• Detection of koi herpesvirus (KHV) in koi carp (Cyprinus carpio L.) imported into Ireland.

      McCleary, S.; Ruane, N. M.; Cheslett, D.; Hickey, C.; Rodger, H.D.; Geoghegan, F.; Henshilwood, K. (Europeand association of fish pathologists, 2011)
      This report described the first detections of koi herpesvirus (KHV) in the Republic of Ireland in imported koi carp. In both cases the KHV suspicions were confirmed by molecular diagnosis and the infected stocks culled.
    • Development & implementation of the Phytotest project

      Kavanagh, S.; Brennan, C.; Lyons, C.; Chamberlain, T.; Salas, R.; Moran, S.; Silke, J.; Maher, M. (Marine Institute, 2008)
      Phytotest is a 3-year research and development project funded through the Marine Institute Strategic Research Programme in Advanced Technologies as part of the National Development plan 2000-2006. The project is a collaboration between the National Diagnostics Centre at NUI Galway and the MI and involves the development of real-time PCR assays for Dinophysis and Pseudo-nitzschia species that are important in Irish waters. In the current final phase of the project, the real-time PCR assays are being transferred to the MI to support the phytoplankton monitoring service.
    • Developments in analysis and toxicology of toxaphene compounds

      de Geus, H-J.; Besselink, H.; Brouwer, A.; Klungsøyr, J.; MacGovern, E.; MacHugh, B.; Nixon, E.; Rimkus, G.G.; Wester, P.G.; de Boer, J. (1998)
      Over the last 50 years toxaphene has been produced and used as a pesticide extensively. The US Environmental Protection Agency banned it in 1982. In the early 1990s the presence of toxaphene in marine fish in Europe caused concern with regard to human health in relation with consumption. This paper gives a brief overview of recent developments in the analytical and toxicological research on toxaphene.
    • Dinoflagellate cysts in Irish coastal sediments - a preliminary report

      O'Mahony, J.H.; Silke, J. (1993)
      Since the mid 1970's the production of bivalve shellfish in Ireland has increased annually to a present level of some 17,000 tonnes. Several problems limit the continued expansion of the industry, most notably the problem of natural biotoxins. These toxins are accumulated in the product by the ingestion of toxic phytoplankton. This causes no obvious ill effects to the shellfish themselves but upon consumption may be transferred to human or other vertebrate consumers causing illness and sometimes death. In Ireland the most common of the toxins are those associated with Diarrhetic Shellfish Poisoning (DSP) which causes diarrhoea. Other more serious toxins which to date have not been confirmed in Ireland are those associated with Paralytic Shellfish Poisoning (PSP) which causes paralysis or even death and Amnesic Shellfish Poisoning (ASP) which causes short term memory loss. Of the phytoplankton species which can result in toxicity, under both bloom and non bloom conditions, the dinoflagellates play an important role. Many of these dinoflagellates have been shown to include a dormant benthic cyst stage in their life cycle. Therefore a better understanding of the dynamics of toxic events may be obtained by studying the distribution and abundance of benthic cysts. There is growing international concern about the transport of harmful aquatic organisms, including cysts, into new areas via the discharge of ships ballast water. Also, as a result of EC directive 91/67/EEC permitting the free movement of shellfish between EU member states there is now increasing concern in Ireland that harmful cysts may be introduced with shipments of imported shellfish. Little research has been carried out on the distribution of dinoflagellate cysts in Irish marine sediments. In this paper preliminary results of a study designed to map the distribution and undertake taxonomic studies on dinoflagellate and other cysts in Ireland are presented and discussed. Also presented are the results of the examination of cysts associated with imported shellfish.
    • The dinophycean genus Azadinium and related species – morphological and molecular characterization, biogeography, and toxins

      Tillmann, U.; Elbrächter, M.; Gottschling, M.; Gu, H.; Jeong, H.J.; Krock, B.; Nézan, E.; Potvin, E.; Salas, R.; Soehner, S. (International Society for the Study of Harmful Algae, 2014)
      Azaspiracids (AZAs) are the most recently discovered group of lipophilic marine biotoxins of microalgal origin. It took about twelve years from the first human poisoning event until a culprit for AZA production was unambiguously identified and described as a novel species, Azadinium spinosum, within a newly created genus. Since then, knowledge on the genus has increased considerably, and an update on the current circumscription of the genus is presented here including various aspects of morphology, phylogeny, biogeography, and toxin production. There are currently five described species: A. spinosum, A. obesum, A. poporum, A. caudatum, and A. polongum. As indicated by molecular sequence variation detected in field samples, there are probably more species to recognize. Moreover, Amphidoma languida has been described recently, and this species is the closest relative of Azadinium based on both molecular and morphological data. Amphidoma and Azadinium are now grouped in the family Amphidomataceae, which forms an independent lineage among other monophyletic major groups of dinophytes. Initially, azaspiracids have been detected in A. spinosum only, but AZA production within the Amphidomataceae appears complex and diverse: A new type of azaspiracid, with a number of structural variants, has been detected in A. poporum and Amphidoma languida, and AZA-2 has now been detected in Chinese strains of A. poporum.
    • Dinophysis species in Irish waters 1990 - 1993

