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This publication constitutes the final report for the research project ST/05/01 “Site investigations and disease management of the pancreas disease virus in Irish farmed salmon”, funded under the NDP Marine RTDI Programme. Work undertaken within the project included longitudinal studies of rainbow trout and Atlantic salmon at sea following the course of infection, testing for vectors and reservoirs of the virus, molecular studies of the virus and an epidemiological investigation of pancreas disease in Ireland. Results have shown that although pancreas disease is endemic in marine farmed Atlantic salmon, no evidence of infection in rainbow trout farmed at sea was found. Serological and molecular based diagnostic methods were shown to be suitable for the screening of fish stocks for the presence of the virus. For the confirmation of clinical outbreaks, farm data and histopathological results should be included. The results also suggest that horizontal transmission of the virus may be the main route of infection between sites. The project also involved the technology transfer of molecular and serological diagnostic methods for pancreas disease between partners and the final chapter includes practical information on management of, and mitigation against, pancreas disease. Pathologies such as pancreas disease, heart and skeletal muscle inflammation and cardiomyopathy syndrome, pose a serious threat to salmonid farming in Ireland, Scotland and Norway. Most significant among this group of diseases is pancreas disease, a viral disease affecting Atlantic salmon during the marine stage of the production cycle. From the first description of pancreas disease in farmed Atlantic salmon from Scotland in 1976 the disease has now become endemic in Ireland and parts of Norway and continues to be significant in Scotland. The causal agent of pancreas disease, a salmonid alphavirus, has now been characterised and a closely related subtype of the virus is known to cause sleeping disease in farmed rainbow trout on continental Europe and in the United Kingdom. The Irish salmon farming industry has estimated that pancreas disease has resulted in a total loss of turnover of €35 million with €12 million loss of profit in the years 2003-2004. The economic impacts are estimated to be in the range of €100 million per year in Norway. In Scotland, pancreas disease and related pathologies are increasingly responsible for significant losses in marine salmon farms but these have yet to be quantified., Funder: Marine Institute

This report details the work undertaken as part of the INTERREG IIIA Irish Sea Marine Aggregates Initiative (IMAGIN) project which aims “to develop recommendations for a strategic policy framework for an administrative and regulatory process, and operational guidelines under which dredging for marine aggregates in the Irish Sea can be sustainably managed.” It considers policy and regulatory issues from an Irish context. Aggregates in the form of sand and gravel deposits are a vital natural resource, providing essential material to support societal needs for infrastructure and the construction industry. Thus, the importance of aggregate supply to the economy of many nations cannot be understated. As a result of Ireland’s economic boom since the early 1990s, the national consumption of aggregates per head of population in Ireland has spiralled upward and is currently standing at four times the European average. At present, all aggregate used in the Irish market is extracted from terrestrial sources. This project set out to examine the marine extraction option for current supply and future Irish demand., Funder: Marine Institute

This document outlines the proceedings of the 8th Irish Shellfish Safety Scientific Workshop. This event was organised by the Marine Institute, the Food Safety Authority of Ireland and Bord Iascaigh Mhara to discuss the methods and advances of food safety with respect to shellfish health., Funder: Marine Institute

The lack of short-term temporal resolution associated with traditional spot sampling for monitoring water quality of dynamic coastal and estuarine waters has meant that many organisations are interesting in autonomous monitoring technologies to provide near real-time semi-continuous data. Such approaches enable capturing short term episodic events (which may be missed or alternatively skew datasets when using spot samples) and provide early warning of water quality problems. New policy drivers such as the Water Framework Directive (WFD) provide added impetus to develop this field. Therefore, as part of the interreg IIIa funded MATSIS project the Marine Institute undertook to develop and pilot an autonomous monitoring station in Dublin Bay (North Bank Monitoring Station NBMS). This report presents the outcome for this pilot study., Funder: Marine Institute

The Food Safety Authority of Ireland in collaboration with the Marine Institute and An Board Iascaigh Mhara (Sea Fisheries Board) has carried out a surveillance study of levels of dioxins (PCDDs), furans (PCDFs) polychlorinated biphenyls (PCBs), and brominated flame retardants (BFRs), specifically polybrominated diphenylethers (PBDEs) and hexabromocyclododecane (HBCD), in a variety of fish species and fishery products, including fresh and processed products available on the Irish market. The study was undertaken because of concern about the possible effects on human health of these bio-persistent environmental contaminants, known to be present in a number of foodstuffs, notably meat, fish, eggs and dairy products. The study showed that levels of PCDDs and PCDFs in Irish fish and fishery products available on the Irish market were well below existing EC legal limits for these contaminants as laid down in Regulation 466/2001. The lowest level was found in a sample of canned tuna (0.012 ng WHO TEQ/kg whole weight) with the highest level found in a farmed salmon sample (0.82 ng WHO TEQ/kg whole weight), compared with the maximum level under the legislation of 4 ng WHO TEQ/kg whole weight. The levels found were also below the new limits for dioxin-like PCBs (dl-PCBs) and for the sum of WHO-TEQs for PCDDs, PCDFs and dioxin-like PCBs, which were introduced in November, 2006 via Regulation 199/2006. The upper-bound mean levels of PCDDs, PCDFs and dioxin-like PCBs expressed as total WHOTEQs ranged from 0.05 – 2.15 ng/kg WHO TEQ whole weight, which can be compared with the new maximum level of 8 ng WHO TEQ/kg whole weight for the sum of PCDDs, PCDFs and dioxin-like PCBs. Results of this study are in line with those from previous FSAI studies on PCDD and PCDF levels in fish and also in meat, milk and eggs, and indicate relatively low levels of these contaminants in fishery produce available in the Irish marketplace. Reductions of PCDD/Fs and dl-PCBs in Irish farmed salmon were observed in comparison to levels measured in a previous FSAI/MI survey in 2001, in which a mean level of 4.02 ng WHO TEQ/kg whole weight was detected compared with 2.15 ng/kg WHO TEQ whole weight in the present study. Similar observations can be made for levels reported in a study carried out by An Board Iascaigh Mhara in 2004, in which a mean level of 1.75 ng WHO TEQ/kg whole weight was reported. Concentrations of brominated flame retardants were also low. The mean PBDE concentrations ranged from, Funder: Marine Institute

