Fromsight to sequence: Underwater visual census vs eDNA metabarcoding for the monitoring of taxonomic and functional fish diversity

Fish monitoring is essential for assessing the effects of natural and
anthropic stressors on marine ecosystems. In this context, environmental
DNA (eDNA) metabarcoding appears to be a promising tool, due to its
efficiency in species detection. However, before this method can be fully
implemented in monitoring programs, more studies are needed to evaluate
its ability to assess the composition of fish assemblages compared with
traditional survey methods that have been used for decades. Here, we used
both eDNA metabarcoding and Underwater Visual Census (UVC) to assess the
taxonomic and functional diversity (presence-absence data) of
Mediterranean fish communities. We collected eDNA samples and performed
UVC strip transects inside and outside four Marine Protected Areas in the
Mediterranean Sea. Samples for eDNA analysis were collected by filtering
seawater simultaneously at the surface and the bottom, and DNA was
amplified using a combination of three sets of primers. We found that eDNA
alone made an outstanding characterisation of fish composition with the
detection of 95% of the 60 taxa identified in this study, whereas UVC
recovered only 58% of them. Functional diversity was better evaluated with
eDNA than with UVC, with the detection of a greater breadth of functional
traits. eDNA was even better at characterising functional than taxonomic
diversity, providing reliable information on ecosystem functioning with
little sampling effort. Together these results suggest that eDNA
metabarcoding offers great potential for surveying complex marine
ecosystems. Combining eDNA metabarcoding and UVC in integrated monitoring
programs would therefore improve monitoring strategies and enhance our
understanding of fish communities, a key step promoting their
conservation.