Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

Abstract

Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research.

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

“…In previous studies on eDNA isolated from water samples, large volumes of water (e.g. 5 L; Wilcox et al, ) were used for filtration, and a study using a comparable volume of water (250 ml water for filtration) obtained variable results (Grey et al, ). It would thus seem advisable, based on our results and those of Grey et al () that a large volume of water be utilized.…”

“…5 L; Wilcox et al, ) were used for filtration, and a study using a comparable volume of water (250 ml water for filtration) obtained variable results (Grey et al, ). It would thus seem advisable, based on our results and those of Grey et al () that a large volume of water be utilized. In the present study, filtration was performed manually using considerably turbid water, which lead to rapid clogging of the filters.…”

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

“…Validation of the biosurveillance tool was considered highly successful because 19 NIS were identified from Departure Bay, of which five were known in BC but not previously recorded for Departure Bay and two were potential new records for BC (Table ). Using multiple gene regions confers two main advantages to increase the number of assigned taxa—variable evolutionary rates are complementary and able to spread detection capacity (Bohle & Gabaldón, ; Cristescu, ; Grey et al, ) and reference sequence data differs greatly among gene regions (Nilsson et al, ).…”

“…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, ; Grey et al, ; Lacoursière‐Roussel et al, ). However, the application is gaining popularity and refinement (Darling & Mahon, ; Holman et al, ; Klymus, Marshall, & Stepien, ; Macher et al, ; Shaw et al, ; Valentini et al, ) due to its power to improve detection efficiency.…”

“…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, ), substrate type (Holman et al, ; Koziol et al, ; Shaw et al, ), and primer choice (Grey et al, ), 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.…”