Biogas slurry application alters soil properties, reshapes the soil microbial community, and alleviates root rot of Panax notoginseng

BACKGROUND: Panax notoginseng is an important herbal medicine in China, where this crop is cultivated by replanting of seedlings. Root rot disease threatens the sustainability of P. notoginseng cultivation. Water flooding (WF) is widely used to control numerous soilborne diseases, and biogas slurry shows positive effects on the soil physiochemical properties and microbial community structure and has the potential to suppress soilborne pathogens. Hence, biogas slurry flooding (BSF) may be an effective approach for alleviating root rot disease of P. notoginseng; however, the underlying mechanism needs to be elucidated. METHODS: In this study, we conducted a microcosm experiment to determine if BSF can reduce the abundance of pathogens in soil and, alleviate root rot of P. notoginseng. Microcosms, containing soil collected from a patch of P. notoginseng showing symptoms of root rot disease, were subjected to WF or BSF at two concentrations for two durations (15 and 30 days), after which the changes in their physicochemical properties were investigated. Culturable microorganisms and the root rot ratio were also estimated. We next compared changes in the microbial community structure of soils under BSF with changes in WF and untreated soils through high-throughput sequencing of bacterial 16S rRNA (16S) and fungal internal transcribed spacer (ITS) genes amplicon. RESULTS: WF treatment did not obviously change the soil microbiota. In contrast, BSF treatment significantly altered the physicochemical properties and reshaped the bacterial and fungal communities, reduced the relative abundance of potential fungal pathogens (Fusarium, Cylindrocarpon, Alternaria, and Phoma), and suppressed culturable fungi and Fusarium. The changes in the microbial community structure corresponded to decreased root rot ratios. The mechanisms of fungal pathogen suppression by BSF involved several factors, including inducing anaerobic/conductive conditions, altering the soil physicochemical properties, enriching the anaerobic and culturable bacteria, and increasing the phylogenetic relatedness of the bacterial community. CONCLUSIONS: BSF application can reshape the soil microbial community, reduce the abundance of potential pathogens, and alleviate root rot in P. notoginseng. Thus, it is a promising practice for controlling root rot disease in P. notoginseng.