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Aquaculture & Fisheries Development Centre
School of Biological, Earth & Environmental Sciences
University College Cork
Annual Report 2013
Aquaculture & Fisheries Development Centre Annual Report 2013
2
AFDC Strategic Vision “To support, stimulate and promote the development of aquaculture and
fisheries, thereby enabling these sectors to achieve their full socio-economic potential by utilising sustainable natural resources”
Aquaculture & Fisheries Development Centre Annual Report 2013
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CONTENTS
Page
Executive Summary 5
Facilities & Specifications 7
Focus on 8
Postgraduate Students Graduated in 2013 16
Research Funding 16
On-going and New Research Grants During 2013 17
Publications 18
Conference Presentations 20
AFDC Personnel 21
Aquaculture & Fisheries Development Centre Annual Report 2013
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Aquaculture & Fisheries Development Centre Annual Report 2013
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2013 was another research active year at The Aquaculture & Fisheries Development Centre in the School of
Biological, Earth & Environmental Sciences at University College Cork. The personnel profile of the centre in
2013 included a Director, Dr Sarah Culloty, a Manager, Dr Maria O’Mahoney, five Principal Investigators in
each of the four thematic areas; Prof. Tom Cross/ Dr Phil McGinnity (Molecular Genetics of Aquatic Animals),
Dr Sarah Culloty (Shellfish Health), Prof. Gavin Burnell (Aquaculture) and Dr Emer Rogan (Marine Mammals
& Fisheries), 2 Senior Researchers, 5 Post-doctoral Researchers, 13 PhD students, 1 MSc student and 3 Re-
search Assistants. During 2013, MSc’s were awarded to 1 AFDC/School of BEES student. A total of 29 pub-
lications in peer-reviewed journals were produced including articles in high impact journals such as Molecular
Ecology, PLoS One and the Journal of Experimental Biology. Two oral presentations were given at interna-
tional conferences.
Two new research projects with a combined funding value of over €223,360 started in 2013. This brings the
tally of research funding at the AFDC to €8.9m for 18 research projects. The profile of research funding at
the AFDC is an amalgamation of Exchequer and EU funding. The research capacity, diversity and strengths
continue to grow through both national and international collaborations. One of the main priorities of the
AFDC is to provide continued support to industry and to enhance industry. The AFDC also continues to play
an important role in the education of undergraduate and postgraduate students within the School of BEES.
Dr Sarah Culloty
Director,
Aquaculture & Fisheries Development Centre
Dr Maria O’Mahoney
Manager,
Aquaculture & Fisheries Development Centre
EXECUTIVE SUMMARY
Aquaculture & Fisheries Development Centre Annual Report 2013
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Aquaculture & Fisheries Development Centre Annual Report 2013
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The Aquaculture & Fisheries Development Centre (AFDC) is a 1200m2 research facility embedded within the
School of Biological, Earth & Environmental Sciences (BEES). The facility includes recirculating fish and
shellfish systems, laboratories (Wet and Dry) and offices. The tank rooms are equipped with marine and
freshwater tropical marine system recirculation units, broodstock conditioning units, shellfish on-growing
units, filter-feeder broodstock conditioning units, a larval culture system and live food culture facilities.
Seawater (Grade A) is delivered to on-site and stored. The AFDC has facilities seawater filtration and UV
treatment if required.
The AFDC is authorised to operate under the European Communities Health of Aquaculture Animals and
Products Regulations 2008 (Authorisation number: 006 / FHA).
FACILITIES & SPECIFICATIONS
The indoor recirculation units consist of mechanical and biological water filtration, water treatment
systems involving UV sterilisation and ozonation, and temperature control conditioning units to
enable full control of environmental parameters/variables. Light intensity and photoperiod are
available in some areas and may be locally controlled on a number of discrete systems. A range of
tank designs and sizes are incorporated which allow fish to be held at each life cycle stage, and
also for the production of research specific systems/units to suit almost any form of aquatic
research with experimental-scale trial replication. The infrastructure at the AFDC also allows for the
Algal culture and live feed production areas are available to support the culture of many species
through their larval stages. A recirculating shellfish nursery system, broodstock holding/
conditioning unit, thermally controlled hatchery and live feed production units are custom designed
to provide a series of systems suitable to the needs of a number of shellfish species. The two tank
rooms of the AFDC are fully backed-up with a 50KVa Generator fitted with an Automatic transfer
Switch (ATS) and Digi-dialler. The dedicated AFDC Laboratory houses water quality analysis
equipment, a Beckman Z2 coulter counter (particle size analyser) and drying oven as well as the
standard laboratory equipment. On site laboratories provide dedicated research facilities and
technical support essential to research at the AFDC.
Additional laboratory facilities available at the AFDC include:
Molecular genetics laboratory
Water quality testing
Wet lab/post mortem room
Tissue culture laboratory
Histology and Immunology laboratory
Aquaculture & Fisheries Development Centre Annual Report 2013
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Focus On Aquaculture Research
Sea Urchin Immunology (PI Prof. Gavin Burnell, PhD Student Ashlie Cipriano)
The sea urchin immunology project is investigating several
aspects of the physiology and anatomy of the purple sea
urchin, Paracentrotus lividus, in aquaculture. P. lividus is a
Lusitanian species, valued commercially for its gonads, which
are a delicacy in European and Pacific/Asian countries. Wild
sea urchin populations worldwide are overfished.
