Functional and taxonomic profiles of soil microbial communities of tropical legume soils from smallholder farmers' fields in Tzaneen, Limpopo province, South Africa.

Abstract

Background: Soil microorganisms play a vital role as the major indicators of soil health in sustainable agricultural farming systems. However, intensive cultivation and unrecommended farmers' soil management practices negatively affect the soil microbial communities, and hence that of the soil health. Here, we investigated the functional and taxonomic diversity of soil microorganisms on six selected smallholder farmers that grow Bambara groundnut (Vigna subterranea) and dry bean (Phaseolus vulgaris) in Limpopo Province, South Africa using metagenomics and phenotypic profiles studies. Five soil samples, randomly collected per farm and pooled into a single representative sample were used. Metagenomics raw read quality control, genome assembly and annotation were performed on the KBase platform while the community level physiological profile analysis was done using Biolog Ecoplates™.

Results: The results indicated that the soil microbial communities in Chosen Generation farm had higher rates of carbon source utilization. Likewise, it showed greater microbial abundance of varying taxonomy in which Actinobacteria, Firmicutes and Proteobacteria were the predominant phyla while Bacillus, Streptomyces, Microvirga and Bradyrhizobium were the most represented genera.

Conclusions: This study reports that soils from the six farms studied are enriched with genetically and physiologically diverse microorganisms that are responsible for crop growth. While soil physico-chemical properties can be associated with microbial diversity in this study, further studies on farming practices such as fertilizer and irrigation are recommended to further explore their possible effects on soil microbes.