• Report on the incidence and implications of phytoplankton blooms on the East Coast and particularly Wexford Harbour, Summer 1984

      Doyle, J.; Dunne, T. (1984)
      The Fisheries Research Centre had a number of reports of discoloured water between Brittas Bay Co. Wicklow and Wexford Harbour and south to Kilmore Quay. Samples of water received from Dr. David Jeffrey, Department of Botany TCD, collected from Penny-come-quick beach, co. Wicklow on June 17th and examined by Tom Dunne in the Laboratory contained dense colonies of Phaeocystis pouchetii - a microscopic algae. Subsequent samples collected by Miss Ann Kiley, Wexford County Council, traced the extent of the bloom as far south as Neamstown near Kilmore Quay. A sample taken at Cullenstown west of Kilmore Quay was clear. Also associated with this bloom were large numbers of needlelike diatoms (Nitzschia spp. More seriously, blooms of another microscopic alga (Prorocentrum minimum) began to develop in early July during the later phase of the Phaeocystis bloom.
    • Reproductive biology and parasite (Perkinsus marinus) prevalence in the eastern oyster, Crassostrea virginica, within a Georgia tidal river

      O'Beirn, F.X.; Walker, R.L.; Jansen, M.L. (Elisha Mitchell Scientific Society, 1997)
      Recruitment, in 1992, of the eastern oyster, Crassostrea virginica, at one site (Flume Dock) within the Sapelo Island National Estuarine Research Reserve (SINERR) was lower than other sampling sites. Recruitment allied with gametogenesis and parasite (Perkinsus marinus) prevalence within the oysters was examined in 1993, in an attempt to explain the differences observed the previous year. Sampling occurred at three sites (Marsh Landing, Jack Hammock, and Flume Dock) along the Duplin River within the SINERR. Oyster recruitment in 1993 was reduced in all sites within the SINERR. No oyster recruitment was recorded at the Flume Dock site during any monthly collections or on collectors deployed for the duration of the sampling study. Oysters developed gametogenically and spawned at the Marsh Landing site two weeks prior to their occurrence at the Jack Hammock site. Gametogenic development in oysters at the Flume Dock site was retarded a further two weeks where the males appeared to spawn six weeks after the females, which could account for reduced recruitment levels at this site. Approximately, twice as many females as males occurred in all sites. Monthly sampling of prevalence and intensity of Perkinsus marinus (Dermo) revealed high levels of both parameters. Smaller oysters did display lower prevalences of Dermo than larger forms.
    • Reproductive Failure of Landlocked Atlantic Salmon from New York's Finger Lakes: Investigations into the Etiology and Epidemiology of the “Cayuga Syndrome”

      Fisher, J.P.; Spitsbergen, J.M.; Rodman, G.; symula, j. (American Fisheries Society, 1995)
      We describe a disease syndrome that afflicts larval, landlocked Atlantic salmon Salmo salar from Cayuga Lake, one of central New York's Finger Lakes. Mortality associated with the “Cayuga syndrome” is 98–100%. Death usually occurs between 650 and 850 centigrade degreedays after fertilization, approximately 2–4 weeks before yolk resorption is complete. Although there is minor temporal variation in the onset of the Cayuga syndrome in progeny from individual females, all sac fry eventually succumb. Incubation of embryos and sac fry under constant, ambient, or reduced temperature regimens slightly alters the degree-day timing of syndrome onset, but does not improve survival. Based on mortality rate, manifestation of the Cayuga syndrome has not changed in the past 10 years, even though incubation waters of varying chemistry and temperature have been used. Mortality of the negative control stocks used for these studies never exceeded 10% from hatching to first feeding. Findings from reciprocal crossbreeding experiments indicate the problem is associated with ova only. A noninfectious etiology is indicated by the lack of consistently identifiable fish pathogens from syndrome-afflicted sac fry and by the failure to transmit the condition horizontally. Suspect contaminants were eliminated as potential causative factors. Epidemiological studies on the viability of other Finger Lakes stocks indicate that Atlantic salmon from Keuka and Seneca lakes are also afflicted (100% mortality). yet those from Skaneateles Lake are not. The cause of this syndrome appears to be nutritional.
    • Review of phytoplankton monitoring 2005

