Abstract
Rhizosphere microbiomes play an essential role in promoting plant growth and health. Although host genotype is known to shape rhizosphere microbial communities, it remains unclear whether core microbial taxa can persist across genetically diverse hosts and contribute to plant performance. Here, we conducted a large-scale analysis of 1005 rhizosphere samples from 335 maize populations to investigate the effects of host genetic variation on rhizosphere microbiota. We observed significant genotype-dependent variation in both bacterial and fungal community diversity and composition. However, community assembly was predominantly governed by stochastic processes, suggesting an evolutionary conservation of rhizosphere microbiota across genotypes. Based on the hypothesis that core microbes may consistently associate with maize independent of genotypes, we identified a core bacterial taxon, ASV245 (Pseudomonas sp.), which was consistently enriched across all maize genotypes. The corresponding strain, designated as WY16, was isolated from maize roots and significantly promoted both stem and root growth by activating maize hormone signaling pathways. These findings highlight the persistence and functional roles of genotype-independent core microbes, deepening our understanding of plant-microbiome interactions and providing new insights for microbiome-based strategies in sustainable agriculture.
Data availability
Bacterial 16S rRNA and fungal ITS1 sequences are available at ScienceDB (https://doi.org/10.57760/sciencedb.29129). Additional data and code are available on GitHub (https://github.com/fxtranquility/R-code).
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Acknowledgements
The authors would like to thank Professor Xiaohong Yang (China Agricultural University) and her team for kindly providing the maize natural-variation population (335 different inbred lines). This work was supported by the Exploratory Research Project of Beijing Academy of Agriculture and Forestry Sciences (TSXM202525), and the Special Program for Creative Ability of Beijing Academy of Agriculture and Forestry Sciences,China (KJCX20251102,KJCX20230113).
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Junnan Fang, Guoliang Wang, Chun Zhang, Guiming Liu, Xuming Wang, and Tianlei Qiu designed the study. Junnan Fang, Guoliang Wang, Chun Zhang, Jiacan Xu, Yuqian Gao, and Yajie Guo conducted the experiments. Junnan Fang performed statistical analyses and wrote the manuscript, and all authors contributed to revisions.
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Fang, J., Wang, G., Zhang, C. et al. Conserved genotype-independent rhizobacteria promote maize growth.
npj Biofilms Microbiomes (2025). https://doi.org/10.1038/s41522-025-00895-4
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DOI: https://doi.org/10.1038/s41522-025-00895-4
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