Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

Seitz, Valerie A.; McGivern, Bridget B.; Daly, Rebecca A.; Chaparro, Jacqueline M.; Borton, Mikayla A.; Sheflin, Amy M.; Kresovich, Stephen; Shields, Lindsay; Schipanski, Meagan E.; Wrighton, Kelly C.; Prenni, Jessica E.

doi:10.1128/aem.00226-22

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

Journal Article · Tue May 10 00:00:00 EDT 2022 · Applied and Environmental Microbiology

DOI:https://doi.org/10.1128/aem.00226-22· OSTI ID:1980752

^[1]; ^[2]; ^[2]; ^[2]; Borton, Mikayla A. ^[2]; Sheflin, Amy M. ^[2]; ^[3]; Shields, Lindsay ^[3]; Schipanski, Meagan E. ^[2]; ^[2]; ^[2]

Colorado State Univ., Fort Collins, CO (United States); Colorado State Univ., Fort Collins, CO (United States)
Colorado State Univ., Fort Collins, CO (United States)
Clemson Univ., SC (United States)

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Nebraska, Lincoln, NE (United States); Colorado State Univ., Fort Collins, CO (United States); Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: SC0014395; SC0019746; AC02-05CH11231

OSTI ID:: 1980752

Journal Information:: Applied and Environmental Microbiology, Journal Name: Applied and Environmental Microbiology Journal Issue: 11 Vol. 88; ISSN 0099-2240

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Microbiology
exometabolomics
metagenomics
rhizodeposition
root exudates
sorghum

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

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References (71)

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