Discovery of the parasite Marteilia cocosarum sp. nov. In common cockle (Cerastoderma edule) fisheries in Wales, UK and its comparison with Marteilia cochillia

Diseases of bivalve molluscs caused by paramyxid parasites of the genus Marteilia have been linked to mass mortalities and the collapse of commercially important shellfish populations. Until recently, no Marteilia spp. have been detected in common cockle (Cerastoderma edule) populations in the British Isles. Molecular screening of cockles from ten sites on the Welsh coast indicates that a Marteilia parasite is widespread in Welsh C. edule populations, including major fisheries. Phylogenetic analysis of ribosomal DNA (rDNA) gene sequences from this parasite indicates that it is a closely related but different species to Marteilia cochillia, a parasite linked to mass mortality of C. edule fisheries in Spain, and that both are related to Marteilia octospora, for which we provide new rDNA sequence data. Preliminary light and transmission electron microscope (TEM) observations support this conclusion, indicating that the parasite from Wales is located primarily within areas of inflammation in the gills and the connective tissue of the digestive gland, whereas M. cochillia is found mainly within the epithelium of the digestive gland. The impact of infection by the new species, here described as Marteilia cocosarum n. sp., upon Welsh fisheries is currently unknown.

Insights into the development of hepatocellular fibrillar inclusions in European flounder (Platichthys flesus) from UK estuaries

Hepatocellular fibrillar inclusions (HFI) are an unusual pathology of unknown aetiology affecting European flounder (Platichthys flesus), particularly from estuaries historically impacted by pollution. This study demonstrated that the HFI prevalence range was 6-77% at several UK estuaries, with Spearman rank correlation analysis showing a correlation between HFI prevalence and sediment concentrations of ∑PBDEs and ∑HBCDs. The data showed that males exhibit higher HFI prevalence than females, with severity being more pronounced in estuaries exhibiting higher prevalence. HFI were not age associated indicating a subacute condition. Electron microscopy confirmed that HFI were modified proliferating rough endoplasmic reticulum (RER), whilst immunohistochemistry provided evidence of VTG production in HFI of male P. flesus. Despite positive labelling of aberrant VTG production, we could not provide additional evidence of xenoestrogen exposure. Gene transcripts (VTG/CHR) and plasma VTG concentrations (>1 μg ml^-1), were only considered elevated in four male fish showing no correlation with HFI severity. Further analysis revealed that reproductively mature female P. flesus i.e. >3-year-old, did not exhibit HFI, whereas males of all ages were affected. This, combined with previous reports that estradiol (E2) can impair mixed function oxygenase activity, supports a hypothesis that harmful chemical metabolites (following phase 1 metabolism of their parent compounds) are potentially responsible for HFIs observed in male and ≤ 3-year-old female fish. Consequently, HFI and xenoestrogenic induced VTG production could be independent of each other resulting from different concurrent toxicopathic mechanisms, although laboratory exposures will likely be the only way to determine the true aetiology of HFI.

The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh

Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible.

De novo transcriptome assembly of the Qatari pearl oyster Pinctada imbricata radiata

The pearl oyster Pinctada imbricata radiata is an iconic species in Qatar, representing an integral part of the nation's cultural heritage and one of the main economic foundations upon which the nation developed. During the early part of the 20th century, nearly half the Qatar population was involved in the pearl oyster industry. However, the fishery has undergone steady decline since the 1930s, and the species is now under threat due to multiple confounding pressures. This manuscript presents the first de novo transcriptome of the Qatari pearl oyster assembled into 30,739 non-redundant coding sequences and with a BUSCO completeness score of 98.4%. Analysis of the transcriptome reveals the close evolutionary distance to the conspecific animal Pinctada imbricata fucata but also highlights differences in immune genes and the presence of distinctive transposon families, suggesting recent adaptive divergence. This data is made available for all to utilise in future studies on the species.

