Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions

Authors: SHAN, JUN - Chinese Academy Of Sciences; SANFORD, ROBERT - University Of Illinois; Chee Sanford, Joanne; OOI, SUSAN - University Of Illinois; LOEFFLER, FRANK - University Of Tennessee; KONSTANTINIDIS, KOSTAS - Georgia Institute Of Technology; YANG, WENDY - University Of Illinois

Submitted to: Global Change Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/11/2021
Publication Date: 5/17/2021
Citation: Shan, J., Sanford, R.A., Chee-Sanford, J.C., Ooi, S., Loeffler, F., Konstantinidis, K., Yang, W.H. 2021. Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions. Global Change Biology. 27(12):2669-2683. https://doi.org/10.1111/gcb.15545.
DOI: https://doi.org/10.1111/gcb.15545

Interpretive Summary: Increasing our understanding of biological nitrous oxide (N2O) reduction is a primary challenge to better predict greenhouse gas fluxes and nitrogen losses from soil ecosystems. N2O is generated from multiple biological and non-biological reactions, but the only known process for consuming N2O is microbial reduction of N2O to dinitrogen (N2). This biological step is catalyzed by nitrous oxide reductase, an enzyme encoded by the microbial gene nosZ. Since 2012 where we first reported the new discovery that nosZ genes are made up of two main groups, Clade I (typical) and Clade II (atypical), studies that include Clade II nosZ are still relatively scant (10%) in a background of hundreds of published studies attempting to characterize microbial N2O reduction in natural systems. Even with increasing reports from sequencing surveys that Clade II nosZ genes dominate over the well-studied Clade I group in many soil systems, few studies consider the full diversity of populations that have the potential to reduce N2O, thus seriously underestimating the biological N2O sink. In this study, we collected a large dataset of published journal articles (631) since 2012 and evaluated their inclusion of Clade II nosZ in methodological approach, and if not, acknowledgments in either their potential role in N2O reduction or limitations in study interpretations based strictly on Clade I nosZ data. The results of our synthesis provides a necessary spotlight on a major gap in the role of nosZ in controlling soil N2O emissions and provides major recommendations to the scientific community to include Clade II nosZ through improved methodological approaches and increasing awareness of inconsistent terminology that describe nosZ in current light. We further make explicit the change from decades-long research on N2O reduction strictly attributed to Clade I previously, to now include a new paradigm shift away from traditional denitrification as the major process responsible for N2O fluxes in soils. The impact of this synthesis is expected to improve access to pertinent literature and available research tools, and highlight the prominence and potential importance of Clade II nosZ in soil N2O emissions studies.

Technical Abstract: Many biotic and abiotic processes contribute to nitrous oxide (N2O) production in the biosphere, but N2O consumption has heretofore been attributed solely to canonical denitrifying microorganisms. The nosZ genes encoding the N2O reductase enzyme (NosZ) responsible for N2O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I possessed only by denitrifiers, and the novel Clade II possessed by highly diverse subgroups of microorganisms, most of which are non-denitrifiers. Clade II N2O reducers could play an important, previously unrecognized role in controlling soil N2O emissions for several reasons, including: (1) the reliance of non-denitrifying N2O reducers on consuming external sources of N2O, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N2O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 630 peer-reviewed original research articles published on nosZ from 2013 to 2018 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 27% in 2018. The census revealed that the slowly spreading awareness of Clade II may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture & Agronomy journals to 31% in Microbiology journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the groups of N2O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N2O reducers in regulating soil N2O emissions.