Rhizosphere metagenomics provides insights into the environmental effect on the secondary metabolism of Ligusticum chuanxiong

Abstract

Rhizosphere microbiomes influence the secondary metabolism of plants, but the mechanism has not been analyzed. This study aimed to explore relationship between abiotic environments, microbiomes and secondary metabolites of Ligusticum chuanxiong. By combining metagenomic, metatranscriptomic, and high-performance liquid chromatography, the microbial community structure and key microbiomes in Ligusticum chuanxiong were identified. Furthermore, the relationship between root-associated microbiomes and the secondary metabolites in Ligusticum chuanxiong was revealed. The microbial community structures of L. chuanxiong differed in each individual. The key microbiome related to secondary metabolism were similar, while there were significant differences in relative abundance across all samples. Four families (Burkholderiaceae, Comamonadaceae, Pseudomonadaceae, and Streptomycetaceae) and four species (Gemmatirosa kalamazoonesis, Luteitalea pratensis, Candidatus Solibacter usitatus, and Sorangium cellulosum) were identified as conservative core microbes, and Chloroflexi was the main biomarker. Functional annotation results showed that the metabolic function strength of the microbial community was positively correlated with the secondary metabolite content. According to correlation results, rhizosphere microbiomes related with secondary metabolites in two aspects including community diversity and microbial abundance. In conclusion, environmental factors might affect secondary metabolites of Ligusticum chuanxiong Hort. by influencing microbial diversity and the abundance of key microbes. This study can provide references for improving the artificial cultivation of Ligusticum chuanxiong, further developing and utilizing this medicinal resource.