Correlation analysis of three coffee species (Coffea arabica, Coffea canephora, and Coffea liberica) rhizosphere microbial communities, soil physicochemical properties and metabolites

Coffee (Coffea L.) is an economically important crop worldwide. C. arabica is widely cultivated for superior flavor, while C. canephora and C. liberica provide valuable traits like pest resistance and stress tolerance. Yunnan, China’s main coffee-producing region, favors C. arabica cultivation, but quality and cultivation challenges remain. This study investigated different coffee varieties’ effects on rhizospheric soil chemical properties, microbial communities, and metabolites using amplicon-based high-throughput sequencing (16S rRNA gene, ITS) and metabolomics. Our results showed coffee varieties significantly altered soil chemical properties and organic carbon content: C. arabica had reduced catalase activity, C. liberica enhanced urease activity. Thirteen phyla, 21 classes, 30 orders, 29 families, 22 genera, and 16 species were detected in 4 soil sample groups. C. arabica enriched Betaproteobacteria; C. liberica enriched Myxococcota and Sphingomonadales, suggesting roles in nitrogen cycling and organic matter decomposition. Microbial communities in C. arabica and C. liberica were dominated by a few abundant taxa, while C. canephora and unplanted soil (CK) had more even, functionally diverse communities; core phyla included Proteobacteria, Actinobacteriota, and Ascomycota. Bacterial communities were sensitive to soil pH and nutrients; fungal groups (Glomerales, Diversisporales) were closely associated with organic matter and enzyme activities. Notably, C. arabica had the most distinct bacterial community, C. liberica the most distinct fungal community, reflecting variety-specific responses. • Coffee variety influences soil properties and enzyme activities. • All coffee varieties shared core phyla including Proteobacteria. • C. arabica exhibited the most distinct bacterial community. • Bacterial communities were highly sensitive to soil pH and nutrient levels.