article · Frontiers in Soil Science
Cowpea is an essential grain legume supporting food security and livelihoods across semiarid regions in Africa. Understanding the soil bacterial communities associated with this crop is important for managing soil fertility. Research examining smallholder cowpea farms in Machakos and Kitui Counties in eastern Kenya revealed marked differences in soil physical and chemical properties at the individual farm level. Analysis of the soil microbiome showed that Actinomycetota was the dominant bacterial group, followed by Pseudomonadota and Bacillota. Crucially, beneficial rhizobial genera capable of nitrogen fixation, primarily Bradyrhizobium, alongside Rhizobium, Ensifer, and Mesorhizobium, were present across all surveyed farms. Overall bacterial composition differed significantly between the two counties, although statistical tests could not confirm the measured soil variables as direct drivers of these differences at the current sample size. These results provide an ecological baseline to guide local soil management.
Cowpeas provide critical nutrition and income for smallholder farmers in dryland regions. Understanding the natural soil bacteria that support crop growth helps agronomists design better farming practices. Identifying native nitrogen-fixing bacteria already adapted to local dry soils offers a path toward improving legume yields and soil fertility naturally, reducing the need for costly external chemical inputs in vulnerable agricultural systems.
This research provides baseline data that could eventually support the development of locally adapted biofertilisers and native rhizobial inoculants for agricultural input suppliers and smallholders. However, the work represents early-stage ecological discovery based on sequencing data. Significant further work, including isolation, functional testing, field trials, and formulation development, is required before any commercial inoculant products can reach the market.
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Introduction 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. Methods This study investigated heterogeneity of soil physicochemical properties 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. Results 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. Preliminary correlation analysis revealed associations between selected soil variables and the distributions of dominant bacterial taxa and rhizobial genera, however none of these pairwise correlations remained significant after Benjamini-Hochberg FDR correction. Discussion Cowpea farm soils in semiarid eastern Kenya harbor compositionally distinct bacterial communities that vary with farm-level edaphic heterogeneity, with native rhizobial genera detected across all sites indicating ecologically relevant symbiotic bacterial resources; a direct test (Mantel test, constrained ordination) did not establish the measured soil variables as significant drivers of this compositional variation at the present sample size. These findings establish a baseline for soil bacterial ecology in Kenyan cowpea systems and demonstrate that site-specific, microbiome-informed strategies are needed for sustainable soil fertility management and effective deployment of native rhizobial inoculants in semiarid smallholder agriculture.
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DOI: 10.3389/fsoil.2026.1911455
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