Nitrospira

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Not to be confused with Nitrospina bacteria.

Nitrospira
Scientific classification e
Domain: Bacteria
Phylum: Nitrospirae
Class: Nitrospira
Order: Nitrospirales
Family: Nitrospiraceae
Genus: Nitrospira
Watson et al. 1986
Type species

Watson et al. 1986
Species

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 .[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, .[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
 

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"" Ushiki et al. 2013

 
 
 

"" Nowka et al. 2015

 
 
 

N. moscoviensis Ehrich et al. 1995

 
 
 

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

 
 
 

"Ca. " van Kessel et al. 2015

 
 

"Ca. " van Kessel et al. 2015

 
 
 
 
 
 
 

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. S2CID 29796511.
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  11. ^ a b c d 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. ^ a b 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. ^ a b c d 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.
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  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.
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