• 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.; Henshilwood, K.; Geoghegan, F.; Fitzgerald, R.D. (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.
    • Phylogenetic analysis of infectious pancreatic necrosis virus in Ireland reveals the spread of a virulent genogroup 5 subtype previously associated with imports

      Ruane, N.M.; McCleary, S.J.; McCarthy, L.J.; Henshilwood, K. (Springer Verlag, 2015)
      Infectious pancreatic necrosis is a significant disease of farmed salmonids resulting in direct economic losses due to high mortality and disease-management costs. Significant outbreaks of the disease occurred in farmed Atlantic salmon in Ireland between 2003 and 2007, associated with imported ova and smolts. As the virus was known to occur in the country since the development of aquaculture in the 1980s, this study examined archived samples to determine whether these older isolates were associated with virulent forms. The study showed that two genotypes of IPNV were present in the 1990s, genotype 3 and genotype 5. A more virulent subtype of the virus first appeared in 2003 associated with clinical outbreaks of IPN, and this subtype is now the most prevalent form of IPNV found in the country. The data also indicated that IPNV in Ireland is more closely related to Scottish and continental European isolates than to Norwegian, Chilean and Australasian genogroup 5 isolates.
    • Phytoplankton and microbial plankton of the Northeast Atlantic Shelf

      Silke, J.; Kennington, K.; Bresnan, E.; Cusack, C. (ICES, 2012)
      The Northeast Atlantic Shelf region includes the sites from all coastal waters of Ireland, the Irish Sea, and western Scottish and Norwegian Sea waters. The region was defined by WGPME to include locations on the northern margin of Europe that were outside the North Sea/English Channel influence. The character of sites in the region are shallow, coastal-water sites ranging from sheltered bays on the south coast of Ireland and fjordic sea lochs of Scotland to fully exposed locations on the west coasts of Ireland and Scotland. Bathymetry of the region ranges from shallow embayments to regions of shallow, exposed continental-shelf waters. The topography of the shelf drops rapidly to 80–100 m within 20 km of the coast, where it extends to the shelf edge as a relatively flat plateau. Time-series of phytoplankton data from the Atlantic Shelf exhibit a typical seasonal pattern of temperate waters, with considerable geographical and temporal variation. The well-mixed winter conditions lead to a region-wide strong spring bloom observed at all sites. The ensuing decrease in nutrient levels lead to a variable summer period characterized by stratified conditions in coastal areas and periodic blooms of mixed or occasionally monospecific diatom and dinoflagellate composition. The growth period tails off in autumn, when a secondary bloom may occur in response to increased mixing and breakdown of the summer thermocline. The seasonal cycle returns to a quiescent winter phase, with generally mixed conditions, light limitation, and increased nutrients return. Seasonal stabilization and destabilization of the water column in this region accounts for most of the natural variation in both phytoplankton species composition and biomass.
    • Polychlorinated Biphenyls and Organochlorines in By-Caught Harbour Porpoises Phocoena phocoena and Common Dolphins Delphinus delphis from Irish Coastal Waters

      Smyth, M.; Berrow, S.; Nixon, E.; Rogan, E. (Royal Irish Academy, 2000)
      Concentrations of 11 organochlorine (OC) pesticides and 10 individual polychlorinated biphenyls (PCB) in blubber and liver from 12 harbour porpoise Phocoena phocoena and eight common dolphins Delphinus delphis incidentally caught in fishing nets in Irish waters are presented. Female harbour porpoises had highest concentrations of OC in blubber and male common dolphins in liver. Harbour porpoises had higher mean concentrations of lindane (121-154 ng/g extractable lipid), dieldrin (116-121 ng/g) and  BHC (54-128 ng/g) but common dolphins had greater overall concentrations of DDT (9444-3998 ng/g). The predominant DDT metabolite was pp-DDE and for the chlordanes was t-nonachlor. Concentrations of ICES 7 PCB (liver-blubber) were similar in both species (4075-7999 ng/g in harbour porpoise and 4076-8945 in common dolphins). The sum of ICES 7 PCB in porpoises ranged from 3041-12270 ng/g extractable lipid in the blubber of females and from 2911-10429 ng/g in males and 798-11074 ng/g in the blubber of female common dolphins and 1555-15883 ng/g in males. Contaminant levels were generally similar to those reported from Scotland but lower than reported from Scandinavia. Ratios of DDT to DDE suggests that there are limited new sources of DDT into the Irish marine environment. These results provide a baseline for monitoring of persistent pollutants in the Irish marine environment.
    • Preliminary recruitment studies of the eastern oyster, Crassostrea virginica, and their potential applications, in coastal Georgia