During 2013, the project investigated different tagging
techniques which would identify individuals whether in
laboratory or field settings. Passive Integrated Transponder
(PIT) tagging was the most successful technique. The
technology involved in PIT tagging is the same at that used by
Veterinarians when micro-chipping cats and dogs and is
programmed with a unique 12-digit identification number that,
when scanned with a handheld scanner and linked to a
database, can provide information about the individual (e.g.
Owner’s information). The use of PIT tags permits repeated
non-destructive identification of individuals, has an indefinite
life span, involves little to no tagging mortality, has a high tag
retention, and no apparent long-term effects on growth and
survival of tagged individuals.
As part of this project, Ashlie is also working on the use of
immunostimulatory agents – immunostimulants, prebiotics,
probiotics, and the synergy between them – to boost the sea
urchins immune system naturally. This application is especially
important in aquaculture due to the ban on antibiotics in fish
farming (Regulations, EC No.1831) and may provide for a
more holistic approach to sea urchin health in culture.
Attaching various tags to the sea urchin, P.
lividus
Using the handheld scanner to retrieve
identification data from the PIT tag
PhD Student Ashlie Cipriano retrieving PIT
tags from P. lividus
Aquaculture & Fisheries Development Centre Annual Report 2013
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As an Irish Research Council Industry-based PhD
Candidate working on the Integrated Multi-trophic
Aquaculture project, Daryl Gunning has been based part-
time in Bantry, Co. Cork at the Daithi O’ Murchu Research
Station (DOMMRS), who are the industry partners in the
project. Whilst based in industry, Daryl has been heavily
involved in the EU FP7 funded IDREEM (Increasing
Industrial Resource Efficiency in European Mariculture)
project (http://www.idreem.eu/cms/about-project/) which
aims to protect the long-term sustainability of European
aquaculture by developing and demonstrating a new
innovative production technology, Integrated Multi-Trophic
Aquaculture (IMTA), and is therefore closely aligned with
his own research.
In addition to the considerable experience gained whilst
based at Industry, Daryl has had an active year
conducting research as part of his own IMTA research
project. During 2013, Daryl conducted sea cucumber
anaesthesia trials using MgCl2, MgSO4 and KCl. The
project also investigated the use of PIT tags attached to
various body locations as a mechanism to physically tag
sea cucumbers.
Three experimental IMTA land-based units were
constructed from recycled Intermediate Bulk Containers
(IBCs). A medium to long term (3-6 month) experiment will
be run from July 2014, monitoring water quality and
growth rates of seaweeds, mussels, sea-cucumbers, and rainbow-trout growing in these recirculation units.
As an alternative to seaweed, Salicornia europaea (a halophytic annual dicot) will be used.
Integrated Multi-Trophic Aquaculture (PI Prof. Gavin Burnell, PhD student Daryl Gunning)
PhD student Daryl Gunning deploying seaweed
longlines as part of the IDREEM project
Aquaculture & Fisheries Development Centre Annual Report 2013
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Focus On Shellfish Health Research
HERPISH (PI Dr Sarah Culloty, Marie Curie Intra-European Fellow Dr Maria Prado-Alvarez)
The project Herpes virus in Irish oysters and identification of
resistant stocks (HERPISH) commenced in June 2013. During
summer time several hatcheries located in areas with different
susceptibility to the ostreid herpes virus were selected and 1 year
old Crassostrea gigas were sampled twice per month to monitor
disease progress and susceptibility to infection. Mortality was
determined in 200 oysters and a total of 60 oysters per sampling
and location were collected and processed for DNA extraction and
histology. In another set of survey, spat from a virus free hatchery
were transferred to two affected areas and were sampled as
described before for 1 year old oysters. Ostreid herpes virus was detected by PCR on gill tissues or total
body tissue depending on the size of the organism. These results were used to determine the prevalence of
infection per site over a 2.5 month period. At the end of the sampling, spat survivors were transferred to the
facilities of the AFDC and keep in a close circuit to carry out an experimental trial. After anesthesia with
Magnesium Chloride, a suspension of purified virus from heavy infected oysters was injected in the adductor
muscle and the mortality rate and the prevalence of infection was determined over a 7 days period. Genomic
material was also kept in order to carry out the genetic analyses proposed for the second year of the project.
Both field and laboratory trials were carried out in 2013
as part of the BIVALIFE project to investigate (a) how
ostreid herpesvirus 1 microVar (OsHV-1 μVar) is
sustaining itself in the environment outside its natural
host the Pacific oyster Crassostrea gigas and (b) the
environmental parameters which might be making
oysters more susceptible to infection with this virus.
Nine samples consisting of 605 individual samples of
invertebrates, sediment, biofilm and water were
collected at Carlingford Lough every two weeks from
July to October. A single sample of invertebrates was
Processing oysters for histology and
the material used
BIVALIFE (PI Dr Sarah Culloty, Research Fellow Dr Sharon Lynch, PhD Student Ms Amy O’Reilly,
Research Assistant Dr Steve Hutton)
Dr Steven Hutton and PhD student Amy O’Reilly
during fieldwork at Carlingford Lough
Aquaculture & Fisheries Development Centre Annual Report 2013
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collected from two non-culture sites at Ardmore and Bullen’s Bay. In 2013, mortalities were minimal (<0.5%)
to absent in Carlingford during the field trial period even though OsHV-1 μVar was detected by polymerase
chain reaction (PCR) in C. gigas (45-100% prevalence) and grouped macroinvertebrates (3-69%). All
invertebrate samples screened at the two control sites, Ardmore and Bullen’s Bay, were negative for OsHV-1
μVar. OsHV-1 μVar was most frequently observed in bivalves followed by gastropods, tunicates,
crustaceans, polychaetes and the chordate. The high prevalence of OsHV-1 μVar in other filter feeding
bivalves, the blue mussel Mytilus edulis and the common cockle Cerastoderma edule, may be due to the
intake of the virus during suspension feeding, while the high prevalence in the shore crab Carcinus maenas
may be due to the ingestion of the virus by feeding on dead or dying infected C. gigas. Grazing gastropods,
including the periwinkle Littorina littorea, may have ingested the virus by feeding on the biofilm. Further
studies are required to indicate if the virus is replicating in these other macroinvertebrate species.
