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Title: Understanding how microbiomes influence the systems they inhabit

Abstract

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods inmore » microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.« less

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1503544
Report Number(s):
PNNL-SA-136262
Journal ID: ISSN 2058-5276
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Nature Microbiology
Additional Journal Information:
Journal Volume: 3; Journal Issue: 9; Journal ID: ISSN 2058-5276
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English

Citation Formats

Hall, Ed K., Bernhardt, Emily S., Bier, Raven L., Bradford, Mark A., Boot, Claudia M., Cotner, James B., del Giorgio, Paul A., Evans, Sarah E., Graham, Emily B., Jones, Stuart E., Lennon, Jay T., Locey, Kenneth J., Nemergut, Diana, Osborne, Brooke B., Rocca, Jennifer D., Schimel, Joshua P., Waldrop, Mark P., and Wallenstein, Matthew D. Understanding how microbiomes influence the systems they inhabit. United States: N. p., 2018. Web. doi:10.1038/s41564-018-0201-z.
Hall, Ed K., Bernhardt, Emily S., Bier, Raven L., Bradford, Mark A., Boot, Claudia M., Cotner, James B., del Giorgio, Paul A., Evans, Sarah E., Graham, Emily B., Jones, Stuart E., Lennon, Jay T., Locey, Kenneth J., Nemergut, Diana, Osborne, Brooke B., Rocca, Jennifer D., Schimel, Joshua P., Waldrop, Mark P., & Wallenstein, Matthew D. Understanding how microbiomes influence the systems they inhabit. United States. doi:10.1038/s41564-018-0201-z.
Hall, Ed K., Bernhardt, Emily S., Bier, Raven L., Bradford, Mark A., Boot, Claudia M., Cotner, James B., del Giorgio, Paul A., Evans, Sarah E., Graham, Emily B., Jones, Stuart E., Lennon, Jay T., Locey, Kenneth J., Nemergut, Diana, Osborne, Brooke B., Rocca, Jennifer D., Schimel, Joshua P., Waldrop, Mark P., and Wallenstein, Matthew D. Fri . "Understanding how microbiomes influence the systems they inhabit". United States. doi:10.1038/s41564-018-0201-z.
@article{osti_1503544,
title = {Understanding how microbiomes influence the systems they inhabit},
author = {Hall, Ed K. and Bernhardt, Emily S. and Bier, Raven L. and Bradford, Mark A. and Boot, Claudia M. and Cotner, James B. and del Giorgio, Paul A. and Evans, Sarah E. and Graham, Emily B. and Jones, Stuart E. and Lennon, Jay T. and Locey, Kenneth J. and Nemergut, Diana and Osborne, Brooke B. and Rocca, Jennifer D. and Schimel, Joshua P. and Waldrop, Mark P. and Wallenstein, Matthew D.},
abstractNote = {Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.},
doi = {10.1038/s41564-018-0201-z},
journal = {Nature Microbiology},
issn = {2058-5276},
number = 9,
volume = 3,
place = {United States},
year = {2018},
month = {8}
}

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