Nitrospira

Nitrospira (from Latin: nitro, meaning "nitrate" and Greek: spira, meaning "spiral") translate into “a nitrate spiral” is a genus of bacteria within the monophyletic clade[1] of Nitrospirae phylum. The first member of this genus was described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina.[2] Populations were initially thought to be limited to marine ecosystems, but it was later discovered to be well-suited for numerous habitats, including activated sludge of wastewater treatment systems,[3] natural biological marine settings (such as the Seine River in France[4] and beaches in Cape Cod[5]), water circulation biofilters in aquarium tanks,[4] terrestrial systems,[5] fresh and salt water ecosystems, and hot springs.[6] Nitrospira is a ubiquitous bacterium that plays a role in the nitrogen cycle[7] by performing nitrite oxidation in the second step of nitrification.[6] Nitrospira live in a wide array of environments including but not limited to, drinking water systems, waste treatment plants, rice paddies, forest soils, geothermal springs, and sponge tissue.[8] Despite being abundant in many natural and engineered ecosystems Nitrospira are difficult to culture, so most knowledge of them is from molecular and genomic data.[9] However, due to their difficulty to be cultivated in laboratory settings, the entire genome was only sequenced in one species, Nitrospira defluvii.[10] In addition, Nitrospira bacteria's 16s rRNA sequences are too dissimilar to use for PCR primers, thus some members go unnoticed.[9] In addition, members of Nitrospira with the capabilities to perform complete nitrification (Comammox bacteria) has also been discovered.[8][11]

Not to be confused with Nitrospina bacteria.

Nitrospira
Scientific classification
Domain: Bacteria
Phylum: Nitrospirae
Class: Nitrospira
Order: Nitrospirales
Family: Nitrospiraceae
Genus: Nitrospira
Species

N. moscoviensis
N. marina

Morphology

For the following description, Nitrospira moscoviensis will be representative of the Nitrospira genus. Nitrospira is a gram-negative nitrite-oxidizing organism with a helical to vibroid morphology (0.9–2.2 × 0.2–0.4 micrometres in size).[12] They are non-planktonic organisms that reside as clumps, known as aggregates, in biofilms.[1] Visualization using Transmission electron microscopy (TEM) confirms star-like protrusions on the outer membrane (6-8 nm thick). The periplasmic space is exceptionally wide (34-41 nm thick),[5] which provides space to accommodate electron-rich molecules.[13] Electron-deprived structures are located in the cytosol and are believed to be glycogen storage vesicles; polyhydroxybutyrate and polyphosphate granules are also identified in the cytoplasm.[12] DNA analysis determined 56.9 +/- 0.4 mol% of the DNA to be guanine and cytosine base pairs.[12]

General Metabolism

Nitrospira are capable of aerobic hydrogen oxidation[14] and nitrite oxidation[6] to obtain electrons, but high concentrations of nitrite have shown to inhibit their growth.[1] The optimal temperature for nitrite oxidation and growth in Nitrospira moscoviensis is 39 °C (can range from 33-44 °C) at a pH range of 7.6-8.0[12] Despite being commonly classified as obligate chemolithotrophs,[5] some are capable of mixotrophy.[6] For instance, under different environments, Nitrospira can choose to assimilate carbon by carbon fixation[6] or by consuming organic molecules (glycerol, pyruvate, or formate[15]). New studies also show that Nitrospira can use urea as a source of nutrient. Urease encoded within their genome can break urea down to CO
2 and ammonia. The CO
2 can be assimilated by anabolism while the ammonia and organic by-product released by Nitrospira allow ammonium oxidizers[6] and other microbes to co-exist in the same microenvironment.[1]

