• Technical Report: Review and Simulate Climate and Catchment Responses at Burrishoole (RESCALE)

      Fealy, R.; Allott, N.; Broderick, C.; de Eyto, E.; Dillane, M.; Erdil, R.M.; Jennings, E.; Hancox, L.; McCrann, K.; Murphy, C.; O'Toole, C.; Poole, R.; Rogan, G.; Ryder, L.; Taylor, D.; Whelan, K.; White, J. (Marine Institute, 2014)
      This report demonstrates that the projected changes in the climate conditions of the Burrishoole catchment, if realised, will have wide ranging implications for all aspects of the catchment system, including water temperature and quality, stream flow hydrology, soil processes, and most notably the well-being of its aquatic environment. While the projected changes in climate and their implications, outlined in this report, are specific to the Burrishoole, they are illustrative of likely changes in similar characteristic catchments along the west coast of Ireland.
    • Temperature and Oxygen Determinations in some Irish Lakes

      Fitzmaurice, P. (Department of Agriculture and Fisheries [Fisheries Division], 1971)
      Information about temperature and dissolved oxygen profiles in Irish lakes has hitherto been lacking. During the period 1966 to 1969 data on temperature and dissolved oxygen content at various depths were determined for a number of Irish lakes. The results are summarised in this paper.
    • Temperature quenching of CDOM fluorescence sensors: temporal and spatial variability in the temperature response and a recommended temperature correction equation

      Ryder, Elizabeth; Jennings, Eleanor; DeEyto, Elvira; Dillane, Mary; NicAonghusa, Caitriona; Pierson, Donald C.; Moore, Karen; Rouen, Martin; Poole, Russell (ASLO, 2012)
      Field-based instruments measuring chromophoric dissolved organic matter (CDOM) fluorescence are often used as a proxy for dissolved organic carbon concentrations in lakes and streams. CDOM fluorescence yield is, however, affected by water temperature at the time of measurement, a factor which varies on both diel and seasonal timescales. A temperature correction must therefore be applied to these data. We present data on temporal and site-specific variability in temperature quenching of CDOM fluorescence for water from a humic lake and one of its main inflows in the west of Ireland. In addition, we present a temperature compensation equation and show that this equation is an improvement on methods previously proposed.
    • Temporal and Spatial Distribution of Ostrea edulis Larvae in Kilkieran Bay, Co. Galway

      Wilson, J H (Department of the Marine, 1987)
      Concentrations and size distributions of Ostrea edulis L larvae were recorded in Kilkieran Bay, Co. Galway, Ireland, during 1984 and 1985. Larvae were most abundant during July and August in both years. Large larvae ≥ 250 µm were homogeneously distributed through the vertical water column. Higher percentages of smaller larvae ≤ 250 µm were recorded at stations near the mouth of the bay than at stations on or near the beds. Variations in tidal amplitude and low salinities caused displacement of larvae from the beds. There were no significant losses of larvae from the inner bay.
    • A test battery approach to the ecotoxicological evaluation of cadmium and copper employing a battery of marine bioassays

      Macken, A; Giltrap, M; Ryall, K; Foley, B; McGovern, E; McHugh, B; Davoren, M (Springer, 2009)
      Heavy metals are ubiquitous contaminants of the marine environment and can accumulate and persist in sediments. The toxicity of metal contaminants in sediments to organisms is dependent on the bioavailability of the metals in both the water and sediment phases and the sensitivity of the organism to the metal exposure. This study investigated the effects of two metal contaminants of concern (CdCl2 and CuCl2) on a battery of marine bioassays employed for sediment assessment. Cadmium, a known carcinogen and widespread marine pollutant, was found to be the least toxic of the two assayed metals in all in vivo tests. However CdCl2 was found to be more toxic to the fish cell lines PLHC-1 and RTG-2 than CuCl2. Tisbe battagliai was the most sensitive species to both metals and the Microtox® and cell lines were the least sensitive (cadmium was found to be three orders of magnitude less toxic to Vibrio fischeri than to T. battagliai). The sensitivity of Tetraselmis suecica to the two metals varied greatly. Marine microalgae are among the organisms that can tolerate higher levels of cadmium. This hypothesis is demonstrated in this study where it was not possible to derive an EC50 value for CdCl2 and the marine prasinophyte, T. suecica. Conversely, CuCl2 was observed to be highly toxic to the marine alga, EC50 of 1.19 mg l-1. The genotoxic effect of Cu on the marine phytoplankton was evaluated using the Comet assay. Copper concentrations ranging from 0.25 to 2.50 mg l-1 were used to evaluate the effects. DNA damage was measured as percent number of comets and normal cells. There was no significant DNA damage observed at any concentration of CuCl2 tested and no correlation with growth inhibition and genetic damage was found.
    • Testes and brain gene expression in precocious male and adult maturing Atlantic salmon (Salmo salar)