      Moran, S.; Silke, J.; Salas, R.; Chamberlain, T.; Lyons, J.; Flannery, J.; Thornton, V.; Clarke, D.; Devilly, L. (Marine Institute, 2006)
      A national phytoplankton monitoring programme, has been in operation in Ireland since 1986, and fulfils requirements of the EU Council Directive 91/492/EEC. This programme provides an important part of the baseline data in the overall integrated shellfish monitoring programme. The analysis of samples received on a regular basis from a site can provide very important information in assembling a population profile for the area. This helps in crucial decisions, for example in Management Cell Decisions - conducted by representatives from the industry, MI, FSAI and DCMNR - when borderline toxin results are present. Phytoplankton monitoring is also hugely important in the Water Framework Directive, which all EU countries must follow, in developing an index of water quality in Ireland and Europe. The Irish Monitoring programme also gives valuable public health information to County Councils, Environmental Health Officer’s and the public during times of bloom events. This paper provides an overview of phytoplankton sampling, analysis and reporting in 2005. The occurrence of potentially toxic and harmful phytoplankton found in Irish coastal and shelf waters in 2005 is also reviewed and the quality scheme in operation is described.
    • Review of phytoplankton monitoring 2006

      Moran, S.; Silke, J.; Salas, R.; Chamberlain, T.; Lyons, J.; Shannon, S. (Marine Institute, 2007)
      This paper provides an overview of phytoplankton sampling, analysis and reporting in 2006. The occurrence of potentially toxic and harmful phytoplankton found in Irish coastal and shelf waters in 2006 is compared with the previous year. The succession of phytoplankton blooms in Bantry is described and environmental data that may explain the onset of toxic species is described.
    • Review of phytoplankton monitoring programme and research activities

      Salas, R.; Chamberlain, T.; Lyons, J.; Hynes, P.; Silke, J. (Marine Institute, 2008)
      This paper provides a review of the activities of the Phytoplankton Unit in the Marine Institute as part of the National Monitoring Programme for 2007 and compares the findings with those recorded during 2005 and 2006., It also presents an overview of the research activities carried out by the phytoplankton team during the year with a focus on culturing phytoplankton and the introduction of real time PCR techniques for phytoplankton identification.
    • Review of the phytoplankton monitoring programme and research activities in 2008

      Salas, R.; Lyons, J.; Hynes, P.; Chamberlain, T.; Silke, J. (Marine Institute, 2009)
      The National Monitoring programme for phytoplankton is a well established programme and this was shown through the improvement and refinement of Phytoplankton shellfish and finfish sites around the country. One important development in the last 2 years has been to increase the number of sentinel sites. A sentinel site is a designated sampling site where a total community Phytoplankton cell count and identification is carried out. The number of sentinel sites has increased from 11 in 2005 to 24 in 2008. This means a better coverage of all the bays around the country. The number of phytoplankton samples analysed in 2008 has seen an increase from the previous year.
    • Risk factors associated with increased mortality of farmed Pacific oysters in Ireland during 2011

      Clegg, T.A.; Morrissey, T.; Geoghegan, F.; Martin, S.W.; Lyons, K.; Ashe, S.; More, S.J. (Elsevier, 2014)
      The Pacific oyster, Crassostrea gigas, plays a significant role in the aquaculture industry in Ireland. Episodes of increased mortality in C. gigas have been described in many countries, and in Ireland since 2008. The cause of mortality events in C. gigas spat and larvae is suspected to be multifactorial, with ostreid herpesvirus 1 (OsHV-1, in particular OsHV-1 μvar) considered a necessary, but not sufficient, cause. The objectives of the current study were to describe mortality events that occurred in C. gigas in Ireland during the summer of 2011 and to identify any associated environmental, husbandry and oyster endogenous factors. A prospective cohort study was conducted during 2010–2012, involving 80 study batches, located at 24 sites within 17 bays. All 17 bays had previously tested positive for OsHV-1 μvar. All study farmers were initially surveyed to gather relevant data on each study batch, which was then tracked from placement in the bay to first grading. The outcome of interest was cumulative batch-level mortality (%). Environmental data at high and low mortality sites were compared, and a risk factor analysis, using a multiple linear regression mixed effects model, was conducted. Cumulative batch mortality ranged from 2% to 100% (median = 16%, interquartile range: 10–34%). The final multivariable risk factor model indicated that batches imported from French hatcheries had significantly lower mortalities than non-French hatcheries; sites which tested negative for OsHV-1 μvar during the study had significantly lower mortalities than sites which tested positive and mortalities increased with temperature until a peak was reached. There were several differences between the seed stocks from French and non-French hatcheries, including prior OsHV-1 μvar exposure and ploidy. A range of risk factors relating to farm management were also considered, but were not found significant. The relative importance of prior OsHV-1 μvar infection and ploidy will become clearer with ongoing selection towards OsHV-1 μvar resistant oysters. Work is currently underway in Ireland to investigate these factors further, by tracking seed from various hatchery sources which were put to sea in 2012 under similar husbandry and environmental conditions.
    • The role of Azadinium spinosum (Dinophyceae) in the production of azaspiracid shellfish poisoning in mussels

