• North Western Waters Atlas 3rd Edition

      Dransfeld, L.; Maxwell, H.W.; Moriarty, M.; Nolan, C.; Kelly, E.; Pedreschi, D.; Slattery, N.; Connolly, P. (Marine Institute, 2015)
      The third edition of the North Western Waters (NWW) Atlas is a joint publication between the Marine Institute and the NWW Advisory Council. This Atlas is intended for policy makers, managers and interested stakeholders and aims to provide a broad overview of the ecosystem of the NWW Advisory Council (AC) area. We have tried to make the science as clear and concise as possible, and keep technical language to a minimum. The information has been presented through a blend of text, tables, figures and images. There is a glossary of terms and a list of more detailed scientific references for those interested in following up certain issues. The first and second editions of the Atlas, published in 2009 and 2011 respectively under the MEFEPO project, were extremely well received and this new edition has been modified in response to stakeholder feedback to provide updated information on the physical and chemical features, habitat types, biological features, birds, mammals, fishing activity and other human activities taking place within the NWW region. We have received valuable contributions from non-governmental organisations, which use citizen science to collect information on the marine ecosystem around us. Whenever citizen science is used to complement the existing knowledge, this is clearly marked in the relevant sections. The North Western Waters (NWW) area is situated in the north east Atlantic off the west coast of Ireland and Scotland, and extends into the Celtic Sea, Irish Sea and the English Channel.
    • Northwest Herring Acoustic Survey Cruise Report and Abundance Estimate, 2007

      O'Donnell, C; Egan, A; Lynch, D; Boyd, J; Wall, D; Goddjin, L (Marine Institute, 2007)
      The northwest and west coast herring acoustic survey programme was first implemented in 1994, with the current winter spawning survey representing the 9th in the time series. The stock in this area is composed of 2 spawning components (autumn and winter), covering a large geographical area. Spawning occurs over a protracted period of over 4-months from late September through to late March. The age profile of the survey stock as generated from trawl samples indicated ages ranging from 1-7 years. Maturity samples indicate the largest proportion of the stock to be in a pre-spawning, spawning or spent state, with small amounts of immature fish, as would be expected at this time. The 2007 survey estimate generated a TSB (total stock biomass) of 14,200 t relating to a SSB (spawning stock biomass) of 13,974 t. Poor weather dominated the survey with almost 25% lost in downtime. As a result the survey area and track lines had to be reduced to compensate and hydrographic stations had to be sacrificed. The poor weather experienced no doubt had an impact on herring schooling behaviour and our detection ability.
    • Northwest Herring Acoustic Survey Report 18 June – 07 July, 2011

      Saunders, Ryan; O'Donnell, Ciaran; Campbell, Andrew; Mullins, Eugene; Sullivan, Mairead; McKeogh, Enda (Marine Institute, 2011)
      The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring acoustic survey programme was first established in 1994. Prior to acoustic estimation, a larval survey programme was conducted from 1981-1986. In the early 1990s, the ICES herring working group (HAWG) identified the need for a dedicated herring acoustic survey in this area (Anon, 1994). From 1994 to 1996 surveys were carried out on this stock during the summer feeding phase. In 1997 a two-survey spawning survey was established covering both autumn and winter components. In 2004, this was modified into single spawning stock survey was carried out early in quarter 1 which continued until 2007. In 2008, it was decided that this survey should be incorporated into the larger coordinated Malin shelf survey on recommendation from SGHERWAY and WGHAWG. The summer 2011 survey represents the forth in the new time series (est. in 2008). The Irish component was carried out to cover, 1) the regions around western Ireland 2) the regions west of Scotland that are usually covered Marine Scotland and 3) northern sector of the Irish Sea survey (AFBI). The survey was coordinated through the ICES Working Group of International Pelagic Surveys (WGIPS). Combined survey data on herring distribution, abundance and age are used to provide a measure of the relative abundance of herring within the Malin shelf stock complex. Survey data on stock numbers at age are submitted to the ICES Herring Assessment Working Group (HAWG) and used in the annual stock assessment process. The northwest and west coast (ICES Divisions VIaS & VIIb) herring stock is composed of 2 of spawning components, autumn and winter spawners. Spawning covers a large geographical area and extends over a 4-month period from late September through to late March (Molloy et al, 2000). Traditionally fishing effort has been concentrated on spawning and pre-spawning aggregations. The autumn spawning component, which mostly occurs within VIIb and VIaS, feeds along the shelf break area to the west of the spawning grounds. The winter spawning component is found further north in VIaS. In VIaS, summer distribution extends from close inshore to the shelf break. Components of the winter spawning fish are known to undertake northward feeding migration into VIaN before returning in the winter to spawn along the Irish coast.
    • Northwest Herring Acoustic Survey Report 2004

