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https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29315
Desulfobacter
2008-03-17T08:13:09Z
<p>Lrastegarzadeh: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
Morphology of strain ''Desulfobacter'' B54T (A) micrograph of cells.Bar, 10 mm. (B and C) Electron micrographs of one cell. Bars, 2 mm.<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [2]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [3,4].<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [5]. The main habitat of Desulfobacter is marine sendiment and brackish water.<br />
<br />
==References==<br />
<br />
[1] Torleiv Lien and Janiche Beeder. 1997.Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation System. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY. Oct., p. 1124–1128 <br />
<br />
[2] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[3] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[4] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[5] [http://books.google.com/books?hl=en&id=VUdeCXm5eHkC&dq=sulphate+reducing+bacteria+larry+barton&printsec=frontcover&source=web&ots=aiyATgKvz_&sig=st9vJjY6Vy8KpSmc63kXEuAMi3w Barton, Larry L. and W. Allen Hamilton. 2007. Sulphate reducing Bacteria Wnvironmental and Engineering system. 1st ed. Cambridge University Press. Cambridge, UK.]<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=29314
Flooded Soils
2008-03-17T08:11:17Z
<p>Lrastegarzadeh: /* Sulfate Reducing Bacteria */</p>
<hr />
<div>[[Image:Floridacrocodile1.jpg|thumb|500px|right|Ding Darling reserve, Sanibel Island, Florida, with an American Crocodile. Wikipedia jimfbleak 13:37, 2 April 2006 (UTC)]] <br />
==Introduction==<br />
[[Image:flooded soil.png|thumb|400px|schematic presentation of flooded soil from[[Y.Chen and Y Avnimelech]]]]<br />
'''Flooded soils''' occur with complete water saturation of soil pores, and generally result in anoxic conditions of the soil environment. Flooded soil environments may include such [[Wikipedia:ecosystem|ecosystem]]<br />
as: rice paddies; wetlands (swamps, marshes, and bogs); compacted soils; and post-rain soils (Scow, 2008). Additionally, similar redox conditions (where oxygen is lacking) can also be found within soil aggregates and along pollutant plumes, and thus many of the concepts discussed in this section may be applied to those environments.<br />
<br />
Oxygen is only sparingly soluble in water and diffuses much more slowly through water than through air (Schlesinger, 1997). What little oxygen that is present in saturated soils in the form of dissolved O<sub>2</sub> is quickly consumed through metabolic processes. Oxygen is used as terminal electron acceptor via respiration by roots, soil microbes, and soil organisms (Sylvia, 2005), and is lost from the soil system in the form of carbon dioxide (CO<sub>2</sub>). Heterotrophic respiration may completely deplete oxygen in flooded soils; and these effects may be observed within only a few millimeters of the soil surface (Schlesinger, 1997). <br />
<br />
Due to the deficiency of oxygen in flooded soils, those organisms inhabiting flooded soils must be able to survive with little to no oxygen. Although energy yields are much greater with oxygen than with any other terminal electron acceptor (see [[#Electron tower]] theory, section 2.1.1), under anoxic conditions anaerobic and facultative microbes can use alternative electron acceptors such as nitrate, ferric iron (Fe III), manganese (IV) oxide, sulfate, and carbon dioxide to produce energy and build biomass. <br />
<br />
Microbial transformations of elements in anaerobic soils play a large role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere (Schlesinger, 1997).<br />
<br />
==Processes ==<br />
[[Image:phenomenon in aggregates.png|thumb|left|200px|Electron acceptor used in aggregates. adjusted from [[Prof. Kate lec #5]]]]<br />
[[Image:phenomena in pollutant plume.png|thumb|200px|Order of electron acceptor in pollutant plume from [[USGS]]]]<br />
In general, flooded soils occur due to seasonal flooding or agricultural activity. <br />
Flooded soils can be often converted into non-flooded soils by the water level fluctuation and drainage. Through this variation of soil conditins, various gases are emitted into the atmosphere and environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changing. <br />
As explained in the [[#Introduction]], microorganisms can use alternative terminal electron acceptors (such as nitrate, perchlorate, sulfate, and carbon dioxide) when dissolved oxygen is absent. Microbes will successively use electron acceptors according to the order of energy yields resulting from electron acceptor utilization indicted on the electron tower (see [[#Electron Tower]] theory). The progression of electron acceptor utilization may also be observed in soil aggregates and pollutant plumes. <br />
<br />
<br />
<br />
<br />
===[http://en.wikipedia.org/wiki/Redox Oxidation/Reduction (Redox) Reaction]===<br />
In redox reactions, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. A classic example well known in the process of cellular respiration is when glucose (the reducing agent) reacts with oxygen (the oxidizing agent)and is oxidized to carbon dioxide. In this reaction, oxygen is reduced to water. Oxygen is the most common and highest energy yielding electron acceptor, and some organisms (strict aerobes) can not live long without it.(6) In flooded soils oxygen is typically not availible. Facultative and strict anaerobic bacteria have the ability to use other oxidizing agents/electron acceptors to carry out respiration. Anaerobic and facultative bacteria will use the electron acceptor which yields the highest energy, or the acceptor which is most readily available. The availibility and concentration of electron acceptors changes as the soil profile increases in depth. <br />
====Electron Tower====<br />
[[Image:Environmental1.gif|thumb|400px|Electron tower [[http://www.microbiologybytes.com/introduction/Environmental.html]]]]<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified as strict aerobes, obligate anaerobes, and facultative anaerobes. Strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, microbes will choose to use nitrate as an electron acceptor (if available). Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptors in the order of electron acceptor having the most reducing energy. Oxygen is the most efficient electron acceptor, while carbon dioxide has the least amount of reduction potential.<br />
====Gleyed Soils and Recovery to Aerobic Conditions====<br />
[[Image:Gleyed soil.png|thumb|200px|left|Gleyed soil from Prof. Scow's lecture note 2008]]<br />
[[Image:Oxidized soil.png|thumb|300px|Oxidized soil from Prof. Scow's lecture note 2008]]<br />
'''Soil Gleying''':<br />
Gleying is a phenomenon in which waterlogged soils are discolored by accumulation of Fe(II) due to reduction of ferric iron into ferrous iron (Lovely 1991).<br />
Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe(III)-reducing fermentative bacteria can be readily isolated from gleyed soils. <br />
The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS<sub>2</sub>) (Wenk and Bulakh 2004).<br />
<br />
'''Recovery to Aerobic Conditions'''<br />
When waterlogged soils drain, the Eh starts to increase as oxygen diffuses into soil pores. Plentiful oxygen represses the activity of anaerobes, which results in an increase of aerobic microbes. If oxygen diffuses deep into the soil profile, the production of H<sub>2</sub>S ceases. Under aerobic conditions, ferrous iron is oxidized by iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals. The gray color in soil changes to a red, yellow, or brown color as these minerals are oxidized. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO<sub>2</sub> (Richardson and Vepraskas 2000).<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise as a result of the buffering capacity of the soil. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succession of anaerobic oxidation processes, the redox potential (Eh) of flooded soils will decrease as a result of the reduced products formed. Approximate values for redox potentials associated with specific oxidation-reduction process are as follows:<br />
<br />
{| width="300" border="1"<br />
|----- bgcolor ="orange"<br />
| width="200" height="23" | Observation<br />
| width="84" | Eh (mV) <br />
|-<br />
| Disappearance of oxygen<br />
| +330<br />
|-<br />
| Disappearance of nitrate<br />
| +220<br />
|-<br />
|Appearance of manganese ions <br />
| +200<br />
|-<br />
| Appearance of ferrous iron ions<br />
| +120 <br />
|-<br />
| Disappearance of sulfate<br />
| -150<br />
|-<br />
|Appearance of methane <br />
| -250<br />
|}<br />
<br />
===Solubility/Mobility of Minerals===<br />
Since the toxicity, solubility, mobility, and bioavailability for a given element or compound is mainly influenced by soil solution reduction potenial and pH, flooded soil conditions play an important role in the mobility of trace metal, nutrients, and minerals.<br />
<br />
<br />
====Plant Nutrient Availability====<br />
[[Image:overwater.jpg|left|frame|What over-watering looks like in a common house plant]]Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a major role in healthy plant growth. In flooded soils, under anaerobic conditions, the pH will tend to rise initially. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants. Microoganisms will begin to use available plants nutrients as alternative electron acceptors, such as sulfate, nitrate and iron(III).<br />
Experiments have been done on soybean plants to show the effects of flooded soils. Flood duration effects on soybean plants resulted in yellowing and abscission of leaves at the lower nodes, stunting, and reduced dry weight and seed yield. Canopy height and dry weight decreased linearly with duration of the flood at both growth stages. Growth rates were 25 to 35% less when soybeans were flooded (3).<br />
<br />
==Key Microbial Processes and Organisms Involved==<br />
The role of microorganisms under flooded soils<br />
===Microbial processes===<br />
====Microbial Activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as [http://en.wikipedia.org/wiki/Electron_acceptor TEA (terminal electron acceptors)]. Some important terminal electron acceptors include iron, nitrate, sulfate, and manganese. These processes are primarily driven by microobial activity. Energy yields of alternative electron acceptors are lower than that of aerobic respiration, in which oxygen is utilized as a TEA (see [[#Electron Tower]] theory. As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of TEA's from the electron tower, and will govern which microbes will thrive, as those able to use these available alternative electron acceptors. Flooding also alters microbial flora in soil by decreasing the O<sub>2</sub> concentration. Fermentation is a major biochemical processes responsible for organic matter decomposition in flooded soils. Eh levels can affect which compounds are fermented. These levels will tend to gradually drop in flooded soils.<br />
<br />
====Fermentation under Anoxic Conditions====<br />
[[Image:anaerobic decomposition.png|thumb|left|300px|Organic matter decomposition pathways . [[Richardson and Vepraskas]]]]<br />
There are many types of fermentative bacteria in soils, such as the genus ''[[Bacillus]]'', ''[[Clostridium]]'', and ''[[Lactobacillus]]''. 4 ATP molecules per molecule of glucose are produced by fermentation, while 38 ATP molecules are produced by aerobic respiration. Although the energy yield via fermentation is less than oxidative phosphorylation, fermentation plays an important role in anaerobic respiration for obligate and facultative anaerobic bacteria, including denitrifier, Fe<sup>3+</sup>, Mn<sup>4+</sup>, SO<sub>4</sub><sup>2-</sup>, reducers, and methanogens. Sugar (glucose or fructose) is broken down into simple compounds (e.g. formate, acetate, and ethanol) during fermentation. Also, numerous fermentation products, such as carbon dioxide, fatty acid, lactic, alcohols, are released into soils. These compounds serve as substrates for other anaerobic bacteria. Thus, low molecular weight organic compounds produced from fermentation influence the reduction of Fe(III), Mn(IV), SO<sub>4</sub><sup>2-</sup>, and CO<sub>2</sub>(Richardson And Vepraskas 2000).<br />
----<br />
<br />
===Organisms involved in Flooded Soils===<br />
====Nitrate Reducing Bacteria====<br />
When available oxygen is depleted and nitrate is available, denitrification, the reduction of NO<sub>3</sub><sup>-</sup> to NO,N<sub>2</sub>,or N<sub>2</sub>, primarily occurs.<br />
Denitrification is carried out by obligate respiratory bacteria belonging to the genra ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''[[Paracoccus denitrificans]]'', ''[[Pseudomonas]]'' and ''[[Thiobacillus]]'' (Knowles, 1982). Nitrate ammonification found in facultative anaerobic bacteria belonging to the genera ''[[Bacillus]]'', ''Citrobacter'' and ''[[Aeromonas]]'', or memebers of the ''[[Enterobacteriaceae]]'' (Cole adn Brown, 1980; Smith adn Zimmerman, 1981; MacFarlane and Herbert, 1982). Strictly anaerobic bacteria belonging to the genus ''[[Clostridium]]'' are also able to reduce nitrate to ammonia (Hasan and Hall, 1975). <br />
Pure culture studies show evidance that nitrate reduction may also occur in the presence of oxygen (Kuenen and and Robertson, 1987).<br />
<br />
====Iron/Manganese Reducing Bacteria====<br />
Most microorganisms can reduce Mn<sup>4+</sup> and Fe <sup>3+</sup>.<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''[[Geobacter]]([[Geobacter metallireducens]] and [[Geobacter sulfurreducens]]),Shewanella putrefaciens,[[Desulfovibrio]], [[Pseudomonas]],'' and ''[[Thiobacillus]]''(Lovley 1993). ''[[Bacillus]], [[Geobacter]],'' and ''[[Pseudomonas]]'' are representative manganese-reducing bacteria. <br />
Different forms of ferric iron oxides exist in drained aerobic soils as well as in waterlogged soils. Not all forms of ferric oxides are equally suitable for reduction by ferric oxide reducer bacteria (Gotoh and Patrick, 1974; Schwertmann and Taylor, 1977). In general, amorphous forms are more efficient for ferric reducer bacteria than crystalline forms (Lovely adn Phillips, 1986). The reduction of ferric oxide may release phosphate and trace elements that are adsorbed to amorphous ferric oxide and thus enhance availablity of these compounds in the soil (Lovely and Phillips, 1986).<br />
<br />
====Sulfate Reducing Bacteria====<br />
Bacteria can use organic compouds as an electron donor and sulfate as an electron acceptor. This reaction for acetate as electron donor is as follows:<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''[[Desulfobacter]]'', ''Desulfobulbus'', ''[[Desulfococcus]]'', ''[[Desulfovibrio]]'', ''[[Desulfosarcina]]'',''Desulfotomaculum'',and ''Desulfonema''(Langston and Bebiano 1998, Sylvia 2004). Some of the sulfate reducing bacteria oxidize the organic componds completely to CO2 and some other stop after producing acetate as an intermaediate of oxidation. Hydrogen sulfide gas produced via anaerobic respiration causes the rotten egg odor.<br />
<br />
====[[Methanogens]]====<br />
Methanogen products less energy than other rueducing reaction because the reduction of carbon dioxide occur under the most anaerobic and reduced conditions(see [[#Electron tower]] section). Thus, the activity of methanogen is repressed until other alternative terminal electron acceptor such as Fe(III), NO<sub>3</sub><sup>-</sup>,and SO<sub>4</sub><sup>2-</sup>, have been depleted.<br />
<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
==Greenhouse Gas Emissions from Flooded Soils==<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively (Schlesinger, 1997). Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. According to Matthews and Fung (1987), an estimated 3.6% of terrestrial land is classified as wetlands, and although this number continues to decline (Schlesinger, 1997) the effect of flooded soils to the global climate is clear. <br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV (see [[#electron tower]] theory, section 2.1.1) (Sylvia, 2005). If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions. <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process (Sylvia, 2005). <br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions (Sylvia, 2005).<br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane (Sylvia, 1998). Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur. (Sylvia, 2005).<br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly (Sylvia, 2005).<br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosytems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. Following is a list of recent journal review articles focused on a range of current research topics related to flooded soil environments for the interested reader: <br />
<br />
1. Shangping Xu, Peter R. Jaffe and Denise L. Mauzerall, A process-based model for methane emission from flooded rice paddy systems, Ecological ModellingVolume 205, Issues 3-4, , 24 July 2007, Pages 475-491.<br />
(http://www.sciencedirect.com/science/article/B6VBS-4NHV759-1/2/3126b5403a44c51c5d8d4160382d848e)<br />
<br />
2. HANK GREENWAY , WILLIAM ARMSTRONG , and TIMOTHY D. COLMER <br />
Conditions Leading to High CO2 (>5 kPa) in Waterlogged–Flooded Soils and Possible Effects on Root Growth and Metabolism <br />
AOBPreview published on July 1, 2006, DOI 10.1093/aob/mcl076.<br />
Ann Bot 98: 9-32.<br />
<br />
3. Kazunori Minamikawa and Naoki Sakai, The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan, Agriculture, Ecosystems & EnvironmentVolume 107, Issue 4, , 30 May 2005, Pages 397-407.<br />
(http://www.sciencedirect.com/science/article/B6T3Y-4FY9M5H-1/2/98a4074277436af97833c16a823b326c)<br />
Keywords: Methane; Water management; Soil redox potential; Oryza sativa L.; Rice yield<br />
<br />
4. Makoto Kimura, Jun Murase and Yahai Lu, Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4), Soil Biology and BiochemistryVolume 36, Issue 9, , September 2004, Pages 1399-1416.<br />
(http://www.sciencedirect.com/science/article/B6TC7-4C9G7KP-4/2/ceb77d1803f5d02e51bb773f3163cdcb)<br />
<br />
5. Sahrawat KL, Fertility and organic matter in submerged rice soils, Current Science. Volume 88, Issues 3-4, 2005, Pages 735-739.<br />
<br />
6. Conrad R, Microbial ecology of methanogens and methanotrophs, Advances in Agronomy. Volume 96, 2007, Pages 1-63.<br />
<br />
7. Ralf Conrad, Christoph Erkel and Werner Liesack, Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil, Current Opinion in BiotechnologyVolume 17, Issue 3, , Environmental biotechnology/Energy biotechnology, June 2006, Pages 262-267.<br />
(http://www.sciencedirect.com/science/article/B6VRV-4JRVFV8-1/2/babb823ea30e51d7445d6861d7d334aa)<br />
<br />
==References==<br />
(1) Lecture 5 of Kate Scow. 2008. Microbial Metabolism. Unpublished, University of California, Davis.<br />
<br />
(2) Schlesinger, W.H. 1997. Biogeochemistry: An Analysis of Global Change. 2nd ed. Elsevier Academic Press, Amsterdam. <br />
<br />
(3) [http://books.google.com/books?id=1l4GAAAACAAJ&dq=soil+microbiology+sylvia&ei=thzbR9j6Hpu8swPmxOXzAQ Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey.]<br />
<br />
(4) [http://books.google.com/books?id=v6cGPMRmPYYC&pg=PA940&dq=J.+Kotz,+P.+Treichel,+G.+Weaver.+2006.+Chemistry+and+Chemical+Reactivity&ei=Bx3bR5yFF5-OtgOdqe3sAQ&sig=2IiJ_hdME4k5k06zd-H35y1cxC8#PPP1,M1 J. Kotz, P. Treichel, G. Weaver. 2006. Chemistry and Chemical Reactivity sixth edition.]<br />
<br />
(5)[http://books.google.com/books?id=xEFIEOjfxx0C&printsec=frontcover&dq=Wetland+richardson&ei=7xvbR4vMH4jysgOg6vnpAQ&sig=bDFNpm0lUibISaIaERoMAu5-K34 J.L Richardson and M.J Vepraskas., 2000 Wetland soils: Genesis, Hydrology, Landscapes, and Classification., CRC press LLC.] <br />
<br />
(6) Flood Duration Effects on Soybean Growth and Yield<br />
http://agron.scijournals.org/cgi/content/abstract/81/4/631<br />
<br />
(7)[http://books.google.com/books?id=pr7kAQAACAAJ&dq=Advances+in+Agricultural+Microbiology,&ei=ddHdR6qDJYG-sgPeyMXyAQ Knowles, R. 1982. Denitrification in Soils, pp. 246-266, In: N.S. Subba Rao (ed.) Advances in Agricultural Microbiology, Butterworth Sci. Pub., London, UK]<br />
<br />
(8) Cole and Brown 1980<br />
<br />
(9) Smith and Zimmerman 1982<br />
<br />
(10) Mac Herbent 1982<br />
<br />
(11)Hasan and Hall 1975<br />
<br />
(12) Kuenen and Roberston 1987<br />
<br />
(13)[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.mi.47.100193.001403?journalCode=micro Derek R. Lovley., 1993., Dissimilatory metal reduction. Annu Rev Microbiol. Vol 47 pp: 263-90.]<br />
<br />
(14) Gotoh and Patrick 1974<br />
<br />
(15) Schwertman and Taylor 1977<br />
<br />
(18) [http://aem.asm.org/cgi/reprint/52/4/751 Derek R. Lovley and Elizabeth J.P Phillips., Availability of Ferric Iron for Microbial Reduction in Bottom Sediments of the Freshwater Tidal Potomac River., Appl Environ Microbiology. 1986, p. 751-757]<br />
<br />
(19) [http://books.google.com/books?id=0GAvKQJ2JuwC&printsec=frontcover&vq=Wenk+H.R+and+Bulakh+A+.,+2004:+Minerals.+Their+constitution+and+origin.+Cambridge+University+Press&source=gbs_summary_r Wenk H.R and Bulakh A ., 2004: Minerals. Their constitution and origin. Cambridge University Press.]<br />
<br />
(20) [http://books.google.com/books?id=9K5I0ZPQd54C&pg=PA219&lpg=PA219&dq=%22LANGSTON%22+%228+Metal+handling%22&source=web&ots=qVFErWWjbn&sig=Iyh9_HN4S6PZU4jdXrMuWbLqcpI&hl=en#PPR11,M1 WJ Langston, MJ Bebianno, ,and GR Burt, ., (1998) "Metal handling strategies in molluscs" In: Langston, WJ, Bebiano, MJ eds. , Metal metabolism in the aquatic environment, Chapman and Hall, London, United Kingdom, pp 219-272]<br />
<br />
(21) Matthews, E. and I. Fung. 1987. Methane Emission from Natural Wetlands: Global Distribution, Area, and Environmental Characteristics of Sources. Global Biogeochemical Cycles 1: 61-86.<br />
<br />
(22) [http://books.google.com/books?id=zHIhWM5R9LcC&printsec=frontcover&dq=Y.Chen+and+Y+Avnimelech&source=gbs_summary_r#PPA118,M1 Y. Chen and Y . Avnimelech., (1986)., The Role of Organic Matter in Modern Agriculture., Springer., Developments in Plant and Soil Sciences , Vol. 25., p118]<br />
<br />
See [[#Current Research]] section for a list of journals for additional information on the topic of flooded soils. <br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=29313
Flooded Soils
2008-03-17T08:10:54Z
<p>Lrastegarzadeh: /* Sulfate Reducing Bacteria */</p>
<hr />
<div>[[Image:Floridacrocodile1.jpg|thumb|500px|right|Ding Darling reserve, Sanibel Island, Florida, with an American Crocodile. Wikipedia jimfbleak 13:37, 2 April 2006 (UTC)]] <br />
==Introduction==<br />
[[Image:flooded soil.png|thumb|400px|schematic presentation of flooded soil from[[Y.Chen and Y Avnimelech]]]]<br />
'''Flooded soils''' occur with complete water saturation of soil pores, and generally result in anoxic conditions of the soil environment. Flooded soil environments may include such [[Wikipedia:ecosystem|ecosystem]]<br />
as: rice paddies; wetlands (swamps, marshes, and bogs); compacted soils; and post-rain soils (Scow, 2008). Additionally, similar redox conditions (where oxygen is lacking) can also be found within soil aggregates and along pollutant plumes, and thus many of the concepts discussed in this section may be applied to those environments.<br />
<br />
Oxygen is only sparingly soluble in water and diffuses much more slowly through water than through air (Schlesinger, 1997). What little oxygen that is present in saturated soils in the form of dissolved O<sub>2</sub> is quickly consumed through metabolic processes. Oxygen is used as terminal electron acceptor via respiration by roots, soil microbes, and soil organisms (Sylvia, 2005), and is lost from the soil system in the form of carbon dioxide (CO<sub>2</sub>). Heterotrophic respiration may completely deplete oxygen in flooded soils; and these effects may be observed within only a few millimeters of the soil surface (Schlesinger, 1997). <br />
<br />
Due to the deficiency of oxygen in flooded soils, those organisms inhabiting flooded soils must be able to survive with little to no oxygen. Although energy yields are much greater with oxygen than with any other terminal electron acceptor (see [[#Electron tower]] theory, section 2.1.1), under anoxic conditions anaerobic and facultative microbes can use alternative electron acceptors such as nitrate, ferric iron (Fe III), manganese (IV) oxide, sulfate, and carbon dioxide to produce energy and build biomass. <br />
<br />
Microbial transformations of elements in anaerobic soils play a large role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere (Schlesinger, 1997).<br />
