• Molecular differentiation of infectious pancreatic necrosis virus isolates from farmed and wild salmonids in Ireland

      McCarthy, L; Swords, D; Ruane, N. M. (Wiley-Blackwell, 2009)
      This study investigated the genotypes and sub-groups of infectious pancreatic necrosis virus (IPNV) present in farmed and wild salmonid fish in Ireland. An 1100-bp portion of the VP2 region of segment A from each of 55 IPNV isolates collected over 2003–2007 was amplified by reverse-transcription–polymerase chain reaction and the product directly sequenced. The nucleotide sequences of each isolate were aligned and compared with each other and with the corresponding sequences of a number of reference isolates. All the 55 sequenced isolates belonged to genogroup 5 (Sp serotype) and could be divided into two subgroups. Irish subgroup 1 consisted of isolates from farmed salmon originating from an Irish salmon broodstock. Irish subgroup 2 consisted of isolates from imported farmed stock and all reported clinical outbreaks of IPN were associated with isolates from subgroup 2. Isolates from wild fish were identical to some isolates from subgroup 2, and therefore are believed to have originated from infected farms. These results highlight the importance of import risk analysis for diseases not listed under current legislation.
    • Molecular methods for monitoring harmful algal bloom species

      Keady, E.; Maher, M. (Marine Institute, 2009)
      Shellfish production can be adversely affected by the presence of harmful microalgae (HABs). Toxins produced by Dinophysis, Alexandrium and Pseudo-nitzschia species can accumulate in shellfish and have the potential to cause serious human illness. In order to satisfy EU legislative requirements pertaining to the production and export of shellfish (EC Hygiene Regulations 2004, No. 853/2004 and No. 854/2004, which replaced the EU Shellfish Hygiene Directive 91/492/EEC in January 2006), monitoring the presence of harmful algal species and biotoxins in coastal waters is performed by EU member states. Routine microscopic monitoring methods are unable to identify certain toxic species, in particular, Alexandrium and Pseudo-nitzschia spp. Electron microscopy is required for species identification and this technique cannot be integrated into a routine monitoring programme. Molecular techniques utilise unique sequence signatures within microorganism genomes for species specific identification. Molecular methods applied for the identification and quantification of HAB species include Fluorescent in-situ hybridisation (FISH) and in-vitro amplification based methods, in particular, real-time PCR.
    • Monitoring of Shellfish Growing Areas - 1993

      Nixon, E.; Rowe, A.; Smith, M.; McLoughlin, D.; Silke, J. (Department of the Marine, 1994-08)
      During 1993, water and shellfish from 19 major growing areas were monitored for chemical parameters in accordance with the 1979 Council Directive 79/923/EC. At each site temperature, salinity, pH, dissolved oxygen and suspended solids measurements were taken and shellfish samples were returned to the laboratory for metal, chlorinated hydrocarbon and algal biotoxin determinations. Generally, water quality in all areas was good and conformed to the guidelines of the Directive. The highest levels of metals recorded were: cadmium in Tralee Bay (0.4 to 0.7µg/g) and Carlingford Lough (0.3 to 0.7µg/g) and lead in Wexford Harbour (0.5µg/g). Mercury in all cases was low with the exception of Cromane during November when levels of 0.3µg/g were detected. Chlorinated hydrocarbons levels were extremely low and indicate the clean nature of Irish shellfish, unpolluted by these synthetic organic compounds. Algal biotoxins were not detected in any samples.
    • Monitoring results for trace metals and organohalogens in shellfish (2015) and physicochemical parameters and trace metals in seawater (2016) in accordance with Shellfish Waters Directive. CHEMREP 2018-003

      Marine Institute (Marine Institute, 2018)
      Directive 2006/113/EC on the Quality Required of Shellfish Waters, also referred to as the Shellfish Waters Directive (SWD) requires the monitoring of, inter alia, certain physicochemical parameters including trace metal contaminants in order to assess and protect the quality of shellfish growing waters and the shellfish harvested from them. The SWD is concerned with the quality of shellfish waters and applied waters designated by the Member States as needing protection or improvement in order to support shellfish (bivalve and gastropod molluscs) life and growth and thus to contribute to the high quality of shellfish products directly edible by man. This report details the Marine Institute’s (MI) monitoring results for physicochemical parameters sampled in seawater and shellfish tissue from designated Shellfish Waters and specifically: Dissolved trace metal concentrations and other physiochemical parameters in seawater sampled from Irish Shellfish Waters in 2016 and trace metal and organohalogen concentrations in shellfish sampled in 2015.
    • Monitoring trace metals and organohalogens in shellfish (2014) and physicochemical parameters and trace metals in seawater (2015) under the Shellfish Waters Directive

