https://microbewiki.kenyon.edu/api.php?action=feedcontributions&user=SciaccaK&feedformat=atommicrobewiki - User contributions [en]2024-03-29T10:43:14ZUser contributionsMediaWiki 1.39.6https://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69541Shewanella woodyi NEU Spring 20122012-02-28T02:32:33Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar Flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. Also, ''S. woodyi'' is a respiratory bacteria, which means that it is non-fermentative. This bacteria is involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants. [1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene, and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
Currently, there is little research available about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family, ''Vibrionaceae'' (Gammaproteobacteria), were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69540Shewanella woodyi NEU Spring 20122012-02-28T02:32:06Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar Flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. Also, ''S. woodyi'' is a respiratory bacteria, which means that it is non-fermentative. This bacteria is involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants. [1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene, and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
Currently, there is little research available about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69539Shewanella woodyi NEU Spring 20122012-02-28T02:30:28Z<p>SciaccaK: /* Cell structure and metabolism */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar Flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. Also, ''S. woodyi'' is a respiratory bacteria, which means that it is non-fermentative. This bacteria is involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants. [1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
Currently, there is little research available about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69538Shewanella woodyi NEU Spring 20122012-02-28T02:29:29Z<p>SciaccaK: /* Description and significance */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar Flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. Also, ''S. woodyi'' is a respiratory bacteria, which means that it is non-fermentative. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants. [1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
Currently, there is little research available about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69537Shewanella woodyi NEU Spring 20122012-02-28T02:28:51Z<p>SciaccaK: /* Cell structure and metabolism */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. Also, ''S. woodyi'' is a respiratory bacteria, which means that it is non-fermentative. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants. [1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
Currently, there is little research available about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69536Shewanella woodyi NEU Spring 20122012-02-28T02:27:23Z<p>SciaccaK: /* Cell structure and metabolism */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes [1]. Also, ''S. woodyi'' is a respiratory bacteria, which means that it is non-fermentative. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants [1].<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
Currently, there is little research available about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69534Shewanella woodyi NEU Spring 20122012-02-28T02:25:25Z<p>SciaccaK: /* Cell structure and metabolism */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. Also, ''S. woodyi'' is a respiratory bacteria, which means that it is non-fermentative. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
Currently, there is little research available about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69533Shewanella woodyi NEU Spring 20122012-02-28T02:13:11Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
Currently, there is little research available about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69532Shewanella woodyi NEU Spring 20122012-02-28T02:12:07Z<p>SciaccaK: /* Cell structure and metabolism */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''S. woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69530Shewanella woodyi NEU Spring 20122012-02-28T02:10:20Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. (2008). Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008). Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69528Shewanella woodyi NEU Spring 20122012-02-28T02:09:00Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Shewanella Woodyi MS32, ATCC 51908. From: <br />
<br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69527Shewanella woodyi NEU Spring 20122012-02-28T02:08:47Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Shewanella Woodyi MS32, ATCC 51908. From: <br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <br />