<br />
==Processes ==<br />
[[Image:phenomenon in aggregates.png|thumb|left|200px|Electron acceptor used in aggregates. adjusted from [[Prof. Kate lec #5]]]]<br />
[[Image:phenomena in pollutant plume.png|thumb|200px|Order of electron acceptor in pollutant plume from [[USGS]]]]<br />
In general, flooded soils occur due to seasonal flooding or agricultural activity. <br />
Flooded soils can be often converted into non-flooded soils by the water level fluctuation and drainage. Through this variation of soil conditins, various gases are emitted into the atmosphere and environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changing. <br />
As explained in the [[#Introduction]], microorganisms can use alternative terminal electron acceptors (such as nitrate, perchlorate, sulfate, and carbon dioxide) when dissolved oxygen is absent. Microbes will successively use electron acceptors according to the order of energy yields resulting from electron acceptor utilization indicted on the electron tower (see [[#Electron Tower]] theory). The progression of electron acceptor utilization may also be observed in soil aggregates and pollutant plumes. <br />
<br />
<br />
<br />
<br />
===[http://en.wikipedia.org/wiki/Redox Oxidation/Reduction (Redox) Reaction]===<br />
In redox reactions, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. A classic example well known in the process of cellular respiration is when glucose (the reducing agent) reacts with oxygen (the oxidizing agent)and is oxidized to carbon dioxide. In this reaction, oxygen is reduced to water. Oxygen is the most common and highest energy yielding electron acceptor, and some organisms (strict aerobes) can not live long without it.(6) In flooded soils oxygen is typically not availible. Facultative and strict anaerobic bacteria have the ability to use other oxidizing agents/electron acceptors to carry out respiration. Anaerobic and facultative bacteria will use the electron acceptor which yields the highest energy, or the acceptor which is most readily available. The availibility and concentration of electron acceptors changes as the soil profile increases in depth. <br />
====Electron Tower====<br />
[[Image:Environmental1.gif|thumb|400px|Electron tower [[http://www.microbiologybytes.com/introduction/Environmental.html]]]]<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified as strict aerobes, obligate anaerobes, and facultative anaerobes. Strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, microbes will choose to use nitrate as an electron acceptor (if available). Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptors in the order of electron acceptor having the most reducing energy. Oxygen is the most efficient electron acceptor, while carbon dioxide has the least amount of reduction potential.<br />
====Gleyed Soils and Recovery to Aerobic Conditions====<br />
[[Image:Gleyed soil.png|thumb|200px|left|Gleyed soil from Prof. Scow's lecture note 2008]]<br />
[[Image:Oxidized soil.png|thumb|300px|Oxidized soil from Prof. Scow's lecture note 2008]]<br />
'''Soil Gleying''':<br />
Gleying is a phenomenon in which waterlogged soils are discolored by accumulation of Fe(II) due to reduction of ferric iron into ferrous iron (Lovely 1991).<br />
Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe(III)-reducing fermentative bacteria can be readily isolated from gleyed soils. <br />
The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS<sub>2</sub>) (Wenk and Bulakh 2004).<br />
<br />
'''Recovery to Aerobic Conditions'''<br />
When waterlogged soils drain, the Eh starts to increase as oxygen diffuses into soil pores. Plentiful oxygen represses the activity of anaerobes, which results in an increase of aerobic microbes. If oxygen diffuses deep into the soil profile, the production of H<sub>2</sub>S ceases. Under aerobic conditions, ferrous iron is oxidized by iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals. The gray color in soil changes to a red, yellow, or brown color as these minerals are oxidized. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO<sub>2</sub> (Richardson and Vepraskas 2000).<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise as a result of the buffering capacity of the soil. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succession of anaerobic oxidation processes, the redox potential (Eh) of flooded soils will decrease as a result of the reduced products formed. Approximate values for redox potentials associated with specific oxidation-reduction process are as follows:<br />
<br />
{| width="300" border="1"<br />
|----- bgcolor ="orange"<br />
| width="200" height="23" | Observation<br />
| width="84" | Eh (mV) <br />
|-<br />
| Disappearance of oxygen<br />
| +330<br />
|-<br />
| Disappearance of nitrate<br />
| +220<br />
|-<br />
|Appearance of manganese ions <br />
| +200<br />
|-<br />
| Appearance of ferrous iron ions<br />
| +120 <br />
|-<br />
| Disappearance of sulfate<br />
| -150<br />
|-<br />
|Appearance of methane <br />
| -250<br />
|}<br />
<br />
===Solubility/Mobility of Minerals===<br />
Since the toxicity, solubility, mobility, and bioavailability for a given element or compound is mainly influenced by soil solution reduction potenial and pH, flooded soil conditions play an important role in the mobility of trace metal, nutrients, and minerals.<br />
<br />
<br />
====Plant Nutrient Availability====<br />
[[Image:overwater.jpg|left|frame|What over-watering looks like in a common house plant]]Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a major role in healthy plant growth. In flooded soils, under anaerobic conditions, the pH will tend to rise initially. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants. Microoganisms will begin to use available plants nutrients as alternative electron acceptors, such as sulfate, nitrate and iron(III).<br />
Experiments have been done on soybean plants to show the effects of flooded soils. Flood duration effects on soybean plants resulted in yellowing and abscission of leaves at the lower nodes, stunting, and reduced dry weight and seed yield. Canopy height and dry weight decreased linearly with duration of the flood at both growth stages. Growth rates were 25 to 35% less when soybeans were flooded (3).<br />
<br />
==Key Microbial Processes and Organisms Involved==<br />
The role of microorganisms under flooded soils<br />
===Microbial processes===<br />
====Microbial Activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as [http://en.wikipedia.org/wiki/Electron_acceptor TEA (terminal electron acceptors)]. Some important terminal electron acceptors include iron, nitrate, sulfate, and manganese. These processes are primarily driven by microobial activity. Energy yields of alternative electron acceptors are lower than that of aerobic respiration, in which oxygen is utilized as a TEA (see [[#Electron Tower]] theory. As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of TEA's from the electron tower, and will govern which microbes will thrive, as those able to use these available alternative electron acceptors. Flooding also alters microbial flora in soil by decreasing the O<sub>2</sub> concentration. Fermentation is a major biochemical processes responsible for organic matter decomposition in flooded soils. Eh levels can affect which compounds are fermented. These levels will tend to gradually drop in flooded soils.<br />
<br />
====Fermentation under Anoxic Conditions====<br />
[[Image:anaerobic decomposition.png|thumb|left|300px|Organic matter decomposition pathways . [[Richardson and Vepraskas]]]]<br />
There are many types of fermentative bacteria in soils, such as the genus ''[[Bacillus]]'', ''[[Clostridium]]'', and ''[[Lactobacillus]]''. 4 ATP molecules per molecule of glucose are produced by fermentation, while 38 ATP molecules are produced by aerobic respiration. Although the energy yield via fermentation is less than oxidative phosphorylation, fermentation plays an important role in anaerobic respiration for obligate and facultative anaerobic bacteria, including denitrifier, Fe<sup>3+</sup>, Mn<sup>4+</sup>, SO<sub>4</sub><sup>2-</sup>, reducers, and methanogens. Sugar (glucose or fructose) is broken down into simple compounds (e.g. formate, acetate, and ethanol) during fermentation. Also, numerous fermentation products, such as carbon dioxide, fatty acid, lactic, alcohols, are released into soils. These compounds serve as substrates for other anaerobic bacteria. Thus, low molecular weight organic compounds produced from fermentation influence the reduction of Fe(III), Mn(IV), SO<sub>4</sub><sup>2-</sup>, and CO<sub>2</sub>(Richardson And Vepraskas 2000).<br />
----<br />
<br />
===Organisms involved in Flooded Soils===<br />
====Nitrate Reducing Bacteria====<br />
When available oxygen is depleted and nitrate is available, denitrification, the reduction of NO<sub>3</sub><sup>-</sup> to NO,N<sub>2</sub>,or N<sub>2</sub>, primarily occurs.<br />
Denitrification is carried out by obligate respiratory bacteria belonging to the genra ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''[[Paracoccus denitrificans]]'', ''[[Pseudomonas]]'' and ''[[Thiobacillus]]'' (Knowles, 1982). Nitrate ammonification found in facultative anaerobic bacteria belonging to the genera ''[[Bacillus]]'', ''Citrobacter'' and ''[[Aeromonas]]'', or memebers of the ''[[Enterobacteriaceae]]'' (Cole adn Brown, 1980; Smith adn Zimmerman, 1981; MacFarlane and Herbert, 1982). Strictly anaerobic bacteria belonging to the genus ''[[Clostridium]]'' are also able to reduce nitrate to ammonia (Hasan and Hall, 1975). <br />
Pure culture studies show evidance that nitrate reduction may also occur in the presence of oxygen (Kuenen and and Robertson, 1987).<br />
<br />
====Iron/Manganese Reducing Bacteria====<br />
Most microorganisms can reduce Mn<sup>4+</sup> and Fe <sup>3+</sup>.<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''[[Geobacter]]([[Geobacter metallireducens]] and [[Geobacter sulfurreducens]]),Shewanella putrefaciens,[[Desulfovibrio]], [[Pseudomonas]],'' and ''[[Thiobacillus]]''(Lovley 1993). ''[[Bacillus]], [[Geobacter]],'' and ''[[Pseudomonas]]'' are representative manganese-reducing bacteria. <br />
Different forms of ferric iron oxides exist in drained aerobic soils as well as in waterlogged soils. Not all forms of ferric oxides are equally suitable for reduction by ferric oxide reducer bacteria (Gotoh and Patrick, 1974; Schwertmann and Taylor, 1977). In general, amorphous forms are more efficient for ferric reducer bacteria than crystalline forms (Lovely adn Phillips, 1986). The reduction of ferric oxide may release phosphate and trace elements that are adsorbed to amorphous ferric oxide and thus enhance availablity of these compounds in the soil (Lovely and Phillips, 1986).<br />
<br />
====Sulfate Reducing Bacteria====<br />
Bacteria can use organic compouds as an electron donor and sulfate as an electron acceptor. This reaction for acetate as electron donor is as follows:<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''Desulfobacter'', ''Desulfobulbus'', ''[[Desulfococcus]]'', ''[[Desulfovibrio]]'', ''[[Desulfosarcina]]'',''Desulfotomaculum'',and ''Desulfonema''(Langston and Bebiano 1998, Sylvia 2004). Some of the sulfate reducing bacteria oxidize the organic componds completely to CO2 and some other stop after producing acetate as an intermaediate of oxidation. Hydrogen sulfide gas produced via anaerobic respiration causes the rotten egg odor.<br />
<br />
====[[Methanogens]]====<br />
Methanogen products less energy than other rueducing reaction because the reduction of carbon dioxide occur under the most anaerobic and reduced conditions(see [[#Electron tower]] section). Thus, the activity of methanogen is repressed until other alternative terminal electron acceptor such as Fe(III), NO<sub>3</sub><sup>-</sup>,and SO<sub>4</sub><sup>2-</sup>, have been depleted.<br />
<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
==Greenhouse Gas Emissions from Flooded Soils==<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively (Schlesinger, 1997). Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. According to Matthews and Fung (1987), an estimated 3.6% of terrestrial land is classified as wetlands, and although this number continues to decline (Schlesinger, 1997) the effect of flooded soils to the global climate is clear. <br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV (see [[#electron tower]] theory, section 2.1.1) (Sylvia, 2005). If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions. <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process (Sylvia, 2005). <br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions (Sylvia, 2005).<br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane (Sylvia, 1998). Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur. (Sylvia, 2005).<br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly (Sylvia, 2005).<br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosytems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. Following is a list of recent journal review articles focused on a range of current research topics related to flooded soil environments for the interested reader: <br />
<br />
1. Shangping Xu, Peter R. Jaffe and Denise L. Mauzerall, A process-based model for methane emission from flooded rice paddy systems, Ecological ModellingVolume 205, Issues 3-4, , 24 July 2007, Pages 475-491.<br />
(http://www.sciencedirect.com/science/article/B6VBS-4NHV759-1/2/3126b5403a44c51c5d8d4160382d848e)<br />
<br />
2. HANK GREENWAY , WILLIAM ARMSTRONG , and TIMOTHY D. COLMER <br />
Conditions Leading to High CO2 (>5 kPa) in Waterlogged–Flooded Soils and Possible Effects on Root Growth and Metabolism <br />
AOBPreview published on July 1, 2006, DOI 10.1093/aob/mcl076.<br />
Ann Bot 98: 9-32.<br />
<br />
3. Kazunori Minamikawa and Naoki Sakai, The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan, Agriculture, Ecosystems & EnvironmentVolume 107, Issue 4, , 30 May 2005, Pages 397-407.<br />
(http://www.sciencedirect.com/science/article/B6T3Y-4FY9M5H-1/2/98a4074277436af97833c16a823b326c)<br />
Keywords: Methane; Water management; Soil redox potential; Oryza sativa L.; Rice yield<br />
<br />
4. Makoto Kimura, Jun Murase and Yahai Lu, Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4), Soil Biology and BiochemistryVolume 36, Issue 9, , September 2004, Pages 1399-1416.<br />
(http://www.sciencedirect.com/science/article/B6TC7-4C9G7KP-4/2/ceb77d1803f5d02e51bb773f3163cdcb)<br />
<br />
5. Sahrawat KL, Fertility and organic matter in submerged rice soils, Current Science. Volume 88, Issues 3-4, 2005, Pages 735-739.<br />
<br />
6. Conrad R, Microbial ecology of methanogens and methanotrophs, Advances in Agronomy. Volume 96, 2007, Pages 1-63.<br />
<br />
7. Ralf Conrad, Christoph Erkel and Werner Liesack, Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil, Current Opinion in BiotechnologyVolume 17, Issue 3, , Environmental biotechnology/Energy biotechnology, June 2006, Pages 262-267.<br />
(http://www.sciencedirect.com/science/article/B6VRV-4JRVFV8-1/2/babb823ea30e51d7445d6861d7d334aa)<br />
<br />
==References==<br />
(1) Lecture 5 of Kate Scow. 2008. Microbial Metabolism. Unpublished, University of California, Davis.<br />
<br />
(2) Schlesinger, W.H. 1997. Biogeochemistry: An Analysis of Global Change. 2nd ed. Elsevier Academic Press, Amsterdam. <br />
<br />
(3) [http://books.google.com/books?id=1l4GAAAACAAJ&dq=soil+microbiology+sylvia&ei=thzbR9j6Hpu8swPmxOXzAQ Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey.]<br />
<br />
(4) [http://books.google.com/books?id=v6cGPMRmPYYC&pg=PA940&dq=J.+Kotz,+P.+Treichel,+G.+Weaver.+2006.+Chemistry+and+Chemical+Reactivity&ei=Bx3bR5yFF5-OtgOdqe3sAQ&sig=2IiJ_hdME4k5k06zd-H35y1cxC8#PPP1,M1 J. Kotz, P. Treichel, G. Weaver. 2006. Chemistry and Chemical Reactivity sixth edition.]<br />
<br />
(5)[http://books.google.com/books?id=xEFIEOjfxx0C&printsec=frontcover&dq=Wetland+richardson&ei=7xvbR4vMH4jysgOg6vnpAQ&sig=bDFNpm0lUibISaIaERoMAu5-K34 J.L Richardson and M.J Vepraskas., 2000 Wetland soils: Genesis, Hydrology, Landscapes, and Classification., CRC press LLC.] <br />
<br />
(6) Flood Duration Effects on Soybean Growth and Yield<br />
http://agron.scijournals.org/cgi/content/abstract/81/4/631<br />
<br />
(7)[http://books.google.com/books?id=pr7kAQAACAAJ&dq=Advances+in+Agricultural+Microbiology,&ei=ddHdR6qDJYG-sgPeyMXyAQ Knowles, R. 1982. Denitrification in Soils, pp. 246-266, In: N.S. Subba Rao (ed.) Advances in Agricultural Microbiology, Butterworth Sci. Pub., London, UK]<br />
<br />
(8) Cole and Brown 1980<br />
<br />
(9) Smith and Zimmerman 1982<br />
<br />
(10) Mac Herbent 1982<br />
<br />
(11)Hasan and Hall 1975<br />
<br />
(12) Kuenen and Roberston 1987<br />
<br />
(13)[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.mi.47.100193.001403?journalCode=micro Derek R. Lovley., 1993., Dissimilatory metal reduction. Annu Rev Microbiol. Vol 47 pp: 263-90.]<br />
<br />
(14) Gotoh and Patrick 1974<br />
<br />
(15) Schwertman and Taylor 1977<br />
<br />
(18) [http://aem.asm.org/cgi/reprint/52/4/751 Derek R. Lovley and Elizabeth J.P Phillips., Availability of Ferric Iron for Microbial Reduction in Bottom Sediments of the Freshwater Tidal Potomac River., Appl Environ Microbiology. 1986, p. 751-757]<br />
<br />
(19) [http://books.google.com/books?id=0GAvKQJ2JuwC&printsec=frontcover&vq=Wenk+H.R+and+Bulakh+A+.,+2004:+Minerals.+Their+constitution+and+origin.+Cambridge+University+Press&source=gbs_summary_r Wenk H.R and Bulakh A ., 2004: Minerals. Their constitution and origin. Cambridge University Press.]<br />
<br />
(20) [http://books.google.com/books?id=9K5I0ZPQd54C&pg=PA219&lpg=PA219&dq=%22LANGSTON%22+%228+Metal+handling%22&source=web&ots=qVFErWWjbn&sig=Iyh9_HN4S6PZU4jdXrMuWbLqcpI&hl=en#PPR11,M1 WJ Langston, MJ Bebianno, ,and GR Burt, ., (1998) "Metal handling strategies in molluscs" In: Langston, WJ, Bebiano, MJ eds. , Metal metabolism in the aquatic environment, Chapman and Hall, London, United Kingdom, pp 219-272]<br />
<br />
(21) Matthews, E. and I. Fung. 1987. Methane Emission from Natural Wetlands: Global Distribution, Area, and Environmental Characteristics of Sources. Global Biogeochemical Cycles 1: 61-86.<br />
<br />
(22) [http://books.google.com/books?id=zHIhWM5R9LcC&printsec=frontcover&dq=Y.Chen+and+Y+Avnimelech&source=gbs_summary_r#PPA118,M1 Y. Chen and Y . Avnimelech., (1986)., The Role of Organic Matter in Modern Agriculture., Springer., Developments in Plant and Soil Sciences , Vol. 25., p118]<br />
<br />
See [[#Current Research]] section for a list of journals for additional information on the topic of flooded soils. <br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=29312
Flooded Soils
2008-03-17T08:10:09Z
<p>Lrastegarzadeh: /* Sulfate Reducing Bacteria */</p>
<hr />
<div>[[Image:Floridacrocodile1.jpg|thumb|500px|right|Ding Darling reserve, Sanibel Island, Florida, with an American Crocodile. Wikipedia jimfbleak 13:37, 2 April 2006 (UTC)]] <br />
==Introduction==<br />
[[Image:flooded soil.png|thumb|400px|schematic presentation of flooded soil from[[Y.Chen and Y Avnimelech]]]]<br />
'''Flooded soils''' occur with complete water saturation of soil pores, and generally result in anoxic conditions of the soil environment. Flooded soil environments may include such [[Wikipedia:ecosystem|ecosystem]]<br />
as: rice paddies; wetlands (swamps, marshes, and bogs); compacted soils; and post-rain soils (Scow, 2008). Additionally, similar redox conditions (where oxygen is lacking) can also be found within soil aggregates and along pollutant plumes, and thus many of the concepts discussed in this section may be applied to those environments.<br />
<br />
Oxygen is only sparingly soluble in water and diffuses much more slowly through water than through air (Schlesinger, 1997). What little oxygen that is present in saturated soils in the form of dissolved O<sub>2</sub> is quickly consumed through metabolic processes. Oxygen is used as terminal electron acceptor via respiration by roots, soil microbes, and soil organisms (Sylvia, 2005), and is lost from the soil system in the form of carbon dioxide (CO<sub>2</sub>). Heterotrophic respiration may completely deplete oxygen in flooded soils; and these effects may be observed within only a few millimeters of the soil surface (Schlesinger, 1997). <br />
<br />
Due to the deficiency of oxygen in flooded soils, those organisms inhabiting flooded soils must be able to survive with little to no oxygen. Although energy yields are much greater with oxygen than with any other terminal electron acceptor (see [[#Electron tower]] theory, section 2.1.1), under anoxic conditions anaerobic and facultative microbes can use alternative electron acceptors such as nitrate, ferric iron (Fe III), manganese (IV) oxide, sulfate, and carbon dioxide to produce energy and build biomass. <br />
<br />
Microbial transformations of elements in anaerobic soils play a large role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere (Schlesinger, 1997).<br />
<br />
==Processes ==<br />
[[Image:phenomenon in aggregates.png|thumb|left|200px|Electron acceptor used in aggregates. adjusted from [[Prof. Kate lec #5]]]]<br />
[[Image:phenomena in pollutant plume.png|thumb|200px|Order of electron acceptor in pollutant plume from [[USGS]]]]<br />
In general, flooded soils occur due to seasonal flooding or agricultural activity. <br />
Flooded soils can be often converted into non-flooded soils by the water level fluctuation and drainage. Through this variation of soil conditins, various gases are emitted into the atmosphere and environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changing. <br />
As explained in the [[#Introduction]], microorganisms can use alternative terminal electron acceptors (such as nitrate, perchlorate, sulfate, and carbon dioxide) when dissolved oxygen is absent. Microbes will successively use electron acceptors according to the order of energy yields resulting from electron acceptor utilization indicted on the electron tower (see [[#Electron Tower]] theory). The progression of electron acceptor utilization may also be observed in soil aggregates and pollutant plumes. <br />
<br />
<br />
<br />
<br />
===[http://en.wikipedia.org/wiki/Redox Oxidation/Reduction (Redox) Reaction]===<br />
In redox reactions, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. A classic example well known in the process of cellular respiration is when glucose (the reducing agent) reacts with oxygen (the oxidizing agent)and is oxidized to carbon dioxide. In this reaction, oxygen is reduced to water. Oxygen is the most common and highest energy yielding electron acceptor, and some organisms (strict aerobes) can not live long without it.(6) In flooded soils oxygen is typically not availible. Facultative and strict anaerobic bacteria have the ability to use other oxidizing agents/electron acceptors to carry out respiration. Anaerobic and facultative bacteria will use the electron acceptor which yields the highest energy, or the acceptor which is most readily available. The availibility and concentration of electron acceptors changes as the soil profile increases in depth. <br />
====Electron Tower====<br />
[[Image:Environmental1.gif|thumb|400px|Electron tower [[http://www.microbiologybytes.com/introduction/Environmental.html]]]]<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified as strict aerobes, obligate anaerobes, and facultative anaerobes. Strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, microbes will choose to use nitrate as an electron acceptor (if available). Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptors in the order of electron acceptor having the most reducing energy. Oxygen is the most efficient electron acceptor, while carbon dioxide has the least amount of reduction potential.<br />
====Gleyed Soils and Recovery to Aerobic Conditions====<br />
[[Image:Gleyed soil.png|thumb|200px|left|Gleyed soil from Prof. Scow's lecture note 2008]]<br />
[[Image:Oxidized soil.png|thumb|300px|Oxidized soil from Prof. Scow's lecture note 2008]]<br />
'''Soil Gleying''':<br />
Gleying is a phenomenon in which waterlogged soils are discolored by accumulation of Fe(II) due to reduction of ferric iron into ferrous iron (Lovely 1991).<br />
Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe(III)-reducing fermentative bacteria can be readily isolated from gleyed soils. <br />
The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS<sub>2</sub>) (Wenk and Bulakh 2004).<br />
<br />
'''Recovery to Aerobic Conditions'''<br />