      O'Donnell, Ciaran; Mullins, Eugene; Egan, Afra; Smith, Turloch; Bunn, Robert; Griffin, Karen; O’Driscol, Patrick; Bicknell, Simon; O’Driscol, Deirdre; Cross, Marcus; et al. (Marine Institute, 2004)
      The objectives of this survey were to: 1). To assess the size of the herring stock in VIaS and VIIb using an EK60 scientific sounder and a 38 kHz mounted within the vessels drop keel. Observe fish marks along the survey track using 18, 120 and 200 kHz; 2). Collect biological data from herring samples within this area and determine composition of marks using a single pelagic mid-water trawl.
    • Northwest Herring Acoustic Survey Report 2005

      O'Donnell, Ciaran; Mullins, Eugene; Johnston, Graham; Power, Ayesha; Beatie, Susan (Marine Institute, 2005)
      The northwest and west coast herring acoustic survey programme was first implemented in 1994. Prior to this a larval survey programme was carried out between 1981 and 1986. The ICES herring working group (HAWG) identified the need for a dedicated herring acoustic survey in this area (Anon, 1993). The stock in this area is composed of a number of spawning components and spawning may extend from September through to March (Molloy et al, 2000). Commercial fishing has targeted the fish during spawning times, no summer matje fishery exists in this area. In VIaS, fishing has traditionally taken place in late December and continues until late February (winter spawners). Traditionally in VIIb, fishing is mainly concentrated on the later months of the year and would be concluded by the early part of the new year (Autumn spawners). The protracted spawning period of herring and the overlap between the two spawning socks in this area (October to February) means that it is difficult to design a survey that covers all spawning fish in one specific survey. A project is currently underway to describe stock structure and discrimination of herring around Ireland. The results of this project may have implications for the design of this survey and for the stock assessment. However, since 1994, acoustic surveys have been carried out, and currently are the only tuning indices available. The current survey makes up the 11th in the time series. The design and execution of this survey has evolved from summer feeding phase surveys, in the mid 1990s until its present winter spawning state.
    • Northwest Herring Acoustic Survey Report 2006

      O'Donnell, Ciaran; Doonan, Ian; Lynch, Deirdre; O’Hea, Brendan; Egan, Afra (Marine Institute, 2006)
      The northwest and west coast herring acoustic survey programme was first implemented in 1994. Prior to this a larval survey programme was carried out between 1981 and 1986. In the early 1990s, the ICES herring working group (HAWG) identified the need for a dedicated herring acoustic survey in this area (Anon, 1994). The stock in this area is composed of 2 spawning components (autumn and winter), covering a large geographical area. Spawning may extend over a 4 month period from late September through to late March (Molloy et al, 2000). Traditionally fishing activity has targeted spawning and pre-spawning aggregations, no summer matje fishery exists in this area, as is the case in the Celtic Sea. In VIaS, fishing has traditionally taken place in late October and continues until late February (winter spawners). Traditionally in VIIb, fishing is mainly concentrated on the later months of the year and would be concluded by the early part of the new year (Autumn spawners). The protracted spawning period of herring and the overlap between the two spawning stocks in this area (October to February) is highly dynamic with variations between annual spawning events of up to 3 weeks. Accurate survey timing is a key component of the design to cover the overlap of peak spawning events. A project is currently underway to describe stock structure and discrimination of herring around Ireland. The results of this project may have implications for the design of this survey and for the stock assessment. However, since 1994, acoustic surveys have been carried out, and currently are the only tuning indices available. The current survey makes up the 13th in the time series. The design and execution of this survey has evolved from summer feeding phase surveys, in the mid 1990s until its present winter spawning state. This is the third survey of this stock carried out by the Celtic Explorer.
    • Northwest Herring Acoustic Survey Report 21 June – 11 July, 2012

