Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring.

Nonindigenous species are introduced worldwide with ballast water (BW). To prevent further introductions, oceanic BW exchange and BW treatment systems are utilized, but their performance needs to be evaluated. To that aim, characterizing BW communities is essential but usually relies on exhaustive sampling and morphological taxonomic identification, which does not always allow fine-scale taxonomic resolution. Through the analysis of BW samples from 11 vessels arriving to the Chesapeake Bay (USA), we evaluated the potential of environmental DNA (eDNA) metabarcoding for BW monitoring by assessing whether the impact of BW management type could be identified, analyzing the influence of BW sampling access locations on communities, and comparing the accuracy of eDNA for taxonomic assignment and identification of nonindigenous taxa. We found that (1) different sampling access locations of the same tank resulted in different communities, (2) communities from treated and exchanged BW differ, (3) signals of source port and of ocean exchange are observed, (4) eDNA metabarcoding results in more diversity than morphological taxonomy, and (5) the nonindigenous copepod Oithona davisae, not reported before in the Chesapeake Bay, is detected. Overall, this study highlights the potential of eDNA metabarcoding for BW monitoring, but more comprehensive sampling will be needed to optimize the approach.

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

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.

Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area.

Current methods for monitoring marine fish (including bony fishes and elasmobranchs) diversity mostly rely on trawling surveys, which are invasive, costly, and time-consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we used environmental DNA (eDNA), the DNA present in the water column as part of shed cells, tissues, or mucus, to provide comprehensive information about fish diversity in a large marine area. Further, eDNA results were compared to the fish diversity obtained in pelagic trawls. A total of 44 5 L-water samples were collected onboard a wide-scale oceanographic survey covering about 120,000 square kilometers in Northeast Atlantic Ocean. A short region of the 12S rRNA gene was amplified and sequenced through metabarcoding generating almost 3.5 million quality-filtered reads. Trawl and eDNA samples resulted in the same most abundant species (European anchovy, European pilchard, Atlantic mackerel, and blue whiting), but eDNA metabarcoding resulted in more detected bony fish and elasmobranch species (116) than trawling (16). Although an overall correlation between fishes biomass and number of reads was observed, some species deviated from the common trend, which could be explained by inherent biases of each of the methods. Species distribution patterns inferred from eDNA metabarcoding data coincided with current ecological knowledge of the species, suggesting that eDNA has the potential to draw sound ecological conclusions that can contribute to fish surveillance programs. Our results support eDNA metabarcoding for broad-scale marine fish diversity monitoring in the context of Directives such as the Common Fisheries Policy or the Marine Strategy Framework Directive.