• Bivalve aquaculture and exotic species: a review of ecological considerations and management issues

      McKindsey, C.W.; Landry, T.; O'Beirn, F.X.; Davies, I.M. (National Shellfisheries Association, 2007)
      Bivalves have been grown and transported for culture for hundreds of years and the introduction of some species outside of their native range for aquaculture has been suggested to be one of the greatest modes of introduction of exotic marine species. However, there has yet to be a thorough assessment of the importance of aquaculture and bivalve culture in particular, to the introduction and spread of exotic species. This paper reviews some of the environmental and ecological implications of the relationship between bivalve aquaculture and the introduction and spread of exotic species, management implications and mitigation strategies. Two broad classes of introductions of exotic species may result from activities associated with bivalve aquaculture. First, the intentional introduction of exotic species into an area for aquaculture purposes, i.e. the ‘‘target’’ species. These are typically foundation or engineering species and may have a considerable influence on receiving ecosystems. Second, the introduction of species that are either associated with introduced bivalves or facilitated by aquaculture activities (i.e. structures or husbandry practices). These may include both ‘‘hitchhiking’’ species (organisms that grow in association with or may be transferred with cultured bivalves) and disease causing organisms.Management options should include the use of risk assessments prior to transfers and quarantines. Various types of mitigation for exotic species have been evaluated but are generally not very successful. Because the risk of exotic species to ecosystems and the bivalve farming industry itself may be great, effort should be directed to better predict and halt introductions of potentially harmful species.
    • Characterisation of norovirus contamination in an Irish shellfishery using real-time RT-qPCR and sequencing analysis

      Rajko-Nenow, Paulina; Keaveney, Sinéad; Flannery, John; O'Flaherty, Vincent; Doré, William (Elsevier, 2012)
      Norovirus (NoV) is the single most important agent of foodborne viral gastroenteritis worldwide. Bivalve shellfish, such as oysters, grown in areas contaminated with human faecal waste may become contaminated with human pathogens including NoV. A study was undertaken to investigate NoV contamination in oysters (Crassostrea gigas) from a shellfishery over a 24 month period from October 2007 to September 2009. Oyster samples were collected monthly from a commercial shellfish harvest area classified as category B under EU regulations, but that had had been closed for commercial harvesting due to its previous association with NoV outbreaks. Real-time reverse transcription quantitative PCR (RT-qPCR) was used to determine the concentration of human NoV genogroups I and II (GI and GII) in monthly samples. Total NoV (GI and GII) concentrations in NoV positive oysters ranged from 97 to 20,080 genome copies g− 1 of digestive tissue and displayed a strong seasonal trend with greater concentrations occurring during the winter months. While NoV GII concentrations detected in oysters during both years were similar, NoV GI concentrations were significantly greater in oysters during the winter of 2008/09 than during the winter of 2007/08. To examine the NoV genotypes present in oyster samples, sequence analysis of nested RT-PCR products was undertaken. Although NoV GII.4 is responsible for the vast majority of reports of outbreaks in the community, multiple NoV genotypes were identified in oysters during this study: GI.4, GI.3, GI.2, GII.4, GII.b, GII.2, GII.12, and GII.e. NoV GI.4 was the most frequently detected genotype throughout the study period and was detected in 88.9% of positive samples, this was followed by GII.4 (43.7%) and GII.b (37.5%). This data demonstrates the diversity of NoV genotypes that can be present in sewage contaminated shellfish and that a disproportionate number of non-NoV GII.4 genotypes can be found in environmental samples compared to the number of recorded human infections associated with non-NoV GII.4 genotypes.
    • Concentration of norovirus during wastewater treatment and its impact on oyster contamination