Ireland has a long history of producing and harvesting native flat oysters, Ostrea edulis. At the start of the nineteenth century, almost every bay and harbour, around the coast had abundant beds of native oysters. Intensive dredging to meet the demands of the markets in Dublin and England depleted the stocks, so that in 1845 the government passed legislation to permit the formation of private oyster beds to improve the ailing stocks. According to the book on “Shellfish & Shellfisheries of Ireland” (Wilkins, 2004) Irish stocks began to collapse between 1850 and 1860. By the second half of the twentieth century, only the beds of Tralee Bay, Galway Bay and Clew Bay were still yielding a good return for local fishermen. The arrival of the oyster parasite Bonamia ostreae in the mid 1980s was an additional blow to the Irish native oyster stocks. This report sets out to document the spread and the impact of the Bonamia ostreae parasite in Irish bays since the 1980s., Funder: Marine Institute

This document outlines the proceedings of the 7th Irish Shellfish Safety Scientific Workshop. This event was organised by the Marine Institute, the Food Safety Authority of Ireland and Bord Iascaigh Mhara to discuss the methods and advances of food safety with respect to shellfish health., Funder: Marine Institute

As it currently stands, the management of the bottom mussel aquaculture in Ireland is a complex process that is governed by three overriding factors; these are; 1) Government policy and regulation, 2) industry and economics and 3) Science and biology. These three factors are influenced by a range of different issues that influence the implementation of resource management either individually or in combination and include, inter alia, aquaculture licensing, carrying capacity, company structure and operating practices, animal health legislation, vessel registration and licensing and North/South agreements, prevailing weather conditions and uncertainty of seed supply. The mussel seed fishery in the Irish Sea, as the primary source of seed, is integral to the continued viability of the bottom mussel sector in Ireland. This report is the outcome of a project initiated over concerns raised regarding the sustainability of the fishery. A goal of this project is to develop and implement a science based management system for the sustainable exploitation of seed mussels in the Irish Sea. A specific goal of the project was to identify environmental drivers governing the distribution and abundance of the seed mussel resources in the Irish Sea. A number of outputs were expected from this project: 1. A literature search and review of existing biological, fisheries, survey and hydrographic data. 2. Studies to estimate adult reproductive cycles and spatfall patterns. 3. Hydrographic models of targeted areas of high mussel population. These models allow for behavioural characteristics of the larval swimming phases. 4. Draft a management strategy to detail the optimum manner in which to effect the sustainable exploitation of the resource, including the hatchery option. This report addresses the final workpackage above, wherein a series of recommendations encompassing both management and research aspects, based upon the scientific outputs of the project, are presented., Funder: Marine Institute

Infectious pancreatic necrosis (IPN) is an economically significant viral disease of salmonid fish worldwide. Infectious pancreatic necrosis is categorised as a List III disease under Annex A of EU Council Directive 91/67/EEC. List III diseases are present within the EU and up to 2004 were regulated under national control programmes within each member state. The disease was first described in freshwater trout in North America in the 1950’s (Wood et al., 1955) and has been reported in Europe since the early 1970’s (Ball et al., 1971). Initially, IPN was regarded as a serious disease affecting rainbow trout fry and fingerlings (Roberts & Pearson, 2005). However as the salmon farming industry began to expand during the 1970’s, incidence of IPN disease in salmon also increased with the result that IPN is now widespread in the salmon farming industry in both Norway and Scotland. The economic loss due to the disease is large and outbreaks may occur in Atlantic salmon juveniles in fresh-water and in post-smolts after transfer to sea-water. Historically in Ireland, isolations of the IPN virus have been rare and occasional outbreaks have occurred in both rainbow trout and Atlantic salmon facilities. The Marine Institute and its predecessor, the Fisheries Research Centre, have been testing farmed and wild fish for disease pathogens since the mid 1980’s. The first reported clinical outbreak of IPN in Atlantic salmon occurred in 2003. However in 2006 severe outbreaks in a number of freshwater salmon hatcheries occurred which were all linked to imports from a specific single source. To date, clinical outbreaks of IPN in Ireland have been associated with imports of infected ova and their subsequent movement within the country. This report reviews the prevalence of the IPN virus in the Irish salmon farming industry and also in wild fish from selected rivers. It describes the steps taken by the industry to control the disease in 2006 and aims to provide some practical solutions to reduce the prevalence of the virus in farmed and wild fish and to prevent future outbreaks of the disease., Funder: Marine Institute

