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Amoebic Gill Disease (AGD), caused by the protozoan extracellular parasite Paramoeba perurans ( P. perurans ) is a disease affecting Atlantic salmon ( Salmo salar ). This study investigated the gill transcriptomic profile of pre-clinical AGD using RNA-sequencing (RNA-seq) technology. RNA-seq libraries generated at 0, 4, 7, 14 and 16 days post infection (dpi) identified 19,251 differentially expressed genes (DEGs) of which 56.2% were up-regulated. DEGs mapped to 224 Gene Ontology (GO) terms including 140 biological processes (BP), 45 cellular components (CC), and 39 molecular functions (MF). A total of 27 reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and 15 Reactome gene sets were identified. The RNA-seq data was validated using real-time, quantitative PCR (qPCR). A host immune response though the activation of complement and the acute phase genes was evident at 7 dpi, with a concurrent immune suppression involving cytokine signalling, notably in interleukins, interferon regulatory factors and tumour necrosis factor-alpha ( tnf- α) genes. Down-regulated gene expression with involvement in receptor signalling pathways (NOD-like, Toll-like and RIG-1) were also identified. The results of this study support the theory that P. perurans can evade immune surveillance during the initial stages of gill colonisation through interference of signal transduction pathways.

Blue mussels (Mytilus spp.) are ecologically and economically important bivalves widespread in both hemispheres. Their relevance to coastal ecosystems and the aquaculture industry has made them extensively studied. The Mytilus complex consists of distinct genetic lineages, including Mytilus edulis, Mytilus galloprovincialis, Mytilus trossulus, and their fertile hybrids. In overlapping areas, they create complex hybrid zones, which have been investigated along European coasts, employing multi‐marker approaches. However, knowledge gaps still exist in the North‐east Atlantic region, in the middle of their hybrid zone around the island of Ireland, regarding their genomic composition, population structure and connectivity. This study addresses these gaps by genotyping 781 individuals from 26 sites encompassing Ireland's hybrid zone, including both wild and farmed stocks from varying environmental conditions. Using a selected panel of 72 SNP markers we examined relationships among genotypic composition, genetic diversity, isolation by distance (IBD) and environmental variables to identify drivers of Mytilus genetic structure. Results confirmed two distinct genetic lineages and their hybrids, with a clear geographic pattern: the east coast of Ireland is dominated by pure M. edulis genotype populations, while the south, west and north coasts exhibit varying degrees of admixture with M. galloprovincialis genotype. Pure M. galloprovincialis populations were identified at specific sites on the west and north coast. Sea current resistance and wave height were significant predictors for both genotype composition and genetic differentiation. This study corroborates previous findings and provides the first comprehensive investigation of Irish Mytilus spp. population structure and connectivity using a multi‐marker approach. The findings highlight the importance of understanding the Mytilus complex's composition and population dynamics to inform sustainable aquaculture practices and monitor potential climate change‐driven shifts in the North‐east Atlantic region.

Topmouth gudgeon is a freshwater fish species native to East Asia. Nowadays, P. parva is spread throughout Europe which is of concern because besides being considered one of the worst aquatic Invasive Alien Species (IAS) in Europe it is also a known vector of Spherotecum destruens, the rosette-like parasite lethal to other fish species. The present study describes the development and validation of a new species-specific assay based on hydrolysis probe chemistry to detect P. parva environmental DNA (eDNA) in water samples collected in a northern region of Italy (Friuli Venezia Giulia). Water samples were collected from 55 sites in an area where partial information on the occurrence of the species is available. eDNA was isolated from all samples and the presence of P. parva eDNA was tested by means of qPCR (quantitative PCR) and microfluidic qdPCR (quantitative digital PCR) techniques. Field results for both qPCR and qdPCR were largely in agreement in terms of detection (presence/absence). Thus, we judged the presence/absence by combining the results from the two methods and found that nine sites showed “strong positive” signal of P. parva eDNA (at least 2 positive replicates), 3 showed “suspected” (only 1 positive replicate), and 42 showed “absent”. The current study shows the strong potential of the newly developed eDNA approach to be a valuable addition to the monitoring of the highly invasive topmouth gudgeon in freshwater ecosystems.

