Long-term farming systems and climatic variability shape soil fungal diversity and community structure in Kenyan tropical agroecosystems

Background Soil fungi play central roles in nutrient cycling, organic matter turnover, and plant-soil interactions. However, their responses to contrasting farming systems, nitrogen inputs, crop phenology, and climate variability in tropical agroecosystems remain poorly documented. Long-term datasets from Sub-Saharan Africa are particularly scarce. Methods This study assessed soil fungal diversity and community composition after 15 years of continuous management in the Farming Systems Comparison Trial (SysCom) at two Kenyan sites representing humid highland (Chuka) and semi-arid lowland (Thika) conditions. Four systems were evaluated: Conventional High-input, Conventional Low-input, Organic High-input, and Organic Low-input. Soil samples were collected across major crop growth stages in cereal and potato rotations. Fungal communities were profiled using ITS-based Illumina MiSeq sequencing and analyzed with DADA2 and phyloseq. Diversity metrics, β-diversity, environmental correlations, and differential abundance were assessed in relation to soil chemical properties and climatic variables. Results Farming system, input intensity, nitrogen form, crop stage, and site climate jointly shaped fungal community structure. Chuka’s wetter conditions supported more stable and diverse assemblages, whereas Thika exhibited stronger temporal turnover linked to rainfall variability. Organic systems especially those integrating legumes and mulches harbored richer and more functionally diverse fungal communities dominated by saprotrophic, mycorrhizal, and entomopathogenic genera (e.g., Mortierella , Glomus , Purpureocillium , Beauveria ). Conventional systems contained higher proportions of opportunistic or xerotolerant taxa such as Fusarium , Aspergillus , and Wallemia . Ammonium-N, available P, and soil pH were the strongest abiotic drivers of community assembly. Fungal succession followed crop phenology, with saprotrophs dominating early crop stages and mutualistic and ligninolytic taxa prevailing toward maturity. Conclusions After 15 years, organic low and high-input systems enhanced fungal richness, evenness, and community stability relative to conventional low-input systems. Integration of organic nutrient sources, legumes, mulches, and adaptive water management promotes diverse and resilient fungal communities in tropical agroecosystems. These results highlight the value of ecological intensification for sustaining soil biodiversity and nutrient cycling under increasing climatic uncertainty.