When waterlogged soils drain, the Eh starts to increase as oxygen diffuses into soil pores. Plentiful oxygen represses the activity of anaerobes, which results in an increase of aerobic microbes. If oxygen diffuses deep into the soil profile, the production of H<sub>2</sub>S ceases. Under aerobic conditions, ferrous iron is oxidized by iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals. The gray color in soil changes to a red, yellow, or brown color as these minerals are oxidized. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO<sub>2</sub> (Richardson and Vepraskas 2000).<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise as a result of the buffering capacity of the soil. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succession of anaerobic oxidation processes, the redox potential (Eh) of flooded soils will decrease as a result of the reduced products formed. Approximate values for redox potentials associated with specific oxidation-reduction process are as follows:<br />
<br />
{| width="300" border="1"<br />
|----- bgcolor ="orange"<br />
| width="200" height="23" | Observation<br />
| width="84" | Eh (mV) <br />
|-<br />
| Disappearance of oxygen<br />
| +330<br />
|-<br />
| Disappearance of nitrate<br />
| +220<br />
|-<br />
|Appearance of manganese ions <br />
| +200<br />
|-<br />
| Appearance of ferrous iron ions<br />
| +120 <br />
|-<br />
| Disappearance of sulfate<br />
| -150<br />
|-<br />
|Appearance of methane <br />
| -250<br />
|}<br />
<br />
===Solubility/Mobility of Minerals===<br />
Since the toxicity, solubility, mobility, and bioavailability for a given element or compound is mainly influenced by soil solution reduction potenial and pH, flooded soil conditions play an important role in the mobility of trace metal, nutrients, and minerals.<br />
<br />
<br />
====Plant Nutrient Availability====<br />
[[Image:overwater.jpg|left|frame|What over-watering looks like in a common house plant]]Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a major role in healthy plant growth. In flooded soils, under anaerobic conditions, the pH will tend to rise initially. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants. Microoganisms will begin to use available plants nutrients as alternative electron acceptors, such as sulfate, nitrate and iron(III).<br />
Experiments have been done on soybean plants to show the effects of flooded soils. Flood duration effects on soybean plants resulted in yellowing and abscission of leaves at the lower nodes, stunting, and reduced dry weight and seed yield. Canopy height and dry weight decreased linearly with duration of the flood at both growth stages. Growth rates were 25 to 35% less when soybeans were flooded (3).<br />
<br />
==Key Microbial Processes and Organisms Involved==<br />
The role of microorganisms under flooded soils<br />
===Microbial processes===<br />
====Microbial Activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as [http://en.wikipedia.org/wiki/Electron_acceptor TEA (terminal electron acceptors)]. Some important terminal electron acceptors include iron, nitrate, sulfate, and manganese. These processes are primarily driven by microobial activity. Energy yields of alternative electron acceptors are lower than that of aerobic respiration, in which oxygen is utilized as a TEA (see [[#Electron Tower]] theory. As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of TEA's from the electron tower, and will govern which microbes will thrive, as those able to use these available alternative electron acceptors. Flooding also alters microbial flora in soil by decreasing the O<sub>2</sub> concentration. Fermentation is a major biochemical processes responsible for organic matter decomposition in flooded soils. Eh levels can affect which compounds are fermented. These levels will tend to gradually drop in flooded soils.<br />
<br />
====Fermentation under Anoxic Conditions====<br />
[[Image:anaerobic decomposition.png|thumb|left|300px|Organic matter decomposition pathways . [[Richardson and Vepraskas]]]]<br />
There are many types of fermentative bacteria in soils, such as the genus ''[[Bacillus]]'', ''[[Clostridium]]'', and ''[[Lactobacillus]]''. 4 ATP molecules per molecule of glucose are produced by fermentation, while 38 ATP molecules are produced by aerobic respiration. Although the energy yield via fermentation is less than oxidative phosphorylation, fermentation plays an important role in anaerobic respiration for obligate and facultative anaerobic bacteria, including denitrifier, Fe<sup>3+</sup>, Mn<sup>4+</sup>, SO<sub>4</sub><sup>2-</sup>, reducers, and methanogens. Sugar (glucose or fructose) is broken down into simple compounds (e.g. formate, acetate, and ethanol) during fermentation. Also, numerous fermentation products, such as carbon dioxide, fatty acid, lactic, alcohols, are released into soils. These compounds serve as substrates for other anaerobic bacteria. Thus, low molecular weight organic compounds produced from fermentation influence the reduction of Fe(III), Mn(IV), SO<sub>4</sub><sup>2-</sup>, and CO<sub>2</sub>(Richardson And Vepraskas 2000).<br />
----<br />
<br />
===Organisms involved in Flooded Soils===<br />
====Nitrate Reducing Bacteria====<br />
When available oxygen is depleted and nitrate is available, denitrification, the reduction of NO<sub>3</sub><sup>-</sup> to NO,N<sub>2</sub>,or N<sub>2</sub>, primarily occurs.<br />
Denitrification is carried out by obligate respiratory bacteria belonging to the genra ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''[[Paracoccus denitrificans]]'', ''[[Pseudomonas]]'' and ''[[Thiobacillus]]'' (Knowles, 1982). Nitrate ammonification found in facultative anaerobic bacteria belonging to the genera ''[[Bacillus]]'', ''Citrobacter'' and ''[[Aeromonas]]'', or memebers of the ''[[Enterobacteriaceae]]'' (Cole adn Brown, 1980; Smith adn Zimmerman, 1981; MacFarlane and Herbert, 1982). Strictly anaerobic bacteria belonging to the genus ''[[Clostridium]]'' are also able to reduce nitrate to ammonia (Hasan and Hall, 1975). <br />
Pure culture studies show evidance that nitrate reduction may also occur in the presence of oxygen (Kuenen and and Robertson, 1987).<br />
<br />
====Iron/Manganese Reducing Bacteria====<br />
Most microorganisms can reduce Mn<sup>4+</sup> and Fe <sup>3+</sup>.<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''[[Geobacter]]([[Geobacter metallireducens]] and [[Geobacter sulfurreducens]]),Shewanella putrefaciens,[[Desulfovibrio]], [[Pseudomonas]],'' and ''[[Thiobacillus]]''(Lovley 1993). ''[[Bacillus]], [[Geobacter]],'' and ''[[Pseudomonas]]'' are representative manganese-reducing bacteria. <br />
Different forms of ferric iron oxides exist in drained aerobic soils as well as in waterlogged soils. Not all forms of ferric oxides are equally suitable for reduction by ferric oxide reducer bacteria (Gotoh and Patrick, 1974; Schwertmann and Taylor, 1977). In general, amorphous forms are more efficient for ferric reducer bacteria than crystalline forms (Lovely adn Phillips, 1986). The reduction of ferric oxide may release phosphate and trace elements that are adsorbed to amorphous ferric oxide and thus enhance availablity of these compounds in the soil (Lovely and Phillips, 1986).<br />
<br />
====Sulfate Reducing Bacteria====<br />
Bacteria can use organic compouds as an electron donor and sulfate as an electron acceptor. This reaction for acetate as electron donor is as follows:<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''[[Desulfobacter]]'', ''Desulfobulbus'', ''Desulfococcus'', ''[[Desulfovibrio]]'', ''[[Desulfosarcina]]'',''Desulfotomaculum'',and ''Desulfonema''(Langston and Bebiano 1998, Sylvia 2004). Some of the sulfate reducing bacteria oxidize the organic componds completely to CO2 and some other stop after producing acetate as an intermaediate of oxidation. Hydrogen sulfide gas produced via anaerobic respiration causes the rotten egg odor.<br />
<br />
====[[Methanogens]]====<br />
Methanogen products less energy than other rueducing reaction because the reduction of carbon dioxide occur under the most anaerobic and reduced conditions(see [[#Electron tower]] section). Thus, the activity of methanogen is repressed until other alternative terminal electron acceptor such as Fe(III), NO<sub>3</sub><sup>-</sup>,and SO<sub>4</sub><sup>2-</sup>, have been depleted.<br />
<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
==Greenhouse Gas Emissions from Flooded Soils==<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively (Schlesinger, 1997). Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. According to Matthews and Fung (1987), an estimated 3.6% of terrestrial land is classified as wetlands, and although this number continues to decline (Schlesinger, 1997) the effect of flooded soils to the global climate is clear. <br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV (see [[#electron tower]] theory, section 2.1.1) (Sylvia, 2005). If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions. <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process (Sylvia, 2005). <br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions (Sylvia, 2005).<br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane (Sylvia, 1998). Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur. (Sylvia, 2005).<br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly (Sylvia, 2005).<br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosytems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. Following is a list of recent journal review articles focused on a range of current research topics related to flooded soil environments for the interested reader: <br />
<br />
1. Shangping Xu, Peter R. Jaffe and Denise L. Mauzerall, A process-based model for methane emission from flooded rice paddy systems, Ecological ModellingVolume 205, Issues 3-4, , 24 July 2007, Pages 475-491.<br />
(http://www.sciencedirect.com/science/article/B6VBS-4NHV759-1/2/3126b5403a44c51c5d8d4160382d848e)<br />
<br />
2. HANK GREENWAY , WILLIAM ARMSTRONG , and TIMOTHY D. COLMER <br />
Conditions Leading to High CO2 (>5 kPa) in Waterlogged–Flooded Soils and Possible Effects on Root Growth and Metabolism <br />
AOBPreview published on July 1, 2006, DOI 10.1093/aob/mcl076.<br />
Ann Bot 98: 9-32.<br />
<br />
3. Kazunori Minamikawa and Naoki Sakai, The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan, Agriculture, Ecosystems & EnvironmentVolume 107, Issue 4, , 30 May 2005, Pages 397-407.<br />
(http://www.sciencedirect.com/science/article/B6T3Y-4FY9M5H-1/2/98a4074277436af97833c16a823b326c)<br />
Keywords: Methane; Water management; Soil redox potential; Oryza sativa L.; Rice yield<br />
<br />
4. Makoto Kimura, Jun Murase and Yahai Lu, Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4), Soil Biology and BiochemistryVolume 36, Issue 9, , September 2004, Pages 1399-1416.<br />
(http://www.sciencedirect.com/science/article/B6TC7-4C9G7KP-4/2/ceb77d1803f5d02e51bb773f3163cdcb)<br />
<br />
5. Sahrawat KL, Fertility and organic matter in submerged rice soils, Current Science. Volume 88, Issues 3-4, 2005, Pages 735-739.<br />
<br />
6. Conrad R, Microbial ecology of methanogens and methanotrophs, Advances in Agronomy. Volume 96, 2007, Pages 1-63.<br />
<br />
7. Ralf Conrad, Christoph Erkel and Werner Liesack, Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil, Current Opinion in BiotechnologyVolume 17, Issue 3, , Environmental biotechnology/Energy biotechnology, June 2006, Pages 262-267.<br />
(http://www.sciencedirect.com/science/article/B6VRV-4JRVFV8-1/2/babb823ea30e51d7445d6861d7d334aa)<br />
<br />
==References==<br />
(1) Lecture 5 of Kate Scow. 2008. Microbial Metabolism. Unpublished, University of California, Davis.<br />
<br />
(2) Schlesinger, W.H. 1997. Biogeochemistry: An Analysis of Global Change. 2nd ed. Elsevier Academic Press, Amsterdam. <br />
<br />
(3) [http://books.google.com/books?id=1l4GAAAACAAJ&dq=soil+microbiology+sylvia&ei=thzbR9j6Hpu8swPmxOXzAQ Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey.]<br />
<br />
(4) [http://books.google.com/books?id=v6cGPMRmPYYC&pg=PA940&dq=J.+Kotz,+P.+Treichel,+G.+Weaver.+2006.+Chemistry+and+Chemical+Reactivity&ei=Bx3bR5yFF5-OtgOdqe3sAQ&sig=2IiJ_hdME4k5k06zd-H35y1cxC8#PPP1,M1 J. Kotz, P. Treichel, G. Weaver. 2006. Chemistry and Chemical Reactivity sixth edition.]<br />
<br />
(5)[http://books.google.com/books?id=xEFIEOjfxx0C&printsec=frontcover&dq=Wetland+richardson&ei=7xvbR4vMH4jysgOg6vnpAQ&sig=bDFNpm0lUibISaIaERoMAu5-K34 J.L Richardson and M.J Vepraskas., 2000 Wetland soils: Genesis, Hydrology, Landscapes, and Classification., CRC press LLC.] <br />
<br />
(6) Flood Duration Effects on Soybean Growth and Yield<br />
http://agron.scijournals.org/cgi/content/abstract/81/4/631<br />
<br />
(7)[http://books.google.com/books?id=pr7kAQAACAAJ&dq=Advances+in+Agricultural+Microbiology,&ei=ddHdR6qDJYG-sgPeyMXyAQ Knowles, R. 1982. Denitrification in Soils, pp. 246-266, In: N.S. Subba Rao (ed.) Advances in Agricultural Microbiology, Butterworth Sci. Pub., London, UK]<br />
<br />
(8) Cole and Brown 1980<br />
<br />
(9) Smith and Zimmerman 1982<br />
<br />
(10) Mac Herbent 1982<br />
<br />
(11)Hasan and Hall 1975<br />
<br />
(12) Kuenen and Roberston 1987<br />
<br />
(13)[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.mi.47.100193.001403?journalCode=micro Derek R. Lovley., 1993., Dissimilatory metal reduction. Annu Rev Microbiol. Vol 47 pp: 263-90.]<br />
<br />
(14) Gotoh and Patrick 1974<br />
<br />
(15) Schwertman and Taylor 1977<br />
<br />
(18) [http://aem.asm.org/cgi/reprint/52/4/751 Derek R. Lovley and Elizabeth J.P Phillips., Availability of Ferric Iron for Microbial Reduction in Bottom Sediments of the Freshwater Tidal Potomac River., Appl Environ Microbiology. 1986, p. 751-757]<br />
<br />
(19) [http://books.google.com/books?id=0GAvKQJ2JuwC&printsec=frontcover&vq=Wenk+H.R+and+Bulakh+A+.,+2004:+Minerals.+Their+constitution+and+origin.+Cambridge+University+Press&source=gbs_summary_r Wenk H.R and Bulakh A ., 2004: Minerals. Their constitution and origin. Cambridge University Press.]<br />
<br />
(20) [http://books.google.com/books?id=9K5I0ZPQd54C&pg=PA219&lpg=PA219&dq=%22LANGSTON%22+%228+Metal+handling%22&source=web&ots=qVFErWWjbn&sig=Iyh9_HN4S6PZU4jdXrMuWbLqcpI&hl=en#PPR11,M1 WJ Langston, MJ Bebianno, ,and GR Burt, ., (1998) "Metal handling strategies in molluscs" In: Langston, WJ, Bebiano, MJ eds. , Metal metabolism in the aquatic environment, Chapman and Hall, London, United Kingdom, pp 219-272]<br />
<br />
(21) Matthews, E. and I. Fung. 1987. Methane Emission from Natural Wetlands: Global Distribution, Area, and Environmental Characteristics of Sources. Global Biogeochemical Cycles 1: 61-86.<br />
<br />
(22) [http://books.google.com/books?id=zHIhWM5R9LcC&printsec=frontcover&dq=Y.Chen+and+Y+Avnimelech&source=gbs_summary_r#PPA118,M1 Y. Chen and Y . Avnimelech., (1986)., The Role of Organic Matter in Modern Agriculture., Springer., Developments in Plant and Soil Sciences , Vol. 25., p118]<br />
<br />
See [[#Current Research]] section for a list of journals for additional information on the topic of flooded soils. <br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29311
Desulfobacter
2008-03-17T08:07:17Z
<p>Lrastegarzadeh: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
Morphology of strain ''Desulfobacter'' B54T (A) micrograph of cells.Bar, 10 mm. (B and C) Electron micrographs of one cell. Bars, 2 mm.<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [2]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [3,4].<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [5]. The main habitat of Desulfobacter is marine sendiment and brackish water.<br />
<br />
==References==<br />
<br />
[1] Torleiv Lien and Janiche Beeder. 1997.Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation System. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY. Oct., p. 1124–1128 <br />
<br />
[2] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[3] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[4] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[5] [http://books.google.com/books?hl=en&id=VUdeCXm5eHkC&dq=sulphate+reducing+bacteria+larry+barton&printsec=frontcover&source=web&ots=aiyATgKvz_&sig=st9vJjY6Vy8KpSmc63kXEuAMi3w Barton, Larry L. and W. Allen Hamilton. 2007. Sulphate reducing Bacteria Wnvironmental and Engineering system. 1st ed. Cambridge University Press. Cambridge, UK.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29310
Desulfobacter
2008-03-17T08:06:14Z
<p>Lrastegarzadeh: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
Morphology of strain ''Desulfobacter'' B54T (A) micrograph of cells.Bar, 10 mm. (B and C) Electron micrographs of one cell. Bars, 2 mm.<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [2]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [3,4].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [5]. The main habitat of Desulfobacter is marine sendiment and brackish water.<br />
<br />
==References==<br />
<br />
[1] Torleiv Lien and Janiche Beeder. 1997.Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation System. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY. Oct., p. 1124–1128 <br />
<br />
[2] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[3] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[4] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[5] [http://books.google.com/books?hl=en&id=VUdeCXm5eHkC&dq=sulphate+reducing+bacteria+larry+barton&printsec=frontcover&source=web&ots=aiyATgKvz_&sig=st9vJjY6Vy8KpSmc63kXEuAMi3w Barton, Larry L. and W. Allen Hamilton. 2007. Sulphate reducing Bacteria Wnvironmental and Engineering system. 1st ed. Cambridge University Press. Cambridge, UK.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29309
Desulfobacter
2008-03-17T07:57:51Z
<p>Lrastegarzadeh: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
Morphology of strain ''Desulfobacter'' B54T (A) micrograph of cells.Bar, 10 mm. (B and C) Electron micrographs of one cell. Bars, 2 mm.<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [2]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [3,4].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [5]. The main habitat of Desulfobacter is marine sendiment and brackish water.<br />
<br />
==References==<br />
<br />
[1] Torleiv Lien and Janiche Beeder. 1997.Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation System. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY. Oct., p. 1124–1128 <br />
<br />
[2] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[3] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[4] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[5] Sulphate reducing bacteria-book)</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29308
Desulfobacter
2008-03-17T07:57:34Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
Morphology of strain ''Desulfobacter'' B54T (A) micrograph of cells.Bar, 10 mm. (B and C) Electron micrographs of one cell. Bars, 2 mm.<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [2]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [3,4].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. The main habitat of Desulfobacter is marine sendiment and brackish water.<br />
<br />
==References==<br />
<br />
[1] Torleiv Lien and Janiche Beeder. 1997.Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation System. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY. Oct., p. 1124–1128 <br />
<br />
[2] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[3] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[4] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[5] Sulphate reducing bacteria-book)</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29307
Desulfobacter
2008-03-17T07:56:59Z
<p>Lrastegarzadeh: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
Morphology of strain ''Desulfobacter'' B54T (A) micrograph of cells.Bar, 10 mm. (B and C) Electron micrographs of one cell. Bars, 2 mm.<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. The main habitat of Desulfobacter is marine sendiment and brackish water.<br />
<br />
==References==<br />
<br />
[1] Torleiv Lien and Janiche Beeder. 1997.Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation System. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY. Oct., p. 1124–1128 <br />
<br />
[2] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[3] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[4] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[5] Sulphate reducing bacteria-book)</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29306
Desulfobacter
2008-03-17T07:51:00Z
<p>Lrastegarzadeh: /* Classification */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
Morphology of strain ''Desulfobacter'' B54T (A) micrograph of cells.Bar, 10 mm. (B and C) Electron micrographs of one cell. Bars, 2 mm.<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. The main habitat of Desulfobacter is marine sendiment and brackish water.<br />
<br />
==References==<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29305
Desulfobacter
2008-03-17T07:37:41Z
<p>Lrastegarzadeh: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. The main habitat of Desulfobacter is marine sendiment and brackish water.<br />
<br />
==References==<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29304
Desulfobacter
2008-03-17T07:37:13Z
<p>Lrastegarzadeh: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. The main habitat of Desulfobacter is marine sendiment and brackish water. <br />
<br />
<br />
<br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29303
Desulfobacter
2008-03-17T07:36:21Z
<p>Lrastegarzadeh: /* Cell Structure and Metabolism */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. The main habitat of Desulfobacter is marine sendiment and brackish water. <br />
<br />
<br />
<br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29302
Desulfobacter
2008-03-17T07:34:56Z
<p>Lrastegarzadeh: /* Species: */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
''D. postgatei'', ''D. hydrogenophilus'', ''D.<br />
latus'', and ''D. curvatus''<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. The main habitat of Desulfobacter is marine sendiment and brackish water. <br />
<br />
<br />
<br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=29301
Flooded Soils
2008-03-17T07:24:13Z
<p>Lrastegarzadeh: /* Sulfate Reducing Bacteria */</p>
<hr />
<div>[[Image:Floridacrocodile1.jpg|thumb|500px|right|Ding Darling reserve, Sanibel Island, Florida, with an American Crocodile. Wikipedia jimfbleak 13:37, 2 April 2006 (UTC)]] <br />
==Introduction==<br />
[[Image:flooded soil.png|thumb|400px|schematic presentation of flooded soil from[[Y.Chen and Y Avnimelech]]]]<br />
'''Flooded soils''' occur with complete water saturation of soil pores, and generally result in anoxic conditions of the soil environment. Flooded soil environments may include such [[Wikipedia:ecosystem|ecosystem]]<br />
as: rice paddies; wetlands (swamps, marshes, and bogs); compacted soils; and post-rain soils (Scow, 2008). Additionally, similar redox conditions (where oxygen is lacking) can also be found within soil aggregates and along pollutant plumes, and thus many of the concepts discussed in this section may be applied to those environments.<br />
<br />
Oxygen is only sparingly soluble in water and diffuses much more slowly through water than through air (Schlesinger, 1997). What little oxygen that is present in saturated soils in the form of dissolved O<sub>2</sub> is quickly consumed through metabolic processes. Oxygen is used as terminal electron acceptor via respiration by roots, soil microbes, and soil organisms (Sylvia, 2005), and is lost from the soil system in the form of carbon dioxide (CO<sub>2</sub>). Heterotrophic respiration may completely deplete oxygen in flooded soils; and these effects may be observed within only a few millimeters of the soil surface (Schlesinger, 1997). <br />
<br />
Due to the deficiency of oxygen in flooded soils, those organisms inhabiting flooded soils must be able to survive with little to no oxygen. Although energy yields are much greater with oxygen than with any other terminal electron acceptor (see [[#Electron tower]] theory, section 2.1.1), under anoxic conditions anaerobic and facultative microbes can use alternative electron acceptors such as nitrate, ferric iron (Fe III), manganese (IV) oxide, sulfate, and carbon dioxide to produce energy and build biomass. <br />
<br />
Microbial transformations of elements in anaerobic soils play a large role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere (Schlesinger, 1997).<br />
<br />
==Processes ==<br />
[[Image:phenomenon in aggregates.png|thumb|left|200px|Electron acceptor used in aggregates. adjusted from [[Prof. Kate lec #5]]]]<br />
[[Image:phenomena in pollutant plume.png|thumb|200px|Order of electron acceptor in pollutant plume from [[USGS]]]]<br />