Integration of biological effects, fish histopathology and contaminant measurements for the assessment of fish health: A pilot application in Irish marine waters

This study investigates the use of a weight of evidence (WOE) approach to evaluate fish health status and biological effects (BEs) of contaminants for assessment of ecosystem health and discusses its potential application in support of the Marine Strategy Framework Directive (MSFD). External fish disease, liver histopathology and several BEs of contaminant exposure including 7-ethoxy resorufin O-de-ethylase (EROD), acetylcholinesterase (AChE), bile metabolites, vitellogenin (VTG) and alkali labile phosphates (ALP) were measured in two flatfish species from four locations in Ireland. Contaminant levels in fish were generally low with PCBs in fish liver below OSPAR environmental assessment criteria (EAC). There were consistencies with low PCB levels, EROD and PAH bile metabolite levels detected in fish. Dab from Cork, Dublin and Shannon had the highest relative prevalence of liver lesions associated with the carcinogenic pathway. An integrated biomarker response (IBR) showed promise to be useful for evaluation of environmental risk, although more contaminant parameters in liver are required for a full assessment with the present study.

Hepatocellular adenoma in a European flatfish (Limanda limanda): Genetic alterations in laser-capture micro-dissected tissue and global transcriptomic approach

Liver tumours in flatfish have been diagnosed using histopathology for decades to monitor the impacts of marine pollution. Here we describe the application of specific gene (retinoblastoma, Rb) profiling in laser capture micro-dissected samples, and a suppression subtractive hybridization (SSH) approach to isolate differentially expressed genes in hepatocellular adenoma (HCA) samples from dab, Limanda limanda. The Rb profiles from apparently normal and HCA micro-dissected samples of fish from the North Sea showed no significant difference, and genotypic heterogeneity within defined histological phenotypes was observed. In the SSH, sequences associated with cell signalling, cell cycle, gene expression regulation, protein transport and protein degradation were isolated. These included up-regulation of arrestin domain containing 3 (arrdc3), Rac-1 and tribbles, and down-regulation of ankyrin repeat/sterile alpha-motif domain-containing protein 1B-like (ANKS1B-like), c-fos, CDKN1B and RhoA-like sequences, previously implicated in mammalian HCA. This study offers new candidates involved in fish liver tumour development.

Diseases of dab (Limanda limanda): Analysis and assessment of data on externally visible diseases, macroscopic liver neoplasms and liver histopathology in the North Sea, Baltic Sea and off Iceland

In the framework of the ICON project (Integrated Assessment of Contaminant Impacts on the North Sea), common dab (Limanda limanda) from seven offshore sampling areas in the North Sea, Icelandic waters and the western Baltic Sea were examined in 2008 for the presence of externally visible diseases and parasites (EVD), macroscopic liver neoplasms (tumours) (MLN) and histopathological liver lesions (LH). Methodologies applied followed standardised ICES and BEQUALM protocols. The EDV results revealed pronounced spatial variation, with dab from the central and northern North Sea sampling areas showing the highest disease prevalence. MLN were recorded only in North Sea dab from the German Bight, Firth of Forth and Ekofisk at a low prevalence. LH results revealed a dominant prevalence of non-specific, mostly inflammatory, lesions and a low prevalence of early toxicopathic non-neoplastic lesions, tumour pre-stages (foci of cellular alteration) and liver tumours. For the analysis and assessment of spatial variation of EVD, a Fish Disease Index (FDI) was calculated for individual dab, summarising data on the presence/absence of EDV, their severity grades, effects on the host and compensating for effects of length, sex and season. FDI data confirmed that the health status of North Sea dab from the offshore areas Dogger Bank, Ekofisk and Firth of Forth was significantly worse than in dab from the German Bight, Icelandic areas and the western Baltic Sea. An assessment of the disease data following ICES/OSPAR criteria was accomplished by applying established numeric background (BAC) and ecological assessment criteria (EAC) for EDV, MLN and LH. The combined assessment of the three disease categories indicated that health effects classified as unacceptable were rare and mainly affected dab from the North Sea. Based on the findings of the present study, it is recommended to monitor wild fish diseases in the context of assessing the impact of hazardous substances and other stressors on the marine environment. The Fish Disease Index (FDI) is regarded as a strong tool for disease data analysis and assessment, suitable as ecosystem health indicator.

