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Title: Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea

Abstract

Despite the explosion of metagenomic sequencing data, using -omics data to indicate 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 normally used to represent the prevalence of a biogeochemical reaction. This method 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. Moreover, 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.

Authors:
ORCiD logo [1];  [2];  [3]; ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mississippi State Univ., Starkville, MS (United States)
  3. Univ. of California, Irvine, CA (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1558043
Report Number(s):
LA-UR-18-21897
Journal ID: ISSN 0095-3628
Grant/Contract Number:  
89233218CNA000001; F260LANL2018
Resource Type:
Accepted Manuscript
Journal Name:
Microbial Ecology
Additional Journal Information:
Journal Volume: 77; Journal Issue: 3; Journal ID: ISSN 0095-3628
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Nitrogen cycle; Comparative genomics; Bacteria Archaea

Citation Formats

Albright, Michaeline B. N., Timalsina, Bibek, Martiny, Jennifer B. H., and Dunbar, John. Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea. United States: N. p., 2018. Web. doi:10.1007/s00248-018-1239-4.
Albright, Michaeline B. N., Timalsina, Bibek, Martiny, Jennifer B. H., & Dunbar, John. Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea. United States. doi:10.1007/s00248-018-1239-4.
Albright, Michaeline B. N., Timalsina, Bibek, Martiny, Jennifer B. H., and Dunbar, John. Mon . "Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea". United States. doi:10.1007/s00248-018-1239-4. https://www.osti.gov/servlets/purl/1558043.
@article{osti_1558043,
title = {Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea},
author = {Albright, Michaeline B. N. and Timalsina, Bibek and Martiny, Jennifer B. H. and Dunbar, John},
abstractNote = {Despite the explosion of metagenomic sequencing data, using -omics data to indicate 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 normally used to represent the prevalence of a biogeochemical reaction. This method 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. Moreover, 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.},
doi = {10.1007/s00248-018-1239-4},
journal = {Microbial Ecology},
number = 3,
volume = 77,
place = {United States},
year = {2018},
month = {8}
}

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