Ecological Function and Diversity of the Endosphere Microbiome in Leaves and Fruits of Coffea arabica L. Across Elevation and Shade Gradients

Coffee is a globally important commodity that supports millions of livelihoods, from smallholder farmers to international traders. However, the sustainability of the coffee value chain is increasingly threatened by environmental changes. In this context, the phytomicrobiome, shaped by both environmental factors and plant genotypes, plays a vital role in plant health, productivity, and the quality of coffee beans. In this study, we explored the diversity and ecological functions of the endosphere microbiome in the leaves and fruits of Coffea arabica L. cultivated under an agroforestry system on Mount Gorongosa, within Gorongosa National Park, Mozambique. Using next‐generation sequencing, we characterized microbial communities along gradients of elevation and shade to assess how environmental variables shape microbiome composition and function. Our findings revealed a rich diversity of microbial communities, with elevation emerging as the primary driver of community structure. Taxonomic analyses showed that both elevation and shade significantly influenced the composition of bacterial and fungal communities. Microbial families such as Debaryomycetaceae, Enterobacteriaceae, Eremotheciaceae, Nocardiaceae, and Pseudonocardiaceae exhibited distinct adaptations to environmental conditions. Notably, we detected the presence of pathogenic genera (e.g., Colletotrichum , Erwinia , Fusarium , and Phaeosphaeria ) without visible disease symptoms, indicating possible plant tolerance to biotic stressors. Predicted functional pathways, including heme biosynthesis and phospholipid metabolism, alongside ecological guilds such as saprotrophs and fungal parasites, suggested microbial adaptations essential to maintaining plant health and coffee quality. Key microbial biomarkers, including Debaryomyces , Eremothecium , and Rhodococcus , emerged as indicators of functional adaptations across environmental gradients, highlighting their potential for informing optimized, environmentally responsive coffee management strategies. Altogether, the results highlight the integral role of coffee‐associated endophytes, in concert with plant genotypes, in shaping innovative, biodiversity‐driven strategies for sustainable coffee production.