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Research Project: Enhancing Crop Resilience to Biotic and Abiotic Stress Through Understanding the Microbiome and Immune Signaling Mechanisms

Location: Plant Gene Expression Center

Title: SRC2

Author
item PETTINGA, DEAN - University Of California Berkeley
item FONSEC-GARCIA, CITLALI - University Of California Berkeley
item KRAUSSE, GENEVEIVE - University Of Arizona
item PLOEMACHER, HANNAH - University Of California Berkeley
item WHEELER, TRAVIS - University Of Arizona
item CLENDINEN, CHEAVIEN - Pacific Northwest National Laboratory
item HANDUKAMBARU, PUBUDU - Pacific Northwest National Laboratory
item EGBERT, ROBERT - Pacific Northwest National Laboratory
item Coleman-Derr, Devin

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/22/2026
Publication Date: N/A
Citation: N/A

Interpretive Summary: The microbial communities associated with roots—the rhizosphere and endosphere—are highly diverse and functionally complex, representing a 'black box' of interactions that govern host health and nutrient access. While large-scale metagenomic studies have established strong correlations between microbial diversity and plant fitness, the sheer complexity of natural microbiomes makes identifying causal relationships a significant challenge. Synthetic Microbial Communities (SynComs) are emerging as essential tools in microbiome sciences because they enable researchers to reduce this complexity to a defined, tractable system. By selecting and combining specific, culturable isolates, SynComs allow for controlled ecological experiments to test hypotheses about inter-species interactions, competition, resource sharing, and the molecular mechanisms that facilitate beneficial host-microbe relationships. Thus, SynComs transition the research field from broad ecological observation to precise, hypothesis-driven experimental systems, which is critical for deciphering the fundamental rules of microbiome assembly and function.

Technical Abstract: The inherent complexity and functional redundancy of natural plant microbiomes presents a formidable barrier to understand the manifold biological interactions therein. Synthetic microbial communities (SynComs) offer a tractable experimental system to decouple these complex interactions. We designed 4 distinct, reduced complexity SynCom variants and assessed their capacities for colonization, stability, and plant growth promotion. To understand the impact on plant performance of our highest-performing SynCom variant, we characterized the host’s longitudinal transcriptional response to SynCom inoculation and validated the results with metabolomics analysis.The top performing SynCom stably colonized sorghum roots and rhizospheres, elicited strong plant growth promotion, and induced dynamic spatiotemporal gene transcription in sorghum roots and shoots defined by enhanced flavonoid production and altered regulation of hormone modulation machinery.The resulting reduced-complexity SynCom is highly stable, soil-independent, preserves plant growth promotion of the original community and provides a proof of concept for the rational design of next-generation microbial products for sustainable agriculture.