      Flannery, John; Keaveney, Sinéad; Rajko-Nenow, Paulina; O’Flaherty, Vincent; Doré, William (American Society for Microbiology, 2012)
      Concentrations of E. coli, FRNA bacteriophage, norovirus genogroup I (NoV GI) and II (NoV GII) in wastewater were monitored weekly over a one-year period at a wastewater treatment plant (WWTP) providing secondary treatment. A total of 49 samples of influent, primary and secondary-treated wastewater were analyzed. Using a real-time RT-qPCR, mean NoV GI and NoV GII concentrations detected in effluent wastewater were 2.53 and 2.63 log10 virus genome copies 100 ml-1 respectively. Mean NoV concentrations in wastewater during the winter period (January to March inclusive) (n=12) were 0.82 (NoV GI) and 1.41 (NoV GII) log units greater than mean concentrations for the rest of the year (n=37). The mean reduction of NoV GI and GII during treatment was 0.80 and 0.92 log units respectively with no significant difference detected in the extent of NoV reductions due to season. No seasonal trend was detected in the concentrations of E. coli or FRNA bacteriophage in wastewater influent and showed mean reductions of 1.49 and 2.13 log units respectively. Mean concentrations of 3.56 and 3.72 log10 virus genome copies 100 ml-1 for NoV GI and GII respectively were detected in oysters sampled adjacent to the WWTP discharge. A strong seasonal trend was observed and concentrations of NoV GI and GII detected in oyster were correlated with concentrations detected in the wastewater effluent. No seasonal difference was detected in concentrations of E. coli or FRNA bacteriophage detected in oysters.
    • Cork Harbour PSP incident

      Doyle, J.; Dunne, T. (1985)
      Gonyaulax tamarensis is one of the principle organisms involved in Paralytic Shellfish Poisoning in Europe and North America. P.S.P. has not been described in Irish waters with the exception of one incidence in Belfast Lough and also in Kerry in the late 1800s, although this cannot be verified. G. tamarensis has only been recorded in Irish waters as individual organisms and no bloom has been described up to this.
    • Creating a weekly Harmful Algal Bloom bulletin

      Leadbetter, A.; Silke, J.; Cusack, C. (Marine Institute, 2018)
      This document describes the procedural steps in creating an information product focused on toxic and harmful phytoplankton. The product is an online Harmful Algal Bloom (HAB) bulletin for aquaculturists, who can face serious operational challenges in the days after a HAB event. Data from satellite, numerical hydrodynamic models and In-situ ocean observations are organised and presented into visual information products. These products are enhanced through local expert evaluation and their interpretation is summarised in the bulletin. This document aims to provide both process overviews (the “what” of the Best Practice in producing the bulletins) and detail procedures (the “how” of the Best Practice”) so that the bulletins may be replicated in other geographic regions.
    • Culture of surfclams Spisula solidissima sp., in coastal Georgia: nursery culture

      O'Beirn, F.X.; Walker, R.L.; Hurley, D.H.; Moroney, D.A. (National Shellfisheries Association, 1997)
      Growth of the Atlantic surfclam, Spisula solidissima solidissima, was compared with that of the southern Atlantic surfclam, Spisula solidissima similis. All experimental animals were reared in upweller units at 20°C and fed cultured algae on a daily basis. Over the 14 wk of the study, the Atlantic surf clams grew markedly better (8.9-mm increase in shell length and a 1,103% increase in biomass) than the southern Atlantic surfclams (6.6-mm increase in shell length and 573% mcrease in biomass). Mortality for both groups was negligible. The mean shell lengths attained for the Atlantic surfclams (15.3 mm) and the southern Atlantic surfclams (13 mm) at the conclusion of the study were large enough to ensure good growth and survival on relocation to a field growout environment. The growth patterns obtained under similm growth conditions further highlight some basic life history differences between these subspecies, which were apparent from other studies.
    • 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.
    • 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.
    • Developments in analysis and toxicology of toxaphene compounds

      de Geus, H-J.; Besselink, H.; Brouwer, A.; Klungsøyr, J.; MacGovern, E.; MacHugh, B.; Nixon, E.; Rimkus, G.G.; Wester, P.G.; de Boer, J. (1998)
      Over the last 50 years toxaphene has been produced and used as a pesticide extensively. The US Environmental Protection Agency banned it in 1982. In the early 1990s the presence of toxaphene in marine fish in Europe caused concern with regard to human health in relation with consumption. This paper gives a brief overview of recent developments in the analytical and toxicological research on toxaphene.
    • Dinoflagellate cysts in Irish coastal sediments - a preliminary report

