Patterns of microbial diversity in three aquatic ecosystems of a Caribbean island

The functioning of various aquatic ecosystems is greatly influenced by the composition of their microbial communities. However, the prokaryotic and eukaryotic organisms present in the microbiome remain to be characterized in the waters of various tropical islands. Here, we used DNA metabarcoding to assess differences in the richness and abundance of prokaryotic and eukaryotic microbial communities in coastal, mangrove, and urban surface waters in Guadeloupe (French West Indies). We found that turnover was an important driving force in these three compartments, and that the urban compartment was the most diverse. We identified 119 prokaryotic and 80 eukaryotic OTUs with differential abundance between these three compartments. Furthermore, functional predictions revealed the importance of photosynthetic organisms (including Bacillariophyceae, Chrysophyceae, Chlorophyceae and Cyanobacteria) in the three compartments, and an enrichment of urban waters in chemoheterotrophic prokaryotes and eukaryotic consumers. Interestingly, we detected several putative harmful algal bloom taxa never before described in Guadeloupe. By cataloging the taxa restricted to particular water bodies, this inventory will facilitate analyses of the long-term effects of urbanization and industrialization on the evolution of microbial assemblages in Guadeloupe.