Beyond traditional biodiversity fish monitoring: environmental DNA metabarcoding and simultaneous underwater visual census detect different sets of a complex fish community at a marine biodiversity hotspot

Significant advances in the study of marine fish communities have been achieved with traditional monitoring methods and recently with novel genetic approaches. eDNA metabarcoding is one of them and a powerful tool for the study of biodiversity still in continuous development. Its applicability in marine ecology and conservation studies may be gauged by comparing its results with those of traditional methods. In the present investigation, we compare results from the underwater visual census (UVC) with eDNA metabarcoding (eDNA) carried out simultaneously in 24 rocky reef sites along the Gulf of California. We developed a two-PCR library preparation protocol followed by high throughput sequencing aimed at teleost fish. Our results show that both methods had different detection capabilities, and each registered different sets of fish taxa from rocky reefs, with some overlap. In particular, eDNA identified taxa from pelagic, demersal, and estuarine habitats beyond the rocky reef itself, suggesting differences in detection mainly attributed to the transport and permanence time of the eDNA in the ocean. Overlap in the detection with both methods increased with taxonomic level. We argue that substantial gaps in sequence reference databases for teleost are at the root of major discrepancies. Our results also confirm that PCR-based eDNA metabarcoding of seawater samples does not reflect patterns in abundance and biomass of species estimated from traditional methods. We discuss how to reconcile the results of eDNA metabarcoding and traditional methods in marine hotspots.