      Jackson, D.; Silke, J. (ICES, 1993)
      The distribution and abundance of Dinophysis species as recorded in the national phytoplankton monitoring programme are described. An apparent spread in the occurrence of Dinophysis to the west coast of Ireland is reported. The lack of correlation between the concentrations of Dinophysis in the water and DSP toxicity in shellfish is reported on and discussed.
    • An ecosystem-based approach and management framework for the integrated evaluation of bivalve aquaculture impacts

      Cranford, P.J.; Kamermans, P.; Krause, G.; Mazurié, J.; Buck, B.H.; Dolmer, P.; Fraser, D.; Van Nieuwenhove, K.; O'Beirn, F.X.; Sanchez-Mata, A.; et al. (Inter Research, 2012)
      An ecosystem-based approach to bivalve aquaculture management is a strategy for the integration of aquaculture within the wider ecosystem, including human aspects, in such a way that it promotes sustainable development, equity, and resilience of ecosystems. Given the linkage between social and ecological systems, marine regulators require an ecosystem-based decision framework that structures and integrates the relationships between these systems and facilitates communication of aquaculture–environment interactions and policy-related developments and decisions. The Drivers-Pressures-State Change-Impact-Response (DPSIR) management framework incorporates the connectivity between human and ecological issues and would permit available performance indicators to be identified and organized in a manner that facilitates different regulatory needs. Suitable performance indicators and modeling approaches, which are used to assess DPSIR framework components, are reviewed with a focus on the key environmental issues associated with bivalve farming. Indicator selection criteria are provided to facilitate constraining the number of indicators within the management framework. It is recommended that an ecosystem-based approach for bivalve aquaculture be based on a tiered indicator monitoring system that is structured on the principle that increased environmental risk requires increased monitoring effort. More than 1 threshold for each indicator would permit implementation of predetermined impact prevention and mitigation measures prior to reaching an unacceptable ecological state. We provide an example of a tiered monitoring program that would communicate knowledge to decision-makers on ecosystem State Change and Impact components of the DPSIR framework.
    • Embryonic and larval development of Spisula solidissima similis (Say, 1822) (Bivalvia: Mactridae)

      Walker, R.L.; O'Beirn, F.X. (California Malacozoological Society, 1996)
      Larvae of the southern surf clam, Spisula solidissima similis (Say, 1822), were reared in the laboratory at a salinity of 25 ppt and a temperature of 20-22°C through the embryonic and early larval development period. Unfertilized eggs averaged 58.5 ± 0.32 (SE) μm, with the size-frequency of eggs being normal. First polar body was observed 22 minutes after fertilization with 50% of eggs exhibiting polar bodies after 26 minutes. Ciliated blastula and trochophore stages occurred at 6 hours and 16.8 hours, respectively. Straight-hinge veligers appeared 39.2 hours after fertilization. Larvae grew to a mean size of 172 μmin the pediveliger phase (range 119 to 212 μm). Larvae were exhibiting active foot-probing by day 8 and continued to do so until day 13 when the cultures suffered heavy mortalities. Early life-history traits of Spisula solidissima similis larvae are compared to those for Spisula solidissima solidissima and Spisula sachalinensis.
    • Enhancement of subtidal eastern oyster, Crassostrea virginica, recruitment using mesh bag enclosures