Biomarkers of general stress in mussels as common indicators for marine biomonitoring programmes in Europe: The ICON experience

This study investigated whether general stress biomarkers in mussels can be applied as common first-tier biomarkers in regional biomonitoring programmes in the North Sea (including Iceland) and western Mediterranean Sea. Stress on Stress (SoS) and lysosomal membrane stability (LMS) biomarkers were analysed in resident mussels (Mytilus sp.) from 8 coastal sites and in transplanted mussels (Mytilus galloprovincialis) from two Spanish Mediterranean coastal sites. The assessment of results, as input to pollution monitoring strategies, was performed jointly for LMS and SoS data from the two regions. Contaminant body burden of the mussels was compared with biomarker results. The results demonstrated that these two general and non-expensive stress biomarkers in mussel can be applied throughout European waters, providing a cost-effective and harmonised approach to screen contaminant-related biological effects within the framework of wide-scale pollution biomonitoring programmes, such as that proposed by the European Union, i.e. the Marine Strategy Framework Directive.

Determining Good Environmental Status under the Marine Strategy Framework Directive: Case study for descriptor 8 (chemical contaminants)

The European Union Marine Strategy Framework Directive (MSFD) requires individual member states to develop a robust set of tools for defining eleven qualitative descriptors of Good Environmental Status (GES), such as demonstrating that "Concentrations of contaminants are at levels not giving rise to pollution effects" (GES descriptor 8). Adopting the recommendations of the ICES/OSPAR Study Group for the Integrated Monitoring of Contaminants and Biological Effects (SGIMC), we present a case study demonstrating how the proposed approach, using chemical contaminant (metals and polycyclic aromatic hydrocarbons and polychlorinated biphenyls) and biological effects (EROD, bile metabolites and pathology) data in different matrices (sediment and biota), could be used to contribute to the determination of GES in a region of the North Sea region off the east coast of the UK.

Spatial and temporal analysis of the risks posed by polychlorinated biphenyl and metal contaminants in dab (Limanda limanda) collected from waters around England and Wales

The metals cadmium, mercury and lead, and the ICES7 CB levels were analysed in the common dab Limanda limanda to investigate whether concentrations of these determinants are at levels above established OSPAR assessment criteria around England and Wales. The results indicate that CB118 is above the OSPAR derived EAC at 22 out of 29 sampled stations, with 15 showing significant reductions. Cadmium is increasing significantly at six stations with two sites in the North Sea breaching corresponding OSPAR EAC. Mean results for all other PCBs and metals stayed below the EAC thresholds, with Hg concentrations even falling below BAC levels at South Eddystone located in the western English Channel. This study shows that PCBs banned over 20years ago are still found at concentrations in fish liver tissues which may pose a health risk to both the individual fish and their predators.

Genetic alterations and cancer formation in a European flatfish at sites of different contaminant burdens

Fish diseases are an indicator for marine ecosystem health since they provide a biological end-point of historical exposure to stressors. Liver cancer has been used to monitor the effects of exposure to anthropogenic pollution in flatfish for many years. The prevalence of liver cancer can exceed 20%. Despite the high prevalence and the opportunity of using flatfish to study environmentally induced cancer, the genetic and environmental factors driving tumor prevalence across sites are poorly understood. This study aims to define the link between genetic deterioration, liver disease progression, and anthropogenic contaminant exposures in the flatfish dab (Limanda limanda). We assessed genetic changes in a conserved cancer gene, Retinoblastoma (Rb), in association with histological diagnosis of normal, pretumor, and tumor pathologies in the livers of 165 fish from six sites in the North Sea and English Channel. The highest concentrations of metals (especially cadmium) and organic chemicals correlated with the presence of tumor pathology and with defined genetic profiles of the Rb gene, from these sites. Different Rb genetic profiles were found in liver tissue near each tumor phenotype, giving insight into the mechanistic molecular-level cause of the liver pathologies. Different Rb profiles were also found at sampling sites of differing contaminant burdens. Additionally, profiles indicated that histological "normal" fish from Dogger sampling locations possessed Rb profiles associated with pretumor disease. This study highlights an association between Rb and specific contaminants (especially cadmium) in the molecular etiology of dab liver tumorigenesis.

Advanced diagnostics applied to fish liver tumours: relating pathology to underlying molecular aetiology

Liver tumours in flatfish have been diagnosed using histopathology for decades in order to monitor the impacts of marine pollution in coastal and estuarine environments. This traditional method has been coupled with molecular analyses of tumours in the liver of the dab, Limanda limanda, in order to elucidate underpinning molecular level aetiology of such disease. A laser capture microdissection technique for molecular investigation of cancer has been applied in fish. The present study provides optimized steps for environmental sample utilisation: a procedure for field sample collection and handling; a method allowing reliable identification of lesions on frozen tissue sections; and, downstream molecular analyses of tumourigenesis markers (retinoblastoma gene) in laser microdissected samples. This approach facilitates the use of wild flatfish as a model of environmentally-induced tumourigenesis, and has wide applicability to any disease pathology for which the underpinning molecular aetiology is required.

