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Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea

Abstract

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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Acknowledgements

We thank Cheryl Kuske and Renee Johansen for comments on previous versions of this manuscript.

Funding

This work was supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research Division, under award number F260LANL2018, and by an Office of Science Graduate Student Research (SCGSR) Fellowship to MA.

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Correspondence to Michaeline B. N. Albright or John Dunbar.

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Albright, M.B.N., Timalsina, B., Martiny, J.B.H. et al. Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea. Microb Ecol 77, 597–606 (2019). https://doi.org/10.1007/s00248-018-1239-4

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Keywords

  • Nitrogen cycle
  • Comparative genomics
  • Bacteria
  • Archaea