Development and validation of a DNA-based multi-species biomonitoring toolkit using a high-throughput qPCR platform: A case study of Irish shellfish species.

Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade-offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled high-throughput quantitative PCR platform (HTqPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 23 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of (off-) target taxa and establishment of reference databases (PHASE 1); selection/development and assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). 42 assays were eventually chosen and validated. Genetic signal not only showed good correlation with direct visual counts by microscopy but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the developmental testing and application of panels of molecular assays for the monitoring and management of natural resources. Once developed, this approach provides a cost and time-effective alternative compared to other multi-species approaches (e.g. metabarcoding). In addition, it is transferable to a wide range of species and will aid future monitoring programmes.

Deep Sea Microplastic Pollution Extends Out to Sediments in the Northeast Atlantic Ocean Margins.

Microplastics are ubiquitous emerging contaminants found in every habitat surveyed, building upon international databases globally. Costs and accessibility often correlate to few deep sea sediment surveys, restricting the number of stations within a given sampling area. An extensive survey of the Porcupine Seabight, Porcupine Bank, the Goban Spur, and south-western canyons resulted in identifying microplastics in deep sea sediment surface layers from 33 of the 44 stations sampled (75%), with a total of 83 particles (74 synthetic and 9 natural) recorded. No microplastic hotspots were identified, and abundances (kg d.w.-1) were not correlated with distance from land, depth, or the presence of macrolitter on the seafloor. Understanding the sources of deep sea microplastics, such as marine traffic, is crucial to developing effective mitigation strategies as well as further monitoring campaigns targeting microplastic pollution in areas with significant deep sea biodiversity such as the Porcupine Seabright.

Size dependent egestion of polyester fibres in the Dublin Bay Prawn (Nephrops norvegicus).

Microplastics (MPs) are an extensive global contaminant in the marine environment, known to be ingested by marine organisms. The presence of MPs in the commercially important marine decapod crustacean Nephrops norvegicus (Dublin Bay Prawn) has been documented for the North-East Atlantic and the Mediterranean, however, uncertainties remain about retention times of MPs in the gastrointestinal tract (GIT) of this species. This study aims to investigate the retention times of polyester MP fibres of three sizes (3, 5, and 10 mm in length) and to determine whether the egestion of MP fibres is size and time dependent. Results suggest that MP fibres of different lengths are retained for different periods of time, with larger MP fibres being retained for longer periods (e.g., minimum 96 h for 10 mm fibres). The present study also assesses for the first time, the size dependent relationship of MP fibres under controlled conditions for N. norvegicus.

Plastics, prawns, and patterns: Microplastic loadings in Nephrops norvegicus and surrounding habitat in the North East Atlantic.

The presence of microplastics (MPs), a contaminant of emerging concern, has attracted increasing attention in commercially important seafood species such as Nephrops norvegicus. This species lend themselves well as bioindicators of environmental contamination owing to their availability, spatial and depth distribution, interactions with seafloor sediment and position in the ecosystem and food chain. This study assesses the abundance of MPs in N. norvegicus and in benthic sediments across six functional units in the North East Atlantic. Assessment of the relationship between MP abundance in N. norvegicus, their biological parameters and their surrounding environment was examined. Despite the lack of statistical significance, MP abundances, size, shape, and polymer type recorded in N. norvegicus mirrored those found in the surrounding environment samples. The three main polymers identified in both organisms and sediment were polystyrene, polyamide (nylons), and polypropylene. The level of MP contamination in N. norvegicus could be related to local sources, with relatively low abundances recorded in this study for the North East Atlantic in comparison to other regional studies. Furthermore, larger organisms contained a lower abundance of MPs, demonstrating no accumulation of MPs in N. norvegicus. Based on the results of this study, data on MP ingestion could be used to study trends in the amount and composition of litter ingested by marine animals towards fulfilling requirements of descriptor 10 of the Marine Strategy Framework Directive.

Assessing microplastic distribution within infaunal benthic communities in a coastal embayment.

