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Theses & Dissertations

Recent Submissions

  • Gill disease in finfish aquaculture with emphasis on amoebic gill disease

    Downes, J.K. (Galway-Mayo Institute of Technology, 2017)
    Gill disease is one of the most significant challenges facing global salmon aquaculture and in terms of economic impact; amoebic gill disease (AGD) caused by the free living protozoan Neoparamoeba perurans is perhaps the most destructive. However, gill disease is often multifactorial, with numerous putative pathogens identified as potentially playing a role. AGD was first described in Irish aquaculture in 1995. Between the years 1995 and 2010, there were sporadic and relatively minor outbreaks of AGD. Since the re-emergence of the disease in 2011/2012, greater focus has been placed on gill health. This research aimed to investigate gill disease and in particular the re-emergence of AGD caused by N. perurans in Irish aquaculture. Through this it was hoped to provide the industry with the tools and information to help improve management of gill disease as well as fish health and welfare. With respect to this, Chapter 2 of this thesis details the effort to develop and validate a real-time TaqMan® PCR assay to detect Neoparamoeba perurans in Atlantic salmon gills. Furthermore, it describes the use of this assay to monitor disease progression on a marine Atlantic salmon farm in Ireland in conjunction with gross gill pathology and histopathology. As molecular diagnosis of AGD remains a high priority for much of the international salmon farming industry, Chapter 3 evaluates the suitability of currently available molecular assays in conjunction with the most appropriate non-destructive sampling methodology. In addition it compares this methodology with traditional screening methods of gill scoring and histopathology. Chapter 4 addresses the complex and multifactorial nature of gill disorders. Co-infections are common on farms and there is a lack of knowledge in relation to interactions and synergistic effects of these agents. The advances in molecular diagnostics have made it possible in Chapter 5 to identify N. perurans as the causative agent in the earliest AGD outbreaks. In addition to this, a number of other putative pathogens were also identified in these early cases of gill disease. Finally, Chapter 6 concludes the findings of this research and how they relate to the current knowledge of gill health and welfare.
  • Optimisation of isolation methods for the azaspiracid group of marine biotoxins and the development of accurate and precise methods of analysis

    Kilcoyle, J. (Dublin Institute of Technology, 2015)
    The two main groups of biotoxins which affect the Irish shellfish industry are azaspiracids (AZAs) and the okadaic acid (OA) group (OA, DTX2, DTX1 and their esters) toxins. Since AZAs were first identified in 1998, well over 30 analogues have been reported. Structural and toxicological data have been described for AZA1–5 (isolated from shellfish). LC-MS/MS is the EU reference method for detection of the AZAs (AZA1, -2 and -3) and the OA group toxins in raw shellfish with the regulatory limit set at 160 μg/kg for each toxin group. Limited supplies of purified toxins for certified reference materials (CRMs) were available for AZA1−3. Little knowledge was also available on the relevance of the additional AZA analogues that had been reported, in terms of human health protection. The analysis of marine biotoxins by LC-MS/MS can be severely affected by matrix interferences. Here, a study was performed on two instruments; a quadrapole time of flight (QToF) and a triple stage quadrupole (TSQ) to assess matrix interferences for AZA1 and OA using a number of tissue types. Enhancement was observed for OA on the QToF while matrix suppression was observed for AZA1 on TSQ. The enhancement on the QToF was overcome by use of an on-line SPE method and matrix matched calibrants, while the suppression on the TSQ was found to be due to late eluting compounds from previous injections and was overcome by employing either a column flush method or an alkaline mobile phase.The isolation of 11 AZA analogues (AZA1−10 and 37-epi-AZA1) from shellfish using an improved procedure (7 steps) is described. Recoveries increased ~2-fold (~ 52%) from previously described isolation procedures. The preparative isolation procedure developed for shellfish was optimised for Azadinium spinosum bulk culture extracts such that only four steps were necessary to obtain purified AZA1 and -2. A purification efficiency of ~70% was achieved, and isolation from 1,200 L of culture yielded 9.3 mg of AZA1 and 2.2 mg of AZA2 (purities >95%). This work demonstrated the feasibility of sustainably producing AZA1 and -2 from A. spinosum cultures. In addition to AZA1 and -2, the novel analogues AZA33, -34 were isolated (also from A. spinosum).Sufficient quantities were purified to enable full structural elucidation, the preparation of reference standards and CRMs, and toxicity studies. Nine of these analogues were fully characterised for the first time (Table 7.1). Structural determination was achieved by NMR and chemical analysis, while toxicity was assessed using the Jurkat T lymphocyte cell assay, mouse intraperitoneal (AZA1−3 and -6) and mouse oral (AZA1−3) administration.The preparation of reference standards for the analogues AZA4−10, 37-epi-AZA1, AZA33 and -34 enabled their relevance in terms of human health protection to be determined. The in vitro and in vivo toxicity studies performed confirmed AZA toxicity.The results from the oral and intraperitoneal mice studies correlated very well, contradicting previous reports and showing that AZA1 is more toxic than AZA2 and -3 and that AZA6 is slightly less toxic than AZA1. Analysis of shellfish (Mytilus edulis) submitted to the Irish biotoxin monitoring programme using the reference standards confirmed previous reports showing that levels of AZA3, -4, -6 and -9 increase following cooking due to heat induced decarboxylation of AZA17, -21, -19 and -23. Very high levels of AZA3 (up to 3-fold that of AZA1) and -6 (up to 3- fold that of AZA2) were detected in some samples (with levels varying most likely due to different rates of metabolism and time of harvesting). As the concentrations of AZA3 and -6 are negligible in raw mussels, yet can increase significantly during the cooking of mussels, the overall concentrations are underestimated by methods used according to current legislation. In cooked shellfish the AZA analogues -4, -5, -7–10, as well as AZA33 and -34, comprise on average ~5% of the total AZA content, however in some samples levels of AZA4 were higher than AZA6. Levels of the 37-epimers in the cooked shellfish extracts were ~ 15% that of the parent analogues.
  • The drivers and dynamics of fisher behaviour in Irish fisheries

