Identification of Bacterial Populations and Functional Mechanisms Potentially Involved in Biochar-Facilitated Antagonism of the Soilborne Pathogen Fusarium oxysporum

Biochar soil amendment alleviates plant disease through microbial-mediated processes but drivers facilitating this “biochar effect” are not fully understood. In this study, cucumber plants were inoculated with and without the fungus Fusarium oxysporum f. sp. radicis-cucumerinum in either biochar-amended or nonamended 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 F. oxysporum f. sp. radicis-cucumerinum-antagonizing capacity. Biochar-amended plants showed lower F. oxysporum f. sp. radicis-cucumerinum-associated growth stagnation compared with nonamended plants, supporting the biochar effect. Their rhizosphere had a more diverse microbiome with higher levels of secondary metabolite-encoding biosynthetic gene clusters (BGCs). Families Pseudonocardiaceae (Lentzea spp.) and Myxococcaceae were significantly more abundant in biochar-amended rhizospheres of F. oxysporum f. sp. radicis-cucumerinum-inoculated plants, and metagenomically assembled genomes (MAGs) from these taxa contained genes encoding enzymes involved in binding and degradation of chitin, and novel BGCs encoding secondary metabolites. Lentzea spp. isolates related to the above MAGs showed in vitro antagonistic activity against F. oxysporum f. sp. radicis-cucumerinum. Collectively, we postulate that biochar amendment generates a “buffering effect” that reduces F. oxysporum f. sp. radicis-cucumerinum-facilitated destabilization of the root-associated microbiome, maintaining beneficial taxa that produce antagonizing enzymes and secondary metabolites that sustain plant health.