Since 1995, when several people became ill following consumption of shellfish from Ireland, azaspiracids (AZAs) have been known as shellfish toxins, causing symptoms associated with gastro-intestinal disorders, including diarrhoea, vomiting, headaches and others. The aims of the ASTOX-project were to provide control tools for the analysis of AZAs in shellfish, i.e. calibration standards and tissue reference materials (RMs), and to clarify the toxicity of AZAs in qualitative and quantitative terms, i.e. to understand the mode of action of AZAs and to derive a No Observable Adverse Effect Level (NOAEL) for safe consumption of shellfish., Funder: Marine Institute

Prior to the present guidelines the assessment, by the Marine Institute on behalf of the Department of Communication, Marine and Natural Resources, of the suitability of dredged materials for disposal at sea had employed provisional action levels as an aid to evaluation. These provisional action levels were based entirely on sediment chemistry. The responsible agencies have decided that these levels now need to be updated and formalised. The approach proposed in this document aims to provide an improved, and more integrated, assessment of the ecological risks associated with individual sediment dredging and disposal activities. It offers flexibility to deal with issues on a case-by-case basis and improves transparency of the decision-making process. The list of parameters to be assessed has been revised and methods for setting numerical guidance values in other countries have been reviewed. Ideally, guidance levels should comprise chemical and ecotoxicological data specifically relating to Irish sediments. In the absence of a comprehensive dataset for Irish sediments, proposed threshold guidance levels have been based on ecotoxicological data from other sources. Wherever possible, lower threshold guidance values have been based on existing Irish background levels of contaminants. Where background data do not exist for a particular parameter, ecotoxicologically-derived values, corresponding to expected no-effect levels, have been taken from reputable sources. Similarly, upper threshold guidance levels (i.e. levels at which effects may be expected) have been based on ecotoxicological data from reputable sources. The assessment strategy has been designed so that decisions concerning the acceptability of sediments for sea disposal will take into account a range of intrinsic and environmental factors i.e. the strategy adopts a Weight of Evidence approach. The guidance will be reviewed and revised as necessary, as more information becomes available. Sampling and storage methodology is presented as well as quality assurance and reporting requirements. Guidance on analytical procedures and approval of analytical laboratories is included., Funder: Marine Institute

This document outlines the proceedings of the 6th Irish Shellfish Safety Scientific Workshop. This event was organised by the Marine Institute, the Food Safety Authority of Ireland and Bord Iascaigh Mhara to discuss the methods and advances of food safety with respect to shellfish health., Funder: Marine Institute

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, water samples from major shellfish growing areas were tested for physicochemical parameters and shellfish were tested for trace metal levels. In 2003, a total of 30 samples were analysed for trace metals. All mercury concentrations measured were below or close to the limit of quantification, 0.03 mg/kg wet weight, which is well within the European maximum level of 0.50 mg/kg wet weight for mercury in bivalve molluscs. Levels of lead were typically low, with a mean of 0.26 mg/kg wet weight and maxima of 1.04 mg/kg wet weight, also below the respective European maximum level of 1.50 mg/kg wet weight. In addition, levels of cadmium were all below the European maximum level of 1 mg/kg wet weight, though the level of cadmium determined at Castlegregory in Tralee Bay was 0.97 mg/kg, close to the European limit. Castlegregory has not been included in the sampling programme since 1994, but will be included in future monitoring. There are no internationally agreed standards or guidelines available for the remaining trace metals in shellfish. A compilation by the OSPAR Commission of standard and guidance values applied by member states of OSPAR indicated the Spanish standard for copper in shellfish of 20 mg/kg wet weight to be the strictest available. This excludes oysters for which a higher standard of 60 mg/kg wet weight has been set, as oysters accumulate copper to higher levels. All copper results were within these Spanish standards. The results obtained provide 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., 2004, 2003a, 2003b; 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 is low in Irish shellfish aquaculture., Funder: Marine Institute

The Marine Institute sample a range of finfish species landed at major Irish ports on an annual basis, in accordance with the monitoring requirements of various European legislation designed to ensure food safety. During 2003, a total of 45 samples from 22 different species of finfish were collected from five major Irish fishing ports and analysed for total mercury concentration in the edible tissue. The concentration of mercury ranged from less than the limit of quantitation (0.03 mg/kg wet weight) to 0.60 mg/kg wet weight with a mean and median of 0.08 and 0.06 mg/kg respectively. The maximum level was found in a dogfish sample (species tentatively identified as Lesser Spotted Dogfish) from Howth. It is most likely that the fish from which this sample was taken were destined for whelk bait and as such there are no human health implications. The remainder of the mercury levels were within the maximum limit of 0.50 mg/kg wet weight for mercury in fishery products set by the EU (1 mg/kg for selected species). This survey confirms previous studies, which show that Irish seafoods are effectively free from mercury contamination. A total of 20 samples were analysed for lead and cadmium. Overall, the levels of lead and cadmium detected in the edible portion of the fish were low and well within the standard values of 0.20 and 0.05 mg/kg wet weight respectively set by the EU. Randomly selected samples were also analysed for other trace metals. There are no internationally agreed standards or guidelines available for the remaining trace metals in fishery products. Therefore results are compared with the strictest standard or guidance value for fish tissue, which are applied by contracting countries to the OSPAR Convention. The levels of these additional contaminants are well below the strictest values listed., Funder: Marine Institute

