Bio-organic fertilizer amendment helps suppress tomato bacterial wilt disease by improving aggregation and enhancing the pathogen inhibition capacity within micro-aggregates

Abstract

Soil structure plays a crucial role in governing the microbial community, which subsequently impacts plant disease suppression. However, typical sampling approaches ignore the importance of the microscale heterogeneity of soil aggregates in determining the microbial function involved in disease suppression. In this study, we examined the microbiomes of different soil particle size classes related to disease suppression in fields from a long-term experiment comparing chemical fertilizer (CF) and bioorganic fertilizer (BF) treatments. Root-adhering soil samples were collected in the 7th tomato cropping cycle across plant growth stages and separated into three soil aggregate size classes. BF resulted in a lower disease incidence and greater soil aggregation than CF. Microaggregates under CF harboured more pathogens compared to macroaggregates as measured by qPCR, while BF reduced the pathogen density in microaggregates. 16S rRNA gene amplicon sequencing shows BF also affected the bacterial community composition of the different soil aggregate classes, and the random forest model reveals that bacterial community composition of microaggregates had significant predictive power with respect to disease incidence. Additionally, by a pot experiment that transferring the microbiomes from different soil aggregates into sterilized substrates, we reconstituted the pathogen inhibition capacity of the soil microbiomes within different soil aggregate size classes on plant roots, the microbial community from microaggregates exhibits critical role in determining pathogen invasion on tomato roots. Overall, our study reveals that fertilization shapes the proportion of soil aggregates and the aggregate-dependent bacterial community composition. BF reduced the proportion of microaggregates and increased the pathogen-inhibiting capacity of the bacterial community in this fraction, which represents the preferred microhabitat of pathogenic Ralstonia solanacearum.