Host-recruited Bacillus and Pseudomonas strains provide potential biocontrol and yield protection against rice bacterial leaf blight.

Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global rice production while growing bactericide resistance and environmental concerns necessitate sustainable disease management alternatives. We employed a microbiome-guided, habitat-specific isolation strategy targeting naturally recovered plants from BLB-endemic hotspots across ten districts of Punjab, Pakistan operating on the ecological premise that plants under pathogen pressure selectively enrich protective microbial taxa, making disease-affected hosts the most coherent source of adapted biocontrol agents. Screening of 1,036 bacterial isolates from rice rhizosphere and phyllosphere using dual-culture antagonism assays yielded six elite strains: Bacillus velezensis, B. amyloliquefaciens, B. subtilis, Pseudomonas fluorescens, and two P. aeruginosa isolates, confirmed by 16 S rRNA and rpoD gene sequencing (> 99% sequence identity). Biochemical profiling revealed multifunctional plant growth-promoting traits including siderophore production, biological nitrogen fixation, indole-3-acetic acid biosynthesis, phosphate solubilization, and hydrogen cyanide production, indicating the potential capacity of selected strains for integrated disease suppression and plant growth promotion. Greenhouse trials across six rice varieties with contrasting genetic resistance backgrounds demonstrated significant reductions in BLB incidence (25-67%) and severity (31-55%) relative to uninoculated controls. Field validation under natural pathogen pressure across two consecutive growing seasons confirmed robust performance, with incidence suppression of 33-65% and severity reduction of 46-67% compared to controls. B. velezensis fsdls3 emerged as the most effective individual agent, achieving 114.5% mean yield protection relative to diseased controls and approaching streptomycin sulfate performance with no statistically significant overall yield difference while outperforming the chemical standard on specific variety-strain combinations. Five of six PGPR agents exceeded the 100% yield protection threshold, delivering agronomic co-benefits including enhanced tillering, increased productive panicles, and elevated total biomass unavailable from chemical bactericide treatment alone. Pronounced cultivar × treatment interactions confirmed that PGPR efficacy is modulated by host genetic background, with resistant varieties carrying pyramided Xa resistance genes showing additive responses to biological treatment. These results establish habitat-adapted, host-recruited PGPR as scientifically credible and ecologically coherent alternatives to chemical bactericides for integrated BLB management in rice.