      Nolan, Cormac; O'Donnell, Ciaran; Campbell, Andrew; Sullivan, Mairead; Mullins, Eugene (Marine Institute, 2012)
      The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring acoustic survey programme was first established in 1994. The summer 2012 survey represents the fifth in the new time series (est. in 2008). The Irish component was carried out to cover, 1) the regions around western Ireland 2) the regions west of Scotland that are usually covered by Marine Scotland and 3) northern sector of the Irish Sea survey (AFBI). The survey was coordinated through the ICES Working Group of International Pelagic Surveys (WGIPS). Combined survey data on herring distribution, abundance and age are used to provide a measure of the relative abundance of herring within the Malin shelf stock complex. Survey data on stock numbers at age are submitted to the ICES Herring Assessment Working Group (HAWG) and used in the annual stock assessment process. The northwest and west coast (ICES Divisions VIaS & VIIb) herring stock is composed of two spawning components, autumn and winter spawners. Spawning covers a large geographical area and extends over a 4-month period from late September through to late March (Molloy et al, 2000). Traditionally, fishing effort has been concentrated on spawning and pre-spawning aggregations. The autumn spawning component, which mostly occurs within VIIb and VIaS, feeds along the shelf break area to the west of the spawning grounds. The winter spawning component is found further north in VIaS. In VIaS, summer distribution extends from close inshore to the shelf break. Components of the winter spawning fish are known to undertake northward feeding migration into VIaN before returning in the winter to spawn along the Irish coast.
    • Northwest Herring Acoustic Survey Report 22nd June – 12th July, 2013

      Nolan, C.; O’Donnell, C.; Campbell, A.; Sullivan, M.; Mullins, E.; Keogh, H. (Marine Institute, 2013)
      The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring acoustic survey programme was first established in 1994.The summer 2013 survey represents the sixth in the new time series (est. in 2008). The survey was coordinated through the ICES Working Group of International Pelagic Surveys (WGIPS). The Irish component was carried out to cover the statistical rectangles between 53°30’-58°30' N and 12°-5° W as laid out in the WGI PS report (ICES, 2012). Combined survey data on herring distribution, abundance and age are used to provide a measure of the relative abundance of herring within the Malin shelf stock complex. Survey data on stock numbers at age are submitted to the ICES Herring Assessment Working Group (HAWG) and used in the annual stock assessment process.The northwest and west coast (ICES Divisions VIaS & VIIb) herring stock is composed of two spawning components, autumn and winter spawners. Spawning covers a large geographical area and extends over a 4-month period from late September through to late March (Molloy et al, 2000). Traditionally, fishing effort has been concentrated on spawning and pre-spawning aggregations. The autumn spawning component, which mostly occurs within VIIb and VIaS, feeds along the shelf break area to the west of the spawning grounds. The larger winter spawning component is found further north in VIa. In VIaS, summer distribution extends from close inshore to the shelf break. Components of the winter spawning fish are known to undertake northward feeding migration into VIaN before returning in the winter to spawn along the Irish coast.
    • Northwest Herring Acoustic Survey Report 22nd June – 12th July, 2014

