Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Tom, Lauren M.; Aulitto, Martina; Wu, Yu-Wei; Deng, Kai; Gao, Yu; Xiao, Naijia; Rodriguez, Beatrice Garcia; Louime, Clifford; Northen, Trent R.; Eudes, Aymerick; Mortimer, Jenny C.; Adams, Paul D.; Scheller, Henrik V.; Simmons, Blake A.; Ceja-Navarro, Javier A.; Singer, Steven W.

doi:10.1186/s40168-022-01377-x

Title: Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Journal Article · Tue Oct 25 00:00:00 EDT 2022 · Microbiome

DOI:https://doi.org/10.1186/s40168-022-01377-x· OSTI ID:1894529

Tom, Lauren M.; Aulitto, Martina; Wu, Yu-Wei; Deng, Kai; Gao, Yu; Xiao, Naijia; Rodriguez, Beatrice Garcia; Louime, Clifford; Northen, Trent R.; Eudes, Aymerick; Mortimer, Jenny C.; Adams, Paul D.; Scheller, Henrik V.; Simmons, Blake A.; Ceja-Navarro, Javier A.; Singer, Steven W.

Abstract Background Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities. Results To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum ( Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea , Filomicrobium , and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes. Conclusions The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1894529

Alternate ID(s):: OSTI ID: 1958750

Journal Information:: Microbiome, Journal Name: Microbiome Vol. 10 Journal Issue: 1; ISSN 2049-2618

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Title: Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

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