Nitrosomonas europaea: Difference between revisions

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==Description and significance==
==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.


[[Image:Nitrosomonas-Photo_by_Stan_Watson,_Woods_Hole_Oceanographic_Institute.jpg|frame|right|Picture of Nitrosomonas europaea. Photo by Stan Watson, Woods Hole Oceanographic Institute. http://genome.jgi-psf.org/finished_microbes/niteu/niteu.home.html]]


[[Image:Nitrosomonas-Photo_by_Stan_Watson,_Woods_Hole_Oceanographic_Institute.jpg|frame|right|Picture of Nitrosomonas europaea. Photo by Stan Watson, Woods Hole Oceanographic Institute]]


''Nitrosomonas europaea'' is a Gram-negative chemolithoautroph with the shape of bacillus. It is an ammonia-oxidizing bacterium that lives in places rich in ammonia and inorganic salt, such as soil, sewage, freshwater, the walls of buildings and on the surface of monuments. It's often found in the polluted areas where the air contains high levels of nitrogen compounds.


''Nitrosomonas europaea'' is a Gram negative chemolithoautroph with the shape of bacillus. It is a nitrite oxidizing bacteria that lives in places rich in ammonia and inorganic salt, such as soil, sewage, freshwater, the walls of buildings and on the surface of monuments. It's often found in the polluted areas where the air contains high levels of nitrogen compounds.  
It is important enough to have its genome sequenced because this organism plays a central role in the availability of nitrogen to plants and hence in limiting C02 fixation. These bacteria are important players in the treatment of industrial and sewage waste in the first step of oxidizing ammonia to nitrite; then other bacteria oxidize nitrite to nitrate. ''N. europaea'' is also capable of degrading a variety of halogenated organic compounds, including trichloroethylene , benzene  and vinyl chloride, which may make it an attractive organism for bioremediation.


It is important enough to have its genome sequenced because this organism plays a central role in the availability of nitrogen to plants and hence in limiting C02 fixation. These bacteria are important players in the treatment of industrial and sewage waste in the first step of oxidizing ammonia to nitrate. ''N. europaea'' is also capable of degrading a variety of halogenated organic compounds, including trichloroethylene , benzene  and vinyl chloride, which may make it an attractive organism for bioremediation.
==Genome structure==


==Genome structure==
Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with approximately 47% transcribed from one strand and approximately 53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO(2) and NH(3) assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of ''N. europaea'' to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.
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?


==Cell structure and metabolism==
==Cell structure and metabolism==
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.


''Nitrosomonas europaea'' is an autotroph. It can obtain the carbon that it needs to grow by getting it from the atmosphere in a process known as "carbon fixation". Carbon fixation is the process of converting carbon in a gaseous form into carbon bound up in organic molecules. This bacterium contains "carboxysomes" (dark spots which can be seen scattered throughout the cell), which store the enzymes used to fix carbon dioxide for cell carbon.
''Nitrosomonas europaea'' is an autotroph. It can obtain the carbon that it needs to grow by getting it from the atmosphere in a process known as "carbon fixation". Carbon fixation is the process of converting carbon in a gaseous form into carbon bound up in organic molecules. This bacterium contains "carboxysomes" (dark spots which can be seen scattered throughout the cell), which store the enzymes used to fix carbon dioxide for cell carbon.


==Ecology==
==Ecology==
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.




[[Image:Nitrification.JPG|frame|right]]
This nitrifying bacterium is the most studied of the ammonia-oxidizing bacteria that are participants in the biogeochemical N cycle. Nitrifying bacteria play a central role in the availability of nitrogen to plants and hence in limiting CO2 fixation. The reaction catalyzed by these bacteria is the first step in the oxidation of ammonia to nitrate. ''N.europaea'' also is capable of degrading a variety of halogenated organic compounds, including trichloroethylene, benzene, and vinyl chloride. The ability of nitrifying organisms to degrade some pollutants may make these organisms attractive for controlled bioremediation in nitrifying soils and waters.


==Pathology==
==Application to Biotechnology==
How does this organism cause disease?  Human, animal, plant hosts?  Virulence factors, as well as patient symptoms.


==Application to Biotechnology==
Conversion of ammonia to dinitrogen in wastewater was tried by ''Nitrosomonas europaea'' because ''Nitrosomonas europaea'' contains ammonia-oxidizing enzyme, nitrite reductase, and nitrous oxide reductase.
Does this organism produce any useful compounds or enzymes?  What are they and how are they used?


==Current Research==
==Current Research==


Enter summaries of the most recent research here--at least three required
 
The dynamics of growth and death of immobilized ''Nitrosomonas
 
europaea'' were studied. For this, the death rate of suspended         
 
cells was determined in the absence of ammonium or oxygen by following the loss of respiration activity and by fluorescein-diacetate (FDA)/ lissamine-green staining techniques. The death rates obtained in the absence of oxygen or ammonium were incorporated in a dynamic growth model and the effects on the performance of the immobilized-cell process was illustrated by model simulations. These model simulations and experimental validation show that if decay of biomass occurs, the biomass concentration in the center of the bead decreases. As a result, the systems react slower to changes in substrate concentrations than if all cells remain viable.