      O'Beirn, F.X.; Heffernan, P.; Walker, R.L. (Elsevier, 1995)
      Oyster recruitment was monitored in Wassaw Sound, Georgia from April through October, 1991. The study was initiated to determine precise recruitment patterns of oysters over the 7 month spawning season. One of the goals was to determine the most suitable time for the collection of natural spat for maricultural, fisheries and recreational purposes. Three sites of varying hydrographic characteristics were chosen in Wassaw Sound. The sites varied in terms of temperature and salinity regimes and in their exposure to wind and wave action. Within each site, oyster recruitment was estimated at three tidal heights; subtidally, at mean low water and intertidally, approximately 2 h above the mean low water mark. Sampling took place so as to measure net recruitment over biweekly (BW), monthly (M) and seasonal ( S) periods. The results indicated that the recruitment of oysters in this region of coastal Georgia is protracted, lasting 6 months (May through October). The levels of recruitment were very high relative to other regions on the east coast of the USA, with peak recruitment for the entire study area (x = 2800 spat m- 2 for BW and x = 3020 spat m- 2 for M) occurring between July and September. The intensity of recruitment varied significantly among the three sites. The most sheltered site in terms of wave exposure experienced the highest recruitment (x =4380 spat m- 2 BW; x = 6260 spat m -2 M). This site also had higher overall water temperatures as well as greater daily temperature fluctuations. The least sheltered site had the lowest numbers of young oysters (x = 1000 spat m- 2 BW; X. = 686 spat m- 2 M), as well as having the most stable temperature regime. The biweekly samples generally experienced higher recruitment subtidally at the three sites. The monthly samples had higher numbers of oyster spat at the mean low water mark while the seasonal samples showed significantly higher recruitment intertidally (up to x =7353 spat m-2 ). The shift in recruitment patterns over time is partially attributed to increased subtidal predation pressure on the recruits. The collection of natural spat in relation to the natural fishery, potential maricultural activity and the recreational fishery is discussed.
    • Preliminary results from a survey of oyster production areas in Ireland for norovirus

      Keaveney, S.; Flannery, J.; Guilfoyle, F.; Doré, J. (2007)
      A survey of 18 oyster production areas in Ireland for norovirus (NoV) contamination was initiated in August 2006. The findings presented are the preliminary results from the first seven months of the survey. Prior to the survey commencing, a simple desk bask sanitary survey of each area was undertaken. This provided an assessment enabling each site to be ranked into 3 categories (low, medium and high) on the basis of the risk of NoV contamination. Samples were collected on a monthly basis and tested for the presence of NoV using semi-quantitative real-time PCR allowing relative quantitation of NoV levels. A correlation was observed between occurrence and levels of NoV detected and the risk categories ascribed to each production area. To date NoV was detected in 60.7, 30.0 and 2.5 percent of samples from the high, medium and low risk categorised areas, respectively. A strong seasonal bias towards increased winter contamination was observed with NoV detected in 15.5 and 50 % of samples in August and February, respectively. The preliminary results from this survey indicate that it may be possible to predict the relative risk of NoV contamination in a shellfish harvesting area. This in conjunction with targeted NoV monitoring using real-time PCR could aid the further development of risk management procedures in shellfisheries.
    • Prevalence of Perkinsus marinus in the eastern oyster, Crassostrea virginica in relation to tidal placement in a Georgia tidal creek