Several laboratory trials were carried out in 2013 to (a) determine the effects of different salinities (20, 35 and
38‰) and (b) different nutrient concentrations (‘Low’, ‘Med’ and ‘High’) on C. gigas spat (4 months old) held
at an elevated temperature (22°C) and exposed to OsHV-1 μVar over a 29 day period. Higher mortalities
were observed in oysters held at the higher salinities (35 and 38 ‰) while minimal mortality was observed in
oysters held at a reduced salinity (20‰), even when oysters were exposed to OsHV-1 μVar. In the nutrient
trial (22°C and 20‰) mortalities were also minimal and although more oysters were becoming infected with
OsHV-1 μVar after week 3, mortalities were not occurring. Reduced salinity may control C. gigas mortality
and reduce the impact of OsHV-1 μVar and its virulence, even when seawater temperatures and nutrients
are elevated.
Dr Steven Hutton processing samples in the Aquaculture laboratory at the
AFDC
Aquaculture & Fisheries Development Centre Annual Report 2013
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Focus On Marine Mammals & Fisheries Research
Beaufort Ecosystem Approach to Fisheries Management (PI Prof Gavin Burnell/ Dr
Emer Rogan, Postdoctoral Researcher Dr Susie Brown)
Funded under the Irish Beaufort Marine
Research Awards, the Ecosystem
Approach to Fisheries Management
(EAFM) is a 7 year €3.9m project involving
a consortium comprising research groups
from University College Cork, Queens
University Belfast, and the Marine Institute.
The EAFM is a move away from traditional
single stock fisheries management and
includes links between fish species and
wider fisheries-ecosystem interactions. In
particular the ecological focus has
broadened from concerns about target
species and resources to concerns about
non target species, including protected species, habitats, ecological communities and socio economics. For
example, if sand-eel stocks are depleted what impacts does this have on both commercial species like cod
and other animals such as dolphins and seabirds.
The School of BEES is conducting Ecological Risk Assessments for the Effects of Fishing (ERAEF) within the
EAFM project, under the work package “Fishing Impacts and Approaches to Management”. These
assessments identify the activities within fisheries with the potential to impact aspects of the ecosystem,
including target and non-target species, habitats and communities. In addition to examining the impact of
fishing activities on the ecosystem as a whole, the school is looking in detail at the interactions between
fisheries and cetacean species. The specific risks posed to cetaceans are being examined with a view to
identifying fisheries and gears with the greatest potential for bycatch of whales and dolphins. Key to this aim
has been the development of an ERAEF procedure which enables the screening of risk to cetacean species
from fishing activities (Brown et al. 2013). A spatially and temporally explicit extension of this ERAEF
procedure is currently being developed to facilitate the mapping of risk to cetacean species from different
fisheries and enable the identification of areas of high bycatch risk. Further to this, investigations into the
feeding ecology of two coastal species (bottlenose dolphins and harbour porpoises) and four pelagic species
(white-sided dolphins, white beaked dolphins, common dolphins and striped dolphins) are contributing to our
understanding of the interactions between fisheries and cetaceans. Dietary information is being collected
Bottlenose dolphins, Tursiops truncatus, in Connemara
Aquaculture & Fisheries Development Centre Annual Report 2013
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from stranded and bycatch animals and is being used to identify dietary preferences; estimate annual food
consumption; assess their role as top predators; and the impacts of overfishing/stock collapse on these
species. In a broader fisheries context ERAEF is being applied to a number of fisheries operating in Irish
waters. Focussing initially on fisheries operating within the Biologically Sensitive Area, these assessments
will examine the impact of fisheries on target species, non-target species, protected species and habitats.
The outputs from these assessments will be used to contribute to management plans for fisheries and the
species and habitats they impact. Further details on the Beaufort EAFM project can be found on the project
website http://www.beaufort-eafm.eu.
The early part of the 2013 (January – May) was spent on
planning and preparing for the summer field season,
including taking training courses for advanced power boat
driving, getting practice in handling and shooting a 0.22
calibre rifle (for bottlenose dolphin biopsies), biopsy
training, attending courses on Personal Survival
Techniques, marine VHF radio and Marine Elementary 1st
Aid. I also attended and presented a poster at the annual
conference of the European Cetacean Society in April
2013. The title of the presentation was “Social structure of
coastal bottlenose dolphins (Tursiops truncatus) in
western Ireland”.
May-August was spent doing fieldwork. I conducted boat-based surveys of bottlenose dolphins in Connemara
(Co. Galway), Mayo and south Donegal with the purpose of gathering photo-identification and biopsy data
during dolphin encounters. I also gave a public talk in Connemara National Park in July 2013. The field
season was funded by the National Parks and Wildlife Service.
