• Decreased Performance of Rainbow Trout Oncorhynchus mykiss Emergence Behaviors Following Embryonic Exposure to Benzo[a]pyrene

      Ostrander, G.K.; Anderson, J.J. (United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, 1990)
      The sublethal effects induced by a model carcinogen and environmental contaminant on salmonid emergence behaviors have been studied. Rainbow trout embryos were exposed for 24 hours to 25 IAg/mL of benzo[a)pyrene 1 week prior to hatching. Exposures occurred during the late organogenesis period of development and allowed assessment of how a single embryonic exposure might affect emergence behaviors nearly 6 weeks later. Though no differences in numbers of alevins successfully emerging were observed, a significant decrease was noted in performance of the upstream orientation behaviors characteristic ofemergence among wild individuals.These findings are discussed in terms ofa model describing the role of upstream swimming behavior after emergence.
    • The deep water fisheries of the Rockall trough: some insights gleaned from Irish survey data

      Kelly, C.J.; Connolly, P.L.; Clarke, M.W. (International Council for the Exploration of the Sea (ICES), 1998)
      The Fisheries Research Centre (FRC) has conducted trawl and longline surveys in the Rockall Trough since 1993, fishing a total of 223 stations over the depth range 201 to 4,945m. Trawls produced greater species diversity and higher discard rates than longlines, which selected larger squalifurm sharks. In 1997, limited selectivity work, based on ten comparative tows, showed that the size range of roundnose grenadier (Coryphaenoides rupestris) caught using a commercial trawl (llOmm), with and without a small mesh end liner (30mm), were similar. This indicates that mesh size, because of poor selectivity and perceived low survival rates of escapees, may not be a useful management tool in the regulation of the trawl fishery.
    • Deep Water Survey, 2008 Celtic Explorer 9th – 22nd September 2008

      O'Hea, B; Johnston, G; Leahy, Y; Mohn, C; Wall, D; Gerritsen, H.D. (Marine Institute, 2009)
      The Marine Institute and the National University of Ireland, Galway conducted a deepwater survey in September 2008. This survey was the third in a series, carried out on the RV Celtic Explorer, gathering fishery and hydrographic data on the continental slope to the north and west of Ireland, and on the Porcupine Bank. The survey objectives were to collect biological data on the main deepwater fish species and invertebrates. Fishing hauls were carried out at four depths, 500m, 1000m, 1500m, and 1800m, in each of three distinct Areas. Six comparative tows were carried out with Scottish Fisheries Science Service scientists aboard the RV Scotia. CTD data was collected along transects in each area. Cetacean observations were carried out by an observer from the Irish Whale and Dolphin Group. The fisheries data collected will provide information for assessment of deepwater stocks, and will provide a time series for CPUE. 122 species of fish were identified, with a further 8 taken ashore for further work.
    • Deep-sea fisheries management: the approach taken by the European Union

      Clarke, Maurice; Patterson, Kenneth (Food and Agriculture Organization of the United Nations, 2005)
      This paper outlines the approach taken by the European Union to the management of deep-sea fish stocks. An extensive range of measures was adopted in 2002, and implementation began in 2003. The scheme, which is binding on EU fishing vessels targeting deep-sea species in the North-East Atlantic, encompasses both input and output controls. In southern Europe and in the Mediterranean, deep-sea fisheries tend to be artisanal in nature, and in some cases of considerable antiquity. In northern community waters deepwater fisheries began in the 1970’s. These diverse fisheries, in several regions create particular problems for fisheries managers. The approach taken by the European Union was to adopt catch restrictions, in the form of total allowable catches for a range of the key deepwater species in the ICES area. In addition, a capacity restriction has been imposed. This requires that vessels that want to land more than a very small amount of some specified deepwater species should hold a license issued by its flag state. The overall capacity (in kilowatts and in gross tonnes) of vessels that can receive licences is limited to recent levels. The capacity limitation scheme is accompanied by a requirement to implement a scientific observer scheme in order to improve the scientific data available for assessment purposes.
    • Deepwater longline survey of the slopes of Porcupine Bank and Porcupine Seabight