      Nolan, Cormac; O'Donnell, Ciaran; Campbell, Andrew; Sullivan, Mairead; Mullins, Eugene (Marine Institute, 2014)
      The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring acoustic survey programme was first established in 1994.The summer 2014 survey represents the seventh in the new time series (est. in 2008). The survey was coordinated through the ICES Working Group of International Pelagic Surveys (WGIPS). The Irish component was carried out to cover the statistical rectangles between 53°30’-58°30' N and 12°-5° W as laid out in the WGIPS report (ICES, 2014). Combined survey data on herring distribution, abundance and age are used to provide a measure of the relative abundance of herring within the Malin shelf stock complex. Survey data on stock numbers at age are submitted to the ICES Herring Assessment Working Group (HAWG) and used in the annual stock assessment process.The northwest and west coast (ICES Divisions VIaS & VIIb) herring stock is composed of two spawning components, autumn and winter spawners. Spawning covers a large geographical area and extends over a 4-month period from late September through to late March (Molloy et al, 2000). Traditionally, fishing effort has been concentrated on spawning and pre-spawning aggregations. The autumn spawning component, which mostly occurs within VIIb and VIaS, feeds along the shelf break area to the west of the spawning grounds. The larger winter spawning component is found further north in VIa. In VIaS, summer distribution extends from close inshore to the shelf break. Components of the winter spawning fish are known to undertake northward feeding migration into VIaN before returning in the winter to spawn along the Irish coast.
    • Northwest Herring Acoustic Survey Report 24th June – 14th July, 2015

      Nolan, C.; Campbell, A.; O’Donnell, C.; Marrinan, M.; Parker, M. (Marine Institute, 2015)
      The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring acoustic survey programme was first established in 1994. The summer 2015 survey represents the eight in the new time series (est. in 2008). The survey was coordinated through the ICES Working Group of International Pelagic Surveys (WGIPS). The Irish component was carried out to cover the statistical rectangles between 53°30’-58°30' N and 12°-5° W as laid out in the WGIPS report (ICES, 2014). For 2015 only Irish data on herring distribution, abundance and age have been used to provide a measure of the relative abundance of herring within the Malin shelf stock complex. Survey data on stock numbers at age are submitted to the ICES Herring Assessment Working Group (HAWG) and used in the annual stock assessment process. The northwest and west coast (ICES Divisions VIaS & VIIb) herring stock is composed of two spawning components, autumn and winter spawners. Spawning covers a large geographical area and extends over a 4-month period from late September through to late March (Molloy et al, 2000). Traditionally, fishing effort has been concentrated on spawning and pre-spawning aggregations. The autumn spawning component, which mostly occurs within VIIb and VIaS, feeds along the shelf break area to the west of the spawning grounds. The larger winter spawning component is found further north in VIa. In VIaS, summer distribution extends from close inshore to the shelf break. Components of the winter spawning fish are known to undertake northward feeding migration into VIaN before returning in the winter to spawn along the Irish coast.
    • Northwest Herring Acoustic Survey Report, 18 June – 07 July, 2010

      O'Donnell, C; Mullins, E; Lyons, K; Sullivan, M; Kavanagh, L; Bunn, R; Beattie, S; McAuliffe, M; Griffin, N; Boyd, J (Marine Institute, 2010)
      The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring acoustic survey programme was first established in 1994. Prior to acoustic estimation, a larval survey programme was conducted from 1981-1986. In the early 1990s, the ICES herring working group (HAWG) identified the need for a dedicated herring acoustic survey in this area (Anon, 1994). From 1994 to 1996 surveys were carried out on this stock during the summer feeding phase. In 1997 a two-survey spawning survey was established covering both autumn and winter components. In 2004, this was modified into single spawning stock survey was carried out early in quarter 1 which continued until 2007. In 2008, it was decided that this survey should be incorporated into the larger coordinated Malin shelf survey on recommendation from SGHERWAY and WGHAWG. The summer 2010 survey represents the third in the new time series (est. in 2008). The Irish component was carried out concurrently with the West of Scotland (MarLab) and Irish Sea surveys (AFBI) and was coordinated through the ICES Working Group of International Pelagic Surveys (WGIPS). Combined survey data on herring distribution, abundance and age are used to provide a measure of the relative abundance of herring within the Malin shelf stock complex. Survey data on stock numbers at age are submitted to the ICES Herring Assessment Working Group (HAWG) and used in the annual stock assessment process. The northwest and west coast (ICES Divisions VIaS & VIIb) herring stock is composed of 2 of spawning components, autumn and winter spawners. Spawning covers a large geographical area and extends over a 4-month period from late September through to late March (Molloy et al, 2000). Traditionally fishing effort has been concentrated on spawning and pre-spawning aggregations. The autumn spawning component, which mostly occurs within VIIb and VIaS, feeds along the shelf break area to the west of the spawning grounds. The winter spawning component is found further north in VIaS. In VIaS, summer distribution extends from close inshore to the shelf break. Components of the winter spawning fish are known to undertake northward feeding migration into VIaN before returning in the winter to spawn along the Irish coast.
    • Northwest Herring Summer Acoustic Survey Cruise Report July 3-22, 2009