Pancreas Disease is the most significant single infectious disease affecting marine salmon farms in Ireland. The first epidemiological studies of Pancreas Disease (PD) in Ireland in the early 1990’s indicated that significant losses occurred in farmed Atlantic salmon in their first year at sea on some individual farms (Menzies et al., 1996). A serological survey for the presence of Salmon Pancreas Disease Virus (SPDV) antibody in 1996 revealed that 53% of Irish sites were positive, but that not all positive sites had recognised clinical signs of PD. This indicated a relatively low incidence and severity of PD at that time (McLoughlin et al., 1998) and this pattern persisted throughout the remainder of the 1990’s. In 2002, a serious increase in both the incidence and severity of PD was reported on farmed Atlantic salmon marine sites in Ireland. An epidemiological survey of Irish sites for 2002 revealed that 59% of sites reported an outbreak of PD, with mortalities averaging 12% (range 1 – 42%; McLoughlin et al., 2003). A recent study using data collected for 2003 and 2004 indicated that PD occurred in 62% and 86% of sites respectively. The average mortality due to PD on affected farms was 18.8% in 2003 and 14.8% in 2004. In response to these significant losses due to PD a range of research initiatives was launched in Ireland and was supported by the Marine Institute. This document gives an overview of the most recent findings from the current projects, carried out in 2004/2005 and also provides an overview of the various actions in Scotland and Norway, where PD has also become a disease of economic significance in salmon aquaculture., Funder: Marine Institute

This document outlines the proceedings of the 5th Irish Shellfish Safety Scientific Workshop. This event was organised by the Marine Institute, the Food Safety Authority of Ireland and Bord Iascaigh Mhara to discuss the methods and advances of food safety with respect to shellfish health., Funder: Marine Institute

A protracted bloom of Karenia mikimotoi was present in summer 2005 along the northern half of the western Irish coastline. The onset of this bloom was identified in late May / early June. This event subsequently dissipated over the month of July and was succeeded by a bloom of the same species in the southwest in late July. The bloom was very intense and resulted in discolouration of seawater and foaming in coastal embayments. Major mortalities of benthic and pelagic marine organisms were observed and a complete decimation of marine faunal communities was reported and observed in several locations. Deaths of echinoderms, polychaetes and bivalve molluscs were observed in County Donegal and Mayo, while farmed shellfish and hatchery raised juvenile bivalve spat suffered significant mortalities along the Galway and Mayo coasts. Reports of dead fish and crustacea were received from Donegal, Galway, West Cork and Kerry. Karenia mikimotoi is one of the most common red tide causative dinoflagellates known in the Northeast Atlantic region, and is also common in the waters around Japan. Blooms of this species often reach concentrations of over several million cells per litre and these densities are often associated with marine fauna mortalities. Although cytotoxic polyethers have been extracted from cultures of the species, the exact mechanism of the toxic effect and resultant devastating damages yet remains unclear. It is known in the literature under several different names as the taxonomy and genetics have been studied. It is now known that previously reported names including Gyrodinium aureolum, G. cf. aureolum, G. nagasakiense and G. mikimotoi are synonymous with the current name given to the organism. The visible effects following the mortalities included noticeable quantities of dead heart urchins (Echinocardium cordata L.) and lugworms (Arenicola marina L.) deposited on beaches. Several species of wild fish were also found dead. The bloom coincided with a period of fine weather and tourists visiting the seaside were concerned about the safety of swimming in waters that were obviously harmful to marine organisms on this scale. A public awareness programme was mounted by the Marine Institute with several radio broadcasts, press releases and a website provided to give up to date pronouncements on the event. While there have been several instances of Karenia mikimotoi blooms reported in Ireland over the past 30 years, this scale of mortalities associated with the 2005 bloom were not previously observed. Recording the scale of this event was facilitated by satellite imagery while direct counts of the cells in seawater by the Marine Institute monitoring programme gave very useful information regarding the size and intensity of this event. The mortalities of marine organisms were documented from reports made by various observers and by Marine Institute field surveys., Funder: Marine Institute

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., Funder: Marine Institute

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 and trace metal levels and chlorinated hydrocarbon concentrations in shellfish are presented. In 2002, a total of 24 samples from 22 different shellfish sites were analysed for chlorinated hydrocarbons and trace metals, including nickel and silver. The median concentration of mercury in shellfish sampled in 2002 was, Funder: Marine Institute

