Microbial Ecology

, Volume 77, Issue 3, pp 597–606 | Cite as

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea

  • Michaeline B. N. AlbrightEmail author
  • Bibek Timalsina
  • Jennifer B. H. Martiny
  • John DunbarEmail author
Environmental Microbiology


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.


Nitrogen cycle Comparative genomics Bacteria Archaea 



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


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.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

248_2018_1239_MOESM1_ESM.docx (1.2 mb)
ESM 1 (DOCX 1179 kb)


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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Bioscience DivisionLos Alamos National LaboratoryLos AlamosUSA
  2. 2.Department of BiochemistryMississippi State UniversityStarkvilleUSA
  3. 3.Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineUSA

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