In general, flooded soils occur due to seasonal flooding or agricultural activity. <br />
Flooded soils can be often converted into non-flooded soils by the water level fluctuation and drainage. Through this variation of soil conditins, various gases are emitted into the atmosphere and environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changing. <br />
As explained in the [[#Introduction]], microorganisms can use alternative terminal electron acceptors (such as nitrate, perchlorate, sulfate, and carbon dioxide) when dissolved oxygen is absent. Microbes will successively use electron acceptors according to the order of energy yields resulting from electron acceptor utilization indicted on the electron tower (see [[#Electron Tower]] theory). The progression of electron acceptor utilization may also be observed in soil aggregates and pollutant plumes. <br />
<br />
<br />
<br />
<br />
===[http://en.wikipedia.org/wiki/Redox Oxidation/Reduction (Redox) Reaction]===<br />
In redox reactions, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. A classic example well known in the process of cellular respiration is when glucose (the reducing agent) reacts with oxygen (the oxidizing agent)and is oxidized to carbon dioxide. In this reaction, oxygen is reduced to water. Oxygen is the most common and highest energy yielding electron acceptor, and some organisms (strict aerobes) can not live long without it.(6) In flooded soils oxygen is typically not availible. Facultative and strict anaerobic bacteria have the ability to use other oxidizing agents/electron acceptors to carry out respiration. Anaerobic and facultative bacteria will use the electron acceptor which yields the highest energy, or the acceptor which is most readily available. The availibility and concentration of electron acceptors changes as the soil profile increases in depth. <br />
====Electron Tower====<br />
[[Image:Environmental1.gif|thumb|400px|Electron tower [[http://www.microbiologybytes.com/introduction/Environmental.html]]]]<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified as strict aerobes, obligate anaerobes, and facultative anaerobes. Strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, microbes will choose to use nitrate as an electron acceptor (if available). Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptors in the order of electron acceptor having the most reducing energy. Oxygen is the most efficient electron acceptor, while carbon dioxide has the least amount of reduction potential.<br />
====Gleyed Soils and Recovery to Aerobic Conditions====<br />
[[Image:Gleyed soil.png|thumb|200px|left|Gleyed soil from Prof. Scow's lecture note 2008]]<br />
[[Image:Oxidized soil.png|thumb|300px|Oxidized soil from Prof. Scow's lecture note 2008]]<br />
'''Soil Gleying''':<br />
Gleying is a phenomenon in which waterlogged soils are discolored by accumulation of Fe(II) due to reduction of ferric iron into ferrous iron (Lovely 1991).<br />
Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe(III)-reducing fermentative bacteria can be readily isolated from gleyed soils. <br />
The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS<sub>2</sub>) (Wenk and Bulakh 2004).<br />
<br />
'''Recovery to Aerobic Conditions'''<br />
When waterlogged soils drain, the Eh starts to increase as oxygen diffuses into soil pores. Plentiful oxygen represses the activity of anaerobes, which results in an increase of aerobic microbes. If oxygen diffuses deep into the soil profile, the production of H<sub>2</sub>S ceases. Under aerobic conditions, ferrous iron is oxidized by iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals. The gray color in soil changes to a red, yellow, or brown color as these minerals are oxidized. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO<sub>2</sub> (Richardson and Vepraskas 2000).<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise as a result of the buffering capacity of the soil. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succession of anaerobic oxidation processes, the redox potential (Eh) of flooded soils will decrease as a result of the reduced products formed. Approximate values for redox potentials associated with specific oxidation-reduction process are as follows:<br />
<br />
{| width="300" border="1"<br />
|----- bgcolor ="orange"<br />
| width="200" height="23" | Observation<br />
| width="84" | Eh (mV) <br />
|-<br />
| Disappearance of oxygen<br />
| +330<br />
|-<br />
| Disappearance of nitrate<br />
| +220<br />
|-<br />
|Appearance of manganese ions <br />
| +200<br />
|-<br />
| Appearance of ferrous iron ions<br />
| +120 <br />
|-<br />
| Disappearance of sulfate<br />
| -150<br />
|-<br />
|Appearance of methane <br />
| -250<br />
|}<br />
<br />
===Solubility/Mobility of Minerals===<br />
Since the toxicity, solubility, mobility, and bioavailability for a given element or compound is mainly influenced by soil solution reduction potenial and pH, flooded soil conditions play an important role in the mobility of trace metal, nutrients, and minerals.<br />
<br />
<br />
====Plant Nutrient Availability====<br />
[[Image:overwater.jpg|left|frame|What over-watering looks like in a common house plant]]Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a major role in healthy plant growth. In flooded soils, under anaerobic conditions, the pH will tend to rise initially. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants. Microoganisms will begin to use available plants nutrients as alternative electron acceptors, such as sulfate, nitrate and iron(III).<br />
Experiments have been done on soybean plants to show the effects of flooded soils. Flood duration effects on soybean plants resulted in yellowing and abscission of leaves at the lower nodes, stunting, and reduced dry weight and seed yield. Canopy height and dry weight decreased linearly with duration of the flood at both growth stages. Growth rates were 25 to 35% less when soybeans were flooded (3).<br />
<br />
==Key Microbial Processes and Organisms Involved==<br />
The role of microorganisms under flooded soils<br />
===Microbial processes===<br />
====Microbial Activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as [http://en.wikipedia.org/wiki/Electron_acceptor TEA (terminal electron acceptors)]. Some important terminal electron acceptors include iron, nitrate, sulfate, and manganese. These processes are primarily driven by microobial activity. Energy yields of alternative electron acceptors are lower than that of aerobic respiration, in which oxygen is utilized as a TEA (see [[#Electron Tower]] theory. As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of TEA's from the electron tower, and will govern which microbes will thrive, as those able to use these available alternative electron acceptors. Flooding also alters microbial flora in soil by decreasing the O<sub>2</sub> concentration. Fermentation is a major biochemical processes responsible for organic matter decomposition in flooded soils. Eh levels can affect which compounds are fermented. These levels will tend to gradually drop in flooded soils.<br />
<br />
====Fermentation under Anoxic Conditions====<br />
[[Image:anaerobic decomposition.png|thumb|left|300px|Organic matter decomposition pathways . [[Richardson and Vepraskas]]]]<br />
There are many types of fermentative bacteria in soils, such as the genus ''[[Bacillus]]'', ''[[Clostridium]]'', and ''[[Lactobacillus]]''. 4 ATP molecules per molecule of glucose are produced by fermentation, while 38 ATP molecules are produced by aerobic respiration. Although the energy yield via fermentation is less than oxidative phosphorylation, fermentation plays an important role in anaerobic respiration for obligate and facultative anaerobic bacteria, including denitrifier, Fe<sup>3+</sup>, Mn<sup>4+</sup>, SO<sub>4</sub><sup>2-</sup>, reducers, and methanogens. Sugar (glucose or fructose) is broken down into simple compounds (e.g. formate, acetate, and ethanol) during fermentation. Also, numerous fermentation products, such as carbon dioxide, fatty acid, lactic, alcohols, are released into soils. These compounds serve as substrates for other anaerobic bacteria. Thus, low molecular weight organic compounds produced from fermentation influence the reduction of Fe(III), Mn(IV), SO<sub>4</sub><sup>2-</sup>, and CO<sub>2</sub>(Richardson And Vepraskas 2000).<br />
----<br />
<br />
===Organisms involved in Flooded Soils===<br />
====Nitrate Reducing Bacteria====<br />
When available oxygen is depleted and nitrate is available, denitrification, the reduction of NO<sub>3</sub><sup>-</sup> to NO,N<sub>2</sub>,or N<sub>2</sub>, primarily occurs.<br />
Denitrification is carried out by obligate respiratory bacteria belonging to the genra ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''[[Paracoccus denitrificans]]'', ''[[Pseudomonas]]'' and ''[[Thiobacillus]]'' (Knowles, 1982). Nitrate ammonification found in facultative anaerobic bacteria belonging to the genera ''[[Bacillus]]'', ''Citrobacter'' and ''[[Aeromonas]]'', or memebers of the ''[[Enterobacteriaceae]]'' (Cole adn Brown, 1980; Smith adn Zimmerman, 1981; MacFarlane and Herbert, 1982). Strictly anaerobic bacteria belonging to the genus ''[[Clostridium]]'' are also able to reduce nitrate to ammonia (Hasan and Hall, 1975). <br />
Pure culture studies show evidance that nitrate reduction may also occur in the presence of oxygen (Kuenen and and Robertson, 1987).<br />
<br />
====Iron/Manganese Reducing Bacteria====<br />
Most microorganisms can reduce Mn<sup>4+</sup> and Fe <sup>3+</sup>.<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''[[Geobacter]]([[Geobacter metallireducens]] and [[Geobacter sulfurreducens]]),Shewanella putrefaciens,[[Desulfovibrio]], [[Pseudomonas]],'' and ''[[Thiobacillus]]''(Lovley 1993). ''[[Bacillus]], [[Geobacter]],'' and ''[[Pseudomonas]]'' are representative manganese-reducing bacteria. <br />
Different forms of ferric iron oxides exist in drained aerobic soils as well as in waterlogged soils. Not all forms of ferric oxides are equally suitable for reduction by ferric oxide reducer bacteria (Gotoh and Patrick, 1974; Schwertmann and Taylor, 1977). In general, amorphous forms are more efficient for ferric reducer bacteria than crystalline forms (Lovely adn Phillips, 1986). The reduction of ferric oxide may release phosphate and trace elements that are adsorbed to amorphous ferric oxide and thus enhance availablity of these compounds in the soil (Lovely and Phillips, 1986).<br />
<br />
====Sulfate Reducing Bacteria====<br />
Bacteria can use organic compouds as an electron donor and sulfate as an electron acceptor. This reaction for acetate as electron donor is as follows:<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''[[Desulfobacter]]'', ''Desulfobulbus'', ''[[Desulfococcus]]'', ''[[Desulfovibrio]]'', ''[[Desulfosarcina]]'',''Desulfotomaculum'',and ''Desulfonema''(Langston and Bebiano 1998, Sylvia 2004). Some of the sulfate reducing bacteria oxidize the organic componds completely to CO2 and some other stop after producing acetate as an intermaediate of oxidation. Hydrogen sulfide gas produced via anaerobic respiration causes the rotten egg odor.<br />
<br />
====[[Methanogens]]====<br />
Methanogen products less energy than other rueducing reaction because the reduction of carbon dioxide occur under the most anaerobic and reduced conditions(see [[#Electron tower]] section). Thus, the activity of methanogen is repressed until other alternative terminal electron acceptor such as Fe(III), NO<sub>3</sub><sup>-</sup>,and SO<sub>4</sub><sup>2-</sup>, have been depleted.<br />
<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
==Greenhouse Gas Emissions from Flooded Soils==<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively (Schlesinger, 1997). Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. According to Matthews and Fung (1987), an estimated 3.6% of terrestrial land is classified as wetlands, and although this number continues to decline (Schlesinger, 1997) the effect of flooded soils to the global climate is clear. <br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV (see [[#electron tower]] theory, section 2.1.1) (Sylvia, 2005). If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions. <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process (Sylvia, 2005). <br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions (Sylvia, 2005).<br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane (Sylvia, 1998). Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur. (Sylvia, 2005).<br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly (Sylvia, 2005).<br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosytems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. Following is a list of recent journal review articles focused on a range of current research topics related to flooded soil environments for the interested reader: <br />
<br />
1. Shangping Xu, Peter R. Jaffe and Denise L. Mauzerall, A process-based model for methane emission from flooded rice paddy systems, Ecological ModellingVolume 205, Issues 3-4, , 24 July 2007, Pages 475-491.<br />
(http://www.sciencedirect.com/science/article/B6VBS-4NHV759-1/2/3126b5403a44c51c5d8d4160382d848e)<br />
<br />
2. HANK GREENWAY , WILLIAM ARMSTRONG , and TIMOTHY D. COLMER <br />
Conditions Leading to High CO2 (>5 kPa) in Waterlogged–Flooded Soils and Possible Effects on Root Growth and Metabolism <br />
AOBPreview published on July 1, 2006, DOI 10.1093/aob/mcl076.<br />
Ann Bot 98: 9-32.<br />
<br />
3. Kazunori Minamikawa and Naoki Sakai, The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan, Agriculture, Ecosystems & EnvironmentVolume 107, Issue 4, , 30 May 2005, Pages 397-407.<br />
(http://www.sciencedirect.com/science/article/B6T3Y-4FY9M5H-1/2/98a4074277436af97833c16a823b326c)<br />
Keywords: Methane; Water management; Soil redox potential; Oryza sativa L.; Rice yield<br />
<br />
4. Makoto Kimura, Jun Murase and Yahai Lu, Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4), Soil Biology and BiochemistryVolume 36, Issue 9, , September 2004, Pages 1399-1416.<br />
(http://www.sciencedirect.com/science/article/B6TC7-4C9G7KP-4/2/ceb77d1803f5d02e51bb773f3163cdcb)<br />
<br />
5. Sahrawat KL, Fertility and organic matter in submerged rice soils, Current Science. Volume 88, Issues 3-4, 2005, Pages 735-739.<br />
<br />
6. Conrad R, Microbial ecology of methanogens and methanotrophs, Advances in Agronomy. Volume 96, 2007, Pages 1-63.<br />
<br />
7. Ralf Conrad, Christoph Erkel and Werner Liesack, Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil, Current Opinion in BiotechnologyVolume 17, Issue 3, , Environmental biotechnology/Energy biotechnology, June 2006, Pages 262-267.<br />
(http://www.sciencedirect.com/science/article/B6VRV-4JRVFV8-1/2/babb823ea30e51d7445d6861d7d334aa)<br />
<br />
==References==<br />
(1) Lecture 5 of Kate Scow. 2008. Microbial Metabolism. Unpublished, University of California, Davis.<br />
<br />
(2) Schlesinger, W.H. 1997. Biogeochemistry: An Analysis of Global Change. 2nd ed. Elsevier Academic Press, Amsterdam. <br />
<br />
(3) [http://books.google.com/books?id=1l4GAAAACAAJ&dq=soil+microbiology+sylvia&ei=thzbR9j6Hpu8swPmxOXzAQ Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey.]<br />
<br />
(4) [http://books.google.com/books?id=v6cGPMRmPYYC&pg=PA940&dq=J.+Kotz,+P.+Treichel,+G.+Weaver.+2006.+Chemistry+and+Chemical+Reactivity&ei=Bx3bR5yFF5-OtgOdqe3sAQ&sig=2IiJ_hdME4k5k06zd-H35y1cxC8#PPP1,M1 J. Kotz, P. Treichel, G. Weaver. 2006. Chemistry and Chemical Reactivity sixth edition.]<br />
<br />
(5)[http://books.google.com/books?id=xEFIEOjfxx0C&printsec=frontcover&dq=Wetland+richardson&ei=7xvbR4vMH4jysgOg6vnpAQ&sig=bDFNpm0lUibISaIaERoMAu5-K34 J.L Richardson and M.J Vepraskas., 2000 Wetland soils: Genesis, Hydrology, Landscapes, and Classification., CRC press LLC.] <br />
<br />
(6) Flood Duration Effects on Soybean Growth and Yield<br />
http://agron.scijournals.org/cgi/content/abstract/81/4/631<br />
<br />
(7)[http://books.google.com/books?id=pr7kAQAACAAJ&dq=Advances+in+Agricultural+Microbiology,&ei=ddHdR6qDJYG-sgPeyMXyAQ Knowles, R. 1982. Denitrification in Soils, pp. 246-266, In: N.S. Subba Rao (ed.) Advances in Agricultural Microbiology, Butterworth Sci. Pub., London, UK]<br />
<br />
(8) Cole and Brown 1980<br />
<br />
(9) Smith and Zimmerman 1982<br />
<br />
(10) Mac Herbent 1982<br />
<br />
(11)Hasan and Hall 1975<br />
<br />
(12) Kuenen and Roberston 1987<br />
<br />
(13)[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.mi.47.100193.001403?journalCode=micro Derek R. Lovley., 1993., Dissimilatory metal reduction. Annu Rev Microbiol. Vol 47 pp: 263-90.]<br />
<br />
(14) Gotoh and Patrick 1974<br />
<br />
(15) Schwertman and Taylor 1977<br />
<br />
(18) [http://aem.asm.org/cgi/reprint/52/4/751 Derek R. Lovley and Elizabeth J.P Phillips., Availability of Ferric Iron for Microbial Reduction in Bottom Sediments of the Freshwater Tidal Potomac River., Appl Environ Microbiology. 1986, p. 751-757]<br />
<br />
(19) [http://books.google.com/books?id=0GAvKQJ2JuwC&printsec=frontcover&vq=Wenk+H.R+and+Bulakh+A+.,+2004:+Minerals.+Their+constitution+and+origin.+Cambridge+University+Press&source=gbs_summary_r Wenk H.R and Bulakh A ., 2004: Minerals. Their constitution and origin. Cambridge University Press.]<br />
<br />
(20) [http://books.google.com/books?id=9K5I0ZPQd54C&pg=PA219&lpg=PA219&dq=%22LANGSTON%22+%228+Metal+handling%22&source=web&ots=qVFErWWjbn&sig=Iyh9_HN4S6PZU4jdXrMuWbLqcpI&hl=en#PPR11,M1 WJ Langston, MJ Bebianno, ,and GR Burt, ., (1998) "Metal handling strategies in molluscs" In: Langston, WJ, Bebiano, MJ eds. , Metal metabolism in the aquatic environment, Chapman and Hall, London, United Kingdom, pp 219-272]<br />
<br />
(21) Matthews, E. and I. Fung. 1987. Methane Emission from Natural Wetlands: Global Distribution, Area, and Environmental Characteristics of Sources. Global Biogeochemical Cycles 1: 61-86.<br />
<br />
(22) [http://books.google.com/books?id=zHIhWM5R9LcC&printsec=frontcover&dq=Y.Chen+and+Y+Avnimelech&source=gbs_summary_r#PPA118,M1 Y. Chen and Y . Avnimelech., (1986)., The Role of Organic Matter in Modern Agriculture., Springer., Developments in Plant and Soil Sciences , Vol. 25., p118]<br />
<br />
See [[#Current Research]] section for a list of journals for additional information on the topic of flooded soils. <br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=29299
Flooded Soils
2008-03-17T07:20:56Z
<p>Lrastegarzadeh: /* Sulfate Reducing Bacteria */</p>
<hr />
<div>[[Image:Floridacrocodile1.jpg|thumb|500px|right|Ding Darling reserve, Sanibel Island, Florida, with an American Crocodile. Wikipedia jimfbleak 13:37, 2 April 2006 (UTC)]] <br />
==Introduction==<br />
[[Image:flooded soil.png|thumb|400px|schematic presentation of flooded soil from[[Y.Chen and Y Avnimelech]]]]<br />
'''Flooded soils''' occur with complete water saturation of soil pores, and generally result in anoxic conditions of the soil environment. Flooded soil environments may include such [[Wikipedia:ecosystem|ecosystem]]<br />
as: rice paddies; wetlands (swamps, marshes, and bogs); compacted soils; and post-rain soils (Scow, 2008). Additionally, similar redox conditions (where oxygen is lacking) can also be found within soil aggregates and along pollutant plumes, and thus many of the concepts discussed in this section may be applied to those environments.<br />
<br />
Oxygen is only sparingly soluble in water and diffuses much more slowly through water than through air (Schlesinger, 1997). What little oxygen that is present in saturated soils in the form of dissolved O<sub>2</sub> is quickly consumed through metabolic processes. Oxygen is used as terminal electron acceptor via respiration by roots, soil microbes, and soil organisms (Sylvia, 2005), and is lost from the soil system in the form of carbon dioxide (CO<sub>2</sub>). Heterotrophic respiration may completely deplete oxygen in flooded soils; and these effects may be observed within only a few millimeters of the soil surface (Schlesinger, 1997). <br />
<br />
Due to the deficiency of oxygen in flooded soils, those organisms inhabiting flooded soils must be able to survive with little to no oxygen. Although energy yields are much greater with oxygen than with any other terminal electron acceptor (see [[#Electron tower]] theory, section 2.1.1), under anoxic conditions anaerobic and facultative microbes can use alternative electron acceptors such as nitrate, ferric iron (Fe III), manganese (IV) oxide, sulfate, and carbon dioxide to produce energy and build biomass. <br />
<br />
Microbial transformations of elements in anaerobic soils play a large role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere (Schlesinger, 1997).<br />
<br />
==Processes ==<br />
[[Image:phenomenon in aggregates.png|thumb|left|200px|Electron acceptor used in aggregates. adjusted from [[Prof. Kate lec #5]]]]<br />
[[Image:phenomena in pollutant plume.png|thumb|200px|Order of electron acceptor in pollutant plume from [[USGS]]]]<br />
In general, flooded soils occur due to seasonal flooding or agricultural activity. <br />
Flooded soils can be often converted into non-flooded soils by the water level fluctuation and drainage. Through this variation of soil conditins, various gases are emitted into the atmosphere and environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changing. <br />
As explained in the [[#Introduction]], microorganisms can use alternative terminal electron acceptors (such as nitrate, perchlorate, sulfate, and carbon dioxide) when dissolved oxygen is absent. Microbes will successively use electron acceptors according to the order of energy yields resulting from electron acceptor utilization indicted on the electron tower (see [[#Electron Tower]] theory). The progression of electron acceptor utilization may also be observed in soil aggregates and pollutant plumes. <br />
<br />
<br />
<br />
<br />
===[http://en.wikipedia.org/wiki/Redox Oxidation/Reduction (Redox) Reaction]===<br />
In redox reactions, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. A classic example well known in the process of cellular respiration is when glucose (the reducing agent) reacts with oxygen (the oxidizing agent)and is oxidized to carbon dioxide. In this reaction, oxygen is reduced to water. Oxygen is the most common and highest energy yielding electron acceptor, and some organisms (strict aerobes) can not live long without it.(6) In flooded soils oxygen is typically not availible. Facultative and strict anaerobic bacteria have the ability to use other oxidizing agents/electron acceptors to carry out respiration. Anaerobic and facultative bacteria will use the electron acceptor which yields the highest energy, or the acceptor which is most readily available. The availibility and concentration of electron acceptors changes as the soil profile increases in depth. <br />
====Electron Tower====<br />
[[Image:Environmental1.gif|thumb|400px|Electron tower [[http://www.microbiologybytes.com/introduction/Environmental.html]]]]<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified as strict aerobes, obligate anaerobes, and facultative anaerobes. Strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, microbes will choose to use nitrate as an electron acceptor (if available). Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptors in the order of electron acceptor having the most reducing energy. Oxygen is the most efficient electron acceptor, while carbon dioxide has the least amount of reduction potential.<br />
====Gleyed Soils and Recovery to Aerobic Conditions====<br />
[[Image:Gleyed soil.png|thumb|200px|left|Gleyed soil from Prof. Scow's lecture note 2008]]<br />
[[Image:Oxidized soil.png|thumb|300px|Oxidized soil from Prof. Scow's lecture note 2008]]<br />
'''Soil Gleying''':<br />
Gleying is a phenomenon in which waterlogged soils are discolored by accumulation of Fe(II) due to reduction of ferric iron into ferrous iron (Lovely 1991).<br />
Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe(III)-reducing fermentative bacteria can be readily isolated from gleyed soils. <br />
The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS<sub>2</sub>) (Wenk and Bulakh 2004).<br />
<br />
'''Recovery to Aerobic Conditions'''<br />