The Marine Institute sample a range of finfish species landed at major Irish ports on an annual basis, in accordance with the monitoring requirements of various European legislation designed to ensure food safety. During 2002, a total of 38 samples from 20 different species of finfish were collected from five major Irish fishing ports and analysed for total mercury concentration in the edible tissue (Common names and species names are listed in Appendix 3). The concentration of mercury ranged from less than the limit of quantitation (0.03 mg/kg wet weight) to 0.46 mg/kg wet weight with a mean and median of 0.09 and 0.06 mg/kg respectively. These levels are within the maximum limit of 0.50 mg/kg wet weight for mercury in fishery products set by the EU (1 mg/kg for selected species). This survey confirms previous studies, which show that Irish seafood is effectively free from mercury contamination. Selected samples were also analysed for other trace metals and chlorinated hydrocarbons. Overall, the levels of lead and cadmium detected in the edible portion of the fish were low and well within the standard values of 0.20 and 0.05 mg/kg wet weight respectively, set by the EU. There are no internationally agreed standards or guidelines available for the remaining trace metals and chlorinated hydrocarbons in fishery products. Therefore results are compared with the strictest standards or guidance values for fish tissue, which are applied by contracting parties to the OSPAR Convention. The levels of these additional contaminants are well below the strictest values listed., Funder: Marine Institute

A diverse seaweed industry has developed in Ireland over the past few decades. The seaweed industry today comprises several sectors, such as biopolymers, agriculture/horticulture, cosmetics, thalassotherapy and human consumption, with the former two sectors being of most economic importance. Approximately sixteen seaweed species are commercially utilised, three of which are of particular commercial importance. These are the calcified red algae, referred to as maërl, which mainly comprises of two species (Phymatolithon calcareum and Lithothamnion corallioides) and are exploited by a single company for agricultural, horticultural, food and cosmetic applications. The other bulk species is the brown alga Ascophyllum nodosum, which is used for alginate extraction and agriculture/horticulture applications. The latter species sustains an industry, which is an important factor in contributing to the maintenance of coastal communities especially in rural areas of the west coast, particularly in the Gaeltacht of Connemara (Guiry 1997, National Seaweed Forum, 2000). Mechanical harvesting of seaweeds in Ireland is limited to the exploitation of maërl. At present, one company has a licence to harvest calcified algae in the south-west of Ireland (Bantry Bay) with 8,000 - 10,000 wet tonnes of maërl being extracted from the seabed annually in recent years. The supply of raw material for the Ascophyllum-processing industry as well as for the other industrial sectors relies on harvesters who harvest the seaweed by hand. Although hand-harvesting provides a source of employment in rural areas along the west coast, the age profile is increasing and the numbers of harvesters are declining due to insufficient recruitment of younger harvesters (National Seaweed Forum 2000; Kelly et al. 2001). With growing demands for seaweeds, it is uncertain whether hand-harvesting will provide sufficient raw material in the long-term. The National Seaweed Forum has evaluated the current state of the Irish Seaweed Industry. The forum was launched by the Minister for Marine and Natural Resources in 1999 and consists of 19 members from state agencies, third-level institutions and industry. In the final report (National Seaweed Forum, 2000) it was stated that the natural sustainable seaweed resources in Ireland are under-utilised and the industrial potential, including high-value applications, has not been fully realised. The National Seaweed Forum identified two key areas as being crucial to the development of the Irish seaweed industry: 1) Seaweed aquaculture was assumed to provide the most cost-effective method to meet growing market demand with high-quality seaweed for specific sectors such as human consumption, cosmetics and biotechnology. Additionally, a seaweed aquaculture industry is expected to create attractive and high-skilled jobs, especially in peripheral communities in coastal areas. This is based on the fact that seaweeds of interest to high quality applications are often not bulk species, which are easy to harvest in large amounts. Therefore, with cultivation you strongly increase volume/area, which facilitates harvesting and also standardises quality. Cultivation of a bulk species such as kelp is economically not feasible in Europe. 2) The development and introduction of harvesting machinery suitable for Irish conditions was thought to have a significant impact on the expansion of a viable Irish seaweed industry. As a measure to ensure long-term continuity of raw-material supply of bulk species (e.g. A. nodosum, Laminaria species) the investigation of mechanical harvesting techniques with emphasis on sustainability and environmental impact were prioritised as an R&D area (National Seaweed Forum, 2000). An initial comprehensive study of hand and mechanical harvesting of Ascophyllum nodosum, including an environmental impact assessment, was conducted in the late 1990s (Kelly et al., 2001). In this study, a device similar to the Norwegian Ascophyllum cutter (a flat-bottomed boat fitted with a Vaughan vertical wet-well chopper pump) was used. When hand and mechanical harvesting were compared, there was no significant difference in environmental impact caused by the two methods, but mechanical harvesting was found to be less effective and more expensive than hand harvesting. At present, kelp species in Ireland such as L. digitata, L. saccharina and Alaria esculenta, are harvested by hand but only in small amounts. This means that the natural sustainable resources of kelps of Irish shores are under-utilised. Due to the economic importance of L. digitata and L. hyperborea for alginate extraction and the growing demand for kelp by the phycocolloid and other industries, the introduction of mechanical harvesting is currently being considered for Ireland. Mechanised harvesting enables the harvester to remove large amounts of biomass from an area in a relatively short time. It is therefore essential to develop a suitable management scheme to ensure sustainable exploitation of natural resources and continuous integrity of marine habitats. The objective of the present study is to provide an extensive literature review on kelp research, harvesting and resource management as essential background knowledge for the development of an appropriate management strategy for Ireland. The report addresses the following topics: • Biology of kelps • Biodiversity of kelp forests and ecological significance of kelps • Commercial kelp harvesting in France and Norway (methods, management and environmental impact) • Investigations of kelp in Ireland (Growth rates, biomass, biodiversity of kelp beds, regeneration potential, kelp resources) • Legal framework for seaweed harvesting in Ireland • Conclusions and recommendations, Funder: Marine Institute