      Guiry, A; Flynn, D; Hubert, S; O'Keeffe, A; LeProvost, O; White, S L; Forde, P F; Davoren, P; Houeix, B; Smith, T J; Cotter, D; Wilkins, N P; Cairns, M T (Biomed Central, 2010)
      Background: The male Atlantic salmon generally matures in fresh water upon returning after one or several years at sea. Some fast-growing male parr develop an alternative life strategy where they sexually mature before migrating to the oceans. These so called ‘precocious’ parr or ‘sneakers’ can successfully fertilise adult female eggs and so perpetuate their line. We have used a custom-built cDNA microarray to investigate gene expression changes occurring in the salmon gonad and brain associated with precocious maturation. The microarray has been populated with genes selected specifically for involvement in sexual maturation (precocious and adult) and in the parr-smolt transformation. Results: Immature and mature parr collected from a hatchery-reared stock in January were significantly different in weight, length and condition factor. Changes in brain expression were small - never more than 2-fold on the microarray, and down-regulation of genes was much more pronounced than up-regulation. Significantly changing genes included isotocin, vasotocin, cathepsin D, anamorsin and apolipoprotein E. Much greater changes in expression were seen in the testes. Among those genes in the testis with the most significant changes in expression were anti-Mullerian hormone, collagen 1A, and zinc finger protein (Zic1), which were down-regulated inprecocity and apolipoproteins E and C-1, lipoprotein lipase and anti-leukoproteinase precursor which were upregulated in precocity. Expression changes of several genes were confirmed in individual fish by quantitative PCR and several genes (anti-Mullerian hormone, collagen 1A, beta-globin and guanine nucleotide binding protein (G protein) beta polypeptide 2-like 1 (GNB2L1) were also examined in adult maturing testes. Down-regulation of anti-Mullerian hormone was judged to be greater than 160-fold for precocious males and greater than 230-fold for November adult testes in comparison to July testes by this method. For anti-Mullerian hormone and guanine nucleotide binding protein beta polypeptide 2-like 1 expression changes in precocious males mirrored mature adults (November) but for collagen 1A and beta-globin the pattern was more complex. Conclusions: Expression changes in the fish brain during the process of precocious sexual maturation were small compared to those in the testes. Microarray analysis suggested down-regulation of housekeeping functions and up-regulation of a small number of specific processes. Transcriptional changes in the testes were much more pronounced with anti-Mullerian hormone playing a major role. Expression profiles for mature parr and maturing adult testes indicate subtle differences in gene expression between these two related groups.
    • Tools for Appropriate Assessment of Fishing and Aquaculture Activities in Marine and Coastal Natura 2000 Sites. Report I: Intertidal and Subtidal Muds.