When waterlogged soils drain, the Eh starts to increase as oxygen diffuses into soil pores. Plentiful oxygen represses the activity of anaerobes, which results in an increase of aerobic microbes. If oxygen diffuses deep into the soil profile, the production of H<sub>2</sub>S ceases. Under aerobic conditions, ferrous iron is oxidized by iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals. The gray color in soil changes to a red, yellow, or brown color as these minerals are oxidized. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO<sub>2</sub> (Richardson and Vepraskas 2000).<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise as a result of the buffering capacity of the soil. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succession of anaerobic oxidation processes, the redox potential (Eh) of flooded soils will decrease as a result of the reduced products formed. Approximate values for redox potentials associated with specific oxidation-reduction process are as follows:<br />
<br />
{| width="300" border="1"<br />
|----- bgcolor ="orange"<br />
| width="200" height="23" | Observation<br />
| width="84" | Eh (mV) <br />
|-<br />
| Disappearance of oxygen<br />
| +330<br />
|-<br />
| Disappearance of nitrate<br />
| +220<br />
|-<br />
|Appearance of manganese ions <br />
| +200<br />
|-<br />
| Appearance of ferrous iron ions<br />
| +120 <br />
|-<br />
| Disappearance of sulfate<br />
| -150<br />
|-<br />
|Appearance of methane <br />
| -250<br />
|}<br />
<br />
===Solubility/Mobility of Minerals===<br />
Since the toxicity, solubility, mobility, and bioavailability for a given element or compound is mainly influenced by soil solution reduction potenial and pH, flooded soil conditions play an important role in the mobility of trace metal, nutrients, and minerals.<br />
<br />
<br />
====Plant Nutrient Availability====<br />
[[Image:overwater.jpg|left|frame|What over-watering looks like in a common house plant]]Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a major role in healthy plant growth. In flooded soils, under anaerobic conditions, the pH will tend to rise initially. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants. Microoganisms will begin to use available plants nutrients as alternative electron acceptors, such as sulfate, nitrate and iron(III).<br />
Experiments have been done on soybean plants to show the effects of flooded soils. Flood duration effects on soybean plants resulted in yellowing and abscission of leaves at the lower nodes, stunting, and reduced dry weight and seed yield. Canopy height and dry weight decreased linearly with duration of the flood at both growth stages. Growth rates were 25 to 35% less when soybeans were flooded (3).<br />
<br />
==Key Microbial Processes and Organisms Involved==<br />
The role of microorganisms under flooded soils<br />
===Microbial processes===<br />
====Microbial Activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as [http://en.wikipedia.org/wiki/Electron_acceptor TEA (terminal electron acceptors)]. Some important terminal electron acceptors include iron, nitrate, sulfate, and manganese. These processes are primarily driven by microobial activity. Energy yields of alternative electron acceptors are lower than that of aerobic respiration, in which oxygen is utilized as a TEA (see [[#Electron Tower]] theory. As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of TEA's from the electron tower, and will govern which microbes will thrive, as those able to use these available alternative electron acceptors. Flooding also alters microbial flora in soil by decreasing the O<sub>2</sub> concentration. Fermentation is a major biochemical processes responsible for organic matter decomposition in flooded soils. Eh levels can affect which compounds are fermented. These levels will tend to gradually drop in flooded soils.<br />
<br />
====Fermentation under Anoxic Conditions====<br />
[[Image:anaerobic decomposition.png|thumb|left|300px|Organic matter decomposition pathways . [[Richardson and Vepraskas]]]]<br />
There are many types of fermentative bacteria in soils, such as the genus ''[[Bacillus]]'', ''[[Clostridium]]'', and ''[[Lactobacillus]]''. 4 ATP molecules per molecule of glucose are produced by fermentation, while 38 ATP molecules are produced by aerobic respiration. Although the energy yield via fermentation is less than oxidative phosphorylation, fermentation plays an important role in anaerobic respiration for obligate and facultative anaerobic bacteria, including denitrifier, Fe<sup>3+</sup>, Mn<sup>4+</sup>, SO<sub>4</sub><sup>2-</sup>, reducers, and methanogens. Sugar (glucose or fructose) is broken down into simple compounds (e.g. formate, acetate, and ethanol) during fermentation. Also, numerous fermentation products, such as carbon dioxide, fatty acid, lactic, alcohols, are released into soils. These compounds serve as substrates for other anaerobic bacteria. Thus, low molecular weight organic compounds produced from fermentation influence the reduction of Fe(III), Mn(IV), SO<sub>4</sub><sup>2-</sup>, and CO<sub>2</sub>(Richardson And Vepraskas 2000).<br />
----<br />
<br />
===Organisms involved in Flooded Soils===<br />
====Nitrate Reducing Bacteria====<br />
When available oxygen is depleted and nitrate is available, denitrification, the reduction of NO<sub>3</sub><sup>-</sup> to NO,N<sub>2</sub>,or N<sub>2</sub>, primarily occurs.<br />
Denitrification is carried out by obligate respiratory bacteria belonging to the genra ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''[[Paracoccus denitrificans]]'', ''[[Pseudomonas]]'' and ''[[Thiobacillus]]'' (Knowles, 1982). Nitrate ammonification found in facultative anaerobic bacteria belonging to the genera ''[[Bacillus]]'', ''Citrobacter'' and ''[[Aeromonas]]'', or memebers of the ''[[Enterobacteriaceae]]'' (Cole adn Brown, 1980; Smith adn Zimmerman, 1981; MacFarlane and Herbert, 1982). Strictly anaerobic bacteria belonging to the genus ''[[Clostridium]]'' are also able to reduce nitrate to ammonia (Hasan and Hall, 1975). <br />
Pure culture studies show evidance that nitrate reduction may also occur in the presence of oxygen (Kuenen and and Robertson, 1987).<br />
<br />
====Iron/Manganese Reducing Bacteria====<br />
Most microorganisms can reduce Mn<sup>4+</sup> and Fe <sup>3+</sup>.<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''[[Geobacter]]([[Geobacter metallireducens]] and [[Geobacter sulfurreducens]]),Shewanella putrefaciens,[[Desulfovibrio]], [[Pseudomonas]],'' and ''[[Thiobacillus]]''(Lovley 1993). ''[[Bacillus]], [[Geobacter]],'' and ''[[Pseudomonas]]'' are representative manganese-reducing bacteria. <br />
Different forms of ferric iron oxides exist in drained aerobic soils as well as in waterlogged soils. Not all forms of ferric oxides are equally suitable for reduction by ferric oxide reducer bacteria (Gotoh and Patrick, 1974; Schwertmann and Taylor, 1977). In general, amorphous forms are more efficient for ferric reducer bacteria than crystalline forms (Lovely adn Phillips, 1986). The reduction of ferric oxide may release phosphate and trace elements that are adsorbed to amorphous ferric oxide and thus enhance availablity of these compounds in the soil (Lovely and Phillips, 1986).<br />
<br />
====Sulfate Reducing Bacteria====<br />
Bacteria can use organic compouds as an electron donor and sulfate as an electron acceptor. This reaction for acetate as electron donor is as follows:<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''[[Desulfobacter]]'', ''Desulfobulbus'', ''[[Desulfococcus]]'', ''[[Desulfovibrio]]'', ''[[Desulfosarcina]]'',''Desulfotomaculum'',and ''Desulfonema''(Langston and Bebiano 1998, Sylvia 2004). Some of the sulfate reducing bacteria carry the reaction to the production of CO2 and some other stop after producing acetate as an intermaediate of oxidation. Hydrogen sulfide gas produced via anaerobic respiration causes the rotten egg odor.<br />
<br />
====[[Methanogens]]====<br />
Methanogen products less energy than other rueducing reaction because the reduction of carbon dioxide occur under the most anaerobic and reduced conditions(see [[#Electron tower]] section). Thus, the activity of methanogen is repressed until other alternative terminal electron acceptor such as Fe(III), NO<sub>3</sub><sup>-</sup>,and SO<sub>4</sub><sup>2-</sup>, have been depleted.<br />
<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
==Greenhouse Gas Emissions from Flooded Soils==<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively (Schlesinger, 1997). Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. According to Matthews and Fung (1987), an estimated 3.6% of terrestrial land is classified as wetlands, and although this number continues to decline (Schlesinger, 1997) the effect of flooded soils to the global climate is clear. <br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV (see [[#electron tower]] theory, section 2.1.1) (Sylvia, 2005). If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions. <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process (Sylvia, 2005). <br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions (Sylvia, 2005).<br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane (Sylvia, 1998). Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur. (Sylvia, 2005).<br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly (Sylvia, 2005).<br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosytems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. Following is a list of recent journal review articles focused on a range of current research topics related to flooded soil environments for the interested reader: <br />
<br />
1. Shangping Xu, Peter R. Jaffe and Denise L. Mauzerall, A process-based model for methane emission from flooded rice paddy systems, Ecological ModellingVolume 205, Issues 3-4, , 24 July 2007, Pages 475-491.<br />
(http://www.sciencedirect.com/science/article/B6VBS-4NHV759-1/2/3126b5403a44c51c5d8d4160382d848e)<br />
<br />
2. HANK GREENWAY , WILLIAM ARMSTRONG , and TIMOTHY D. COLMER <br />
Conditions Leading to High CO2 (>5 kPa) in Waterlogged–Flooded Soils and Possible Effects on Root Growth and Metabolism <br />
AOBPreview published on July 1, 2006, DOI 10.1093/aob/mcl076.<br />
Ann Bot 98: 9-32.<br />
<br />
3. Kazunori Minamikawa and Naoki Sakai, The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan, Agriculture, Ecosystems & EnvironmentVolume 107, Issue 4, , 30 May 2005, Pages 397-407.<br />
(http://www.sciencedirect.com/science/article/B6T3Y-4FY9M5H-1/2/98a4074277436af97833c16a823b326c)<br />
Keywords: Methane; Water management; Soil redox potential; Oryza sativa L.; Rice yield<br />
<br />
4. Makoto Kimura, Jun Murase and Yahai Lu, Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4), Soil Biology and BiochemistryVolume 36, Issue 9, , September 2004, Pages 1399-1416.<br />
(http://www.sciencedirect.com/science/article/B6TC7-4C9G7KP-4/2/ceb77d1803f5d02e51bb773f3163cdcb)<br />
<br />
5. Sahrawat KL, Fertility and organic matter in submerged rice soils, Current Science. Volume 88, Issues 3-4, 2005, Pages 735-739.<br />
<br />
6. Conrad R, Microbial ecology of methanogens and methanotrophs, Advances in Agronomy. Volume 96, 2007, Pages 1-63.<br />
<br />
7. Ralf Conrad, Christoph Erkel and Werner Liesack, Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil, Current Opinion in BiotechnologyVolume 17, Issue 3, , Environmental biotechnology/Energy biotechnology, June 2006, Pages 262-267.<br />
(http://www.sciencedirect.com/science/article/B6VRV-4JRVFV8-1/2/babb823ea30e51d7445d6861d7d334aa)<br />
<br />
==References==<br />
(1) Lecture 5 of Kate Scow. 2008. Microbial Metabolism. Unpublished, University of California, Davis.<br />
<br />
(2) Schlesinger, W.H. 1997. Biogeochemistry: An Analysis of Global Change. 2nd ed. Elsevier Academic Press, Amsterdam. <br />
<br />
(3) [http://books.google.com/books?id=1l4GAAAACAAJ&dq=soil+microbiology+sylvia&ei=thzbR9j6Hpu8swPmxOXzAQ Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey.]<br />
<br />
(4) [http://books.google.com/books?id=v6cGPMRmPYYC&pg=PA940&dq=J.+Kotz,+P.+Treichel,+G.+Weaver.+2006.+Chemistry+and+Chemical+Reactivity&ei=Bx3bR5yFF5-OtgOdqe3sAQ&sig=2IiJ_hdME4k5k06zd-H35y1cxC8#PPP1,M1 J. Kotz, P. Treichel, G. Weaver. 2006. Chemistry and Chemical Reactivity sixth edition.]<br />
<br />
(5)[http://books.google.com/books?id=xEFIEOjfxx0C&printsec=frontcover&dq=Wetland+richardson&ei=7xvbR4vMH4jysgOg6vnpAQ&sig=bDFNpm0lUibISaIaERoMAu5-K34 J.L Richardson and M.J Vepraskas., 2000 Wetland soils: Genesis, Hydrology, Landscapes, and Classification., CRC press LLC.] <br />
<br />
(6) Flood Duration Effects on Soybean Growth and Yield<br />
http://agron.scijournals.org/cgi/content/abstract/81/4/631<br />
<br />
(7)[http://books.google.com/books?id=pr7kAQAACAAJ&dq=Advances+in+Agricultural+Microbiology,&ei=ddHdR6qDJYG-sgPeyMXyAQ Knowles, R. 1982. Denitrification in Soils, pp. 246-266, In: N.S. Subba Rao (ed.) Advances in Agricultural Microbiology, Butterworth Sci. Pub., London, UK]<br />
<br />
(8) Cole and Brown 1980<br />
<br />
(9) Smith and Zimmerman 1982<br />
<br />
(10) Mac Herbent 1982<br />
<br />
(11)Hasan and Hall 1975<br />
<br />
(12) Kuenen and Roberston 1987<br />
<br />
(13)[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.mi.47.100193.001403?journalCode=micro Derek R. Lovley., 1993., Dissimilatory metal reduction. Annu Rev Microbiol. Vol 47 pp: 263-90.]<br />
<br />
(14) Gotoh and Patrick 1974<br />
<br />
(15) Schwertman and Taylor 1977<br />
<br />
(18) [http://aem.asm.org/cgi/reprint/52/4/751 Derek R. Lovley and Elizabeth J.P Phillips., Availability of Ferric Iron for Microbial Reduction in Bottom Sediments of the Freshwater Tidal Potomac River., Appl Environ Microbiology. 1986, p. 751-757]<br />
<br />
(19) [http://books.google.com/books?id=0GAvKQJ2JuwC&printsec=frontcover&vq=Wenk+H.R+and+Bulakh+A+.,+2004:+Minerals.+Their+constitution+and+origin.+Cambridge+University+Press&source=gbs_summary_r Wenk H.R and Bulakh A ., 2004: Minerals. Their constitution and origin. Cambridge University Press.]<br />
<br />
(20) [http://books.google.com/books?id=9K5I0ZPQd54C&pg=PA219&lpg=PA219&dq=%22LANGSTON%22+%228+Metal+handling%22&source=web&ots=qVFErWWjbn&sig=Iyh9_HN4S6PZU4jdXrMuWbLqcpI&hl=en#PPR11,M1 WJ Langston, MJ Bebianno, ,and GR Burt, ., (1998) "Metal handling strategies in molluscs" In: Langston, WJ, Bebiano, MJ eds. , Metal metabolism in the aquatic environment, Chapman and Hall, London, United Kingdom, pp 219-272]<br />
<br />
(21) Matthews, E. and I. Fung. 1987. Methane Emission from Natural Wetlands: Global Distribution, Area, and Environmental Characteristics of Sources. Global Biogeochemical Cycles 1: 61-86.<br />
<br />
(22) [http://books.google.com/books?id=zHIhWM5R9LcC&printsec=frontcover&dq=Y.Chen+and+Y+Avnimelech&source=gbs_summary_r#PPA118,M1 Y. Chen and Y . Avnimelech., (1986)., The Role of Organic Matter in Modern Agriculture., Springer., Developments in Plant and Soil Sciences , Vol. 25., p118]<br />
<br />
See [[#Current Research]] section for a list of journals for additional information on the topic of flooded soils. <br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29297
Desulfobacter
2008-03-17T07:01:57Z
<p>Lrastegarzadeh: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. The main habitat of Desulfobacter is marine sendiment and brackish water. <br />
<br />
<br />
<br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29295
Desulfobacter
2008-03-17T06:52:49Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. <br />
The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29294
Desulfobacter
2008-03-17T06:51:42Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3]. <br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29290
Desulfobacter
2008-03-17T06:31:15Z
<p>Lrastegarzadeh: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3]. <br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29285
Desulfobacter
2008-03-17T06:18:56Z
<p>Lrastegarzadeh: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3]. <br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Isolate Sulfitobacter sp. EE-36 was isolated from the salt marsh on the coast of Georgia, US. Phylogenetically it belongs to the Sulfitobacter genus, which has been isolated from numerous places. Originally Sulfitobacter was isolated from the Black Sea, although it proved to be abundant in other environments, such as coastal and open ocean environments, an Antarctic lake and in symbiosis with sea animals. Sulfitobacter is particularly abundant in environments with a constant source of inorganic sulphur, like the Black Sea sediment or seafloor. Sulfitobacter sp. EE-36 stands out for its high inorganic sulphur oxidation activity. It is able to oxidize sulfite and thiosulfate, possibly to conserve energy for growth. It also grows on DMSP and glycine betaine as sole carbon sources<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29284
Desulfobacter
2008-03-17T06:14:32Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3]. <br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4].<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29283
Desulfobacter
2008-03-17T06:13:05Z
<p>Lrastegarzadeh: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3]. <br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. <br />
<br />
<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
1-Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
[4] Sulphate reducing bacteria-book)<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29282
Desulfobacter
2008-03-17T06:10:25Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2 in anoxic codition. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology [1]. The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [2,3]. <br />
Micobiological and molecular studies have suggested the presence of different sulfate reducing bacteria (SBR)in oxic and anoxic layers of soil profile. Dsulfobater, Desulfobulbus and desulfotomoculum species were detected in restricly anoxic conition while Desulfococcus, Desolfonema, and Desulfovibrio species appear to be perdominantly in oxic layers [4]. <br />
<br />
<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
1-Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29276
Desulfobacter
2008-03-17T05:45:02Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2. Desulfobacter is mainly found in brackish and marine environemnt and has a oval or vibrio morphology (1). The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [21,30].<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
1-Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29274
Desulfobacter
2008-03-17T05:36:49Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
Desulfobacter is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2. Desulfobacter is mainly common in brackish and marine environemnt (1). The genus desulfobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [21,30].<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
1-Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29271
Desulfobacter
2008-03-17T05:30:44Z
<p>Lrastegarzadeh: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
"Desulfobacter" is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2. Desulfobacter is mainly common in brackish and marine environemnt (1). The genus "desulfobacter" includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [21,30].<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
1-Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy <br />
Paustian© 1999-2004.</span>]<br />
<br />
[1] Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29267
Desulfobacter
2008-03-17T05:27:40Z
<p>Lrastegarzadeh: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
"Desulfobacter" is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2. Desulfobacter is mainly common in brackish and marine environemnt (1). The genus "desulfobacter" includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [21,30].<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
1-Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy Paustian© 1999-2004.</span>]<br />
<br />
[2] Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
[3] Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334.<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29265
Desulfobacter
2008-03-17T05:23:39Z
<p>Lrastegarzadeh: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
"Desulfobacter" is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2. Desulfobacter is mainly common in brackish and marine environemnt (1). The genus "desulfobacter" includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [21,30].<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
1-Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy Paustian© 1999-2004.</span>]<br />
<br />
Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Talk:Geomicrobiology&diff=29263
Talk:Geomicrobiology
2008-03-17T05:08:50Z
<p>Lrastegarzadeh: </p>
<hr />
<div>Good job. Minor points: in section "Microbial Energetics", your picture is not readable. You can resize the picture to make it useful for readers. Also you missed the reference and description of the picture.<br />
<br />
<br />
Just out of curiousity, what about phosphorous? I know the only source of P is from the mineral apatite (ie, not atmospheric). I'm not sure about the relationships with microbes with P... Just a thought... Heather<br />
<br />
I agree that chemical formulas would be a good addition to the site. Overall what you have looks great, Heather<br />
<br />
Hey Guys! This page is looking pretty good! My recommendations are as follows: 1. First of all, I do not understand how you could have written an entire page on Geomicrobiology without mentioning the word lithoautotroph. You should probably work this word into your page and define it. 2. For the different chemicals that are broken down by microorganisms, please inform us as to whether the microorganisms are doing this because they are obtaining specific nutrients from the rock, or if this is a side effect of another process. 3. How do these different processes aid other soil organisms? 4. Taking the time to integrate your links into the text instead of using a "click here" strategy would be valuable. 5. Please provide chemical formulas and energy budgets for each process mentioned. References and existing information look good! [[User:Metotman|Metotman]] 21:53, 15 March 2008 (UTC)<br />
----<br />
<br />
Very nice reference section! One last thing: I noticed that you don't have any links to microbes on the MicrobeWiki, even though you have some listed in your sections. If the exampls listed have pages on MicrobeWiki, the way you create a link is by flanking the organism name with two square brackets, like so ''[[Methylobacterium]]''. The apostrophes italicize the name.[[User:Jmmullane|Jmmullane]] 05:40, 15 March 2008 (UTC)<br />
----<br />
In the section on microbial energetics, maybe you could mention why fermentation yields less ATP than respiration (lack of e- transport chain, etc.). It might also be helpful to mention e- carriers and how they eliminate the need for TEAs in fermentation.[[User:Jmmullane|Jmmullane]] 05:32, 15 March 2008 (UTC)<br />
----<br />
Great job with the page! It seems like you covered everything. One suggestion: instead of saying "for more information follow this link", tell us what page it will be going to/what additional information we can expect to find there. [[User:Aebellows|Aebellows]] 07:11, 14 March 2008 (UTC)<br />
----<br />
<br />
<br />
"ATP is heterotrophically generated by fermentation or respiration." This is true, but can't ATP be generated by autotrophs as well, otherwise how would they survive.<br />
<br />
I think it is important to include the chemical equations involved in these transformations. Example: in the Sufur section you could add: <br />
SO32- + 6 H+ 6 e- --> H2S + H2O + 2 OH-<br />
<br />
[[User:Icclark|Icclark]] 06:08, 14 March 2008 (UTC) <br />
---- <br />
<br />
Nice page! One suggestion: under the Microbial energetics section, you say that "a nice summary can be found at:_________" with an image to the side. You might say that the image is the summary, because right now it looks like you forgot to post a link to somewhere.[[User:Njblackburn|Njblackburn]] 04:36, 14 March 2008 (UTC)<br />
----<br />
Also, if you want a numbered list to be a list down the page, rather than in a paragraph, put an extra line between the sentences<br />
<br />
1) like<br />
<br />
2) this<br />
<br />
[[User:Njblackburn|Njblackburn]] 04:36, 14 March 2008 (UTC)<br />
----<br />
<br />
I agree!! I aslo added uranium which seems to have an interesting relationship with Iron and nitrate[[User:Egrgutierrez|Egrgutierrez]] 03:12, 14 March 2008 (UTC)----<br />
<br />
Wow, your page looks really great! I love the warm and inviting into, and I thought everything was really well written. I don't really have any good suggestions for your group other than one small point: where you have a list of processes in the beginning, you may want to change that to "processes and environments", since you are including hot springs on the list. Otherwise, I think it's perfecto! Heather<br />
