Abstract
Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.
Highlights
Environmental DNA surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data
We demonstrated that the type of environmental sample in Environmental DNA (eDNA) metabarcoding studies affects the measured community composition, indicating that the most comprehensive assessment of biodiversity in a given community comes from the collection of multiple environmental sample types
We demonstrate that type of environmental sample can affect the detection of both whole community composition and particular species of concern
Summary
Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Such surveys often focus on the detection of a specific taxonomic group that are being targeted, with no ability to retrospectively separate mis-identified species in light of new species discoveries This is of critical importance for biodiversity monitoring as an increasing number of studies are revealing the widespread presence of molecular cryptic species (i.e. morphologically similar but genetically distinct species[8]). Validity and replicability rely on appropriate experimental design and an understanding of the effects of methodological choices during sampling, sequencing library preparation and bioinformatic analysis[23,24] It is well-established that eDNA surveys are highly informative and can complement other biodiversity monitoring methods[25], eDNA studies assessing how different sampling techniques affect species detectability remain rare[26]. Specific sampling and surveying protocols are needed to study marine organisms in these environments, with eDNA surveys offering huge potential for early detection and management of NIS
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