Comammox

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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. [1] Nitrification has traditionally thought to be a two-step process, where ammonia-oxidizing bacteria and archaea oxidize ammonia to nitrite and then nitrite-oxidizing bacteria convert to nitrate. [2] [3] Complete conversion of ammonia into nitrate by a single microorganism was first predicted in 2006. [1] In 2015 the presence of microorganisms that could carry out both conversion processes was discovered within the genus Nitrospira, and the nitrogen cycle was updated. [4] [5] Within the genus Nitrospira, the major ecosystems comammox are primarily found in natural aquifers and engineered ecosystems. [6]

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Complete nitrification step yield more energy (∆G°′ = −349 kJ mol−1 NH3) than either single oxidation alone (∆G°′ = −275 kJ mol−1 NH3 for ammonia oxidation to nitrite and ∆G°′ = −74 kJ mol−1 NO2− for nitrite oxidation to nitrate). [5]

Comammox Nitrospira Bacteria

Complete nitrification of oxidizing ammonia to nitrate is energetically advantageous for Nitrospira . [5] Due to the previous research done on Nitrospira, it was thought that all Nitrospira use nitrite as their energy source. [1] Therefore, comammox Nitrospira were not discovered until 2015. [5] All discovered nitrifiers belong to sublineage II of the genus Nitrospira. [3] The genome of the nitrifying chemolithoautotrophic bacterium from the genus Nitrospira encodes for both ammonia and nitrite oxidation. [5] The genes associated with the growth by ammonia oxidation to nitrate are ammonia monooxygenase and hydroxylamine dehydrogenases genes (e.g. amoA gene and hao cluster). [5] This shows that complete nitrifying Nitrospira serve as cornerstones of the nitrogen-cycling microbial communities found in the environment. Nearly two years after the discovery of comammox organisms, Nitrospira inopinata was the first complete nitrifier to be isolated in pure culture. [7] Kinetic and physiological analysis of Nitrospira inopinata demonstrated that this complete nitrifier has a high affinity for ammonia, slow growth rate, low maximum rate of ammonia oxidation, and high yield. [7] [6] The discovery of comammox Nitrospira provides a view into the modular evolution of the nitrogen cycle and expands upon the complexity of the evolutionary history of nitrification. [5]

Ecosystem of Comammox

Comammox have been identified in many ecosystems, including natural freshwater and terrestrial ecosystems. Notably commamox genes were not found to be abundant in oceans. Additionally, the use of engineered ecosystems for comammox could be used for ammonium removal during water and wastewater treatment. [3] Comammox have been found in many engineered systems including aquaculture biofiltration units, drinking water treatment and distribution systems, and wastewater treatment plants. [3] [6] The growth of comammox in these engineered ecosystems co-occur with ammonia-oxidizing bacteria and/or archaea, and in some cases outnumber other ammonia-oxidizing prokaryotes. [3] [6] [8] [9] The ecosystem of comammox is currently unknown in terms of biogeography, including their distribution and abundance, due to the influences of process configuration and chemical composition of the treated wastewater. [3] [6] Following these findings, it was determined that comammox may out-select canonical nitrite oxidizing bacteria in the genus Nitrospira in some engineered environments, suggesting the potentially important role for comammox in efficient biological nitrogen removal in wastewater treatment processes. [3]

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Related Research Articles

<span class="mw-page-title-main">Nitrogen cycle</span> Biogeochemical cycle by which nitrogen is converted into various chemical forms

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 biological and physical processes. Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earth's atmosphere (78%) is atmospheric nitrogen, making it the largest source of nitrogen. However, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems.

<span class="mw-page-title-main">Nitrification</span> Biological oxidation of ammonia/ammonium to nitrate

Nitrification is the biological oxidation of ammonia to nitrate via the intermediary nitrite. Nitrification is an important step in the nitrogen cycle in soil. The process of complete nitrification may occur through separate organisms or entirely within one organism, as in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.