      O'Mahony, J.H.; Silke, J. (1993)
      Since the mid 1970's the production of bivalve shellfish in Ireland has increased annually to a present level of some 17,000 tonnes. Several problems limit the continued expansion of the industry, most notably the problem of natural biotoxins. These toxins are accumulated in the product by the ingestion of toxic phytoplankton. This causes no obvious ill effects to the shellfish themselves but upon consumption may be transferred to human or other vertebrate consumers causing illness and sometimes death. In Ireland the most common of the toxins are those associated with Diarrhetic Shellfish Poisoning (DSP) which causes diarrhoea. Other more serious toxins which to date have not been confirmed in Ireland are those associated with Paralytic Shellfish Poisoning (PSP) which causes paralysis or even death and Amnesic Shellfish Poisoning (ASP) which causes short term memory loss. Of the phytoplankton species which can result in toxicity, under both bloom and non bloom conditions, the dinoflagellates play an important role. Many of these dinoflagellates have been shown to include a dormant benthic cyst stage in their life cycle. Therefore a better understanding of the dynamics of toxic events may be obtained by studying the distribution and abundance of benthic cysts. There is growing international concern about the transport of harmful aquatic organisms, including cysts, into new areas via the discharge of ships ballast water. Also, as a result of EC directive 91/67/EEC permitting the free movement of shellfish between EU member states there is now increasing concern in Ireland that harmful cysts may be introduced with shipments of imported shellfish. Little research has been carried out on the distribution of dinoflagellate cysts in Irish marine sediments. In this paper preliminary results of a study designed to map the distribution and undertake taxonomic studies on dinoflagellate and other cysts in Ireland are presented and discussed. Also presented are the results of the examination of cysts associated with imported shellfish.
    • The dinophycean genus Azadinium and related species – morphological and molecular characterization, biogeography, and toxins

      Tillmann, U.; Elbrächter, M.; Gottschling, M.; Gu, H.; Jeong, H.J.; Krock, B.; Nézan, E.; Potvin, E.; Salas, R.; Soehner, S. (International Society for the Study of Harmful Algae, 2014)
      Azaspiracids (AZAs) are the most recently discovered group of lipophilic marine biotoxins of microalgal origin. It took about twelve years from the first human poisoning event until a culprit for AZA production was unambiguously identified and described as a novel species, Azadinium spinosum, within a newly created genus. Since then, knowledge on the genus has increased considerably, and an update on the current circumscription of the genus is presented here including various aspects of morphology, phylogeny, biogeography, and toxin production. There are currently five described species: A. spinosum, A. obesum, A. poporum, A. caudatum, and A. polongum. As indicated by molecular sequence variation detected in field samples, there are probably more species to recognize. Moreover, Amphidoma languida has been described recently, and this species is the closest relative of Azadinium based on both molecular and morphological data. Amphidoma and Azadinium are now grouped in the family Amphidomataceae, which forms an independent lineage among other monophyletic major groups of dinophytes. Initially, azaspiracids have been detected in A. spinosum only, but AZA production within the Amphidomataceae appears complex and diverse: A new type of azaspiracid, with a number of structural variants, has been detected in A. poporum and Amphidoma languida, and AZA-2 has now been detected in Chinese strains of A. poporum.
    • Dinophysis species in Irish waters 1990 - 1993

      Jackson, D.; Silke, J. (ICES, 1993)
      The distribution and abundance of Dinophysis species as recorded in the national phytoplankton monitoring programme are described. An apparent spread in the occurrence of Dinophysis to the west coast of Ireland is reported. The lack of correlation between the concentrations of Dinophysis in the water and DSP toxicity in shellfish is reported on and discussed.
    • An ecosystem-based approach and management framework for the integrated evaluation of bivalve aquaculture impacts

