• Ichthyophthiriosis ‘White-spot Disease’

      Marine Institute (Marine Institute, 2011)
      This leaflet gives information on ichthyophthiriosis ‘white-spot disease’. The disease, also known as “Ich”, affects most species of freshwater fish and has a worldwide distribution.
    • Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs

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

      Duggan, Deirdre E.; Farnsworth, Keith D.; Kraak, Sarah B. M. (Elsevier, 2013)
      Interaction with ecological models can improve stakeholder participation in fisheries management. Problems exist in efficiently communicating outputs to stakeholders and an objective method of structuring stakeholder differences is lacking. This paper aims to inform the design of a multi-user communication interface for fisheries management by identifying functional stakeholder groups. Intuitive categorisation of stakeholders, derived from survey responses, is contrasted with an evidence-based method derived from analysis of stakeholder literature. Intuitive categorisation relies on interpretation and professional judgement when categorising stakeholders among conventional stakeholder groups. Evidence-Based categorisation quantitatively characterises each stakeholder with a vector of four management objective interest strength values (Yield, Employment, Profit and Ecosystem Preservation). Survey respondents agreed little in forming intuitive groups and the groups were poorly defined and heterogeneous in interests. In contrast the Evidence-Based clusters were well defined and largely homogeneous, so more useful for identifying functional relations with model outputs. The categorisations lead to two different clusterings of stakeholders and suggest unhelpful stereotyping of stakeholders may occur with the Intuitive categorisation method. Stakeholder clusters based on literature-evidence show a high degree of common interests among clusters and is encouraging for those seeking to maximise dialogue and consensus forming.
    • Identifying the role of environmental drivers in organic carbon export from a forested peat catchment

      Ryder, Elizabeth; DeEyto, Elvira; Dillane, Mary; Poole, Russell; Jennings, Eleanor (Elsevier, 2014)
      Carbon export in streams draining peat catchments represents a potential loss of carbon from long-term stores to downstream aquatic systems and ultimately, through mineralisation, to the atmosphere. There is now a large body of evidence that dissolved organic carbon (DOC) export has increased significantly in recent decades at many sites, although there is still debate about the drivers of this increase. In this study, DOC export and particulate organic carbon (POC) export were quantified from a forested peatland catchment in the west of Ireland over two years at a fine temporal resolution. The principle drivers of change in stream DOC and POC concentrations were investigated using a general additive modelling (GAM) approach. The study period included drought conditions in the early summer of 2010 and clearfelling of some commercial forestry in early 2011. The results indicated that annual loads of 9.5 t DOC km2 year− 1 and 6.2 t POC km2 year− 1 were exported from the catchment in 2010. This combined annual load of 15.7 t C km2 year− 1 would represent between 0.01% and 0.02% of typical estimates for peat soil carbon storage in the region. Soil temperature, river discharge and drought explained 59.7% the deviance in DOC concentrations, while soil temperature, river discharge, and rainfall were the significant drivers of variation in POC concentrations, explaining 58.3% of deviance. Although clearfelling was not a significant factor in either model, large spikes in POC export occurred in 2011 after the first forestry clearance. The results illustrate the complexity of the interactions between climate and land management in driving stream water carbon export. They also highlight the sensitivity of peatland carbon stores to changes in temperature and precipitation, which are projected to be more extreme and variable under future climate scenarios.
    • Impact Assessment of Hand and Mechanical Harvesting of Ascophyllum nodosum on Regeneration and Biodiversity

