Diversity of soil bacterial communities in response to fonio genotypes and pedoclimatic conditions in Benin

In sub-Saharan regions, soil fertility is a major concern for plant productivity, influenced by physical, chemical, and biological components. Among biological properties, the recruitment of soil microbial communities by plant roots is influenced by both physico-chemical soil properties and plant characteristics, dependent on species or genotypes. Here, rhizosphere bacterial communities associated with five fonio genotypes cultivated under three locations were investigated. Rhizosphere soils were collected for high-throughput 16S rRNA gene sequencing to characterize soil bacterial diversity. Additional parameters were assessed to classify soil fertility at three locations and to evaluate relationships between the bacterial community’s composition and soil fertility variables. PCA revealed a clear effect of location, whereas genotype had no significant impact on soil chemical properties or enzyme activities. Overall, soils were low in fertility, with Boukoumbe soil standing out for its higher chemical values and enzyme activities. For example, Boukoumbe reached 1.48% organic carbon, compared to 0.61% in Gogounou and 0.36% in Ina. Similarly, total nitrogen and available phosphorus were also higher in Boukoumbe. Regarding bacterial community, there is no impact of location and genotype on their richness and diversity. However, Bray-Curtis index revealed a significant difference in bacterial community structure among locations, but not among fonio genotypes. This suggests, in rhizosphere, bacterial community structure is more modulated by soil properties than crop genotypes. Proteobacteria and Bacteroidota were most abundant phyla, varying significantly across locations. Moraxellaceae and Oxalobacteraceae bacteria were most abundant families within Proteobacteria, while Chitinophagaceae and Weekselleceae dominated in Bacteroidota. Our study highlighted the significant roles of soil pH, as well as sulfate and nitrate content, in shaping bacterial communities. These findings offer valuable insights into the bacterial communities associated with fonio and their key drivers. This will support future research in identifying plant-growth bacteria that improve soil fertility and health, and crop productivity.