Ecology-guided Bacillus SynCom from a rice–duckweed core reveals division of labor for concurrent growth promotion and sheath blight suppression

TL;DR

This study creates a synthetic bacterial community from a rice-duckweed ecosystem that boosts plant growth and fights disease, showing how ecological principles can guide effective microbial consortia.

Contribution

A top-down, ecology-guided method for assembling a multifunctional Bacillus synthetic community with greenhouse-proven efficacy and mechanistic clarity.

Findings

The SynCom reduced sheath blight by 70% and promoted rice growth without phytotoxicity.

Individual strains specialized in distinct functions like auxin production and antimicrobial compound synthesis.

The community showed resilience to member loss due to functional redundancy and complementarity.

Abstract

Ecologically derived synthetic communities can provide robust plant benefits, yet generalizable rules for assembling multifunctional consortia remain limited. We hypothesized that a “top-down” community assembled from an ecological core would yield complementary functions and resilience superior to reductionist mixes.

We distilled an eight-member, Bacillus-dominated synthetic community (hereafter referred to as SynCom) from a rice–duckweed agroecosystem by targeting taxa consistently shared across soil, root and shoot niches. Under greenhouse conditions, the SynCom concurrently promoted rice growth and suppressed sheath blight caused by Rhizoctonia solani, reducing the final disease index by 70% without detectable phytotoxicity. Leave-one-member perturbations (−Dx), combined with untargeted LC–MS profiling and qRT-PCR of biosynthetic genes, revealed a division-of-labor architecture: individual strains specialized in auxin production, siderophore-linked iron mobilization, or lipopeptide/polyketide-based antagonism. These complementary yet partially redundant contributions mapped members, metabolite pools, plant outcomes and rendered community performance resilient to single-member loss. Across −Dx contrasts, the complete SynCom uniquely recovered the full suite of plant-growth metabolites (e.g., indole-3-acetic acid, acetoin/2,3-butanediol) together with antimicrobial chemistries (e.g., surfactin, bacillomycin, fengycin, difficidin). We formalize an assembly heuristic, ecological core, complementary functions, redundancy check, that links ecological origin to predictable, multi-trait performance.

A top-down, ecology-guided route can generate a multifunction SynCom with demonstrated greenhouse efficacy and mechanistic transparency. By coupling-member perturbations with multi-omics readouts, our study provides a transferable rule for building resilient plant-associated consortia and a tractable framework for future genetic and in-plant chemical confirmations.

Video Abstract

Video Abstract

The online version contains supplementary material available at 10.1186/s40168-026-02360-6.

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