There is almost no systematic information about the state of marine ecosystems in Aruba. A recent report commissioned by the United Nations Development Program (Pantin 2011) also noted an almost complete lack of information on Aruba’s ecological resources, carrying capacity, limits of acceptable change and the existing level of environmental stress. The Government of Aruba therefore aims to create an assessment program to monitor the status and changes in the reef communities along its coastline. CARMABI, a Curaçaoan foundation specializing in tropical marine research, was selected to conduct the baseline assessment in collaboration with the Scripps Institution of Oceanography (U.S.A.) and the Global Coral Reef Monitoring Network (U.S.A.).
Human activities can degrade the quality of coral reefs, cause a decline in fish species richness and functional diversity and an erosion of the ecosystem services provided. Environmental DNA metabarcoding (eDNA) has been proposed as an alternative to Underwater Visual Census (UVC) to offer more rapid assessment of marine biodiversity to meet management demands for ecosystem health indices. Taxonomic information derived from sequenced eDNA can be combined with functional traits and phylogenetic positions to generate a variety of ecological indices describing ecosystem functioning. Here, we inventoried reef fish assemblages of two contrasted coastal areas of Cura¸cao, (i) in close proximity to the island’s capital city and (ii) in a more remote area under more limited anthropogenic pressure. We sampled eDNA by filtering large volumes of sea water (2 x 30L) along 2km boat transects, which we coupled with species ecological properties related to habitat use, trophic level and body size to investigate the difference in fish taxonomic composition, functional and phylogenetic indices recovered from eDNA metabarcoding between these two distinct coastal areas. Despite no marked difference in species richness, we found a higher phylogenetic diversity in proximity to the city, but a higher functional diversity on the more isolated reef. Composition differences between coastal areas were associated with different frequencies of reef fish families. Because of a partial reference database, eDNA only partly matched those detected with UVC, but eDNA surveys nevertheless provided rapid and robust species occupancy responses to contrasted environments. eDNA metabarcoding coupled with functional and phylogenetic diversity assessment can serve the management of coastal habitats under increasing threat from global changes.