Nitrification

All members of this genus have the nitrite oxidoreductase genes, and thus are all thought to be nitrite-oxidizers.[9] Ever since nitrifying bacteria were discovered it was accepted that nitrification occurred in two steps, although it would be energetically favourable for one organism to do both steps.[16] Recently some Nitrospira members with the abilities to perform complete nitrification (Comammox bacteria) have also been discovered.[8][11][17] The discovery of Commamox organisms within Nitrospira redefine the way bacteria contribute to the Nitrogen cycle and thus a lot of future studies will be dedicated to it.[8]

With these new findings there's now a possibility to mainly use complete nitrification instead of partial nitrification in engineered systems like wastewater treatment plants because complete nitrification results in lower emissions of the greenhouse gases: nitrous oxide and nitric oxide, into the atmosphere.[18]

Genome

After sequencing and analyzing the DNA of Nitrospira members researchers discovered both species had genes encoding ammonia monooxygenase (Amo) and hydroxlyamine dehydrogenase (hao), enzymes that ammonia-oxidizing bacteria (AOB), use to convert ammonia into nitrite.[8][11][17] The bacteria possess all necessary sub-units for both enzymes as well as the necessary cell membrane associated proteins and transporters to carry out the first step of nitrification.[8] Origins of the Amo gene are debatable as one study found that it is similar to other AOB[3], while another study found the Amo gene to be genetically distinct from other lineages.[11] Current findings indicate that the hao gene is phylogenetically distinct from the hao gene present in other AOB, meaning that they acquired them long ago, likely by horizontal gene transfer.[8]

Nitrospira also carry the genes encoding for all the sub-units of nitrite oxidoreductase (nxr), the enzyme that catalyzes the second step of nitrification.[8]

