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Nitrobacter
Nitrobacter winogradskyi str. Nb-255
Scientific classification
Kingdom:
Bacteria
Phylum:
Proteobacteria
Class:
Alphaproteobacteria
Order:
Rhizobiales
Family:
Bradyrhizobiaceae
Genus:
Nitrobacter

Winogradsky 1892
Type species
Nitrobacter winogradskyi
Species

N. alkalicus
N. hamburgensis
N. vulgaris
N. winogradskyi

Nitrobacter is a genus comprised of rod-shaped, gram-negative, and chemoautotrophic bacteria.[1] The name Nitrobacter derives from the Latin neuter gendernoun nitrum, nitri, alkalis; the Ancient Greek noun βακτηρία,  βακτηρίᾱς, rod. They are non-motile and reproduce via budding or binary fission.[2][3] Nitrobacter cells are obligate aerobes and have a doubling time of about 13 hours.[1]

Nitrobacter play an important role in the nitrogen cycle by oxidizing nitrite to nitrate in soil and marine systems.[2] Unlike plants, where electron transfer in photosynthesis provides the energy for carbon fixation, Nitrobacter uses energy from the oxidation of nitrite ions, NO2−, into nitrate ions, NO3−, to fulfill their energy needs. Nitrobacter fix carbon dioxide via the Calvin cycle for their carbon requirements.[1] Nitrobacter belongs to the α-subclass of the Proteobacteria.[3][4]

Morphology and Characteristics

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Nitrobacter are gram-negative bacteria and are either rod-shaped, pear-shaped or pleomorphic.[1][2] They are typically 0.5-0.9 x 1.0-2.0μm in size and have a intracytomembrane polar cap.[5][2] Due to the presence of cytochromes c, they are often yellow in cell suspensions.[5] The nitrate oxydizing system on membranes is cytoplasmic.[2] Nitrobacter cells have been shown to recover following extreme CO2 exposure and are non-motile.[6][5][2]

Phylogeny

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16s rRNA sequence analysis phylogenetically places Nitrobacter within the class of Alphaproteobacteria.  Pairwise evolutionary distance measurements within the genus are low compared to other genera, at less than 1%.[6] Nitrobacter are also closely related to other species within the alpha subdivision, including the photosynthetic Rhodopseudomonas palustris, the root-nodulating Bradyrhizobium japonicum, Blastobacter denitrificans, and the human pathogens Afipia felis, and Afipia clevelandensis.[6] Nitrobacter bacteria are presumed to evolve from photosynthetic ancestors, and there are evidences that the nitrification phenotype evolved separately from photosynthetic bacteria on multiple occasions for individual nitrifying genera and species.[6]

All known nitrite-oxidizing prokaryotes are restricted to a handful of phylogenetic groups. Beyond that, nitrite oxidation is known to occur only in the genus Nitrospira of the phylum Nitrospirae,[7] and the genus Nitrolancetus from the phylum Chloroflexi.[8] Before 2004, nitrite oxidation was believed to only occur within Proteobacteria, it is likely that further scientific inquiry will expand the list of known nitrite oxidizing species even more.[9] The low diversity of species performing nitrite oxidation notably contrasts with other processes associated with the nitrogen cycle in the ocean, such as denitrification and N-fixation, where a diverse range of taxa perform analogous functions. This might change as future research identifies new prokaryotic species.[8]

Nitrification

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Nitrification is a crucial component of the nitrogen cycle, especially in the oceans. The oxidation of nitrite (NO2-) into nitrate (NO3-) in nitrification is a crucial step, as photosynthetic organisms such as phytoplankton are only able to take up nitrogen in the form of nitrate. For this reason, nitrification is a source of nitrate for much of the planktonic primary production that occurs in the world's oceans. Nitrification is the source of half of the nitrate consumed by phytoplankton globally.[10] Phytoplankton are major contributors to oceanic production, and are therefore important for the oceanic biological pump. The process of nitrification is crucial for separating recycled production from production leading to export. Biologically metabolized nitrogen returns to the inorganic dissolved nitrogen pool in the form of ammonia. Microbe-mediated nitrification converts that ammonia into nitrate, which can subsequently be taken up by phytoplankton and recycled.[10]

The nitrite oxidation reaction performed by the Nitrobacter is as follows;

2NO2− + H2O → NO3− + 2H+ + 2e−

2H+ + 2e− + ½O2 → H2O [9]

The Gibbs' Free Energy yield for nitrite oxidation is:

ΔGο = -74 kJ mol-1 NO2-

In the oceans, nitrite-oxidizing bacteria such as Nitrobacter are usually found in close proximity to ammonia-oxidizing bacteria.[11] These two reactions together make up the process of nitrification. The nitrite-oxidation reaction generally proceeds more quickly in ocean waters, and it is therefore not a rate-limiting step in nitrification. For this reason, it is rare for nitrite to accumulate in ocean waters.