---<br />
<br />
Leslie, I think its coming together very nicely what do you think .... anything you want me to do?[[User:Calgilbert|Calgilbert]] 21:14, 13 March 2008 (UTC)<br />
----<br />
Hey Neel: you've got great suggestions...thank-you thank-you! :) [[User:Lapeacock|Leslie Peacock]] 12:00, 13 March 2008 (UTC)<br />
----<br />
<br />
Also the page might benefit from the addition of ecological significance section for this topic. [[User:Njppatel|Njppatel]] 18:26, 13 March 2008 (UTC)<br />
----<br />
Good Idea Njppatel I will look into it[[User:Calgilbert|Calgilbert]] 18:49, 13 March 2008 (UTC)<br />
----<br />
Looks great, i would suggest under the microorganisms involved you add some specific example of organisms involved in geomicrobiology[[User:Njppatel|Njppatel]] 18:23, 13 March 2008 (UTC)<br />
---- <br />
Thank you for the sugesttion Njppatel, but i belive there already are some specific examples listed[[User:Calgilbert|Calgilbert]] 18:49, 13 March 2008 (UTC)<br />
----<br />
I would suggest to put the link to the existing microbe page in wiki, for example [[Pseudomonas putida]].<br />
[[User:Tantayotai|Tantayotai]] 00:38, 13 March 2008 (UTC) <br />
----<br />
Thank you for the suggestion I have added the link[[User:Calgilbert|Calgilbert]] 18:49, 13 March 2008 (UTC)<br />
----<br />
You don't need to geomicrobiology methods section because those methods are common to all the sections in the wiki, unless you can justify some very specific methods for geomicrobiology itself.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
I went ahead and deleted this section.[[User:Calgilbert|Calgilbert]] 19:09, 12 March 2008 (UTC)<br />
----<br />
<br />
Also I don't know that the category "geomicrobiology habitats" will work well in your section unless you want to do some special environments like hot springs or volcanic soils.<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
I would suggest organizing the category process by the different elements: e.g. iron, manganese, mercury, selenium sulfur (you don't have to go too far with this, just focus on main ones)<br />
<br />
You might want to maintain that type of organization then when you talk about specific organisms OR you can have the organisms as a subcategory under each element.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<br />
<br />
Good start - did you look around to see if any microbes that are important to different geomicrobiology processes have pages already?<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:42, 10 February 2008 (UTC)</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Talk:Carbon_cycle&diff=29262
Talk:Carbon cycle
2008-03-17T05:00:39Z
<p>Lrastegarzadeh: </p>
<hr />
<div>Great job, nice graphics. I have couple minor suggestions:<br />
I think this sentense "The major function of microbes in the Carbon Cycle is as decomposers-- degraders of complex organic molecules that would otherwise permanently sequester carbon." needs to be reworded to make it more clear what would happen otherwise...<br />
Also when you say "These decomposers also release CO2, contributing to the rising concentration in the atmosphere." this suggests that in general the CO2 is the final byproduct of all the biodegradations. you may want to mention that that is not always the case. <br />
<br />
This page is beautiful! I absolutely love the images of compound types. Great job! There may be a couple places which may need citations throughout the body of the page. Looks super!<br />
<br />
Hey Guys! The page is looking good! I really liked the links you included to the Nitrogen Cycle page. Here are a few more suggestions: 1. Name some of the enzymes responsible for breaking down different types of Carbon chains and provide links to wikipidia for them. 2. Provide quantitative information relating to the relative affect of each greenhouse gas relative to others - how much impact does each molecule have? Relative abundance in the atmosphere would be useful as well. 3. I'm a little confused as to why you have a Nitrious Oxide section on a carbon page. 4. The first time you use a chemical formula in a section (ex: CaCO3 under the Acid Rain section), give us the written name of the compound (Calcium Carbonate). 5. For each step in the Carbon Cycle, provide us with chemical formulas and energy budgets. 6. It would be useful to interlink how different levels of carbon complexity affect other organisms in the soil. What is the significance of breaking down these large chains? I really like the diagrams on this page, they make your discriptions very clear. Additionally, I like the method of citation used on this page. I think this page is coming along well. [[User:Metotman|Metotman]] 21:34, 15 March 2008 (UTC)<br />
----<br />
<br />
<br />
Great job!! However, I make two suggestions. <br />
Why don’t you guys add chemical reaction equations related to decomposition of various carbon sources?. <br />
Additionally, you mentioned intermediates produced from complex substrates though, I’d like you to put '''metabolic pathway diagram''' on your page in order to explain how these intermediates are involved in metabolic pathways. [[User:Jokang|Sungho]] 20:07, 14 March 2008 (UTC) <br />
----"Thank you for the suggestion. I added some diagrams from Chapter 13 from the textbook. Enjoy!"[[User:Jmmullane|Jmmullane]] 03:43, 15 March 2008 (UTC)<br />
----<br />
What ever happened to the Verticillium page? Jaime set it up, and I don't think she should be the one to have to fill it in. Come on other group people! Help us out! [[User:Jmmullane|Jmmullane]] 06:56, 14 March 2008 (UTC)<br />
----<br />
<br />
Looks good. In general, though, you have not cited of your work. <br />
<br />
"I went back and cited as much of the material as I could. Some of the sections were written by other people in my group, so I cited to them to the best of my abilities. If I have mis-referenced anything, please let me know." [[User:Jmmullane|Jmmullane]] 20:33, 14 March 2008 (UTC)<br />
----<br />
<br />
The references section needs some reformatting as well. <br />
<br />
If you have any specific suggestions on what needs reformatting and how we should go about it, I would be happy to entertain them. [[User:Jmmullane|Jmmullane]] 06:41, 14 March 2008 (UTC)<br />
<br />
The list in the Humus section needs clarification.<br />
<br />
Methane is produced by carbon dioxide reduction (anaerobic respiration) and acetate fermentation (fermentation), not always by C02 reduction. You indicate this, but also say that methanogenesis is always anaerobic respiration. <br />
[[User:Icclark|Icclark]] 05:51, 14 March 2008 (UTC)<br />
----<br />
Whoa!! Great Page...NEXT LEVEL!!!! my eyes are poppin out. i am not gonna pick nits. Congrats your page is very handsome [[User:Pbwebb|Pbwebb]] 04:43, 14 March 2008 (UTC)<br />
----<br />
Hey dudes: we still need a microbe page and 2 more current research papers![[User:Njblackburn|Njblackburn]] 04:15, 14 March 2008 (UTC)<br />
----<br />
Also, I went through and subscripted (thanks for the note!), but if you notice any that I missed, feel free to fix them.[[User:Njblackburn|Njblackburn]] 04:17, 14 March 2008 (UTC)<br />
----<br />
<br />
I thought you guys did a great job too! I really liked the images. I think you guys should check for a couple of typos and that the "what organic matter does in the soil" section could be expanded a little, like how those effects work. -Annie[[User:Aebellows|Aebellows]] 03:25, 14 March 2008 (UTC) ----<br />
<br />
Very nice work!! It could be important to complement this good information with issues associated with the carbon cycle in the ocean[[User:Egrgutierrez|Egrgutierrez]] 03:19, 14 March 2008 (UTC)----<br />
<br />
Maybe you guys could talk more about acid rain. The causes, short term effects, long term effects... -david la````[[User:Dtla|Dtla]] 02:51, 14 March 2008 (UTC)<br />
"Thanks for the suggestion. I added some more info about acid rain. I hope you find it satisfactory!" [[User:Jmmullane|Jmmullane]] 06:36, 14 March 2008 (UTC)<br />
<br />
-I really love your first image! The quotes below are copied from your site and pasted here so you'd understand my comments:<br />
-“Humus is composed mainly of humin, humic acid, and fulvic acid.”- I think humin, humic acid, and fulvic acid are more chemical extraction products of humus, rather than actual components of humus…. I’m not sure if this would be better rephrased?? …<br />
-Under the “humics” section, you have a list of effects of humus to soil…this is also in the previous section…Not sure if you meant to do that? I would suggest eliminating the list in the humics section and just have the other list.<br />
One more suggestion may be to add images of the different carbon compounds you discuss- just a thought...<br />
Overall really great job- The page looks terrific! -Heather<br />
---------------<br />
Page is great, the diagram on the greenhouse effect really helped solidify the information, and can help those who are not yet familiar with this environmental problem. [[User:Njppatel|Njppatel]] 18:20, 13 March 2008 (UTC)<br />
----<br />
<br />
Looks great, perhaps you could add a section on ecological significance of the carbon cycle[[User:Njppatel|Njppatel]] 18:18, 13 March 2008 (UTC)<br />
----<br />
<br />
Your page looks good and well organize. To make the subscirpt font, < sub >your text< /sub >, do not for get to delete space between them when you use. [[User:Tantayotai|Tantayotai]] 00:26, 13 March 2008 (UTC) <br />
----<br />
I've added a link to a blank page on Verticillium (under chitin degradation). And I'm certainly not going to stay up to fill the whole thing in.<br />
[[User:Njblackburn|Njblackburn]] 06:51, 11 March 2008 (UTC)<br />
----<br />
<br />
So, what happened to group member #4? And who was in charge of our microbe page that we had to write? I feel that I've done more than my share (thanks Jess for filling in so much, too). <br />
[[User:Njblackburn|Njblackburn]] 06:11, 11 March 2008 (UTC)<br />
----<br />
I would modify the heading of Decomposition of organic..... to include "and the microorganisms involved" Then you can include some info on the players in each category if there is specific info available AND make nice links to the existing microbe pages. There should be a lot of these pages.<br />
<br />
This way you can eliminate the section on just microbes and integrate it into each important process. If there are no really specific organisms, e.g. with the sugars section, you can just say that metabolism of these compounds is by a broad group of microorganisms.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:55, 10 March 2008 (UTC) ----<br />
<br />
[[User:Kmscow|Kate Scow]] 01:45, 10 March 2008 (UTC)<br />
<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<br />
Ok, guys: we need to do this wiki. I'm sorry that I haven't gotten to it until today, but I don't any other effort here either. I'm going to work through some of it, but what I leave undone had better get done by tomorrow.<br />
[[User:Njblackburn|Njblackburn]] 19:37, 9 March 2008 (UTC)<br />
----<br />
I would suggest not breaking out geo/bio/hydro/atmosphere unless you really want to go into detail about this. Please include the 2 main sections in the lecture:<br />
# Decomposition of organic matter--<br />
and then cover all the different chemical components of plant materials e.g. monomers, cellulose, hemicellulose, lignin, etc<br />
# Formation of humic substances<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
You might want to link the microbial types directly to the processes rather than split it out alone.<br />
<br />
E.g. cellulose decomposition is where you would discuss a little about the organisms involved and you can link this to the organisms already listed in the wiki. A lot of these organisms start with "cellu"<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
You don't need to have an Edits and Dates section at the end either - all this information is collected under "History". I noticed you wrote "Jaime and Alex". I can see that Jaime made edits but not Alex. So please make sure you log in yourselves when editing, so that we can attribute work - [[User:Irina.chakraborty|Irina C]] 22:52, 10 February 2008 (UTC)<br />
<br />
Good start - You don't need to have a list of your sections at the start of your page because a content list is automatically generated if you use heading formats for the title of each section. Also you used internal link formatting for the items in "List of Topics". You only need to do this if you are creating new pages for each item - this would make sense if we were going to add a lot of detail. Instead each item is just a section within your page, so does not require a link to its own page.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 22:22, 10 February 2008 (UTC)<br />
<br />
----<br />
Has anyone seen the template for our page we need to write about a microbe? Jess and I have gone through and put in a bunch of links, but I'm not sure how to create an entirely new page. (~Jaime)<br />
----<br />
<br />
Could you make the pictures smaller. Those pictures are really pretty.</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Talk:Carbon_cycle&diff=29261
Talk:Carbon cycle
2008-03-17T04:58:15Z
<p>Lrastegarzadeh: </p>
<hr />
<div>Great job, nice graphics. I have couple minor suggestions:<br />
I think this sentense "The major function of microbes in the Carbon Cycle is as decomposers-- degraders of complex organic molecules that would otherwise permanently sequester carbon." needs to be reworded to make it more clear what would happen otherwise...<br />
Also when you say "These decomposers also release CO2, contributing to the rising concentration in the atmosphere." you are making it very general that CO2 is the byproduct of all the biodegradations. you may want to mention that that is not always the case. <br />
<br />
This page is beautiful! I absolutely love the images of compound types. Great job! There may be a couple places which may need citations throughout the body of the page. Looks super!<br />
<br />
Hey Guys! The page is looking good! I really liked the links you included to the Nitrogen Cycle page. Here are a few more suggestions: 1. Name some of the enzymes responsible for breaking down different types of Carbon chains and provide links to wikipidia for them. 2. Provide quantitative information relating to the relative affect of each greenhouse gas relative to others - how much impact does each molecule have? Relative abundance in the atmosphere would be useful as well. 3. I'm a little confused as to why you have a Nitrious Oxide section on a carbon page. 4. The first time you use a chemical formula in a section (ex: CaCO3 under the Acid Rain section), give us the written name of the compound (Calcium Carbonate). 5. For each step in the Carbon Cycle, provide us with chemical formulas and energy budgets. 6. It would be useful to interlink how different levels of carbon complexity affect other organisms in the soil. What is the significance of breaking down these large chains? I really like the diagrams on this page, they make your discriptions very clear. Additionally, I like the method of citation used on this page. I think this page is coming along well. [[User:Metotman|Metotman]] 21:34, 15 March 2008 (UTC)<br />
----<br />
<br />
<br />
Great job!! However, I make two suggestions. <br />
Why don’t you guys add chemical reaction equations related to decomposition of various carbon sources?. <br />
Additionally, you mentioned intermediates produced from complex substrates though, I’d like you to put '''metabolic pathway diagram''' on your page in order to explain how these intermediates are involved in metabolic pathways. [[User:Jokang|Sungho]] 20:07, 14 March 2008 (UTC) <br />
----"Thank you for the suggestion. I added some diagrams from Chapter 13 from the textbook. Enjoy!"[[User:Jmmullane|Jmmullane]] 03:43, 15 March 2008 (UTC)<br />
----<br />
What ever happened to the Verticillium page? Jaime set it up, and I don't think she should be the one to have to fill it in. Come on other group people! Help us out! [[User:Jmmullane|Jmmullane]] 06:56, 14 March 2008 (UTC)<br />
----<br />
<br />
Looks good. In general, though, you have not cited of your work. <br />
<br />
"I went back and cited as much of the material as I could. Some of the sections were written by other people in my group, so I cited to them to the best of my abilities. If I have mis-referenced anything, please let me know." [[User:Jmmullane|Jmmullane]] 20:33, 14 March 2008 (UTC)<br />
----<br />
<br />
The references section needs some reformatting as well. <br />
<br />
If you have any specific suggestions on what needs reformatting and how we should go about it, I would be happy to entertain them. [[User:Jmmullane|Jmmullane]] 06:41, 14 March 2008 (UTC)<br />
<br />
The list in the Humus section needs clarification.<br />
<br />
Methane is produced by carbon dioxide reduction (anaerobic respiration) and acetate fermentation (fermentation), not always by C02 reduction. You indicate this, but also say that methanogenesis is always anaerobic respiration. <br />
[[User:Icclark|Icclark]] 05:51, 14 March 2008 (UTC)<br />
----<br />
Whoa!! Great Page...NEXT LEVEL!!!! my eyes are poppin out. i am not gonna pick nits. Congrats your page is very handsome [[User:Pbwebb|Pbwebb]] 04:43, 14 March 2008 (UTC)<br />
----<br />
Hey dudes: we still need a microbe page and 2 more current research papers![[User:Njblackburn|Njblackburn]] 04:15, 14 March 2008 (UTC)<br />
----<br />
Also, I went through and subscripted (thanks for the note!), but if you notice any that I missed, feel free to fix them.[[User:Njblackburn|Njblackburn]] 04:17, 14 March 2008 (UTC)<br />
----<br />
<br />
I thought you guys did a great job too! I really liked the images. I think you guys should check for a couple of typos and that the "what organic matter does in the soil" section could be expanded a little, like how those effects work. -Annie[[User:Aebellows|Aebellows]] 03:25, 14 March 2008 (UTC) ----<br />
<br />
Very nice work!! It could be important to complement this good information with issues associated with the carbon cycle in the ocean[[User:Egrgutierrez|Egrgutierrez]] 03:19, 14 March 2008 (UTC)----<br />
<br />
Maybe you guys could talk more about acid rain. The causes, short term effects, long term effects... -david la````[[User:Dtla|Dtla]] 02:51, 14 March 2008 (UTC)<br />
"Thanks for the suggestion. I added some more info about acid rain. I hope you find it satisfactory!" [[User:Jmmullane|Jmmullane]] 06:36, 14 March 2008 (UTC)<br />
<br />
-I really love your first image! The quotes below are copied from your site and pasted here so you'd understand my comments:<br />
-“Humus is composed mainly of humin, humic acid, and fulvic acid.”- I think humin, humic acid, and fulvic acid are more chemical extraction products of humus, rather than actual components of humus…. I’m not sure if this would be better rephrased?? …<br />
-Under the “humics” section, you have a list of effects of humus to soil…this is also in the previous section…Not sure if you meant to do that? I would suggest eliminating the list in the humics section and just have the other list.<br />
One more suggestion may be to add images of the different carbon compounds you discuss- just a thought...<br />
Overall really great job- The page looks terrific! -Heather<br />
---------------<br />
Page is great, the diagram on the greenhouse effect really helped solidify the information, and can help those who are not yet familiar with this environmental problem. [[User:Njppatel|Njppatel]] 18:20, 13 March 2008 (UTC)<br />
----<br />
<br />
Looks great, perhaps you could add a section on ecological significance of the carbon cycle[[User:Njppatel|Njppatel]] 18:18, 13 March 2008 (UTC)<br />
----<br />
<br />
Your page looks good and well organize. To make the subscirpt font, < sub >your text< /sub >, do not for get to delete space between them when you use. [[User:Tantayotai|Tantayotai]] 00:26, 13 March 2008 (UTC) <br />
----<br />
I've added a link to a blank page on Verticillium (under chitin degradation). And I'm certainly not going to stay up to fill the whole thing in.<br />
[[User:Njblackburn|Njblackburn]] 06:51, 11 March 2008 (UTC)<br />
----<br />
<br />
So, what happened to group member #4? And who was in charge of our microbe page that we had to write? I feel that I've done more than my share (thanks Jess for filling in so much, too). <br />
[[User:Njblackburn|Njblackburn]] 06:11, 11 March 2008 (UTC)<br />
----<br />
I would modify the heading of Decomposition of organic..... to include "and the microorganisms involved" Then you can include some info on the players in each category if there is specific info available AND make nice links to the existing microbe pages. There should be a lot of these pages.<br />
<br />
This way you can eliminate the section on just microbes and integrate it into each important process. If there are no really specific organisms, e.g. with the sugars section, you can just say that metabolism of these compounds is by a broad group of microorganisms.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:55, 10 March 2008 (UTC) ----<br />
<br />
[[User:Kmscow|Kate Scow]] 01:45, 10 March 2008 (UTC)<br />
<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<br />
Ok, guys: we need to do this wiki. I'm sorry that I haven't gotten to it until today, but I don't any other effort here either. I'm going to work through some of it, but what I leave undone had better get done by tomorrow.<br />
[[User:Njblackburn|Njblackburn]] 19:37, 9 March 2008 (UTC)<br />
----<br />
I would suggest not breaking out geo/bio/hydro/atmosphere unless you really want to go into detail about this. Please include the 2 main sections in the lecture:<br />
# Decomposition of organic matter--<br />
and then cover all the different chemical components of plant materials e.g. monomers, cellulose, hemicellulose, lignin, etc<br />
# Formation of humic substances<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
You might want to link the microbial types directly to the processes rather than split it out alone.<br />
<br />
E.g. cellulose decomposition is where you would discuss a little about the organisms involved and you can link this to the organisms already listed in the wiki. A lot of these organisms start with "cellu"<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
You don't need to have an Edits and Dates section at the end either - all this information is collected under "History". I noticed you wrote "Jaime and Alex". I can see that Jaime made edits but not Alex. So please make sure you log in yourselves when editing, so that we can attribute work - [[User:Irina.chakraborty|Irina C]] 22:52, 10 February 2008 (UTC)<br />
<br />
Good start - You don't need to have a list of your sections at the start of your page because a content list is automatically generated if you use heading formats for the title of each section. Also you used internal link formatting for the items in "List of Topics". You only need to do this if you are creating new pages for each item - this would make sense if we were going to add a lot of detail. Instead each item is just a section within your page, so does not require a link to its own page.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 22:22, 10 February 2008 (UTC)<br />
<br />
----<br />
Has anyone seen the template for our page we need to write about a microbe? Jess and I have gone through and put in a bunch of links, but I'm not sure how to create an entirely new page. (~Jaime)<br />
----<br />
<br />
Could you make the pictures smaller. Those pictures are really pretty.</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29221
Desulfobacter
2008-03-17T01:09:44Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
"Desulfobacter" is a mesophilic gram-negative genera that is capable of oxidizing organic substrate completely to CO2. Desulfobacter is mainly common in brackish and marine environemnt (1). The genus "desulfobacter" includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria and could be used as a biomarker for these bacteria [21,30].<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
1-Lary L. Barton Biotechnology handbooks. Vol. 8-Sulfate reducing bacteria. 1995 Plenum Press, New York.<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy Paustian© 1999-2004.</span>]<br />
<br />
[http://ecosystems.mbl.edu/pimo/projects.html PIMO Database].<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29220
Desulfobacter
2008-03-17T00:38:48Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