Monitoring the nutritional health of cetaceans has become increasingly important in a changing environment, where multiple stressors impact animals. Particularly for those species that require consumption of energy‐dense prey, such as the common dolphin. Thus far, no uniform measure for monitoring body condition has been recommended across cetaceans, and species‐specific measures may need to be developed if employed as a population condition indicator under Descriptor 1 of the Marine Strategy Framework Directive. Here, nine morphometric body condition indices were applied to long‐term common dolphin stranding data sets originating from Ireland and the UK. We report a recent decline in the nutritional health of common dolphins in the Celtic Seas ecoregion comparing animals from 2017 to 2019 to animals from 1990 to 2006, with an increase in cases of animals dying due to starvation. Using ordinal regression trees, ventral blubber thickness (VBT) was identified as the most important index to predict nutritional status, defined at necropsy, followed by the scaled mass index (SMI). Using generalised linear models, both the VBT and SMI indices differentiated individuals that died from chronic and acute causes of death (i.e., bycatch), where animals in chronic conditions had significantly thinner VBT and lower SMI. Both significant temporal and seasonal patterns in VBT were identified, with poorer body conditions observed during the autumn and better body conditions observed during the spring, as well as an overall decline detected in VBT during the study period. While VBT was positively correlated with total body length, SMI showed the opposite trend. The VBT index is recommended for monitoring nutritional health within the species when total body length and season are considered. Further research is needed to understand the underlying causes for the observed decline, including shifts in prey availability and/or quality, to inform targeted conservation management strategies. The nutritional health of stranded common dolphins in the Celtic Seas ecoregion has recently declined, as evidenced by a decrease in nutritional status and an increase in starvation‐related deaths. Ventral blubber thickness was identified as the most reliable predictor of nutritional status when comparing various morphometric indices using ordinal regression tree analysis. We recommend using ventral blubber thickness while considering body length and seasonal variations to monitor the health of these dolphins and to inform conservation strategies.

Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While still in its infancy, the application of environmental DNA (eDNA) metabarcoding approaches is revolutionizing marine biodiversity monitoring capability. Indeed, the analysis of eDNA in conjunction with the collection of multidisciplinary optoacoustic and environmental data, can provide a more comprehensive monitoring of deep-sea biodiversity. Here, we describe the potential for acquiring eDNA as a core component for the expanding ecological monitoring capabilities through cabled observatories and their docked Internet Operated Vehicles (IOVs), such as crawlers. Furthermore, we provide a critical overview of four areas of development: (i) Integrating eDNA with optoacoustic imaging; (ii) Development of eDNA repositories and cross-linking with other biodiversity databases; (iii) Artificial Intelligence for eDNA analyses and integration with imaging data; and (iv) Benefits of eDNA augmented observatories for the conservation and sustainable management of deep-sea biodiversity. Finally, we discuss the technical limitations and recommendations for future eDNA monitoring of the deep-sea. It is hoped that this review will frame the future direction of an exciting journey of biodiscovery in remote and yet vulnerable areas of our planet, with the overall aim to understand deep-sea biodiversity and hence manage and protect vital marine resources.

Predators forage by balancing the energy content of prey with the energy required to capture it, selecting prey based on their foraging strategy. In the Celtic Seas ecoregion, recent dietary data are lacking for the common dolphin ( Delphinus delphis ) despite concerns about declining body conditions and changes in prey communities over recent decades. Using conventional stomach content analysis of a large sample set (n = 138) collected over three decades, combined with statistical modelling, we provided updated insights into common dolphin foraging ecology in the region. We examined dietary composition, trophic level, daily prey consumption, and gross energy intake in relation to explanatory variables, including time period, season, sex, maturity status, total body length, body condition, and cause of death. Results indicated that common dolphins fed at higher trophic levels on prey of lower energy content than in more southern European waters. Common dolphins were identified as facultative generalists, with Trisopterus spp. as the most important prey, though its importance slightly declined in the latter period of the study. Foraging patterns varied across all variables, likely reflecting shifts in prey availability, reproductive needs, dolphin movement patterns, and physiological constraints. Limitations of stomach content analysis were identified, with stomach contents only representing 18% of their daily required intake, underscoring the need for large sample sizes to achieve robust dietary assessments. Findings provide critical insights into their foraging ecology within the Celtic Seas ecoregion, data essential for supporting future ecosystem-based management approaches, amid ongoing ecosystem and prey community changes.

Documenting temporal and spatial occurrence trends of Non-Indigenous Species (NIS) is essential to understand vectors and pathways of introduction, and for horizon scanning for future introductions. This study provides an overview of marine NIS found in the Republic of Ireland up to 2020. Taxonomic groups, species origin, and location of first reporting (counties) were compiled and analysed focusing on the last three decades. While the unambiguous characterisation of introduction events is challenging, analysis of 110 species corroborated the global weight of evidence that shipping activities to/from ports and marinas are the most likely vectors and pathways in Ireland. A comparable review study for the Netherlands revealed that most NIS were first introduced to mainland Europe and subsequently would take on average >15 years to reach Ireland. In the last two decades there has been an increase in NIS-focused surveys in Ireland. Incorporating data from these surveys in centralized national repositories such as the National Biodiversity Data Centre, will strongly aid the evaluation of potential NIS management responses. Furthermore, the availability of robust baseline data as well as predictions of future invaders and their associated vectors and pathways will facilitate the effective application of emerging monitoring technologies such as DNA-based approaches.

