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Title: Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle

Journal Article · · mBio (Online)
 [1];  [2];  [3];  [4];  [5];  [6];  [6];  [7]
  1. Georgia Inst. of Technology, Atlanta, GA (United States). School of Civil and Environmental Engineering
  2. Georgia Inst. of Technology, Atlanta, GA (United States). School of Biology
  3. Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology
  4. US Dept. of Agriculture (USDA), Urbana, IL (United States). Agricultural Research Service (ARS)
  5. Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Geology
  6. Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering
  7. Georgia Inst. of Technology, Atlanta, GA (United States). School of Civil and Environmental Engineering; Georgia Inst. of Technology, Atlanta, GA (United States). School of Biology.
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Microbial activities in soils, such as (incomplete) denitrification, represent major sources of nitrous oxide (N2O), a potent greenhouse gas. The key enzyme for mitigating N2O emissions is NosZ, which catalyzes N2O reduction to N2. We recently described “atypical” functional NosZ proteins encoded by both denitrifiers and nondenitrifiers, which were missed in previous environmental surveys (R. A. Sanford et al., Proc. Natl. Acad. Sci. U. S. A. 109:19709–19714, 2012, doi:10.1073/pnas.1211238109). Here, we analyzed the abundance and diversity of both nosZ types in whole-genome shotgun metagenomes from sandy and silty loam agricultural soils that typify the U.S. Midwest corn belt. First, different search algorithms and parameters for detecting nosZ metagenomic reads were evaluated based on in silico-generated (mock) metagenomes. Using the derived cutoffs, 71 distinct alleles (95% amino acid identity level) encoding typical or atypical NosZ proteins were detected in both soil types. Remarkably, more than 70% of the total nosZ reads in both soils were classified as atypical, emphasizing that prior surveys underestimated nosZ abundance. Approximately 15% of the total nosZ reads were taxonomically related to Anaeromyxobacter, which was the most abundant genus encoding atypical NosZ-type proteins in both soil types. Further analyses revealed that atypical nosZ genes outnumbered typical nosZ genes in most publicly available soil metagenomes, underscoring their potential role in mediating N2O consumption in soils. Therefore, this study provides a bioinformatics strategy to reliably detect target genes in complex short-read metagenomes and suggests that the analysis of both typical and atypical nosZ sequences is required to understand and predict N2O flux in soils.

Research Organization:
Univ. of Tennessee, Knoxville, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
SC0006662
OSTI ID:
1626129
Journal Information:
mBio (Online), Vol. 5, Issue 3; ISSN 2150-7511
Publisher:
American Society for Microbiology (ASM)Copyright Statement
Country of Publication:
United States
Language:
English

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Nitrous Oxide Reduction by an Obligate Aerobic Bacterium, Gemmatimonas aurantiaca Strain T-27 journal April 2017
Peaks of in situ N 2 O emissions are influenced by N 2 O-producing and reducing microbial communities across arable soils journal September 2017
Resolving N 2 O respiration pathways: a tale of two NosZ clades : Resolving N journal November 2017
The diversity of the N2O reducers matters for the N2O:N2 denitrification end-product ratio across an annual and a perennial cropping system journal September 2015
Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer journal November 2019
Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors journal December 2016
Greenhouse Gas Production and Transport in Desert Soils of the Southwestern United States journal November 2018
Temperature determines the diversity and structure of N 2 O-reducing microbial assemblages journal March 2018
Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem journal April 2016
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Geochemical and Microbiological Studies of Nitrous Oxide Variations within the New NEEM Greenland Ice Core during the Last Glacial Period journal February 2016
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Microbial nitrous oxide emissions in dryland ecosystems: mechanisms, microbiome and mitigation: Microbial regulation of dryland N 2 O emissions journal June 2017
Methylotrophs in natural habitats: current insights through metagenomics journal June 2015
The soil N cycle: new insights and key challenges journal January 2015
Biochar reduces the efficiency of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) mitigating N2O emissions journal February 2019
Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils journal March 2018
Aerobic denitrification: A review of important advances of the last 30 years journal August 2015
Role of heterotrophic aerobic denitrifying bacteria in nitrate removal from wastewater journal May 2020
Phylogenetic and functional potential links pH and N2O emissions in pasture soils journal October 2016
Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions journal December 2014
Geochemical and Microbiological Studies of Nitrous Oxide Variations within the New NEEM Greenland Ice Core During the Last Glacial Period text January 2016
Dominance of bacterial ammonium oxidizers and fungal denitrifiers in the complex nitrogen cycle pathways related to nitrous oxide emission journal May 2018
Consumption of N2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27 journal December 2019
Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution journal November 2018
Biokinetic Characterization and Activities of N2O-Reducing Bacteria in Response to Various Oxygen Levels journal April 2018
Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions journal July 2017
Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem journal July 2014
Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen journal June 2016
Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States journal August 2018
Underexplored microbial metabolisms for enhanced nutrient recycling in agricultural soils journal January 2017

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