      ABPmer (ABP Marine Environmental Research Ltd, 2013)
      Ireland has many coastal and marine habitats and species that are of national and international conservation importance. The value of these has been recognised by the designation of a number of Special Areas of Conservation and Special Protected Areas through the EU Habitats Directive (92/43/EEC) and EU Birds Directive (2009/147/EC). Together these sites form part of the European network of Natura 2000 sites. This report and accompanying annexes is part of a series of documents that present a risk assessment tool developed by ABPmer to assess the effects of fishing and aquaculture activities on the Annex I habitats and Annex II species present in Natura 2000 sites. The tool is designed to support the preparation of screening statements and Appropriate Assessments. Specifically this report presents the project deliverables for the assessment of intertidal and subtidal mud habitats and describes the potential use of the risk assessment tool.
    • Tools for Appropriate Assessment of Fishing and Aquaculture Activities in Marine and Coastal Natura 2000 Sites. Report II: Intertidal and Subtidal Sands

      ABPmer (ABP Marine Environmental Research Ltd, 2013)
      Ireland has many coastal and marine habitats and species that are of national and international conservation importance. The value of these has been recognised by the designation of a number of Special Areas of Conservation and Special Protected Areas through the EU Habitats Directive (92/43/EEC) and EU Birds Directive (2009/147/EC). Together these sites form part of the European network of Natura 2000 sites.This report and accompanying annexes is part of a series of documents that present a risk assessment tool developed by ABPmer to assess the effects of fishing and aquaculture activities on the Annex I habitats and Annex II species present in Natura 2000 sites. The tool is designed to support the preparation of screening statements and Appropriate Assessments. Specifically this report presents the project deliverables for the assessment of intertidal and subtidal sand habitats and describes the potential use of the risk assessment tool.
    • Tools for Appropriate Assessment of Fishing and Aquaculture Activities in Marine and Coastal Natura 2000 Sites. Report III: Intertidal and Subtidal Muddy Sands and Sandy Muds

      ABPmer (ABP Marine Environmental Research Ltd, 2013)
      Ireland has many coastal and marine habitats and species that are of national and international conservation importance. The value of these has been recognised by the designation of a number of Special Areas of Conservation and Special Protected Areas through the EU Habitats Directive (92/43/EEC) and EU Birds Directive (2009/147/EC). Together these sites form part of the European network of Natura 2000 sites. This report and accompanying annexes is part of a series of documents that present a risk assessment tool developed by ABPmer to assess the effects of fishing and aquaculture activities on the Annex I habitats and Annex II species present in Natura 2000 sites. The tool is designed to support the preparation of screening statements and Appropriate Assessments. Specifically this report presents the project deliverables for the assessment of vegetation dominated communities (Saltmarsh and seagrass) and describes the potential use of the risk assessment tool.
    • Tools for Appropriate Assessment of Fishing and Aquaculture Activities in Marine and Coastal Natura 2000 Sites. Report IV: Intertidal and Subtidal Mixed Sediments

      ABPmer (ABP Marine Environmental Research Ltd, 2013)
      Ireland has many coastal and marine habitats and species that are of national and international conservation importance. The value of these has been recognised by the designation of a number of Special Areas of Conservation and Special Protected Areas through the EU Habitats Directive (92/43/EEC) and EU Birds Directive (2009/147/EC). Together these sites form part of the European network of Natura 2000 sites. This report and accompanying annexes is part of a series of documents that present a risk assessment tool developed by ABPmer to assess the effects of fishing and aquaculture activities on the Annex I habitats and Annex II species present in Natura 2000 sites. The tool is designed to support the preparation of screening statements and Appropriate Assessments. Specifically this report presents the project deliverables for the assessment of intertidal and subtidal mixed sediments habitats and describes the potential use of the risk assessment tool.
    • Tools for Appropriate Assessment of Fishing and Aquaculture Activities in Marine and Coastal Natura 2000 Sites. Report V: Intertidal and Subtidal Coarse Sediments

      ABPmer (ABP Marine Environmental Research Ltd, 2013)
      Ireland has many coastal and marine habitats and species that are of national and international conservation importance. The value of these has been recognised by the designation of a number of Special Areas of Conservation and Special Protected Areas through the EU Habitats Directive (92/43/EEC) and EU Birds Directive (2009/147/EC). Together these sites form part of the European network of Natura 2000 sites. This report and accompanying annexes is part of a series of documents that present a risk assessment tool developed by ABPmer to assess the effects of fishing and aquaculture activities on the Annex I habitats and Annex II species present in Natura 2000 sites. The tool is designed to support the preparation of screening statements and Appropriate Assessments. Specifically this report presents the project deliverables for the assessment of coarse sediments and describes the potential use of the risk assessment tool.
    • Tools for Appropriate Assessment of Fishing and Aquaculture Activities in Marine and Coastal Natura 2000 Sites. Report VI: Biogenic Reefs (Sabellaria, Native Oyster, Maerl).