      Kelly, L; Collier, L; Costello, M J; Diver, M; McGarvey, S; Kraan, S; Morrissey, J; Giury, M D (Marine Institute, 2001)
      This preliminary study assessed over an 18-month period the effect of mechanical and hand harvesting on seaweed regeneration and biodiversity while also assessing the costs and benefits of mechanical means of harvesting Ascophyllum nodosum in Ireland. Two study sites were used, one in Clew Bay Co. Mayo and the other in south Connemara, Co. Galway, each typical of different types of shore that harvesting takes place from. Sampling was quantitative, stratified by height on the shore and conducted before and after harvesting. According to the results of this preliminary study traditional hand harvesting was clearly more effective and cost efficient than the mechanical harvesting. However, it is recognised that this trial was a first of its kind for mechanical harvesting of seaweed in Ireland and as such could be expected to encounter various operational and design difficulties that with modification could result in greater harvesting efficiency in the future. Rare species of fauna were generally typical of sediment and sublittoral rather than Ascophyllum biotopes. Species richness differed between the Connemara site with 97 taxa and the Clew Bay site with 87 taxa, and varied from the upper to lower shore at both sites. Richness varied over time but an effect of harvesting was not detected. Ascophyllum nodosum cover decreased significantly after harvesting and was nearing recovery after 17 months in Connemara and 11 months in Clew Bay. No significant effects or changes in red algae or Fucus serratus could be attributed to harvesting. However, increases in ephemeral algae cover in the midshore after harvesting may have been facilitated by removal of the Ascophyllum canopy. Fucus vesiculosus significantly increased in cover after harvesting at both sites. At the Connemara site the abundance of the periwinkle Littorina obtusata increased in the control and decreased in the hand-harvested sections of seashore during the winter. The species was less abundant at the Clew Bay site and no significant seasonal or harvesting trends were apparent. The numbers and cover of other animals, both mobile and sessile, were low which limited analysis. However, the cover of sessile fauna was significantly variable over time in hand-harvested sections at both sites whereas controls were not.
    • Impact of early infestation with the salmon louse Lepeophtheirus salmonis on the subsequent survival of outwardly migrating Atlantic salmon smolts from a number of rivers on Ireland's south and west coasts

      Jackson, D.; Cotter, D.; Ó Maoiléidigh, N.; O'Donohoe, P.; White, J.; Kane, F.; Kelly, S.; McDermott, T.; McEvoy, S.; Drumm, A.; Cullen, A. (Elsevier, 2011)
      The potential impact of sea lice infestation on outwardly migrating Atlantic salmon smolts has been investigated by treating populations of ranched salmon, prior to release, with a prophylactic sea lice treatment conferring protection from sea lice infestation, for up to 9 weeks. Established populations of ranched Atlantic salmon with well described rates of return were chosen to investigate the potential contribution of early infestation with the salmon louse, Lepeophtheirus salmonis to mortality in Atlantic salmon. Results of five releases from four locations are presented and compared with a time series of releases from Lough Furnace in Newport, County Mayo. The results of this study would suggest that infestation of outwardly migrating salmon smolts with the salmon louse (L. salmonis) was a minor component of the overall marine mortality in the stocks studied.
    • The Impact of Eel Fyke Netting on Other Fisheries

      Moriarty, C (Department of Tourism, Fisheries and Forestry, 1986)
      The small fyke net was introduced to Ireland in 1963 and has been operated extensively in tidal water ever since. Experiments in freshwater began in Lough Corrib in 1967, conducted by the then Department of Agriculture and Fisheries. In 1970 operation by professional fishermen under special authorisations began. It has been effectively demonstrated by the Department's experiments, by information furnished by the professional fishermen and by observations by local fishermen and the Department's officials that fyke nets could be used for eel fishing without harmful effects on other fish stocks. As a result, the fyke net was listed as a "scheduled engine" in the Fisheries Act, 1980
    • Impact of inter-lab variation on the estimation of epidemiological cut-off values for disc diffusion susceptibility test data for Aeromonas salmonicida

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

      Jackson, D; Cotter, D; Newell, J; McEvoy, S; O'Donohoe, P; Kane, F; McDermott, T; Kelly, S; Drumm, A (John Wiley and Sons, 2013)
      Sea lice infestation as a source of marine mortality of outwardly migrating Atlantic salmon smolts has been investigated by treating groups of ranched salmon, prior to release, with a prophylactic sea lice treatment conferring protection from sea lice infestation. A number of studies have been carried out in Ireland using both established ranched populations and groups of hatchery reared fish imprinted for 5–8 weeks in the sites of experimental releases. In this study, data on 352 142 migrating salmon from twenty-eight releases, at eight locations along Ireland's South and West coasts covering a 9-year period (2001 to 2009) are reviewed. Both published and new data are presented including a previously unpublished time series. The results of a meta-analysis of the combined data suggest that while sea lice-induced mortality on outwardly migrating smolts can be significant, it is a minor and irregular component of marine mortality in the stocks studied and is unlikely to be a significant factor influencing conservation status of salmon stocks.
    • Impact of naturally spawning captive-bred Atlantic salmon on wild populations: depressed recruitment and increased risk of climate-mediated extinction

