Resistant and Susceptible Lima Bean Genotypes Differentially Recruit Rhizosphere and Phyllosphere Bacteria in Response to the Fungal Pathogen Colletotrichum truncatum

Plant‐associated microbiomes play a pivotal role in host health and disease resistance. However, resistant plants can recruit distinct and more interactive bacterial communities, and these genotype‐driven microbiome changes can enhance resistance to plant pathogens. In this study, we assessed the bacterial communities in the rhizosphere and phyllosphere of two lima bean genotypes contrasting in resistance to anthracnose, under inoculated and non‐inoculated conditions with Colletotrichum truncatum . The V4 region of the 16S rRNA gene was amplified for rhizosphere communities, while the V5–V7 region was amplified for endophytic phyllosphere communities. Bacterial community structure varied significantly among genotypes and C. truncatum inoculation within each compartment. Principal coordinate analysis showed significant shifts in the resistant genotype after inoculation within both rhizosphere and phyllosphere communities. In the rhizosphere, the susceptible genotype showed higher bacterial diversity than the resistant genotype when inoculated. Genus‐level composition formed distinct clusters, with resistant genotypes showing greater exclusivity of taxa between C. truncatum ‐inoculated and non‐inoculated plants. Network analysis revealed compartment‐specific responses, with the phyllosphere of inoculated resistant plants showing higher connectivity and predominantly positive interactions, indicating a more cooperative and structured bacterial community under pathogen infection. Overall, our findings demonstrate that resistant genotypes restructure their microbiomes in response to pathogen infection, enriching beneficial taxa and forming more interconnected, cooperative bacterial networks across compartments.