After the field season I analysed the identification photographs collected during the surveys and submitted a
progress report and a biopsy report on the 2013 field season to the NPWS. I also started working on an
abundance estimate for bottlenose dolphins occurring in the waters in Connemara, Co. Galway, and on an
abundance estimate for a wider area covering Connemara, Mayo and south Donegal. In addition, I deployed
a passive acoustic monitoring device, a C-POD, in Saint John’s point, Co. Donegal. The purpose of the
deployment is to give an indication of habitat use and occupancy rates of bottlenose dolphins in this area.
West Coast of Ireland Bottlenose Dolphin Project (PI Dr Emer Rogan, PhD Student Milaja
Nykanen)
PhD student Milaja Nykanen conducting a boat
survey during her fieldwork season 2013
Aquaculture & Fisheries Development Centre Annual Report 2013
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The focus of activities in 2013 and beyond was divided in two elements; the first was orientated towards the
completion of ongoing work programmes and the fulfilment of the contractual commitments associated with
the various contracted research projects acquired during the lifetime of Beaufort Fish Population Genetics
Award and the second element was focused on the continued acquisition of new research grants. The project
achieved a significant milestone in 2013 by surpassing €2.5m in external funding since the projects
commencement in June 2008.
The Beaufort Marine Research Award in Fish Population Genetics is a joint project with Queen’s University
Belfast and the Marine Institute and is funded by the Irish Government under the Sea Change Programme. In
keeping with the priorities of the Beaufort genetics research programme, the majority of new grants are
focused on the key species (i.e. Atlantic salmon, Atlantic cod, brown trout and lobsters). However, additional
research projects in collaboration with our Beaufort project partners in Queen’s University Belfast, focusing
on other species of strategic value from economic and/or conservation perspectives (e.g. sea bass, marine
and river lampreys, eels, European perch, oysters) are also been undertaken by the group. Dr Tom Reed,
supported by the Beaufort, has being preparing an application for funding through the prestigious European
Research Councils starter grants. ERC Starting Grants aim to support up-and-coming research leaders who
are about to establish a proper research team and to start conducting independent research in Europe. The
scheme targets promising researchers who have the proven potential of becoming independent research
leaders. In 2013, seven scientific papers have been published by the group at UCC with numerous additional
papers published in press or in review for 2014.
In respect of personnel matters, in Cork, Dr Jens Carlsson was appointed as Lecturer in Zoology at the
School of Biological and Environment Science in University College Dublin. The vacant position has now
been filled by Dr Tom Reed (http://www.ucc.ie/en/afdc/peopleandcontacts/tomreed/). Dr Eileen Dillane
continues in her role as laboratory supervisor in UCC. Mr Brian Clarke and Mr Trevor Stafford were
employed as research assistants funded by the Atlantic Area Inter-Reg programme as part of the AARC
project. Mr Ross O’Neill commenced a study for MSc on the biology and genetics of sea bass
(Dincentrarchus labrax) in 2013. Dr Ciar O’Toole, funded and supervised as part of the Beaufort Award,
successfully completed her PhD research for a thesis entitled the ‘Biological significance of molecular
variation in salmonid fish’.
During 2013, progress continued on previously established projects which were acquired under the Beaufort
Fish Population Genetics Award. These included the CSTP, Lobster (NELCO V-notching), Lobster (Kilkeel
Focus On Molecular Genetics of Aquatic Animals Research
Beaufort Fish Population Genetics (Prof Tom Cross - Grantee/ Dr Phil McGinnity - Principal
Investigator, Senior Researcher Dr Jamie Coughlan, Senior Researcher Dr Tom Reed, Research Sup-
port Officer Dr Eileen Dillane, PhD Student Ciar O’Toole)
Aquaculture & Fisheries Development Centre Annual Report 2013
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Development Association), Reciprocal transfer experiment, Burrishoole pedigree, Girnock Burn pedigree,
West Greenland GSI, Jamie Magee’s trout studies in the Burrishoole, Cathy Johnson’s studies in Donegal
and the Bush, Ciar O’Toole’s studies in the Burrishoole, Newfoundland and Lough Currane, Update NGSI,
EirCOD, Galloway brown trout population genetics studies and IFI brown trout studies. New research
initiatives started in 2013 include an additional ranching element to the common garden experiment
undertaken in the Bunowen River as part of the Atlantic ARC project extension. The objective here is to
obtain some estimate of the relative marine performance of the some of the candidate populations assessed
in freshwater. The ESB have generously sponsored an assessment of the provenance of the contemporary
wild salmon population returning to the upper river. The key management question here is whether these
fish originate from natural spawning or are the product of the stocking programme. The outcome of the
investigation will inform the best strategy for stock rebuilding. As part of an MSc research project Mr Ross
O’Neill has undertaken an investigation into the distribution of European sea bass (Dicentrarchus labrax) in
Irish waters.
Polymorphic microsatellite DNA loci were used
here in three studies during this PhD, one on
Salmo salar and two on S. trutta. In 2013, all
laboratory work was completed, data analysis was
carried out and the thesis was written and
submitted on the 4th January 2014. Final results
showed, in the case of S. salar, that the survival of
native fish and non-natives from a nearby
catchment, and their hybrids, differed significantly
during a common-garden experiment. Overall
survival of non-natives was 35% of natives. These
results imply a genetic basis and suggest local
adaptation can occur in salmonids across
relatively small geographic distances. In the first case study with S. trutta, the species was investigated as an
invasive in Newfoundland, eastern Canada. Genetic investigation provided a clear example of the structure
of two expanding waves of spread along coasts. Finally, the genetics of anadromous S. trutta from the
Waterville catchment in south western Ireland were studied and used to assign very large rod caught sea
trout individuals (so called “specimen” sea trout) back to region of origin. All these studies provide results
which will contribute to future management of the species. It might be concluded that the overarching
message from this thesis is to highlight the importance of maintaining genetic diversity in salmonid
populations as vital for their long-term productivity and resilience.