The genus sulphobacter includes acetateutelizing sulphate-reducing bacteria. 10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria<br />
and hence has been proposed as a biomarker for these bacteria [21,30].<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Comparison of the phospholipid ester-linked fatty acid biomarkers of acetate-oxidising sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132,1815-1825.<br />
<br />
30-Dowling, N.J., Nichols, P.D. and White, D.C. (1988)Phospholipid fatty acid and infra-red spectroscopic analysis of a sulfate-reducing consortium. FEMS Microbiol.Ecol. 53, 325-334<br />
<br />
<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy Paustian© 1999-2004.</span>]<br />
<br />
[http://ecosystems.mbl.edu/pimo/projects.html PIMO Database].<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29219
Desulfobacter
2008-03-17T00:36:42Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
The genus sulphobacter includes acetateutelizing sulphate-reducing bacteria.<br />
10 Methyl 16:0 is an unusual bacterial phospholipid fatty acids (PLFA) characteristic of Desulfobacter-type sulphate-reducing bacteria<br />
and hence has been proposed as a biomarker for these bacteria [21,30].<br />
<br />
21-Dowling, N.J., Widdel, F. and White, D.C. (1986) Com-<br />
<br />
<br />
<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy Paustian© 1999-2004.</span>]<br />
<br />
[http://ecosystems.mbl.edu/pimo/projects.html PIMO Database].<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29206
Desulfobacter
2008-03-17T00:19:29Z
<p>Lrastegarzadeh: /* Description and Significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
<br />
<br />
<br />
This rod-shaped bacterium is identified as anaerobically growing, motile organism. Desulfovibrio is known as a sulfate reducing bacterium, which has put it to the forefront of biological research. Because of its metal corroding ability, which has consequently led to numerous health and safety concerns in industry, a means to neutralize and better understand Desulfovibrio species is the goal of research on Desulfovibrio (ITQB). The organism however also shows potential for bioremediation, in that it may undergo anaerobic conversion of pollutants in the soil.<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy Paustian© 1999-2004.</span>]<br />
<br />
[http://ecosystems.mbl.edu/pimo/projects.html PIMO Database].<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29198
Desulfobacter
2008-03-16T23:53:21Z
<p>Lrastegarzadeh: /* Species: */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2289&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy Paustian© 1999-2004.</span>]<br />
<br />
[http://ecosystems.mbl.edu/pimo/projects.html PIMO Database].<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Desulfobacter&diff=29197
Desulfobacter
2008-03-16T23:50:04Z
<p>Lrastegarzadeh: New page: {{Biorealm Genus}} [[Image:.jpg|thumb|350px|right| ==Classification== ===Higher order taxa:=== Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobactera...</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[Image:.jpg|thumb|350px|right|<br />
<br />
==Classification==<br />
<br />
===Higher order taxa:===<br />
<br />
Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae<br />
<br />
===Species:===<br />
<br />
''Desulfosarcina variablis, Desulfosarcina sp. CME1''<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2299&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy] Genome'''<br />
|}<br />
<br />
==Description and Significance==<br />
<br />
<br />
==Genome Structure==<br />
<br />
<br />
<br />
==Cell Structure and Metabolism==<br />
<!-- the only way I know to do multiple images is to create the "frame" yourself by using tables like the one i setup here for you. http://en.wikipedia.org/wiki/Help:Table gives great help on the construction of tables if you get in a jam. Drew T. 6.5.06 --><br />
{| border="1" cellpadding="5" cellspacing="0" style="background-color:#f9f9f9;" width="425" align="left"<br />
|-<br />
|[[Image:bbb.jpg|center]]<br><br />
[[Image:ddd.jpg|center]]<br><br />
''D. variabilis'' contains significant quantities of AEG-P (top), and almost 20% of the alkyl-glycerol bond is present as DPG lipids, also known as "cardiolipin" (bottom). Note that the DPGs contain either ether or ester linkages in the core lipids.[http://www.chemistry.montana.edu/chem524/pdf/Julian%20lipids%20RCM%20%202004.pdf Sturt ''et al'']<!-- watch your links any webpage that has a %20 is a space and your converter will change it to a " "(space) which will cancel your links so be careful. Drew T. 6.5.06 --><br />
|}<br />
<br />
<!-- the following table was built to center the text vertically and to push teh next section down past the pictures. Drew T. 6.5.06 --><br />
<br />
{| align="right" style="width:350px; height:390px" border="0px"<br />
|- <br />
| valign="center"|Sulfate reducers have a wide range of cellular morphologies, including rods, vibrios, ovals, spheres and even tear-dropped or onion shaped cells. Some are motile, others are not. Most sulfate-reducing bacteria are mesophilic, but a few thermophiles are known. ''Desulfosarcina variabilis'' is mesophilic, and contains bacterial core lipids (see images on left). The dominant phospholipid headgroups in ''D. variabilis'' are Phosphoethanolamine PE (48%) and Phosphoglycerol PG (33%). One study has found that ''Desulfosarcina variabilis'' solely contained n-hexadecyl ether side chains. For more information on tetraether lipids found in Archaea, click [http://biology.kenyon.edu/Microbial_Biorealm/archaea/sulfolobus/sulfolobus.html#tetra here].<br />
|}<br />
<br style="clear:both" /><br />
==Ecology==<br />
<br />
Although sulfate reduction is thought to be an anaerobic process, sulfate-reducing bacteria (SRB) are also important in aerobic environments if they can proliferate in anaerobic zones. For example, in marine sediments and in aerobic wastewater treatment systems, sulfate reduction accounts for up to 50% of the mineralization of organic matter. Furthermore, sulfate reduction strongly stimulates microbially enhanced corrosion of metals. <br />
[[Image:plum_island_estuary_aerial.jpg|frame|center|The Plum Island Estuary Microbial Observatory ([http://ecosystems.mbl.edu/pimo/projects.html PIMO]), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Among SRBs identified, relatives of ''Desulfosarcina variabilis'' and D''esulfobacterium anilini'' were found to be persistent in the sediment.]]<br />
<br />
==References==<br />
<br />
<div align="left"><br />
<br />
[http://www.arches.uga.edu/ Arches], specifically p.10 [http://www.arches.uga.edu/~whitman/coursedocs/mibo4300/natural populations and methods.PDF here].<br />
<br />
[http://www.bact.wisc.edu/Microtextbook/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=104&page=1 Microbiology Textbook.<span class="pn-sub"> Copyright, Timothy Paustian© 1999-2004.</span>]<br />
<br />
[http://ecosystems.mbl.edu/pimo/projects.html PIMO Database].<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11734887&dopt=Abstract Rutters H, Sass H, Cypionka H, Rullkotter J. "Monoalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina variabilis and Desulforhabdus amnigenus." <span title="Archives of microbiology.">Arch Microbiol.</span> 2001 Dec;176(6):435-442. Epub 2001 Sep 19.]<br />
<br />
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106533 Santegoeds, Cecilia M.; Timothy G. Ferdelman, Gerard Muyzer, and Dirk de Beer. "Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms." Appl Environ Microbiol. 1998 October; 64(10): 3731–3739. Copyright © 1998, American Society for Microbiology.]<br />
<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15052572&dopt=Abstract Sturt, Helen F.; Roger E. Summons, Kristin Smith, Marcus Elvert, and Kai-Uwe Hinrichs. "Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology." Rapid Commun. Mass Spectrom. 2004; 18: 617–628.]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=28100
Flooded Soils
2008-03-09T19:20:45Z
<p>Lrastegarzadeh: /* Ion reducing bacteria */</p>
<hr />
<div>==Introduction==<br />
[[Image:flooded soil.png|thumb|300px|schematic presentation of flooded soil from[[Y.Chen and Y Avnimelech]]]]<br />
When the pore spaces in soils are saturated with water, oxygen dissolved in water is gradually depleted because oxygen is used as terminal electron acceptor for respiration by some aerobes and the facultative anaerobes. This results in anaerobic condition of soils. This anoxic condition can be found in soil aggregates and pollutants plume. Under anoxic condition, some microbes can use alternative electron acceptors such as nitrate, ferric, manganese (IV) oxide, sulfate, and carbon dioxide. Anaerobic reduction processes do not occure simultaneously, but one after another according to presence of appropriate electron aceptors as well as the cometitive electron acceptors.<br />
<br />
==Process ==<br />
In general, flooded soil condition occurs due to seasonal flooding or agricultural activity. <br />
The flooded soils condition can be often converted into non-flooded soil condition by the water level fluctuation and drainage. Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed. <br />
As explained in the introduction, microorganism can use alternative terminal electron acceptor when dissolved oxygen is absent. They successively use electron acceptor according to the order of electron acceptor utilization based on electron tower. The order change of electron acceptor utilization is observed in soil aggregates and pollutant plume. <br />
(Figure aggregates and pollutant plume)<br />
<br />
===Oxidation/reduction (redox) reaction===<br />
====Electron tower====<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified into the strict aerobes, obligate anaerobes, and facultative anaerobes. The strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, they start to use nitrate as electron acceptor. Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptor in the order of electron acceptor having more reducing energy. Oxygen is most efficient electron acceptor, while carbon dioxide has the less reducing energy. <br />
(figure electron tower)<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobe and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by Iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by Denitrifier) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by Methanogeous)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by Manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succetion of anaerobic oxidation processes, the redox potential (Eh) of the flooded soil will decrease as a result of the reduced products formed. The approximate redox potential values that indicate the start and end of a specific reduction oxidation process are as follows: (How to make a table??)<br />
Observation Eh (mV)<br />
Disappearance of oxygen +330<br />
Disappearance of nitrate +220<br />
Appearance of manganese ions +200<br />
Appearance of ferrous ions +120<br />
Disappearance of sulfate -150<br />
Appearance of methane -250<br />
<br />
===Solubility/mobility of mineral===<br />
Since the toxicity, solubility, mobility,and bioavailability of a given element or compounds are mainly influenced by soil solution redox potenial and pH, flooded soil condition plays an important role in mobility of trace metal, nutrients, and mineral.<br />
<br />
===Effects on life===<br />
<br />
In flooded conditions microorganisms can no longer use oxygen, or it is severly limited<br />
<br />
====Plant nutrient availability====<br />
Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a main role in a healthy plant growth process. In flooded soils, under anaerobic conditions the pH value wil tend to rise. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants<br />
<br />
====Microorganism activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as TEA (terminal electron acceptors). Iron is reduced from Fe<sup>3+</sup> to Fe<sup>2+</sup> during iron repiration. Manganese is also reduced. These processes occur because of microoganism activity. Energy yields are lower than for aerobic respiration.(1)<br />
<br />
==Key Microorganisms & exchanges of gases==<br />
The role of microorganisms under flooded soil<br />
===nitrate reducing bacteria===<br />
Denitrification is carried out by obligate respiratory bacteria belonging to the genra ''Agrobactterium'', ''Alcaligenes'', ''Bacillus'', Paracoccus'', ''Pesudomonas'' and ''Thiobacillus'' (Knowles, 1982). Nitrate ammonification found in facultative anaerobe bacteria belonging to the genera ''Bacillus'', ''Citrobacter'' and ''Aeromonas'', or in the memebers of the Enterobacteriaceae (Cole adn Brown, 1980; Smith adn Zimmerman, 1981; MacFarlane and Herbert, 1982). Strictly anaerobic bacteria belonging to the genus ''Clostridium'' are also able to reduce nitrate to ammonia (Hasan and Hall, 1975). <br />
Pure culture studies show evidance that nitrate reduction does occure in presence of oxygen (Kuenen and and Robertson, 1987).<br />
<br />
===Methaneous bacteria===<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
===Iron reducing bacteria===<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''G. metallireducens'', ''G. sulfurreducens'', and ''Shewanella putrefaciens''.Different forms of ferric oxides exist in aaerobic drained as well as in waterlogged soils. Not all of these ferric oxides are equally suitable for reduction by ferric oxide reducer bacteria (Gotoh and Patrick, 1974; Schwertmann and Taylor, 1977). In general, amorphous forms are more efficient for ferric reducer bacteria than crystalline forms (Lovely adn Phillips, 1986). The reduction of ferric oxide may release phosphate and trace elements that are adsorbed to the amorphous ferric oxide and thus enhance availablity of these compounds in the soil (Lovely and Phillips, 1986).<br />
<br />
===Sulfate reducing bacteria===<br />
Bacteria can use acetate as electron donor and sulfate as electron acceptor. This reaction is as follow;<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''Desulfobacterales'', ''Desulfovibrionales'', and ''Syntrophobacterales'' (Langston and Bebiano 1998). Hydrogen sulfide gas produced via anaerobic respiration cause the rotten egg odor.<br />
<br />
===Manganese reducing bacteria===<br />
<br />
==Current Research==<br />
Green house gases(nitrous oxides, methane, carbon dioxide ) emission from flooded soil(rice paddy,riverine, estuarine, and lacustrine sediments)<br />
<br />
==References==<br />
<br />
(1) Kate Scow lecture 5<br />
<br />
x Appl Environ Microbiol, June 1998, p. 2181-2186, Vol. 64, No. 6<br />
http://aem.asm.org/cgi/content/full/64/6/2181<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=28098
Flooded Soils
2008-03-09T19:20:18Z
<p>Lrastegarzadeh: /* Ion reducing bacteria */</p>
<hr />
<div>==Introduction==<br />
[[Image:flooded soil.png|thumb|300px|schematic presentation of flooded soil from[[Y.Chen and Y Avnimelech]]]]<br />
When the pore spaces in soils are saturated with water, oxygen dissolved in water is gradually depleted because oxygen is used as terminal electron acceptor for respiration by some aerobes and the facultative anaerobes. This results in anaerobic condition of soils. This anoxic condition can be found in soil aggregates and pollutants plume. Under anoxic condition, some microbes can use alternative electron acceptors such as nitrate, ferric, manganese (IV) oxide, sulfate, and carbon dioxide. Anaerobic reduction processes do not occure simultaneously, but one after another according to presence of appropriate electron aceptors as well as the cometitive electron acceptors.<br />
<br />
==Process ==<br />
In general, flooded soil condition occurs due to seasonal flooding or agricultural activity. <br />
The flooded soils condition can be often converted into non-flooded soil condition by the water level fluctuation and drainage. Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed. <br />
As explained in the introduction, microorganism can use alternative terminal electron acceptor when dissolved oxygen is absent. They successively use electron acceptor according to the order of electron acceptor utilization based on electron tower. The order change of electron acceptor utilization is observed in soil aggregates and pollutant plume. <br />
(Figure aggregates and pollutant plume)<br />
<br />
===Oxidation/reduction (redox) reaction===<br />
====Electron tower====<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified into the strict aerobes, obligate anaerobes, and facultative anaerobes. The strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, they start to use nitrate as electron acceptor. Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptor in the order of electron acceptor having more reducing energy. Oxygen is most efficient electron acceptor, while carbon dioxide has the less reducing energy. <br />
(figure electron tower)<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobe and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by Iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by Denitrifier) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by Methanogeous)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by Manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succetion of anaerobic oxidation processes, the redox potential (Eh) of the flooded soil will decrease as a result of the reduced products formed. The approximate redox potential values that indicate the start and end of a specific reduction oxidation process are as follows: (How to make a table??)<br />
Observation Eh (mV)<br />
Disappearance of oxygen +330<br />
Disappearance of nitrate +220<br />
Appearance of manganese ions +200<br />
Appearance of ferrous ions +120<br />
Disappearance of sulfate -150<br />
Appearance of methane -250<br />
<br />
===Solubility/mobility of mineral===<br />
Since the toxicity, solubility, mobility,and bioavailability of a given element or compounds are mainly influenced by soil solution redox potenial and pH, flooded soil condition plays an important role in mobility of trace metal, nutrients, and mineral.<br />
<br />
===Effects on life===<br />
<br />
In flooded conditions microorganisms can no longer use oxygen, or it is severly limited<br />
<br />
====Plant nutrient availability====<br />
Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a main role in a healthy plant growth process. In flooded soils, under anaerobic conditions the pH value wil tend to rise. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants<br />
<br />
====Microorganism activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as TEA (terminal electron acceptors). Iron is reduced from Fe<sup>3+</sup> to Fe<sup>2+</sup> during iron repiration. Manganese is also reduced. These processes occur because of microoganism activity. Energy yields are lower than for aerobic respiration.(1)<br />
<br />
==Key Microorganisms & exchanges of gases==<br />
The role of microorganisms under flooded soil<br />
===nitrate reducing bacteria===<br />
Denitrification is carried out by obligate respiratory bacteria belonging to the genra ''Agrobactterium'', ''Alcaligenes'', ''Bacillus'', Paracoccus'', ''Pesudomonas'' and ''Thiobacillus'' (Knowles, 1982). Nitrate ammonification found in facultative anaerobe bacteria belonging to the genera ''Bacillus'', ''Citrobacter'' and ''Aeromonas'', or in the memebers of the Enterobacteriaceae (Cole adn Brown, 1980; Smith adn Zimmerman, 1981; MacFarlane and Herbert, 1982). Strictly anaerobic bacteria belonging to the genus ''Clostridium'' are also able to reduce nitrate to ammonia (Hasan and Hall, 1975). <br />
Pure culture studies show evidance that nitrate reduction does occure in presence of oxygen (Kuenen and and Robertson, 1987).<br />
<br />
===Methaneous bacteria===<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
===Ion reducing bacteria===<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''G. metallireducens'', ''G. sulfurreducens'', and ''Shewanella putrefaciens''.Different forms of ferric oxides exist in aaerobic drained as well as in waterlogged soils. Not all of these ferric oxides are equally suitable for reduction by ferric oxide reducer bacteria (Gotoh and Patrick, 1974; Schwertmann and Taylor, 1977). In general, amorphous forms are more efficient for ferric reducer bacteria than crystalline forms (Lovely adn Phillips, 1986). The reduction of ferric oxide may release phosphate and trace elements that are adsorbed to the amorphous ferric oxide and thus enhance availablity of these compounds in the soil (Lovely and Phillips, 1986).<br />
<br />
===Sulfate reducing bacteria===<br />
Bacteria can use acetate as electron donor and sulfate as electron acceptor. This reaction is as follow;<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''Desulfobacterales'', ''Desulfovibrionales'', and ''Syntrophobacterales'' (Langston and Bebiano 1998). Hydrogen sulfide gas produced via anaerobic respiration cause the rotten egg odor.<br />
<br />
===Manganese reducing bacteria===<br />
<br />
==Current Research==<br />
Green house gases(nitrous oxides, methane, carbon dioxide ) emission from flooded soil(rice paddy,riverine, estuarine, and lacustrine sediments)<br />
<br />
==References==<br />
<br />
(1) Kate Scow lecture 5<br />
<br />
x Appl Environ Microbiol, June 1998, p. 2181-2186, Vol. 64, No. 6<br />
http://aem.asm.org/cgi/content/full/64/6/2181<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=28075
Flooded Soils
2008-03-09T18:51:17Z
<p>Lrastegarzadeh: /* nitrate reducing bacteria */</p>
<hr />
<div>==Introduction==<br />
<br />
When the pore spaces in soils are saturated with water, oxygen dissolved in water is gradually depleted because oxygen is used as terminal electron acceptor for respiration by some aerobes and the facultative anaerobes. This results in anaerobic condition of soils. This anoxic condition can be found in soil aggregates and pollutants plume. Under anoxic condition, some microbes can use alternative electron acceptors such as nitrate, ferric, manganese (IV) oxide, sulfate, and carbon dioxide. Anaerobic reduction processes do not occure simultaneously, but one after another according to presence of appropriate electron aceptors as well as the cometitive electron acceptors.<br />
<br />
==Process ==<br />
In general, flooded soil condition occurs due to seasonal flooding or agricultural activity. <br />
The flooded soils condition can be often converted into non-flooded soil condition by the water level fluctuation and drainage. Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed. <br />
As explained in the introduction, microorganism can use alternative terminal electron acceptor when dissolved oxygen is absent. They successively use electron acceptor according to the order of electron acceptor utilization based on electron tower. The order change of electron acceptor utilization is observed in soil aggregates and pollutant plume. <br />
(Figure aggregates and pollutant plume)<br />
<br />
===Oxidation/reduction (redox) reaction===<br />
====Electron tower====<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified into the strict aerobes, obligate anaerobes, and facultative anaerobes. The strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, they start to use nitrate as electron acceptor. Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptor in the order of electron acceptor having more reducing energy. Oxygen is most efficient electron acceptor, while carbon dioxide has the less reducing energy. <br />
(figure electron tower)<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobe and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by Iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by Denitrifier) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by Methanogeous)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by Manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succetion of anaerobic oxidation processes, the redox potential (Eh) of the flooded soil will decrease as a result of the reduced products formed. The approximate redox potential values that indicate the start and end of a specific reduction oxidation process are as follows: (How to make a table??)<br />
Observation Eh (mV)<br />
Disappearance of oxygen +330<br />
Disappearance of nitrate +220<br />
Appearance of manganese ions +200<br />
Appearance of ferrous ions +120<br />
Disappearance of sulfate -150<br />
Appearance of methane -250<br />
<br />
===Solubility/mobility of mineral===<br />
Since the toxicity, solubility, mobility,and bioavailability of a given element or compounds are mainly influenced by soil solution redox potenial and pH, flooded soil condition plays an important role in mobility of trace metal, nutrients, and mineral.<br />