      McGinnity, P; Jennings, E; deEyto, E; Allott, N; Samuelsson, P; Rogan, G; Whelan, K; Cross, T (Royal Society Publishing, 2009)
      The assessment report of the 4th International Panel on Climate Change confirms that global warming is strongly affecting biological systems and that 20–30% of species risk extinction from projected future increases in temperature. It is essential that any measures taken to conserve individual species and their constituent populations against climate-mediated declines are appropriate. The release of captive bred animals to augment wild populations is a widespread management strategy for many species but has proven controversial. Using a regression model based on a 37-year study of wild and sea ranched Atlantic salmon (Salmo salar) spawning together in the wild, we show that the escape of captive bred animals into the wild can substantially depress recruitment and more specifically disrupt the capacity of natural populations to adapt to higher winter water temperatures associated with climate variability. We speculate the mechanisms underlying this seasonal response and suggest that an explanation based on bio-energetic processes with physiological responses synchronized by photoperiod is plausible. Furthermore, we predict, by running the model forward using projected future climate scenarios, that these cultured fish substantially increase the risk of extinction for the studied population within 20 generations. In contrast, we show that positive outcomes to climate change are possible if captive bred animals are prevented from breeding in the wild. Rather than imposing an additional genetic load on wild populations by releasing maladapted captive bred animals, we propose that conservation efforts should focus on optimizing conditions for adaptation to occur by reducing exploitation and protecting critical habitats. Our findings are likely to hold true for most poikilothermic species where captive breeding programmes are used in population management.
    • Impacts of climate change on harmful algal blooms

      Bresnan, E.; Davidson, K.; Edwards, M.; Fernand, L.; Gowen, R.; Hall, A.; Kennington, K.; McKinney, A.; Milligan, S.; Raine, R.; Silke, J. (Marine Climate Change Impacts Partnership, 2013)
      High biomass Harmful Algal Blooms (HABs) such as Karenia mikimotoi and shellfish toxin producing HAB species continue to be observed in UK and Republic of Ireland waters. Regional differences continue to be seen in the distribution of HABs in UK and RoI waters with impacts mainly observed in the south and west coast of Ireland and regions in the UK with a strong Atlantic influence, e.g. Regions 1, 3, 4, 6 and 7. There is little monitoring aside from the continuous plankton recorder (CPR) in Region 8. The impacts from HABs in Wales, Northern Ireland and the Isle of Man are generally low. Since the last MCCIP report card was issued, blooms of Karenia mikimotoi have caused problems in Ayrshire, Scotland, and also in the north-west coast of Ireland where concerns about the quantity of dead wild fish washing on shore during an event in Ireland in 2012 resulted in two beaches being closed to the public. No clear trend that can be attributed to climate change can be observed in the incidence of shellfish toxin producing HABs since the last report card was issued. During the last two years the incidence of some shellfish toxins has continued to decrease (e.g. paralytic shellfish poisoning toxins in Scotland). High concentrations of yessotoxins (YTX) and azaspiracids (AZAs) have been recorded for the first time in Scotland. Northern Ireland enforced its first shellfish harvesting closure for high concentrations of domoic acid (the toxin responsible for amnesic shellfish poisoning, ASP) in 2012. A recent survey in Scottish waters (Regions 1, 6 and 7) has revealed the presence of domoic acid in the urine and faeces of harbour seals (Phoca vitulina). The impacts of these toxins on the health of marine mammals are unknown and a more detailed study is currently being undertaken. Many of the future impacts of climate change are unknown. Increasing sea surface temperatures as a result of climate change may increase the potential for blooms of species that are not currently found in UK and RoI waters through range expansion or human mediated introduction. There is evidence that no new HAB species have become established during the last two years. An increase in the duration of stratification of the water column may influence the abundance of HABs in UK and RoI waters. This is particularly relevant in shelf areas and Region 8, an area where offshore high biomass K. mikimotoi blooms have been hypothesized to initiate and impact coastal areas along the west of Ireland and Regions 6, 7 and 1. Conversely, an increase in wind speed and duration may reduce the duration of stratification in the water column. This may result in a decrease of some HAB dinoflagellate species and an increase in HAB diatom species. Little is known about the impacts of ocean acidification or changes in offshore circulation on the incidence of HABs. The role of offshore blooms in seeding coastal blooms (e.g. of K. mikimotoi) remains unknown and the lack of monitoring in Region 8 and on the shelf edge compounds this knowledge gap.
    • Impacts of Increased Atmospheric CO2 on Ocean Chemistry and Ecosystems

