Multi-omics reveal resistance mechanisms and pathogens associated with root rot disease in Panax quinquefolius

Our findings show that Bacillus amyloliquefaciens and Aspergillus fumigatus significantly enhanced plant height, stem diameter, and fresh root weight of P. quinquefolius. The activities of key plant defense enzymes, including peroxidase (POD) and lipoxygenase (LOX), were markedly increased, resulting in a notable reduction in root rot incidence. Soil physicochemical analyses revealed that these microbial treatments increased the levels of available phosphorus (AP), available potassium (AK), and total potassium (TK), as well as the activities of soil urease (S-UE) and acid phosphatase (S-ACP), thereby improving soil fertility and nutrient uptake. Microbiome profiling showed that these microbes reshaped the rhizosphere microbial community, promoting the recruitment of beneficial taxa and constructing a more stable microbial network. Integrated transcriptomic and metabolomic analyses revealed that B. amyloliquefaciens upregulated key genes such as pyruvate kinase, isocitrate dehydrogenase, and enolase, and facilitated the accumulation of defense-related metabolites like hydroxyacetone.