Functional 16S rRNA Genomic Analysis of Herbicide-treated Soil Inocula from Legume and Cereal-based Cropping Systems in Smallholder Agroecosystems of Northern Ghana

The increasing reliance on herbicides for weed management in smallholder farming systems across sub-Saharan Africa has raised concerns about their long-term effects on soil microbial communities that sustain soil health and crop productivity. This study evaluated the impact of herbicide application on the diversity and population structure of plant growth-promoting microorganisms (PGPM) in agricultural soils collected from 15 farmers’ fields in the Upper West Region of Ghana. Soil samples were obtained from herbicide-treated farms and untreated reference sites under legume- and cereal-based cropping systems. Bacterial community composition was characterized using 16S rRNA gene amplicon sequencing, with taxonomic classification performed using the Kraken2 pipeline within the Galaxy platform. Untreated soils consistently exhibited greater microbial taxonomic richness than herbicide-treated soils at both the phylum (29–34 vs. 21–32) and genus (248–495 vs. 182–338) levels. Herbicide application reduced the relative abundance of beneficial phyla, including Firmicutes, Planctomycetes, and Actinobacteria, while enriching stress-tolerant groups such as Acidobacteria and Chloroflexi. At the genus level, important plant growth-promoting taxa, such as Bradyrhizobium , Burkholderia , Streptomyces , Conexibacter , and Planctomyces declined markedly, whereas xenobiotic-degrading genera including Rhodoplanes , Sphingomonas , Geodermatophilus , and Nocardioides increased, indicating microbial adaptation to herbicide-derived compounds. Principal component analysis and agglomerative hierarchical clustering revealed distinct shifts in microbial community composition following herbicide application. Overall, these findings demonstrate that herbicide use alters beneficial soil microbial communities, potentially reducing microbial activities associated with ecosystem functioning such as biological nitrogen fixation, phosphate solubilization and biocontrol, highlighting the need for environmentally-friendly herbicide management strategies that preserve soil health and agricultural productivity.