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Title: Genome-centric view of carbon processing in thawing permafrost

Abstract

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Lastly, our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1];  [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1];  [1]; ORCiD logo [4]; ORCiD logo [5];  [5]; ORCiD logo [6]; ORCiD logo [6];  [7];  [7];  [5];  [8]; ORCiD logo [9]; ORCiD logo [3]; ORCiD logo [1]
  1. Univ. of Queensland, Brisbane, QLD (Australia)
  2. The Ohio State Univ., Columbus, OH (United States); Univ. of California, Davis, CA (United States)
  3. The Ohio State Univ., Columbus, OH (United States)
  4. Rochester Institute of Technology, Rochester, NY (United States)
  5. Florida State Univ., Tallahassee, FL (United States)
  6. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  7. Univ. of New Hampshire, Durham, NH (United States)
  8. Stockholm Univ., Stockholm (Sweden)
  9. Univ. of Arizona, Tucson, AZ (United States)
Publication Date:
Research Org.:
Univ. of Queensland, Brisbane, QLD (Australia). Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1506092
Alternate Identifier(s):
OSTI ID: 1481644
Grant/Contract Number:  
SC0010580; SC0016440
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 560; Journal Issue: 7716; Related Information: Raw DNA and RNA sequencing data: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA386568; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; Permafrost; Metagenomics; Bacteria; Archaea

Citation Formats

Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I., and Tyson, Gene W. Genome-centric view of carbon processing in thawing permafrost. United States: N. p., 2018. Web. doi:10.1038/s41586-018-0338-1.
Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I., & Tyson, Gene W. Genome-centric view of carbon processing in thawing permafrost. United States. doi:10.1038/s41586-018-0338-1.
Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I., and Tyson, Gene W. Mon . "Genome-centric view of carbon processing in thawing permafrost". United States. doi:10.1038/s41586-018-0338-1. https://www.osti.gov/servlets/purl/1506092.
@article{osti_1506092,
title = {Genome-centric view of carbon processing in thawing permafrost},
author = {Woodcroft, Ben J. and Singleton, Caitlin M. and Boyd, Joel A. and Evans, Paul N. and Emerson, Joanne B. and Zayed, Ahmed A. F. and Hoelzle, Robert D. and Lamberton, Timothy O. and McCalley, Carmody K. and Hodgkins, Suzanne B. and Wilson, Rachel M. and Purvine, Samuel O. and Nicora, Carrie D. and Li, Changsheng and Frolking, Steve and Chanton, Jeffrey P. and Crill, Patrick M. and Saleska, Scott R. and Rich, Virginia I. and Tyson, Gene W.},
abstractNote = {As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Lastly, our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.},
doi = {10.1038/s41586-018-0338-1},
journal = {Nature (London)},
number = 7716,
volume = 560,
place = {United States},
year = {2018},
month = {7}
}

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Cited by: 27 works
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