Dogwhelk and periwinkle specimens were collected from six bays/estuaries in 2000, where Tributyl Tin (TBT) contamination was suspected. In four estuaries, shells of dead Pacific oysters were collected from 7 sites in the vicinity of culture installations. Observations on imposex in dogwhelks, intersex in periwinkles and shell thickness in the Pacific oysters were used to assess the degree of TBT contamination. The results showed low levels of contamination, which are unlikely to have detrimental effects to mollusc culture or fisheries in Mulroy Bay, Valentia Harbour or Tralee Bay. Thickening of oyster shells was detected in Carlingford Lough, Waterford Harbour, Cork Harbour and Fountainstown. The small degree of thickening was considered unlikely to affect marketability., Funder: Marine Institute

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, Funder: Marine Institute

In the early 1990’s pancreas disease (PD) was shown to be the most significant cause of mortality in Irish farmed salmon (Wheatley et al., 1995, Menzies et al., 1996, Crockford et al., 1999). At that time the aetiology of PD was uncertain but in 1995 it was conclusively shown that PD was caused by a virus subsequently named salmon pancreas disease virus (SPDV), (Nelson et al., 1995, McLoughlin et al., 1996). It has since been further classified and named salmonid alphavirus (Weston et al., 1999, Weston et al., 2002). The clinical and histopathological features of naturally occurring pancreas disease in farmed Atlantic salmon in Ireland were described by Murphy et al., 1992 and McLoughlin et al., 2002. The original epidemiological studies of PD in Ireland indicated that mortality rates up to 48% have occurred in farmed Atlantic salmon in their first year in the sea on some individual fish farms (Menzies et al., 1996). PD was recorded in over 70% of marine sites monitored and the majority of PD outbreaks occurred during August to October (Crockford et al., 1999). A serological survey for the presence of SPDV antibody in 1996 revealed 53% of the sites (9/17) were positive and that not all positive sites had recognised clinical signs of PD. This indicated a relatively low incidence and severity of PD at that time (McLoughlin et al., 1998). This pattern persisted until 2002 when there was a serious increase in both the incidence and severity of PD reported on farmed Atlantic salmon marine sites in Ireland. In order to identify factors associated with this re-emergence of PD in Irish farmed salmon, an in-depth epidemiological investigation was carried out on all marine sites. In trying to identify the cause of a disease from epidemiological studies the concept of time, place and individual is paramount, i.e. why did a particular disease occur in a particular animal or group of animals at a particular time in a particular place? Epidemiological study designs are chosen so that predictor variables are measured in affected and non-affected “units”. These “units” may be cells, animals, pens, farms or countries. The association between these predictor variables and disease is then examined. Where associations are demonstrated then risk factors for disease can be identified. A risk factor is a predictor variable associated with the disease. However the identification of a risk factor does not imply causation. The strength, consistency, temporality and dose response effect of the risk factor add weight to it being causal but only an intervention study where the risk factor is added or omitted can confirm this. Individual or univariate analysis of the relationship between a predictor variable and disease may result in an association being demonstrated. However it is dangerous to read too much into univariate analyses as factors which have been ignored, not measured or not seen as important may have a confounding effect. Multivariate analysis is used to try to provide estimates of association adjusted for the effect of confounding factors is a much more accurate and powerful epidemiological tool, but was of limited application in this snapshot survey of a single production cycle. This report aims to describe the occurrence and severity of PD in Irish farmed salmon in 2002-2003 and to identify risk factors associated with the re-emergence of severe PD. Finally, recommendations are made on how PD can be managed to reduce its serious impact on the health, welfare and productivity of Irish farmed salmon., Funder: Marine Institute

