Tropical orchard soil microbiomes shaped by crop management harbor azole-resistant Candida tropicalis clade 4 as an integrated community member

Soil microbial communities represent one of the planet's most diverse ecosystems, performing essential ecological functions including nutrient cycling, plant growth promotion, and biological disease suppression. Agricultural practices reshape these communities, yet their interactions with agrochemical residues and opportunistic pathogens remain poorly characterized. We investigated how orchard management, azole fungicide residues, and Candida tropicalis presence influence soil microbial composition and functional profiles across 55 orchard soils (papaya, grape, wax apple) in Taiwan using 16S rRNA and ITS metabarcoding. Orchard management was the primary determinant of microbial community structure, explaining 10–11% of compositional variance and significantly structuring both bacterial and fungal functional guilds. Predictive functional annotation via FAPROTAX and FUNGuild revealed orchard-specific metabolic profiles, mostly enriched for anaerobic fermentation, iron respiration, and methanol oxidation. Neither C. tropicalis presence nor azole residues significantly altered overall community composition. However, cumulative azole burden selectively suppressed fungal but not bacterial diversity. Cross-kingdom co-occurrence analysis revealed that C. tropicalis clade 4 showed exclusively positive co-occurrence with 8 microbial taxa. These findings demonstrate that agricultural management overwhelms pathogenic and chemical drivers in structuring soil microbiomes, while total azole concentration exposure drives shifts in fungal diversity, and the C. tropicalis clade 4 may act as integrated community members.