• Effective use of ecosystem and biological knowledge in fisheries

      Rivot, E.; Massiot-Granier, F.; Pulkkinen, H.; Chaput, C.; Mäntyniemi, S.; Pakarinen, T.; Prévost, E.; White, J.; Romakkaniemi, A. (2013)
      North Atlantic (NA) stock assessments address the marine phase, estimating returns to home waters, with Pre-Fishery Abundance (PFA) estimated through raising of national (or regional) annual catches by exploitation rates and attributing unreported catch and natural mortality ranges in Monte Carlo simulations. Baltic stocks in contrast, are estimated through integrated Bayesian life cycle state-space models including riverine and sea phases (Michielsens et al., 2008). There is presently no interaction between the two methodologies.We detail the two approaches specifying similarities in biology, as a prerequisite to their harmonization for parallel inference and risk analysis, independent of scales, available data and management objectives. Through aggregations of scale and availability, assimilations of data differ. For the Baltic much is performed within the forecasting framework, and while aggregations in the NA case are disparate, finer scale details are available. In the Baltic a scale of “river” is used as the geographical unit, while in the NA, 3 geo-regions are treated independently, each operating at arbitrary regional scales. To harmonize NA and Baltic approaches, a multi-scale integrated life cycle model in a Hierarchical Bayesian Modelling (HBM) framework is proposed for the NA to capture inherent complexities from mixing of life cycle age and stage cohorts, which is currently not addressed. A stage-structured life cycle approach is proposed, incorporating freshwater and marine phase variability of life histories (survival and life history choices) and auto-regenerated cohort dynamics. This represents a large change in both the modelling and statistical inference framework.Key structural hypotheses and common informative prior distributions for modelling demographic processes, for both NA and Baltic models are developed. Together with the Bayesian methodology these form the core of the harmonization process. To harmonize modelling of the demographic process the following items are necessary:  State-space representation of all life stages including those not directly observed to explicitly separate out modeling of the demographic and observation processes, so as the harmonization of the models for the core ecological process can be thought independently from the data availability.  Age/stage-based demographic models to integrate biological and ecological knowledge of population dynamics, characterized by seaward migrations of smolts and spawning migration of adults back to freshwater, accommodating intra- and inter-population variability in life history traits.  Probabilistic demographic transitions and between-years variability of certain parameters to capture both environmental and demographic stochasticity.  Variable egg to juvenile density-dependent average survival, of classical survival functions.  Common approach to forecast yearly variations of marine post-smolts survival.
    • Effects of cooking and heat treatment on concentration and tissue distribution of okadaic acid and dinophysistoxin-2 in mussels (Mytilus edulis)

      McCarron, P; Kilcoyne, J; Hess, P (Elsevier, 2008)
      Using high performance liquid chromatography with mass spectrometry the influence of conventional steaming and other heat treatments on the level of azaspiracids, okadaic acid and dinophysistoxin-2 in mussels (Mytilus edulis) was investigated. A prior study looking at the influence of steaming on the concentration and distribution of azaspiracids showed significant increases in concentration as a result. Described is a follow-up study using two separate mussel samples, where the contribution of water loss during steaming to increases of toxin levels was examined. In addition to water loss it was demonstrated that heating of fresh azaspiracid contaminated mussels resulted in significant increases in the quantity of the desmethyl analogue (azaspiracid-3) measured. A systematic heat treatment experiment confirmed these findings and showed that azaspiracid-3 was the most thermally instable of the three regulated azaspiracid analogues. In parallel, the same studies were carried out for okadaic acid and dinophysistoxin-2 also naturally present in the samples used. Concentration increases correlated with water loss during steaming. More so than for azaspiracids, increased distribution of okadaic acid and dinophysistoxin-2 from the digestive glands to the remainder tissues was observed as a result of the processes examined. This suggests that analysis of whole flesh tissues, as opposed to dissected digestive glands, is more appropriate for regulatory purposes, particularly if cooked samples are being analysed. The findings of the studies reported here have importance in terms of the methodology applied in regulatory phycotoxin monitoring programmes. Therefore, options for sample pre-treatment are discussed.
    • The effects of drainage on the flora and fauna of a tributary of the River Boyne