      Salas, Rafael; Tillmann, Urban; John, Uwe; Kilcoyne, Jane; Burson, Amanda; Cantwell, Caoimhe; Hess, Philipp; Jauffrais, Thierry; Silke, Joe (Elsevier, 2011)
      Azaspiracids (AZAs) are a group of lipophilic polyether compounds first detected in Ireland which have been implicated in shellfish poisoning incidents around Europe. These toxins regularly effect shellfish mariculture operations including protracted closures of shellfish harvesting areas for human consumption. The armoured dinoflagellate Azadinium spinosum Elbrächter et Tillmann gen. et sp. nov. (Dinophyceae) has been described as the de novo azaspiracid toxin producer; nonetheless the link between this organism and AZA toxin accumulation in shellfish has not yet been established. In August 2009, shellfish samples of blue mussel (Mytilus edulis) from the Southwest of Ireland were analysed using liquid chromatography–tandem-mass spectrometry (LC–MS/MS) and were found to be above the regulatory limit (0.16 μg g−1 AZA-equiv.) for AZAs. Water samples from this area were collected and one algal isolate was identified as A. spinosum and was shown to produce azaspiracid toxins. This is the first strain of A. spinosum isolated from Irish waters. The Irish A. spinosum is identical with the other two available A. spinosum strains from Scotland (3D9) and from Denmark (UTHE2) in its sequence of the D1–D2 regions of the LSU rDNA. A 24 h feeding trial of blue mussels (M. edulis) using an algal suspension of the Irish A. spinosum culture at different cell densities demonstrated that A. spinosum is filtered, consumed and digested directly by mussels. Also, LC–MS/MS analysis had shown that AZAs were accumulating in the shellfish hepatopancreas. The toxins AZA1 and -2 were detected in the shellfish together with the AZA analogues AZA3, AZA6, AZA17 and -19 suggesting that AZA1 and -2 are metabolised in the shellfish within the first 24 h after ingestion of the algae. The levels of AZA17 detected in the shellfish hepatopancreas (HP) were equivalent to the levels of AZA1 but in the remainder tissues the levels of AZA17 were four to five times higher than that of AZA1, only small quantities of AZA3 and -19 were present with negligible amounts of AZA6 detected after the 24 h period. This could have implications in the future monitoring of these toxins given that at present according to EU legislation only AZA1–AZA3 is regulated for. This is the first report of blue mussels’ (M. edulis) feeding on the azaspiracid producing algae A. spinosum from Irish waters.
    • Salmon Mortalities at Inver Bay and McSwyne’s Bay Finfish farms, County Donegal, Ireland, during 2003

