Nitrospira Japonica
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''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 of the
Nitrospirota Nitrospirota is a phylum of bacteria. It includes multiple genera, such as ''Nitrospira'', the largest. The first member of this phylum, ''Nitrospira marina'', was discovered in 1985. The second member, ''Nitrospira moscoviensis'', was discovered ...
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 ''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 of the Nitrospirota phylum. The first member of this genus was d ...
''. 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 The activated sludge process is a type of biological wastewater treatment process for treating sewage or industrial wastewaters using aeration and a biological floc composed of bacteria and protozoa. It uses air (or oxygen) and microorganisms ...
of
wastewater treatment Wastewater treatment is a process used to remove contaminants from wastewater and convert it into an effluent that can be returned to the water cycle. Once returned to the water cycle, the effluent creates an acceptable impact on the environme ...
systems, natural biological marine settings (such as the Seine River in France and beaches in Cape Cod), water circulation
biofilter Biofiltration is a pollution control technique using a bioreactor containing living material to capture and biologically degrade pollutants. Common uses include processing waste water, capturing harmful chemicals or silt from surface runoff, and ...
s in aquarium tanks, terrestrial systems, fresh and salt water ecosystems, and hot springs. Nitrospira is a ubiquitous bacterium that plays a role in the nitrogen cycle by performing nitrite oxidation in the second step of nitrification. ''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. 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. However, due to their difficulty to be cultivated in laboratory settings, the entire genome was only sequenced in one species, ''
Nitrospira defluvii ''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 of the Nitrospirota phylum. The first member of this genus was d ...
''. In addition, ''Nitrospira'' bacteria's
16s rRNA 16S rRNA may refer to: * 16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The g ...
sequences are too dissimilar to use for PCR primers, thus some members go unnoticed. In addition, members of Nitrospira with the capabilities to perform complete
nitrification ''Nitrification'' is the biological oxidation of ammonia to nitrite followed by the oxidation of the nitrite to nitrate occurring through separate organisms or direct ammonia oxidation to nitrate in comammox bacteria. The transformation of amm ...
(
comammox Comammox (COMplete AMMonia OXidation) is the name attributed to an organism that can convert ammonia into nitrite and then into nitrate through the process of nitrification. Nitrification has traditionally thought to be a two-step process, where amm ...
bacteria) has also been discovered and cultivated.


Morphology

For the following description, ''
Nitrospira moscoviensis ''Nitrospira moscoviensis'' was the second bacterium classified under the most diverse nitrite-oxidizing bacteria phylum, ''Nitrospirae''. It is a gram-negative, non-motile, facultative lithoauthotropic bacterium that was discovered in Moscow, Ru ...
'' will be representative of the Nitrospira genus. Nitrospira is a
gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
nitrite The nitrite polyatomic ion, ion has the chemical formula . Nitrite (mostly sodium nitrite) is widely used throughout chemical and pharmaceutical industries. The nitrite anion is a pervasive intermediate in the nitrogen cycle in nature. The name ...
-oxidizing organism with a helical to vibroid morphology (0.9–2.2 × 0.2–0.4
micrometre The micrometre ( international spelling as used by the International Bureau of Weights and Measures; SI symbol: μm) or micrometer (American spelling), also commonly known as a micron, is a unit of length in the International System of Unit ...
s in size). They are non-
planktonic Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a crucia ...
organisms that reside as clumps, known as aggregates, in
biofilm A biofilm comprises any syntrophic consortium of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular ...
s. Visualization using
Transmission electron microscopy Transmission electron microscopy (TEM) is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image. The specimen is most often an ultrathin section less than 100 nm thick or a suspension on a g ...
(TEM) confirms star-like protrusions on the outer membrane (6-8 nm thick). The
periplasmic space The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the ''periplasmic space'' in gram-negative bacteria. Using cryo-electron microscopy it has been found tha ...
is exceptionally wide (34-41 nm thick), which provides space to accommodate electron-rich molecules. Electron-deprived structures are located in the cytosol and are believed to be
glycogen Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. The polysaccharide structure represents the main storage form of glucose in the body. Glycogen functions as one o ...
storage vesicles;
polyhydroxybutyrate Polyhydroxybutyrate (PHB) is a polyhydroxyalkanoate (PHA), a polymer belonging to the polyesters class that are of interest as bio-derived and biodegradable plastics. The poly-3-hydroxybutyrate (P3HB) form of PHB is probably the most common type ...
and
polyphosphate Polyphosphates are salts or esters of polymeric oxyanions formed from tetrahedral PO4 (phosphate) structural units linked together by sharing oxygen atoms. Polyphosphates can adopt linear or a cyclic ring structures. In biology, the polyphosphate e ...
granules are also identified in the cytoplasm. DNA analysis determined 56.9 +/- 0.4 mol% of the DNA to be
guanine Guanine () ( symbol G or Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is called ...
and
cytosine Cytosine () ( symbol C or Cyt) is one of the four nucleobases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an am ...
base pairs.


