Difference between revisions of "Nitrobacter hamburgensis"

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Classification
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{{Curated}}
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae; Nitrobacter; Nitrobacter hamburgensis
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{{Biorealm Genus}}
  
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==Classification==
  
Description and significance
 
Nitrobacter hamburgensis, gram negative bacteria, was isolated from soil of the Old Botanic Garden in Hamburg and of a corn field in Yucatan.  The main types of environments they inhabit are soil, building sandstone, and sewage sludge.  Its cells are 0.5-0.8 x 1.2-2.0 m in size.  They are pleomorphic; mostly pear-shaped and motile via one subpolar to lateral flagellum.  Intracytoplasmic membranes appear as caps of flattened vesicles or membrane vesicles in the central region of the cell.  The bacteria have an enzyme capable of oxidizing nitrite.  This is why it is important to sequence the genome of N. hamburgensis
 
  
[edit]Genus
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Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae; Nitrobacter; ''Nitrobacter hamburgensis'' (1)
Enterococcus faecalis
 
  
[edit]Description and significance
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==Description and significance==
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated. Include a picture or two (with sources) if you can find them.  
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''Nitrobacter hamburgensis'', a gram-negative bacteria, was isolated from soil of the Old Botanic Garden in Hamburg and of a corn field in Yucatan.  The main types of environments they inhabit are soil, building sandstone, and sewage sludge. Its cells are 0.5-0.8 x 1.2-2.0 m in size.  They are mostly pear-shaped and motile via one subpolar to lateral flagellum.  Intracytoplasmic membranes appear as caps of flattened vesicles or membrane vesicles in the central region of the cell. (2)  The bacteria have an enzyme capable of oxidizing nitrite (3).  This is why it is important to sequence the genome of ''N. hamburgensis''.
  
[edit]Genome structure
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==Genome structure==
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence? Does it have any plasmids? Are they important to the organism's lifestyle?
 
  
[edit]Cell structure and metabolism
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There is one circular DNA chromosome and three circular DNA plasmids.  The chromosome has 4,406,967 nucleotides.  Plasmid 1 has 294,829 nucleotides, 2 has 188,318 nucleotides, and 3 has 121,408 nucleotides. (1)
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.  
 
  
[edit]Ecology
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==Cell structure and metabolism==
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.
 
  
[edit]Pathology
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''N. hamburgensis'' gains energy from oxidation of nitrite to nitrate via the enzyme nitrite oxidoreductase (NOR). It has a maximum doubling time of 10 to 18 hours. (3)
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.  
 
  
[edit]Application to Biotechnology
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==Ecology==
Does this organism produce any useful compounds or enzymes? What are they and how are they used?
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''Nitrobacter hamburgensis'' is an example of nitrite-oxidizing bacteria.  This bacteria has the capability of metabolizing nitrogen in nitrite form in its environment.  It is found mainly in soil and freshwater. (4,6,7)  (See Current Research section for a summary of the work of ''Nitrobacter hamburgensis'' and nitrobacter.)
  
[edit]Current Research
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==Pathology==
Enter summaries of the most recent research here--at least three required
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As of present, there is no evidence for ''Nitrobacter hambugensis'' having pathological characteristics.
  
[edit]References
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==Application to Biotechnology==
example:
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The nitrification feature of ''Nitrobacter hamburgensis'' has been appreciated.  The bacteria has provided a solution to removing high levels of nitrogen from municipal effluents of wastewater treatment plants.  Biofilms with different nitrifying bacteria including ''N. hamburgensis'' have been constructed.  Before the invention of these biofilms very large and expensive reactors were used for this purpose. (4)
  
Glockner, F. O., M. Kube, M. Bauer, H. Teeling, T. Lombardot, W. Ludwig, D. Gade, A. Beck, K Borzym, K Heitmann, R. Rabus, H. Schlesner, R. Amann, and R. Reinhardt. 2003. "Complete genome sequence of the marine planctomycete Pirellula sp. strain 1." Proceedings of the National Acedemy of Sciences, vol. 100, no. 14. (8298-8303)  
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(See Current Research section for more on this topic and other specific examples of ''Nitrobacter hamburgensis''' involvement in biotechnology)
  
De la Maza, Luis M., Marie T. Pezzlo, and Janet T. Shigei. Color Atlas of Medical Bacteriology. Washington, DC: American Society for Microbiology, 2004.  
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==Current Research==
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This section summarizes some of the current research on ''Nitrobacter hamburgensis''. While this organism has long-been described, this species in particular has not sparked current research interest. After exhausting my resources I was only able to find two articles about ''Nitrobacter hamburgensis'' that were recently published. The other two articles are about nitrobacter species in general.
  
