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Title: Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

Abstract

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae,Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to usemore » carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.« less

Authors:
 [1];  [2];  [2];  [3];  [2];  [4];  [5];  [6];  [6];  [5];  [7];  [8];  [2];  [9]; ORCiD logo [2];  [10];  [11];  [12];  [13];  [4] more »;  [14];  [15];  [16];  [11];  [1] « less
  1. Univ. of Colorado, Boulder, CO (United States)
  2. Univ. of California, Riverside, CA (United States)
  3. Univ. of Kansas, Lawrence, KS (United States)
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  5. Univ. of California, Merced, CA (United States)
  6. Univ. of Arizona, Tucson, AZ (United States)
  7. Pennsylvania State Univ., University Park, PA (United States)
  8. Louisiana State Univ., Baton Rouge, LA (United States)
  9. Idaho State Univ., Pocatello, ID (United States)
  10. Univ. of Washington, Seattle, WA (United States)
  11. Univ. of Illinois at Urbana-Champaign, IL (United States)
  12. Argonne National Lab. (ANL), Argonne, IL (United States)
  13. Northwestern Univ., Evanston, IL (United States)
  14. Univ. of Pennsylvania, Philadelphia, PA (United States)
  15. Duke Univ., Durham, NC (United States)
  16. Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); National Science Foundation (NSF)
OSTI Identifier:
1599173
Alternate Identifier(s):
OSTI ID: 1646563
Report Number(s):
LLNL-JRNL-791438
Journal ID: ISSN 2150-7511; 156495
Grant/Contract Number:  
AC02-06CH11357; ICER-1541047; EF-1550920; AC52-07NA27344; SCW1478
Resource Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 10; Journal Issue: 5; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; critical zone; metagenomics; microbial ecology; microbial traits; soil microbiology

Citation Formats

Brewer, Tess E., Aronson, Emma L., Arogyaswamy, Keshav, Billings, Sharon A., Botthoff, Jon K., Campbell, Ashley N., Dove, Nicholas C., Fairbanks, Dawson, Gallery, Rachel E., Hart, Stephen C., Kaye, Jason, King, Gary, Logan, Geoffrey, Lohse, Kathleen A., Maltz, Mia R., Mayorga, Emilio, O’Neill, Caitlin, Owens, Sarah M., Packman, Aaron, Pett-Ridge, Jennifer, Plante, Alain F., Richter, Daniel D., Silver, Whendee L., Yang, Wendy H., and Fierer, Noah. Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons. United States: N. p., 2019. Web. https://doi.org/10.1128/mBio.01318-19.
Brewer, Tess E., Aronson, Emma L., Arogyaswamy, Keshav, Billings, Sharon A., Botthoff, Jon K., Campbell, Ashley N., Dove, Nicholas C., Fairbanks, Dawson, Gallery, Rachel E., Hart, Stephen C., Kaye, Jason, King, Gary, Logan, Geoffrey, Lohse, Kathleen A., Maltz, Mia R., Mayorga, Emilio, O’Neill, Caitlin, Owens, Sarah M., Packman, Aaron, Pett-Ridge, Jennifer, Plante, Alain F., Richter, Daniel D., Silver, Whendee L., Yang, Wendy H., & Fierer, Noah. Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons. United States. https://doi.org/10.1128/mBio.01318-19
Brewer, Tess E., Aronson, Emma L., Arogyaswamy, Keshav, Billings, Sharon A., Botthoff, Jon K., Campbell, Ashley N., Dove, Nicholas C., Fairbanks, Dawson, Gallery, Rachel E., Hart, Stephen C., Kaye, Jason, King, Gary, Logan, Geoffrey, Lohse, Kathleen A., Maltz, Mia R., Mayorga, Emilio, O’Neill, Caitlin, Owens, Sarah M., Packman, Aaron, Pett-Ridge, Jennifer, Plante, Alain F., Richter, Daniel D., Silver, Whendee L., Yang, Wendy H., and Fierer, Noah. Tue . "Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons". United States. https://doi.org/10.1128/mBio.01318-19. https://www.osti.gov/servlets/purl/1599173.
@article{osti_1599173,
title = {Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons},
author = {Brewer, Tess E. and Aronson, Emma L. and Arogyaswamy, Keshav and Billings, Sharon A. and Botthoff, Jon K. and Campbell, Ashley N. and Dove, Nicholas C. and Fairbanks, Dawson and Gallery, Rachel E. and Hart, Stephen C. and Kaye, Jason and King, Gary and Logan, Geoffrey and Lohse, Kathleen A. and Maltz, Mia R. and Mayorga, Emilio and O’Neill, Caitlin and Owens, Sarah M. and Packman, Aaron and Pett-Ridge, Jennifer and Plante, Alain F. and Richter, Daniel D. and Silver, Whendee L. and Yang, Wendy H. and Fierer, Noah},
abstractNote = {While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae,Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.},
doi = {10.1128/mBio.01318-19},
journal = {mBio (Online)},
number = 5,
volume = 10,
place = {United States},
year = {2019},
month = {10}
}

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