      Clarke, M; Hareide, N; Hoey, S (Marine Institute, 2001)
      This survey took place over a period of 12 days in November and December 1999 on the western slope of the Porcupine Bank and the western and eastern slopes of the Porcupine Seabight. Fishing was carried out in five separate areas, in depths between 400 and 2,000 meters. The primary objective of the survey was to obtain samples of chondricthyan and teleost fish for the Marine Institute (MI) deepwater research programme, for contaminant analysis of fish by the MI chemistry section and for food technology analysis at the Teagase National Food Centre. The survey was carried out on a commercial long-liner, using commercial deep-water autoline gear. In total 18 species of chondricthyan, 24 species of teleost fish and 1 species of cephalopod were taken. Among the most abundant species in the catch were bird beak dogfish, leafscale gulper shark, Portuguese dogfish and mora. Over the entire survey, discarding was estimated as 42% of the total catch. The main species discarded were birdbeak dogfish, black mouth dogfish and greater lantern shark. Catch per 1,000 hooks (CPU E) was highest abundances were found in the western and northwestern slope of the Porcupine Bank. The catch rates in the slopes of the Porcupine Seabight were considerable lower. CPUE compared with rates from previous years in the northwestern slope, showed a reduction for the commercial species Portuguese dogfish and leafscale gulper shark.
    • Deepwater longline survey on the continental slopes of Porcupine Bank, Rockall Bank and Hatton Bank

      Clarke, M; Moore, S J (Marine Institute, 2002)
      A deepwater survey programme has been operated since 1993 by the Marine Institute (MI), in the deep waters of the Rockall Trough and Porcupine Bank. The first leg of the present survey took place over a period of 12 days in August 2000 on the Western slope of the Porcupine Bank and the western slopes of Rockall Bank and Hatton Bank. The second leg took place on the slopes and shelves of the Porcupine Bank. Fishing was carried out in depths between 150 and 1,800 meters. The primary objective of the survey was to obtain biological samples of chondricthyan and teleost fish, for contaminant analysis of fish by the MI chemistry section and for food technology analysis at the Teagase National Food Centre. The survey was carried out on the commercial long-liner "An Capall Bán," using commercial deepwater autoline gear. In total 26 species of chondricthyan and 24 species of teleost fish were taken. Among the most abundant species in the catch were birdbeak dogfish (22%), leafscale gulpershark (14%), Portuguese dogfish (8%), tusk (17%) and mora (8%). Over the entire survey, discarding was estimated at 43% of the total catch. The main species discarded were bird beak dogfish and greater lantern shark. Catch per unit effort showed that highest abundances were found in the northwestern slope of the Porcupine Bank at 600 - 700 metres and in the western slopes of Rockall Bank and Hatton Bank at 1,000 to 1,200 metres depths.
    • Deepwater Survey Report 2006

      Hareide, N; O'Hea, B; Johnston, G; Leahy, Y; McCormick, E; Trueman, C; Wall, D; Gerritsen, H.D. (Marine Institute, 2006)
      The Marine Institute fisheries science services carried out a deepwater survey in 2006, to revisit earlier survey areas from the nineties and investigate the impact of the high levels of exploitation on the abundance and biological parameters of the deepwater species. The survey was carried out in three areas, two of which were located on the western continental slope and the third on the northern slope of the Porcupine Bank. Hauls were made at four depths, 500m, 750m, 1000m and 1500 meters. Eight comparative tows were made with the Scottish research vessel, RV Scotia. The object of the survey was to collect biological information on the main deepwater fish species, and also to collect benthic invertebrates and bottom sediment samples. CTD transects, grab sampling, and cetacean studies were also carried out. 126 species of fish were identified along with 131 species of invertebrates. The survey will be the basis for further collaborative work with FRS in future years, and provide a timeseries for CPUE for the main deepwater species.
    • Deepwater Trawl and Longline Surveys in 1995

