Divergent sucker-corm endophytic microbiota underpins the progressive decline of Fusarium-wilt incidence in resistant bananas across ratoon cycles

Fusarium wilt of banana, caused by <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> (Foc), threatens global banana production. Resistant cultivars exhibit reduced disease incidence after successive ratoon cycles, but the underlying micro-ecological mechanisms remain unclear. This study represents the first longitudinal analysis of corm endophytic microbiota across ratoon cycles in banana, revealing temporal dynamics that underpin progressive disease resistance. A three-cycle field trial with three biological replicates per cultivar per cycle was conducted in a Foc-infested orchard in Guangxi, China. Corm tissues were sampled from resistant ('Bao Dao Jiao' and 'Gui Jiao 9') and susceptible 'Williams B6' bananas (<i>n</i> = 3 biological replicates per group) at plant crop (cycle 1) and third ratoon (cycle 3). 16S rRNA amplicons were sequenced via Illumina NovaSeq. Alpha- and beta-diversity, taxonomic composition, and predicted functions (PICRUSt2) were analyzed. Resistant cultivars maintained significantly higher Chao1 and Shannon indices than the susceptible cultivar, with divergence intensified across ratoon cycles (<i>p</i> < 0.05). Community structure was shaped primarily by cultivar rather than maternal health status. Resistant genotypes enriched <i>Proteobacteria</i> and <i>Actinobacteria</i>, alongside beneficial genera (<i>Halomonas</i>, <i>Nesterenkonia</i>, <i>Aliihoeflea</i>). Functional predictions revealed enrichment in carbohydrate metabolism, membrane transport, and xenobiotic degradation pathways in resistant cultivars. Disease incidence declined significantly from 34-39% (cycle 1) to 4-8% (cycle 3) in resistant cultivars, whereas susceptible cultivars remained at 44-59%. Resistant bananas continuously recruit beneficial endophytes during ratooning, assembling a stable microbiome that reinforces Fusarium wilt resistance. These findings provide microbial targets for breeding and biocontrol strategies.