Biological Significance of Molecular Variation in Salmonid Fish (Supervisors Prof. Tom Cross &
Dr Phil McGinnity, PhD Student Ciar O’Toole)
The Atlantic Salmon Salmo salar
Aquaculture & Fisheries Development Centre Annual Report 2013
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Allocation of research funding (%) on-going during
2013 from different funding bodies.
MSc Theses
O’Grady, E. 2013. Modelling thresholds in parasite life-cycles
using delayed exchange of stability - with particular reference to
the Unikaryon legeri problem. Supervisors: Dr Sarah Culloty, Dr
Tom Kelly, Dr Dmitri Rachinskii (School of Mathematics).
PhD Theses
McCarthy, M. 2013. Ecotoxicology of marine biotoxins in bivalve
shellfish. Supervisors: Prof. John O’Halloran (School of BEES),
Prof. Frank Van Pelt (School of Pharmacy), Prof. Kevin James
(UCC/CIT).
Morgan, E. 2013. Synecology in soft sediment bivalves: the influence of parasites, physiological processes,
and environmental stressors on health and disease. Supervisors: Dr Sarah Culloty, Dr Ruth Ramsay (School
of BEES).
Ribeiro Santos, A.M.A. 2013. The life history and ecology of black scabbardfish (Alphanopus carbo Lowe
1839) in the north-east Atlantic. Supervisor: Dr Emer Rogan.
POSTGRADUATE STUDENTS GRADUATED IN 2013
RESEARCH FUNDING
During 2013, eighteen research projects to the value of €8.9m were on-going at the AFDC. New projects to
the value of €223,360 started in 2013. National funding sources, through the Marine Institute, Inland Fisheries
Ireland, Irish Research Council, National Parks and Wildlife Service and the School of Biological, Earth and
Environmental Sciences, University College Cork, account for 69% of the total research funding for 2013.
The proportion of funding for research through European Union funding (Framework 7 and the European Re-
gional Development Fund) at the AFDC has increased from 29% in 2012 to 31% in 2013.
School of BEES/AFDC PhD Graduates 2013
Aquaculture & Fisheries Development Centre Annual Report 2013
17
2013 Funding
Burnell, G.B. The ecological and economic contribution of the detritivore component to novel marine
Integrated Multi-tophic Aquaculture (IMTA) systems. Irish Research Council, 2013-2017. €32,000.
Culloty, S.C. Herpes virus in Irish oysters and identification of resistant stocks (HERPISH). FP7 Marie Curie
Intra-European Fellowship, 2013-2015. €191,360.
2012 Funding
Culloty, S.C. Bridging the gap between science and producers to support the European marine mollusc
production sector (EUROSHELL). EU FP7 Funding, 2012-2014. €18,168.
Burnell, G.B. & Culloty, S.C. The effect of pre- and probiotics on marine invertebrates in aquaculture.
School of BEES Crawford Hayes Scholarship, 2012-2015. €72,000.
2011 Funding
Culloty, S.C. Bioengineered micro-encapsulation of active agents delivered to shellfish (BEADS). EU FP7
Capacities Support for SME’s Funding Programme, 2011-2013. €303,899.
Culloty, S.C. Management of infectious diseases in oysters and mussels in Europe (BIVALIFE). EU FP7
Funding, 2011-2014. €256,410.
Rogan, E. The genetic structure, foraging ecology, movement patterns and habitat choices of bottlenose
dolphins (Tursiops truncatus) along the west coast of Ireland. National Parks and Wildlife Service, 2011-
2015. €45,000.
Rogan, E. The genetic structure, foraging ecology, movement patterns and habitat choices of bottlenose
dolphins (Tursiops truncatus) along the west coast of Ireland. School of BEES Crawford Hayes Scholarship,
2011-2015. €72,000.
2010 Funding
Culloty, S.C. Establishing the scientific bases and technical procedures and standards to recover the
European flat oyster production through strategies to tackle the main constraint bonamiosis
(OYSTERECOVER). EU FP7 Funding, 2010-2013, €730,894.
McGinnity, P., Cross, T.F. & Coughlan, J. Atlantic aquatic resource conservation (AARC). European
Regional Development Fund (ERDF): INTERREG 4 Atlantic Area Programme, 2010-2013, €255,429.
McGinnity, P. & Cross, T.F. IFI Strategic Partnership Project – Setting Conservation Limits. National
Salmon Conservation Stamp. IFI Research Partnership Project, Inland Fisheries Ireland. €80,000.
2009 Funding
Culloty, S.C. Shellfish productivity in the Irish Sea: working towards a sustainable future (SUSFISH). ERDF
INTERREG 4A, 2009-2013, €618,399.
McGinnity, P. & Cross, T.F. Celtic Sea Trout project: Genetic Stock Identification of sea trout stocks. EU
INTERREG, 2009-2013, €359,830.
McGinnity, P., Cross, T.F. & Coughlan, J. IFI Strategic Partnership Project. Inland Fisheries Ireland.
(Research grant award to Beaufort consortium. 2009-2013, €320,000.