The two-step conversion of ammonia to nitrate observed in bacteria species such as Nitrobacter is puzzling to researchers.[12][13] Complete nitrification, the conversion of ammonia to nitrate in a single step, has an energy yield (∆G°′) of −349 kJ mol−1 NH3, while the energy yields for the ammonia-oxidation and nitrite-oxidation steps of the observed two-step reaction are −275 kJ mol−1 NH3, and −74 kJ mol−1 NO2−, respectively.[12] These values indicate that it would be energetically favourable for an organism to carry out complete nitrification from ammonia to nitrate, rather than conduct only one of the two steps. The evolutionary motivation for a decoupled, two-step nitrification reaction is an area of ongoing research. In 2015, it was discovered that the genus Nitrospira possesses all the enzymes required for carrying out complete nitrification in one step, suggesting that this reaction does in fact occur.[12][13] This discovery raises questions about evolutionary capability of Nitrobacter to conduct only nitrite-oxidation.

Metabolism and Growth

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Nitrobacter oxidize nitrite as a source of energy and reductant, and use CO2 as a carbon source.[11] Nitrite is not a particularly favourable substrate from which to gain energy. Thermodynamically, the nitrite oxidation reaction gives a yield (∆G°′) of only -74  kJ mol−1 NO2−.[12] As a result, Nitrobacter has developed a highly specialized metabolism to derive energy from the oxidation of nitrite.

Nitrobacter may reproduce by budding or binary fission.[5][2] Carboxysomes, which aid carbon fixation, are found in lithoautotrophically and mixotrophically grown cells. Additional energy conserving inclusions are PHB granules and polyphosphates. When both nitrite and organic substances are present, cells can exhibit biphasic growth, first the nitrite is used and after a lag phase, organic matter is oxidized. Chemoorganotroph growth is slow and unbalanced, thus more poly-β-hydroxybutyrate granules are seen that distort the shape and size of the cells.

The enzyme responsible for the oxidation of nitrite to nitrate in Nitrobacter is Nitrite oxidoreductase (NXR), which is encoded by the gene nxrA.[14] NXR is composed of two subunits, and likely forms an αβ-heterodimer.[15] The enzyme exists within the cell on specialized membranes in the cytoplasm which can be folded into vesicles or tubes.[15] The α-subunit is thought to be the location of nitrite oxidation, and the β-subunit is an electron channel from the membrane.[15] The direction of the reaction catalyzed by NXR can be reversed depending on oxygen concentrations.[15] The region of the nxrA gene which encodes for the β-subunit of the NXR enzyme is similar in sequence to the iron-sulfur centers of bacterial ferredoxins, and to the β-subunit of the enzyme nitrate reductase, found in Escherichia coli.[16]

Ecology and Distribution

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The Aquatic Nitrogen Cycle. The conversion of nitrite to nitrate is facilitated by species in the genera of Nitrobacter and Nitrospira.[17]

Nitrobacter are widely distributed in both aquatic and land environments.[2] Nitrifying bacteria have an optimum growth between 25-30°C, and cannot survive past the upper limit of 49°C or the lower limit of 0°C, limiting their distribution even though they encompass a variety of habitats.[1] Nitrobacter have an optimum pH between 7.3 and 7.5, and will die in temperatures exceeding 120 °F (49 °C) or below 32 °F (0 °C).[1] According to Grundmann, Nitrobacter seem to grow optimally at 38 °C and at a pH of 7.9, but Holt states that Nitrobacter grow optimally at 28 °C and grows within a pH range of 5.8 -8.5 and has a pH optima between 7.6 and 7.8.[18][3]

Nitrobacter's primary ecological role is to oxidize nitrite to nitrate which is readily absorbed by plants. This role is also essential in aquaponics.[1][19] Since all Nitrobacter are obligate aerobes, oxygen along with phosphorous tend to be the limiting factors of their capability to perform nitrogen fixation.[1] The greater impact of Nitrosomonas and Nitrobacter in both oceanic and terrestrial ecosystems are due to their effect on the process of eutrophication.[20] The distribution and differences in nitrification rate across the Nitrobacter genus may be attributed to differences in the plasmids amongst the species, as data presented in Schutt (1990) imply, habitat specific plasmid DNA was induced by adaptation for some of the lakes that were investigated.[21] A follow up study performed by Navarro et al. (1995) showing a 60MDa plasmid and a 37 MDa plasmid in freshwater and sediment Nitrobacter populations.[20] In conjunction with Schutts’ (1990) study, Navarro et al. (1995) illustrated genomic features that may play crucial roles in determining the distribution and ecological impact of Nitrobacter. Nitrifying bacteria in general tend to be less abundant than their heterotrophic counterparts, as the oxidizing reactions they perform have a low energy yield and most of their energy production goes toward carbon-fixation rather than growth and reproduction.[1]