      ABPmer (ABP Marine Environmental Research Ltd, 2013)
      Ireland has many coastal and marine habitats and species that are of national and international conservation importance. The value of these has been recognised by the designation of a number of Special Areas of Conservation and Special Protected Areas through the EU Habitats Directive (92/43/EEC) and EU Birds Directive (2009/147/EC). Together these sites form part of the European network of Natura 2000 sites. This report and accompanying annexes is part of a series of documents that present a risk assessment tool developed by ABPmer to assess the effects of fishing and aquaculture activities on the Annex I habitats and Annex II species present in Natura 2000 sites. The tool is designed to support the preparation of screening statements and Appropriate Assessments. Specifically this report presents the project deliverables for the assessment of Biogenic Reefs (Sabellaria, Native Oyster, Maerl)and describes the potential use of the risk assessment tool.
    • Tools for Appropriate Assessment of Fishing and Aquaculture Activities in Marine and Coastal Natura 2000 Sites. Report VII: Intertidal and Subtidal Reefs.

      ABPmer (ABP Marine Environmental Research Ltd, 2013)
      Ireland has many coastal and marine habitats and species that are of national and international conservation importance. The value of these has been recognised by the designation of a number of Special Areas of Conservation and Special Protected Areas through the EU Habitats Directive (92/43/EEC) and EU Birds Directive (2009/147/EC). Together these sites form part of the European network of Natura 2000 sites. This report and accompanying annexes is part of a series of documents that present a risk assessment tool developed by ABPmer to assess the effects of fishing and aquaculture activities on the Annex I habitats and Annex II species present in Natura 2000 sites. The tool is designed to support the preparation of screening statements and Appropriate Assessments. Specifically this report presents the project deliverables for the assessment of littoral and sublittoral reefs and associated biological assemblages and describes the potential use of the risk assessment tool.
    • Tools for Appropriate Assessment of Fishing and Aquaculture Activities in Marine and Coastal Natura 2000 Sites. Report VIII: Vegetation Dominated Communities (Saltmarsh and Seagrass).

      ABPmer (ABP Marine Environmental Research Ltd, 2013)
      Ireland has many coastal and marine habitats and species that are of national and international conservation importance. The value of these has been recognised by the designation of a number of Special Areas of Conservation and Special Protected Areas through the EU Habitats Directive (92/43/EEC) and EU Birds Directive (2009/147/EC). Together these sites form part of the European network of Natura 2000 sites. This report and accompanying annexes is part of a series of documents that present a risk assessment tool developed by ABPmer to assess the effects of fishing and aquaculture activities on the Annex I habitats and Annex II species present in Natura 2000 sites. The tool is designed to support the preparation of screening statements and Appropriate Assessments. Specifically this report presents the project deliverables for the assessment of vegetation dominated communities (saltmarsh and seagrass)and describes the potential use of the risk assessment tool.
    • The Torrey Canyon Disaster: A review of methods employed to combat large scale oil pollution

      Griffith, David de G (Department of Agriculture and Fisheries (Fisheries Division), 1969)
      In this review an attempt has been made to collate the central points of the most important of the multitudinous reports which have appeared in connection with the Torrey Canyon oil pollution. The content has been limited to the biological aspects of a large-scale oil spillage and its subsequent treatment, although the importance of tourist amenities also receives consideration in the discussion. Consequently, several related topics which lie outside the scope of the biologist have either been omitted or just mentioned in passing: they include the technical problems of the salvage of oil from a crippled tanker, the control or collection of floating oil, and the administrative organisational requirements for effective action in an emergency of this kind.
    • Toward design criteria in constructed oyster reefs: oyster recruitment as a function of substrate type and tidal height

