Can organic amendments override environmental filtering of soil microbiomes? Evidence from 20 years across contrasting tropical agricultural sites.

Soil microbial communities underpin ecosystem functions critical for sustainable agriculture, yet understanding of how long-term management shapes these communities in tropical agroecosystems remains limited, particularly in sub-Saharan Africa where soil health challenges are most acute. Using four long-term experiments (~20 years) across contrasting agroecological zones in Kenya, we investigated whether sustained organic resource management can override environmental filtering to reshape soil microbial communities. We combined amplicon sequencing of prokaryotic (16S rRNA) and fungal (ITS2) communities with quantification of nitrogen-cycling functional genes to assess how organic amendments (farmyard manure, Tithonia diversifolia, Zea mays stover) and mineral nitrogen fertilization shaped microbial diversity, community composition, and functional potential. Site-level edaphic properties dominated community variation, explaining 30% and 28% of prokaryotic and fungal β-diversity, respectively. Despite strong environmental control, farmyard manure created distinguishable community patterns across all sites, significantly affecting all 66 responsive prokaryotic genera and achieving 96% reclassification success for fungal communities. Prokaryotes responded predominantly to farmyard manure through enrichment of copiotrophic Firmicutes, while fungi demonstrated dual sensitivity to both farmyard manure and T. diversifolia, recruiting distinct decomposer guilds based on substrate biochemistry. Functional gene responses were amplified in sandy, nutrient-poor soils, where farmyard manure increased ammonia-oxidizing bacteria by over 1000% compared to controls. Mineral nitrogen fertilization alone produced no distinct community composition and suppressed specific nitrogen-cycling genes, demonstrating that organic resource management drives long-term microbial community development. These findings provide decadal-scale evidence that sustained organic amendments generate predictable microbial responses across heterogeneous tropical landscapes, informing integrated soil fertility management in sub-Saharan Africa.