      O'Beirn, F.X.; Dean, C.C.; Walker, R.L. (Marine Environmental Sciences Consortium of Alabama, 1994)
      This experiment was designed to evaluate the effects tidal zonation and bottom placement of the eastern oyster, Crassostrea virginica, have on the prevalence and intensity of the oyster parasite, Perkinsus marinus a suspected causative agent for subtidal oyster mortalities experienced in the coastal waters of Georgia. Twelve growout bags (1 m x 0.5 m; 12.7 mm mesh), each containing 200 oysters, were placed in Jointer Creek, Georgia In March 1992. Bags (3 replicates each) were placed lntertidally and subtidally on the creek bottom and offbottom. Ten oysters per bag were removed monthly for twelve months beginning March 1992, and were inspected for prevalence and intensity of Perkinsus marinus, using the thioglycollate method. Oyster mortality and shell length data were also evaluated. Neither prevalence (p = 0.3505) nor intensity levels (p = 0.2993) of Perkinsus marinus in oysters were significantly different among the treatments. Although there were no significant differences In prevalence or intensity of the pathogen among treatments, the intertidal offbottom treatment had the lowest values most frequently. Perkinsus marinus was present in all replicates every month. Prevalence and intensity of infection followed the typically observed pattern of maximum values in summer and fall and minimum levels in winter. Subtidal bottom oysters experienced higher mortalities (p = 0.0022), but the prevalence and intensity of Perklnsus marinus in oysters were not significantly different between treatments. It appears therefore, that the oyster parasite, Perkinsus marinus is not the discerning factor in the higher mortalities witnessed in oysters placed subtidally on the bottom in the southeastern U.S. coastal waters.
    • Proceedings of the 8th Irish Shellfish Safety Workshop

      McMahon, T.; Deegan, B.; Silke, J.; Ó Cinneide, M. (Marine Institute, 2008)
      This document outlines the proceedings of the 8th Irish Shellfish Safety Scientific Workshop. This event was organised by the Marine Institute, the Food Safety Authority of Ireland and Bord Iascaigh Mhara to discuss the methods and advances of food safety with respect to shellfish health.
    • Proceedings of the 9th Irish Shellfish Safety Scientific Workshop

      Gilmartin, M.; Silke, J. (Marine Institute, 2009)
      The 9th Irish Shellfish Safety Workshop was held on the 20th March, 2009, in Kenmare, County Kerry. The Workshop was co-sponsored by the Marine Institute, Bord Iascaigh Mhara, the Food Safety Authority of Ireland, and the Sea Fisheries Protection Authority, with support from IFA Aquaculture. The topics addressed at the workshop included an update on the National Biotoxin monitoring programme, and a number of research projects with Irish participation and international perspectives on toxin detection. Finding mechanisms to improve our product was a common theme with presentations on improving food safety, increasing productivity, providing easily applied test methods, and research in support of the shellfish industry. The focus of the three Workshop sessions was on a review of the year, research and legislation.
    • Real-time PCR detection of Dinophysis species in Irish coastal waters