      Connolly, P L; Kelly, C J (Marine Institute, 1997)
      Two surveys were carried out in 1995 as part of the continuing deep water fish research programme at the Fisheries Research Centre. The trawl survey fished areas on the eastern slopes of the Rockall Trough and on two seamounts of the mid-Atlantic ridge approximately 300 miles north of the Azores. The deep water longline trip was the first such survey carried out by the Fisheries Research Centre and concentrated on previously fished grounds in the Rockall Trough and on new areas along the slope of the Porcupine Bank. Both surveys were carried out in conjunction with an Bord Iascaigh Mhara (BIM) and the objective was to locate commercial quantities of deep water fish and to obtain samples for biological analyses. The trawl survey was conducted on a chartered fishing vessel using a commercial otter trawl, fitted with a small mesh cod-end liner. Twenty-six trawling operations were carried out in the depth range 750m-1,400m, of which 21 produced fish catches. Longlines were set between 542m and 1,521m and only one line was lost. Thirteen chondricthian and 38 species of teleost fish were recorded from the catches. The most abundant species in the catches were Portuguese shark, roundnose grenadier, black scabbard, Baird's smoothhead, blue ling and orange roughy. Length, weight, sex, maturity and catch data together with samples of otoliths and gonads were collected. Discards were monitored from both fishing methods. In comparison with the trawl, longline catches produced larger specimens of fewer species which were more dominated by sharks. Overall catch rates for the longlines were similar to Norwegian data for the Rockall area. Trawl catch rates showed a decrease since the last Irish survey in this area in 1993.
    • Defining value per unit effort in mixed métier fisheries

      Davies, S.; Minto, C.; Officer, R.; Lordan, C. (Elsevier, 2015)
      Value achieved from time spent at sea is a central driver of fishing decisions and fishing behaviors. Value per unit effort (VPUE) is an important indicator of economic performance in itself and a useful metric within integrated mixed fisheries models. A time series of Irish first sale prices and total per trip landings values (VPT) highlight heterogeneity in fish prices and VPTs achieved by the Irish fleet spatially and temporally, as well as variability with species targeting. This investigation compared models to standardize fishing trip VPUE accounting for species targeting (métier groupings), engine power (a kW proxy for vessel size), seasonal and annual variability, fishing effort, and individual vessels (encompassing variability in vessel characteristics and skipper effects). Linear mixed effects models incorporating random vessel effects and within-group variance between métier groupings performed best at describing the variability in the dataset. All investigated factors were important in explaining variability, and thus important in standardizing VPUE. Models incorporating fishing days (days with reported fishing activity) and engine power as separate variables resulted in improved AIC values. Therefore, fishing days were considered to be the most appropriate effort measure to generate VPUE. The effort unit traditionally applied in measures of per unit effort, fishing hours, performed comparatively poorly in relation to VPT.
    • Definition, dynamics and stability of métiers in the Irish otter trawl fleet

      Davie, Sarah; Lordan, Colm (Elsevier, 2011)
      The Irish otter trawl fleet operates in a complex multi-species multi-gear fishery, spanning a wide geographic area, and involving around 275 trawlers. Factorial and clustering methods were applied to 2003 fishing trip data to define thirty-three métiers. Definitions were based on six trip characteristics taken from logbooks, namely: fishing gear, mesh size, vessel length, species composition, area, and month. Métiers exploiting demersal species or species groups are characterised by single vessel bottom otter trawls, typically with mesh sizes of 70 mm or more, operating year round. This includes nine Nephrops dominated métiers highlighting the importance of this species to the fleet. Many demersal métiers are characterised by groups of species, such as mixed whitefish or slope species. Métiers exploiting pelagic species are often focussed on single species, and are typically seasonal, mid-water trawling (often paired) with mesh sizes less than 70 mm. Pelagic métiers account for the majority of landings by over an order of magnitude in several cases. Demersal métiers account for the majority of fishing trips and effort, (primarily Nephrops métiers), and vessels (primarily mixed species métiers). The new métier definitions were found to be appropriate remained relevant despite declining fleet landings and effort between 2003 and 2006. Species compositions within these métiers have generally remained similar to the proportions defined in 2003. These robust métier definitions present opportunities to improve fisheries sampling, assessment and management. Although métiers pose complexity challenge for such applications they can be used the building blocks for appropriate management units.
    • Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland

      Dillane, E; McGinnity, P; Coughlan, J P; Cross, M C; deEyto, E; Kenchington, E; Prodöhl, P; Cross, T F (Wiley-Blackwell, 2008)
      Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography and thus knowledge of landscape features (for example, as characterised within Geographical Information Systems) has the potential, to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.
    • Demystify - A collection of Artworks produced for the BlueFish Project

