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 analyzing animal diets. Currently, metabarcoding, a PCR-based method, is the method of choice for analyzing such data. However, this method has limitations, specifically PCR bias, which can result in the overestimation of the importance of certain taxa and the failure to detect other taxa because they do not amplify. The present study compared metabarcoding with metagenomics, a marker-free method, to assess the diversity of prey items in the feces of a critically endangered South African estuarine pipefish, Syngnathus watermeyeri, and its widely distributed congener (S. temminckii) to investigate the potential dietary competition. Our results showed a distinct difference between the diets of S. watermeyeri and S. temminckii, with the former mainly consuming calanoid copepods and the latter preferring caridean shrimp. Metagenomics produced more species identifications than metabarcoding; however, most of the species identified are not present in South Africa. The identifications made by both methods mostly belonged to the same families, but some prey items were identified only by either method. Both methods would benefit from a complete reference database of South African estuarine macroinvertebrates.