General metabolism

Nitrospira are capable of aerobic hydrogen oxidation and nitrite oxidation to obtain electrons, but high concentrations of nitrite have shown to inhibit their growth. The optimal temperature for nitrite oxidation and growth in ''
Nitrospira moscoviensis ''Nitrospira moscoviensis'' was the second bacterium classified under the most diverse nitrite-oxidizing bacteria phylum, ''Nitrospirae''. It is a gram-negative, non-motile, facultative lithoauthotropic bacterium that was discovered in Moscow, Ru ...
'' is 39 °C (can range from 33-44 °C) at a pH range of 7.6-8.0 Despite being commonly classified as obligate
chemolithotrophs Lithotrophs are a diverse group of organisms using an inorganic substrate (usually of mineral origin) to obtain reducing equivalents for use in biosynthesis (e.g., carbon dioxide fixation) or energy conservation (i.e., ATP production) via aerobic ...
, some are capable of
mixotroph A mixotroph is an organism that can use a mix of different sources of energy and carbon, instead of having a single trophic mode on the continuum from complete autotrophy at one end to heterotrophy at the other. It is estimated that mixotrophs comp ...
y. For instance, under different environments, Nitrospira can choose to assimilate carbon by
carbon fixation Biological carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide) is converted to organic compounds by living organisms. The compounds are then used to store energy and as ...
or by consuming organic molecules (
glycerol Glycerol (), also called glycerine in British English and glycerin in American English, is a simple triol compound. It is a colorless, odorless, viscous liquid that is sweet-tasting and non-toxic. The glycerol backbone is found in lipids known ...
,
pyruvate Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic aci ...
, or
formate Formate (IUPAC name: methanoate) is the conjugate base of formic acid. Formate is an anion () or its derivatives such as ester of formic acid. The salts and esters are generally colorless.Werner Reutemann and Heinz Kieczka "Formic Acid" in ''Ull ...
). New studies also show that Nitrospira can use
urea Urea, also known as carbamide, is an organic compound with chemical formula . This amide has two amino groups (–) joined by a carbonyl functional group (–C(=O)–). It is thus the simplest amide of carbamic acid. Urea serves an important r ...
as a source of nutrient.
Urease Ureases (), functionally, belong to the superfamily of amidohydrolases and phosphotriesterases. Ureases are found in numerous bacteria, fungi, algae, plants, and some invertebrates, as well as in soils, as a soil enzyme. They are nickel-containin ...
encoded within their genome can break urea down to and
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous was ...
. The can be assimilated by
anabolism Anabolism () is the set of metabolic pathways that construct molecules from smaller units. These reactions require energy, known also as an endergonic process. Anabolism is the building-up aspect of metabolism, whereas catabolism is the breaking-do ...
while the ammonia and organic by-product released by Nitrospira allow ammonium oxidizers and other microbes to co-exist in the same microenvironment.