      Cranford, P.J.; Kamermans, P.; Krause, G.; Mazurié, J.; Buck, B.H.; Dolmer, P.; Fraser, D.; Van Nieuwenhove, K.; O'Beirn, F.X.; Sanchez-Mata, A.; et al. (Inter Research, 2012)
      An ecosystem-based approach to bivalve aquaculture management is a strategy for the integration of aquaculture within the wider ecosystem, including human aspects, in such a way that it promotes sustainable development, equity, and resilience of ecosystems. Given the linkage between social and ecological systems, marine regulators require an ecosystem-based decision framework that structures and integrates the relationships between these systems and facilitates communication of aquaculture–environment interactions and policy-related developments and decisions. The Drivers-Pressures-State Change-Impact-Response (DPSIR) management framework incorporates the connectivity between human and ecological issues and would permit available performance indicators to be identified and organized in a manner that facilitates different regulatory needs. Suitable performance indicators and modeling approaches, which are used to assess DPSIR framework components, are reviewed with a focus on the key environmental issues associated with bivalve farming. Indicator selection criteria are provided to facilitate constraining the number of indicators within the management framework. It is recommended that an ecosystem-based approach for bivalve aquaculture be based on a tiered indicator monitoring system that is structured on the principle that increased environmental risk requires increased monitoring effort. More than 1 threshold for each indicator would permit implementation of predetermined impact prevention and mitigation measures prior to reaching an unacceptable ecological state. We provide an example of a tiered monitoring program that would communicate knowledge to decision-makers on ecosystem State Change and Impact components of the DPSIR framework.
    • Embryonic and larval development of Spisula solidissima similis (Say, 1822) (Bivalvia: Mactridae)

      Walker, R.L.; O'Beirn, F.X. (California Malacozoological Society, 1996)
      Larvae of the southern surf clam, Spisula solidissima similis (Say, 1822), were reared in the laboratory at a salinity of 25 ppt and a temperature of 20-22°C through the embryonic and early larval development period. Unfertilized eggs averaged 58.5 ± 0.32 (SE) μm, with the size-frequency of eggs being normal. First polar body was observed 22 minutes after fertilization with 50% of eggs exhibiting polar bodies after 26 minutes. Ciliated blastula and trochophore stages occurred at 6 hours and 16.8 hours, respectively. Straight-hinge veligers appeared 39.2 hours after fertilization. Larvae grew to a mean size of 172 μmin the pediveliger phase (range 119 to 212 μm). Larvae were exhibiting active foot-probing by day 8 and continued to do so until day 13 when the cultures suffered heavy mortalities. Early life-history traits of Spisula solidissima similis larvae are compared to those for Spisula solidissima solidissima and Spisula sachalinensis.
    • Enhancement of subtidal eastern oyster, Crassostrea virginica, recruitment using mesh bag enclosures

      O'Beirn, F.X.; Walker, R.L.; Heffernan, P.B. (National Shellfisheries Association, 1996)
      Eastern oysters, Crassostrea virginica, in the southeastern United States are found predominantly in the intertidal zone. In this study, mesh bags (3 and 6 mm) were deployed over collecting frames, and the patterns of oyster settlement on these collectors were compared against unmeshed controls at three tidal heights (intertidal, low water, and subtidal) over three sampling regimes (biweekly, monthly, and seasonal) at two sites. Within the biweekly sampling regime, the meshed collectors and controls had similar patterns of settlement at the respective tidal heights. For monthly samplers, mesh treatments maintained higher settlement subtidally whereas controls had highest settlement on the collectors at mean low-water level. Controls had highest recruitment intertidally for seasonal collectors, whereas mesh treatments had higher recruitment lower in the intertidal zone. Conclusions from this experiment were that the use of mesh-covered collectors enhanced subtidal oyster recruitment. Causes of observed increases in subtidal settlement in mesh collectors over unmeshed controls over time could be the result of a combination of factors: predator exclusion, larval entrainment, or reduced desiccation, which seemed to overcome the detrimental effects of increased fouling, resulting in reduced flow and possible hypoxic conditions within the mesh bags. Given the degree of recruitment and the sizes of the recruits attained within the mesh bags, the use of these methods to attain juveniles for commercial purposes would appear to be both feasible and viable, particularly for long periods (up to 6 1110) of deployment.
    • Environmental factors associated with invasion: modeling occurrence data from a coordinated sampling programme for Pacific oysters

