16S rRNA-based genetic diversity and symbiotic efficiency of indigenous cowpea-nodulating rhizobia from semiarid Eastern Kenya

Indigenous rhizobia that nodulate cowpea ( Vigna unguiculata ) can support locally adapted biofertilizers for semiarid farming systems, yet their genetic diversity and symbiotic performance in Eastern Kenya remain poorly characterized. In this study, we isolated nodule-associated bacteria from cowpea root nodules collected from smallholder farms in Machakos and Kitui Counties and evaluated nodulation and plant growth under greenhouse conditions. We recovered 70 isolates and grouped them into 19 morphotypes on the basis of colony and biochemical traits, but only 15 isolates (21.4%) formed nodules. The phenotypes of the identified isolates varied in terms of nodulation (16.20 ± 1.39 to 51.70 ± 4.68 nodules plant ^− 1 ) and biomass. The symbiotic efficiency ranged from 37.88% to 157.04% relative to the nitrogen-supplemented control, and eight isolates (53.3%) exceeded 100%. Three isolates (M-34, M-17, and M-27) presented the highest efficiencies (~ 140–157%) and outperformed the nitrogen-supplemented control and the reference strain ( Bradyrhizobium sp. USDA 3456). Partial 16S rRNA sequencing assigned isolates to Rhizobium (53.3%), Bradyrhizobium (40.0%), and one isolate was identified as Mesorhizobium plurifarium , representing one of the first documented associations of this species with cowpea in Eastern Africa. Closely related isolates differed markedly in efficiency, indicating that taxonomic identity alone does not predict symbiotic performance. These results identify high-performing indigenous strains for further evaluation as candidates for locally adapted cowpea inoculants.