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See also

References
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  2. Stanley W. Watson; Eberhard Bock; Frederica W. Valois; John B. Waterbury; Ursula Schlosser (1986). "Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite-oxidizing bacterium". Arch Microbiol. 144 (1): 1–7. doi:10.1007/BF00454947.
  3. Wagner, Michael; Loy, Alexander; Nogueira, Regina; Purkhold, Ulrike; Lee, Natuschka; Daims, Holger (2002). "Microbial community composition and function in wastewater treatment plants". Antonie van Leeuwenhoek. 81 (1/4): 665–680. doi:10.1023/A:1020586312170. PMID 12448762.
  4. Hovanec, Timothy A.; Taylor, Lance T.; Blakis, Andrew; Delong, Edward F. (1998). "Nitrospira-Like Bacteria Associated with Nitrite Oxidation in Freshwater Aquaria". Applied and Environmental Microbiology. 64 (1): 258–264. doi:10.1128/AEM.64.1.258-264.1998. ISSN 0099-2240. PMC 124703. PMID 16349486.
  5. Watson, Stanley W.; Bock, Eberhard; Valois, Frederica W.; Waterbury, John B.; Schlosser, Ursula (February 1986). "Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite-oxidizing bacterium". Archives of Microbiology. 144 (1): 1–7. doi:10.1007/BF00454947.
  6. Koch, Hanna; Lücker, Sebastian; Albertsen, Mads; Kitzinger, Katharina; Herbold, Craig; Spieck, Eva; Nielsen, Per Halkjaer; Wagner, Michael; Daims, Holger (8 September 2015). "Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus". Proceedings of the National Academy of Sciences. 112 (36): 11371–11376. doi:10.1073/pnas.1506533112. PMC 4568715. PMID 26305944.
  7. Lucker, S.; Wagner, M.; Maixner, F.; Pelletier, E.; Koch, H.; Vacherie, B.; Rattei, T.; Damste, J. S. S.; Spieck, E.; Le Paslier, D.; Daims, H. (12 July 2010). "A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria". Proceedings of the National Academy of Sciences. 107 (30): 13479–13484. doi:10.1073/pnas.1003860107. PMC 2922143. PMID 20624973.
  8. van Kessel, Maartje A. H. J.; Speth, Daan R.; Albertsen, Mads; Nielsen, Per H.; Camp, Huub J. M. Op den; Kartal, Boran; Jetten, Mike S. M.; Lücker, Sebastian (2015). "Complete nitrification by a single microorganism". Nature. 528 (7583): 555–9. doi:10.1038/nature16459. PMC 4878690. PMID 26610025.
  9. Pester, Michael; Maixner, Frank; Berry, David; Rattei, Thomas; Koch, Hanna; Lücker, Sebastian; Nowka, Boris; Richter, Andreas; Spieck, Eva (2014-10-01). "NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira". Environmental Microbiology. 16 (10): 3055–3071. doi:10.1111/1462-2920.12300. ISSN 1462-2920. PMID 24118804.
  10. Lucker, S.; Wagner, M.; Maixner, F.; Pelletier, E.; Koch, H.; Vacherie, B.; Rattei, T.; Damste, J. S. S.; Spieck, E.; Le Paslier, D.; Daims, H. (12 July 2010). "A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria". Proceedings of the National Academy of Sciences. 107 (30): 13479–13484. doi:10.1073/pnas.1003860107. PMC 2922143. PMID 20624973.
  11. Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra; Han, Ping; Herbold, Craig; Albertsen, Mads; Jehmlich, Nico; Palatinszky, Marton; Vierheilig, Julia (2015). "Complete nitrification by Nitrospira bacteria". Nature. 528 (7583): 504–9. doi:10.1038/nature16461. PMC 5152751. PMID 26610024.
  12. Ehrich, Silke; Behrens, Doris; Lebedeva, Elena; Ludwig, Wolfgang; Bock, Eberhard (July 1995). "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. PMID 7646315.
  13. Haaijer, Suzanne C. M.; Ji, Ke; Niftrik, Laura van; Hoischen, Alexander; Speth, Daan; Jetten, Mike S. M.; Damsté, Jaap S. Sinninghe; Op den Camp, Huub J. M. (2013). "A novel marine nitrite-oxidizing Nitrospira species from Dutch coastal North Sea water". Frontiers in Microbiology. 4: 60. doi:10.3389/fmicb.2013.00060. PMC 3600790. PMID 23515432.
  14. Koch, H.; Galushko, A.; Albertsen, M.; Schintlmeister, A.; Gruber-Dorninger, C.; Lucker, S.; Pelletier, E.; Le Paslier, D.; Spieck, E.; Richter, A.; Nielsen, P. H.; Wagner, M.; Daims, H. (28 August 2014). "Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation". Science. 345 (6200): 1052–1054. doi:10.1126/science.1256985. PMID 25170152.
  15. Daims, H.; Nielsen, J. L.; Nielsen, P. H.; Schleifer, K.-H.; Wagner, M. (1 November 2001). "In Situ Characterization of Nitrospira-Like Nitrite-Oxidizing Bacteria Active in Wastewater Treatment Plants". Applied and Environmental Microbiology. 67 (11): 5273–5284. doi:10.1128/AEM.67.11.5273-5284.2001. PMC 93301. PMID 11679356.
  16. Costa, Engràcia; Pérez, Julio; Kreft, Jan-Ulrich (2006). "Why is metabolic labour divided in nitrification?". Trends in Microbiology. 14 (5): 213–219. doi:10.1016/j.tim.2006.03.006. PMID 16621570.
  17. Palomo, Alejandro; Fowler, S Jane; Gülay, Arda; Rasmussen, Simon; Sicheritz-Ponten, Thomas; Smets, Barth F (2016-04-29). "Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp". The ISME Journal. 10 (11): 2569–2581. doi:10.1038/ismej.2016.63. ISSN 1751-7370. PMC 5113852. PMID 27128989.
  18. Rodriguez-Caballero, A.; Ribera, A.; Balcázar, J.L.; Pijuan, M. (2013). "Nitritation versus full nitrification of ammonium-rich wastewater: Comparison in terms of nitrous and nitric oxides emissions". Bioresource Technology. 139: 195–202. doi:10.1016/j.biortech.2013.04.021. PMID 23665516.
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