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Fisheries enforcement relies on visual catch identification and quantification at sea or when landed. Silage (fish dissolved in acid) and fish blocks (block frozen fish) are promising methods for on-board processing and storage of low-value catches. We examined the use of non-destructive sampling and two DNA-based methods, quantitative PCR (qPCR) and metabarcoding, to assess species composition and relative abundance in industrial grade experimental silage and fish blocks. We demonstrate the ability to identify and quantify DNA from fish species in both products. qPCR analysis of small silage samples collected over 21 days detected all target control species. DNA from one species (Atlantic wolffish) was consistently overrepresented while, for three species of gadoids (Atlantic cod, haddock and whiting), the DNA content matched input tissue proportions with high accuracy. qPCR and metabarcoding of fish blocks, sampled as run-off water and exterior swabs, provided consistent species detection, with the highest variance observed in quantification from swab samples. Our analysis shows that DNA-based methods have significant potential as a tool for species identification and quantification of complex on-board-processed seafood products and are readily applicable to taxonomically and morphologically similar fish. There is, however, a need for establishing DNA/weight calibration factors for primary fisheries species.

Monitoring, understanding, and communicating the impact of offshore oil and gas exploration and production (E&P) activities on marine mammal (MM) biodiversity can be challenging. Here, we share methods, results, and experiences accumulated during seven years of monitoring MM and underwater sound in a mature E&P activity area in the North-East Atlantic. We collected data on the distribution and behaviour of MM, their prey and changes associated with impulsive (e.g., seismic) and continuous (e.g., platform) sound generated by E&P operations. A program was created as an incentive for offshore staff to report systematically incidental MM sightings. Underwater acoustic recorders were placed around producing facilities and across a 3D seismic survey area before, during and after acquisition. A 2nd Generation Environmental Sample Processor (ESP) was deployed to collect and analyse environmental DNA (eDNA) from seawater to identify MM species and their potential prey. Monitoring data were shared with relevant stakeholders through publications in scientific journals, presentations at conferences and meetings, or through social media. Our data provided evidence of MM activity in the E&P activity area year-round. A total of eight species were sighted from platforms and vessels; harbour porpoise being the most common MM. Harbour porpoises were recorded as being within 800m of the platform three times more often than at stations further away. Near installations, acoustic data showed porpoises actively searched for prey whilst eDNA confirmed the presence of prey species - validating a strong reef-effect. Decrease in porpoise echolocation to 8-12 km from an active seismic vessel, is suggestive of a temporary displacement of animals in the corresponding area. There was no large scale or long-term displacement as harbour porpoises were detected again in the area few hours after airgun operations ended. The results indicate that despite elevated sound level in the E&P area, porpoise distribution appears to be linked to higher availability of prey around the artificial reef created by subsea O&G structures. The monitoring efforts generate valuable scientific knowledge, which form a sound basis to support management and regulation of E&P activities in Denmark. Additionally, several simultaneous tangible benefits resulted from the study such as staff awareness of biodiversity and increased stakeholder interactions. Results and methodologies may be used by HSE practitioners and O&G project managers to assess the potential impact of sound generated by O&G industry on marine mammals. Our success illustrates the value of long-term monitoring and should inspire and support HSE practitioners in their future environmental monitoring initiatives.

Biomass assesment of fish stocks is a difficult task that often involves costly fisheries trawl surveys. Trawl surveys rarely return replicate samples, as trawling attempts are expensive and difficult to reproduce. Furthermore, traditional benthic trawling is often detrimental to habitats and the organisms associated with the sea bottom. The rapidly developing field of environmental DNA (eDNA) analysis offers a new approach to non-invasive monitoring of fish. In the present study, we develop and test species-specific primers and probes for qPCR detection of eDNA from Atlantic herring (Clupea harengus ), Atlantic cod ( Gadus morhua ), European flounder ( Platichthys flesus ), European plaice ( Pleuronectes platessa), and Atlantic mackerel ( Scomber scombrus ) in the Baltic Sea. A recently published qPCR system was applied for European eel (Anguilla anguilla ). Filtered water samples were collected during a stratified benthic trawl survey, enabling parallel comparisons of eDNA concentrations with biomass caught by trawling. No significant correlation was found between eDNA concentrations and the biomass of fish caught by the trawl, although an association was observed between the measured concentrations of eDNA and the known distributions and main abundances of cod, herring, plaice and flounder. This indicates that while eDNA concentrations may not be directly comparable to results from existing methods – likely because aquatic eDNA concentrations are not controlled by the same combinations of factors as e.g. trawl biomass catch – eDNA analysis could prove a useful supplement for monitoring fish stocks in the future.

Application of environmental DNA (eDNA) analysis has attracted the attention ofresearchers, advisors and managers of living marine resources and biodiversity. The apparent simplicity and cost-effectiveness of eDNA analysis make it highly attractive as species distributions can be revealed from water samples. Further, species-specific analyses indicate that eDNA concentrations correlate with biomass and abundance, suggesting the possibility for quantitative applications estimating abundance and biomass of specific organisms in marine ecosystems, such as for stock assessment. However, the path from detecting occurrence of an organism to quantitative estimates is long and indirect, not least as eDNA concentration depends on several physical, chemical and biological factors which influence its production, persistence and transport in marine ecosystems. Here, we provide an overview of basic principles in relation to eDNA analysis with potential for marine fisheries application. We describe fundamental processes governing eDNA generation, breakdown and transport andsummarize current uncertainties about these processes. We describe five major challenges in relation to application in fisheries assessment, where there is immediate need for knowledge building in marine systems, and point to apparent weaknesses of eDNA compared to established marine fisheries monitoring methods. We provide an overview of emerging applications of interest to fisheries management and point to recent technological advances, which could improve analysis efficiency. We advise precaution against exaggerating the present scope for application of eDNA analysis in fisheries monitoring, but also argue that with informed insights into strengths andlimitations, eDNA analysis can become an integrated tool in fisheries assessment and management

While genetics has assisted fisheries management for over 50 years, genetic applications aiming to alleviate or eliminate discards have received little attention. In this chapter, we focus on how genetics can be applied under the EU Landing Obligation, to identify and prevent unwanted catches and to estimate the composition of products made from such catches. Three themes are covered: (i) the genetic identification of bycatch; (ii) the genetic analysis of species composition in nutritional products made from unwanted fish; (iii) the potential of using so-called environmental DNA (DNA shedded from aquatic organisms into the water) to reduce bycatch. For all themes, we introduce and explain the relevant genetic techniques, including data formats and analyses. We present the most significant limitations of the methodologies for their implementation in fisheries and provide examples of their use through relevant case studies. Finally, we discuss the potential future perspectives, with emphasis on the rapid progress in portable and automatic DNA devices, which may revolutionize the use of real-time onsite genetic analyses.