Comparative metabarcoding of the cassava rhizoplane bacteriome in wetland and upland fields reveals Bacillus-mediated suppression of stem and root rot

Abstract Cassava ( Manihot esculenta Crantz) stem and root rot caused by Fusarium falciforme is a major constraint to production. This study characterised rhizoplane bacteriome shifts across agroecosystems with contrasting disease incidence and identified microbial indicators and potential biocontrol agents using 16S rRNA gene amplicon sequencing, culture-dependent isolation, and functional assays. Microbial richness was highest in diseased wetlands (Chao1: 601.60 ± 10.37), followed by healthy wetlands (581.20 ± 14.39) and uplands (547.97 ± 5.74), while evenness remained comparable among ecosystems. Pseudomonadota dominated all sites (~ 64%). Bacteroidota, Planctomycetota, and Actinomycetota were enriched in healthy wetlands but declined in diseased sites, whereas Verrucomicrobiota increased in diseased roots (7.35%). Pseudomonas dominated uplands (29.7%), while Aeromonas, Salmonella, and Devosia were associated with disease. The conserved core microbiome comprised Aquicella, Enterobacter, Klebsiella, Sodalis , and Salmonella. Network analysis identified Geminigeraceae as a keystone taxon and revealed predominantly cooperative interactions between bacteria and fungi. Among 195 isolates, Bacillus subtilis ULB_36 and Bacillus stercoris ULB_12 exhibited strong inhibition of F. falciforme (83.33% and 78.52%), significantly reduced disease severity, and enhanced plant growth, comparable to fungicide treatments. These findings demonstrate that cassava stem and root rot are associated with disruption of the rhizoplane bacteriome and the loss of beneficial taxa. Agroecosystem-specific microbial signatures and core bacteriome members provide insights into cassava–microbe interactions, while native Bacillus strains offer promising niche-adapted biocontrol solutions for sustainable management of cassava stem and root rot.