      O'Donnell, C; Mullins, E; Saunders, R; Lyons, K; Blaszkowski, M; Sullivan, M; Hoare, D; Bunn, R (Marine Institute, 2009)
      The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring acoustic survey programme was first established in 1994. Prior to acoustic estimation a larval survey programme was conducted between 1981 and 1986. In the early 1990s, the ICES herring working group (HAWG) identified the need for a dedicated herring acoustic survey in this area (Anon, 1994). From 1994 to 1996 surveys were carried out on this stock during the summer feeding phase. In 1997 a two-survey spawning survey was established covering both autumn and winter components. In 2004, a single spawning stock survey was carried out early in quarter 1 and continued until 2007. In 2008, it was decided that this survey should be incorporated into the larger coordinated Malin shelf survey as recommended by SGHERWAY and WGHAWG. This survey was the second in a new time series and a step away from the traditional spawning stock surveys. The Irish survey was carried out concurrently with the West of Scotland (MarLab) and Irish Sea surveys (AFBI) and was coordinated through the ICES Planning Group of International Pelagic Surveys (PGIPS). Combined survey data on herring distribution, abundance and age will be used to provide a measure of the relative abundance of herring within the Malin shelf stock complex. Survey data on stock numbers at age are submitted to the ICES Herring Assessment Working Group (HAWG) and used in the annual stock assessment process. The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring stock is composed of 2 of spawning components, autumn and winter spawners. Spawning covers a large geographical area and extends over a 4-month period from late September through to late March (Molloy et al, 2000). Traditionally fishing effort has been concentrated on spawning and pre- pawning aggregations. The autumn spawning component, which mostly occurs within VIIb, feeds along the shelf break area to the west of the spawning grounds. In VIaS, summertime distribution extends from close inshore to the shelf break. A component of this the winter spawning fish are known to undertake northward feeding migration into VIaN before returning in the winter to spawn along the Irish coast. Up to 40 vessels commonly participate in the fishery, many of which are based in the Co. Donegal port of Killybegs. The fleet is made up of 20 RSW (Refrigerated Seawater) vessels of 40-70m in length; 20 polyvalent trawlers 10 of which are vessels of 22-40m and 10 of less than 25m.
    • Northwest Herring Summer Acoustic Survey Cruise Report June 19 - July 8, 2008