2008 Funding
Burnell, G. & Cummins, V. Beaufort Marine Research Award: Ecosystem Approach to Fisheries
Management. Irish Government NDP administered by the Marine Institute, 2008-2015, €1,860,004.
Cross, T.F. & McGinnity, P. Irish cod breeding programme. Marine Institute, 2008-2015, €213,088.
Cross, T.F. & McGinnity, P. Beaufort Marine Research Award: Fish population genetics. Irish Government
ON-GOING & NEW RESEARCH GRANTS DURING 2013
Aquaculture & Fisheries Development Centre Annual Report 2013
18
NDP administered by the Marine Institute, 2008-2015. €2,710,236.
Rogan E. & Codling, E. Develop and test through simulation a suite of measures that will contribute to
rebuilding depleted fish stocks in waters around Ireland. Marine Institute, 2008-2014. €627,633.
1. Bourret V., Kent M.P., Hayes B.J., Primmer C.R., Vasemagi A., Karlsson S., Hindar K., McGinnity P.,
Verspoor E., Bernatchez L. & Lien S. 2013. SNP-array reveals genome wide patterns associated with
geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo
salar). Molecular Ecology, 22, 532–551.
2. Brown S.L., Reid D. & Rogan E. 2013. A risk-based approach to rapidly screen vulnerability of
cetaceans to impacts from fisheries bycatch. Biological Conservation, 168: 78-87.
3. Cronin M., Zuur A.F. & Rogan E. 2013. A modelling framework to optimize timing of haulout counts for
estimating harbour seal (Phoca vitulina) abundance. NAMMCO Scientific Publications, doi: http://
dx.doi.org/10.7557/3.2686.
4. Carlsson J., Gauthier D., Carlsson J.E.L., Coughlan J.P., Dillane E., Fitzgerald R.D., Keating F.U.,
McGinnity P., Mirimin L. & Cross T.F. 2013. Rapid, economical single nucleotide polymorphism and
microsatellite discovery based on de novo assembly of a reduced representation genome in a non-
model organism: a case study of Atlantic cod. Journal of Fish Biology, 82: 944–958.
5. Davenport J., Cotter E., Rogan E., Kelliher D. & Murphy C. 2013. Structure, material characteristics
and function of the upper respiratory tract of the pygmy sperm whale. Journal of Experimental Biology,
doi: 10.1242/jeb.083782.
6. Ensing D., Crozier W.W., Boylan P., O’Maoiléidigh N. & McGinnity P. 2013. An analysis of Genetic
Stock Identification on a small geographical scale using microsatellite makers, and its application in the
management of a Mixed-Stock fishery for Atlantic salmon (Salmo salar L.) in Ireland. Journal of Fish
Biology, 82 (6): 2080-2094.
7. Friedland K.D., Shank B.V., Todd C.D., McGinnity P. & Nyee, J. 2013. Differential response of
continental stock complexes of Atlantic salmon (Salmo salar) to the Atlantic Multi-decadal Oscillation.
Journal of Marine Systems, 133: 77-78.
8. Gauthier D., Audemard C.A., Carlsson J.E., Darden T.L., Denson M.R., Reece K.S. & Carlsson J.
2013. Genetic Population Structure of US Atlantic Coastal Striped Bass (Morone saxatilis). Journal of
Heredity, 104 (4): 510-520.
9. Greco G., Svaldo Lanero T., Torrassa S., Young R., Vassali M., Cavaliere A., Rolandi R., Pelucchi El,
Faimali M. & Davenport J. 2013. Microtopography of the eye surface of the crab Carcinus maenas : an
atomic force microscope study suggesting a possible antifouling potential. Journal of the Royal Society
Interface 2013 10, 20130122. doi: 10.1098/rsif.2013.0122.
10. Hammond P.S., Macleod K., Berggren P., Borchers D.L., Burt L., Cañadas A., Desportes, G., Donovan,
G.P., Gilles A., Gillespie D., Gordon J., Hiby L., Kuklik I., Leaper R., Lehnert K., Leopold M., Lovell P.,
Oien N., Paxton C.G.M., Ridoux V., Rogan E., Samarra F., Schieidat M., Sequeira M., Siebert U., Skov
H., Swift R., Tasker M.L., Teilmann J.M., Van Canneyt O., Vazquez J.A. 2013. Cetacean abundance
and distribution in European Atlantic shelf waters to inform conservation and management. Biological
Conservation, 164: 107-122.
11. Hedger R.D., de Eyto E., Dillane M., Diserud O., Hindar K., McGinnity P., Poole R. & Rogan G. 2013.
Improving abundance estimates from electrofishing removal sampling. Fisheries Research, 137: 104–
115.
12. Keenan K., Bradley C.R., Magee J.J., Hynes R.A., Kennedy R.J., Crozier W.W., Poole R., Cross T.F.,
McGinnity P. & Prodöhl P. A. 2013. Beaufort Trout MicroPlex: A high throughput multiplex platform
comprising 38 informative microsatellite loci for use in brown trout and sea trout (Salmo trutta L.)
PUBLICATIONS
Aquaculture & Fisheries Development Centre Annual Report 2013
19
population genetics studies. Journal of Fish Biology, 82 (6):1789-804.
13. Keenan K., McGinnity P., Cross T., Crozier W.W. & Prodohl P. 2013. diveRsity: An R package for the
estimation and exploration of population genetics parameters and their associated errors. Methods in
Ecology and Evolution, 4 (8): 782-788.
14. Lynch S.A., Dillane E., Carlsson J. & Culloty S.C. 2013. Development and Assessment of a
Sensitive and Cost-Effective Polymerase Chain Reaction to Detect Ostreid Herpes virus 1 and Variants.