      O'Beirn, F.X.; Luchenbach, M.W.; Nestlerode, J.A.; Coates, G.M. (National Shellfisheries Association, 2000)
      Restoration of degraded oyster reef habitat generally begins with the addition of substrate that serves as a reef base and site for oyster spat attachment. Remarkably, little is known about how substrate type and reef morphology affect the development of oyster populations on restored reefs. Three-dimensional, intertidal reefs were constructed near Fisherman's Island, Virginia: two reefs in 1995 using surfclam (Spisula solidissima) shell and six reefs in 1996 using surfclam shell, oyster shell, and stabilized coal ash. We have monitored oyster recruitment and growth quarterly at three tidal heights (intertidal, mean low water, and subtidal) on each reef type since their construction. Oyster recruitment in 1995 exceeded that observed in the two subsequent years. High initial densities on the 1995 reefs decreased and stabilized at a mean of 418 oyster/m2. Oyster settlement occurred on all reef types and tidal heights in 1996; however, postsettlement mortality on the surfclam shell and coal ash reefs exceeded that on the oyster shell reefs, which remained relatively constant throughout the year (mean = 935 oysters/m2). Field observations suggest that predation accounts for most of the observed mortality and that the clam shell and coal ash reefs, which have little interstitial space, suffer greater predation. Oyster abundance was consistently greatest higher in the intertidal zone on all reefs in each year studied. The patterns observed here lead to the preliminary conclusion that the provision of spatial refugia (both intertidal and interstitial) from predation is an essential feature of successful oyster reef restoration in this region. In addition, high levels of recruitment can provide a numerical refuge, whereby the oysters themselves will provide structure and increase the probability of an oyster population establishing successfully on the reef.
    • Toxic phytoplankton in Irish waters

      Silke, J.; McMahon, T.; Nolan, A. (1995)
      The subject of harmful and toxic marine algae has recently gained a growing public and scientific interest both in Ireland and abroad because of the occurrence of these toxins in shellfish.
    • Toxicological risks to humans of toxaphene residues in fish

      Leonards, P.E.G.; Besselink, H.; Klungsøyr, J.; McHugh, B.; Nixon, E.; Rimkus, G.G.; Brouwer, A.; de Boer, J. (Wiley, 2011)
      A revised risk assessment for toxaphene was developed, based on the assumption that fish consumers are only exposed to toxaphene residues that differ substantially from technical toxaphene due to environmental degradation and metabolism. In vitro studies confirmed that both technical toxaphene and degraded toxaphene inhibit gap junctional intercellular communication that correlates with the mechanistic potential to cause tumour promotion. In vivo rat studies established the NOAEL for degraded and technical toxaphene at the highest dose tested in the bioassay. Toxaphene residue intakes from European fishery products were estimated and compared to the provisional tolerable daily intakes (TDIs) from various regulatory agencies including Canada, the United States, Germany. The estimated intake was also compared to a new calculated provisional MATT pTDI. The MATT pTDI is based upon new toxicological information (in vivo rat studies) developed on a model for environmental toxaphene residues rather than technical toxaphene. A MATT pTDI (1.08 mg total toxaphene for a person of 60 kg) for tumour promotion potency was adopted for use in Europe and is hitherto referred to as the MATT pTDI. These new data result in a better estimate of safety and a higher TDI than previously used. Based on realistic fish consumption data and recent baseline concentration data of toxaphene in European fishery products the toxaphene intake for the consumers of Germany, Ireland, Norway and The Netherlands was estimated. For an average adult fish consumer the average daily intake of toxaphene was estimated to be 1.2 µg, and 0.4, 0.5, and 0.2 µg for the consumers of Norway, Germany, Ireland, and The Netherlands, respectively. The toxaphene intake of these average fish consumers was far below the MATT pTDI of 1.08 mg/60 kg body weight. In conclusion, based on the most relevant toxicological studies and the most realistic estimates of fish consumption and recent concentrations of toxaphene in European fishery products, adverse health effects are unlikely for the average European consumer of fishery products. In no case is the MATT pTDI exceeded.
    • Trace Metal and Chlorinated Hydrocarbon Concentrations in Shellfish and Fin-Fish from Irish Waters - 1996