Nitrification

All members of this genus have the
nitrite oxidoreductase Nitrite oxidoreductase (NOR or NXR) is an enzyme involved in nitrification. It is the last step in the process of aerobic ammonia oxidation, which is carried out by two groups of nitrifying bacteria: ammonia oxidizers such as '' Nitrosospira'', ''N ...
genes, and thus are all thought to be nitrite-oxidizers. Ever since
nitrifying bacteria Nitrifying bacteria are chemolithotrophic organisms that include species of genera such as ''Nitrosomonas'', ''Nitrosococcus'', ''Nitrobacter'', '' Nitrospina'', ''Nitrospira'' and '' Nitrococcus''. These bacteria get their energy from the oxidation ...
were discovered it was accepted that nitrification occurred in two steps, although it would be energetically favourable for one organism to do both steps. Recently ''Nitrospira'' members with the abilities to perform complete
nitrification ''Nitrification'' is the biological oxidation of ammonia to nitrite followed by the oxidation of the nitrite to nitrate occurring through separate organisms or direct ammonia oxidation to nitrate in comammox bacteria. The transformation of amm ...
(
comammox Comammox (COMplete AMMonia OXidation) is the name attributed to an organism that can convert ammonia into nitrite and then into nitrate through the process of nitrification. Nitrification has traditionally thought to be a two-step process, where amm ...
bacteria) have also been discovered and cultivated as in the case of ''
Nitrospira inopinata ''Nitrospira inopinata'' is a bacterium from the phylum Nitrospirota. This phylum contains nitrite-oxidizing bacteria playing role in nitrification. However ''N. inopinata'' was shown to perform complete ammonia oxidation to nitrate thus being the ...
''. The discovery of commamox organisms within ''Nitrospira'' redefine the way bacteria contribute to the
Nitrogen cycle The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biologi ...
and thus a lot of future studies will be dedicated to it. 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 Wastewater treatment is a process used to remove contaminants from wastewater and convert it into an effluent that can be returned to the water cycle. Once returned to the water cycle, the effluent creates an acceptable impact on the environmen ...
because complete nitrification results in lower emissions of the
greenhouse gas A greenhouse gas (GHG or GhG) is a gas that Absorption (electromagnetic radiation), absorbs and Emission (electromagnetic radiation), emits radiant energy within the thermal infrared range, causing the greenhouse effect. The primary greenhouse ...
es:
nitrous oxide Nitrous oxide (dinitrogen oxide or dinitrogen monoxide), commonly known as laughing gas, nitrous, or nos, is a chemical compound, an oxide of nitrogen with the formula . At room temperature, it is a colourless non-flammable gas, and has a ...
and
nitric oxide Nitric oxide (nitrogen oxide or nitrogen monoxide) is a colorless gas with the formula . It is one of the principal oxides of nitrogen. Nitric oxide is a free radical: it has an unpaired electron, which is sometimes denoted by a dot in its che ...
, into the atmosphere.


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 Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous was ...
into nitrite. 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. Origins of the Amo gene are debatable as one study found that it is similar to other AOB while another study found the Amo gene to be genetically distinct from other lineages. 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 Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
. ''Nitrospira'' also carry the genes encoding for all the sub-units of nitrite oxidoreductase (nxr), the enzyme that catalyzes the second step of nitrification.


Phylogeny

The currently accepted taxonomy is based on the
List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclature ...
(LSPN) and the
National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...
(NCBI). Phylogeny is based on GTDB 07-RS207 by
Genome Taxonomy Database The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to breaking up parap ...


See also

*
Nitrogen cycle The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biologi ...
*
List of bacterial orders This article lists the orders of the Bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S ...
*
List of bacteria genera This article lists the genera of the bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI). However many taxonomic names are ...


References


External links


MicrobeWiki -- Nitrospira
{{Taxonbar, from=Q3024630 Nitrospirota Bacteria genera