Using eDNA to biomonitor fishes in a tropical lake

Background: Environmental DNA (eDNA) is an effective approach for detecting vertebrates and plants in various ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the future goal to detect possible invasion of the Amazon sailfin catfish Pterygoplichthys pardalis. Methodology/Principal Findings: Replicate sediment and water samples were collected from eight stations in Lake Bacalar on three occasions in 2015-2016. Each sample was stored in the presence or absence of lysis buffer to permit comparison of eDNA recovery. Short fragments (184-187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers, and then sequenced on Ion Torrent PGM and S5, before their source species were identified using custom reference sequence databases constructed on BOLD. The eDNA sequences from water samples delivered coverage for substantially more species than those from sediments. In total, the eDNA sequences derived from 47 species of fishes, 2 1 amphibians, 15 birds, 76 mammals, and 3 reptiles. Although all 73 species are known from this region, six of the fish species represent new records for Lake Bacalar. Sequences for 2 birds, 21 mammal and 1 reptile were only detected from sediments, while 51 species were only found in water. Because DNA from the sailfin catfish was not detected in any field samples, we conducted a mock eDNA experiment to ensure that our methodology and PCR primers are appropriate for the detection of Pterigoplichthys species. Conclusions/Significance: We developed field sampling protocols and a NGS pipeline that enables fish eDNA recovery from tropical aquatic ecosystems with potential to detect invasive Pterigoplichthys species.