http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69526Shewanella woodyi NEU Spring 20122012-02-28T02:08:33Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Shewanella Woodyi MS32, ATCC 51908. From: <br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69525Shewanella woodyi NEU Spring 20122012-02-28T02:08:15Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Shewanella Woodyi MS32, ATCC 51908. From: <br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: <p>http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69520Shewanella woodyi NEU Spring 20122012-02-28T02:02:24Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Shewanella Woodyi MS32, ATCC 51908. From: <br />
http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641522649<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69519Shewanella woodyi NEU Spring 20122012-02-28T02:00:36Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69518Shewanella woodyi NEU Spring 20122012-02-28T02:00:15Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008). Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69517Shewanella woodyi NEU Spring 20122012-02-28T01:59:04Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008), Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69514Shewanella woodyi NEU Spring 20122012-02-28T01:57:23Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] National Center for Biotechnology Information. (2008) Shewanella woodyi ATCC 51908: A luminous marine bacteria isolated from squid ink. From: http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. Web: <http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730><br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008), Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69513Shewanella woodyi NEU Spring 20122012-02-28T01:56:52Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] National Center for Biotechnology Information. (2008) http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. Web: <http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730><br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008), Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69512Shewanella woodyi NEU Spring 20122012-02-28T01:56:12Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. Web: <http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730><br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008), Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69510Shewanella woodyi NEU Spring 20122012-02-28T01:55:56Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. Web: <http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730><br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008), Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol,''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69509Shewanella woodyi NEU Spring 20122012-02-28T01:54:42Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. ''Int J Syst Bacteriol'' 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. ''FEMS Microbiology Ecology'' 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. ''Journal of Bacteriology'' 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). ''Prokaryotes'' 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. Web: <http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730><br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008), Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69508Shewanella woodyi NEU Spring 20122012-02-28T01:52:28Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. ''Journal of Fish Diseases'', 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. (2008), Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.''190:10, 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69507Shewanella woodyi NEU Spring 20122012-02-28T01:49:42Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. Journal of Fish Diseases, 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69500Shewanella woodyi NEU Spring 20122012-02-28T01:22:46Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic <i>Shewanella marisflavi</i> infecting sea cucumber, <i>Apostichopus japonicus</i>. Journal of Fish Diseases, 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69499Shewanella woodyi NEU Spring 20122012-02-28T01:21:58Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., Qiao, G., Li, Q., Zhou, W., Won, K. M., Xu, D.-H. and Park, S.-I. (2010), Biological characteristics and pathogenicity of a highly pathogenic Shewanella marisflavi infecting sea cucumber, Apostichopus japonicus. Journal of Fish Diseases, 33: 865–877.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69496Shewanella woodyi NEU Spring 20122012-02-28T01:11:42Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69495Shewanella woodyi NEU Spring 20122012-02-28T01:07:48Z<p>SciaccaK: /* Genome structure */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA. [3]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: [http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730]<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69494Shewanella woodyi NEU Spring 20122012-02-28T01:05:25Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: [http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730]<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69493Shewanella woodyi NEU Spring 20122012-02-28T01:04:09Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on January 21, 2012. From: [http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730]<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69492Shewanella woodyi NEU Spring 20122012-02-28T01:03:22Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9] Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69490Shewanella woodyi NEU Spring 20122012-02-28T00:57:09Z<p>SciaccaK: /* Cell structure and metabolism */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. ''S. woodyi'' is able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and contributes to the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69489Shewanella woodyi NEU Spring 20122012-02-28T00:52:52Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10] Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69488Shewanella woodyi NEU Spring 20122012-02-28T00:52:30Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[10]Urbanczyk, H., Ast, J.C., Kaeding, A. J., Oliver, J. D., and Dunlap, P. D. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae. ''J. Bacteriol.'' May 2008 vol. 190 no. 10 3494-350. From: doi: 10.1128/JB.00101-08<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69487Shewanella woodyi NEU Spring 20122012-02-28T00:47:29Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi'' and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages. [10]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69486Shewanella woodyi NEU Spring 20122012-02-28T00:44:48Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
There is not much current research about this bacteria, but a study was done in 2008 about the horizontal gene transfer of the lux gene, which encodes the proteins involved in luminescence. Horizontal gene transfer plays a huge role in the evolution of bacteria, and genera in the family ''Vibrionaceae'' (Gammaproteobacteria) were studied including ''Shewanella'' (''Shewanella woodyi and ''Shewanella hanedai'') to show a pattern of incidence of the lux gene and how it must have been started in an ancestor of the ''Vibrionaceae'' and then was horizonatally transfered to members of ''Shewanellaceae'' and ''Enterobacteriaceae''. Since most of the species of these families lack the lux gene, the scattered incidence most likely is from horizontal transfer, but this study tried to show some evidence since there has been no phylogenetic tests performed. An evolutionary approach was used to test for the horizontal gene transfer of the lux gene from ''Vibrionaceae''. They examined the incongruence of phylogenies of 300 strains of luminous bacteria based on housekeeping genes and multiple lux genes, and the results showed that horizonatal gene transfer of the lux gene is actually very rare. Surprisingly, the findings from this research lacked evidence for horizontal gene transfer, so it supports the other idea that the scattered incdence of the lux gene may have been due to vertical inheritance with a loss of this gene from multiple lineages.<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69396Shewanella woodyi NEU Spring 20122012-02-27T23:00:11Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
No other current research was found about this bacteria, but in the past ten years much work has been done on making the genomes for the bacteria in the genus, ''Shewanella''.<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69395Shewanella woodyi NEU Spring 20122012-02-27T22:59:32Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article posted to Decoded Science on January 21, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
No other current research was found about this bacteria, but in the past ten years much work has been done on making the genomes for this genus group, ''Shewanella''.<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69394Shewanella woodyi NEU Spring 20122012-02-27T22:57:08Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
An article from January 23, 2012 showed how ''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69393Shewanella woodyi NEU Spring 20122012-02-27T22:53:00Z<p>SciaccaK: /* Cell structure and metabolism */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite are used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69346Shewanella woodyi NEU Spring 20122012-02-27T02:26:14Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP is degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69345Shewanella woodyi NEU Spring 20122012-02-27T02:25:26Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP in degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism. [9]<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69344Shewanella woodyi NEU Spring 20122012-02-27T02:24:52Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
''S.woodyi'' was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. ''S. woodyi'' has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP in degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism [9].<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69343Shewanella woodyi NEU Spring 20122012-02-27T02:23:43Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
"S.woodyi" was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. "S. woodyi" has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP in degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism [9].<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69338Shewanella woodyi NEU Spring 20122012-02-27T01:27:03Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
http://www.sciencedirect.com/science/article/pii/S0167701211001308<br />
http://www.biomedcentral.com/1471-2164/12/S1/S3<br />