      Kochmann, J.; O’Beirn, F.X.; Yearsley, J.; Crowe, T.P. (Springer Netherlands, 2013)
      Documenting establishment and spread of invasive species requires extensive co-ordinated sampling programmes. Identifying the factors promoting or inhibiting local establishment of an invasive species can improve capacity to predict further spread and underpin strategies to limit spread. Here, a structured sampling programme was used to assess the current distribution of feral populations of Pacific oysters, Crassostrea gigas, in Ireland. Sixty-nine sites were sampled using a standardised protocol combining semi-quantitative and quantitative approaches. Sites were chosen to represent variation in proximity to aquaculture and a range of environmental variables. Oyster populations were found at 18 locations, with densities ranging from single individuals to nine individuals per m2. The broad size range of oysters found is indicative of more than one recruitment event. Logistic regression indicated that feral oysters were positively associated with the presence of hard substrata or biogenic reef, long residence times of embayments and large intertidal areas. There was also a tendency for oysters to occur disproportionately in bays with aquaculture, but >500 m from it. Small-scale analysis within sites showed that oysters were almost exclusively attached to hard substrata and mussel shell. The approach taken here provides a rigorous repeatable methodology for future monitoring and a detailed basis for the prediction of further spread.
    • Environmental occurrence, analysis, and toxicology of toxaphene compounds

      de Geus, H.-J.; Besselink, H.; Brouwer, A.; Klungsøyr, J.; McHugh, B.; Nixon, E.; Rimkus, G.G.; Wester, P.G.; de Boer, J. (1999)
      Toxaphene production, in quantities similar to those of polychlorinated biphenyls, has resulted in high toxaphene levels in fish from the Great Lakes and in Arctic marine mammals (up to 10 and 16 microg g-1 lipid). Because of the large variabiliity in total toxaphene data, few reliable conclusions can be drawn about trends or geographic differences in toxaphene concentrations. New developments in mass spectrometric detection using either negative chemical ionization or electron impact modes as well as in multidimensional gas chromatography have recently led researchers to suggest congener-specific approaches. Several nomenclature systems have been developed for toxaphene compounds. Although all systems have specific advantages and limitations, it is suggested that an international body, such as the International Union of Pure and Applied Chemistry, make an attempt to obtain uniformity in the literature. Toxicologic information on individual chlorobornanes is scarce, but some reports have recently appeared. Neurotoxic effects of toxaphene exposure such as those on behavior and learning have been reported. Technical toxaphene and some individual congeners were found to be weakly estrogenic in in vitro test systems; no evidence for endocrine effects in vivo has been reported. In vitro studies show technical toxaphene and toxaphene congeners to be mutagenic. However, in vivo studies have not shown genotoxicity; therefore, a nongenotoxic mechanism is proposed. Nevertheless, toxaphene is believed to present a potential carcinogenic risk to humans. Until now, only Germany has established a legal tolerance level for toxaphene--0.1 mg kg-1 wet weight for fish.
    • Establishing boundary classes for the classification of UK marine waters using phytoplankton communities

      Devlin, M.; Best, M.; Coates, D.; Bresnan, E.; O'Boyle, S.; Parke, R.; Silke, J.; Cusack, C.; Skeats, J. (Elsevier, 2007)
      This paper presents a description of three of the proposed phytoplankton indices under investigation as part of a classification framework for UK and ROI marine waters. The three indices proposed for the classification process are (i) phytoplankton biomass measured as chlorophyll, (ii) the frequency of elevated phytoplankton counts measuring individual species and total cell counts and (iii) seasonal progression of phytoplankton functional groups through the year. Phytoplankton biomass is calculated by a 90th percentile measurement of chlorophyll over the growing season (April to September) compared to a predetermined reference value. Calculation of functional groups and cell counts are taken as proportional counts derived from the presence of the indicator species or group as compared to the total phytoplankton count. Initial boundary conditions for the assessment of high/good status were tested for each index. Chlorophyll reference conditions were taken from thresholds developed for previous EU directives with the setting of offshore concentrations as a reference condition. Thresholds for elevated counts of phytoplankton taxa were taken from previous EU assessments describing counts that could be impact negatively on the environment. Reference seasonal growth curves are established using phytoplankton counts from ‘‘high status’’ waterbodies. To test the preliminary boundaries for each index, a risk assessment integrating nutrient enrichment and susceptibility for coastal and transitional waters was carried out to identify WFD waterbodies in England and Wales at different levels of risk. Waterbodies assessed as having low or medium risk from nutrient enrichment were identified as type 1 and type 2 waterbodies, and waterbodies assessed as high risk were identified as type 3 waterbodies. Phytoplankton data was extracted from the risk assigned waterbodies and applied to each phytoplankton index to test the robustness of the preliminary classification ranges for each phytoplankton index.