Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 113, Issue 29, Pages 8033-8040Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1601070113
Keywords
nitrification; nitrogen fixation; ammonia assimilation; metagenomics; dissimilatory nitrite reduction
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Funding
- US Department of Education Graduate Assistance in Areas of National Need Fellowship
- US Department of Energy, Office of Science, Office of Biological and Environmental Research Grant [DE-PS02-09ER09-25]
- Direct For Biological Sciences [1457160] Funding Source: National Science Foundation
- Division Of Environmental Biology [1457160] Funding Source: National Science Foundation
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Microorganisms drive much of the Earth's nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little-studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N-cycling specialists or generalists. For instance, taxa within the Deltaproteo bacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait-based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils.
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