Developing an Original Soil Microbial Diversity Index for Assessing Agricultural Soil Health Under Nigerian Smallholder Farming Systems

This dissertation develops and validates an original Soil Microbial Diversity Health Index (SMDHI) for assessing agricultural soil health under smallholder farming systems across Nigeria, providing a scientifically grounded and practically accessible microbial indicator tool for use by national soil monitoring programmes. Soil microbial diversity is increasingly recognised as a fundamental dimension of soil health, but no Nigeria-specific standardised microbial assessment framework exists, and published international frameworks are designed for temperate agricultural contexts that do not reflect Nigerian soil biology. This study characterises soil microbial communities using shotgun metagenomics, 16S and ITS rRNA amplicon sequencing, and functional gene profiling across 240 agricultural soils representing 6 agroecological zones and 8 management systems. Reference microbial communities from 60 uncultivated natural ecosystem soils provide baseline values for index calibration. Structural equation modelling links microbial diversity parameters to soil function indicators (nitrogen mineralisation, phosphorus solubilisation, organic matter decomposition, disease suppression). A composite SMDHI is developed integrating weighted alpha diversity, functional gene richness, and biomass ratio metrics. The SMDHI is validated against independent crop yield and soil function data from 80 validation sites. The dissertation proposes the SMDHI as an original theoretical and applied contribution, demonstrating 74 percent explained variance in soil function performance across validation sites. The SMDHI is designed for deployment through two-tiered assessment: full metagenomics for research contexts and a validated short qPCR proxy battery for ADP routine monitoring. Keywords: soil microbial diversity, health index, smallholder farming, metagenomics, Nigeria.