      O’Dowd, Colin; Cave, Rachel; McGovern, Evin; Ward, Brian; Kivimae, Caroline; McGrath, Triona; Stengel, Dagmar; Westbrook, Guy (Marine Institute, 2011)
      Ocean pH is a function of the seawater carbonate system, which is a function of both the influx of CO2 from the atmosphere and the resulting concentration of CO2 in the water (i.e. pCO2). Uptake of anthropogenic carbon dioxide from the atmosphere is reducing ocean pH; a phenomenon referred to as ocean acidification. It is estimated that there has been a decrease of 0.1 pH units in the surface waters of the world’s oceans since the start of the industrial revolution with a reduction of 0.3 – 0.5 forecast by 2100. There is growing concern over the potential consequences of ocean acidification for marine ecosystems and the services they provide for mankind. This project was aimed at enabling the capability and developing the expertise within Ireland to measure and quantify the flux of CO2 into (or out of) the ocean; to monitor seasonal trends in pCO2 and CO2 fluxes; to determine the current baseline state and variability of the carbonate system; and to evaluate the potential impact of future changes on ecosystems with the ultimate aim of contributing to more informed policy development.
    • The implications of Alexandrium tamarense resting cysts in an area of shellfish aquaculture in Ireland

      Silke, J.; McMahon, T. (1998)
      The Irish Marine Institute's Fisheries Research Centre carry out a monitoring programme for the detection of algal toxins in shellfish. This programme is carried out under EU Directive 91/492. During the course of this programme the North Channel area of Cork Harbour has been the only location in Ireland where toxins causing Paralytic Shellfish Poisoning (PSP) have been detected in shellfish above the regulatory limit. For short periods during each of the summers of 1996,1997 and 1998, PSP toxins were found in mussels{Mytilus edulis) from this area above the regulatory limit period necessitating a ban on harvesting. Oysters {Crassostrea gigas) from the same area remained below the regulatory threshold. The dinoflagellate Alexandrium tamarense, a known vector of PSP toxins, was observed in the area during each of the toxic events. The exact origin of the populations of A. tamarense was unknown. A. tamarense is known to produce a cyst stage as part of its life cycle. These cysts can remain viable in the sediments for several years. A survey of the distribution of cysts of A. tamarense in the surface sediments in Cork Harbour was carried out in order to determine if they were potentially seeding the area. They were detected in 6 sites, and successfully germinated to yield vegetative cells. The results of the survey are presented and discussed.
    • Improved Isolation Procedure for Azaspiracids from Shellfish, Structural Elucidation of Azaspiracid-6 and Stability studies

      Kilcoyne, Jane; Keogh, Adela; Clancy, Ger; Le Blanc, Pat; Burton, Ian; Quilliam, Michael A.; Hess, Philipp; Miles, Christopher O. (ACS Publications, 2012)
      Azaspiracids are a group of lipophilic polyether toxins produced by the small dinoflagellate Azadinium spinosum. They may accumulate in shellfish and can result in illnesses when consumed by humans. Research into analytical methods, chemistry, metabolism, and toxicology of azaspiracids has been severely constrained by the scarcity of high-purity azaspiracids. Consequently, since their discovery in 1995, considerable efforts have been made to develop methods for the isolation of azaspiracids in sufficient amounts and purities for toxicological studies, in addition to the preparation of standard reference materials. A seven-step procedure was improved for the isolation of azaspiracids-1–3 (1, 2, and 3) increasing recoveries 2-fold as compared to previous methods and leading to isolation of sufficiently purified azaspiracid-6 (6) for structural determination by NMR spectroscopy. The procedure, which involved a series of partitioning and column chromatography steps, was performed on 500 g of Mytilus edulis hepatopancreas tissue containing 14 mg of 1. Overall yields of 1 (52%), 2 (43%), 3 (43%), and 6 (38%) were good, and purities were confirmed by NMR spectroscopy. The structure of 6 was determined by one- and two-dimensional NMR spectroscopy and mass spectrometry. The stability of 6 relative to 1 was also assessed in three solvents in a short-term study that demonstrated the greatest stability in aqueous acetonitrile.
    • Improving abundance estimates from electrofishing removal sampling