Histopathology of mussels (Mytilus sp.) from the Tamar estuary, UK

This study assessed numerous histological parameters as markers of health status in mussels (Mytilus spp.) collected from several locations along a contamination gradient on the River Tamar and two coastal sites on the north and south coast of Cornwall, UK. Twenty-seven health parameters were assessed including the presence of pathogens, inflammatory lesions, non-specific pathologies and reproductive condition. Logistic regression showed that reproductive condition and inflammatory lesions showed changes indicative of a contamination gradient response. Mussel populations further upstream within the Tamar were relatively less developed compared to mussels situated downstream in the estuary. Compared to coastal locations, mussels sampled within the Tamar also exhibited a higher prevalence of inflammatory lesions that increased at locations situated furthest upstream. Similarly, levels of lipofuscin within the kidney epithelium were highest in mussels sampled within the estuary and Whitsand Bay compared to Trebarwith Strand. The most prevalent pathogens observed during this survey included Rickettsia/Chlamydia-like organisms (R/CLO), gill ciliates including Ancistrum mytili, the copepod Mytilicola intestinalis, Ciliophora-like organisms and Marteilia sp. Marteilia sp. was observed in 31% of the mussels sampled from the Cremyll Ferry site. Generally, the range and prevalence of pathogens was highest from the two estuarine locations at Cremyll Ferry and Wilcove. No significant differences were observed between estuarine sampling sites and Whitsand Bay with respect to median epithelial cell height of digestive tubules, however mussels from Trebarwith Strand did exhibit a reduced median epithelial cell height compared to mussels sampled from other sampling sites. Species genotyping was also undertaken during this study in order to consider any histological differences in relation to species. Results are discussed in relation to histopathology health parameters and biological effects monitoring.

Laser-assisted microdissection: a new tool for aquatic molecular parasitology

Laser-assisted microdissection (LMD) has been developed to isolate distinct cell populations from heterogeneous tissue sections, cytological preparations, or live cell samples. Downstream applications typically include gene expression studies using real-time PCR and array platforms, diagnostic PCR, and protein expression studies. LMD techniques are now commonplace in mainstream biological research and clearly have suitable applications in the field of aquatic pathology and parasitology. The present study used LMD to isolate 2 dinoflagellate parasites (Hematodinium spp.) from formalin-fixed paraffin-embedded tissue sections from 2 crustacean hosts, Cancer pagurus and Portunus trituberculatus. DNA was isolated from LMD parasite preparations, and partial regions (up to 300 bp) of the small subunit and the first internal transcribed spacer region of the rRNA gene complex from the Hematodinium spp. were PCR amplified using diagnostic primers. The amplification products were sequenced to confirm the identity of the targeted regions. The techniques, applications, and limitations of LMD to address questions in aquatic molecular pathology and parasitology are discussed.

Direct sampling of organisms from the field and knowledge of their phenotype: key recommendations for environmental metabolomics

Critical questions must be addressed to evaluate the potential of metabolomics for studying free-living wildlife. First, can metabolomics identify stress-induced phenotypes in animals experiencing a highly variable environment or must animals be stabilized in a controlled laboratory prior to sampling? Second, is knowledge of species and phenotype (gender and age) required to interpret metabolomics data? To address these questions, we characterized the metabolic variability of the mussel and determined if inherent variability masked the metabolic response to an environmental stressor, hypoxia. Specifically, we compared metabolic fingerprints of adductor muscle and mantle from four groups of Mytilus galloprovincialis: animals sampled directly from the field with and without hypoxia and those stabilized in a laboratory for 60 h, also with and without hypoxia. Contrary to expectation, laboratory stabilization increased metabolic variability in adductor muscle, thereby completely masking the response to hypoxia. The principal source of metabolic variability in mantle was shown to be gender-based, highlighting the importance of phenotypic anchoring of samples to known life history traits. We conclude that direct field sampling is recommended for environmental metabolomics since it minimizes metabolic variability and enables stress-induced phenotypic changes to be observed. Furthermore, we recommend that species and phenotype of the study organism must be known for meaningful interpretation of metabolomics data.