    Davie, S. (Galway Mayo Institute of Technology, 2013)
    It is widely acknowledged within the scientific community that a single species approach to European mixed fisheries can result in species-specific advice inconsistent with multi-species management objectives. Within the reformed Common Fisheries Policy a move toward mixed fisheries and ecosystem based management is encouraged. The overall objective of this research was to improve understanding of the complex targeting behaviour undertaken by commercial fishers. Whereby, improved understanding will enhance the ability to predict the responses to future mixed fisheries management measures and changing economic conditions within the Irish fishing industry. Irish métiers (groups of homogeneous fishing trips) highlight the complexity of fishing activities within the Irish fleet, having identified 33 otter trawl métiers and 19 in the remainder of the fleet. Métier dynamics identified over compensation to introduced management, resulting in effort displacement and increased temporal specific fishing pressure. Therefore were deemed as appropriate base units for all subsequent analyses. Two economic variables, operational fishing cost and trip landings value, considered to represent important drivers were developed. This lead to application of a general additive model to estimate and predict fuel consumption estimates according to fleet segment definitions. A linear mixed effects model with random vessel effect was developed as a method of standardising value generating an index of value per unit effort. This identified kilowatt fishing days as the most appropriate effort measure. The final investigation stage successfully amalgamated the knowledge gained into the formulation of novel Markov transition probability for a multinomial model to predict fisher métier strategy choice. This is to be incorporated into management strategy evaluation, aiding the assessment and possible impacts of future management proposals on the Irish fleet and commercial stocks around Ireland. Developments presented will benefit the progression toward optimising sustainability within a mixed fisheries approach to management through incorporation of economic considerations.
  • An investigation into the detection and identification of OsHV-1 µvar virus and associated risk factors causing mortalities in Crassostrea gigas in Ireland.

    Morrissey, Teresa (Galway-Mayo Institute of Technology (GMIT), 2014)
    The Oyster Herpes Virus micro variant, OsHV-1μvar, is an emerging disease affecting Crassostrea gigas oysters which has caused significant mortalities in France, Ireland, and the UK (Jersey and Kent, England) between the summer of 2008 and 2012.The present MSc. study was carried out in 2 parts. The first part of the study aimed to characterize and further elucidate the strains of OsHV-1 present in C. gigas oysters sampled in Ireland by further examining sequence data obtained from animals collected from 30 bays during mortality outbreaks between 2003-2012. Part two of this study investigated the detection of OsHV-1 µvar and associated risk factors during mortality outbreaks. The current study provides some insights into mortality events affecting farmed Pacific oyster production in Ireland. The epidemiological study conducted found that batch mortality was lower in 2011, compared with earlier years, in association with lower OsHV-1 µvar viral loads.
  • Passive Sampling for Quality Monitoring of Irish Marine Waters