Marine anthropogenic litter is increasing in prevalence in both the marine environment and its inhabitants. This study assesses the levels of anthropogenic microplastics in benthic infauna from 20 subtidal stations in Galway Bay, Ireland. Microplastics were removed from the organisms using an alkaline digestion (KOH) and their synthetic origin was confirmed by µFTIR spectroscopic analysis. The average number of microplastics recorded for all organisms was 0.79 ± 1.14 particles individual-1, similar to previously published results on subtidal fauna of the North Sea. Fibres were the dominant particle type (98%) and the majority were identified as natural (cellulose, cotton). Synthetic polymers identified included PVA (polyvinyl acetate), EPDM (synthetic rubber), PE (polyethylene) and PVC (polyvinyl chloride). Fibres less than 1 mm made up 55% of the recovered lengths. Colours recorded in the organisms were mainly blue and were reflective of the surrounding habitats. Of the five phyla collected, the highest incidence and uptake was associated with the Annelida. A significant difference in ingested MPs was only evident when depth (greater and less than 30 m) was considered as a factor. In addition, no significant differences were found between either the numbers of ingested MPs and phyla or feeding strategies. The results indicate that future studies should follow an ecosystem-based approach to monitor MPs levels in an area where specific bioindicator(s) have not been identified or are unsuitable.

Differences in microplastic abundances within demersal communities highlight the importance of an ecosystem-based approach to microplastic monitoring.

Plastic pollution is prevalent in all habitats and microplastic ingestion has been recorded in several different species examined to date. However, most studies have focused solely on commercial species. This study investigates microplastics (MPs) by assessing the levels present in a mixed demersal trawl at two sites in a coastal embayment. MPs were recovered from species' gastrointestinal tracts and polymers identified with µFTIR spectroscopic analysis. Particles recovered comprised 20% natural fibres. The majority of MPs were identified as PE, PVDF, and PETE. Results show an average MP range of 0.11-4.67 MPs individual-1. Fluctuating trendlines for MPs within species suggest that their bioavailability is influenced by several factors. Individual species show significant differences in ingested MP between trawls; however, when the entire trawl community is assessed there is no significant difference between sites. These results suggest that future studies should follow an ecosystem-based approach to monitor MPs.

Ischnomesus harrietae sp. nov., a new benthic asellote (Crustacea: Isopoda: Ischnomesidae) from bathyal bottoms of the southern Bay of Biscay.

A new species of Ischnomesidae (Crustacea: Isopoda: Asellota), Ischnomesus harrietae sp. nov. is described from the southern Bay of Biscay. This new species is distinctive due to the presence of numerous pedestal setae arranged in longitudinal rows on pereonite 5. Because of this morphological peculiarity, it can be easily distinguished from the four other Ischnomesus species previously reported from bathyal/abyssal bottoms of the European continental margin. Within its known distributional area, the new species inhabits sandy and muddy bottoms between 619 and 1099 m, with a maximum abundance of 41.8 individuals per 100 m2 recorded at approximately 700 m on the Arcachon Plateau. Another new species is also reported, Ischnomesus sp.1, represented by one specimen only and briefly described. An identification key to European species of Ischnomesus is provided.

Understanding the challenges of palliative care in everyday clinical practice: an example from a COPD action research project.

Palliative care seeks to improve the quality of life for patients suffering from the impact of life-limiting illnesses. Palliative care encompasses but is more than end-of-life care, which is defined as care during the final hours/days/weeks of life. Although palliative care policies increasingly require all healthcare professionals to have at least basic or non-specialist skills in palliative care, international evidence suggests there are difficulties in realising such policies. This study reports on an action research project aimed at developing respiratory nursing practice to address the palliative care needs of patients with advanced chronic obstructive pulmonary disease (COPD). The findings suggest that interlevel dynamics at individual, team, interdepartmental and organisational levels are an important factor in the capacity of respiratory nurses to embed non-specialist palliative care in their practice. At best, current efforts to embed palliative care in everyday practice may improve end-of-life care in the final hours/days/weeks of life. However, embedding palliative care in everyday practice requires a more fundamental shift in the organisation of care.