Design, implementation and evaluation of a soil microbiome biofertilizer for tropical crop yield in controlled trials

Thesis Abstract

Designing, implementing, and evaluating a soil microbiome biofertilizer to enhance tropical crop yield in controlled trials addresses the pervasive constraint of declining soil fertility and suboptimal nutrient use efficiency in smallholder and commercial tropical agro-ecosystems. The study aims to develop a consortium-based biofertilizer that modulates rhizosphere microbial communities to promote nutrient acquisition, plant growth, and resilience under variable tropical environmental conditions. Specific objectives are (1) to formulate a consortium comprising Bacillus velezensis, Pseudomonas fluorescens, and Azospirillum brasilense engineered for synergistic phosphate solubilization, nitrogen fixation, and phytohormone production; (2) to optimize carrier material and application rate for compatibility with maize and sorghum under greenhouse and screenhouse settings; (3) to evaluate agronomic performance, soil enzyme activities, and microbial diversity using controlled field-macrotile trials across three tropical sites; (4) to quantify yield components, nutrient uptake, and drought/pest resilience indicators; and (5) to develop a decision-support framework for farm-scale deployment. The methodology adopts a mixed-methods design anchored in pragmatic realism. A dual-phase experimental approach comprises a controlled greenhouse experiment with a factorial arrangement (biofertilizer vs. conventional fertilizer × moisture regime optimal vs. drought-stressed) and a field trial conducted across three tropical sites with distinct edaphic profiles. The population includes maize and sorghum cultivars with plot-level replication (n = 4) in greenhouse trials and randomized complete block design across field sites (n = 6 blocks per site; total plots per site = 12). Microbial inoculants are prepared using standardized fermentation and carrier-adhesion protocols, with carrier materials (biochar, peat, and alginate bead) tested for viability over 12 weeks. Data collection instruments include soil physicochemical assays (pH, CEC, soil organic carbon, inorganic N and P), enzyme assays (dehydrogenase, phosphatase, urease), plant biometric measurements (height, leaf area index, root length density), yield components (grain weight, kernel number, harvest index), and nutrient analyses (macro- and micronutrient content via ICP-OES). Microbial community dynamics are monitored by 16S rRNA gene amplicon sequencing (Illumina MiSeq, V3-V4 region) and metagenomic potential via shotgun sequencing for functional profiling; gene abundance associated with nitrogen fixation (nifH), phosphate solubilization (gcd, pqqC), and phytohormone pathways (acdS) are quantified by qPCR. Data analysis employs a hierarchical linear model to assess treatment effects on yield and soil-plant parameters, with ANOVA and post hoc Tukey tests for multiple comparisons. Regression analyses examine relationships between microbial functional gene abundance and agronomic outcomes. Community composition is analyzed using alpha/beta diversity metrics (Shannon, Simpson, Bray-Curtis) and ordination (PCA/NMDS), with PERMANOVA to test treatment effects. Structural equation modeling (SEM) tests causal pathways linking biofertilizer application, microbial mediation, soil health indicators, and crop yield. The study anticipates that the biofertilizer will enhance grain yield by 12–25% under optimal moisture and 6–15% under drought stress, accompanied by increased soil phosphatase activity and greater nifH gene abundance relative to controls. Expected shifts in microbial communities toward taxa associated with nutrient cycling and plant growth promotion are hypothesized, with improved root system architecture observed via root imaging in treated plots. The contribution to knowledge includes empirical evidence on consortium-based soil microbiome interventions tailored for tropical agro-ecosystems, an integrated framework linking microbial ecology to agronomic performance, and a decision-support toolkit for farmers and extension services. The study informs policy and practice by quantifying yield gains, nutrient use efficiency, and resilience benefits under climate variability, while identifying optimal carrier matrices and application regimes for scalable deployment. Final conclusions are expected to advocate for the adoption of targeted microbiome biofertilizers as a sustainable alternative or complement to chemical inputs in tropical cropping systems, with recommendations for site-specific formulation, quality control standards, regulatory considerations, and avenues for future research on long-term impacts and biodiversity effects.