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:
-
[1];
[1]
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mississippi State Univ., Starkville, MS (United States)
- 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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