Bio-Fertilizer Amendment Alleviates The Replanting Disease By Reshaping Leaf And Root Microbiome

A growing problem in intensive agricultural systems is replanting disease. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields and characterized the associated microbiota by bacterial 16S rRNA gene sequencing and qRT-PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium, and enhancing positive connections of the bacterial community across the two compartments. Bio-fertilizer had a positive and indirect effect as indicated by a structural equation models on both yield and quality by shaping the leaf microbiota rather than the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving the plant-microbe interactions.