Nitrospira

Nitrospira
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
Species
  • "Ca. N. alkalitolerans"
  • "Ca. N. bockiana"
  • "Ca. N. inopinata"
  • "Ca. N. kreftii"
  • "Ca. N. nitrificans"
  • "Ca. N. nitrosa"
  • "Ca. N. salsa"
  • N. calida
  • N. defluvii
  • N. japonica
  • N. lenta
  • N. marina
  • N. moscoviensis

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 nutrient. 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.[17] Recently Nitrospira members with the abilities to perform complete nitrification (comammox bacteria) have also been discovered[8][11][18] 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.[19]

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][18] 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)[20] and the National Center for Biotechnology Information (NCBI).[21] Phylogeny is based on Annotree v1.2.0[22][23] which uses the GTDB 05-RS95 (Genome Taxonomy Database)[24][25]

Nitrospira
 

"N. defluvii" Nowka et al. 2015

 
 
 

"N. japonica" Ushiki et al. 2013

 
 
 

"N. lenta" Nowka et al. 2015

 
 
 

N. moscoviensis Ehrich et al. 1995

 
 
 

"Ca. N. inopinata" Daims et al. 2015

 
 
 

"Ca. N. nitrosa" van Kessel et al. 2015

 
 

"Ca. N. nitrificans" van Kessel et al. 2015

 
 
 
 
 
 
 

See also

References

  1. 1 2 3 4 Fujitani, Hirotsugu; Ushiki, Norisuke; Tsuneda, Satoshi; Aoi, Yoshiteru (October 2014). "Isolation of sublineage I by a novel cultivation strategy". Environmental Microbiology. 16 (10): 3030–3040. doi:10.1111/1462-2920.12248. PMID 25312601.
  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. S2CID 29796511.
  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. S2CID 21315850.
  4. 1 2 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. 1 2 3 4 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. S2CID 29796511.
  6. 1 2 3 4 5 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. 1 2 3 4 5 6 7 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. 1 2 3 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. 1 2 3 4 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. 1 2 Kits, K. Dimitri; Sedlacek, Christopher J.; Lebedeva, Elena V.; Han, Ping; Bulaev, Alexandr; Pjevac, Petra; Daebeler, Anne; Romano, Stefano; Albertsen, Mads; Stein, Lisa Y.; Daims, Holger (September 2017). "Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle". Nature. 549 (7671): 269–272. doi:10.1038/nature23679. ISSN 1476-4687. PMC 5600814. PMID 28847001.
  13. 1 2 3 4 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. S2CID 2702110.
  14. ↑ 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.
  15. ↑ 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. S2CID 206559794.
  16. ↑ 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.
  17. ↑ 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.
  18. 1 2 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.
  19. ↑ 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.
  20. ↑ Euzéby JP. ""Nitrospirae"". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
  21. ↑ Sayers. "Nitrospirae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
  22. ↑ "AnnoTree v1.2.0". AnnoTree.
  23. ↑ Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research. 47 (9): 4442–4448. doi:10.1093/nar/gkz246. PMC 6511854. PMID 31081040.
  24. ↑ "GTDB release 05-RS95". Genome Taxonomy Database.
  25. ↑ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
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