Seasonal variations in the composition and diversity of rhizosphere soil microbiome of bamboo plants as infected by soil-borne pathogen and screening of associated antagonistic strains

As the occurrence and severity of soil-borne diseases are strongly season-dependent, the ecological processes that shift plant microbiome compositions and functions upon pathogen infection in different seasons are rarely studied. In this study, we compared the differences in fungal and bacterial communities in rhizosphere soil between healthy and diseased bamboo plants throughout the four seasons at the main bamboo production site in China and investigated how basal rot disease caused by Fusarium proliferatum affected the composition, structure and ecological functions of rhizosphere-associated microorganisms. The results showed that diseased bamboo plants enriched the highest abundance of Fusarium genus in rhizosphere soil while receiving largely increased stem lesion area in summer. Microbiome analysis further proved that healthy bamboo plants harbored more ecologically beneficial microbial taxa that might function as biological protectants in their rhizosphere soil than diseased plants at the same season. Three individual strains with biocontrol potentials were further isolated and identified as Trichoderma spirale, Bacillus velezensis and Streptomyces mirabilis. The antagonistic tests further demonstrated their inhibition effects on the growth and pathogenicity of the pathogenic fungus F. proliferatum in vitro and in vivo. This study advances our understanding of soil-borne pathogen mediated changes in microbiome structure and function in plant rhizosphere soil and provides potential biocontrol strains for increasing plant resistance against basal rot disease.