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Recent research has investigated the benefits of using nitrifying bacteria in neutralizing wastewater.  Researchers have constructed biofilms with different nitrifying bacteria including ''N. hamburgensis''.  They were successful in removing high levels of nitrogen in a short amount of time from municipal effluents from wastewater treatment plants.  The biofilms are sufficient alternatives for the treatment of industrial wastewater that otherwise requires very large and expensive reactors for efficient bioremediation of effluents. (4)
  
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Other current research has identified evidence that the previously published sequence of norX in ''N. hamburgensis X14''(T) contains an invalid base "insertion," which resulted in a frameshift and a misidentified start codon. (5)
  
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Going along the lines of neutralizing wastewater, nitrobacter and another nitrifying bacteria have been found in the Seine River in France.  Agricultural and urban pollution result in high concentrations of nitrogen in the Seine River and hence in the waster water treatment plants downstream of the river.  Scientists have identified nitrobacter as one of the bacteria responsible for oxidizing nitrite products upstream of the plant (in the freshwater).  Nitrobacter was also found as the main bacteria in the waste water effluents.  The overall result is nitrified waste water that flows into the sea. (6)
  
Edited by Richard A. Martinez of UC San Diego, student of Rachel Larsen.  
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The final research I will summarize describes the quorum sensing of nitrobacter bacteria. Quorum sensing is a term used to define a feature of bacteria that requires a certain number of them for something to happen.  For example, researchers have discovered that nitrobacter can oxidize nitrite in soil which has been exposed to diesel fuel for a long period of time.  They found that a large population of the bacteria is required for the nitrification to take place. (7)
  
Retrieved from "http://microbewiki.kenyon.edu/index.php/Enterococcus_faecalis"
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==References==
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1. www.ncbi.nlm.nih.gov/genomes/lproks.cgi
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2. E. Bock et al. 1983. “New facultative lithoautotrophic nitrite-oxidizing bacteria.” Archives of Microbiology, vol. 136, no.4. (281-284)
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3. Jens Aamand, Thomas Ahl, and Eva Spieck. 1996. "Monoclonal Antibodies Recognizing Nitirite Oxidoreductase fo Nitrobacter hamburgensis, N. winogradskyi, and N. vulgaris." Applied and Environmental Microbiology, vol. 67, no. 7. (2352-5)
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4. Franco-Rivera A, Paniaqua-Michel S, Zamora-Castro J. 2007.  “Characterization and performance of constructed nitrifying biofilms during nitrogen bioremediation of a wastewater effluent.” Journal of industrial microbiology and biotechnology, vol. 34, no. 4. (279-287)
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5. Maron PA, Coeur C, Pink C, Clays-Josserand A, Lensi R, Richaume-A Potier. 2006. "Validation of the correct start codon of norX/nxrX and universality of the norAXB/nxrAXB gene cluster in nitrobacter species." Current Microbiology, vol 53, no 3. (255-257)
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6. Aurelie Cebron and Josette Garnier. 2005. "Nitrobacter and Nitrospira genera as representatives of nitrite-oxidizing bacteria: Detection, quantification and growth along the lower Seine River (France)." Water Research, vol 39, no 20. (4979-92) 
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7. Deni J and Penninckx MJ. 2004. "Influence of long-term diesel fuel pollution on nitrite-oxidizing activity and population size of nitrobacter spp in soil." Microbiol Res, vol 159, no 4. (323-329)
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Edited by Rashonda Butler student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
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KMG

Latest revision as of 15:23, 7 July 2011

This is a curated page. Report corrections to Microbewiki.

A Microbial Biorealm page on the genus Nitrobacter hamburgensis

Classification

Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae; Nitrobacter; Nitrobacter hamburgensis (1)

Description and significance

Nitrobacter hamburgensis, a gram-negative bacteria, was isolated from soil of the Old Botanic Garden in Hamburg and of a corn field in Yucatan. The main types of environments they inhabit are soil, building sandstone, and sewage sludge. Its cells are 0.5-0.8 x 1.2-2.0 m in size. They are mostly pear-shaped and motile via one subpolar to lateral flagellum. Intracytoplasmic membranes appear as caps of flattened vesicles or membrane vesicles in the central region of the cell. (2) The bacteria have an enzyme capable of oxidizing nitrite (3). This is why it is important to sequence the genome of N. hamburgensis.

