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Title: Selection, Succession, and Stabilization of Soil Microbial Consortia

Abstract

Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures inmore » soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments. The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.« less

Authors:
ORCiD logo [1];  [2];  [2];  [2];  [3];  [2]; ORCiD logo [1]; ORCiD logo [2];  [2]; ORCiD logo [2]; ORCiD logo [4];  [5]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Washington State Univ., Pullman, WA (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Iowa State Univ., Ames, IA (United States)
  4. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Washington State Univ., Pullman, WA (United States); Arctic Univ. of Norway, Tromsø (Norway)
  5. Northern Arizona Univ., Flagstaff, AZ (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1530884
Alternate Identifier(s):
OSTI ID: 1577277
Report Number(s):
PNNL-SA-138630; PNNL-SA-146173
Journal ID: ISSN 2379-5077
Grant/Contract Number:  
AC0576RL01830; AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
mSystems
Additional Journal Information:
Journal Volume: 4; Journal Issue: 4; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; chitin; microbial consortia; microbiome; microbiome stability; model microbiome; N-acetylglucosamine; species volatility; succession; fungi; soil microbiology

Citation Formats

Zegeye, Elias K., Brislawn, Colin J., Farris, Yuliya, Fansler, Sarah J., Hofmockel, Kirsten S., Jansson, Janet K., Wright, Aaron T., Graham, Emily B., Naylor, Dan, McClure, Ryan S., Bernstein, Hans C., and Caporaso, J. Gregory. Selection, Succession, and Stabilization of Soil Microbial Consortia. United States: N. p., 2019. Web. doi:10.1128/mSystems.00055-19.
Zegeye, Elias K., Brislawn, Colin J., Farris, Yuliya, Fansler, Sarah J., Hofmockel, Kirsten S., Jansson, Janet K., Wright, Aaron T., Graham, Emily B., Naylor, Dan, McClure, Ryan S., Bernstein, Hans C., & Caporaso, J. Gregory. Selection, Succession, and Stabilization of Soil Microbial Consortia. United States. doi:10.1128/mSystems.00055-19.
Zegeye, Elias K., Brislawn, Colin J., Farris, Yuliya, Fansler, Sarah J., Hofmockel, Kirsten S., Jansson, Janet K., Wright, Aaron T., Graham, Emily B., Naylor, Dan, McClure, Ryan S., Bernstein, Hans C., and Caporaso, J. Gregory. Tue . "Selection, Succession, and Stabilization of Soil Microbial Consortia". United States. doi:10.1128/mSystems.00055-19. https://www.osti.gov/servlets/purl/1530884.
@article{osti_1530884,
title = {Selection, Succession, and Stabilization of Soil Microbial Consortia},
author = {Zegeye, Elias K. and Brislawn, Colin J. and Farris, Yuliya and Fansler, Sarah J. and Hofmockel, Kirsten S. and Jansson, Janet K. and Wright, Aaron T. and Graham, Emily B. and Naylor, Dan and McClure, Ryan S. and Bernstein, Hans C. and Caporaso, J. Gregory},
abstractNote = {Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments. The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.},
doi = {10.1128/mSystems.00055-19},
journal = {mSystems},
number = 4,
volume = 4,
place = {United States},
year = {2019},
month = {5}
}

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