Screening biocontrol agents based on pathogen-induced rhizosphere microbiome modulation and synergistic defense response of cotton

• The rhizosphere microbiome was reconstituted through pathogen induction. • B. amyloliquefaciens with high inhibition on V. dahlia was screened. • B. amyloliquefaciens induced cotton to defense pathogen through multi-pathway. Control of cotton Verticillium wilt still faces significant challenge due to the frequent genetic variation and persistent survival of Verticillium dahliae . Here, we developed a method to reconstruct rhizosphere microbiome based on the “cry for help” hypothesis of pathogen-induced rhizosphere microbiome modulation and to fast isolate antagonistic microorganisms. The drench-inoculated cotton with V. dahliae V592 triggered to enrich soil bacterial species and induced the enrichment of beneficial bacteria in cotton rhizosphere, in which Bacillus amyloliquefaciens E2 with 76.47 % inhibition rate against V. dahliae V592 was obtained. The pot experiment confirmed the ultra-high colonization of B. amyloliquefaciens E2 in cotton root (7.92 × 10 6 CFU/g) and stems (3.91 × 10 6 CFU/g). This strain resulted in 66.67 % of control efficacy on cotton Verticillium wilt and reduced the disease index by 45.83 (from 68.75 to 22.92). The application of B. amyloliquefaciens E2 efficiently inhibited colonization of V. dahliae V592 in cotton root, promoted cotton growth, induced ROS burst and callose deposition in cotton leaves, enhanced root vigor (70.72 %), and upregulated the defense-related gene ( POD , SOD , PAL , PPO and PR10 ) expression (3.5-fold to 9.8-fold), thus demonstrating synergistically induced defense responses of cotton plants. The present study provides an effective application of ’cry for help’ concept for fast screening biocontrol agents, and the obtained B. amyloliquefaciens E2 shows the potential for application.