      Kavanagh, S.; Brennan, C.; O’Connor, L.; Moran, S.; Salas, R.; Lyons, J.; Silke, J.; Maher, M. (Springer Verlag, 2010)
      Diarrhetic shellfish toxin-producing Dinophysis species occur in Irish coastal waters throughout the year. Dinophysis acuta and Dinophysis acuminata are the most commonly occurring species and are responsible for the majority of closures of Irish mussel farms. This study describes the development of a qualitative real-time polymerase chain reaction (PCR) assay for identification of D. acuta and D. acuminata in Irish coastal waters. DNA sequence information for the D1-D2 region of the large ribosomal sub-unit (LSU) was obtained, following single-cell PCR of D. acuta and D. acuminata cells isolated from Irish coastal locations. PCR primers and hybridization probes, specific for the detection of D. acuta, were designed for real-time PCR on the LightCycler™. The LightCycler™ software melt curve analysis programme determined that D. acuta was identified by a melt-peak at 61°C, while D. acuminata cells produced a melt peak at 48°C. The limit of detection of the real-time PCR assay was determined to be one to ten plasmid copies of the LSU D1-D2 target region for both species and one to five D. acuminata cells. Lugol's preserved water samples were also tested with the assay. The real-time PCR assay identified Dinophysis species in 100% of samples found to contain Dinophysis species by light microscopy and had a greater than 90% correlation with light microscopy for identification of D. acuta and D. acuminata in the samples. The assay can identify and discriminate D. acuta and D. acuminata at low numbers in Irish waters and has the potential to add value to the Irish phytoplankton monitoring programme.
    • REDRISK: reduction of the virus risk in shellfish harvesting areas

      Guilfoyle, F.; Keaveney, S.; Flannery, J.; Doré, B. (Marine Institute, 2006)
      Filter feeding bivalve shellfish can accumulate human pathogenic bacteria and viruses if grown in sewage-contaminated waters. Current consumer protection legislation relies on classification of harvesting areas based on their sanitary quality, using E coli as an indicator of sewage contamination. Advances in viral monitoring have shown that E coli can underestimate the extent of the contamination. The most common cause of gastroenteritis associated with shellfish is norovirus, commonly known as winter vomiting virus. The REDRISK project was undertaken to investigate the main environmental factors that cause viral contamination in shellfish. The REDRISK project is part of a EU research pillar with parallel research being undertaken in the UK, France and Spain. A recently developed technique to quantify norovirus in shellfish, real-time PCR, has been used in the REDRISK project. Clew Bay, in Co. Mayo was chosen as the study area in Ireland. The bay is generally considered to have good water quality but with certain areas subject to intermittent sewage contamination. The cooperation of local producers and organisations such as the Clew Bay Marine Forum and the Native Oyster Co-op greatly helped the project. The project was divided into a two-phased approach. Phase one involved the identification of contamination sources impacting the bay through a sanitary survey and selection of appropriate sites for further study. Results of the first phase of this study were presented previously at this forum (Keaveney, et al 2006) and the characteristics of the sites selected for study and locations within the bay are shown in table 1 and figure 1 respectively. The second phase of the project focused on monitoring environmental conditions and microbiological levels in shellfish to identify environmental conditions leading to viral contamination. This paper reports the finding of this monitoring.
    • Report on analysis of shellfish samples for the presence of Yessotoxins (YTX)

      Marine Institute (Marine Institute, 2001)
      In order to determine the cause of the positive mouse bioassay results obtained in mussel samples from several shellfish production areas (including Bantry Bay, Kenmare Bay, Cromane and Lough Foyle), samples were sent in December 2000 and January 2001 for analysis. Positive mouse bioassay results were obtained, using the Yasumoto (1978) assay, in the EU Reference Laboratory and using the Yasumoto (l 984) assay in the Italian Reference Laboratory. ASP toxins, Azaspiracid, Okadaic acid and DTXs were not detected. Yessotoxin, homoYessotoxins and analogues of Yessotoxins were not detected in the samples sent to the EU Reference Laboratory or the Italian Reference Laboratory. Prof. Yasumoto detected the presence of Yessotoxin and 45-hydroxyYessotoxin at the Japan Food Research Laboratory. 45-hydroxyYessotoxin is a shellfish metabolite of Yessotoxin, which occurs with time as the YTX is oxidised by the shellfish. The shellfish samples in which Yessotoxin and 45-hydroxy Yessotoxin were detected were taken from Bantry Bay, Roaring Water Bay (Summer 2000) and Mulroy Bay. If the initial detection of Yessotoxin and 45-hydroxyYessotoxin is confirmed in other samples, the Irish biotoxin management regime and the production cycles for shellfish (in particular mussels) will have to be adapted to encompass YTX.