<br />
===Effects on life===<br />
<br />
In flooded conditions microorganisms can no longer use oxygen, or it is severly limited<br />
<br />
====Plant nutrient availability====<br />
Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a main role in a healthy plant growth process. In flooded soils, under anaerobic conditions the pH value wil tend to rise. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants<br />
<br />
====Microorganism activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as TEA (terminal electron acceptors). Iron is reduced from Fe<sup>3+</sup> to Fe<sup>2+</sup> during iron repiration. Manganese is also reduced. These processes occur because of microoganism activity. Energy yields are lower than for aerobic respiration.(1)<br />
<br />
==Key Microorganisms & exchanges of gases==<br />
The role of microorganisms under flooded soil<br />
===nitrate reducing bacteria===<br />
Denitrification is carried out by obligate respiratory bacteria belonging to the genra ''Agrobactterium'', ''Alcaligenes'', ''Bacillus'', Paracoccus'', ''Pesudomonas'' and ''Thiobacillus'' (Knowles, 1982). Nitrate ammonification found in facultative anaerobe bacteria belonging to the genera ''Bacillus'', ''Citrobacter'' and ''Aeromonas'', or in the memebers of the Enterobacteriaceae (Cole adn Brown, 1980; Smith adn Zimmerman, 1981; MacFarlane and Herbert, 1982). Strictly anaerobic bacteria belonging to the genus ''Clostridium'' are also able to reduce nitrate to ammonia (Hasan and Hall, 1975). <br />
Pure culture studies show evidance that nitrate reduction does occure in presence of oxygen (Kuenen and and Robertson, 1987).<br />
<br />
===Methaneous bacteria===<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
===Ion reducing bacteria===<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''G. metallireducens'', ''G. sulfurreducens'', and ''Shewanella putrefaciens''.<br />
<br />
===Sulfate reducing bacteria===<br />
Bacteria can use acetate as electron donor and sulfate as electron acceptor. This reaction is as follow;<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''Desulfobacterales'', ''Desulfovibrionales'', and ''Syntrophobacterales'' (Langston and Bebiano 1998). Hydrogen sulfide gas produced via anaerobic respiration cause the rotten egg odor.<br />
<br />
===Manganese reducing bacteria===<br />
<br />
==Current Research==<br />
Green house gases(nitrous oxides, methane, carbon dioxide ) emission from flooded soil(rice paddy,riverine, estuarine, and lacustrine sediments)<br />
<br />
==References==<br />
<br />
(1) Kate Scow lecture 5<br />
<br />
x Appl Environ Microbiol, June 1998, p. 2181-2186, Vol. 64, No. 6<br />
http://aem.asm.org/cgi/content/full/64/6/2181<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=28065
Flooded Soils
2008-03-09T18:20:15Z
<p>Lrastegarzadeh: /* Eh */</p>
<hr />
<div>==Introduction==<br />
<br />
When the pore spaces in soils are saturated with water, oxygen dissolved in water is gradually depleted because oxygen is used as terminal electron acceptor for respiration by some aerobes and the facultative anaerobes. This results in anaerobic condition of soils. This anoxic condition can be found in soil aggregates and pollutants plume. Under anoxic condition, some microbes can use alternative electron acceptors such as nitrate, ferric, manganese (IV) oxide, sulfate, and carbon dioxide. Anaerobic reduction processes do not occure simultaneously, but one after another according to presence of appropriate electron aceptors as well as the cometitive electron acceptors.<br />
<br />
==Process ==<br />
In general, flooded soil condition occurs due to seasonal flooding or agricultural activity. <br />
The flooded soils condition can be often converted into non-flooded soil condition by the water level fluctuation and drainage. Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed. <br />
As explained in the introduction, microorganism can use alternative terminal electron acceptor when dissolved oxygen is absent. They successively use electron acceptor according to the order of electron acceptor utilization based on electron tower. The order change of electron acceptor utilization is observed in soil aggregates and pollutant plume. <br />
(Figure aggregates and pollutant plume)<br />
<br />
===Oxidation/reduction (redox) reaction===<br />
====Electron tower====<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified into the strict aerobes, obligate anaerobes, and facultative anaerobes. The strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, they start to use nitrate as electron acceptor. Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptor in the order of electron acceptor having more reducing energy. Oxygen is most efficient electron acceptor, while carbon dioxide has the less reducing energy. <br />
(figure electron tower)<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobe and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by Iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by Denitrifier) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by Methanogeous)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by Manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succetion of anaerobic oxidation processes, the redox potential (Eh) of the flooded soil will decrease as a result of the reduced products formed. The approximate redox potential values that indicate the start and end of a specific reduction oxidation process are as follows: (How to make a table??)<br />
Observation Eh (mV)<br />
Disappearance of oxygen +330<br />
Disappearance of nitrate +220<br />
Appearance of manganese ions +200<br />
Appearance of ferrous ions +120<br />
Disappearance of sulfate -150<br />
Appearance of methane -250<br />
<br />
===Solubility/mobility of mineral===<br />
Since the toxicity, solubility, mobility,and bioavailability of a given element or compounds are mainly influenced by soil solution redox potenial and pH, flooded soil condition plays an important role in mobility of trace metal, nutrients, and mineral.<br />
<br />
===Effects on life===<br />
<br />
In flooded conditions microorganisms can no longer use oxygen, or it is severly limited<br />
<br />
====Plant nutrient availability====<br />
Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a main role in a healthy plant growth process. In flooded soils, under anaerobic conditions the pH value wil tend to rise. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants<br />
<br />
====Microorganism activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as TEA (terminal electron acceptors). Iron is reduced from Fe<sup>3+</sup> to Fe<sup>2+</sup> during iron repiration. Manganese is also reduced. These processes occur because of microoganism activity. Energy yields are lower than for aerobic respiration.(1)<br />
<br />
==Key Microorganisms & exchanges of gases==<br />
The role of microorganisms under flooded soil<br />
===nitrate reducing bacteria===<br />
Denitrification is carried out by denitrifier such as ''Pseudomonas stutzeri'', ''Pseudomonas aeruginosa'', and ''Paracoccus denitrificans'' (Carlson and Ingraham 1983)<br />
<br />
===Methaneous bacteria===<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
===Ion reducing bacteria===<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''G. metallireducens'', ''G. sulfurreducens'', and ''Shewanella putrefaciens''.<br />
<br />
===Sulfate reducing bacteria===<br />
Bacteria can use acetate as electron donor and sulfate as electron acceptor. This reaction is as follow;<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''Desulfobacterales'', ''Desulfovibrionales'', and ''Syntrophobacterales'' (Langston and Bebiano 1998). Hydrogen sulfide gas produced via anaerobic respiration cause the rotten egg odor.<br />
<br />
===Manganese reducing bacteria===<br />
<br />
==Current Research==<br />
Green house gases(nitrous oxides, methane, carbon dioxide ) emission from flooded soil(rice paddy,riverine, estuarine, and lacustrine sediments)<br />
<br />
==References==<br />
<br />
(1) Kate Scow lecture 5<br />
<br />
x Appl Environ Microbiol, June 1998, p. 2181-2186, Vol. 64, No. 6<br />
http://aem.asm.org/cgi/content/full/64/6/2181<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=28062
Flooded Soils
2008-03-09T18:08:30Z
<p>Lrastegarzadeh: /* Eh */</p>
<hr />
<div>==Introduction==<br />
<br />
When the pore spaces in soils are saturated with water, oxygen dissolved in water is gradually depleted because oxygen is used as terminal electron acceptor for respiration by some aerobes and the facultative anaerobes. This results in anaerobic condition of soils. This anoxic condition can be found in soil aggregates and pollutants plume. Under anoxic condition, some microbes can use alternative electron acceptors such as nitrate, ferric, manganese (IV) oxide, sulfate, and carbon dioxide. Anaerobic reduction processes do not occure simultaneously, but one after another according to presence of appropriate electron aceptors as well as the cometitive electron acceptors.<br />
<br />
==Process ==<br />
In general, flooded soil condition occurs due to seasonal flooding or agricultural activity. <br />
The flooded soils condition can be often converted into non-flooded soil condition by the water level fluctuation and drainage. Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed. <br />
As explained in the introduction, microorganism can use alternative terminal electron acceptor when dissolved oxygen is absent. They successively use electron acceptor according to the order of electron acceptor utilization based on electron tower. The order change of electron acceptor utilization is observed in soil aggregates and pollutant plume. <br />
(Figure aggregates and pollutant plume)<br />
<br />
===Oxidation/reduction (redox) reaction===<br />
====Electron tower====<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified into the strict aerobes, obligate anaerobes, and facultative anaerobes. The strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, they start to use nitrate as electron acceptor. Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptor in the order of electron acceptor having more reducing energy. Oxygen is most efficient electron acceptor, while carbon dioxide has the less reducing energy. <br />
(figure electron tower)<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobe and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by Iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by Denitrifier) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by Methanogeous)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by Manganese reducing bacteria)<br />
<br />
====Eh====<br />
During the succetion of anaerobic oxidation processes, the redox potential (Eh) of the flooded soil will decrease as a result of the reduced products formed. The approximate redox potential values that indicate the start and end of a specific reduction oxidation process are as follows<br />
<br />
===Solubility/mobility of mineral===<br />
Since the toxicity, solubility, mobility,and bioavailability of a given element or compounds are mainly influenced by soil solution redox potenial and pH, flooded soil condition plays an important role in mobility of trace metal, nutrients, and mineral.<br />
<br />
===Effects on life===<br />
<br />
In flooded conditions microorganisms can no longer use oxygen, or it is severly limited<br />
<br />
====Plant nutrient availability====<br />
Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a main role in a healthy plant growth process. In flooded soils, under anaerobic conditions the pH value wil tend to rise. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants<br />
<br />
====Microorganism activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as TEA (terminal electron acceptors). Iron is reduced from Fe<sup>3+</sup> to Fe<sup>2+</sup> during iron repiration. Manganese is also reduced. These processes occur because of microoganism activity. Energy yields are lower than for aerobic respiration.(1)<br />
<br />
==Key Microorganisms & exchanges of gases==<br />
The role of microorganisms under flooded soil<br />
===nitrate reducing bacteria===<br />
Denitrification is carried out by denitrifier such as ''Pseudomonas stutzeri'', ''Pseudomonas aeruginosa'', and ''Paracoccus denitrificans'' (Carlson and Ingraham 1983)<br />
<br />
===Methaneous bacteria===<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
===Ion reducing bacteria===<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''G. metallireducens'', ''G. sulfurreducens'', and ''Shewanella putrefaciens''.<br />
<br />
===Sulfate reducing bacteria===<br />
Bacteria can use acetate as electron donor and sulfate as electron acceptor. This reaction is as follow;<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''Desulfobacterales'', ''Desulfovibrionales'', and ''Syntrophobacterales'' (Langston and Bebiano 1998). Hydrogen sulfide gas produced via anaerobic respiration cause the rotten egg odor.<br />
<br />
===Manganese reducing bacteria===<br />
<br />
==Current Research==<br />
Green house gases(nitrous oxides, methane, carbon dioxide ) emission from flooded soil(rice paddy,riverine, estuarine, and lacustrine sediments)<br />
<br />
==References==<br />
<br />
(1) Kate Scow lecture 5<br />
<br />
x Appl Environ Microbiol, June 1998, p. 2181-2186, Vol. 64, No. 6<br />
http://aem.asm.org/cgi/content/full/64/6/2181<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=28060
Flooded Soils
2008-03-09T17:53:33Z
<p>Lrastegarzadeh: /* Eh */</p>
<hr />
<div>==Introduction==<br />
<br />
When the pore spaces in soils are saturated with water, oxygen dissolved in water is gradually depleted because oxygen is used as terminal electron acceptor for respiration by some aerobes and the facultative anaerobes. This results in anaerobic condition of soils. This anoxic condition can be found in soil aggregates and pollutants plume. Under anoxic condition, some microbes can use alternative electron acceptors such as nitrate, ferric, manganese (IV) oxide, sulfate, and carbon dioxide. Anaerobic reduction processes do not occure simultaneously, but one after another according to presence of appropriate electron aceptors as well as the cometitive electron acceptors.<br />
<br />
==Process ==<br />
In general, flooded soil condition occurs due to seasonal flooding or agricultural activity. <br />
The flooded soils condition can be often converted into non-flooded soil condition by the water level fluctuation and drainage. Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed. <br />
As explained in the introduction, microorganism can use alternative terminal electron acceptor when dissolved oxygen is absent. They successively use electron acceptor according to the order of electron acceptor utilization based on electron tower. The order change of electron acceptor utilization is observed in soil aggregates and pollutant plume. <br />
(Figure aggregates and pollutant plume)<br />
<br />
===Oxidation/reduction (redox) reaction===<br />
====Electron tower====<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified into the strict aerobes, obligate anaerobes, and facultative anaerobes. The strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, they start to use nitrate as electron acceptor. Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptor in the order of electron acceptor having more reducing energy. Oxygen is most efficient electron acceptor, while carbon dioxide has the less reducing energy. <br />
(figure electron tower)<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobe and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by Iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by Denitrifier) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by Methanogeous)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by Manganese reducing bacteria)<br />
<br />
====Eh====<br />
during the succetion of electron decreasing in Eh(V) with soil depth<br />
<br />
===Solubility/mobility of mineral===<br />
Since the toxicity, solubility, mobility,and bioavailability of a given element or compounds are mainly influenced by soil solution redox potenial and pH, flooded soil condition plays an important role in mobility of trace metal, nutrients, and mineral.<br />
<br />
===Effects on life===<br />
<br />
In flooded conditions microorganisms can no longer use oxygen, or it is severly limited<br />
<br />
====Plant nutrient availability====<br />
Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a main role in a healthy plant growth process. In flooded soils, under anaerobic conditions the pH value wil tend to rise. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants<br />
<br />
====Microorganism activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as TEA (terminal electron acceptors). Iron is reduced from Fe<sup>3+</sup> to Fe<sup>2+</sup> during iron repiration. Manganese is also reduced. These processes occur because of microoganism activity. Energy yields are lower than for aerobic respiration.(1)<br />
<br />
==Key Microorganisms & exchanges of gases==<br />
The role of microorganisms under flooded soil<br />
===nitrate reducing bacteria===<br />
Denitrification is carried out by denitrifier such as ''Pseudomonas stutzeri'', ''Pseudomonas aeruginosa'', and ''Paracoccus denitrificans'' (Carlson and Ingraham 1983)<br />
<br />
===Methaneous bacteria===<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
===Ion reducing bacteria===<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''G. metallireducens'', ''G. sulfurreducens'', and ''Shewanella putrefaciens''.<br />
<br />
===Sulfate reducing bacteria===<br />
Bacteria can use acetate as electron donor and sulfate as electron acceptor. This reaction is as follow;<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''Desulfobacterales'', ''Desulfovibrionales'', and ''Syntrophobacterales'' (Langston and Bebiano 1998). Hydrogen sulfide gas produced via anaerobic respiration cause the rotten egg odor.<br />
<br />
===Manganese reducing bacteria===<br />
<br />
==Current Research==<br />
Green house gases(nitrous oxides, methane, carbon dioxide ) emission from flooded soil(rice paddy,riverine, estuarine, and lacustrine sediments)<br />
<br />
==References==<br />
<br />
(1) Kate Scow lecture 5<br />
<br />
x Appl Environ Microbiol, June 1998, p. 2181-2186, Vol. 64, No. 6<br />
http://aem.asm.org/cgi/content/full/64/6/2181<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh
https://microbewiki.kenyon.edu/index.php?title=Flooded_Soils&diff=28059
Flooded Soils
2008-03-09T17:45:07Z
<p>Lrastegarzadeh: /* Introduction */</p>
<hr />
<div>==Introduction==<br />
<br />
When the pore spaces in soils are saturated with water, oxygen dissolved in water is gradually depleted because oxygen is used as terminal electron acceptor for respiration by some aerobes and the facultative anaerobes. This results in anaerobic condition of soils. This anoxic condition can be found in soil aggregates and pollutants plume. Under anoxic condition, some microbes can use alternative electron acceptors such as nitrate, ferric, manganese (IV) oxide, sulfate, and carbon dioxide. Anaerobic reduction processes do not occure simultaneously, but one after another according to presence of appropriate electron aceptors as well as the cometitive electron acceptors.<br />
<br />
==Process ==<br />
In general, flooded soil condition occurs due to seasonal flooding or agricultural activity. <br />
The flooded soils condition can be often converted into non-flooded soil condition by the water level fluctuation and drainage. Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed. <br />
As explained in the introduction, microorganism can use alternative terminal electron acceptor when dissolved oxygen is absent. They successively use electron acceptor according to the order of electron acceptor utilization based on electron tower. The order change of electron acceptor utilization is observed in soil aggregates and pollutant plume. <br />
(Figure aggregates and pollutant plume)<br />
<br />
===Oxidation/reduction (redox) reaction===<br />
====Electron tower====<br />
Electron tower theory explains the utilization order of electron acceptor for respiration. <br />
Depending on the type of electron acceptors used by microorganisms, microbes can be classified into the strict aerobes, obligate anaerobes, and facultative anaerobes. The strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, they start to use nitrate as electron acceptor. Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptor in the order of electron acceptor having more reducing energy. Oxygen is most efficient electron acceptor, while carbon dioxide has the less reducing energy. <br />
(figure electron tower)<br />
<br />
===Variation of pH and Eh===<br />
====pH====<br />
Neutral pH soil<br />
<br />
When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes. The half reactions of hydrogen consumption are as follow; <br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobe and aerobes)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by Iron reducing bacteria)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by Denitrifier) <br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by Methanogeous)<br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by Manganese reducing bacteria)<br />
<br />
====Eh====<br />
decreasing in Eh(V) with soil depth<br />
<br />
===Solubility/mobility of mineral===<br />
Since the toxicity, solubility, mobility,and bioavailability of a given element or compounds are mainly influenced by soil solution redox potenial and pH, flooded soil condition plays an important role in mobility of trace metal, nutrients, and mineral.<br />
<br />
===Effects on life===<br />
<br />
In flooded conditions microorganisms can no longer use oxygen, or it is severly limited<br />
<br />
====Plant nutrient availability====<br />
Flooded soils can prevent efficient gas exchange between the plant root and the soil. pH plays a main role in a healthy plant growth process. In flooded soils, under anaerobic conditions the pH value wil tend to rise. Denitrification of soil nitrate to nitrogen gas plays a major role in the rise of pH levels. Flooding results in poor soil aeration because the supply of oxygen to flooded soil is severely limited. Oxygen deficiency is likely the most important environmental factor that triggers growth inhibition and injury in flooded plants<br />
<br />
====Microorganism activity====<br />
In anaerobic respiration oxygen is replaced by other compounds as TEA (terminal electron acceptors). Iron is reduced from Fe<sup>3+</sup> to Fe<sup>2+</sup> during iron repiration. Manganese is also reduced. These processes occur because of microoganism activity. Energy yields are lower than for aerobic respiration.(1)<br />
<br />
==Key Microorganisms & exchanges of gases==<br />
The role of microorganisms under flooded soil<br />
===nitrate reducing bacteria===<br />
Denitrification is carried out by denitrifier such as ''Pseudomonas stutzeri'', ''Pseudomonas aeruginosa'', and ''Paracoccus denitrificans'' (Carlson and Ingraham 1983)<br />
<br />
===Methaneous bacteria===<br />
Methanogen (e.g ''Methanobacterium formicum'', ''Methanobacterium bryantii'', ''Methanobacterium thermo-autrotrophicum'', and etc ) can use CO<sub>2</sub> and produce methane (Langston and Bebiano 1998)<br />
<br />
===Ion reducing bacteria===<br />
Ferrous iron is used as electron acceptor by iron-reducing bacteria such as ''G. metallireducens'', ''G. sulfurreducens'', and ''Shewanella putrefaciens''.<br />
<br />
===Sulfate reducing bacteria===<br />
Bacteria can use acetate as electron donor and sulfate as electron acceptor. This reaction is as follow;<br />
<br />
<br />
CH<sub>3</sub>COO<sup>-</sup> + SO<sub>4</sub><sup>2-</sup> + 3 H<sup>+</sup> ---> 2CO<sub>2</sub> + H<sub>2</sub>S + 2 H<sub>2</sub>O<br />
<br />
<br />
This reaction is carried out by sulfate-reducing bacteria such as ''Desulfobacterales'', ''Desulfovibrionales'', and ''Syntrophobacterales'' (Langston and Bebiano 1998). Hydrogen sulfide gas produced via anaerobic respiration cause the rotten egg odor.<br />
<br />
===Manganese reducing bacteria===<br />
<br />
==Current Research==<br />
Green house gases(nitrous oxides, methane, carbon dioxide ) emission from flooded soil(rice paddy,riverine, estuarine, and lacustrine sediments)<br />
<br />
==References==<br />
<br />
(1) Kate Scow lecture 5<br />
<br />
x Appl Environ Microbiol, June 1998, p. 2181-2186, Vol. 64, No. 6<br />
http://aem.asm.org/cgi/content/full/64/6/2181<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Lrastegarzadeh