Journal of Shellfish Research, 32 (3), 657-664.
15. Lynch, S.A., Villalba, A., Abollo, E., Engelsma, M., Stokes, N. & Culloty, S.C. 2013. The occurrence of
haplosporidian parasites, Haplosporidium nelsoni and Haplosporidium sp., in oysters in Ireland.
Journal of Invertebrate Pathology, 112: 208-212.
16. Luque, P. L., Pierce, G. J., Learmonth, J. A., Rogan, E., Boon, J. & Lockyer, C.H. (2013). Are
Mineralization Anomalies in Common Dolphin Teeth Associated with Life-History Events And/Or The
Exposure to Anthropogenic Pollutants?Journal of Zoology, 291 (3): 194-204
17. Mackenzie C.L., Bell M.C., Birchenough S.N.R., Culloty S.C., Sanderson W.G., Whiteley N.M. &
Malham, S.K. 2013. Future socio-economic and environmental sustainability of the Irish Sea requires a
multi-disciplinary approach with industry and research collaboration, and cross-border partnership.
Ocean & Coastal Management, 8: 1-6.
18. Maloy A.P., Culloty S.C. & Slater J.W. 2013. Dietary analysis of small planktonic consumers: a case
study with marine bivalve larvae. Journal of Plankton Research. doi: 10.1093/plankt/fbt027.
19. Maloy A.P., Nelle P., Culloty S.C., Slater J.W. & Harrod, C. 2013. Identifying trophic variation in a
marine suspension feeder: DNA-and stable isotope-based dietary analysis in Mytilus spp. Marine
biology, 160 (2), 479-490.
20. Morgan E., O'Riordan R.M. & Culloty S.C. (2013). Climate change impacts on potential recruitment in
an ecosystem engineer. Ecology and Evolution, 393, 581-594.
21. Moura, A.E., Natoli, A., Rogan, E. & Rus Hoelzel, A. (2013). Evolution of Functional Genes in
Cetaceans Driven by Natural Selection on a Phylogenetic and Population Level. Evolutionary Biology,
40 (3): 341-354.
22. Moura, A. E., Natoli, A., Rogan E. & Hoelzel, A. (2013). Atypical Panmixia In A European Dolphin
Species (Delphinus delphis): Implications For The Evolution Of Diversity Across Oceanic Boundaries,
Journal of Evolutionary Biology, 26 (1): 63-75.
23. O'Farrell B., Benzie J.A.H., McGinnity P., de Eyto, E., Dillane E., Coughlan J. & Cross T. 2013.
Selection and Phylogenetics of Salmonid MHC Class I: Wild Brown Trout (Salmo trutta) Differ from a
Non-Native Introduced Strain. PLoS ONE, 8 (5): e63035.
24. Outerbridge M. & Davenport J. 2013. Malaclemys terrapin (Diamondback Terrapin). Dredging foraging
behavior. Herpetological Review, 44: 307-308.
25. Pazhayamadom D.G., Kelly C.J., Rogan E. & Codling E. 2013. Self-starting CUSUM approach for
monitoring data poor fisheries. Fisheries Research, 145: 114-127.
26. Santos A.R., Minto C., Connolly P. & Rogan E. 2013. Oocyte dynamics and reproductive strategy of
Aphanopus carbo in the NE Atlantic—Implications for fisheries management. Fisheries Research, 143:
161-173.
27. Santos A.R., Trueman C., Connolly P. & Rogan E. 2013. Trophic ecology of black scabbardfish,
Aphanopus carbo in the NE Atlantic—Assessment through stomach content and stable isotope
analyses. Deep Sea Research Part I: Oceanographic Research Papers, 77: 1-10.
28. Sullivan T., Broszeit S., O’Sullivan K.P.A., McAllen R., Davenport J. & Regan F. 2013. High resolution
monitoring of episodic stratification events in an enclosed marine system. Estuarine, Coastal and Shelf
Science 123: 26-33.
Aquaculture & Fisheries Development Centre Annual Report 2013
20
29. Thrupp T.J., Lynch S.A., Wootton E.C., Malham S.K., Vogan C.L., Culloty S.C. & Rowley A.F. 2013.
Infection of juvenile edible crabs, Cancer pagurus by a haplosporidian-like parasite. Journal of
Invertebrate Pathology, 114 (1): 92–99.
Published Abstracts
1. Prado-Alvarez M., Darmody G., Lynch S., Maloy A., Cotterill J., Wontner-Smith T. & Culloty S.C.
2013. In vivo immunostimulation of the flat oyster Ostrea edulis and tissue targeting by microspheres
uptake. Fish & Shellfish Immunology, 34 (6): 1731.
Non-Peer Reviewed Publications
1. Robert R., Sanchez J.L., Perez-Paralle L., Ponis E., Kamermans P. & O’Mahoney M. 2013. A glimpse
of the mollusc industry in Europe. Aquaculture Europe, 38 (1): 5-11.
Books
1. Allan G. & Burnell G. (Ed.s) 2013. Advances in aquaculture hatchery technology. Woodhead
Publishing Series in Food Science, Technology and Nutrition No. 242.
Oral Presentations
1. Cipriano A., Culloty S.C., Burnell G. & Ryan P. 2013. External and internal tagging methods for
Paracentrotus lividus. Asian-Pacific Aquaculture 2013, 11th-13th December, Ho Chi Minh City,
Vietnam.