      McCarthy, D T (Department of Agriculture and Fisheries (Fisheries Division), 1975)
      Arterial drainage helps in the process of land reclamation by lowering the level of the existing river bed and allowing the ground water to run off more quickly. In recent years the Rivers Corrib, Dee-Glyde, and Moy have been drained. The effects of drainage on the fish stocks and the invertebrate fauna of the River Moy have been described by Toner, 0'Riordan and Twomey (1965). In 1968 investigations commenced into the effects of drainage on the invertebrate fauna and flora as well as fish stocks in the Trimblestown, or Athboy, River, a tributary of the River Boyne. The Boyne rises 6.4 km from Edenderry and flows north-east for 112 km to the sea at Drogheda. It has fifteen tributary streams and two lakes in its catchment area of 2,693 square km. A section of the Trimblestovn River which rises at the foot of Slieve na Calligh, Co Westmesth and flows south-east for 35 km to meet the Boyne at the town of Trim was selected. Its shallowness and accessibility made it particularly suitable for the study. The study area 4.8km north of Athboy town, was 146 metres long and averaged 6.1 metres wide. The river flows for its entire length over Carboniferous limestone end the bed of the river consists of gavel and sandy silt, with scattered boulders and some mud in the quieter areas. There are a few pools in this section, the river being composed of riffle areas alternating with flats. The normal flow at this point was 0.77 cubic metres per second, the pH was 7.6 and the alkalinity as CaCo3 was 310 p.p.m. From 1968 and 1970, 57 invertebrate fauna samples from standard areas (0.093 sq.m) were taken with a suber stream bottom sampler. The plant life was mapped and an assessment of the fish population was made, by the depletion method.
    • The Effects of Drainage on the Trimblestown River

      McCarthy, D. T. (Department of Agriculture and Fisheries [Fisheries Division], 1977)
      The effects of arterial drainage on the macro-invertebrates and flora of a salmon nursery stream are described. A section of the Trimblestown River, Co. Meath was sampled from 1968 to 1974. In drainage operations of this kind the substratum where insect life predominates is removed, also fish and salmonid ova and fry life is affected by mechanical disturbance. A Surber stream-bottom sampler covering an area of 1 square ft (O.093m2) was used to take 107 samples. Wet and dry weights of the fauna were determined. A survey of the aquatic flora, pre- and post-drainage is also described. The fauna and flora were seriously depleted after drainage but recovered rapidly both in numbers and biomass a year after drainage was completed. There was an increase in the growth of emergent vegetation after drainage. Filamentous algae and Chara sp. recolonised the bed of the river replacing two submerged species (Fontinalis sp and Rorippa nasturtium) which had been abundant prior to drainage.
    • The effects of growth phase and light intensity on toxin production by Dinophysis acuminata from the northeastern United States

      Tong, M; Kulis, D M; Fux, E; Smith, J L; Hess, P; Zhou, Q; Anderson, D M (Elsevier, 2011)
      For many years, the study of toxic Dinophysis species was primarily restricted to field populations until it was recently demonstrated that some of these organisms can be mixotrophically cultured in the laboratory with the ciliate prey, Myrionecta rubra, which had previously been fed with cryptophytes of the genus Teleaulax and Geminigera. Here we investigated the influence of growth phase and light intensity on the production of diarrhetic shellfish poisoning (DSP) toxins and pectenotoxins (PTXs) in cultures of Dinophysis acuminata from the northeastern United States. The cell toxin content of okadaic acid (OA), dinophysistoxin-1 (DTX1), pectenotoxin-2 (PTX2), and the okadaic acid diol ester (OA-D8) varied significantly with growth phase under all light treatments, at 6 °C. Each toxin quota remained low during middle and late exponential phases, but significantly increased by mid-plateau phase. DTX1 and OA-D8 were variable through plateau phase, while OA and PTX2 significantly decreased as the culture aged. Although maximum toxin content was not achieved until middle plateau phase, the rate of toxin production was generally greatest during exponential growth. The low and relatively constant cellular toxin levels observed during exponential and early-plateau phase indicate a balance between toxin production and growth, whereas in the middle-plateau phase, toxin production continues even though the cells are no longer capable of dividing, leading to higher toxin quotas. Light was required for Dinophysis growth and the production of all toxins, however, there was no significant difference in growth rates or toxin quotas between the higher light treatments ranging from 65 to 300 μmol photons/sq.m/s. These results demonstrate that DSP production in D. acuminate is constitutive, and that specific toxins are differentially produced or accumulated during the cells’ growth phase, possibly in response to changes to their environment.
    • The effects of intertidal oyster (Crassostrea gigas) culture on the spatial distribution of waterbirds

