Comammox—a newly discovered nitrification process in the terrestrial nitrogen cycle
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Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, is a pivotal component of the biogeochemical nitrogen cycle. Nitrification was conventionally assumed as a two-step process in which ammonia oxidation was thought to be catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria (NOB). This long-held assumption of labour division between the two functional groups, however, was challenged by the recent unexpected discovery of complete ammonia oxidizers within the Nitrospira genus that are capable of converting ammonia to nitrate in a single organism (comammox). This breakthrough raised fundamental questions on the niche specialization and differentiation of comammox organisms with other canonical nitrifying prokaryotes in terrestrial ecosystems.
Materials and methods
This article provides an overview of the recent insights into the genomic analysis, physiological characterization and environmental investigation of the comammox organisms, which have dramatically changed our perspective on the aerobic nitrification process. By using quantitative PCR analysis, we also compared the abundances of comammox Nitrospira clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a wide range of soil pH.
Results and discussion
Comammox Nitrospira are environmentally widespread and numerically abundant in natural and engineered habitats. Physiological data, including ammonia oxidation kinetics and metabolic versatility, and comparative genomic analysis revealed that comammox organisms might functionally outcompete other canonical nitrifiers under highly oligotrophic conditions. These findings highlight the necessity in future studies to re-evaluate the niche differentiation between ammonia oxidizers and their relative contribution to nitrification in various terrestrial ecosystems by including comammox Nitrospira in such comparisons.
The discovery of comammox and their broad environmental distribution added a new dimension to our knowledge of the biochemistry and physiology of nitrification and has far-reaching implications for refined strategies to manipulate nitrification in terrestrial ecosystems and to maximize agricultural productivity and sustainability.
KeywordsAmmonia oxidation Comammox Complete nitrification Niche separation Nitrite oxidation Nitrospira
This work was financially supported by Natural Science Foundation of China (41230857) and the Australian Research Council (DE150100870; DP160101028).
- Arp D, Bottomley PJ (2006) Nitrifier: more than 100 years from isolation to genome sequences. Microbe 1:229–234Google Scholar
- Camejo PY, Domingo JS, McMahon KD, Moguera DR (2017) Genome-enabled insights into the ecophysiology of the comammox bacterium Candidatus Nitrospira nitrosa. mSystems. https://doi.org/10.1128/mSystems.00059-17
- Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M et al (2015) Complete nitrification by Nitrospira bacteria. Nature 528:504–509Google Scholar
- Hink L, Nicol GW, Prosser JI (2016) Archaea produce lower yields of N2O than bacteria during aerobic ammonia oxidation in soil. Environ Microbiol. https://doi.org/10.1111/1462-2920.13282
- Hu HW, Trivedi P, He JZ, Singh BK (2017) Microbial nitrous oxide emissions in dryland ecosystems: mechanisms, microbiome and mitigation. Environ Microbiol. https://doi.org/10.1111/1462-2920.13795
- Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P et al (2017) Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature. https://doi.org/10.1038/nature23679
- Palomo A, Pedersen AG, Fowler SJ, Dechesne A, Sicheritz-Ponten T, Smets BF (2017) Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira. bioRxiv. https://doi.org/10.1101/138586
- Pinto AJ, Marcus DN, Ijaz UZ, Bautista-de lose Santos QM, Dick GJ, Raskin L (2015) Metagenomic evidence for the presence of comammox Nitrospira-like bacteria in a drinking water system. mSphere 1:e00054–e00015Google Scholar
- Shi XZ, Hu HW, Zhu-Barker X, Hayden H, Wang JT, Suter H, Chen D, He JZ (2017) Nitrifier-induced denitrification is an important source of soil nitrous oxide and can be inhibited by a nitrification inhibitor 3,4-dimethylpyrazole phosphate. Environ Microbiol. https://doi.org/10.1111/1462-2920.13872
- Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N et al (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 14:3122–3145Google Scholar
- van Kessel MA, Speth DR, Albertsen M, Nielsen PH, den Camp HJO, Kartal B et al (2015) Complete nitrification by a single microorganism. Nature 528:555–559Google Scholar