Abstract
Environmental DNA (eDNA) surveys are an increasingly important tool for biodiversity monitoring, providing unprecedented levels of resolution and sensitivity. Nevertheless, eDNA studies focussing on the detection of novel and resident species remain rare, and little is known about the effects that different environmental sample types have on species detectability. Here we evaluated the ability of eDNA metabarcoding to detect marine species by collecting sediment and water samples and performing eDNA metabarcoding of 18S rRNA and COI genes. We detected vastly different species assemblages between the studied environmental samples; with sediment containing significantly higher number of operational taxonomic units than water. We then compared the obtained datasets with previously published biodiversity surveys and found excellent concordance among different survey techniques, as well as novel species introductions. We conclude that careful consideration of type of environmental sample is needed when conducting biodiversity monitoring using eDNA, especially for studies focusing on community change.