      Gittings, T; O'Donoghue, P.D. (Marine Institute, 2012)
      Atkins was commissioned by the Marine Institute to provide ornithological services in relation to the appropriate assessment of aquaculture and fisheries activities on coastal Special Protecion Areas for birds (SPA's). Intertidal culture of the Pacific Oyster using oyster trestles is widespread in Ireland and occurs in 16 SPAs and the potential impact of this activity on waterbird populations will be an issue in a number of Appropriate Assessments. Therefore, a research programme was designed by Atkins, in consultation with the Marine Institute, to fill this information gap. This research programme included a review of the distribution of intertidal oyster culture in Ireland in relation to coastal Special Areas, and other areas of importance for waterbirds and extensive and intensive studies of the relationship between waterbird distribution and intertidal oyster culture.
    • Effects of temperature and salinity on the survival and development of larval and juvenile Palaemon serratus (Decapoda: Palaemonidae) from Irish waters

      Kelly, Eoghan; Tully, Oliver; Browne, Ronan (Cambridge University Press, 2012)
      The combined effects of temperature and salinity on the survival and development of larval and juvenile Palaemon serratus from the west coast of Ireland were investigated. Survival over time was measured at thirty combinations of temperature and salinity ranging from 10–19°C and 9–34‰ in a fully factorial design. Salinity had a stronger influence than temperature on survival at all larval stages except stage V. For juveniles the main effect changed from temperature between 100 and 200 degree days to salinity between 200 and 600 degree days and temperature between 600 and 800 degree days. Estimates of time taken to 50% mortality showed that juveniles tolerated lower salinities for longer periods and exhibited optimal salinity values which were 3% lower than larvae, at temperatures between 10 and 15°C. Larval stage durations were found to be influenced by temperature but not salinity. Comparison with published data suggests that populations of P. serratus have adapted to local conditions of temperature and salinity. The results presented here have practical implications for fisheries assessment and management, as the incorporation of environmental effects into stock–recruitment models can improve their predictive capacity.
    • Effects of weather-related episodic events in lakes: an analysis based on high-frequency data

      Jennings, Eleanor; Jones, Stuart; Arvola, Lauri; Staehr, Peter A.; Gaiser, Evelyn; Jones, Ian D.; Weathers, Kathleen C.; Weyhenmeyer, Gesa A.; Chiu, Chih-Yu; de Eyto, Elvira (Wiley-Blackwell, 2012)
      Summary 1. Weather-related episodic events are typically unpredictable, and their duration is often short. Abiotic and biological responses are often missed in routine monitoring. These responses are, however, now of particular relevance given projected changes in extreme weather conditions. 2. We present data from high-frequency monitoring stations from lakes in Europe, North America and Asia that illustrate two classes of abiotic effects of weather events: (i) generally short-lived effects of storms on lake thermal structure and (ii) the more prolonged effects of high rainfall events on dissolved organic matter levels and water clarity. We further relate these abiotic effects to changes in dissolved oxygen or in chlorophyll a levels. 3. Three differing causes for weather-related decreases in surface dissolved oxygen levels were observed: (i) entrainment of anoxic water from depth, (ii) reduction in primary productivity and (iii) increased mineralisation of organic carbon delivered from the catchment. 4. The duration of in-lake effects tended to be longer for events driven by weather conditions with a longer return period, that is, conditions that were relatively more severe and less frequent at a site. While the susceptibility of lakes to change was related in part to the severity of the meteorological drivers, the impacts also depended on site-specific factors in some cases. 5. The availability of high-frequency data at these sites provided insight into the capacity of the lakes to absorb current and future pressures. Several of the changes we observed, including increases in carbon availability, decreases in photosynthetically active radiation and increased disturbance, have the capacity to shift lakes towards an increased degree of heterotrophy. The magnitude and direction of any such change will, however, also depend on the magnitude and direction of climate change for a given location and on lake and catchment characteristics.
    • 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.
    • EMFF Offshore Reef Survey, Sensitive Ecosystem Assessment and ROV Exploration of Reef - SeaRover 2018 Cruise Report

      O’Sullivan, D.; Leahy, Y.; Healy, L.; Shipboard Scientific Party (Marine Institute, 2018)
      This report presents preliminary findings of a 2018 offshore reef survey of Ireland’s Northwest continental margin and Rockall Bank. The survey is part of an extensive three year project, beginning 2017, that is coordinated and led by Ireland’s Marine Institute and INFOMAR (Integrated Mapping for the Sustainable Development of Ireland’s Marine Resources) and funded by the European Maritime and Fisheries Fund (EMFF) Marine Biodiversity Scheme and the National Parks and Wildlife Service (NPWS). The objectives of the project are to implement the EMFF’s Marine Biodiversity Scheme - Natura Fisheries by mapping offshore reef habitats with a view to protecting them from deterioration due to fishing pressures. The reef project aligns with sub-article 6.2 of the Habitats Directive (EC 92/43/EEC) which requires member states to take measures to avoid deterioration of protected habitats. The overarching aim is to quantify the abundance and distribution of offshore biogenic and geogenic reef habitat in Irish waters to fulfil Ireland’s legal mandate and to generate baseline data from which appropriate monitoring of Reef habitat within Special Areas of Conservation (SAC) can be established. The initial survey in July 2017 (O’Sullivan et al. 2017) primarily focussed on the Continental margin west and northwest of Ireland. The second survey leg took place in July 2018 aboard the ILV Granuaile. The survey vessel was equipped with the Marine Institute’s remotely operated vehicle (ROV) Holland 1 to observe seabed features and biological associations along the northwest continental shelf and the eastern flank of the Rockall Bank
    • EMFF Offshore Reef Survey, Sensitive Ecosystem Assessment and ROV Exploration of Reef - SeaRover 2019 Cruise Report