<span class="mw-page-title-main">Denitrification</span> Microbially facilitated process

Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denitrification as a type of respiration that reduces oxidized forms of nitrogen in response to the oxidation of an electron donor such as organic matter. The preferred nitrogen electron acceptors in order of most to least thermodynamically favorable include nitrate (NO3−), nitrite (NO2−), nitric oxide (NO), nitrous oxide (N2O) finally resulting in the production of dinitrogen (N2) completing the nitrogen cycle. Denitrifying microbes require a very low oxygen concentration of less than 10%, as well as organic C for energy. Since denitrification can remove NO3−, reducing its leaching to groundwater, it can be strategically used to treat sewage or animal residues of high nitrogen content. Denitrification can leak N2O, which is an ozone-depleting substance and a greenhouse gas that can have a considerable influence on global warming.

<span class="mw-page-title-main">Anammox</span> Anaerobic ammonium oxidation, a microbial process of the nitrogen cycle

Anammox, an abbreviation for "anaerobic ammonium oxidation", is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a great surprise for the scientific community. In the anammox reaction, nitrite and ammonium ions are converted directly into diatomic nitrogen and water.

Nitrosomonas europaea is a Gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite and lives in several places such as soil, sewage, freshwater, the walls of buildings and on the surface of monuments especially in polluted areas where the air contains high levels of nitrogen compounds.

<i>Nitrosomonas</i> Genus of bacteria

Nitrosomonas is a genus of Gram-negative bacteria, belonging to the Betaproteobacteria. It is one of the five genera of ammonia-oxidizing bacteria and, as an obligate chemolithoautotroph, uses ammonia as an energy source and carbon dioxide as a carbon source in presence of oxygen. Nitrosomonas are important in the global biogeochemical nitrogen cycle, since they increase the bioavailability of nitrogen to plants and in the denitrification, which is important for the release of nitrous oxide, a powerful greenhouse gas. This microbe is photophobic, and usually generate a biofilm matrix, or form clumps with other microbes, to avoid light. Nitrosomonas can be divided into six lineages: the first one includes the species Nitrosomonas europea, Nitrosomonas eutropha, Nitrosomonas halophila, and Nitrosomonas mobilis. The second lineage presents the species Nitrosomonas communis, N. sp. I and N. sp. II, meanwhile the third lineage includes only Nitrosomonas nitrosa. The fourth lineage includes the species Nitrosomonas ureae and Nitrosomonas oligotropha and the fifth and sixth lineages include the species Nitrosomonas marina, N. sp. III, Nitrosomonas estuarii and Nitrosomonas cryotolerans.

Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. Denitrification is performed by a variety of denitrifying bacteria that are widely distributed in soils and sediments and that use oxidized nitrogen compounds such as nitrate and nitrite in the absence of oxygen as a terminal electron acceptor. They metabolize nitrogenous compounds using various enzymes, including nitrate reductase (NAR), nitrite reductase (NIR), nitric oxide reductase (NOR) and nitrous oxide reductase (NOS), turning nitrogen oxides back to nitrogen gas or nitrous oxide.

<i>Nitrobacter</i> Genus of bacteria

Nitrobacter is a genus comprising rod-shaped, gram-negative, and chemoautotrophic bacteria. The name Nitrobacter derives from the Latin neuter gender noun nitrum, nitri, alkalis; the Ancient Greek noun βακτηρία, βακτηρίᾱς, rod. They are non-motile and reproduce via budding or binary fission. Nitrobacter cells are obligate aerobes and have a doubling time of about 13 hours.

Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

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 of inorganic nitrogen compounds. Types include ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Many species of nitrifying bacteria have complex internal membrane systems that are the location for key enzymes in nitrification: ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase.

Nitrospira 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 described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. 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, natural biological marine settings, water circulation biofilters 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. In addition, Nitrospira bacteria's 16S rRNA 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 has also been discovered and cultivated.

<i>Nitrosopumilus</i> Genus of archaea

Nitrosopumilus maritimus is an extremely common archaeon living in seawater. It is the first member of the Group 1a Nitrososphaerota to be isolated in pure culture. Gene sequences suggest that the Group 1a Nitrososphaerota are ubiquitous with the oligotrophic surface ocean and can be found in most non-coastal marine waters around the planet. It is one of the smallest living organisms at 0.2 micrometers in diameter. Cells in the species N. maritimus are shaped like peanuts and can be found both as individuals and in loose aggregates. They oxidize ammonia to nitrite and members of N. maritimus can oxidize ammonia at levels as low as 10 nanomolar, near the limit to sustain its life. Archaea in the species N. maritimus live in oxygen-depleted habitats. Oxygen needed for ammonia oxidation might be produced by novel pathway which generates oxygen and dinitrogen. N. maritimus is thus among organisms which are able to produce oxygen in dark.

