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

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.

A new approach to molecular biosurveillance of invasive species using DNA metabarcoding

“…This conspicuous pattern indicates that assessed community structure is influenced by substrate type, which is supported by recent aquatic eDNA metabarcoding studies (Holman et al, 2019;Koziol et al, 2019). Aquatic metabarcoding is typically performed on filtered water samples; however, it is becoming apparent that additional substrate types need to be incorporated given mounting evidence for substrate bias in community biodiversity studies (Koziol et al, 2019) and NIS studies (Holman et al, 2019). Differences in community structure between surveys explained a smaller proportion of total variance but were still significant for all assigned species (R 2 = .08; p < .01; Figure 3c) and NIS (R 2 = .05; p < .01; Figure 3d).…”

“…explained the highest proportion of total variance for all assigned taxa (R 2 = .25; p < .01; Figure 3a) and NIS (R 2 = 0.17; p < .01; Figure 3b). This conspicuous pattern indicates that assessed community structure is influenced by substrate type, which is supported by recent aquatic eDNA metabarcoding studies (Holman et al, 2019;Koziol et al, 2019). Aquatic metabarcoding is typically performed on filtered water samples; however, it is becoming apparent that additional substrate types need to be incorporated given mounting evidence for substrate bias in community biodiversity studies (Koziol et al, 2019) and NIS studies (Holman et al, 2019).…”

“…Metabarcoding for NIS detection is in its infancy and thus far has largely been applied within an exploratory context using "universal" or "near-universal" primers (Borrell, Miralles, Do Huu, Mohammed-Geba, & Garcia-Vazquez, 2017;Grey et al, 2018;Lacoursière-Roussel et al, 2018). However, the application is gaining popularity and refinement (Darling & Mahon, 2011;Holman et al, 2019;Klymus, Marshall, & Stepien, 2017;Macher et al, 2018;Shaw et al, 2016;Valentini et al, 2016) due to its power to improve detection efficiency. There are unique differences between metabarcoding for NIS detection and for its more classical application to describe community biodiversity, and these differences necessitate an entirely revised technical and logistical framework.…”

“…Field-based DNA sampling considerations are equally important for maximizing NIS detection efficiency. Community biodiversity and NIS detection identified through metabarcoding are highly dependent on sampling effort (i.e., number of samples/replicates; Grey et al, 2018), substrate type (Holman et al, 2019;Koziol et al, 2019;Shaw et al, 2016), and primer choice , all of which need to be tailored to the species of interest to maximize the chances of detection. For example, early NIS detection in the Northeast Pacific relies on capturing individuals that are either rare or have a non-uniform distribution within the vast ocean ecosystem.…”

Linking Environmental DNA and RNA for Improved Detection of the Marine Invasive Fanworm Sabella spallanzanii

“…Sample type and volume have been shown to have a significant effect on recovered biodiversity but also on particular detections of certain organisms (Moyer et al, 2014;Nascimento et al, 2018). Sampling strategies need to be adapted toward the target species' biological traits and life cycle (Rees et al, 2014;Furlan and Gleeson, 2017;Harper et al, 2018;Holman et al, 2019). Sabella spallanzanii has a very short free-swimming larval phase (2-3 weeks) but primarily lives attached to hard substrates, typical to invasive hull foulers (Lee et al, 2018).…”