Drivers of promiscuous soybean associated rhizobia diversity in un-inoculated soil in Malawi

Increasing legume cultivation and yields on smallholder farms is challenged by low soil rhizobia bacteria populations and limited access to rhizobia inoculants. However, by understanding the environmental drivers of rhizobia diversity in un-inoculated soils to improve nodulation success for smallholder farmers. Soils were collected from 39 smallholder farms in the Ekwendeni region of northern Malawi. Soils were categorized by cropping history and analyzed for Mehlich-3 phosphorus, calcium, magnesium, potassium, iron, particle size distribution, organic matter (OM) content and pH. Rhizobia bacteria were isolated using Tropical Glycine cross (TGx) soybean (Glycine max) variety 1740-2F as a trap crop. Genomic fingerprints of extracted rhizobia were created using rep-PCR with the BOX A1R primer and diversity indexes calculated from resulting fingerprints. Genomic fingerprinting of rhizobia resulted in 32 clusters with 70 % fingerprint similarity. Soil OM and carbon strongly influenced the presence of 6 clusters, Ca of 4 clusters, pH of 3 clusters, and Mg, K, Clay of three clusters each. Recent soybean production resulted in a greater number of nodules (16) than other histories (10), and uncultivated soils had a different rhizobia community structure than cultivated soils. Soil rhizobia are subject to a complex ecology in which plant communities as well as OM, clay, and nutrient (Mg, K, Fe and P) content select for community structure. Identifying the drivers and preferred environments of high performing rhizobia strains could improve nodulation in low-input agriculture environments.