    White, Philip (Dublin Institute of Technology, 2014)
    This study details the steps involved in fabrication, deployment and retrieval of mainly polydimethyl siloxane (PDMS) passive sampling devices deployed in a number of locations in and around Ireland in an attempt to derive dissolved water concentrations of contaminants in-situ. PDMS samplers were initially deployed in the Burrishoole catchment, Co. Mayo in conjunction with the collection of biological tissues and sediment to investigate the source of elevated dioxins in the catchment. Passive samplers were used to generate dissolved water concentrations of persistent organic pollutants (POPs) and also to successfully screen for the presence of dioxins in the water column. The dioxin profile present was also found in sediment and biological tissue and through statistical profiling potential sources were identified as being possibly related to the use of technical pentachlorophenol in the catchment though no direct evidence was found. Passive samplers (PDMS and SPMD) were then deployed at various depths on the M6 weather buoy, 400 miles off the West Coast of Ireland, in conjunction with temperature and salinity monitors to test how the technology would fare over a long period deployment (585 days) in a harsh, dynamic environment. The PDMS samplers were almost completly lost where the SPMDs last better (80 % recovered). Dissolved water concentrations estimated using both sampler types were found to be very low (<ppb) with polyaromatic hydrocarbons found in higher levels than polychlorinated biphenlys, and organochlorine compounds. The use of statistical analysis suggests that passive samplers can also be used to differentiate different water masses by investigating contaminant loadings at each depth sampled. Finally passive samplers were deployed in various inshore and inland waters across Ireland with the results indicating that the remote West of Ireland had the lowest levels of dissolved water concentrations estimated. Many estuaries and inland water bodies had levels of contaminants higher than the west of Ireland with the heavily industrialised Cork and Dublin sites having the highest levels estimated. The separation of sites based on concentrations found indicated that assessment criteria could be generated in an Irish context (IRef) which could be used to classify a site in relation to ‘background’ levels found in the West of Ireland and at M6. The results generated during this study were then assessed based on various legislative requirements and assessment criteria such as the Water Framework Directive (WFD) and the Oslo Paris convention (OSPAR). Results from the WFD assessment indicate that concentrations found at all sites were below the EQS values set down. However this EQS value is based on total water concentration hence the EQS was modified to a dissolved water concentration basis. This reduced the total water EQS values by up to 80 % for some analytes however in most locations the dissolved water concentrations found were at or below this dissolved water EQS value indicating that the levels of contaminants from across Ireland are below the EQS values generated as part of the WFD. Assessments were also made on the concentrations found across Ireland using background assessment criteria (BAC) suggested by OSPAR. The results indicate that the levels across Ireland are above the BAC for most compounds with the M6 weather buoy faring better. Concentrations from “pristine” Irish sites were then chosen to generate reference criteria on an Irish basis (IRef) which were found to be below the concentration levels suggested as part of the BAC assessment criteria in the majority of locations.
  • Aspects of the biology of three exploited deepwater sharks Centrophorus squamosus, Centroscymnus coelolepis and Deania calceus (Elasmobranchii: Squalidae) from the continental slopes of the Rockall Trough and Porcupine Bank

