Background 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. Results 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. Conclusions 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. <MediaObject ID="MOESM5"> <VideoObject FileRef="MediaObjects/40168_2026_2360_MOESM5_ESM.mp4" VideoID="CsSnFs9bJm4u8wtG-CzUEk"> <Caption Language="En" xml:lang="en"> <CaptionContent> Video Abstract </CaptionContent> </Caption> </VideoObject> </MediaObject>

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

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2026年2月25日

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Yingjie Song,
Qingxia Chen,
Shasha Luo,
Shuang Li,
Ruimin He,
Xinyan Yang,
Dachun Shen,
Chunlin Long,
Sizhao Liu,
Guohua Zhong,
Yuxing An,
Yinglin Lu

摘要

Background

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.

Results

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.

Conclusions

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