Compositional Shifts in Microbial Diversity under Traditional Banana Cropping Systems of Sub-Saharan Africa

Abstract

Improvements in the crop productivity, soil health, and sustainable intensification should be premised on the better understanding of interactions between the cropping systems and soil microbial diversity. In this study, we assessed variations in the microbial communities across the traditional banana-based cropping systems of contrasting monocrop vigor (vigorous or V vs. non-vigorous or NV) and the cropping system (monocrop or MC vs. intercropped or IC) using 16S rDNA (V3–V4) and ITS2 amplicon deep sequencing via Illumina platform. Sequencing results of the bacterial and fungal communities showed high variability among MC and V cropping systems. The abundances of Proteobacteria, Firmicutes, and Actinobacteria were significantly higher in NV (non-vigorous) and V (vigorous) cropping systems; and the abundances of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes in the MC (monocropping) than IC (intercropping). There were high relative abundances of Pseudomonas (6.1–37.43%), Bacillus (4.5–20.4%), Rhizobium (1.4–6.5%), and Devosia (1.5–6.7%) in the cropping systems. The dominant family of fungal class Incertae_sedis was Mortierellales, which accounted for 8.79–41.12% of total taxa. This result indicated that the cropping systems are vital for supporting the dynamic microbial diversity specifically beneficial for bacterial communities that helps in promoting synergistic plant-soil interactions and total productivity under resource poor conditions of smallholder farmers in sub-Saharan Africa (SSA).