Sclerotia-Mediated Soil Microbiome Modulation in Rice–Rapeseed Cropping Systems

<i>Rhizoctonia solani</i> (Rs) and <i>Sclerotinia sclerotiorum</i> (Ss) are devastating pathogens of rice and rapeseed, contributing 20-69% and 10-50% of yield losses, respectively. These pathogens develop resistant overwintering and/or oversummering sclerotia, which serve as inocula for infection in the subsequent season under favorable conditions. The present study was designed to investigate the month-wise variation in microbial diversity by mixing Rs and Ss sclerotia separately in rice-rapeseed rotation field soil, thereby identifying key microbial players associated with specific sclerotia and their implications for subsequent crops. Therefore, we incubated 2.5 g of Rs and Ss sclerotia in 100 g of soil for 3 months to mimic the field conditions and subjected month-wise soil samples to 16S rRNA and ITS2 sequencing. Data analysis of bacterial communities revealed diversity, richness, and evenness in Ss treated soil samples compared to the control, while fungal communities exhibited less diversity. These results were also evident in PCoA and hierarchical clustering, where control and treated samples were scattered in 16S rRNA and ITS sequencing. Genus level diversity exhibited enrichment of bacterial genera with known beneficial potential, notably <i>Acidibacter</i>, <i>Stenotrophobacter</i>, <i>Sphingomonas</i>, <i>Flavisolibacter</i>, <i>Gaiella</i>, and <i>Neobacillus</i> in control. Beneficial bacterial genera such as <i>Ramlibacter</i>, <i>Geomonas</i>, <i>Kofleria</i>, <i>Nitrospira</i>, and <i>Paraflavitalea</i> were enriched in Ss treated soil samples. The addition of Ss and Rs sclerotia activated several beneficial fungi, notably <i>Trichoderma</i>, <i>Talaromyces</i>, <i>Clonostachys</i> in Ss treated samples, and <i>Vermispora</i>, <i>Hyalorbilia</i>, <i>Mortierella</i>, <i>Lecanicillium</i> in Rs treated samples. Additionally, Rs treated soil samples also activated pathogenic genera, including <i>Typhula</i>, <i>Fusarium</i>, and <i>Rhizoctonia</i>. Sclerotia in soil modulates the microbiome and activates beneficial and pathogenic microbes. During the off-season, the <i>Sclerotinia</i> inoculum pressure in the soil reduces, and it is safe to grow crops next season. Whereas, in the case of <i>Rhizoctonia</i> infected soil, it is suggested to avoid growing crops susceptible to wilt, root rot, and blight. However, field experiments to understand the pathogen-pathogen interactions around the sclerotiosphere require further exploration.