    Clarke, Maurice (National University of Ireland, 2000)
    Aspects of the biology of three exploited sharks (Elasmobranchii: Squalidae) from the continental slopes of the Rockall Trough and Porcupine Bank (NE Atlantic) were examined using specimens taken during trawl and long-line surveys (December 1995 to December 1999) and commercial samples obtained from trawlers (March 1997 to June 1998). The species under study were Centroscymnus coelolepis, Centrophorus squamosus, and Deania calceus. The entire depth range (300 m – 1,800 m) of each species was sampled. C. squamosus and D. calceus were abundant between 700 m and 900 m. C. coelolepis was more abundant deeper (1,300 m) but gravid females were more abundant in shallower waters. Small specimens of each species were absent from the study area. Trawls and long-lines selected for different size ranges of C. coelolepis and D. calceus, though not C. squamosus. Deepwater bobbin and French high headline trawls did not select for different size ranges of C. coelolepis. Unlike the other species D. calceus is not landed. Discard rates from long-liners exceeded 40 % of total catch depending on depth fished. While percentage discard rates from trawlers were lower, an estimated 745 t of this species were discarded in 1996 alone. Sexual maturity was achieved at large size, more than 75 % of maximum length in each species. No evidence of seasonal cycles in reproduction was found from spermatogenic analysis or the occurrence of maturity stages. Mean ovarian fecundity was low; C. squamosus, 8, C. coelolepis and D. calceus 13. Dorsal spine sections were used for age estimation. Significant positive regressions of spine width and total length were found and the growth rates of first and second spines were not significantly different. Estimates of 21-70 years (C. squamosus) and 11-35 years (D. calceus) were obtained. Agreement within 1 year was found for more than 93 % of D. calceus and 88 % of C. squamosus first and second spines. Empirical and von Bertalanffy growth data suggest that growth had slowed down or ceased before the onset of maturity. Estimates of natural mortality (M) for C. squamosus (0.066 – 0.087) and D. calceus (0.116-0.177) were low. Fishing mortality (F) for D. calceus was estimated to have reached the level of M for females but below M for males. This study suggests that these species have conservative life-history strategies. No management plan currently exists for the multi-species deepwater fishery in the northeast Atlantic. In the absence of suitable abundance indices, stock assessment should be based on known life history parameters of target and by-catch species. Such an approach will facilitate the rational management of the fishery. Correspondance à: Maurice Clarke, Marine Institute, Abbotstown, Dublin 15, République d’Irlande. Aspects de la biologie de trois requins profonds, Centrophorus squamosus, Centroscymnus coelolepis et Deania calceus (Elasmobranchii: Squalidae) du talus continental du Fossé de Rockall et du Banc de Porcupine.
  • The diatom Pseudo-nitzschia (Peragallo) in Irish waters

    Cusack, Caroline K. (National University of Ireland, Galway, 2002)
    The objectives of this study were to: 1. Determine which Pseudo-nitzschia species are present in Irish waters using light microscopy, scanning and transmission electron microscopy; 2. Investigate the hydrographic conditions that relate to the distribution of the genus Pseudo-nitzschia; 3. Determine which species are capable of producing domoic acid in unialgal cultures; 4. Compare SSU and ITS1 and part of the 5.8S ribosomal DNA sequences of Irish Pseudo-nitzschia isolates with available sequences of Pseudo-nitzschia isolates from other geographic regions; 5. Examine the efficacy of existing oligonucleotide probes to aid identification of Pseudo-nitzschia strains in Irish waters.
  • Biological changes in Celtic Sea and southwest of Ireland herring, based on a long-term data archival project

    Lynch, Deirdre (Trinity College Dublin, 2011)
    The herring fishery in the Celtic Sea and Division VIIj has been commercially important for many years. The Marine Institute has been collecting biological data for this herring stock since 1959. This stock is assessed by ICES annually. However, this is the first study of long term biological trends. The biological data consists of total length, weight, sex, maturity and age of the commercial catches. This study looks at mean length and mean weight at age, growth rate, condition factor and maturity ogives from 1959 to 2007. Environmental factors that may explain the biological trends are also investigated. These data consist of sea surface temperature (SST) for the Celtic Sea and the Irish Sea from 1970 to 2004, North Atlantic Oscillation (NAO) indices from 1958 to 2001 and Calanus spp. abundance for the Celtic Sea and Division VIIj from 1958 to 2007. In addition, data from the ICES stock assessment is consulted and this consists of spawning stock biomass (SSB), fishing mortality (F) and recruitment (R) from 1958 to 2008. The results show that mean length and mean weight at age peaked in the 1970s and declined thereafter. It was found that the condition factor over time declined. The results also illustrate that the growth rates were faster in the 1960s and 1970s than in the 1980s and 1990s. It can be seen that maturation for 1 winter ring increased in the early 1970s and has remained at a high level since then. This study looks at possible explanations for the biological trends and found that it was unlikely to be due to fishing mortality or density dependence. There have been changes in the proportions of autumn and winter spawners in this area over time but it is unlikely that this influenced the trends. Evidence suggests that the changes in the biological data over time may be influenced by environmental factors. NAO shows a significant negative correlation with growth rate in length. There is evidence to suggest that increased SST in the Irish Sea and Celtic Sea is associated with reduced size/weight at age and condition. Calanus abundance shows some positive correlations with mean length and mean weight and is a favourable influence on herring growth. These changes in the biology of the stock have implications for its future management. Declining growth results in more individual fish per tonne of landings which exerts a greater fishing mortality than in the past. This study has allowed for a better understanding of the biology of the stock. Biological data has been routinely collected for other herring stocks around Ireland and similar studies should be performed on these herring stocks in the future.
  • Arsenic in Irish marine waters and its potential as a water mass tracer

