DNA metabarcoding unveils niche overlapping and competition among Caribbean sea urchins

Detailed information of trophic interactions among consumer–resources in food webs is usually limited due to the lack of accurate identification of eaten food resources. The use of DNA-metabarcoding has been proven useful for molecular identification of the numerous taxa present in stomach contents. Here, we characterize the diet and trophic behavior of four sea urchin species inhabiting shallow waters of Puerto Rico using this molecular technique. We extracted, sequenced, and analyzed DNA from the gut content of a total of 60 individuals collected at three sites at the northeastern coast of Puerto Rico. Our results demonstrated that seaweeds were the dominant food source for the four sea urchin species at all three sites, but also small protists, fungi and metazoans were important components of sea urchin’s diet. Interspecific differences in diet were also found among sites. PERMANOVA analysis detected significant differences among species (Pseudo-F 1.755, p < 0.001), and among sites (Pseudo-F 2.52, p < 0.001). A SIMPER analysis showed that in all cases the main taxa causing differences between species and sites were macroalgae (Rhodophyta, Chlorophyta and Ochrophyta) with some contribution of small eukaryotes (Apicomplexa and Bacillariophyta). This diet characterization in sea urchins revealed a generalist omnivore behavior, but with a clear dominance of algae as a main dietary component. Thus, we found a potential inter-specific competition due to niche overlapping, which seems to be more common than initially thought