Integrated Metagenomics and Metabolomics Analysis Reveals Changes in the Microbiome and Metabolites in the Rhizosphere Soil of Different Varieties of <em>Thlaspi arvense </em>L.

Pennycress (Thlaspi arvense L.), a representative and economically valuable cover crop, supports and enhances key ecological processes throughout its life cycle via its root system. It is hypothesized that pennycress selectively modulates its rhizosphere microbial community through root-derived metabolites, which may influence both the crop’s growth and the subsequent crops in rotation. However, systematic investigations comparing the rhizosphere microbiomes and metabolomes among different pennycress lines remain limited. This study employed metagenomic and metabolomic approaches to examine the dynamic changes in the rhizosphere microbial community and metabolite profiles of three pennycress lines with significantly different total alkaloid contents. The goal was to elucidate the interactions between microbes and metabolites. Results indicated significant differences in microbial community structure across the cultivars. JiL67 maintained stable community diversity, while LiN54 (with the lowest alkaloid content) showed reduced diversity. HeL43 (with the highest alkaloid content) exhibited increased diversity but also potential community homogenization, accompanied by the significant enrichment of microbial taxa capable of alkaloid tolerance. Metabolomic analysis identified metabolites such as Portulacaxanthin II, Oleanolic acid, and Soraphen A as significantly enriched in the rhizosphere soil of pennycress. This study reveals the shifts in rhizosphere microbial communities and metabolites linked to different pennycress lines and uncovers their interactive mechanisms, providing a scientific foundation for developing more economically efficient pennycress cultivation strategies.