      Cronin, M.; Cusack, C.; Geoghegan, F.; Jackson, D.; McGovern, E.; McMahon, T.; O'Beirn, F.X.; Ó Cinneide, M.; Silke, J. (Marine Institute, 2004)
      This report details the investigations into a major mortality of farmed salmon at Inver Bay and McSwyne’s Bay, Co. Donegal in July 2003. Previous reports were provided on 29th July 2003 and on 11th August 2003. The information is based upon analysis and research by MI scientists, a review of environmental data, survey reports by external consultants, inputs from veterinary practitioners who visited the site, reports from DCMNR staff in Killybegs, and site visits made by DCMNR / MI inspectors. Following a review meeting of the principal investigators on the 9th October, 2003, MI proceeded to carry out further scientific investigations. DCMNR also commissioned Kirk McClure Morton Consulting Engineers (KMM) to carry out a parallel investigation of the mortalities at Inver Bay and McSwynes Bay salmon farms. MI provided support as required to the KMM study, the report for which was furnished to DCMNR and MI on 11 February 2004. (KMM, 2004) MI wishes to acknowledge the high level of co-operation and assistance that it received from the owners and staff of Creevin Fish Farm Ltd, Eany Fish Products Ltd and Ocean Farms Ltd. It also wishes to acknowledge the assistance of veterinary practitioners, DCMNR staff and others in the course of this investigation.
    • A sensitive liquid chromatography/tandem mass spectrometry method for the determination of natural and synthetic steroid estrogens in seawater and marine biota, with a focus on proposed Water Framework Directive Environmental Quality Standards

      Ronan, J.; McHugh, B. (Wiley, 2013)
      RATIONALE: Trace levels of natural and synthetic steroid estrogens estrone (E1), 17b-estradiol (E2) and 17a-ethynyl estradiol (EE2) have been demonstrated to exert adverse effects in exposed organisms. E2 and EE2 have been proposed for inclusion in the Water Framework Directive (WFD) list of priority pollutants; however, the detection and accurate quantification of these compounds provide significant challenges, due to the low detection limits required. METHODS: A sensitive method combining ultrasonication, solid-phase extraction (SPE) and liquid chromatography/tandem mass spectrometry, with electrospray ionisation in negative mode (LC/ESI-MS/MS), capable of determining E1, E2 and EE2 at concentrations between 0.07 and 60 ng/L for seawater and between 0.4 and 200 ng/g wet weight in Mytilus spp. is reported. Recoveries at the limit of quantification (LOQ) ranged from 95 to 102% and 88 to 100% for water and tissue, respectively. Salinity (12 to 35%) and typical marine particulate matter loadings (between 10 and 100 mg/L) were not found to affect analyte recoveries. RESULTS: The first detection of E1 by LC/MS/MS in Irish marine waters (Dublin Bay, at 0.76 ng/L) is reported. Steroids were not detected in Galway Bay, or in any mussel samples from Dublin, Galway and Clare. The level of E2 detected in the dissolved water phase was below the proposed WFD Environmental Quality Standard (EQS) in other surface waters. CONCLUSIONS: The proposed method is suitable for the detection of E1, E2 and EE2 at biologically relevant concentrations and, due to the specificity offered, is not subject to potential interferences from endogenous E1 and E2 which often complicate the interpretation of estrogenic biomarker assays.
    • Simulated sunlight inactivation of norovirus and FRNA bacteriophage in seawater

      Flannery, J.; Rajko-Nenow, P.; Keaveney, S.; O'Flaherty, V.; Doré, W. (Wiley, 2013)
      Aims: To investigate norovirus (NoV) and F-specific RNA (FRNA) bacteriophage inactivation in seawater under simulated sunlight and temperature conditions representative of summer (235 W m−2; 17°C) and winter (56 W m−2; 10°C) conditions in Ireland. Methods and Results: Inactivation experiments were carried out using a collimated beam of simulated sunlight and 100 ml of filtered seawater seeded with virus under controlled temperature conditions. NoV concentrations were determined using RT-qPCR, and FRNA bacteriophage concentrations were determined using RT-qPCR and by plaque assay. For all virus types, the fluence required to achieve a 90% reduction in detectable viruses (S90 value) using RT-qPCR was not significantly different between summer and winter conditions. S90 values for FRNA bacteriophage determined by plaque assay were significantly less than those determined by RT-qPCR. Unlike S90 values determined by RT-qPCR, a significant difference existed between summer and winter S90 values for infectious FRNA bacteriophage. Conclusions: This study demonstrated that RT-qPCR significantly overestimates the survival of infectious virus and is therefore unsuitable for determining the inactivation rates of viruses in seawater. Significance and Impact of the Study: Results from this study provide initial data on the inactivation of NoV and FRNA bacteriophage in seawater under representative summer and winter conditions and will be of interest to shellfish and water management agencies alike.
    • Small intestinal injuries in mice caused by a new toxin, Azaspiracid, isolated from Irish mussels

