eDNA metabarcoding vs metagenomics: an assessment of dietary competition in two estuarine pipefishes

Understanding the dietary preferences of endangered species can be useful in implementing conservation strategies, including habitat restoration, translocation, and captive breeding. Environmental DNA (eDNA) from feces provides a non-invasive method for analysing animal diets. Currently, metabarcoding, PCR-based approach, is choice such data. However, this has limitations, specifically PCR bias, which result overestimation importance certain taxa failure to detect other because they do not amplify. The present study compared metabarcoding with metagenomics, PCR-free method, assess diversity prey items critically South African estuarine pipefish, Syngnathus watermeyeri , its widely distributed congener S. temminckii investigate potential competition. results showed distinct difference between diets former mainly consuming calanoid copepods latter preferring caridean shrimp. In each case, single dominated sequences generated by metabarcoding. Metagenomics produced more identifications, although same trend was found regarding preference that shrimp, approach identified additional, albeit yet unidentified, copepod as being important diet . We conclude lower number using most likely amplification resulting key missing analysis. These findings suggest metagenomics only complementary molecular analysis, but may some cases outperform even strongly affected lack reference than majority originate genomic regions have been sequenced putative question.