J Plant Ecol ›› 2026, Vol. 19 ›› Issue (4): rtag016.DOI: 10.1093/jpe/rtag016

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Exogenous Bacillus promotes enrichment of native microbes to assemble synthetic communities for plant growth promotion

Hui Nie1, Jingyi Zeng1, Qianqian Liu1, Xiongfei Zhang1, Lianhao Sun1, Jie Lin1, Chong Li2, Nan Wang3, Haidong Li1, Xin Liu1, * and Jinchi Zhang1, *   

  1. 1.Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China;
    2.Department of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2H1, Canada;
    3.Center for Ecological Civilization Construction, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
    *Corresponding authors.E-mails:liuxinswc@njfu.edu.cn(X.L.);zhangjc8811@gmail.com (J.Z.)
  • Received:2025-10-03 Revised:2025-11-24 Accepted:2026-01-12 Online:2026-01-23 Published:2026-08-01
  • Supported by:
    We thank everyone who contributed to the collection of the experimental data, especially Ms. Wensui Li and Mr. Lianhao Sun. We also thank the editor and reviewers, whose comments greatly improved the quality of this manuscript.

外源芽孢杆菌促进本土微生物富集并组装合成群落进而促进植物生长

Abstract: Plants recruit beneficial microbes to support growth and defense, but how exogenous inoculants interact with native microbiomes to influence plant performance remains unclear. We found that Bacillus thuringiensis NL-11 promoted the enrichment of indigenous taxa, including 45 amplicon sequence variants (ASVs). From a nonredundant isolate collection, we linked enriched ASVs to isolates (based on 16S rRNA identity) to build a 12-member SynCom (SynCom12), and adding B. thuringiensis NL-11 produced BSynCom12 to test the growth effects. Neither SynCom12 nor BSynCom12 exceeded the growth promotion of B. thuringiensis NL-11 alone. Therefore, we designed a simplified synthetic community, SynComC, which consisted of two strains (NJ158 and NJ63) with strong rhizosphere colonization capabilities and high abundance with the help of NL-11, and whose growth-promoting ability exceeded that of SynCom12 and BSynCom12. Moreover, coinoculation of B. thuringiensis NL-11 with SynComC yielded the highest stability in bacterial co-occurrence networks. Community assembly analyses further showed that NL-11 alone increased deterministic assembly, whereas NL-11/SynComC coinoculation restored stochastic dominance. Metagenomics revealed an enrichment of plant hormone signaling, plant-pathogen interactions, MAPK signaling and isoflavonoid biosynthesis in the inoculated groups (NL-11, SynComC and BSynComC). Our SynCom assembly strategy, guided by colonization capacity and coinoculation with native partners, effectively promotes plant growth and informs rational design of synthetic communities.

Exogenous inoculant Bacillus thuringiensis NL-11 enriches specific indigenous rhizosphere taxa and enables the rational assembly of synthetic communities. A colonization-guided, simplified two-member consortium (SynComC; NJ158 and NJ63), especially when co-inoculated with NL-11, delivers superior plant growth promotion and higher co-occurrence network stability, highlighting an effective “exogenous strain + native partners” design principle.

Key words: microbial inoculant, synthetic community, community simplification, rhizospheric microbial community, multi-omics

摘要:
植物可招募有益微生物以支持生长与防御,但目前学术界仍不清楚外源接种剂如何与本土微生物组互作,并影响植物生长。本研究发现,苏云金芽孢杆菌(Bacillus thuringiensis NL-11)可促进本土类群富集,共包括45个扩增子序列变体(ASVs)。基于非冗余分离菌株库,本研究依据16S rRNA序列一致性将富集ASVs与分离菌株关联,构建了由12个成员组成的合成群落SynCom12;进一步加入B. thuringiensis NL-11形成BSynCom12,用于检验促生效应。然而,SynCom12与BSynCom12的促生效果均未超过NL-11单独接种。基于此,我们设计了简化合成群落SynComC,该群落由两株具备较强根际定殖能力、并在NL-11协助下可维持较高丰度的菌株(NJ158与NJ63)组成,其促生能力优于SynCom12与BSynCom12。并且,B. thuringiensis NL-11与SynComC协同接种可使细菌共现网络表现出最高稳定性。群落组装分析表明,NL-11单独接种增强了确定性组装过程,而NL-11/SynComC协同接种则恢复了随机过程的主导地位。宏基因组结果显示,接种处理(NL-11、SynComC与BSynComC)富集了与植物激素信号传导、植物—病原互作、MAPK信号通路以及异黄酮生物合成相关的功能。综上所述,基于定殖能力并结合与本土伙伴协同接种的SynCom构建策略能够有效促进植物生长,并为合成群落的理性设计提供依据。

关键词: 微生物接种剂, 合成群落, 群落简化, 根际微生物群落, 多组学