Diverse banana endophytes reveal potential genotype-driven community structure affected by domestication

Plant endophytic microbiomes play critical roles in plant health, productivity, and stress tolerance, however, their relationship with host genotype remains poorly understood. This study focused on endophytic microbiomes of six banana (Musa spp.) cultivars grown under shared environmental conditions to determine how genotype influences microbial diversity and structure. We used deep amplicon sequencing to investigate the endophytic microbiomes from above- and below-ground tissues of wild diploid cultivars Musa balbisiana, M. balbisiana "Thai Black", and M. textilis, and domesticated triploid cultivars Dwarf Cavendish, Williams Hybrid, and hybrid FHIA-25, grown in sympatry. Across all samples, dominant genera included Pseudomonas, Acinetobacter, Enterobacter, Devosia, and Rhizobium, while 27.4% of ASVs were unclassified. Although many core taxa were shared, each cultivar and tissue harbored distinct low-abundance microbial taxa. Beta diversity analyses revealed that banana cultivar explained a small but significant proportion of community variation (Bray-Curtis R ² = 2.7%, p = 0.002; Weighted UniFrac R ² = 2.9%, p = 0.005), whereas tissue type and domestication contributed less to overall variation. PICRUSt2 predicted functional differences among endophytic communities across banana cultivars, with 49 pathways differing between wild and domesticated plants, including enrichment of lipid metabolism, biotin biosynthesis, and aromatic compound degradation in domesticated cultivars. However, because domestication status and ploidy differed among the selected cultivars, these effects could not be fully separated in the current study. Together, these results indicate that banana genotype influences endophytic microbiome composition and predicted function, although host genotype accounted for only a modest proportion of the observed variation, highlighting the importance of additional ecological and environmental factors in shaping plant-associated microbial communities.