Influence of root secretions of understory Chinese herbal medicines on the characterization of inter-root microbial communities

Medicinal herbs often encounter significant succession barriers during cultivation, with the accumulation of root secretions identified as a key driver of changes in soil microbial communities and subsequent barriers. Investigating the effects of understory herb root secretions on soil microbial ecology is crucial for for improving soil health, optimizing cultivation practices, and promoting sustainable agricultural development. Compare the compositional characteristics of inter-root soil microbial communities of Panax notoginseng, Polygonatum sibiricum, and Wasabia japonica in natural and understory forests, and analyze soil physicochemical properties to provide a scientific basis for disease prevention and wild-like cultivation. Collect inter-root soils from natural and understory forests, analyze the species composition and diversity of soil bacterial and fungal communities, and determine soil physicochemical properties using high-throughput sequencing. This study explored the effects of root secretions from Panax notoginseng, Polygonatum sibiricum, and Wasabia japonica on soil microbes and metabolic pathways. Compared to the unplanted control, there were 329, 250, and 193 differential secretions in the three plants, with some in common. Lipids were the major component (60.25% in Panax notoginseng, 56.12% in Polygonatum sibiricum, 66.10% in Wasabia japonica). Compared to natural woodland (RCK), 22, 20, and 15 metabolic pathways were enriched in the Panax notoginseng, Polygonatum sibiricum, and Wasabia japonica plantation woodland, respectively, mainly involving amino-acid, fatty-acid, and secondary-metabolite synthesis. Soil factors were correlated with microbial abundance. Strong microbiome-metabolome correlations and clear groupings among experimental groups (RCK, RPN, RPS, REW) were found. Metabolite analyses showed positive correlations (phenylalanine - small molecules, 3-hydroxypropionic acid - short-chain fatty acids) and a negative one (phenylalanine - pyruvate). Root secretions’ effects on soil varied, linked to soil factors and metabolites, offering insights into understory herb ecological effects. Root secretions of the three plants significantly affect understory soil microbial communities. Secretions are mainly lipids, lipids-like substances, and organic acids, with significant differences among plants, reflecting their unique metabolic adaptations. Microbial community analysis showed that Panax notoginseng plantation soil significantly enhanced bacterial community diversity, in the soil, particularly increasing the abundance of Ascomycota and Acidobacteria. However, the presence of Fusarium spp. and Cysticercus spp. species among the fungal communities warrants special attention due to their potential impact on plant health. To improve soil health and optimize the growth environment of Panax notoginseng, it is essential to implement measures that enhance soil organic matter content and promote microbial diversity.