      Donnelly, Felicity (Marine Institute, 2021)
      The BLUEFISH project (2017 to 2021) focused on the Irish Sea and Celtic Sea region and set out to provide region wide adaptation strategies for the benefit of coastal communities, with a focus on fisheries and aquaculture. BLUEFISH assessed and disseminated knowledge on the risks and opportunities for commercial fish and shellfish under climate change scenarios. It has provided options that will help coastal communities adapt to climate change in the area of food security and the Blue Economy. BLUEFISH developed a series of targeted work-packages (WP) with stakeholders. WP2 focused on developing our understanding of the Irish Sea and Celtic Sea ecosystem in order to provide a framework for forward looking climate adaptation guidelines. Linking art and science to portray and explain these ecosystem goods and services and to depict plausible climate change impacts was an integral part of WP2. This compendium presents the various forms of artwork that were produced for the Marine Institute as part of the outputs from WP2. The climate change issue demands considerable public investment to reverse. This investment will only arise if the general public is supportive and this support is only likely if climate change issues are widely understood. The use of art to connect with people may be an effective way to change attitudes and win support for the societal actions required to reverse the impacts of climate change. The art forms presented in this compendium portray the importance of the ocean to the economies of coastal communities. This art also shows the potential impacts of climate change on these communities in a powerful way. The images can create anxiety about the future but the intent is to provide a deeper understanding of climate change and that the solutions presented for our coastal communities, expressed through the medium of art, will stimulate a long overdue debate and provide hope and inspiration for the future. The art outputs from WP2 also include the “Demystify animation” which can also make a valuable contribution to the debate in Ireland and in Wales. While the oceans are in a parlous state they also provide hope. If the ocean is managed more sustainably, species and ecosystems could revive, and could become better sources of sustainable food, energy, materials, livelihoods and, ultimately, planetary well-being.
    • DEPLOY: Smart Demonstration of Online Water Quality Monitoring on the River Lee, Cork, Ireland

      Regan, Fiona; Lawlor, Antóin; O’Flynn, Brendan; Wallace, John (Environmental Protection Agency, 2011)
      The DEPLOY project was a successful technology demonstration, showcasing how state-of-the-art technology can be used to achieve continuous, real-time monitoring of a river catchment. The project involved the collection of in-situ environmental data over a period of 12 months from a network of stations located in the River Lee Catchment, in Co. Cork. DEPLOY has demonstrated that this technology can be used to track fluctuations in a number of water quality parameters such as temperature, dissolved oxygen and pH across a catchment. This, in turn, has demonstrated the benefits of this approach over more traditional means of monitoring that are likely to miss much of the temporal variability associated with these parameters. This technology demonstration of a truly heterogeneous water quality monitoring networked system was one of the first of its kind in Ireland and showed how data could be collected from a number of locations and viewed in real or near real time. DEPLOY represented an important collaboration among research centres, the National Centre for Sensor Research (NCSR) at Dublin City University (DCU), and the Tyndall National Institute (TNI), commercial partner Intelligent Data Systems and the relevant River Basin District (the South Western River Basin District). The assembled project team had the technical and analytical expertise to successfully deploy, maintain, continuously collect environmental and water quality data and evaluate the effects of long-term sensor deployment on water quality monitoring systems and sensor data from a number of sites. The findings were then disseminated to the widest possible audience through the project website (http:// www.deploy.ie). While the potential of this technology is clear, the DEPLOY project also identified a number of gaps, particularly in the area of in-situ nutrient analysis. Further technological development in this area will be required if the goal of achieving a complete in-situ water quality monitoring solution is to be achieved. DEPLOY is a technology demonstration project that began planning, station selection and design in August 2008. It aimed to show how state-of-the-art technology could be implemented for cost-effective, continuous, real-time monitoring of a river catchment. The DEPLOY project is seen as an important building block in the realisation of a wide-area autonomous network of sensors capable of monitoring the spatial and temporal distribution of important water quality and environmental target parameters. The deployment demonstrates SN capability in collecting real-time water quality data and can act as a test bed to implement and evaluate water quality monitoring systems and deployment infrastructure (wireless data transfer mechanisms, novel sensors, sensor interfacing, etc.).
    • Design and make an explorer's paper maché submarine

      Marine Institute (Marine Institute, 2013)
      Get inspiration from books, movies and lots of imagination from the students to learn how a submarine works. The students should consider the technology of the future and produce drawings of the submarine featuring the design plans for inside and outside the vessel. Once completed, the students are to create a paper maché of a Super Future Explorers Submarine. Each student should compose and present a short story about their submarine explaining how its future technology works.
    • Desk Study Report: National, International and EU Legal Instruments Relevant to the Development of a Marine Spatial Planning Framework in Ireland