Increasing public and media awareness of the unique nature of European deep-water corals has put the focus firmly on the need for sustainable management of European offshore living resources. The well documented destruction of deep-water corals off Norway and potentially along the entire European margin combined with extremely slow coral habitat recovery rates, has created a sense of urgency to move towards implementation of the appropriate management measures to ensure the long-term survival of this spectacular and important habitat. In the process, deep-water coral conservation has become in many ways a paradigm for a shift away from traditional sectoral driven resource management approaches, towards an inclusive integrated ecosystem approach to the management of European offshore resources. The EU Fifth Framework Programme, in an effort to increase the socio-economic impact of its R&D projects strongly encouraged the formation of scientist-stakeholder partnerships and development of a suitable research-product delivery mechanism. The major (€2.1 million) European Union funded research project: the Atlantic Coral Ecosystem Study successfully responded to these new challenges in a number of innovative ways. In particular, the establishment of an ACES project-stakeholder partnership through consultative workshops, provided a means for stakeholders to prioritise the scientific research and created a forum for rapid dissemination of scientific results. Complementary initiatives arising from these meetings, such as the formation of the ad hoc Irish Coral Task Force, provided a mechanism whereby scientific findings could be translated into policy advice for the appropriate national authorities. This report serves as a record of the consultative process undertaken during two stakeholder workshops held in Galway on 23rd June 2000 and 24th June 2002. Section A contains conclusions and summary records of the two meetings. Section B contains a series of papers presented at the workshops to provide detailed information on: cold-water coral research and conservation initiatives; fishing related issues; oil and gas related issues and conservation legislation and legal issues. The 2000 meeting was sponsored by the Atlantic Coral Ecosystem Study, while the 2002 meeting was sponsored by the Marine Institute (Ireland), as part of its support for the Irish Coral Task Force and ACES. Between the first and the second meeting, the need for scientific advice to support the designation of Special Areas of Conservation to protect corals under the EU Habitats Directive became a clear priority. Finally, it is obvious that much work remains to be done to achieve effective protection of deep-water corals and similarly threatened 'hot spots' of marine biodiversity along the European shelf and slope. It is also clear, however, that successful implementation of conservation measures will require on-going dialogue with stakeholders, and their participation in the decision making process., Funder: Marine Institute

Concerns over recent expansion of the aquaculture sectors in Mulroy Bay have lead to several investigations on environmental quality within the area, including a recent report (in 2000) for the Irish Marine Institute by the Centre for Marine Resources and Mariculture (C-Mar, 2000). This study reported on changes in the physical and chemical environment within Muloy Bay over a two year data collection period, and from data collected by Marine Harvest Ireland, and related observed changes to aquaculture (notably salmon farming) outputs. The study also involved sediment bioassays using sediment collected in Mulroy Bay and a variety of test organisms to investigate whether any toxicants were present that may affect the benthic community. The current study was commissioned by the Marine Institute to draw together the results of long term monitoring of water and sediment quality, and hydrography, within Mulroy Bay collected by the Institute of Aquaculture (IoA), Stirling, on behalf of Marine Harvest Ireland since 1986. The study examines trends in the physical and chemical environment within Mulroy Bay (predominantly using IoA data) since recording began, and relates results to the present activities within the bay. The aims of the study are: • to produce a carrying capacity model for Mulroy Bay as a whole • to produce maps of waste dispersion from fish cage sites • to assess the environmental sustainability of current aquaculture activities in Mulroy Bay, Funder: Marine Institute

The European Union project “Investigation into the monitoring, analysis and toxicity of toxaphene” (MATT), involving participants from The Netherlands, Ireland, Norway and Germany, began in 1997. Analytical methodology, concentration information and statistical interpretation of results for three indicator congeners, CHB’s 26, 50 and 62, are presented. Data from 55 samples, covering 18 different fish species, from Irish waters are documented. Concentrations were lowest in shellfish and in fish species having low lipid content and were highest in medium/high lipid species. Males from a number of fish species were shown to contain significantly higher concentrations than observed in female fish. Overall no samples were shown to exceed existing German MRL or Canadian TDI recommendations., Funder: Marine Institute

The Marine Institute sample a range of finfish species landed at major Irish ports on an annual basis, in accordance with the monitoring requirements of various European legislation designed to ensure food safety. During 2001, a total of 44 samples from 20 different species of finfish were collected from six major Irish fishing ports and analysed for total mercury concentration in the edible tissue. The concentration of mercury ranged from less than the limit of quantitation (0.03 mg/kg wet weight) to 0.42 mg/kg wet weight with a mean and median of 0.09 and 0.07 mg/kg respectively. These levels are within the maximum limit of 0.50 mg/kg wet weight for mercury in fishery products set by the EC (1 mg/kg for selected species). This survey confirms previous studies, which show that Irish seafood is effectively free from mercury contamination. Selected samples were also analysed for other trace metals and chlorinated hydrocarbons. Overall, the levels of lead and cadmium detected in the edible portion of the fish were low and well within the standard values of 0.20 and 0.05 mg/kg wet weight respectively, set by the EU. There are no internationally agreed standards or guidelines available for the remaining trace metals and chlorinated hydrocarbons in fishery products. Therefore results are compared with the strictest standard or guidance value for fish tissue, which are applied by contracting parties to the OSPAR Convention. The levels of these additional contaminants are well below the strictest values listed., Funder: Marine Institute

