Integrating invasive species risk assessment into environmental DNA metabarcoding reference libraries

Environmental DNA (eDNA) metabarcoding has shown promise as a tool for estimating biodiversity and early detection of invasive species. In aquatic systems, advantages of this method include the ability to concurrently monitor biodiversity and detect incipient invasions simply through the collection and analysis of water samples. However, depending on the molecular markers chosen for a given study, reference libraries containing target sequences from present species may limit the usefulness of eDNA metabarcoding. To explore the extent of this issue and how it may be resolved to aid biodiversity and invasive species early detection goals, we focus on fishes in the well-studied Laurentian Great Lakes region. First, we provide a synthesis of species currently known from the region and of non-indigenous species identified as threats by international, national, regional, and introduction pathway-specific fish risk assessments. With these species lists, we then evaluate 23 primer pairs commonly used in fish eDNA metabarcoding with available databases of sequence coverage and species specificity. Finally, we identify established and potentially invasive non-indigenous fish that should be prioritized for genetic sequencing to ensure robust eDNA metabarcoding for the region. Our results should increase confidence in using eDNA metabarcoding for fisheries conservation and management in the Great Lakes region and help prioritize reference sequencing efforts. The ultimate utility of eDNA metabarcoding approaches will come when conservation management of existing fish communities is integrated with early detection efforts for invasive species surveillance to assess total fish biodiversity.

Ballast water-mediated species spread risk dynamics and policy implications to reduce the invasion risk to the Mediterranean Sea

This study helps understand the ballast water-mediated species spread risk dynamics in the Mediterranean and examine potential policy options for ballast water management to further reduce species spread risk in the region. Results show that Gibraltar, Suez, and Istanbul remained high-risk ports from 2012 to 2018, and they are hub ports connecting several clusters. We reveal ballast water management implications for both the Mediterranean region and individual hub ports respectively. To further reduce the risks of individual Mediterranean hub ports beyond the IMO standards, the most effective (cost-effective) regulatory method is to set more stringent regulation towards such hub ports besides the IMO regulation. To further reduce the risks of the Mediterranean as a whole, the most effective (cost-effective) regulatory scenario is to set more stringent regulation towards all Mediterranean ports besides the IMO regulation. The barge-based method is the most cost-effective technology to achieve stricter regulations.

Integrated Biological Risk and Cost Model Analysis Supports a Geopolitical Shift in Ballast Water Management

This work evaluates efficacies of plausible ballast water management strategies and standards by integrating a global species spread risk assessment with a policy cost-effectiveness analysis. Specifically, we consider species spread risks and costs of port- and vessel-based strategies under both current organism concentration standards and stricter standards proposed by California. For each scenario, we estimate species spread risks and patterns using a higher-order analysis of a global ship-borne species spread model and estimate fleet costs for vessel- and barge-based ballast water treatment systems for each standard. We find that stricter standards may reduce species spread risk by a factor of 17 globally and would greatly simplify the complex network of ship-borne species spread. The current policy of IMO standards is most cost-effectively achieved through ship-based treatment, and that any additional risk reduction will be most cost-effectively achieved by port-based (or barge-based) technologies, particularly if these are strategically implemented at the top ports within the largest clusters. Barge-based ballast water management would require a shift in governance, and we suggest that this next level of policymaking could be feasible for special areas designated by the IMO, by State or multistate authorities, or by voluntary port applications.

Network analysis of ballast-mediated species transfer reveals important introduction and dispersal patterns in the Arctic

Rapid climate change has wide-ranging implications for the Arctic region, including sea ice loss, increased geopolitical attention, and expanding economic activity resulting in a dramatic increase in shipping activity. As a result, the risk of harmful non-native marine species being introduced into this critical region will increase unless policy and management steps are implemented in response. Using data about shipping, ecoregions, and environmental conditions, we leverage network analysis and data mining techniques to assess, visualize, and project ballast water-mediated species introductions into the Arctic and dispersal of non-native species within the Arctic. We first identify high-risk connections between the Arctic and non-Arctic ports that could be sources of non-native species over 15 years (1997-2012) and observe the emergence of shipping hubs in the Arctic where the cumulative risk of non-native species introduction is increasing. We then consider how environmental conditions can constrain this Arctic introduction network for species with different physiological limits, thus providing a tool that will allow decision-makers to evaluate the relative risk of different shipping routes. Next, we focus on within-Arctic ballast-mediated species dispersal where we use higher-order network analysis to identify critical shipping routes that may facilitate species dispersal within the Arctic. The risk assessment and projection framework we propose could inform risk-based assessment and management of ship-borne invasive species in the Arctic.

Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method

The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol in these environments, seawater samples were collected in a commercial port and methodologies for concentrating and purifying eDNA were tested for their effect on eukaryotic DNA yield and subsequent richness of Operational Taxonomic Units (OTUs). Different filter materials [Cellulose Nitrate (CN) and Glass Fibre (GF)], with different pore sizes (0.5 µm, 0.7 µm and 1.2 µm) and three previously published liquid phase extraction methods were tested. The number of eukaryotic OTUs detected differed by a factor of three amongst the method combinations. The combination of CN filters with phenol-chloroform-isoamyl alcohol extractions recovered a higher amount of eukaryotic DNA and OTUs compared to GF filters and the chloroform-isoamyl alcohol extraction method. Pore size was not independent of filter material but did affect the yield of eukaryotic DNA. For the OTUs assigned to a highly successful non-indigenous species, Styelaclava, the two extraction methods with phenol significantly outperformed the extraction method without phenol; other experimental treatments did not contribute significantly to detection. These results highlight that careful consideration of methods is warranted because choice of filter material and extraction method create false negative detections of marine eukaryotic OTUs and underestimate taxonomic richness from environmental samples.

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

Because significant global changes are currently underway in the Arctic, creating a large-scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio-temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large-scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern-based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well-mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI-based eDNA metabarcoding may quickly improve large-scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.

Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs

Following decades of ecologic and economic impacts from a growing list of nonindigenous and invasive species, government and management entities are committing to systematic early- detection monitoring (EDM). This has reinvigorated investment in the science underpinning such monitoring, as well as the need to convey that science in practical terms to those tasked with EDM implementation. Using the context of nonindigenous species in the North American Great Lakes, this article summarizes the current scientific tools and knowledge - including limitations, research needs, and likely future developments - relevant to various aspects of planning and conducting comprehensive EDM. We begin with the scope of the effort, contrasting target-species with broad-spectrum monitoring, reviewing information to support prioritization based on species and locations, and exploring the challenge of moving beyond individual surveys towards a coordinated monitoring network. Next, we discuss survey design, including effort to expend and its allocation over space and time. A section on sample collection and analysis overviews the merits of collecting actual organisms versus shed DNA, reviews the capabilities and limitations of identification by morphology, DNA target markers, or DNA barcoding, and examines best practices for sample handling and data verification. We end with a section addressing the analysis of monitoring data, including methods to evaluate survey performance and characterize and communicate uncertainty. Although the body of science supporting EDM implementation is already substantial, research and information needs (many already actively being addressed) include: better data to support risk assessments that guide choice of taxa and locations to monitor; improved understanding of spatiotemporal scales for sample collection; further development of DNA target markers, reference barcodes, genomic workflows, and synergies between DNA-based and morphology-based taxonomy; and tools and information management systems for better evaluating and communicating survey outcomes and uncertainty.

Evaluation of Blue Crab, Callinectes sapidus, Megalopal Settlement and Condition during the Deepwater Horizon Oil Spill

The Blue Crab, Callinectes sapidus, is a commercially, culturally, and ecologically significant species in the Gulf of Mexico (GOM), whose offshore stages were likely impacted by the Deepwater Horizon oil spill (DWH). To test for DWH effects and to better understand the planktonic ecology of this species, we monitored Callinectes spp. megalopal settlement and condition at sites within and outside of the spill extent during and one year after the DWH. We tested for DWH effects by comparing 2010 settlement against baseline data available for two sites, and by testing for differences in settlement and condition inside and outside of the spill extent. We also developed time series models to better understand natural drivers of daily settlement variation (seasonal and lunar trends, hydrodynamics, wind) during 2010 and 2011. Overall, we found that neither megalopal settlement nor body weight were significantly reduced at oiled sites, but that high unexplained variation and low statistical power made detection of even large effects unlikely. Time series models revealed remarkably consistent and relatively strong seasonal and lunar trends within sites (explaining on average 28% and 9% of variation, respectively), while wind and hydrodynamic effects were weak (1–5% variation explained) and variable among sites. This study provides insights into DWH impacts as well as the natural drivers of Callinectes spp. megalopal settlement across the northern GOM.