Genome structure

There is one circular DNA chromosome and three circular DNA plasmids. The chromosome has 4,406,967 nucleotides. Plasmid 1 has 294,829 nucleotides, 2 has 188,318 nucleotides, and 3 has 121,408 nucleotides. (1)

Cell structure and metabolism

N. hamburgensis gains energy from oxidation of nitrite to nitrate via the enzyme nitrite oxidoreductase (NOR). It has a maximum doubling time of 10 to 18 hours. (3)

Ecology

Nitrobacter hamburgensis is an example of nitrite-oxidizing bacteria. This bacteria has the capability of metabolizing nitrogen in nitrite form in its environment. It is found mainly in soil and freshwater. (4,6,7) (See Current Research section for a summary of the work of Nitrobacter hamburgensis and nitrobacter.)

Pathology

As of present, there is no evidence for Nitrobacter hambugensis having pathological characteristics.

Application to Biotechnology

The nitrification feature of Nitrobacter hamburgensis has been appreciated. The bacteria has provided a solution to removing high levels of nitrogen from municipal effluents of wastewater treatment plants. Biofilms with different nitrifying bacteria including N. hamburgensis have been constructed. Before the invention of these biofilms very large and expensive reactors were used for this purpose. (4)

(See Current Research section for more on this topic and other specific examples of Nitrobacter hamburgensis' involvement in biotechnology)

Current Research

This section summarizes some of the current research on Nitrobacter hamburgensis. While this organism has long-been described, this species in particular has not sparked current research interest. After exhausting my resources I was only able to find two articles about Nitrobacter hamburgensis that were recently published. The other two articles are about nitrobacter species in general.

Recent research has investigated the benefits of using nitrifying bacteria in neutralizing wastewater. Researchers have constructed biofilms with different nitrifying bacteria including N. hamburgensis. They were successful in removing high levels of nitrogen in a short amount of time from municipal effluents from wastewater treatment plants. The biofilms are sufficient alternatives for the treatment of industrial wastewater that otherwise requires very large and expensive reactors for efficient bioremediation of effluents. (4)

Other current research has identified evidence that the previously published sequence of norX in N. hamburgensis X14(T) contains an invalid base "insertion," which resulted in a frameshift and a misidentified start codon. (5)

Going along the lines of neutralizing wastewater, nitrobacter and another nitrifying bacteria have been found in the Seine River in France. Agricultural and urban pollution result in high concentrations of nitrogen in the Seine River and hence in the waster water treatment plants downstream of the river. Scientists have identified nitrobacter as one of the bacteria responsible for oxidizing nitrite products upstream of the plant (in the freshwater). Nitrobacter was also found as the main bacteria in the waste water effluents. The overall result is nitrified waste water that flows into the sea. (6)

The final research I will summarize describes the quorum sensing of nitrobacter bacteria. Quorum sensing is a term used to define a feature of bacteria that requires a certain number of them for something to happen. For example, researchers have discovered that nitrobacter can oxidize nitrite in soil which has been exposed to diesel fuel for a long period of time. They found that a large population of the bacteria is required for the nitrification to take place. (7)

References

1. www.ncbi.nlm.nih.gov/genomes/lproks.cgi

2. E. Bock et al. 1983. “New facultative lithoautotrophic nitrite-oxidizing bacteria.” Archives of Microbiology, vol. 136, no.4. (281-284)

3. Jens Aamand, Thomas Ahl, and Eva Spieck. 1996. "Monoclonal Antibodies Recognizing Nitirite Oxidoreductase fo Nitrobacter hamburgensis, N. winogradskyi, and N. vulgaris." Applied and Environmental Microbiology, vol. 67, no. 7. (2352-5)

4. Franco-Rivera A, Paniaqua-Michel S, Zamora-Castro J. 2007. “Characterization and performance of constructed nitrifying biofilms during nitrogen bioremediation of a wastewater effluent.” Journal of industrial microbiology and biotechnology, vol. 34, no. 4. (279-287)

5. Maron PA, Coeur C, Pink C, Clays-Josserand A, Lensi R, Richaume-A Potier. 2006. "Validation of the correct start codon of norX/nxrX and universality of the norAXB/nxrAXB gene cluster in nitrobacter species." Current Microbiology, vol 53, no 3. (255-257)

6. Aurelie Cebron and Josette Garnier. 2005. "Nitrobacter and Nitrospira genera as representatives of nitrite-oxidizing bacteria: Detection, quantification and growth along the lower Seine River (France)." Water Research, vol 39, no 20. (4979-92)

7. Deni J and Penninckx MJ. 2004. "Influence of long-term diesel fuel pollution on nitrite-oxidizing activity and population size of nitrobacter spp in soil." Microbiol Res, vol 159, no 4. (323-329)

Edited by Rashonda Butler student of Rachel Larsen and Kit Pogliano

KMG