Journal
MICROBIAL ECOLOGY
Volume 77, Issue 3, Pages 597-606Publisher
SPRINGER
DOI: 10.1007/s00248-018-1239-4
Keywords
Nitrogen cycle; Comparative genomics; Bacteria; Archaea
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Funding
- U.S. Department of Energy, Office of Science, Biological and Environmental Research Division [F260LANL2018]
- Office of Science Graduate Student Research (SCGSR) Fellowship
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Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.
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