Exploring the Coffee Fruit Microbiome under Different Management Practices and its Correlation with Beverage Quality Criteria in Costa Rica

The microbiome associated with coffee berries plays a vital role in shaping the sensory profile of coffee beverages. This study examined the bacterial and fungal communities present in the epiphytic and endophytic microbiota of Coffea arabica L. berries grown under two contrasting agronomic practices: conventional and sustainable practices in Costa Rica. The microbial composition and diversity in the harvested berries were evaluated using high-throughput sequencing of the 16 S rRNA gene and ITS region. Additionally, sensory analysis was performed to explore the potential relationship between microbial community structure and in-cup quality attributes. Amplicon sequencing yielded 5,617,926 and 4,413,659 high-quality bacterial and fungal sequences, respectively. Alpha diversity analysis revealed greater fungal richness and uniformity in the sustainable system, whereas the bacterial richness was comparable between the two treatments. Core microbiome analysis identified 17 fungal and 17 bacterial genera shared across all farms, with Glomeromycota and Mucoromycota found exclusively in sustainably managed farms. Functional predictions for fungi suggest increased saprotrophic activity under sustainable practices. Despite the absence of statistically significant differences in sensory scores between treatments, Spearman’s correlation analysis revealed stronger positive associations between microbial taxa and sensory traits in sustainable berries. A novel symbolic dimension reduction approach using Uniform Variety Approximation Projections (UMAP) and Canberra distance projected the integrated dataset (sensory, brix, and color) into a conceptual space defined solely by treatment and variables. The method distinguished between both treatments and identified six significant subgroups. This study represents the first comprehensive investigation of the microbial communities associated with coffee berries in Costa Rican farms. The findings support the hypothesis that sustainable agricultural practices influence the microbiota of coffee berries, shaping both their microbial diversity and functional potential. The research provides new insights into the ecological and functional dynamics of coffee berry microbiomes, and their implications for coffee quality and sustainable production strategies.