Identification of bacterial populations and functional mechanisms potentially involved in biochar-facilitated antagonism of the soilborne pathogen Fusarium oxysoporum

Abstract

Biochar soil amendment alleviates plant disease through microbial-mediated processes, but drivers facilitating this "biochar effect" are not fully understood. In this study, cucumbers were inoculated with and without the fungus Fusarium oxysporum f.sp. radicis-cucumerinum (FORC) in either biochar-amended or non-amended soils, and disease severity was assessed. Amplicon sequencing and shotgun metagenomics were then applied to identify bacteria and associated mechanisms potentially involved in pathogen inhibition, and candidate bacteria were tested for in-vitro FORC-antagonizing capacity. Biochar-amended plants showed lower FORC-associated growth stagnation compared with non-amended plants, supporting the "biochar effect". Their rhizosphere had a more diverse microbiome with higher levels of secondary metabolite-encoding biosynthetic gene clusters (BGCs). Pseudonocardiaceae (Lentzea spp.) and Myxococcaceae were significantly more abundant in biochar-amended rhizospheres of FORC-inoculated plants, and metagenome assembled genomes (MAG) from these taxa contained enzymes involved in binding and degradation of chitin, and novel BGCs encoding secondary metabolites. Lentzea spp. isolates related to the above MAG showed in-vitro antagonistic activity against FORC. Collectively, we postulate that biochar amendment generates a "buffering effect" that reduces FORC-facilitated destabilization of the root-associated microbiome, maintaining beneficial taxa that produce antagonizing enzymes and secondary metabolites that sustain plant health.