      O'Beirn, F.X.; Walker, R.L.; Heffernan, P.B. (National Shellfisheries Association, 1996)
      Eastern oysters, Crassostrea virginica, in the southeastern United States are found predominantly in the intertidal zone. In this study, mesh bags (3 and 6 mm) were deployed over collecting frames, and the patterns of oyster settlement on these collectors were compared against unmeshed controls at three tidal heights (intertidal, low water, and subtidal) over three sampling regimes (biweekly, monthly, and seasonal) at two sites. Within the biweekly sampling regime, the meshed collectors and controls had similar patterns of settlement at the respective tidal heights. For monthly samplers, mesh treatments maintained higher settlement subtidally whereas controls had highest settlement on the collectors at mean low-water level. Controls had highest recruitment intertidally for seasonal collectors, whereas mesh treatments had higher recruitment lower in the intertidal zone. Conclusions from this experiment were that the use of mesh-covered collectors enhanced subtidal oyster recruitment. Causes of observed increases in subtidal settlement in mesh collectors over unmeshed controls over time could be the result of a combination of factors: predator exclusion, larval entrainment, or reduced desiccation, which seemed to overcome the detrimental effects of increased fouling, resulting in reduced flow and possible hypoxic conditions within the mesh bags. Given the degree of recruitment and the sizes of the recruits attained within the mesh bags, the use of these methods to attain juveniles for commercial purposes would appear to be both feasible and viable, particularly for long periods (up to 6 1110) of deployment.
    • Environmental factors associated with invasion: modeling occurrence data from a coordinated sampling programme for Pacific oysters

      Kochmann, J.; O’Beirn, F.X.; Yearsley, J.; Crowe, T.P. (Springer Netherlands, 2013)
      Documenting establishment and spread of invasive species requires extensive co-ordinated sampling programmes. Identifying the factors promoting or inhibiting local establishment of an invasive species can improve capacity to predict further spread and underpin strategies to limit spread. Here, a structured sampling programme was used to assess the current distribution of feral populations of Pacific oysters, Crassostrea gigas, in Ireland. Sixty-nine sites were sampled using a standardised protocol combining semi-quantitative and quantitative approaches. Sites were chosen to represent variation in proximity to aquaculture and a range of environmental variables. Oyster populations were found at 18 locations, with densities ranging from single individuals to nine individuals per m2. The broad size range of oysters found is indicative of more than one recruitment event. Logistic regression indicated that feral oysters were positively associated with the presence of hard substrata or biogenic reef, long residence times of embayments and large intertidal areas. There was also a tendency for oysters to occur disproportionately in bays with aquaculture, but >500 m from it. Small-scale analysis within sites showed that oysters were almost exclusively attached to hard substrata and mussel shell. The approach taken here provides a rigorous repeatable methodology for future monitoring and a detailed basis for the prediction of further spread.
    • Environmental occurrence, analysis, and toxicology of toxaphene compounds

      de Geus, H.-J.; Besselink, H.; Brouwer, A.; Klungsøyr, J.; McHugh, B.; Nixon, E.; Rimkus, G.G.; Wester, P.G.; de Boer, J. (1999)
      Toxaphene production, in quantities similar to those of polychlorinated biphenyls, has resulted in high toxaphene levels in fish from the Great Lakes and in Arctic marine mammals (up to 10 and 16 microg g-1 lipid). Because of the large variabiliity in total toxaphene data, few reliable conclusions can be drawn about trends or geographic differences in toxaphene concentrations. New developments in mass spectrometric detection using either negative chemical ionization or electron impact modes as well as in multidimensional gas chromatography have recently led researchers to suggest congener-specific approaches. Several nomenclature systems have been developed for toxaphene compounds. Although all systems have specific advantages and limitations, it is suggested that an international body, such as the International Union of Pure and Applied Chemistry, make an attempt to obtain uniformity in the literature. Toxicologic information on individual chlorobornanes is scarce, but some reports have recently appeared. Neurotoxic effects of toxaphene exposure such as those on behavior and learning have been reported. Technical toxaphene and some individual congeners were found to be weakly estrogenic in in vitro test systems; no evidence for endocrine effects in vivo has been reported. In vitro studies show technical toxaphene and toxaphene congeners to be mutagenic. However, in vivo studies have not shown genotoxicity; therefore, a nongenotoxic mechanism is proposed. Nevertheless, toxaphene is believed to present a potential carcinogenic risk to humans. Until now, only Germany has established a legal tolerance level for toxaphene--0.1 mg kg-1 wet weight for fish.
    • Establishing boundary classes for the classification of UK marine waters using phytoplankton communities

