A novel functional screening method for generation of a synthetic microbial community: Case study with control of Fusarium wilt in pigeonpea

Abstract Conventional methods to combat phytopathogens have ecological implications: chemical fertilizers pollute the environment, while bioinoculants are often inconsistent under field conditions. Microbiome‐assisted rhizosphere engineering aims to re‐structure the rhizosphere microbiome to promote plant growth and/or mitigate stress. This study employs a strategy based on rhizosphere engineering to combat stress caused by Fusarium udum in Cajanus cajan, by generating synthetic microbial communities (SMCs). We used a culture bank of indigenous bacterial strains belonging to the family Bacillaceae, isolated from the rhizosphere of C. cajan with biocontrol activity against Fusarium, and plant growth‐promoting (PGP) properties. Various possible combinations of compatible strains were generated, followed by a novel iterative deconvolution technique to establish strains exhibiting enhanced biocontrol traits, when present in a community of other strains. A scoring scheme aided selection of strains for the SMCs, which were tested using in vitro and in planta experiments. Estimating growth attributes and stress markers in plants treated with constituted SMCs helped to select an SMC with maximum biocontrol potential against Fusarium wilt of pigeonpea. A robust SMC was generated with indigenous multi‐trait plant growth promoting bacterial strains for sustainable mitigation of Fusarium induced biotic stress with proven efficacy in the host, C. cajan .