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Nitrospira
Genus of bacteria From Wikipedia, the free encyclopedia
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Nitrospira (from Latin: nitro, meaning "nitrate" and Greek: spira, meaning "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 in the United States[5]), water circulation biofilters in aquarium tanks,[4] terrestrial systems,[5] fresh and salt water ecosystems, agricultural lands[6] and hot springs.[7] Nitrospira is a ubiquitous bacterium that plays a role in the nitrogen cycle[8] by performing nitrite oxidation in the second step of nitrification.[7] 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.[9] 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.[10] However, due to their difficulty to be cultivated in laboratory settings, the entire genome was only sequenced in one species, Nitrospira defluvii.[11] In addition, Nitrospira bacteria's 16S rRNA sequences are too dissimilar to use for PCR primers, thus some members go unnoticed.[10] In addition, members of Nitrospira with the capabilities to perform complete nitrification (comammox bacteria) has also been discovered[9][12] and cultivated.[13]
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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).[14] 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.[15] 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.[14] DNA analysis determined 56.9 +/- 0.4 mol% of the DNA to be guanine and cytosine base pairs.[14]
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General metabolism
Nitrospira are capable of aerobic hydrogen oxidation[16] and nitrite oxidation[7] 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[14] Despite being commonly classified as obligate chemolithotrophs,[5] some are capable of mixotrophy.[7] For instance, under different environments, Nitrospira can choose to assimilate carbon by carbon fixation[7] or by consuming organic molecules (glycerol, pyruvate, or formate[17]). New studies also show that Nitrospira can use urea as a source of nutrients.[18] 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[7] and other microbes to co-exist in the same microenvironment.[1]
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Nitrification
All members of this genus have the nitrite oxidoreductase genes, and thus are all thought to be nitrite-oxidizers.[10] 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.[19] Recently Nitrospira members with the abilities to perform complete nitrification (comammox bacteria) have also been discovered[9][12][20] and cultivated as in the case of Nitrospira inopinata.[13] 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.[9]
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.[21]
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.[9][12][20] 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.[9] 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.[12] 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.[9]
Nitrospira also carry the genes encoding for all the sub-units of nitrite oxidoreductase (nxr), the enzyme that catalyzes the second step of nitrification.[9]
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Phylogeny
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[22] and the National Center for Biotechnology Information (NCBI).[23] Phylogeny is based on GTDB 09-RS220 by Genome Taxonomy Database[24][25][26]
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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
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See also
References
External links
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