ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microbial Symbioses
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1638130
Rhizosphere Domestication Enhances Root Colonization and Plant Growth Promotion Performance of Bacillus velezensis SQR9
Provisionally accepted
Zhengqi Wang1Yike Zhao1Jiahui Shao1Jingjing Wang1
Weibing Xun1Xinli Sun1
Zhihui Xu1
Youzhi Miao1
Guidong Huang2Derui Liu3Ruifu Ruifu Zhang1
Qirong SHEN1
Nan Zhang1*- 1Nanjing Agricultural University, Nanjing, China
- 2Foshan University, Foshan, China
- 3Hubei Yishizhuang Agricultural Technology Co., Ltd., Yichang 443100, China, Yichang, China
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The overuse of chemical fertilizers has caused severe soil degradation and environmental pollution, necessitating sustainable alternatives such as microbial fertilizers containing plant growth-promoting rhizobacteria (PGPR). However, application of laboratory-developed microbial inoculants usually reveals impaired performance, attributing to complicated field conditions including plant genotype, soil property, and interaction with indigenous microbiota. Currently, traditional microbial breeding methods such as random mutagenesis and genetic engineering, could not be so appropriate for screening agents with comprehensive phenotypes (e.g., root colonization and plant growth-promotion effects). In the present study, we developed a rhizosphere domestication strategy for PGPR strain Bacillus velezensis SQR9, involving 20 cycles (approximately 160 generations in total) of in situ transfer and evolution in pepper rhizosphere. Evolved strains achieved 1.5~2.9-fold greater root colonization than the ancestral strain. A three-step phenotypic screening of 45 evolved strains firstly identified 29 candidates showing enhanced indole-3-acetic acid (IAA) production, biofilm formation, or siderophore production compared to the ancestor. Subsequent screening picked 6 strains with superior plant growth-promoting effects than the ancestor in hydroponic system. Final pot experiment confirmed the evolved strain 9P41 as the optimal performer, of which the inoculated pepper plants exhibiting 11.4% greater height, 28.7% longer roots, 21.0% higher aboveground biomass, and 29.1% increased underground biomass compared to plants treated with the ancestor. Genomic resequencing identified adaptive mutations in mlnD, smc, and fhuC genes are potentially associated with phenotypic improvements of strain 9P41. This rhizosphere adapted domestication strategy
Keywords: Rhizosphere domestication, experimental evolution, PGPR, Microbial fertilizers, sustainable agriculture
Received: 30 May 2025; Accepted: 14 Jul 2025.
Copyright: © 2025 Wang, Zhao, Shao, Wang, Xun, Sun, Xu, Miao, Huang, Liu, Zhang, SHEN and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Nan Zhang, Nanjing Agricultural University, Nanjing, China
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