Nitrospira
Nitrospira | |
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Scientific classification ![]() | |
Domain: | Bacteria |
Phylum: | Nitrospirota |
Class: | Nitrospira |
Order: | Nitrospirales |
Family: | Nitrospiraceae |
Genus: | Nitrospira Watson et al. 1986 |
Type species | |
Nitrospira marina Watson et al. 1986
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Species | |
See text |
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 the Nitrospirota 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] and cultivated.[12]
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).[13] 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.[14] 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.[13] DNA analysis determined 56.9 +/- 0.4 mol% of the DNA to be guanine and cytosine base pairs.[13]
General metabolism
Nitrospira are capable of aerobic hydrogen oxidation[15] 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[13] 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[16]). New studies also show that Nitrospira can use urea as a source of nutrients.[17] Urease encoded within their genome can break urea down to CO2 and ammonia. The CO2 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.[18] Recently Nitrospira members with the abilities to perform complete nitrification (comammox bacteria) have also been discovered[8][11][19] and cultivated as in the case of Nitrospira inopinata.[12] 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.[20]
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][19] 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]
Phylogeny
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[21] and the National Center for Biotechnology Information (NCBI).[22] Phylogeny is based on GTDB 08-RS214 by Genome Taxonomy Database[23][24][25]
Nitrospira |
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Species incertae sedis:
- "Ca. N. alkalitolerans" Daebeler et al. 2020
- "Ca. N. bockiana" Lebedeva et al. 2008
- "N. calida" Lebedeva et al. 2011
- N. marina Watson et al. 1986
- "Ca. N. salsa" Haaijer et al. 2013
- "N. tepida" Keuter et al. 2023
See also
References
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- ^ 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. Bibcode:1986ArMic.144....1W. doi:10.1007/BF00454947. S2CID 29796511.
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- ^ a b Hovanec TA, Taylor LT, Blakis A, Delong EF (1998). "Nitrospira-Like Bacteria Associated with Nitrite Oxidation in Freshwater Aquaria". Applied and Environmental Microbiology. 64 (1): 258–264. Bibcode:1998ApEnM..64..258H. doi:10.1128/AEM.64.1.258-264.1998. ISSN 0099-2240. PMC 124703. PMID 16349486.
- ^ a b c d Watson SW, Bock E, Valois FW, Waterbury JB, Schlosser U (February 1986). "Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite-oxidizing bacterium". Archives of Microbiology. 144 (1): 1–7. Bibcode:1986ArMic.144....1W. doi:10.1007/BF00454947. S2CID 29796511.
- ^ a b c d e f Koch H, Lücker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H (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.
- ^ Lucker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Damste JS, 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. Bibcode:2010PNAS..10713479L. doi:10.1073/pnas.1003860107. PMC 2922143. PMID 20624973.
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- ^ a b c Pester M, Maixner F, Berry D, Rattei T, Koch H, Lücker S, Nowka B, Richter A, Spieck E (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. Bibcode:2014EnvMi..16.3055P. doi:10.1111/1462-2920.12300. ISSN 1462-2920. PMID 24118804.
- ^ Lucker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Damste JS, 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. Bibcode:2010PNAS..10713479L. doi:10.1073/pnas.1003860107. PMC 2922143. PMID 20624973.
- ^ a b c d Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J (2015). "Complete nitrification by Nitrospira bacteria". Nature. 528 (7583): 504–9. Bibcode:2015Natur.528..504D. doi:10.1038/nature16461. PMC 5152751. PMID 26610024.
- ^ a b Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY, Daims H (September 2017). "Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle". Nature. 549 (7671): 269–272. Bibcode:2017Natur.549..269K. doi:10.1038/nature23679. ISSN 1476-4687. PMC 5600814. PMID 28847001.
- ^ a b c d Ehrich S, Behrens D, Lebedeva E, Ludwig W, Bock E (July 1995). "A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium,Nitrospira moscoviensis sp. nov. and its phylogenetic relationship". Archives of Microbiology. 164 (1): 16–23. Bibcode:1995ArMic.164...16E. doi:10.1007/BF02568729. PMID 7646315. S2CID 2702110.
- ^ Haaijer SC, Ji K, Niftrik Lv, Hoischen A, Speth D, Jetten MS, Damsté JS, Op den Camp HJ (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.
- ^ Koch H, Galushko A, Albertsen M, Schintlmeister A, Gruber-Dorninger C, Lucker S, Pelletier E, Le Paslier D, Spieck E, Richter A, Nielsen PH, Wagner M, Daims H (28 August 2014). "Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation". Science. 345 (6200): 1052–1054. Bibcode:2014Sci...345.1052K. doi:10.1126/science.1256985. hdl:2066/133107. PMID 25170152. S2CID 206559794.
- ^ Daims H, Nielsen JL, Nielsen PH, Schleifer KH, 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. Bibcode:2001ApEnM..67.5273D. doi:10.1128/AEM.67.11.5273-5284.2001. PMC 93301. PMID 11679356.
- ^ Koch H, Lücker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H (2015-09-08). "Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira". Proceedings of the National Academy of Sciences. 112 (36): 11371–11376. Bibcode:2015PNAS..11211371K. doi:10.1073/pnas.1506533112. ISSN 0027-8424. PMC 4568715. PMID 26305944.
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- ^ Rodriguez-Caballero A, Ribera A, Balcázar J, 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. Bibcode:2013BiTec.139..195R. doi:10.1016/j.biortech.2013.04.021. PMID 23665516.
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- ^ Sayers. "Nitrospirae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
- ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
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