      Hedger, Richard D; De Eyto, Elvira; Dillane, Mary; Diserud, Ola; Hindar, Kjetil; McGinnity, Philip; Poole, Russell; Rogan, Ger (Elsevier, 2013-01)
      Estimates of fish abundance from electrofishing surveys depend on accurate estimation of capture probability. We examine in this paper how estimates of capture probability and abundance of Atlantic salmon from multi-pass removal sampling can be improved by comparing the results of an experimental programme of closed electrofishing sites within selected rivers in west-central Norway, and those obtained from open electrofishing sites established for monitoring long-term juvenile Atlantic salmon population abundance within the Burrishoole catchment, western Ireland. We first establish that the Carle & Strub method provides a more robust estimate of population abundance than the Zippin and Seber methods. We then show how prior information on capture probability may be used to improve the accuracy of the abundance estimate in open sites. We also show that the use of prior information with single-pass electrofishing may improve the accuracy of the abundance estimate so that it is comparable with that of multi-pass electrofishing in terms of stock prediction while requiring less sampling effort
    • Improving underwater visibility using vignetting correction

      Sooknanan, K.; Kokaram, A.; Baugh, G.; Corrigan, D.; Wilson, J.; Harte, N. (IEEE, 2012)
      Underwater survey videos of the seafloor are usually plagued with heavy vignetting (radial falloff) outside of the light source beam footprint on the seabed. In this paper we propose a novel multi-frame approach for removing this vignetting phenomenon which involves estimating the light source footprint on the seafloor, and the parameters for our proposed vignetting model. This estimation is accomplished in a bayesian framework with an iterative SVD-based optimization. Within the footprint, we leave the image contents as is, whereas outside this region, we perform vignetting correction. Our approach does not require images with different exposure values or recovery of the camera response function, and is entirely based on the attenuation experienced by point correspondences accross multiple frames. We verify our algorithm with both synthetic and real data, and then compare it with an existing technique. Results obtained show significant improvement in the fidelity of the restored images.
    • In vitro and in vivo tumor promoting potency of technical toxaphene, UV-irradiated toxaphene, and biotransformed toxaphene

      Besselink, H.T.; Nixon, E.; McHugh, B.; Klungsøyr, J.; Brouwer, A. (2000)
      Toxaphene, a complex mixture of polychlorinated camphenes, was first introduced in 1945 by Hercules Co. as Hercules 3965. Until the mid 1980s, it was mass produced and widely used as an insecticide, and was also used as a piscicide to control rough fish in various water systems. The lipophilic, persistent, and volatile nature of toxaphene has contributed to its global dispersion throughout the fresh water and marine environment. In addition to bioaccumulation in biota inhabiting these regions, it is also been detected in humans. Human exposure mainly occurs through the consumption of toxaphene contaminated fish. Information on the carcinogenicity and general toxicology of weathered and biotransformed TT would be of major interest. To mimic the weathered toxaphene found in fish, we developed a so-called 'realistic exposure' procedure for toxaphene. This procedure makes use of cod that were exposed to TT. Toxaphene residues that were extracted from cod liver (CLE), were then used in in vitro and in vivo studies to obtain information on its tumor promoting potency. Besides CLE, we also studied the tumor promoting properties of UV-irradiated toxaphene (UVT) and TT.
    • In-situ and remote monitoring of environmental water quality

      Cleary, John; Hayes, Jer; Diamond, Dermot (2011)
    • Indexing and selection of well-lit details in underwater video using vignetting estimation

      Sooknanan, K.; Kokaram, A.; Corrigan, D.; Wilson, J.; Harte, N. (IEEE, 2012)
      Video is an important tool in underwater surveys today, yet its useful field of view is restricted to image details within well lit regions on the seafloor. In this paper we present a novel vignetting-based weighting scheme for selecting these well lit details for use in the creation of a wide area view (mosaic) of the surveyed seafloor. Apart from this detail selection novelity,two other contributions are made. Firstly, because some of these scenes contain very little image texture, we introduce a hybrid homography estimation procedure that uses both feature-based and exhaustive searching techniques. Secondly, to facilitate cross referencing with the video, sections of the mosaic were indexed with the frame number in which the respective image details was selected from. We test our algorithm with real seabed survey video, whose scientific mission was population census of the particular species of lobster, Nephrops norvegicus. High quality mosaics were obtained that captured image details from well lit regions of the scene, which expert marine biologists agreed was a useful analysis tool. This work was supported by the Science Foundation Ireland PI Programme: SFI-PI 08/IN.1/I2112, and was done in collaboration with the Marine Institute Galway.
    • Infectious Haematopoietic Necrosis

      Marine Institute (Marine Institute, 2011)
      This leaflet gives information on infectious haematopoietic necrosis. This disease is caused by a single stranded RNA virus of the family Rhabdoviridae, genus Novirhabdoviridae. IHN is listed as a non-exotic disease under EU Directive 2006/88/EC, and is notifiable in Ireland, according to S.I. No. 261 of 2008.