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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #426518
Research Project: Enhancing Crop Resilience to Biotic and Abiotic Stress Through Understanding the Microbiome and Immune Signaling Mechanisms

Location: Plant Gene Expression Center

Title: Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth

Author
item FONSECA-GARCIA, CITLALI - University Of California Berkeley
item PETTINGA, DEAN - University Of California Berkeley
item CADDELL, DANIEL - University Of California Berkeley
item PLOEMACHER, HANNAH - University Of California Berkeley
item LOUIE, KATHERINE - Joint Genome Institute
item BOWEN, BENJAMIN - Joint Genome Institute
item PARK, JOELLE - University Of California Berkeley
item SANCHEZ, JESUS - University Of California Berkeley
item ZIMIC-SHEEN, ALEN - University Of California Berkeley
item TRAXLER, MATTHEW - University Of California Berkeley
item NORTHEN, TRENT - Joint Genome Institute
item Coleman-Derr, Devin

Submitted to: The ISME Journal: Multidisciplinary Journal of Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/12/2025
Publication Date: 11/26/2025
Citation: Fonseca-Garcia, C., Pettinga, D., Caddell, D., Ploemacher, H., Louie, K., Bowen, B.P., Park, J., Sanchez, J., Zimic-Sheen, A., Traxler, M.F., Northen, T.R., Coleman-Derr, D.A. 2025. Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 23(11). Article e3003526. https://doi.org/10.1371/journal.pbio.3003526.
DOI: https://doi.org/10.1371/journal.pbio.3003526

Interpretive Summary: The crop microbiome carries out several ecological functions including providing the host access to nutrients, protection from pathogens, and plant growth promotion through specialized metabolites. Over the last several years research in a wide variety of crops has shown that during periods of drought crops rewire their microbiomes, recruiting much larger fractions of the bacterial genus Streptomyces to live in their roots. To date, it is unclear if this new relationship is universally conserved across all individual strains of Streptomyces, or if this increase is beneficial to crop fitness and productivity. Here we investigate whether all Streptomyces behave similarly in terms of drought enrichment and measure the extent to which these diverse Streptomyces are valuable for crop protection and yield enhancement.

Technical Abstract: The genus Streptomyces is consistently enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment of Streptomyces in field-grown sorghum roots and identified multiple closely related but distinct ASVs with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for in-depth phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that drought enrichment (DE) scores, determined through mono-association experiments in sterile sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified gene clusters involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces enrichment under drought is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, enrichment in the root microbiome does not predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe–host–environment interactions under abiotic stress.