Environmental DNA sampling protocols for the surveillance of marine non-indigenous species in Irish coastal waters

Drop it all: extraction-free detection of targeted marine species through optimized direct droplet digital PCR

Molecular biomonitoring programs increasingly use environmental DNA (eDNA) for detecting targeted species such as marine non-indigenous species (NIS) or endangered species. However, the current molecular detection workflow is cumbersome and time-demanding, and thereby can hinder management efforts and restrict the "opportunity window" for rapid management responses. Here, we describe a direct droplet digital PCR (direct-ddPCR) approach to detect species-specific free-floating extra-cellular eDNA (free-eDNA) signals, i.e., detection of species-specific eDNA without the need for filtration or DNA extraction, with seawater samples. This first proof-of-concept aquarium study was conducted with three distinct marine species: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analysing aquarium marine water samples using an optimized species-specific ddPCR assay. The results demonstrated the consistent detection of S. spallanzanii and B. neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 h. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. This study represents the first step in assessing the feasibility of direct-ddPCR technology for the detection of marine species. Our results provide information that could aid in the development of new technology, such as a field development of ddPCR systems, which could allow for automated continuous monitoring of targeted marine species, enabling point-of-need detection and rapid management responses.

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases. Logistic constraints in ports prompt the development of simple, easy-to-deploy samplers. We tested a new device called polyamide mesh for ports organismal monitoring (POMPOM) with a high surface-to-volume ratio. POMPOMS were deployed inside a fishing and recreational port in the Mediterranean alongside conventional settlement plates. We also compiled a curated database with cytochrome oxidase (COI) sequences of Mediterranean NIS. COI metabarcoding of the communities settled in the POMPOMs captured a similar biodiversity than settlement plates, with shared molecular operational units (MOTUs) representing ca. 99% of reads. 38 NIS were detected in the port accounting for ca. 26% of reads. POMPOMs were easy to deploy and handle and provide an efficient method for NIS surveillance.

Non-indigenous aquatic fauna in transitional waters from the Spanish Mediterranean coast: A comprehensive assessment

Understanding drivers of spatial variation in non-indigenous species (NIS) is a key goal in invasion biology, but comprehensive assessments providing high-resolution data are extremely scarce. Anthropogenic modifications to transitional waters facilitate the invasion of NIS where they cause both ecological and economic important damage. By screening validated data sources, we conducted a comprehensive assessment of non-indigenous aquatic fauna in Spanish Mediterranean transitional waters (30 sites), as well as assessed introduction pathways, native regions, NIS assemblage patterns and temporal introduction rate. One hundred and twenty-nine NIS were inventoried, with 72 % established and more than half listed before 1980. Two intentional (release, escape) and two unintentional (contaminant, stowaway) introduction pathways were dominant. Recorded NIS originated mostly from North America and Asia. A clear nested pattern in NIS assemblages was observed across sites, suggesting secondary spread from the most invaded waters placed in the northern regions. Our updated inventory should be pivotal for designing prevention protocols and informing specific management plans on non-indigenous fauna in transitional waters.

Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea

Gathering comprehensive marine biodiversity data can be difficult, costly and time consuming, preventing adequate knowledge of diversity patterns in many areas worldwide. We propose fishing ports as "natural" sinks of biodiversity information collected by fishing vessels probing disparate habitats, depths, and environments. By combining rapid environmental DNA metabarcoding (eDNA) surveys and data from public registers and Automatic Identification Systems, we show significant positive relationships between fishing fleet activities (i.e. fishing effort and characteristics of the fishing grounds) and the taxonomic fish assemblage composition in eleven Mediterranean fishing ports. Overall, we identified 160 fish and 123 invertebrate OTUs, including at least seven non-indigenous species, in some instances well beyond their known distribution areas. Our findings suggest that eDNA assessments of fishing harbours' waters might offer a rapid way to monitor marine biodiversity in unknown or under-sampled areas, as well as to reconstruct fishing catches, often underreported in several regions.

Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring

Marinas are high-priority targets for marine non-indigenous species (NIS), where they compose a large portion of the biofouling communities. The practicality of water samples collection makes environmental DNA (eDNA) metabarcoding an interesting tool for routine NIS surveys. Here the effectiveness of water-eDNA-metabarcoding to identify biofouling NIS, in 10 marinas from western France, was examined. Morphological identification of specimens collected in quadrats brought out 18 sessile benthic NIS beneath floating pontoons. Water-eDNA-metabarcoding detected two thirds of them, failing to detect important NIS. However, sampling and bioinformatics filtering steps can be optimized to identify more species. In addition, this method allowed the detection of additional NIS from neighboring micro-habitats. Caution should, however, be taken when reporting putative novel NIS, because of errors in species assignment. This work highlights that water-eDNA-metabarcoding is effective for active (targeted) NIS surveys and could be significantly improved for its further use in marine NIS passive surveys.