Argan fruit microbiomes: influence of biogeographic and soil driven environmental factors

Argan tree (Sideroxylon spinosum L.), also known as Argania spinosa, is an endemic woodland species in Morocco. Its fruit has multiple uses for food, cosmetics, and traditional medicine. Despite their importance, argan fruit microbiomes remain unexplored. In this study, we investigated the diversity and biogeographical patterns of the microbial communities associated with argan fruits. Bacterial and fungal communities were characterized from 36 argan trees across four locations, Agadir, Essaouira, Rabat and Berkane, along a 1,000 km transect, with altitudes ranging from 66 to 794 m above sea level. Our finding revealed significant variation in both fresh (p = 0.0108) and dry (p = 0.0191) fruit weights across locations, suggesting a geographic influence on fruit biomass. Alpha diversity analysis showed significantly higher bacterial richness in Agadir (p < 0.05), while fungal diversity did not differ significantly across sites (p > 0.05). Pantoea was the dominant bacterial genus (up to 89.0%), and Hanseniaspora was the dominant fungal genus (up to 82.4%). We also found correlations between microbial genera and environmental factors, such as altitude, soil pH, nutrient levels and calcium carbonate content. Pantoea abundance was positively correlated with clay content (p = 0.045). Alternaria abundance was positively associated with soil pH (p = 0.0092) and negatively associated with electric conductivity (p = 0.0026) and nitrate concentration (p = 0.039). No significant differences in microbial community composition were detected among locations. This study reveals distinct biogeographic patterns in the Argan fruit-associated microbiome, shaped by soil properties and geographic location. Core taxa, including Pantoea and Hanseniaspora, were consistently dominant, alongside site-specific microbial signatures. These findings provide a foundation for microbiome-informed strategies to support Argan tree conservation and sustainable cultivation.