A model was developed to forecast and compare changes in species presence assessed with either eDNA or traditional observations. We use it to explore how ecosystem conditions could affect the suitability of eDNA for Environmental Impact Assessment. First, a deterministic model simulated the dynamics of the impacted population (called “receptor” in EIA) and their shed DNA fragment concentrations. Second, random distributions of receptor organisms and eDNA fragment quantities at steady state were simulated within the impacted spatial domain (called “project area”). Then, simple random samplings were performed for both the receptor and eDNA. Third, post‐sampling processes (eDNA extraction, amplification, and analysis) were simulated to estimate the taxon detection probability. Fourth, we simulated an impact by modifying the growth, mortality, and mobility (null, passive, and active) parameters of the receptor taxon. eDNA detection probability curves were then estimated for a range of environmental sample volumes by fitting a Weibull cumulative distribution function. A F‐like statistic compared detection curves before and after impact. Statistically significant differences were detected with eDNA in impact scenarios where receptor taxon growth rate decreased and receptor mobility was null or passive. In scenarios where the project area accumulates DNA shed from multiple categories of the same taxon (e.g., from dead organisms if mortality increased or when individuals can cross project area boundaries), it is difficult to assess impact. Our study shows that results obtained from eDNA sampling will not always agree with an impact classically assessed on a receptor population. One reason is that sources of the total eDNA pool are not identified. The modeling highlights the need: to do preliminary testing of sample sizes, to develop new approaches that will identify sources from the pool of extracted DNA, and to improve descriptions of the ecogeochemical processes required to forecast shed DNA reactivity. This study considers how eDNA information could be utilized within Environmental Impact Assessment to forecast an impact on designated receptor organisms. The tool estimates detection probability curves for a range of sample volumes described by a Weibull cumulative distribution function. A F‐like statistic compares the detection curve parameters before and after impact. Scenario analysis suggests that if a potential impact would reduce growth and increase mortality rates of the receptor (whether a mobile or immobile species), then a significant difference could be assessed. More generally, impacts could be detected with sufficient certainty using eDNA if both the population dynamics of the receptor and the dynamics of DNA shed into the environment are adequately well‐known.

Conservation and management of protected species, particularly of elusive species such as pinnipeds, is hampered by knowledge gaps. In the case of studies using genetic data these are often attributed to a lack of representative samples. Therefore, there is a pressing need for the development of minimally invasive sampling protocols suitable for genetic analyses of pinnipeds. The present study evaluated the applicability of various protocols for the collection and processing of samples from harbour seals ( Phoca vitulina ) and grey seals ( Halichoerus grypus ), encompassing seven source sample types (blood, skin, hair (plucked/moulted), urine, buccal swabs, scat) and three different extraction methods. Protocols were designed for minimally invasive sampling, but also to evaluate differences in their performance based on cost and time of execution in comparison to traditional sampling approaches. The performance of each protocol was measured following successful DNA isolation, molecular sex determination and sequencing of a mitochondrial DNA fragment (control region). Protocols using plucked hair, urine and buccal swab samples proved effective for collection from individuals in captivity, whereas scat was most applicable for non-invasive sampling in the wild. Furthermore, following a pilot study on scat samples, DNA was found to be viable for genetic analysis after exposure to ambient conditions for up to four weeks. This study provides a useful assessment of the suitability of various minimal and non-invasively collected samples for DNA isolation, amplification and mitochondrial sequencing, enabling the effective design of future sampling strategies and a significant increase of samples available for genetic analysis of pinnipeds.

The understanding of population structure and gene flow of marine pelagic species is paramount to monitoring, management and conservation studies. Such studies are often hampered by the potentially high dispersal behavior of the species, the lack of obvious geographical barriers in the marine environment and the scarce sample availability. Short-beaked common dolphins (Delphinus delphis) are widespread in coastal and open-ocean habitats of the North Atlantic Ocean, nevertheless population structure and migratory patterns are poorly understood. Furthermore, concern has been raised about the status of the species because large numbers of dolphins have been taken incidentally in several fisheries throughout the North Atlantic in the past decades. In the present study, a large number of individual samples were obtained from seasonal and spatial aggregations of common dolphins from western (wNA) and eastern North Atlantic (eNA) regions, mostly using opportunistic sampling (i.e. from incidental entanglement in fishing gear or beach-cast carcasses). Genetic variability was investigated using nuclear (14 microsatellite loci) and mitochondrial (360 bp of the control region) genetic markers. Levels of genetic diversity were relatively high in all sampled areas and no evidence of recent reduction of effective population size (i.e. bottleneck) was detected at the nuclear loci. Significant population structure was detected between the two main regions (wNA and eNA) where it appeared to be more pronounced at mitochondrial (F ST = 0.018, P < 0.001) than nuclear markers (F ST = 0.005, P < 0.05), indicating the presence of at least two genetically distinct populations of common dolphins in the North Atlantic Ocean. In contrast, no significant genetic structure was detected between temporal aggregations of dolphins from within the same region, suggesting possible seasonal movement patterns at a regional scale. The observed levels of genetic differentiation between classes of markers are discussed here as a possible consequence of migratory patterns or recent population subdivision.