Winter nutrient concentrations in the western Irish Sea have been monitored annually from 1990 to 2000. Surface samples have been taken between Dundalk Bay and Carnsore Point and analysed for total oxidised nitrogen (TOxN), ortho-phosphate (ortho-P), silicate and salinity. More recently monitoring has been extended into the Celtic Sea. Data from this monitoring programme are presented in detail, along with comparisons to existing data sets. The spatial distribution of nutrients and salinity are presented for each year in contour or classed plots (depending on sample coverage for the particular year). Salinity values were representative of those expected in the Irish Sea and TOxN, ortho-P and silicate values were in general agreement with previous studies. A short summary of studies on nutrient levels in estuaries on the western Irish Sea is presented. In addition, riverine input data supplied by the Environmental Protection Agency (EPA) is used to evaluate the relative magnitude of nutrient inputs from riverine and oceanic sources. Nutrient concentrations are considered using an ecological quality objectives (EcoQOs) approach, proposed as part of the Oslo Paris Convention’s (OSPAR) ‘Common Procedure for Identification of the Eutrophication Status of the Maritime Area’, in partial consideration of the trophic status of the western Irish Sea. Although there is evidence for nutrient enrichment in some estuarine waters and possibly to a lesser extent in some coastal waters, there is little evidence for generally elevated nutrient levels in coastal and offshore waters in the western Irish Sea. Salinity regression curves were calculated for TOxN and ortho-P values in order to generate salinity-normalised concentrations for trend determinations. Regression and trend analysis were carried out on the sample area as a whole and also on regions defining the north, mid, and south western Irish Sea. Trend analysis has been performed, based on nutrient-salinity regressions, using Trend-Y-Tector. A decrease in TOxN over the study period (ranging from 4 to13%) is observed in all regions analysed with the exception of the south west Irish Sea, where a 5% increase was indicated. Analysis of trends in ortho-P concentration showing decreasing trends ranging from 20 to 33%. On visual examination, trends in TOxN are not as intuitively apparent as trends in ortho-P concentrations, therefore it may not be prudent to draw conclusions from them at this stage. Trend analysis of riverine inputs shows an increase in TOxN by 17% and no apparent trend in ortho-P levels. These trends are not consistent with trends observed in the Irish Sea. On the basis of this assessment, it is recommended that this monitoring be continued. The design of future nutrient monitoring surveys is considered, with a view to improving the efficacy of the monitoring regime., Funder: Marine Institute

This paper gives a summary of previously published results of studies on the dispersal of oxytetracycline from the vicinity of a typical salmon farm. These studies showed the environmental impact of occasional treatments to be negligible. Concentrations of oxytetracycline (OTC) were measured in the benthic sediments and in mussel Mytilus edulis sampled in the vicinity of an inshore salmon farm on the west coast of Ireland. Concentrations between 1.0 μg/g and 14.7 μg/g were observed in sediments within 120 m from the farm. Concentrations declined exponentially with time, reaching low levels after 32 days and reduced to traces at 66 days. The highest concentrations were observed in the top 2 cm of sediment, falling to trace levels at a depth of 10 cm. The half-life of OTC persistence in mussels was found to be approximately 2 days. Residues in unpolluted sediment beneath the cages were never present in high concentrations and were flushed out rapidly. In the presence of excessive quantities of unconsumed food pellets on the seabed and in anoxic sediment, the persistence of OTC was significantly prolonged. Monitoring the quality of the sediment could therefore provide adequate indication of any risk of accumulation of antibiotic, without the need for elaborate chemical analyses. Residues in sediment, invertebrates and salmon could account for not more than 1.3% of total input of OTC. It was concluded that the antibiotic was very rapidly dispersed in the environment and its use in salmon therapy posed no material risk to human or environmental health., Funder: Marine Institute

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, the Marine Institute collected water and shellfish samples from major shellfish growing areas and analysed for physicochemical parameters, trace metal levels and chlorinated hydrocarbon concentrations. Since, with the exception of mercury, there are no currently applicable European standards for the concentration of these contaminants in shellfish, the levels were compared with the available standards and guidance values for human consumption, as compiled by the Oslo and Paris Commission (OSPAR) countries. 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 cadmium in oyster tissue, which was slightly elevated in the 1999 samples from Clew Bay, Inner Tralee Bay, Aughinish Limerick and Kilkieran. However these levels did not exceed the Dutch human consumption standard value or the EU maximum limit of 1.0 mg/kg wet weight due to apply from 2002. This survey confirms previous studies which show Irish shellfish products are effectively free from trace metal and chlorinated hydrocarbon contamination., Funder: Marine Institute

A programme monitoring water quality was carried out at 11 sites in Kilkieran Bay, Co. Galway from 1984 to the 1998, for the most part. Continuous monthly readings were recorded at 5 of these sites. Three sites were sampled for temperature, salinity, nitrate, nitrite and phosphate. Three replicate samples were taken at each sampling event. While salinity remained relatively stable throughout, temperature varied considerably between winter and summer months (e.g. Lettercallow, 3.5-18.5ºC), at each of the sites. Nutrient levels were highest in winter months at all sites. The innermost sites tended to have lower salinities and lower nutrient levels. However, there were no statistical differences in nutrient levels among the sites and from year to year. These findings suggest that there was no appreciable increase (or decrease) in nutrient loading within Kilkieran Bay. It is recommended that sampling within the bay is defined according to the broad geographic regions outlined and that intensive sampling was not necessary., Funder: Marine Institute