      Devlin, M.; Best, M.; Coates, D.; Bresnan, E.; O'Boyle, S.; Parke, R.; Silke, J.; Cusack, C.; Skeats, J. (Elsevier, 2007)
      This paper presents a description of three of the proposed phytoplankton indices under investigation as part of a classification framework for UK and ROI marine waters. The three indices proposed for the classification process are (i) phytoplankton biomass measured as chlorophyll, (ii) the frequency of elevated phytoplankton counts measuring individual species and total cell counts and (iii) seasonal progression of phytoplankton functional groups through the year. Phytoplankton biomass is calculated by a 90th percentile measurement of chlorophyll over the growing season (April to September) compared to a predetermined reference value. Calculation of functional groups and cell counts are taken as proportional counts derived from the presence of the indicator species or group as compared to the total phytoplankton count. Initial boundary conditions for the assessment of high/good status were tested for each index. Chlorophyll reference conditions were taken from thresholds developed for previous EU directives with the setting of offshore concentrations as a reference condition. Thresholds for elevated counts of phytoplankton taxa were taken from previous EU assessments describing counts that could be impact negatively on the environment. Reference seasonal growth curves are established using phytoplankton counts from ‘‘high status’’ waterbodies. To test the preliminary boundaries for each index, a risk assessment integrating nutrient enrichment and susceptibility for coastal and transitional waters was carried out to identify WFD waterbodies in England and Wales at different levels of risk. Waterbodies assessed as having low or medium risk from nutrient enrichment were identified as type 1 and type 2 waterbodies, and waterbodies assessed as high risk were identified as type 3 waterbodies. Phytoplankton data was extracted from the risk assigned waterbodies and applied to each phytoplankton index to test the robustness of the preliminary classification ranges for each phytoplankton index.
    • Factors affecting the concentration of domoic acid in scallop, Pecten maximus

      Bogan, Y. (2006)
      Domoic acid, a neurotoxin produced by some Pseudo-nitzschia species, can accumulate in shellfish, consumption of which can result in Amnesic Shellfish Poisoning. Since its detection in Irish king scallop, Pecten maximus, regulatory monitoring of toxin levels in product entering the human food chain has been undertaken. Only limited data exist on factors that may influence variability in scallop DA concentration in the field. DA concentration in scallop tissues from a range of sites around Ireland, analysed using HPLC-PDA, exhibited high concentrations in hepatopancreas (max. 3834.4 (μg.g-1), much lower in gonad (max. 61.3 μg.g-1) and even lower concentrations in adductor muscle (max. 31.8 μg.g-1). Toxin concentration in hepatopancreas and scallop size usually exhibited no relationship and there was little support for the hypothesis that shellfish size influenced toxin concentration. DA concentration exhibited site-specific relationships with water depth. Toxin concentration in suspended scallops compared to seabed scallops exhibited a statistically significant difference on only one sampling occasion. Attempts to correlate the occurrence of DA in bivalves with the abundance of cells of Pseudo-nitzschia species were unsuccessful. Given the extent of field variability in DA concentration, a landings-based approach to toxin management rather than an area-based approach would reduce the risks of poisoning.
    • Gill damage to Atlantic salmon (Salmo salar) caused by the common jellyfish (Aurelia aurita) under experimental challenge

      Baxter, E.J.; Sturt, M.M.; Ruane, N.M.; Doyle, T.K.; McAllen, R.; Harman, L.; Rodger, H.D. (PLoS ONE, 2011)
      Background: Over recent decades jellyfish have caused fish kill events and recurrent gill problems in marine-farmed salmonids. Common jellyfish (Aurelia spp.) are among the most cosmopolitan jellyfish species in the oceans, with populations increasing in many coastal areas. The negative interaction between jellyfish and fish in aquaculture remains a poorly studied area of science. Thus, a recent fish mortality event in Ireland, involving Aurelia aurita, spurred an investigation into the effects of this jellyfish on marine-farmed salmon. Methodology/Principal Findings: To address the in vivo impact of the common jellyfish (A. aurita) on salmonids, we exposed Atlantic salmon (Salmo salar) smolts to macerated A. aurita for 10 hrs under experimental challenge. Gill tissues of control and experimental treatment groups were scored with a system that rated the damage between 0 and 21 using a range of primary and secondary parameters. Our results revealed that A. aurita rapidly and extensively damaged the gills of S. salar, with the pathogenesis of the disorder progressing even after the jellyfish were removed. After only 2 hrs of exposure, significant multi-focal damage to gill tissues was apparent. The nature and extent of the damage increased up to 48 hrs from the start of the challenge. Although the gills remained extensively damaged at 3 wks from the start of the challenge trial, shortening of the gill lamellae and organisation of the cells indicated an attempt to repair the damage suffered. Conclusions: Our findings clearly demonstrate that A. aurita can cause severe gill problems in marine-farmed fish. With aquaculture predicted to expand worldwide and evidence suggesting that jellyfish populations are increasing in some areas, this threat to aquaculture is of rising concern as significant losses due to jellyfish could be expected to increase in the future.
    • Growth and survival of Spisula solidissima similis larvae fed different rations of Tahitian strain Isochrysis species