History

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Sergei Nikolaievich Winogradsky

In 1890, Ukrainian-Russian microbiologist Sergei Winogradsky successfully isolated the first pure cultures of nitrifying bacteria which are capable of growth in the absence of organic matter and sunlight. The exclusion of organic material by Winogradsky in the preparation of his cultures is recognized as a contributing factor to his success in isolating the microbes.[22] In 1891, English chemist Robert Warington proposed a two-stage mechanism for nitrification, mediated by two distinct genera of bacteria. The first stage is proposed as the conversion of ammonia to nitrite and the second the oxidation of nitrite to nitrate.[23] Winogradsky named the bacteria responsible for the oxidation of nitrite to nitrate Nitrobacter in his subsequent study on microbial nitrification in 1892.[24] Winslow et al. proposed the type species Nitrobacter winogradsky in 1917.[25] The species was officially recognized in 1980.[26]

Main Species

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See also

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References

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  1. ^ a b c d e f g h i http://www.bioconlabs.com/nitribactfacts.html
  2. ^ a b c d e f g h i j k l Spleck, Eva; Bock, Eberhard (2004). Bergey’s Manual ® of Systematic Bacteriology Volume Two: The PRoteobacteria, Part A Introductory Essays. Springer. pp. 149–153. ISBN 978-0-387-241-43-2.
  3. ^ a b c Grundmann, GL; Neyra, M; Normand, P (2000). "High-resolution phylogenetic analysis of NO2--oxidizing Nitrobacter species using the rrs-rrl IGS sequence and rrl genes". International Journal of Systematic and Evolutionary Microbiology. 50 (Pt 5): 1893–8. doi:10.1099/00207713-50-5-1893. PMID 11034501.
  4. ^ Grunditz, C; Dalhammar, G (2001). "Development of nitrification inhibition assays using pure cultures of Nitrosomonas and Nitrobacter". Water research. 35 (2): 433–40. doi:10.1016/S0043-1354(00)00312-2. PMID 11228996.
  5. ^ a b c d Pillay, B.; Roth, G.; Oellermann, A. (1989). "Cultural characteristics and identification of marine nitrifying bacteria from a closed prawnculture system in Durban". South African Journal of Marine Science. 8 (1): 333–343.
  6. ^ a b c d Teske, A; Alm, E; Regan, J M; Toze, S; Rittmann, B E; Stahl, D A (1994-11-01). "Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria". Journal of Bacteriology. 176 (21): 6623–6630. ISSN 0021-9193. PMC 197018. PMID 7961414.{{cite journal}}: CS1 maint: PMC format (link)
  7. ^ Ehrich, Silke; Behrens, Doris; Lebedeva, Elena; Ludwig, Wolfgang; Bock, Eberhard. "A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium,Nitrospira moscoviensis sp. nov. and its phylogenetic relationship". Archives of Microbiology. 164 (1): 16–23. doi:10.1007/bf02568729.
  8. ^ a b Sorokin, Dimitry Y; Lücker, Sebastian; Vejmelkova, Dana; Kostrikina, Nadezhda A; Kleerebezem, Robbert; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Le Paslier, Denis; Muyzer, Gerard (2017-03-09). "Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi". The ISME Journal. 6 (12): 2245–2256. doi:10.1038/ismej.2012.70. ISSN 1751-7362. PMC 3504966. PMID 22763649.{{cite journal}}: CS1 maint: PMC format (link)
  9. ^ a b Zehr, Jonathan P.; Kudela, Raphael M. (2011-01-01). "Nitrogen cycle of the open ocean: from genes to ecosystems". Annual Review of Marine Science. 3: 197–225. doi:10.1146/annurev-marine-120709-142819. ISSN 1941-1405. PMID 21329204.
  10. ^ a b Yool, Andrew; Martin, Adrian P.; Fernández, Camila; Clark, Darren R. (2007-06-21). "The significance of nitrification for oceanic new production". Nature. 447 (7147): 999–1002. doi:10.1038/nature05885. ISSN 0028-0836.