      O'Donnell, C; Saunders, R; Lynch, D; Mullins, E; Lyons, K; Wragg, O; Smith, T; Hoare, D; Blaszkowski, M (Marine Institute, 2008)
      The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring acoustic survey programme was first established in 1994. A larval survey programme was initially carried out between 1981 and 1986. In the early 1990s, the ICES herring working group (HAWG) identified the need for a dedicated herring acoustic survey in this area (Anon, 1994). From 1994 to 1996 surveys were carried out on this stock during the summer feeding phase. In 1997 a two-survey spawning aggregation program was established covering both autumn and winter components. In 2004, a single spawning stock survey was carried out early in quarter 1 and continued until 2007, whereupon it was decided that this survey should be incorporated into the larger coordinated Malin shelf survey. This survey will be the first in a new time series and a step away from the traditional spawning stock surveys. The Irish survey will be carried out concurrently with the West of Scotland (MarLab) and Irish Sea surveys (AFBI) and was coordinated through the ICES Planning Group of Herring Acoustic Surveys (PGHERS). Combined survey data on herring distribution, abundance and age will be used to provide a measure of the relative abundance of herring within the Malin shelf stock complex. Survey data on stock numbers at age are submitted to the ICES Herring Assessment Working Group (HAWG) and used in the annual stock assessment process. The northwest and west coast (ICES Divisions VIaS & VIIb, c) herring stock is composed of 2 of spawning components (Autumn and Winter spawners) covering a large geographical area, which extends over a 4-month period from late September through to late March (Molloy et al, 2000). Traditionally fishing effort has been concentrated on spawning and pre-spawning aggregations. In Vlas, fishing begins in late Novemember and continues until late March (winter spawners). Further south in Vlllb, peak fishing takes place from October to December (Autumn spawners). The protracted spawning period of herring and the overlap between the two spawning stocks in this area (October to February) is highly dynamic with variations between annual spawning events of up to 3 weeks. Up to 40 vessels commonly participate in the fishery, many of which are based in the Co. Donegal port of Killybegs. The fleet is made up of 20 RSW (Refrigerated Seawater) vessels of 40-70m in length; 20 polyvalent trawlers 10 of which are vessels of 22-40m and 10 of less than 25m.
    • Note on the Growth-Rate of Herrings in the Irish Sea

      Farran, G. (Conseil International pour l'Exploration de la Mer (ICES), 1928)
    • Notes On Some Irish Estuarine And Inshore Fishes (With records of the distribution of shads by Eileen Twomey, M.Sc )

      Bracken, J J; Kennedy, M (Department of Agriculture and Fisheries (Fisheries Division), 1967)
      This paper brings together data collected in various ways by the authors, over a period of years. Some of the material described is a by-product of investigations, the primary results of which have already been published. Other material is supplementary to data previously published.
    • Novel azaspiracids produced by Amphidomataceae

      Krock, B.; Tillmann, U.; Jeong, H.J.; Potvin, E.; Salas, R.; Kilcoyne, J.; Gu, H. (Alfred-Wegener-Institut für Polar- und Meeresforschung, 2012)
    • The novel use of pop-off satellite tags (PSATs) to investigate the migratory behaviour of European sea bass Dicentrarchus labrax

      O'Neill, R.; Ó Maoiléidigh, N.; McGinnity, P.; Bond, N.; Culloty, S. (Wiley, 2018)
      A total of 12 adult European sea bass Dicentrarchus labrax were tagged with pop‐off satellite archival tags (PSAT) in Irish coastal waters and in offshore waters in the north‐east Celtic Sea between 2015 and 2016. Archived data were successfully recovered from five of the 12 tags deployed, three from fish released in inshore Irish waters and two from fish released offshore in the eastern Celtic Sea. All three fish tagged in inshore waters were found to undertake migrations into the open ocean coinciding with the spawning period. These fish also exhibited fidelity to inshore sites post‐migration, returning to the same general location (within c. 73 km, which is roughly the predicted mean accuracy of the method) of their original release site. Although the number of tracks obtained here was limited, some degree of aggregation between inshore and offshore tagged fish in the eastern Celtic Sea was noted during the expected spawning period suggesting PSATs can provide new information on specific spawning locations of European sea bass.
    • Nucleic acid tests for toxic phytoplankton in Irish waters-phytotest: Marine Strategic RTDI project AT/04/02/02 - research update

      Maher, M.; Kavanagh, S.; Brennan, C.; Moran, M.; Salas, R.; Lyons, J.; Silke, J. (Marine Institute, 2007)
      The Phytotest project is a 3 year collaborative project funded through the Marine Strategic Programme in Advanced Technologies as part of the National Development plan 2000-2006. The project partners include the National Diagnostics Centre at NUI Galway and MI. The overall objective of the project is the development of nucleic acid tests (molecular methods) for the identification of key toxic phytoplankton species in Irish waters. In the final year of the programme the aim is to transfer the molecular methods developed in the project into MI to support their monitoring service. Currently, the monitoring for phytoplankton species in Irish waters is performed by light microscopy which can easily identify some plankton species based on distinctive morphological traits. Other species in particular, Pseudonitzschia spp. and Alexandrium spp. cannot be identified to species level by light microscopy. Identification of these species requires more sophisticated microscopic techniques such as scanning electron microscopy (SEM) and transmission electron microscopy (TEM). These techniques cannot easily be integrated into a routine testing environment. Molecular methods utilise unique information contained within an organism’s genome in order to identify it. This genetic information can be exploited in a range of molecular test platforms enabling microorganisms to be identified to species level. Additionally, there has been a major drive towards the development of highly automated platforms to support molecular tests for high-throughput testing in routine laboratory settings.
    • Numerical modelling of blue mussel (Mytilus edulis) bacterial contamination

