Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling
Abstract
Soil microorganisms determine the fate of soil organic matter (SOM), and their activities compose a major component of the global carbon (C) cycle. For this work, we employed a multisubstrate, DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interacted within soil. We identified and tracked 1,286 bacterial taxa that assimilated 13C in an agricultural soil over a period of 48 d. Overall 13C-assimilation dynamics of bacterial taxa, defined by the source and timing of the 13C they assimilated, exhibited low phylogenetic conservation. We identified bacterial guilds composed of taxa that had similar 13C assimilation dynamics. We show that C-source bioavailability explained significant variation in both C mineralization dynamics and guild structure, and that the growth dynamics of bacterial guilds differed significantly in response to C addition. We also demonstrate that the guild structure explains significant variation in the biogeographical distribution of bacteria at continental and global scales. These results suggest that an understanding of in situ growth dynamics is essential for understanding microbial contributions to soil C cycling.more »
- Authors:
-
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853,
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853,, Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany,
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853,, Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104
- Publication Date:
- Research Org.:
- Cornell Univ., Ithaca, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)
- OSTI Identifier:
- 1831533
- Alternate Identifier(s):
- OSTI ID: 1863898; OSTI ID: 2228485; OSTI ID: 2228924
- Grant/Contract Number:
- SC0004486; SC0010558; SC0016364
- Resource Type:
- Published Article
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 118 Journal Issue: 47; Journal ID: ISSN 0027-8424
- Publisher:
- Proceedings of the National Academy of Sciences
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; DNA-SIP; bacterial; soil; carbon cycling; ecology
Citation Formats
Barnett, Samuel E., Youngblut, Nicholas D., Koechli, Chantal N., and Buckley, Daniel H. Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. United States: N. p., 2021.
Web. doi:10.1073/pnas.2115292118.
Barnett, Samuel E., Youngblut, Nicholas D., Koechli, Chantal N., & Buckley, Daniel H. Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. United States. https://doi.org/10.1073/pnas.2115292118
Barnett, Samuel E., Youngblut, Nicholas D., Koechli, Chantal N., and Buckley, Daniel H. Fri .
"Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling". United States. https://doi.org/10.1073/pnas.2115292118.
@article{osti_1831533,
title = {Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling},
author = {Barnett, Samuel E. and Youngblut, Nicholas D. and Koechli, Chantal N. and Buckley, Daniel H.},
abstractNote = {Soil microorganisms determine the fate of soil organic matter (SOM), and their activities compose a major component of the global carbon (C) cycle. For this work, we employed a multisubstrate, DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interacted within soil. We identified and tracked 1,286 bacterial taxa that assimilated 13C in an agricultural soil over a period of 48 d. Overall 13C-assimilation dynamics of bacterial taxa, defined by the source and timing of the 13C they assimilated, exhibited low phylogenetic conservation. We identified bacterial guilds composed of taxa that had similar 13C assimilation dynamics. We show that C-source bioavailability explained significant variation in both C mineralization dynamics and guild structure, and that the growth dynamics of bacterial guilds differed significantly in response to C addition. We also demonstrate that the guild structure explains significant variation in the biogeographical distribution of bacteria at continental and global scales. These results suggest that an understanding of in situ growth dynamics is essential for understanding microbial contributions to soil C cycling. We interpret these findings in the context of bacterial life history strategies and their relationship to terrestrial C cycling.},
doi = {10.1073/pnas.2115292118},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 47,
volume = 118,
place = {United States},
year = {Fri Nov 19 00:00:00 EST 2021},
month = {Fri Nov 19 00:00:00 EST 2021}
}
https://doi.org/10.1073/pnas.2115292118
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