Narrow-spectrum resource-utilizing bacteria drive the stability of synthetic communities through enhancing metabolic interactions

Wei Wang, Yanwei Xia, Panpan Zhang, Mengqing Zhu, Shiyi Huang, Xinli Sun, Zhihui Xu, Nan Zhang, Weibing Xun, Qirong Shen, Youzhi Miao () and Ruifu Zhang
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Wei Wang: Nanjing Agricultural University
Yanwei Xia: Nanjing Agricultural University
Panpan Zhang: Nanjing Agricultural University
Mengqing Zhu: Nanjing Agricultural University
Shiyi Huang: Nanjing Agricultural University
Xinli Sun: Nanjing Agricultural University
Zhihui Xu: Nanjing Agricultural University
Nan Zhang: Nanjing Agricultural University
Weibing Xun: Nanjing Agricultural University
Qirong Shen: Nanjing Agricultural University
Youzhi Miao: Nanjing Agricultural University
Ruifu Zhang: Nanjing Agricultural University

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract The importance of synthetic microbial communities in agriculture is increasingly recognized, yet methods for constructing targeted communities using existing microbial resources remain limited. Here, six plant-beneficial bacterial strains with distinct functions and rhizosphere resource utilization profiles are selected to construct stable, multifunctional communities for plant growth promotion. Metabolic modeling reveals that narrower resource utilization correlates with increased metabolic interaction potential and reduced metabolic resource overlap, contributing to greater community stability. Integrated analyses further consistently confirm the central roles of narrow-spectrum resource-utilizing strains, Cellulosimicrobium cellulans E and Pseudomonas stutzeri G, which form metabolic interaction networks via secretion of asparagine, vitamin B12, isoleucine, and their precursors or derivatives. Two synthetic communities, SynCom4 and SynCom5, have high stability in the tomato rhizosphere and increase plant dry weight by over 80%. Our study elucidates the relationship between resource utilization width and community stability, providing a rational strategy for designing stable, multifunctional microbial communities for specific habitats.

Date: 2025
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DOI: 10.1038/s41467-025-61432-7

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