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United States Department of Agriculture

Agricultural Research Service

Title: Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils

item Wu, Qingzhong
item Thomas, Sara
item Wagner, Ryan
item Cruz-garcia, Claribel
item Rodriguez, Gina
item Massol-deya, Arturo
item Ritalahti, Kirsti
item Sanford, Robert
item Chee Sanford, Joanne
item Loffler, Frank

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2012
Publication Date: 10/19/2012
Citation: Sanford, R.A., Wagner, D.D., Wu, Q., Chee-Sanford, J.C., Thomas, S.H., Cruz-Garcia, C., Rodriguez, G., Massol-Deya, A., Ritalahti, K.M., Nissen, S., Konstantidis, K.T., Loeffler, F.E. 2012. Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. Proceedings of the National Academy of Sciences. 109:19709-19714.

Interpretive Summary: Concerns over greenhouse gas emissions has prompted a major interest in understanding source processes and mitigating effects.Agricultural soils are a significant source of nitrous oxide (N2O), a potent greenhouse gas, and a major intermediate and product of microbial N-metabolic activities. Conventional understanding of N-cycling in soil has primarily focused on dentrification as the main source and consumption of N2O in soils. Beyond denitrifying bacteria, other metabolic groups may also significantly affect N2O flux in natural environments. In this study, we investigated a unique bacterial genus, Anaeromyxobacter, a non-denitrifier capable of growth using N2O for respiration. Anaeromyxobacter is commonly found in a wide range of environments, often in high relative abundances, and most recently found in a large number of agricultural soils in the Midwestern U.S. The enzyme nitrous oxide reductase mediates N2O reduction, and is encoded by the gene nosZ. Using genetic probes we designed based on nosZ sequences found in all Anaeromyxobacter, we found widespread distribution and abundances of novel nosZ genes not previously identified and distinct from those found in true denitrifiers. These results, along with computational analyses of the genomes of numerous other non-denitrifying bacteria that indicate the presence of nosZ, suggest that N2O respiration may be a common function apart from true denitrifiers.An understanding of the ecological significance of Anaeromyxobacter and other non-denitrifiers in affecting N2O flux in soil will expand the current knowledge of N-cycling. The results suggest that our current understanding of N-cycling in soils is incomplete, and the further impact of this work expands the existing genetic markers used to monitor bacteria and N-cycling genes.

Technical Abstract: Members of the Anaeromyxobacter genus are versatile, facultative microaerophilic myxobacteria distributed in soils, aquifers and freshwater sediments. Anaeromyxobacter spp. grow with nitrate as electron acceptor via dissimilatory reduction to ammonium. Remarkably, the analysis of four available Anaeromyxobacter spp. genomes revealed the presence of complete nosZ gene clusters suggesting non-denitrifiers contribute to nitrous oxide (N2O) turnover. Physiological studies confirmed that Anaeromyxobacter spp. use N2O as an electron acceptor for growth, and this respiratory process yielded 2.85-4.08 x 108 cells per µmol of N2O reduced. Electron donors supporting N2O reduction by Anaeromyxobacter dehalogenans strain 2CP-C included succinate, lactate, acetate, formate and hydrogen (H2). Oxygen (3%), 0.42 mM nitrate or 2 mM soluble ferric iron did not inhibit N2 formation and were reduced concomitantly with N2O. A computational analysis detected complete nosZ gene clusters in other non-denitrifying bacterial genera including Desulfitobacterium, Geobacillus and Salinibacter) and one archaeal Pyrobaculum genus, indicating that N2O respiration in non-denitrifiers may not be uncommon. The application of Anaeromyxobacter nosZ-specific PCR primers indicated that N2O reduction is a shared feature of this genus. A nosZ gene-based survey of distinct agroecological regions in the North American cornbelt targeting Anaeromyxobacter sequences demonstrated widespread distribution and abundance of novel nosZ genes not previously identified in soil (64 of 76 samples). These finding indicate that non-dentrifying myxobacteria, as well as other bacterial groups, may affect N2O flux from agricultural soils. The occurrence of nosZ in non-denitrifying organisms in agricultural soils suggests that the current tools to monitor and understanding of microbes affecting N2O flux from agricultural soils is incomplete.

Last Modified: 10/16/2017
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