      Slater, Anne-Michelle; Kennedy, Alison; Grist, Dr. Berna; Barnes, Jerry; Berne, Sybil (Marine Institute, 2014-11)
      This study reviewed all international, European and national law relevant for the development of a framework for marine spatial planning (MSP) for Irish waters. The report details the identification of a range of options for MSP for Ireland and the criteria for testing these options. It explains the process of refining and developing both the options and the criteria in conjunction with the Enablers Task Force (ETF) to form preliminary conclusions.
    • Detection of human viruses in shellfish and update on REDRISK research project, Clew Bay, Co. Mayo

      Keaveney, S.; Guilfoyle, F.; Flannery, J.; Doré, B. (Marine Institute, 2006)
      This paper describe the progress in norovirus detection methods and initial results from the REDRISK study.
    • Detection of koi herpesvirus (KHV) in koi carp (Cyprinus carpio L.) imported into Ireland.

      McCleary, S.; Ruane, N. M.; Cheslett, D.; Hickey, C.; Rodger, H.D.; Geoghegan, F.; Henshilwood, K. (Europeand association of fish pathologists, 2011)
      This report described the first detections of koi herpesvirus (KHV) in the Republic of Ireland in imported koi carp. In both cases the KHV suspicions were confirmed by molecular diagnosis and the infected stocks culled.
    • Development & implementation of the Phytotest project

      Kavanagh, S.; Brennan, C.; Lyons, C.; Chamberlain, T.; Salas, R.; Moran, S.; Silke, J.; Maher, M. (Marine Institute, 2008)
      Phytotest is a 3-year research and development project funded through the Marine Institute Strategic Research Programme in Advanced Technologies as part of the National Development plan 2000-2006. The project is a collaboration between the National Diagnostics Centre at NUI Galway and the MI and involves the development of real-time PCR assays for Dinophysis and Pseudo-nitzschia species that are important in Irish waters. In the current final phase of the project, the real-time PCR assays are being transferred to the MI to support the phytoplankton monitoring service.
    • Development and Demonstration of Viable Hatchery and Ongoing Methodologies for Seaweed Species with Identified Commercial Potential

      Dring, Matthew; Edwards, Maeve; Watson, Lucy (Marine Institute, 2013)
      The main objectives of this project were to develop and conduct trials of industry-scale hatchery and ongrowing methodologies for three seaweed species with commercial potential. These included two edible red algae, Palmaria palmata and Porphyra sp., and the large brown kelp Laminaria digitata. During the project the large brown kelp Saccharina latissima was added to the work programme. In addition to developing ongrowing methodologies for each of the seaweed species, the project aim was to provide a platform for transferring the results and knowledge gained during the project, which would support the creation of new business opportunities in Ireland’s seaweed aquaculture sector.
    • Development of a Management Strategy for the Reduction/Elimination of Sea Lice Larvae, Lepeophtheirus salmonis, Parasites of Salmon and Trout

      O'Donoghue, G; Costelloe, M; Costelloe, J (Marine Institute, 1998)
      Sea lice are copepod ectoparasites of fish, belonging to the family Caligidae. Their importance to marine salmonid culture stems from the extensive damage they may inflict on hosts through feeding and contact abrasion. The principal species associated with cultured salmonids is Lepeophtheirus salmonis (Kroyer, 1838), a large salmonid-specific species reported as a problem for aquaculture in a number of countries. The objectives of the present study were: (a) to examine the production and distribution of larval stages of Lepeophtheirus salmonis within a cage containing Salmo salar in order to identify specific spawning cues and larval frequencies and intensities; (b) to identify precisely the behavioural patterns of sea lice larvae over a variety of tidal and diurnal cycles; (c) to monitor environmental parameters and (d) having identified the specifics of spawning and larval behaviour, to identify potential management strategies for the elimination of a high percentage of sea lice larvae produced on fish farms. Larval plankton samples along with mobile lice samples were taken during two growing cycles on a fish farm on the west coast of Ireland. Highest densities of larvae were recovered during neap tides following synchronous spawning episodes within the female population. Gravid females were recorded during the winter months; however, spawning intensity remained low until late Spring. Sea lice larvae migrated vertically within the water column with highest densities recorded during slack water normally associated with high tide. The results of this study increases our knowledge of the complex behaviour and life cycle of the louse. The occurrence and the location of high densities of larvae within salmon cages have been identified. This information provides a sound basis from which management strategies can be developed in order to reduce lice intensities on the farm.