      Ito, E.; Satake, M.; Ofuji, K.; McMahon, T.; Silke, J.; James, K.; Yasumoto, T. (UNESCO, 2001)
      Pathological changes of the small intestine caused by a new toxin, azaspiracid, from Irish mussels were studied. Human poisoning cases included both diarrhetic shellfish and paralitic shellfish poisoning symptoms. The present paper focused on the former. Injuries were observed in the Upper part of the small intestine, where lamina propria in the villi became atrophied at the initial stage, followed by desquamation of epithelial cells and shortening of villi. The injuries were different from the DSP toxin okadaic acid; 1) they developed very slowly after a lag time of about 3 hr, 2) recovery was very late, 3) initial target and process were different.
    • Stable isotope analysis of baleen reveals resource partitioning among sympatric rorquals and population structure in fin whales

      Ryan, C.; McHugh, B.; Trueman, C.N.; Sabin, R.; Deaville, R.; Harrod, C.; Berrow, S.D.; O'Connor, I. (Inter-Research, 2013)
      Stable isotope analysis is a useful tool for investigating diet, migrations and niche in ecological communities by tracing energy through food-webs. In this study, the stable isotopic composition of carbon and nitrogen in keratin was measured at growth increments of baleen plates from 3 sympatric species of rorquals (Balaenoptera acutrostrata, B. physalus and Megaptera novaeangliae), which died between 1985 and 2010 in Irish and contiguous waters. Bivariate ellipses were used to plot isotopic niches and standard ellipse area parameters were estimated via Bayesian inference using the SIBER routine in the SIAR package in R. Evidence of resource partitioning was thus found among fin, humpback and minke whales using isotopic niches. Highest δ15N values were found in minke whales followed by humpback, and fin whales. Comparison between Northeast Atlantic (Irish/UK and Biscayan) and Mediterranean fin whale isotopic niches support the current International Whaling Commission stock assessment of an isolated Mediterranean population. Significantly larger niche area and higher overall δ 15N and δ 13C values found in fin whales from Irish/UK waters compared to those sampled in adjacent regions (Bay of Biscay and Mediterranean) suggest inshore foraging that may be unique to fin whales in Ireland and the UK. Isotopic profiles support spatial overlap but different foraging strategies between fin whales sampled in Ireland/UK and the Bay of Biscay. Stable isotope analysis of baleen could provide an additional means for identifying ecological units, thus supporting more effective management for the conservation of baleen whales.
    • Summary Report on 2015 Residue Monitoring of Irish Farmed Finfish and 2015 Border Inspection Post Fishery and Fishery Product Sample Testing

      Residues Monitoring Programme, Chemistry Section, Marine Environmental Food Safety Services (Marine Institute, 2017)
      On behalf of the Department of Agriculture, Food and Marine (DAFM), the Marine Institute carries out monitoring of chemical residues in finfish for aquaculture sector. This monitoring is set out in the annual National Residue Control Plan, which is approved by the European Commission, and is an important component of the DAFM food safety controls and is implemented under a service contract with the Food Safety Authority of Ireland. Since 1999, the Marine Institute has implemented the National Residues Monitoring Programme for aquaculture. This is carried out on behalf of the Sea Fisheries Protection Authority, which is the responsible organisation for residue controls on farmed finfish. The outcome for residues levels in farmed finfish during 2015 remains one of consistently low occurrence. In 2015, in excess of 676 tests and a total of 1,845 measurements were carried out on 128 samples (i.e. 124 target samples & 4 suspect samples) of farmed finfish for a range of chemical substances, including banned and unauthorised substances, various authorised veterinary treatments and environmental contaminants.
    • Summary Report on 2016 Residue Monitoring of Irish Farmed Finfish and 2016 Border Inspection Post Fishery Product Testing undertaken at the Marine Institute