    Anninou, Pinelopi (National University of Ireland, Galway, 2007)
    Arsenic is a metalloid, met in both reduced (+3) and oxidised (+5) states, in a variety of inorganic and organic compounds. It is naturally and anthropogenically introduced. Globally, anthropogenic loads of arsenic exceed the natural ones. It is highly toxic, especially inorganic arsenic. Its toxicity is due to structural similarities with the essential nutrient phosphate. The phenomenon is natural and known as competitive inhibition. First order speciation between hydride (mostly inorganic) and non-hydride (mostly organic) arsenic took place during this project. An in-house, batch type system of hydride generation, electrothermal atomic absorption spectrometry was used. This study has produced baseline concentrations in aquatic environments (rivers, lakes, mines, coastal, shelf edge, oceanic), mainly from the west coast of Ireland. The measured concentrations fall within normal for seawater (15-20nM) and fresh water (0-5nM). Exceptionally high concentration (~50nM) was observed in the effluent of the Avoca Mines, in Co. Wicklow; low concentrations are restored up and downstream of the mines. Results coupled to phosphate findings, showed biological uptake of arsenic being much slower process than physical mixing of water masses. Mixing of coastal seawater with fresh water of low arsenic resulted in near linear increase in the concentration of hydride arsenic with increasing salinity (rivers Corrib and Shannon plumes). This is reversed at high salinities for a small salinity range, where fronts are formed between mixed coastal and open ocean seawater (Thermal Shelf Edge). It is proposed that enhanced biological activity in the highly active frontal zones removes arsenic from the dissolved phase. In the open ocean the positive distribution is restored to some degree, but overall a wide range of arsenic concentrations characterises different water masses despite the small salinity range. Among water masses, Mediterranean Sea Outflow Water displays great potential of being traced by its distinctive arsenic concentration.
  • Phytoplankton precision trials in the enumeration and identification of marine microalgae through the scheme "Biological Effects Quality Assurance in Monitoring Programmes (BEQUALM)"

    Salas, Rafael Gallardo (2011)
    Scientists are coming under increased pressure in recent years to show that results they obtain arising from their scientific work are quality assured and stand up to scrutiny by independent expert auditors. This has meant that the methodologies used by laboratories involved in making these measurements have to be validated and fit for purpose and has led to the adoption of internationally recognised standard protocols. These protocols must be underpinned by robust quality systems and must be accredited to an international standard. In order for laboratories to become accredited in particular methods, they have to fulfil a series of prerequisites but a compulsory one is the participation in a proficiency testing scheme. Proficiency testing schemes are independent assessor organisations which coordinate regular inter-calibration and intercomparative studies between laboratories with a common purpose. What happens, though when proficiency testing schemes do not exist for a particular scientific measurement? This study presents results from two inter-comparison exercises at European level between phytoplankton monitoring laboratories in the enumeration and identification of marine microalgae using the Utermöhl cell counting method. Microalgae are a very important ecological component of the marine ecosystem and have also become important ecological indicators of hydro-climatic change, ocean acidification and eutrophication. Member states of the European Union are obliged to monitor for toxic and harmful algae which can cause problems and devastation in the natural environment, have detrimental effects on human health if contaminated fish and shellfish are eaten, can cause huge economic losses to the aquaculture industry and impact directly in coastal communities. This study shows how an intercomparison of this kind is designed and organised, how samples are set up, materials homogenised and reference values obtained. It demonstrates the importance of using the right technique and best practice, based on experience, to analyse samples and how important it is to design the exercise to be statistically robust, both quantitatively and qualitatively. The taxonomy quiz in 2009 showed that there was no evidence that video clips were better audit trail tools than images or vice versa. The quantitative measure suggested that there was evidence of good agreement between virtually all the analysts and the reference value for all species except one (P.micans). However, there was evidence of lack of reproducibility between and within laboratories. The qualitative measure calculated indicated that analysts are more likely to identify a toxic organism as a non toxic organism than the other way around. The results from the enumeration data in the 2010 exercise showed that there was lack of reproducibility across laboratories using different counting strategies and volume sub-sampled and analysed. These results when compared to a set of hypothesised means used as reference values suggested that cell counts were potentially underestimated by as much as 30% and that this underestimation was most likely due to test method effects.