Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments

Abstract

Monitoring introduction and spread of nonindigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability, and the time‐consuming morphological approach used for taxonomic identification. Metabarcoding represents a promising alternative for rapid comprehensive port biological baseline surveys, but its application in this context requires further assessments. We applied metabarcoding (based on barcodes of the cytochrome c oxidase subunit I and of the 18S ribosomal RNA gene) to 192 port samples collected (a) from diverse habitats (water column—including environmental DNA and zooplankton, sediment, and fouling structures), (b) at different sites (from inner to outer estuary), and iii) during the four seasons of the year. By comparing the biodiversity metrics derived from each sample group, we show that each sampling method resulted in a distinct community profile and that environmental DNA alone cannot substitute for organismal sampling, and that, although sampling at different seasons and locations resulted in higher observed biodiversity, operational results can be obtained by sampling selected locations and seasons. By assessing the taxonomic composition of the samples, we show that metabarcoding data allowed the detection of previously recorded nonindigenous species as well as to reveal presence of new ones, even if in low abundance. Synthesis and application. Our comprehensive assessment of metabarcoding for port biological baseline surveys sets the basics for cost‐effective, standardized, and comprehensive monitoring of nonindigenous species and for performing risk assessments in ports. This development will contribute to the implementation of the recently entered into force International Convention for the Control and Management of Ships' Ballast Water and Sediments.

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

“…However, studies employing both eDNA and bulk organismal samples suggest that eDNA alone cannot replace organismal sampling (e.g. Leduc et al 2019, Huhn et al 2020, Rey et al 2020, Westfall et al 2020). Currently, it would probably work best as an early alert system or exploratory method to be used as a complement to conventional approaches such as in situ visual confirmation (Borrell et al 2018, Holman et al 2019, Rey et al 2020, specimen collection (Leduc et al 2019, Huhn et al 2020 or followed by active surveillance with digital drop PCR (ddPCR) or quantitative PCR (qPCR) (Wood et al 2019).…”

“…1B). Zooplankton sampling has been conducted in ships ballast water (Zaiko et al 2015a,b, Ghabooli et al 2016, Darling et al 2018, Lin et al 2020, boats bilge water (Fletcher et al 2017), and in sea water in ports and marinas or nearby natural habitats , Zaiko et al 2015c, Abad et al 2016, Stefanni et al 2018, Couton et al 2019, Leduc et al 2019, Rey et al 2020, Westfall et al 2020. The monitoring of larvae in plankton samples in ports or in the close vicinities, may provide key information about NIS introduction status or detect their presence at an earlier stage (Couton et al 2019).…”

“…Compared to water, the collection of sediments to survey eukaryotic organisms has received much less attention, and to our knowledge has been attempted only in 6 studies (Table S2, Fig. 1B, Koziol et al 2018, Holman et al 2019, Leduc et al 2019, Shang et al 2019, Shaw et al 2019, Rey et al 2020. Metabarcoding of eDNA extracted from sediments can provide a rapid screen for a wide range of taxa in ballast tanks and marine port sediments (Holman et al 2019, Shang et al 2019, Shaw et al 2019.…”

“…Early detection through metabarcoding can help prevent spread to new locations, where they can result in toxic blooms and have devastating impacts on ecosystems (Shang et al 2019, Shaw et al 2019). On the other hand, benthic invertebrates have been only surveyed in two studies using metabarcoding in NIS surveillance (Leduc et al 2019, Rey et al 2020. Benthic habitats can be very complex and benthic communities very patchy, which increases the possibility of missing taxa when sampling invertebrates from sediments (Leduc et al 2019).…”

“…Despite the great potential of DNA metabarcoding to improve NIS monitoring in marine and coastal ecosystems (Pochon et al 2013, Ardura et al 2015, Zaiko et al 2015a,b,c, Borrell et al 2018, Westfall et al 2020, the widespread and routine implementation of this method is still highly dependent on reliable and cost-effective standardization (Leese et al 2016, Rey et al 2020. In this study, we carried out a comprehensive compilation and evaluation of methodologies employed across the full workflow (e.g.…”