      Marine Institute (Marine Institute, 2018)
      On behalf of the Department of Agriculture, Food and Marine (DAFM), the Marine Institute carries out monitoring of chemical residues in finfish for aquaculture sector. This monitoring is set out in the annual National Residue Control Plan, which is approved by the European Commission, and is an important component of the DAFM food safety controls and is implemented under a service contract with the Food Safety Authority of Ireland. Since 1999, the Marine Institute has implemented the National Residues Monitoring Programme for aquaculture. This is carried out on behalf of the Sea Fisheries Protection Authority, which is the responsible organisation for residue controls on farmed finfish. The outcome for residues levels in farmed finfish during 2016 remains one of consistently low occurrence. In 2016, in excess of 691 tests and a total of 1,933 measurements were carried out on 136 samples (i.e. 126 target samples & 10 suspect samples) of farmed finfish for a range of chemical substances, including banned and unauthorised substances, various authorised veterinary treatments and environmental contaminants.
    • Summary Report on 2017 Residue Monitoring of Irish Farmed Finfish and 2017 Border Inspection Post Fishery Product Testing undertaken at the Marine Institute

      Marine Institute (Marine Institute, 2018-11-27)
      On behalf of the Department of Agriculture, Food and Marine (DAFM), the Marine Institute carries out monitoring of chemical residues in finfish for aquaculture sector. This monitoring is set out in the annual National Residue Control Plan, which is approved by the European Commission, and is an important component of the DAFM food safety controls and is implemented under a service contract with the Food Safety Authority of Ireland. Since 1999, the Marine Institute has implemented the National Residues Monitoring Programme for aquaculture. This is carried out on behalf of the Sea Fisheries Protection Authority, which is the responsible organisation for residue controls on farmed finfish. The outcome for residues levels in farmed finfish during 2017 remains one of consistently low occurrence. In 2017, in excess of 775 tests and a total of 2,250 measurements were carried out on 141 samples of farmed finfish for a range of chemical substances, including banned and unauthorised substances, various authorised veterinary treatments and environmental contaminants.
    • Summary Report on 2018 Residue Monitoring of Irish Farmed Finfish & 2018 Border Inspection Post Fishery Product Testing undertaken at the Marine Institute

      Glynn, D.; McGovern, E.; Kelly, C.; Moffat, R.; Farragher, E. (Marine Institute, 2019)
      On behalf of the Department of Agriculture, Food and Marine (DAFM), the Marine Institute carries out monitoring of chemical residues in finfish for aquaculture sector. This monitoring is set out in the annual National Residue Control Plan, which is approved by the European Commission, and is an important component of the DAFM food safety controls and is implemented under a service contract with the Food Safety Authority of Ireland. Since 1999, the Marine Institute has implemented the National Residues Monitoring Programme for aquaculture. This is carried out on behalf of the Sea Fisheries Protection Authority, which is the responsible organisation for residue controls on farmed finfish. In 2018, in excess of 920 tests and a total of 2,611 measurements were carried out on 171 samples of farmed finfish for a range of residues. Implementation of the Aquaculture 2018 Plan involves taking samples at both farm and processing plant: • 123 target samples taken at harvest: 110 farmed salmon and 13 freshwater trout. • 48 target samples were taken at other stages of production: 40 salmon smolts and 8 freshwater trout. All 2018 samples were compliant. For target sampling of farmed fish, a summary table of the residue results from 2005 - 2018 is outlined in Table 1. Overall, the outcome for aquaculture remains one of consistently low occurrence of residues in farmed finfish, with no non-compliant target residues results for the period 2006-2014, 0.11% and 0.10% non-compliant target residues results in 2015 and 2016 respectively and no non-compliant target results in 2017 and 2018.
    • Survey of toxaphene concentrations in fish from European waters

      McHugh, B.; Nixon, E.; Klungsoyr, J.; Besselink, H.; Brouwer, A.; Rimkus, G.; Leonards, P.; de Boer, J. (2000)
      Toxaphene, a suspected carcinogen, is a broad spectrum chlorinated pesticide. The objective of this study was to provide information on the toxicological risks posed by toxaphene to the consumer of fish from European waters. The levels of 3 toxaphene congeners in various fish species from different geographical locations were determined. These data were then used to provide information on the exposure of toxaphene to the consumer of fish.