Metagenomic insights into the interactions between <i>Chaetomium</i> , tomato and the <i>Fusarium–Meloidogyne</i> complex

Abstract The elite fungal microbials namely Chaetomium globosum Cg6 and Cg40 were used as a liquid bioformulation for seed dressing, seedling root dipping and soil application. The treatment effectively suppressed the wilt complex caused by Fusarium–Meloidogyne (FOL + RKN) under greenhouse and field conditions in tomato crops. An in vitro study on the volatiles by GC‐MS‐TD revealed the presence of potential antimicrobial compounds with antifungal activity which was further up‐regulated in the presence of the pathogen FOL. The Cg40 strain produced an array of compounds such as n‐hexane, Cyclotrisiloxane, hexamethyl, 1,4 Pentadiene, Butanoic acid ethyl ester, Cyclopentasiloxane decamethyl and decane which showed antimicrobial and plant growth promotion activity. Microbial diversity in (i) bioagent (Cg40) alone, (ii) bioagent challenged with Fusarium and Meloidogyne was assessed through transcriptomic analysis via Illumina sequencing. The results suggested that the relative abundance of several bacterial taxa namely actinobacteria, acidobacteria, gammaproteobacteria and chloroflexi in Cg40 treated plants. The diversity of microbial communities was predominantly higher for bioagent Cg40 alone (150837‐actinobacteria, Chaetomium 4) compared to Cg40 challenged with Fusarium and RKN. The amplification of antimicrobial genes namely chitinase (1500 bp), xylanase (660 bp) responsible for hydrolysing the fungal cell wall was detected in Cg40 by polymerase chain reaction. Soil application of the liquid bioformulation as seed treatment, seedling root dipping and soil drenching of Chaetomium globosum Cg40 resulted in the least wilt severity, enhanced plant height, early flowering and fruit yield at both field locations studied. These findings contribute to eco‐friendly sustainable agriculture by demonstrating how microbials can be employed to manage harmful plant pathogens thereby enhancing soil and crop health as well as productivity.