"S.woodyi" was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. "S. woodyi" has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP in degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism [9].<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69337Shewanella woodyi NEU Spring 20122012-02-27T01:25:04Z<p>SciaccaK: /* References */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
http://www.sciencedirect.com/science/article/pii/S0167701211001308<br />
http://www.biomedcentral.com/1471-2164/12/S1/S3<br />
"S.woodyi" was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. "S. woodyi" has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP in degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism [9].<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
[9]Stone, Marcia. (2012) Nitric Oxide: A Newly Discovered Potential Target for Biofilm Control. Published on Decoded Science on january 21, 2012. From:http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69336Shewanella woodyi NEU Spring 20122012-02-27T01:21:12Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
http://www.sciencedirect.com/science/article/pii/S0167701211001308<br />
http://www.biomedcentral.com/1471-2164/12/S1/S3<br />
"S.woodyi" was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. "S. woodyi" has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP in degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism [9].<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69335Shewanella woodyi NEU Spring 20122012-02-27T01:19:52Z<p>SciaccaK: /* Current Research */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
http://www.sciencedirect.com/science/article/pii/S0167701211001308<br />
http://www.biomedcentral.com/1471-2164/12/S1/S3<br />
"S.woodyi" was used in a study about how bacteria go about making biofilms. This involves quorum sensing, how the cells communicate with each other, and biofilm formation and bioluminescence are used for this research. It is agreed upon that a signaling molecule is involved called bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP), but this study showed how nitric oxide, which is a signaling molecule in mammals, is also a regulator in bacteria impacting biofilms. "S. woodyi" has a gene called H-NOX near the c-di-GMP gene and they directly interact. The H-NOX gene is heme-nitic oxide/oxygen binding, so when there is nitric oxide, c-di-GMP in degraded. The absence of nitric oxide up-regulates the c-di-GMP activity. When the concentration of the c-di-GMP goes up, bacteria enter biofilms. This was the first study to show how nitric oxide plays a role in c-di-GMP metabolism.<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaKhttps://microbewiki.kenyon.edu/index.php?title=Shewanella_woodyi_NEU_Spring_2012&diff=69328Shewanella woodyi NEU Spring 20122012-02-27T00:58:51Z<p>SciaccaK: /* Cell structure and metabolism */</p>
<hr />
<div>{{Uncurated}}<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella; woodyi [3]<br />
<br />
==Description and significance==<br />
[[File:shewa.jpg|200px|thumb|left|Figure 1: Polar flagellum [1]]] <br />
<br />
Named after J. Woodland Hastings, a famous American biologist recognized for his work about bacterial bioluminescence, ''Shewanella woodyi'' is a gram negative bacterium found to have some unique characteristics and play a couple of important environmental roles [1,4]. It is a bacilli shaped bacterium and is generally between one to two micrometers in length [1,4]. ''S. woodyi'' is entirely marine and can be found in deep-sea environments therefore making it barophilic (tolerant to high pressure) [1,2]. Although other species within the Shewanella genus are psychrophilic, ''S. woodyi'' is instead mesophilic growing at an optimal temperature around 25°C [1,2]. Each ''S. woodyi'' bacterial cell possesses a single polar flagellum making it motile, as seen in Figure 1 [1]. This bacterium is also luminescent, meaning it can emit light[1].<br />
<br />
It is well known that the ocean acts as a sink for harmful compounds from both terrestrial and aquatic environments. ''S. woodyi'' is significant in that it helps reduce the levels of select toxic compounds that collect in the sediment on the ocean floor [2,6]. Additionally, this bacterium also plays a role in carbon and nitrogen cycling through its anaerobic capabilities [2,6,7].<br />
<br />
==Genome structure==<br />
<br />
[[File:ChromosomalMap.jpg|200px|thumb|right|Figure 2: Chromosomal Map [3]]] <br />
<br />
<i> S. woodyi</i> has a circular DNA chromosome of 5,935,403 bases, of which 86.02% are coding bases. This chromosome has a G+C content of 43.7%. The entire chromosome can be seen in Figure 2. These base pairs code for 5,085 genes in total, with 96.81%, or 4,923 genes, coding for proteins. The remaining 3.19%, or 162 genes, code for RNA.<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Shewanella woodyi'' is a gram negative, luminescent, nonsporulating rod (0.4-1.0 by 1.4-2.0 pm) with an unsheathed flagellum as was mentioned above. For this bacteria's metabolism, it is catalase and oxidase positive and most strains produce amylase. All strains do produce gelatinase but are unable to make lipase, chtinase, and agarase. They are able to metabolize D-galactose, cellobiose, D-glucuronic acid, acetate, a-ketoglutarate,propionate, succinate, L-alanine, L-threonine, L-leucine, L-serine, and putrescine. Oxygen and nitrite is used by these cells as electron acceptors for their metabolic processes. This bacteria is also involved in carbon and nitrogen fixation in its marine environment and the biodegradation of pollutants.[1]<br />
