Ecological processes influencing bacterial community assembly across plant niche compartments

Abstract

Understanding microbial community assembly in plants is critical for advancing agricultural sustainability. This study investigated microbial diversity and community assembly mechanisms across six compartments of tomato plants: bulk soil, rhizosphere, root, stem, flower, and seed. Using 16S rRNA amplicon sequencing, we observed that microbial richness was highest in the bulk soil and rhizosphere, with significant reductions in internal plant tissues. Co-occurrence network analysis identified distinct microbial hubs in each compartment, such as Bacillus in the root and seed, highlighting critical interactions influencing microbial dynamics. Ecological process modeling revealed that deterministic processes, such as selection, dominated in below-ground compartments, whereas stochastic processes like drift were more influential in above-ground tissues, reflecting differences in niche specificity and ecological stability. Dispersal limitation emerged as a key driver in soil-associated compartments, structuring microbial diversity. These findings advance our understanding of the ecological mechanisms shaping plant microbiomes and suggest targeted microbiome management strategies to enhance crop health, productivity, and resilience. Future research integrating functional genomics, temporal dynamics, and environmental factors is necessary to uncover the broader implications of plant-associated microbiomes.

Keywords

community assembly / ecological process partitioning / neutral theory / niche theory / sink–source analysis

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2025 The Author(s). mLife published by John Wiley & Sons Australia, Ltd on behalf of Institute of Microbiology, Chinese Academy of Sciences.