      Environmental Team, Chemistry Section, Marine Environment & Food Safety Services (Marine Institute, 2017)
      Directive 2006/113/EC on the Quality Required of Shellfish Waters, also referred to as the Shellfish Waters Directive (SWD) requires the monitoring of, inter alia, certain physicochemical parameters including trace metal contaminants in order to assess and protect the quality of shellfish growing waters and the shellfish harvested from them. Sixty-four areas have been designated as Shellfish Waters (SWs) under SI 268 of 2006, SI 55 of 2009 and SI 464 of 2009. The SWD is concerned the quality of shellfish waters and applied waters designated by the Member States as needing protection or improvement in order to support shellfish (bivalve and gastropod molluscs) life and growth and thus to contribute to the high quality of shellfish products directly edible by man. The Marine Institute undertakes a monitoring programme to meet the requirements of the Water Framework Directive (WFD) 2000/60/EC Transitional and Coastal (TraC) Waters and physico-chemical elements of the SWD.
    • Morphological and molecular characterization of the small armoured dinoflagellate Heterocapsa minima (Peridiniales, Dinophyceae)

      Salas, R.; Tillmann, U.; Kavanagh, S. (Taylor and Francis, 2014)
      The dinophycean genus Heterocapsa is of considerable interest as it contains a number of bloom-forming and/or harmful species. Fine structure of organic body scales is regarded as the most important morphological feature for species determination but currently is unknown for the species H. minima described by Pomroy 25 years ago. Availability of a culture of H. minima collected in the south-west of Ireland allowed us to provide important information for this species, including cell size, cell organelle location, thecal plate pattern, body scale fine structure and molecular phylogeny. Light microscopy revealed the presence of one reticulate chloroplast, an elongated centrally located nucleus, and the presence of one pyrenoid surrounded by a starch sheath. Scanning electron microscopy (SEM) of the thecal plate pattern indicated that Pomroy erroneously designated the narrow first cingular plate as a sulcal plate. In addition, SEM revealed as yet unreported details of the apical pore complex and uncommon ornamentations of hypothecal plates. Organic body scales of H. minima were about 400 nm in size, roundish, with a small central hole and one central, six peripheral and three radiating spines. They differ from other body scales described within this genus allowing for positive identification of H. minima. Heterocapsa minima shares gross cell morphological features (hyposome smaller than episome, elongated nucleus in the middle of the cell, one pyrenoid located in the episome on its left side) with H. arctica (both subspecies H. arctica subsp. arctica and H. arctica subsp. frigida), H. lanceolata and H. rotundata. These relationships are reflected in the phylogenetic trees based on LSU and ITS rDNA sequence data, which identified H. arctica (both subspecies), H. rotundata and H. lanceolata as close relatives of H. minima.
    • A multi-year comparison of Spirolide profiles in planktonic field samples from the North Sea and adjacent waters

      Krock, B.; Tillmann, U.; Alpermann, T.; Salas, R.; Cembella, A.D. (Alfred-Wegener-Institut für Polar- und Meeresforschung in der Helmholtz-Gemeinschaft, 2010)
      Alexandrium ostenfeldii isolates from distinct geographical locations showed almost identical profiles, primarily consisting of 20-methyl spirolide G (20-meG). Whereas the Scottish isolate produces only this variant, the Irish isolate additionally yields slight amounts of 13-desmethyl spirolide C (13-desmeC). These profiles were also reflected in the field data, where 20-meG was the most abundant spirolide throughout all samples and years.
    • New insights into the causes of human illness due to consumption of azaspiracid contaminated shellfish

      Chevallier, O.P.; Graham, S.F.; Alonso, E.; Duffy, C.; Silke, J.; Campbell, K.; Botana, L.M.; Elliott, C.T. (Nature Publishing Group, 2015)
      Azaspiracid (AZA) poisoning was unknown until 1995 when shellfish harvested in Ireland caused illness manifesting by vomiting and diarrhoea. Further in vivo/vitro studies showed neurotoxicity linked with AZA exposure. However, the biological target of the toxin which will help explain such potent neurological activity is still unknown. A region of Irish coastline was selected and shellfish were sampled and tested for AZA using mass spectrometry. An outbreak was identified in 2010 and samples collected before and after the contamination episode were compared for their metabolite profile using high resolution mass spectrometry. Twenty eight ions were identified at higher concentration in the contaminated samples. Stringent bioinformatic analysis revealed putative identifications for seven compounds including, glutarylcarnitine, a glutaric acid metabolite. Glutaric acid, the parent compound linked with human neurological manifestations was subjected to toxicological investigations but was found to have no specific effect on the sodium channel (as was the case with AZA). However in combination, glutaric acid (1mM) and azaspiracid (50nM) inhibited the activity of the sodium channel by over 50%. Glutaric acid was subsequently detected in all shellfish employed in the study. For the first time a viable mechanism for how AZA manifests itself as a toxin is presented.
    • Norovirus genotypes present in oysters and in effluent from a wastewater treatment plant during the seasonal peak of infections in Ireland in 2010

