Molecular Assessment of Soil Microbiome Changes Following Organic and Inorganic Fertilizer Application in Smallholder Farms in Benue State

Soil microbial communities are fundamental drivers of nutrient cycling, organic matter decomposition, and plant health, and their composition is sensitive to fertilizer management practices. Understanding how organic and inorganic fertilizer applications alter soil microbiome structure in Nigerian smallholder farming systems is essential for sustainable agricultural productivity. This study assessed soil microbiome changes following organic (poultry manure) and inorganic (NPK) fertilizer applications in smallholder yam farms in Benue State, North Central Nigeria. Soil samples were collected from plots under three treatments (organic, inorganic, and unfertilized control) at baseline, 4 weeks, and 12 weeks post-application. Total microbial community DNA was extracted and the V3-V4 region of the bacterial 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform. Bacterial community diversity indices (Shannon, Simpson) and taxonomic composition were analyzed using QIIME 2. Organic fertilizer plots showed significantly higher alpha diversity and increased relative abundance of Actinobacteria and Verrucomicrobia compared to inorganic and control plots at 12 weeks. Inorganic fertilizer application was associated with a relative enrichment of nitrogen-fixing Rhizobiales at 4 weeks, with diversity declining thereafter. These findings provide molecular evidence for distinct microbiome responses to contrasting fertilizer inputs in Benue State yam agroecosystems. Keywords: soil microbiome, 16S rRNA amplicon sequencing, fertilizer, smallholder farming, Benue State.