Functional divergence in the rhizosphere microbiome of Codonopsis pilosula drives a soil carbon allocation trade-off

Rhizosphere microorganisms play pivotal roles in soil organic carbon dynamics; yet, their relationship with soil carbon cycling remains unclear under plant intraspecific variation, particularly for medicinal species with distinct metabolic traits. Here, we investigate how six varieties of Codonopsis pilosula (BT, CD, WD, WY1, WY3, WY4) influence the trade-off between soil organic matter (SOM) and microbial biomass carbon (MBC) through modulation of rhizosphere microbial communities. The results showed that a significant negative correlation was observed between SOM and MBC across varieties (P = 0.0025). The BT variety exhibited a rapid carbon turnover phenotype, marked by low SOM, high MBC, and enhanced peroxidase activity. In contrast, WD and WY3 adopted a carbon-accumulating strategy, sustaining high SOM with moderate to low MBC. Plant variety emerged as the dominant factor structuring rhizosphere bacterial and fungal communities. The BT variety specifically enriched taxa involved in recalcitrant carbon degradation, such as Nitrospira and Chryseolinea. Functional prediction further revealed enrichment of nitrification and lignin degradation pathways in BT microbiomes, whereas denitrification was prominent in WY4. Network analyses underscored strong associations among SOM, MBC, and carbon-cycling enzymes with microbial network modules, suggesting that environmental factors modulate carbon processes via microbiome interactions. Our findings unveil a mechanism by which plant genetic variation mediates soil carbon allocation through rhizosphere community restructuring, providing a foundation for genotype-specific breeding and microbiome management to optimize soil carbon sequestration.