      Rajow-Nenow, P.; Waters, A.; Keaveney, S.; Flannery, J.; Tuite, G.; Coughlan, S.; O’Flaherty, V.; Doré, W. (American Society for Microbiology, 2013)
      We determined norovirus (NoV) concentrations in effluent from a wastewater treatment plant and in oysters during the peak period of laboratory-confirmed cases of NoV infection in Ireland in 2010 (January to March). Weekly samples of influent, secondary treated effluent, and oysters were analyzed using real-time quantitative reverse transcription-PCR for NoV genogroup I (GI) and genogroup II (GII). The mean concentration of NoV GII (5.87 104 genome copies 100 ml 1) in influent wastewater was significantly higher than the mean concentration of NoV GI (1.40 104 genome copies 100 ml 1). The highest concentration of NoV GII (2.20 105 genome copies 100 ml 1) was detected in influent wastewater during week 6. Over the study period, a total of 931 laboratory-confirmed cases of NoV GII infection were recorded, with the peak (n 171) occurring in week 7. In comparison, 16 cases of NoV GI-associated illness were reported during the study period. In addition, the NoV capsid N/S domain was molecularly characterized for selected samples. Multiple genotypes of NoV GI (GI.1, GI.4, GI.5, GI.6, and GI.7) and GII (GII.3, GII.4, GII.6, GII.7, GII.12, GII.13, and GII.17), as well as 4 putative recombinant strains, were detected in the environmental samples. The NoV GII.4 variant 2010 was detected in wastewater and oyster samples and was the dominant strain detected in NoV outbreaks at that time. This study demonstrates the diversity of NoV genotypes present in wastewater during a period of high rates of NoV infection in the community and highlights the potential for the environmental spread of multiple NoV genotypes.
    • Novel azaspiracids produced by Amphidomataceae

      Krock, B.; Tillmann, U.; Jeong, H.J.; Potvin, E.; Salas, R.; Kilcoyne, J.; Gu, H. (Alfred-Wegener-Institut für Polar- und Meeresforschung, 2012)
    • Nucleic acid tests for toxic phytoplankton in Irish waters-phytotest: Marine Strategic RTDI project AT/04/02/02 - research update

      Maher, M.; Kavanagh, S.; Brennan, C.; Moran, M.; Salas, R.; Lyons, J.; Silke, J. (Marine Institute, 2007)
      The Phytotest project is a 3 year collaborative project funded through the Marine Strategic Programme in Advanced Technologies as part of the National Development plan 2000-2006. The project partners include the National Diagnostics Centre at NUI Galway and MI. The overall objective of the project is the development of nucleic acid tests (molecular methods) for the identification of key toxic phytoplankton species in Irish waters. In the final year of the programme the aim is to transfer the molecular methods developed in the project into MI to support their monitoring service. Currently, the monitoring for phytoplankton species in Irish waters is performed by light microscopy which can easily identify some plankton species based on distinctive morphological traits. Other species in particular, Pseudonitzschia spp. and Alexandrium spp. cannot be identified to species level by light microscopy. Identification of these species requires more sophisticated microscopic techniques such as scanning electron microscopy (SEM) and transmission electron microscopy (TEM). These techniques cannot easily be integrated into a routine testing environment. Molecular methods utilise unique information contained within an organism’s genome in order to identify it. This genetic information can be exploited in a range of molecular test platforms enabling microorganisms to be identified to species level. Additionally, there has been a major drive towards the development of highly automated platforms to support molecular tests for high-throughput testing in routine laboratory settings.
    • Observations on a bloom of Flagellate "X" in the West of Ireland

      Dunne, T. (ICES, 1984)
      In July 1983 major mortalities of farmed trout and salmon were associated with a bloom of an unidentified organism hitherto unrecorded in Ireland. Three further blooms occurred in 1984, two of which were associated with mortalities. The morphology of this organism (Flagellate "X") as observed in 1983 is described.
    • Observed sequential occurrence of phytoplankton and zooplankton in the Dunkellin Estuary, Galway Bay, Ireland