<br />
==Ecology==<br />
<br />
Originally found in squid ink, ocean floor sediment, and among detritus from the Alboran Sea, this bacterium can be found in a wide range of areas [1]. It thrives at 25°C in a deep-sea environment where it can use detritus and other compounds present for energy [1,2,7]. Research in the past few years has suggested that these bacteria can use almost any electron acceptor for anaerobic respiration [7]. The only criteria seems to be that the electron acceptor must be more electronegative than sulfate [7].<br />
<br />
High pressure and cold temperatures are two major factors that ''S. woodyi'' must overcome in its environment. Usually under these conditions, cell membranes become very rigid and stiff. ''S. woodyi'' avoids this problem by producing large amounts of polyunsaturated fatty acids in order to create a very lipid rich membrane [2,5]. This characteristic allows for a more fluid membrane even under high pressures and lower temperatures.<br />
<br />
Many of these characteristics that ''S. woodyi'' have acquired to live in their environment are a result of horizontal gene transfer from other species [6]. For example, ''S. woodyi'' inherited its Na+/H+ antiporter pump from other bacteria that were already expressing that particular gene [6]. As a result, this bacteria is able to regulate the concentration of sodium in the cell in order to live in high salinity waters.<br />
<br />
==Pathology==<br />
<br />
While other species of <i> Shewanella</i> are known pathogens (ie. <i>Shewanella marisflavi</i> isolate AP629 is pathogenic to sea cucumber), <i>S. woodyi</i> has not proven to be a pathogenic organism. [8]<br />
<br />
==Current Research==<br />
http://www.decodedscience.com/nitric-oxide-a-newly-discovered-potential-target-for-biofilm-control/9730<br />
http://www.sciencedirect.com/science/article/pii/S0167701211001308<br />
http://www.biomedcentral.com/1471-2164/12/S1/S3<br />
<br />
==Cool Factor==<br />
<br />
[[File:Rdx pathway 2.png|200px|thumb|left|Figure 3: RDX degradation pathways [6]]]<br />
<br />
As previously mentioned, ''S. woodyi'' plays a role in alleviating the environment of toxic compounds. There are several organisms which also complete similar tasks and remove harmful components from the air or soil, however, not many are capable of degrading compounds such as RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) along with other explosives [6]. ''S. woodyi'' contains cytochrome c genes and nitroreductases which allow for the break down of RDX into nitric oxide and carbon dioxide [6]. This pathway is shown on the right side of Figure 3 [6]. Although ''Shewanella halifaxensis'' and ''Shewanella sediminis'' are more efficient at breaking down RDX than ''S. woodyi'' and can use both degradation pathways shown in Figure 3, ''S. woodyi'' is still capable of this activity making it unique from many other microorganisms [6]. This factor also makes it even more important to the countless animals that depend on non-polluted waters for better survival. Recent research has suggested that in the presence of explosive compounds, such as RDX, bacteria in the ''Shewanella'' genus, including ''S. woodyi'', actually thrive [6].<br />
<br />
==References==<br />
<br />
[1] Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.<br />
[2] Kato, C., and Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiology Ecology 35, 223-230.<br />
[3] "Shewanella Woodyi MS32, ATCC 51908." Integrated Microbial Genomes. U.S. Department of Energy Joint Genome Institute. Web. 02 Feb. 2012.<br />
[4] http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=ShowDetailView&TermToSearch=17455<br />
[5] Wang, F., Xiao, X., Ou, H., Gai, Y., and Wang, F. (2009). Role and regulation of fatty acid biosynthesis in the response of S. pizotolerans WP3 to different temperatures and pressures. Journal of Bacteriology 191, 2574-2584.<br />
[6] Zhao, J., Deng, Y., Manno, D., and Hawari, J. (2010). Genomic evolution for a cold marine lifestyle and in-situ explosive biodegration. PLoS ONE 5, online.<br />
[7] Nealson, K.H., and Scott, J. Ecophysiology of the Genus Shewanella. (2006). Prokaryotes 6, 1133-1151.<br />
[8] Li, H., G. Qiao, Q. Li, W. Zhou, K. M. Won, D-H Xu, and S-I Park. "Biological Characteristics and Pathogenicity of a Highly Pathogenic Shewanella Marisflavi Infecting Sea Cucumber, Apostichopus Japonicus." Journal of Fish Diseases 33.11 (2010): 865-77. Wiley Online Library. Blackwell Publishing Ltd, 6 Oct. 2010. Web.<br />
<br />
[http://ijs.sgmjournals.org/content/49/2/705.short Venkateswaran, K., Moser, D.P., Dollhopf, M.E., Lies, D.P., Saffarini, D.A., MacGregor, B.J., Ringelberg, D.B., White, D.C., Nishijima, M., Sano, H., Burghardt, J., Stackebrandt, E., and Nealson, K.H. "Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.". ''International Journal of Systematic and Evolutionary Microbiology''. 1999. Volume 49. p. 705-724.]</div>SciaccaK