Insect herbivory reshapes rhizosphere bacterial and fungal networks in a stage-specific manner

Plants interact with diverse above- and belowground biota, with defense phenotypes shaped by these multiorganismal networks, particularly in the rhizosphere. We tested how insect herbivory reorganizes rhizosphere microbiomes across plant phenology and how it differs from mechanical damage. In Arabidopsis thaliana exposed to feeding by the generalist caterpillar Spodoptera frugiperda at pre-flowering, flowering, and post-flowering stages, we profiled rhizosphere communities and compared them to mechanically wounded plants. Bacterial alpha diversity was driven largely by phenology, whereas fungal alpha diversity was more sensitive to injury type. PCA revealed clear, treatment-specific separations within each stage, indicating compositional remodeling beyond diversity shifts. Herbivory increased Streptomyces, Sphingomonas, and Acinetobacter, while mechanical injury produced distinct, stage-dependent bacterial signatures, including Dyella and Pseudolabrys. Fungal responses were stage contingent: fermentative yeasts before flowering and saprotrophic or opportunistic genera after flowering. Co-occurrence networks under both injuries exhibited more positive correlations, with herbivory enhancing bacteria-fungi connectivity. Functional inference showed strong, stage-dependent restructuring: symbiotroph and endophyte guilds clustered at flowering, and post-flowering communities were enriched for hydrogenotrophy, nitrogen fixation, and pathogen/pathotroph functions. Herbivory further elevated inferred chemotrophy, fermentation, and nitrate reduction, whereas mechanical injury reduced chemotrophy, saprotroph abundance, and nitrate-reducing functions. Together, these results indicate that insect herbivory is a biologically distinct disturbance that reorganizes rhizosphere communities and interaction networks in a phenology-dependent manner, underscoring aboveground-belowground linkages with implications for crop resistance and productivity.

Plants rely on soil-dwelling microbes around their roots to grow and defend themselves. Yet we know little about how insects reshape root‑zone communities as plants develop, or whether this differs from simple wounding. We studied Arabidopsis thaliana fed on by the generalist caterpillar Spodoptera frugiperda before, during, and after flowering and compared these plants to those with mechanical damage. We found that insect feeding, not just injury, acts as a distinct disturbance that reorganizes the root‑zone microbial community in stage‑specific ways. It altered which microbes were present and how they interacted, strengthening links between bacteria and fungi and shifting likely nutrient and defense functions. These results reveal strong connections between aboveground attack and belowground life, with practical implications for breeding and managing crops for resilience and productivity.