      Byrne, P.; O'Mahony, J.H.T. (ICES, 1993)
      The Dunkellin is a small tidally-dominated estuary to the south-east of Galway Bay in western Ireland. The plankton of the estuary was studied for 18 months between December 1984 and July 1986. This paper presents results on the variation in the sequential occurrenCe of phytoplankton and zooplankton between the inner and outer estuary. Phytoplankton and microzooplankton occurred in high numbers in the spring to autumn months. Highest abundances of phytoplankton and microzooplankton (non-tintinnid ciliates and tintinnid ciliates) were recorded 10 the Inner estuary, whereas mesozooplankton were predominant in the outer reaches.
    • The occurrence of DSP toxicity in Ireland

      Jackson, D.; Silke, J.; Doyle, J.; Nixon, E.; Taaffe, B. (ICES, 1993)
      The geographical and temporal variations in the occurrence of DSP in Ireland are presented and the implications of the resulting closures on aquaculture operations and fisheries are discussed. Prior to 1992 DSP toxicity had been confined to the southwest and south coasts but in 1992 a protracted occurrence of DSP was recorded in Killary Harbour on the west coast.
    • The oceanography of southwest Ireland: current research activities

      Raine, R.; Whelan, D.; Conway, N.; Joyce, B.; Moloney, M.; Hoey, M.J.; Patching, J.W. (Fisheries Research Centre, 1993)
      The coastal waters of Ireland are rich in physical features affecting both chemistry and biology. Amongst these are the tidal fronts of the Irish Sea (Le Fevre, 1986) and the Irish Shelf Front on the Atlantic coast lying along the 200m iso bath (Huang et al., 1991). Recently, an upwelling system has been described in the vicinity of the Fastnet Rock (Roden, 1986; Raine et al., 1990). Coastal upwelling systems are ecologically very important and are generally extremely productive, as nutrients brought up to the sea surface can stimulate extensive phytoplankton growth. This paper describes further satellite and ship-based investigations which are currently being carried out to examine the mechanisms driving the upwelling system and its effect on local ecology.
    • Organisms associated with oysters cultured in floating systems in Virginia, USA

      O'Beirn, F.X.; Ross, P.G.; Luckenbach, M.W. (National Shellfisheries Association, 2004)
      The number and abundance of macro-fauna! taxa was estimated from six floating structures (floats) used to culture the Eastern oyster (Crassostrea virginica) near Chincoteague Island, Virginia, USA. After a 10-mo grow-out period, all organisms found among and attached to the cultured oysters were counted. The final mean size of oysters was 80.5 (14.7 SD) mm. Overall, 45 species of macrofauna were recorded with the number of species in the floats ranging from 24 to 36. There was no relationship between the number of taxa and the density of oysters in the floats. Total abundances of associated organisms were estimated at 12,746/float to 92,602/float. These findings highlight the diverse (taxonomic and trophic) and abundant nature of communities associated with cultured oysters. They also provide a baseline set of information that may help more clearly define the interactions between oyster culture and the environment.
    • An outbreak of francisellosis in wild-caught Celtic Sea Atlantic cod, Gadus morhua L., juveniles reared in captivity

      Ruane, N.M.; Bolton-Warberg, M.; Rodger, H.D.; Colquhoun, D.J.; Geary, M.; McCleary, S.J.; O´Halloran, K.; Maher, K.; O´Keeffe, D.; Mirimin, L.; et al. (Wiley, 2013)
    • Overview of trends in plankton communities

      Licandro, P.; Head, E.; Gislason, A.; Benfield, M.C.; Harvey, M.; Margonski, P.; Silke, J. (ICES, 2011)
      Phytoplankton and zooplankton occupy pivotal positions within marine ecosystems. These small organisms fuel and support the foodwebs upon which almost all higher organisms depend. Fisheries and related economic activities are highly dependent on the production, size, and composition of zooplankton which, in turn, rely on primary production by phytoplankton. In addition to their role as prey for herbivorous zooplankton, phytoplankton absorb enormous quantities of dissolved CO2 via photosynthesis. Zooplankton then plays an essential role in the biological pump by consuming phytoplankton and transporting carbon from the upper ocean to the deep ocean, where it is sequestered for hundreds to thousands of years. Given the ecological and economic importance of phyto‐ and zooplankton, it is essential to understand and predict how they are likely to respond to climate change. Climate‐related hydrographic changes may also directly affect the abundance and composition of zooplankton, shifting the distribution of dominant species, changing the structure of the zooplankton community, and altering the timing, duration, and efficiency of zooplankton reproductive cycles. Ocean acidification through increased carbon dioxide dissolution in the upper ocean is lowering the pH in surface waters. A lower pH could impair the physiology and ultimately the abundance of many phytoplankton and zooplankton species. It is important to understand how phytoplankton and zooplankton are likely to respond to climate‐induced changes in the ocean. This section explores what is known about the sensitivity of phytoplankton and zooplankton to climate change and summarizes the trends that are evident in plankton communities within the ICES Area.
    • Pea Crab, Pinna theres ostreum Say, 1817, in the eastern Oyster, Crassostrea virginica (Gmelin, 1791): prevalence and apparent adverse effects on oyster gonad development

