Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

Biodiversity monitoring in aquatic ecosystems is challenging as it requires taxonomic expertise and is difficult to automate. One expedient approach is the use of environmental DNA (eDNA) surveys to infer species incidence from nucleic acids found in environmental samples. An advantage of eDNA surveys is that they allow rapid detection of non-indigenous species (NIS), lessening the time from introduction to discovery and increasing the likelihood of successful control and / or eradication. Despite this, relatively few studies have compared eDNA and traditional surveys for the study of NIS, or examined the differences between metabarcoding of different environmental sample types. We evaluated the ability of eDNA to detect a broad range of native and NIS in urban coastal environments, and compared the results with previously published traditional surveys. We collected water and sediment samples from the same sites and then performed eDNA metabarcoding of 18S rRNA and COI genes. We found very different patterns of biodiversity in water and sediment samples; with sediment containing more than two times the number of operational taxonomic units (OTUs) than seawater in some cases. The findings showed the presence of as much variation in assemblage diversity among environmental sample types as amongst geographically-segregated sampling sites. Additionally, species detection within phyla was not consistent in water or sediment samples, indicating that at a broad scale sample type does not perfectly predict taxa detected. We found almost perfect agreement in species detection from eDNA and traditional surveys. Additionally, eDNA metabarcoding detected three previously undocumented species introductions. Finally, our work provided a novel high-resolution biodiversity dataset for urban marine environments. Synthesis and applications: Our study showed that the type of eDNA sample dramatically affects the detected biodiversity and that eDNA metabarcoding is accurate for the detection of notorious NIS. Natural resource managers, ecological practitioners and researchers should consider the benefits of integrating molecular tools such as eDNA into applied ecology.