      O'Sullivan, D.; Healy, L.; Leahy, Y. (Marine Institute, 2019)
      This report presents preliminary findings of the 2019 offshore reef survey over the Porcupine Seabight and adjacent areas. The survey is the final leg of an extensive three year project, beginning in 2017, that was coordinated and led by Ireland’s Marine Institute and INFOMAR (Integrated Mapping for the Sustainable Development of Ireland’s Marine Resource) and funded by the European Maritime and Fisheries Fund (EMFF) Marine Biodiversity Scheme and the National Parks and Wildlife Service (NPWS).
    • English 5th and 6th Class - Marine Litter and What is in the News (English and Irish version available)

      Marine Institute (Marine Institute., 2014)
      The aim of the lesson plan is for the children to explore new interests and perspectives through reading about the effects of marine litter. The students will continue to develop a range of comprehension strategies to deal with narrative, expository and representational reading materials.
    • English 5th and 6th Class - The Energy Debate (English and Irish version available)

      Marine Institute (Marine Institute., 2014)
      The aim of the lesson plan is for the children to develop cognitive abilities in developing ideas and discuss issues of major concern relating to energy. The students will justify and defend particular opinions or attitudes they have developed and try to persuade others to support a particular point of view.
    • English 5th and 6th Class: Marine TV - An investigative report on the marine science survey aboard the RV Celtic Explorer

      Marine Institute (Marine Institute, 2018)
      The aim of the lesson plan is for the children to learn how to use key media questions: Who? What? Where? When? Why? How? They will work in groups to write a script where they can play different characters aboard the research vessel, allowing them to work collaboratively and use their imaginations.
    • English 5th and 6th Class: Storyboard your own deep sea voyage of discovery

      Marine Institute (Marine Institute, 2018)
      The lesson introduces students to how stories are developed for film. Students will draft a storyboard for a film imagining they are a team of marine scientists embarking on their own underwater voyage of discovery. They will interpret marine and scientific language and through a combination of the real and the imaginary, develop their own storyboard and film.
    • English: 1st and 2nd Class - My Boat Story – Reading activities (English and Irish versions available)

      Marine Institute (Marine Institute., 2014)
      The aim of the lesson plan is for the children to continue to experience the reading process being modelled through receptiveness to language. The children will also engage in shared reading activities.
    • English: 1st and 2nd Class – Soundscapes and the Big Blue Sea (English & Irish version)

      Marine Institute (Marine Institute., 2014)
      The aim of the lesson plan is for the children to develop receptiveness to language by listening to stories and responding to them; listening to sounds and responding to them; and using gestures and movement to extend the meaning of what he/she is saying.
    • English: 3rd and 4th Class - Marine TV and reporting on Marine Pollution (English and Irish version available)

      Marine Institute (Marine Institute., 2014)
      The aim of the lesson plan is for the children to learn how to use key media questions: Who? What? Where? When? Why? How? The children will discuss cause and effect in relation to processes and events and predict possible outcomes. They will also explore reactions to ideas through improvisational drama.
    • English: 3rd and 4th Class –Jigsaw discussions on Ireland’s Mackerel Fishery (English and Irish version available)

      Marine Institute (Marine Institute, 2014)
      The aim of the lesson plan is for the children to develop their reading skills while learning about Ireland’s Mackerel Fishery. The children will learn skimming, scanning, note taking and summarizing. The children will explore non-fiction texts for a variety of purposes. They will also get to use information retrieval techniques in cross curricular settings.
    • English: Juniors and Seniors Infants Class - Ocean Swap Game and Marine Vo-back-ulary

      Marine Institute (Marine Institute., 2014)
      The aim of the lesson plan is for the children to experience, recognise and observe simple oral commands while participating in games relating to marine animals.