Nitrite oxidoreductase 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, Nitrosomonas, and Nitrosococcus convert ammonia to nitrite, while nitrite oxidizers such as Nitrobacter and Nitrospira oxidize nitrite to nitrate. NXR is responsible for producing almost all nitrate found in nature.

<span class="mw-page-title-main">SHARON Wastewater Treatment</span>

SHARON is a sewage treatment process. A partial nitrification process of sewage treatment used for the removal of ammonia and organic nitrogen components from wastewater flow streams. The process results in stable nitrite formation, rather than complete oxidation to nitrate. Nitrate formation by nitrite oxidising bacteria (NOB) is prevented by adjusting temperature, pH, and retention time to select for nitrifying ammonia oxidising bacteria (AOB). Denitrification of waste streams utilizing SHARON reactors can proceed with an anoxic reduction, such as anammox.

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 in 1995.

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, Russia in 1995. The genus name, Nitrospira, originates from the prefix “nitro” derived from nitrite, the microbe’s electron donor and “spira” meaning coil or spiral derived from the microbe’s shape. The species name, moscoviensis, is derived from Moscow, where the species was first discovered. N. moscoviensis could potentially be used in the production of bio-degradable polymers.

Nitrososphaera gargensis is a non-pathogenic, small coccus measuring 0.9 ± 0.3 μm in diameter. N. gargensis is observed in small abnormal cocci groupings and uses its archaella to move via chemotaxis. Being an Archaeon, Nitrososphaera gargensis has a cell membrane composed of crenarchaeol, its isomer, and a distinct glycerol dialkyl glycerol tetraether (GDGT), which is significant in identifying ammonia-oxidizing archaea (AOA). The organism plays a role in influencing ocean communities and food production.

<span class="mw-page-title-main">Cattle urine patches</span> Grass damage by cattle urine

Urine patches in cattle pastures generate large concentrations of the greenhouse gas nitrous oxide through nitrification and denitrification processes in urine-contaminated soils. Over the past few decades, the cattle population has increased more rapidly than the human population. Between the years 2000 and 2050, the cattle population is expected to increase from 1.5 billion to 2.6 billion. When large populations of cattle are packed into pastures, excessive amounts of urine soak into soils. This increases the rate at which nitrification and denitrification occur and produce nitrous oxide. Currently, nitrous oxide is one of the single most important ozone-depleting emissions and is expected to remain the largest throughout the 21st century.

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 first comammox bacterium to be discovered.

Anammox is a wastewater treatment technique that removes nitrogen using anaerobic ammonium oxidation (anammox). This process is performed by anammox bacteria which are autotrophic, meaning they do not need organic carbon for their metabolism to function. Instead, the metabolism of anammox bacteria convert ammonium and nitrite into dinitrogen gas. Anammox bacteria are a wastewater treatment technique and wastewater treatment facilities are in the process of implementing anammox-based technologies to further enhance ammonia and nitrogen removal.

References

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  2. ↑ Winogradsky, Serge (1892). "Contributions a la morphologie des organismes de la nitrification". Arch. Sci. Biol. 1: 87–137.
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  8. ↑ Roots, Paul; Wang, Yubo; Rosenthal, Alex F.; Griffin, James S.; Sabba, Fabrizio; Petrovich, Morgan; Yang, Fenghua; Kozak, Joseph A.; Zhang, Heng; Wells, George F. (2019-06-15). "Comammox Nitrospira are the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor". Water Research. 157: 396–405. doi:10.1016/j.watres.2019.03.060. ISSN   0043-1354.
  9. ↑ Cotto, Irmarie; Dai, Zihan; Huo, Linxuan; Anderson, Christopher L.; Vilardi, Katherine J.; Ijaz, Umer; Khunjar, Wendell; Wilson, Christopher; De Clippeleir, Haydee; Gilmore, Kevin; Bailey, Erika; Pinto, Ameet J. (2020-02-01). "Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems". Water Research. 169: 115268. doi:10.1016/j.watres.2019.115268. ISSN   0043-1354.
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