Can Organic Amendments Override Environmental Filtering of Soil Microbiomes? Evidence From 20 Years Old Agricultural Field Trials in Contrasting Tropical Sites

ABSTRACT Soil microbial communities underpin ecosystem functions critical for sustainable agriculture, yet our understanding of how long‐term management of tropical agroecosystems shapes these communities remains limited. This is particularly the case in sub‐Saharan Africa where soil health challenges are most acute for food security. Using four long‐term (~20 years) experiments across contrasting agroecological zones in Kenya, we studied how organic inputs (farmyard manure, Tithonia diversifolia , Zea mays stover; applied at 4 Mg C ha −1 year −1 ) and nitrogen fertilizer (±120 kg N ha −1 per season as calcium ammonium nitrate) affect soil microbial communities. We combined amplicon sequencing of prokaryotic (16S rRNA) and fungal (ITS2) communities with quantification of nitrogen‐cycling functional genes to examine microbial diversity, community composition, and functional potential. Site‐level edaphic properties were the main correlate of community variation, namely 30% and 28% of prokaryotic and fungal β‐diversity, respectively. Despite this strong environmental control, farmyard manure created distinguishable community patterns across all sites, significantly affecting 65 prokaryotic genera and achieving 96% reclassification success for fungal communities. Prokaryotic and fungal communities exhibited contrasting response patterns: prokaryotes responded predominantly to farmyard manure through enrichment of copiotrophic Bacillota (formerly Firmicutes), while fungi were sensitive to both farmyard manure and T. diversifolia green manure, recruiting distinct decomposer guilds based on substrate biochemistry. Functional gene responses were amplified at the driest, most nutrient‐poor site, where farmyard manure led to a 30‐fold increase in the abundance of ammonia‐oxidizing bacteria compared to the control treatment. Mineral nitrogen fertilization alone did not produce distinct community composition but modestly reduced specific nitrogen‐cycling genes. This demonstrates that organic resource management, not mineral inputs, drives long‐term microbial community development. These findings provide decadal‐scale evidence that sustained organic amendments can generate predictable microbial responses across environmentally heterogeneous tropical landscapes, informing integrated soil fertility management strategies for sub‐Saharan Africa.