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

Soil fungi play important roles in organic matter decomposition, nutrient cycling, and plant-soil interactions. However, their responses to contrasting farming systems, input intensity, crop phenology, and climatic variability in tropical agroecosystems remain insufficiently documented particularly in Sub-Saharan Africa where long-term datasets are scarce. This study assessed soil fungal diversity and community composition after more than 15 years of continuous management in the Farming Systems Comparison in the Tropics (SysCom) trial at two Kenyan sites representing contrasting agroecological conditions: a humid highland site (Chuka) and semi-arid site (Thika). Four farming systems were evaluated: conventional high input (Conv-High), conventional low input (Conv-Low), organic high input (Org-High), and organic low input (Org-Low). Soil samples were collected across key crop growth stages in cereal- and potato-based rotations. Fungal communities were characterized using ITS-based Illumina MiSeq sequencing and analyzed using DADA2 and phyloseq. Prior to diversity analyses, sequence data were rarefied to an equal sequencing depth to account for uneven sequencing effort (17,500 reads per sample for Chuka and 32,300 reads per sample for Thika). Alpha and beta diversity, ordination, and exploratory differential abundance analyses were conducted in relation to soil chemical properties and site conditions. Fungal community composition varied across farming systems, input intensity, crop growth stages, seasons, and sites. Differences in alpha diversity were generally modest and context-dependent across sites and seasons, whereas clearer patterns were observed in community composition. Organic systems were frequently associated with higher relative abundances of taxa such as Mortierella, Purpureocillium, Beauveria, Serendipita, and Flammulina, while conventional systems were more often associated with taxa including Fusidium, Cladosporium, Alternaria, and Wallemia. Associations between fungal community composition and soil chemical variables particularly ammonium-N, available phosphorus, and pH were detected at the semi-arid Thika site but not at the humid Chuka site, highlighting strong site-specific responses. Crop growth stage and season were also associated with shifts in the relative abundance of fungal taxa, as indicated by exploratory differential abundance analyses. This long-term study shows that soil fungal community composition in Kenyan tropical agroecosystems varies with management intensity, crop development, and site conditions. The findings underscore the importance of long-term, context-aware research for understanding how diversified nutrient management and cropping practices are associated with soil fungal community patterns in tropical farming systems.