Defined synthetic microbial communities colonize and benefit field-grown sorghum

Fonseca-García, Citlali; Pettinga, Dean; Wilson, Andrew; Elmore, Joshua R.; McClure, Ryan; Atim, Jackie; Pedraza, Julie; Hutmacher, Robert; Turumtay, Halbay; Tian, Yang; Eudes, Aymerick; Scheller, Henrik V.; Egbert, Robert G.; Coleman-Derr, Devin

doi:10.1093/ismejo/wrae126

Defined synthetic microbial communities colonize and benefit field-grown sorghum

Journal Article · Wed Jul 10 00:00:00 EDT 2024 · The ISME Journal

DOI:https://doi.org/10.1093/ismejo/wrae126· OSTI ID:2500269

Fonseca-García, Citlali ^[1]; Pettinga, Dean ^[1]; Wilson, Andrew ^[2]; Elmore, Joshua R. ^[2]; McClure, Ryan ^[2]; Atim, Jackie ^[3]; Pedraza, Julie ^[3]; Hutmacher, Robert ^[4]; Turumtay, Halbay ^[5]; Tian, Yang ^[6]; Eudes, Aymerick ^[6]; Scheller, Henrik V. ^[7]; Egbert, Robert G. ^[2]; Coleman-Derr, Devin ^[1]

USDA‐ARS, Albany, CA (United States). Plant Gene Expression Center; University of California, Berkeley, CA (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
University of California, Parlier, CA (United States)
West Side Research and Extension Center, Five Points, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division; Karadeniz Technical University, Trabzon (Turkey)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division
University of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division

The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced microbes must survive, and the absence of adaptation to the specific metabolic and environmental demands of the rhizosphere. Here, in this study, we engineered a synthetic rhizosphere community (SRC1) with the anticipation that it would exhibit a selective advantage in colonizing the host Sorghum bicolor, thereby potentially fostering its growth. SRC1 was assembled from bacterial isolates identified either for their potential role in community cohesion through network analysis or for their ability to benefit from host-specific exudate compounds. The growth performance of SRC1 was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field. Our findings reveal that SRC1 cohesion is most robust when cultivated in the presence of the plant host under laboratory conditions, with lineages being lost from the community when grown either in vitro or in a native field setting. We establish that SRC1 effectively promotes the growth of both above- and below-ground plant phenotypes in both laboratory and native field contexts. Furthermore, in laboratory conditions, these growth enhancements correlate with the transcriptional dampening of lignin biosynthesis in the host. Collectively, these results underscore the potential utility of synthetic microbial communities for modulating crop performance in controlled and native environments alike.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); US Dept. of Agriculture (USDA)

Grant/Contract Number:: AC05-76RL01830; AC02-05CH11231

OSTI ID:: 2500269

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 1 Vol. 18; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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