      Bloxham, M; Rowe, A; McGovern, E; Smyth, M; Nixon, E (Marine Institute, 1998-11)
      In accordance with the monitoring requirements of the 1979 Council Directive 79/923/EC on the quality of shellfish waters, water and shellfish samples were collected from 22 major shellfish growing areas and analysed for physicochemical parameters, trace metal levels and chlorinated hydrocarbon concentrations. Fin-fish were also collected from five Irish fishing ports and analysed for total mercury content in compliance with the European Commission's Decision of 19 May 1993 on mercury in fisheries products. Selected samples of fin-fish were also analysed for trace metal and chlorinated hydrocarbon concentration. As there are no generally accepted European standards for the concentration of these contaminants in shellfish or fin-fish, the levels were compared with the available standards and guidance values compiled by the Oslo and Paris Commission (OSPAR) countries for human consumption. As in previous years, the water quality from shellfish growing areas was good and conformed to the guidelines and requirements of the Directive. Petroleum hydrocarbons were not observed in any of the shellfish waters or as deposits on the shellfish. Chlorinated hydrocarbon levels were very low, evidence of the clean, unpolluted nature of Irish shellfish and shellfish producing waters. Trace metal levels were consistently low with the exception of lead in mussel tissue from Wexford Harbour, which was elevated, and cadmium in oyster tissue, which was slightly elevated in some samples but did not exceed the Dutch human consumption tolerance value of 1.0mg/kg. The concentration of mercury in fin-fish selected from catches at Irish fishing ports ranged from 0.02 to 0.27µg/g wet weight. These levels were well within the maximum limits set down in the EC Decision for mercury in fisheries products. Chlorinated hydrocarbon and trace metal levels were also very low in fish tissue. This survey confirms previous studies that show Irish fishery products are effectively free from trace metal and chlorinated hydrocarbon contamination.
    • Trace Metal and Chlorinated Hydrocarbon Concentrations in Shellfish from Irish Waters 2001

      Glynn, D; Tyrrell, L; McHugh, B; Rowe, A; Monaghan, E; Costello, J; McGovern, E (Marine Institute, 2003)
      Major shellfish growing areas were sampled in accordance with the monitoring requirements of Council Directive 79/923/EEC, on the quality required of shellfish waters, and Council Directive 91/492/EEC, laying down the health conditions for the production and placing on the market of live bivalve molluscs. Data for physicochemical parameters in water, trace metal levels and chlorinated hydrocarbon concentrations in shellfish are presented. In 2001, a total of 23 samples from 20 different shellfish sites were analysed for trace metals and chlorinated hydrocarbons. The median concentration of mercury in shellfish sampled in 2001 was <0.03 mg/kg wet weight, with a maximum of 0.04 mg/kg wet weight which is well within the maximum limit of 0.50 mg/kg wet weight for mercury in bivalve molluscs set by the EU. The levels of lead and cadmium detected were low, with means of 0.20 and 0.24 mg/kg wet weight and maxima of 0.37 and 0.74 mg/kg wet weight respectively, also within the respective maximum levels of 1.50 and 1 mg/kg wet weight set by the EU. There are no internationally agreed standards or guidelines available for the remaining trace metals and chlorinated hydrocarbons in shellfish. However these results were compared with the strictest standard or guidance values for shellfish, which are applied by contracting countries to OSPAR, and were found to be well below the strictest values listed. This is evidence of the clean, unpolluted nature of Irish shellfish and shellfish producing waters. As in previous years, the water quality from shellfish growing areas was good and conformed to the requirements of the Directive. Petroleum hydrocarbons were not visible in any of the shellfish waters or as deposits on the shellfish. This survey confirms previous studies (Glynn et al., 2003; McGovern et al., 2001; Bloxham et al., 1998; Smyth et al., 1997 and Nixon et al., 1995, 1994, and 1991), which show that contamination from trace metals and chlorinated hydrocarbons is low in Irish shellfish aquaculture.