  11. ^ a b "Nitrification Network". nitrificationnetwork.org. Retrieved 2017-03-24.
  12. ^ a b c d Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra; Han, Ping; Herbold, Craig; Albertsen, Mads; Jehmlich, Nico; Palatinszky, Marton; Vierheilig, Julia (2015-12-24). "Complete nitrification by Nitrospira bacteria". Nature. 528 (7583): 504–509. doi:10.1038/nature16461. ISSN 0028-0836. PMC 5152751. PMID 26610024.{{cite journal}}: CS1 maint: PMC format (link)
  13. ^ a b van Kessel, Maartje A. H. J.; Speth, Daan R.; Albertsen, Mads; Nielsen, Per H.; Op den Camp, Huub J. M.; Kartal, Boran; Jetten, Mike S. M.; Lücker, Sebastian (2015-12-24). "Complete nitrification by a single microorganism". Nature. 528 (7583): 555–559. doi:10.1038/nature16459. ISSN 0028-0836. PMC 4878690. PMID 26610025.{{cite journal}}: CS1 maint: PMC format (link)
  14. ^ Poly, Franck; Wertz, Sophie; Brothier, Elisabeth; Degrange, Valérie (2008-01-01). "First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA". FEMS Microbiology Ecology. 63 (1): 132–140. doi:10.1111/j.1574-6941.2007.00404.x. ISSN 1574-6941.
  15. ^ a b c d Garrity, George M. (2001-01-01). Bergey's Manual® of Systematic Bacteriology. Springer Science & Business Media. ISBN 9780387241456.
  16. ^ Kirstein, K.; Bock, E. (1993-01-01). "Close genetic relationship between Nitrobacter hamburgensis nitrite oxidoreductase and Escherichia coli nitrate reductases". Archives of Microbiology. 160 (6): 447–453. ISSN 0302-8933. PMID 8297210.
  17. ^ Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra; Han, Ping; Herbold, Craig; Albertsen, Mads; Jehmlich, Nico; Palatinszky, Marton; Vierheilig, Julia (2015-12-24). "Complete nitrification by Nitrospira bacteria". Nature. 528 (7583): 504–509. doi:10.1038/nature16461. ISSN 1476-4687. PMC 5152751. PMID 26610024.{{cite journal}}: CS1 maint: PMC format (link)
  18. ^ a b c d e Holt, John G.; Hendricks Bergey, David (1993). R.S. Breed (ed.). Bergey's Manual of Determinative Bacteriology (9th ed.). USA: Lippincott Williams and Wilkins. ISBN 0-683-00603-7.
  19. ^ Hu, Zhen; Lee, Jae Woo; Chandran, Kartik; Kim, Sungpyo; Brotto, Ariane Coelho; Khanal, Samir Kumar (2015-07-01). "Effect of plant species on nitrogen recovery in aquaponics". Bioresource Technology. International Conference on Emerging Trends in Biotechnology. 188: 92–98. doi:10.1016/j.biortech.2015.01.013.
  20. ^ a b Navarro, E.; Degrange, V.; Bardin, R. (1995-01-01). Balvay, Gérard (ed.). Space Partition within Aquatic Ecosystems. Developments in Hydrobiology. Springer Netherlands. pp. 43–48. doi:10.1007/978-94-011-0293-3_3. ISBN 9789401041294.
  21. ^ Schütt, Christian (1990-01-01). Overbeck, Jürgen; Chróst, Ryszard J. (eds.). Aquatic Microbial Ecology. Brock/Springer Series in Contemporary Bioscience. Springer New York. pp. 160–183. doi:10.1007/978-1-4612-3382-4_7. ISBN 9781461279914.
  22. ^ Winogradsky, Sergei (1890). "Recherches sur les Organismes de la Nitrification". Milestone in Microbiology. 110: 1013–1016.
  23. ^ "Investigations upon Nitrification and the Nitrifying Organisms". Science. 18: 48–52. 1891.
  24. ^ Winogradsky, Sergei (1892). "Contributions a la morphologie des organismes de la nitrification". Archives of Biological Science. 1: 86–137.
  25. ^ Winslow, Charles-Edward (1917). "The Characterization and Classification of Bacterial Types". Science. 39: 77–91.
  26. ^ D., Skerman, V. B.; Vicki., Mcgowan,; Andrews., Sneath, Peter Henry; committee., International committee on systematic bacteriology. Judicial commission. Ad hoc (1989-01-01). Approved lists of bacterial names. American society for microbiology. ISBN 9781555810146. OCLC 889445817.{{cite book}}: CS1 maint: extra punctuation (link) CS1 maint: multiple names: authors list (link)
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