Functional and taxonomic shifts in rhizosphere microbiomes of summer legume cover crops

Legume cover crops are increasingly incorporated into sustainable production systems, yet their influence on rhizosphere microbial communities remains poorly characterized, particularly for underutilized warm-season species. In this study, we investigated rhizosphere bacterial communities associated with cowpea ( Vigna unguiculata ), tepary bean ( Phaseolus acutifolius ), and sunn hemp ( Crotalaria juncea ) in an organic production system using 16S rRNA amplicon sequencing and compared them with fallow soils. All legume species were associated with shifts in bacterial community composition relative to fallow soil, with increased relative abundance of copiotrophic taxa such as Proteobacteria , while fallow soils were dominated by oligotrophic groups within Actinobacteriota . Distinct species-specific recruitment patterns were observed: tepary bean rhizospheres showed higher relative abundance of Rhizobiales , associated with taxa involved in biological nitrogen fixation, whereas cowpea and sunn hemp supported bacterial groups linked to organic matter turnover and plant growth. Weighted UniFrac analyses indicated clear separation between cover-cropped and fallow soils, accounting for approximately 54% of community variation. Functional predictions using PICRUSt2 suggested representation of pathways related to central carbon metabolism, amino acid biosynthesis, and siderophore production under legume rhizospheres. Predicted pathways associated with nitrogen metabolism also tended to be more represented under cover crops, although no pathways remained significant after false discovery rate correction. Overall, these findings indicate that summer legume cover crops are associated with shifts in rhizosphere bacterial communities and predicted functional potential relative to fallow soils. These findings highlight the potential of species selection in shaping rhizosphere microbial communities in organic production systems and provide a foundation for future studies investigating microbial processes associated with cover cropping.