      O'Beirn, F.X.; Walker, R.L. (California Malacozoological Society, 1999)
      Incidence of pea crab, Pinnotheres ostreum Say 1817, infestation in the eastern oyster, Crassostrea virginica (Gmelin, 1791), was recorded and related to oyster gametogenic activity over 18 months. Sampling occurred at twO tidal heights (high intertidal HI and low intertidal LI) at two sites (House Creek, HC and Skidaway River, SR) in Wassaw Sound, Georgia. Overall, incidence rates were 3% HC LI, 1 % HC HI, 8% SR LI, and 4% SR HI. At both tidal heights at HC, no differences were observed in gonad area between those oysters with and without pea crabs. At SR (where overall incidences were higher), oysters without pea crabs had significantly higher gonad area values than those oysters with pea crabs present. These results suggest that at higher incidences of pea crab infestation, oyster reproductive capabilities could be impacted, and support the claim that the pea crab/oyster relationship is a parasitic one.
    • Performance of the EU Harmonised Mouse Bioassay for Lipophilic Toxins for the Detection of Azaspiracids in Naturally Contaminated Mussel (Mytilus edulis) Hepatopancreas Tissue Homogenates Characterised by Liquid Chromatography coupled to Tandem Mass Spectrometry

      Hess, P.; Butter, T.; Petersen, A.; Silke, J.; McMahon, T. (Elsevier, 2009)
      Azaspiracids (AZAs) are a group of lipophilic polyether toxins that were discovered in shellfish from Ireland in 1995, following a food poisoning incident. Both the limited availability of pure AZAs and the co-occurrence in shellfish of other toxins in combination with AZAs have so far prevented an in-depth evaluation of the performance of the EU reference test, the mouse bioassay (MBA), for this toxin group at the regulatory limit. The present study evaluated the performance of the mouse bioassay at the example of a mussel tissue homogenate, naturally contaminated with AZAs, diluted with uncontaminated tissues to appropriate concentration levels. Concentrations were determined using liquid chromatography coupled to tandem mass spectrometry (LC-MS-MS) (7 levels ranging from levels less than the limit of quantification to a maximum of ca. 2.24 mg/kg in hepatopancreas, which corresponds to a maximum whole flesh AZA1-equivalent of ca. 0.34 mg/kg). Replicate homogenates of each concentration level were analysed by MBA on 7 independent occasions over 6 weeks. Inhomogeneity between replicate aliquot portions was evaluated using LC-MS-MS and ranged from 1.8 to 6.6% RSD for the six levels contaminated above quantification limits. This variation was similar to the variability of the LC-MS-MS method within a batch, and the difference between replicate aliquots could thus be considered negligible. Other uncertainties considered in the study included the short- and long-term variability of the LC-MS-MS method, toxic equivalence factors, relative response factors in mass spectrometric detection, additional analogues and matrix effects. A concentration-response curve was modelled as a 4-parametric logistic fit to a sigmoidal function, with an LC50 of 0.70 mg AZA1-equivalent/kg hepatopancreas tissue. Furthermore, the mathematical model of the lethality data from this study suggests that occasional negative mouse assays at high concentrations, previously observed in the Irish statutory monitoring, are at least partly due to the biological variation of mice and can be understood on a statistical basis. The mathematical model of the concentration-response curve also describes the probability of a positive mouse bioassay at the current regulatory limit of 0.16 mg/kg to be ca. 95%. Therefore, it appears that the mouse bioassay performs very well in the implementation of this limit. Hence, the present study very strongly suggests that the MBA and LC-MS-MS techniques can be considered equivalent in the implementation of the current regulatory limit of 0.16 mg/kg for Azaspiracids in shellfish.