==References==
==References==
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]


# Patrick Chain et al. (May 2003). "Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea". Journal of Bacteriology 185: 2759-2773.  
# Patrick Chain et al. (May 2003). "Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea". Journal of Bacteriology 185: 2759-2773.  
Line 78: Line 73:


# DOE JOINT GENOME INSTITUTE - US Department of Energy Office of Science http://genome.jgi-psf.org/finished_microbes/niteu/niteu.home.html
# DOE JOINT GENOME INSTITUTE - US Department of Energy Office of Science http://genome.jgi-psf.org/finished_microbes/niteu/niteu.home.html
# DJW, Microbial of the Week 1999, Nirosomonas europae. http://web.umr.edu/~microbio/BIO221_1999/N_europaea.html
# Nagatsuta, Midori-ku, Yokohama "Conversion of ammonia to dinitrogen in wastewater by Nitrosomonas europaea". Department of Bioengineering, Tokyo Institute of Technology http://cat.inist.fr/?aModele=afficheN&cpsidt=1056630


# Wikipedia http://en.wikipedia.org/wiki/Nitrosomonas_europaea
# Wikipedia http://en.wikipedia.org/wiki/Nitrosomonas_europaea
# Stacy Heather "Nitrosomonas europaea" http://web.umr.edu/~microbio/BIO221_1999/N_europaea.html


Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
KMG

Latest revision as of 21:25, 14 December 2015

This is a curated page. Report corrections to Microbewiki.

A Microbial Biorealm page on the genus Nitrosomonas europaea

Classification

Higher order taxa

Domain; Phylum; Class; Order; family [Others may be used. Use NCBI link to find]

Domain: Prokaryota

Phylum: Proteobacteria

Class: Beta Proteobacteria

Order: Nitrosomonadales

Family: Nitrosomonadaceae

Genus: Nitrosomonas

Species: N. europea

Species

NCBI: Taxonomy

Nitrosomonas europaea

Description and significance

Picture of Nitrosomonas europaea. Photo by Stan Watson, Woods Hole Oceanographic Institute. http://genome.jgi-psf.org/finished_microbes/niteu/niteu.home.html


Nitrosomonas europaea is a Gram-negative chemolithoautroph with the shape of bacillus. It is an ammonia-oxidizing bacterium that lives in places rich in ammonia and inorganic salt, such as soil, sewage, freshwater, the walls of buildings and on the surface of monuments. It's often found in the polluted areas where the air contains high levels of nitrogen compounds.

It is important enough to have its genome sequenced because this organism plays a central role in the availability of nitrogen to plants and hence in limiting C02 fixation. These bacteria are important players in the treatment of industrial and sewage waste in the first step of oxidizing ammonia to nitrite; then other bacteria oxidize nitrite to nitrate. N. europaea is also capable of degrading a variety of halogenated organic compounds, including trichloroethylene , benzene and vinyl chloride, which may make it an attractive organism for bioremediation.

Genome structure

Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with approximately 47% transcribed from one strand and approximately 53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO(2) and NH(3) assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.

Cell structure and metabolism

Nitrosomonas europaea is an autotroph. It can obtain the carbon that it needs to grow by getting it from the atmosphere in a process known as "carbon fixation". Carbon fixation is the process of converting carbon in a gaseous form into carbon bound up in organic molecules. This bacterium contains "carboxysomes" (dark spots which can be seen scattered throughout the cell), which store the enzymes used to fix carbon dioxide for cell carbon.

Ecology

This nitrifying bacterium is the most studied of the ammonia-oxidizing bacteria that are participants in the biogeochemical N cycle. Nitrifying bacteria play a central role in the availability of nitrogen to plants and hence in limiting CO2 fixation. The reaction catalyzed by these bacteria is the first step in the oxidation of ammonia to nitrate. N.europaea also is capable of degrading a variety of halogenated organic compounds, including trichloroethylene, benzene, and vinyl chloride. The ability of nitrifying organisms to degrade some pollutants may make these organisms attractive for controlled bioremediation in nitrifying soils and waters.

Application to Biotechnology

Conversion of ammonia to dinitrogen in wastewater was tried by Nitrosomonas europaea because Nitrosomonas europaea contains ammonia-oxidizing enzyme, nitrite reductase, and nitrous oxide reductase.

Current Research

The dynamics of growth and death of immobilized Nitrosomonas

europaea were studied. For this, the death rate of suspended

cells was determined in the absence of ammonium or oxygen by following the loss of respiration activity and by fluorescein-diacetate (FDA)/ lissamine-green staining techniques. The death rates obtained in the absence of oxygen or ammonium were incorporated in a dynamic growth model and the effects on the performance of the immobilized-cell process was illustrated by model simulations. These model simulations and experimental validation show that if decay of biomass occurs, the biomass concentration in the center of the bead decreases. As a result, the systems react slower to changes in substrate concentrations than if all cells remain viable.

References

  1. Patrick Chain et al. (May 2003). "Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea". Journal of Bacteriology 185: 2759-2773.
  1. John G. Holt, Noel R. Krieg, editor, editor-in-chief (1984) Bergey's manual of systematic bacteriology volume2 page1809- 1825
  1. DOE JOINT GENOME INSTITUTE - US Department of Energy Office of Science http://genome.jgi-psf.org/finished_microbes/niteu/niteu.home.html
  1. DJW, Microbial of the Week 1999, Nirosomonas europae. http://web.umr.edu/~microbio/BIO221_1999/N_europaea.html
  1. Nagatsuta, Midori-ku, Yokohama "Conversion of ammonia to dinitrogen in wastewater by Nitrosomonas europaea". Department of Bioengineering, Tokyo Institute of Technology http://cat.inist.fr/?aModele=afficheN&cpsidt=1056630
  1. Wikipedia http://en.wikipedia.org/wiki/Nitrosomonas_europaea
  1. Stacy Heather "Nitrosomonas europaea" http://web.umr.edu/~microbio/BIO221_1999/N_europaea.html

Edited by student of Rachel Larsen and Kit Pogliano

KMG