      Dabrowski, T.; Dore, W.; Lyons, K.; Nolan, G. (Elsevier, 2014)
      Bivalve shellfish such as oysters and mussels can concentrate human pathogens when grown in areas impacted by municipal wastewater. Under EU regulation this risk to consumers is controlled by determining the sanitary quality of bivalve shellfish production areas based on the concentration of Escherichia coli present in shellfish flesh. The authors present a modelling approach to simulate an uptake of E. coli from seawater and subsequent depuration by Mytilus edulis. The model that dynamically predicts E. coli concentration in the mussel tissue is embedded within a 3-D numerical modelling system comprising hydrodynamic, biogeochemical, shellfish ecophysiological and the newly proposed microbial modules. The microbial module has two state variables, namely, the concentrations of E. coli in water and in the mussel tissue. Novel formulations to calculate the filtration rates by mussels and the resulting uptake of bacteria are proposed; these rates are updated at every computational time step. Concentrations of E. coli in seawater are also updated accordingly taking into account the amounts ingested by mussels. The model has been applied to Bantry Bay in the south-west of Ireland. The results indicate that the model is capable of reproducing the official classification of shellfish waters in the bay based on monthly sampling at several stations. The predicted filtration rates and ratios of E. coli in water and mussels also compare well with the literature. The model thus forms a tool that may be used to assist in the classification of shellfish waters at much greater spatial and temporal detail than that offered by a field monitoring programme. Moreover, it can also aid in designing an efficient monitoring programme. The model can also be utilised to determine the contribution of individual point sources of pollution on the microbial loading in mussels and, when incorporated into an operational framework, it can provide a short-term forecasting of microbial contamination in a shellfishery. Also, the model can be easily extended to include other shellfish and pathogen species.
    • Numerical modelling of spatio-temporal variability of growth of Mytilus edulis (L.) and influence of its cultivation on ecosystem functioning

      Dabrowski, T.; Lyons, K.; Curé, M.; Berry, A.; Nolan, G. (Elsevier, 2013)
      One of the key needs of the aquaculture industry is the implementation of effective management methods to ensure the sustainability, economic viability and minimization of negative impacts on both human and ecosystem well-being. The authors developed a Fortran 90 implementation of the dynamic energy budget (DEB) model for Mytilus edulis. The model has been further developed to include physiological interactions with the ecosystem and coupled to a biogeochemical nutrient–phytoplankton–zooplankton–detritus (NPZD) model. Phytoplankton and detritus uptakes, oxygen utilisation, CO2 production, NH4 excretion, egestion of faeces, and assimilation of food are modelled. A novel approach was derived that accounts for the allocation of C and N in mussel flesh and shell organic fraction. The DEB–NPZD model has been subsequently coupled to a high resolution three dimensional numerical coastal ocean model of the south–west coast of Ireland, where approximately 80% of national rope mussel is produced annually. Simulations have been carried out for the time period July 2010–June 2011, for which the field data on mussel biometrics and ambient seawater properties were collated. The model accurately reproduced the spatio-temporal variability in blue mussel growth. It is also shown that the ecosystem dynamics is affected by the presence of aquaculture farms. The modelling system presented allows for the assessment of the impacts of aquaculture activities on water quality, quantification of the production and ecological carrying capacities and improvement of our understanding of the ecosystem functioning with particular emphasis on interactions between various trophic levels.