      Hurley, D.H.; Walker, R.L.; O'Beirn, F.X. (National Shellfisheries Association, 1997)
      Laboratory-spawned veliger-stage larvae of the southern Atlantic surfclam, Spisula solidissima similis (Say 1822), were reared to late pediveliger stage on five different cell concentrations of Tahitian strain Isochrysis species (T-Iso) to determine an optimal food ration for this subspecies. Larvae were fed daily 0, 50,000, 100,000, 200,000, or 300,000 cells/mL of T-Iso. Day-old veliger larvae were stocked in 150 (1-L) replicate flasks at mean densities of 0.7 or 0.8 larvae/mL for trials A and B, respectively. Larval growth and survival were assessed every 2 days over the 14-day trial penods. Significantly greater growth and survival of larvae occurred in both trials in the lower food rations of 50,000 and 100,000 cells/mL. A reduction in larval growth rate and survival was observed at the higher ration treatments. A decline in overall larval health may be associated with the deliterious effects of surplus ration degradation.
    • Harmful and nuisance algal blooms in Irish coastal waters 1990 - 1993

      Silke, J.; Jackson, D. (ICES, 1993)
      Algal blooms occur naturally around our coast. These high concentrations of planktonic algae are associated with favourable conditions of light and nutrients, and often occur at stratification/ mixing fronts. Many blooms are completely harmless, and form the diet of shellfish and zooplankton. Some colour the water red or brown. A few species are toxic and can cause fish kills or make shellfish unsafe to eat. The Fisheries Research Centre monitors phytoplankton in order to detect any toxic or potentially harmful blooms. The harmful and nuisance algal events from 1990 to 1993 are described.
    • Harmful phytoplankton events caused by variability in the Irish Coastal Current along the west of Ireland

      O'Boyle, S.; Nolan, G.; Raine, R. (UNESCO IOC, 2001)
      Frequent sampling in summer along the western and northwestern coasts of Ireland showed the rapid onshore development of blooms of potentially harmful phytoplankton species. In both 1998 and 1999, concentrations of Gyrodinium cf. aureolum rose by four orders of magnitude to over one million cells per litre in Donegal Bay(northwestern Ireland) in less than 10days. The rapid development of these populations was linked to advection resulting from unfavourable wind-forcing of the Irish Coastal Current (ICG) which runs northwards along the western Irish coast. Current measurements showed that after a particular sequence of changes in wind direction phytoplankton populations could be rapidly advected from areas of slack circulation on the shelf via the ICC into aquaculturally sensitive coastal zones such as Donegal Bay. The model presented is similar to one already demonstrated for the occurrence of toxic events in the bays of southwestern Ireland. Other historical harmful events along the west and northwest coasts relating to substantial losses in both finfish and shellfish culture could also be explained using the model. These include the G. aureolum bloom of 1992, the Prorocentrum balticum bloom in 1997.
    • Histological examination of the gills as a method of detecting asymptomatic carriers of A. Salmonicida in Atlantic salmon (Salmo salar)

      McArdle, J.F.; Dooley-Martyn, C.; McKiernan, F. (European Association of Fish Pathologists, 1986)
    • Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs

      Donohoe, O. H.; Henshilwood, K.; Way, K.; Hakimjavadi, R.; Stone, D. M.; Walls, D. (PLoS ONE, 2015)
      MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.
    • Impact of inter-lab variation on the estimation of epidemiological cut-off values for disc diffusion susceptibility test data for Aeromonas salmonicida

      Smith, P.; Ruane, N.M.; Douglas, I.; Carroll, C.; Kronvall, G.; Fleming, G.T.A. (Elsevier, 2007)
      Two laboratories investigated the susceptibility of 106 Aeromonas salmonicida strains (from Denmark, France, Ireland, Norway and Scotland) to erythromycin, gentamicin, oxytetracycline and oxolinic acid using the disc diffusion protocols (M42-A) published by the Clinical and Laboratory Standards Institute. In studies of susceptibility to florfenicol an additional 15 Canadian strains were included. Comparison of the data generated by the two laboratories demonstrated that for each disc both detected a similar pattern of distribution but that there was a significant numerical difference in the zone sizes they recorded. Analysis of the extent of this lateral shift between the data generated in two laboratories indicated that the application of a single laboratory-independent epidemiological cut-off value for each disc could result in disagreement between the laboratories as to whether a strain should be classified as wild-type or non wild-type. Normalised resistance interpretation was employed to generate epidemiological cut-off values from the data obtained by each laboratory. The use of these laboratory-specific cut-off values resulted in both laboratories achieving complete agreement as to the classification of all strains to all agents.