Association of Soil Physicochemical Properties with Bacterial Microbiome Structures in Cowpea Farms from Semiarid Eastern Kenya

Cowpea ( Vigna unguiculata [L.] Walp.) is an important grain legume in semiarid Africa, where it contributes to food security and livelihood resilience in smallholder farming systems. However, information on the soil bacterial microbiome associated with cowpea production in semiarid eastern Kenya remains limited. This study investigated soil physicochemical heterogeneity and bacterial community structure in cowpea farms from Machakos and Kitui Counties via 16S rRNA amplicon next-generation sequencing (NGS), with the aim of improving the understanding of belowground microbial patterns in these production systems. Most measured soil physicochemical properties varied significantly among farms, indicating substantial field-level heterogeneity, whereas county-level differences were less pronounced. Across all the samples, the bacterial communities were dominated by Actinomycetota, followed by Pseudomonadota, Bacillota, Chloroflexota, and Acidobacteriota. Rhizobial genera of agronomic relevance, including Bradyrhizobium , Rhizobium , Ensifer , and Mesorhizobium , were detected across farms, with Bradyrhizobium showing the highest relative abundance. The alpha-diversity indices varied among the samples, while the beta-diversity analysis revealed significant differences in the bacterial community composition between the counties. Correlation analysis further revealed associations between selected soil variables and the distributions of dominant bacterial taxa and rhizobial genera. Cowpea farm soils in semiarid eastern Kenya harbor distinct bacterial communities associated with farm-level edaphic heterogeneity and measurable compositional turnover across sites. The detection of rhizobial genera across farms suggests the potential ecological relevance of native bacterial populations in these systems. This study provides a baseline for understanding the soil bacterial microbiome structure in Kenyan cowpea production systems and supports the need for site specific, microbiome-informed approaches for sustainable soil fertility management.