2. Cipriano A., Culloty S.C., Burnell G. & Ryan P. 2013. Effects of immunostimulants on the purple sea
urchin Paracentrotus lividus. Asian-Pacific Aquaculture 2013, 11th-13th December, Ho Chi Minh City,
Vietnam.
3. Lynch S.A., Villalba A., Engelsma M., Stokes N.A., Burreson E. & Culloty S.C. 2013. A parasite can
have a significant impact on the ecology of the cockle Cerastoderma edule. SUSFISH 4Sea
Conference, 12th - 13th March 2013, Welsh Government Buildings, Llandudno Junction, Wales, UK.
Poster Presentations
1. Prado-Alvarez M., Darmody G., Lynch S., Maloy A., Cotterill J., Wontner-Smith T. & Culloty
S.C. 2013. In vivo immunostimulation of the flat oyster Ostrea edulis and tissue targeting by
microspheres uptake. 1st International Conference of Fish and Shellfish Immunology, 25th-28th June
2013, Vigo, Spain.
2. Flannery G., Lynch S. & Culloty S.C. 2013. Investigating the existence of a vector or reservoir of
Bonamia ostreae. 16th European Association of Fish Pathologists (EAFP) Conference, 4th September
2013, Tampere, Finland.
3. Lynch S.A. & Culloty S.C. 2013. Haplosporidium nelsoni and Haplosporidium amoricanum detected in
Irish oysters. SUSFISH 4Sea Conference, 12th - 13th March 2013, Welsh Government Buildings
Llandudno Junction, Wales, UK.
4. Lynch S.A., Morgan E. & Culloty S.C. 2013. Investigation into the prevalence and distribution of
pathogens in cultured and wild populations of mussels Mytilus spp. in Ireland. SUSFISH 4Sea
Conference, 12th - 13th March 2013, , Welsh Government Buildings Llandudno Junction, Wales, UK.
5. Lynch S.A., Cross M., O’ Grady, E., Morgan E., O’ Riordan R. & Culloty S. 2013. Shellfish
productivity in the Irish Sea: working towards a sustainable future (SUSFISH). SUSFISH 4Sea
Conference,12th - 13th March 2013, Welsh Government Buildings Llandudno Junction, Wales, UK.
CONFERENCE PRESENTATIONS
Aquaculture & Fisheries Development Centre Annual Report 2013
21
AFDC PERSONNEL
Dr Sarah Culloty, Director of the AFDC is PI with
the Shellfish Health research group and Senior
Lecturer with the School of BEES.
Professor Tom Cross, is PI with the Molecular
Genetics research group and Professor Emeritus
with the School of BEES.
Prof. Gavin Burnell is PI with the Aquaculture
Research Group. Gavin is also Vice Head of the
School of BEES and Acting Head of Zoology.
Dr Emer Rogan is PI with the Marine Mammals
and Fisheries Research Group and Senior
Lecturer with the School of BEES.
Dr Phil McGinnity is the Beaufort Marine
Research Award Principal Investigator with the
Molecular Genetics research group.
Prof. John Davenport is Professor Emeritus with
the School of BEES and has a particular interest
in aquaculture and the environment.
Dr Eileen Dillane is Postdoctoral Researcher with
the Molecular Genetics of Aquatic Animals Re-
search Group.
Dr Sharon Lynch is Postdoctoral Researcher with
the Shellfish Health Research Group working on a
range of projects within the group.
Dr Sarah Kraak, Postdoctoral Researcher with the
Marine Mammals and Fisheries Research Group,
working on the SeaChange project.
Dr Susie Brown is Postdoctoral Researcher with
the Marine Mammals and Fisheries Research
Group working on the Beaufort EAFM project.
Dr Maria Prado Alvarez, is Postdoctoral
Researcher with the Shellfish Health Research
Group working on oyster herpes virus.
Anneli Englund is a PhD student with the Marine
Mammals and Fisheries Research Group working
on vocalisations in marine mammals.
Deepak George Pazhayamadom is a PhD
student with the Marine Mammals and Fisheries
Research Group working on the application of
Signal Detection Methods to the Fisheries
Management.
Dr Jens Carlsson is Senior Researcher with the
Beaufort Fish Population Genetics project with
the Molecular Genetics of Aquatic Animals (until
July 2013)
Dr Jamie Coughlan is Senior Researcher with the
Beaufort Fish Population Genetics project with the
Molecular Genetics of Aquatic Animals.
Principal Investigators
Manager
Dr Maria O’Mahoney is Manager of the AFDC. Maria‘s
research background is in the application of novel
technologies to the aquaculture of sea urchins and abalone.
Researchers
Dr Thomas Reed is Senior Researcher with the
Beaufort Fish Population Genetics project with
the Molecular Genetics of Aquatic Animals (latter
half of 2013)
Aquaculture & Fisheries Development Centre Annual Report 2013
22
Emer Morgan is a PhD student with the Shellfish
Health Research Group working on the ERDF
funded SUSFISH project.
Grace Flannery is a PhD student with the
Shellfish Health Research Group. Grace’s
research is part of the EU FP7
OYSTERECOVER project.
Maud Cross is a PhD student with the Shellfish
Health Research Group. Maud’s research is part
of the EU FP7 SUSFISH project.
Moira McCarthy is a PhD student with the EU
FP7 Environment and Climate Change: Impacts
& Responses project. This project is supervised
by Prof. John O’Halloran (School of BEES), Dr
Frank van Pelt and Prof. Kevin James.
Ashlie Cipriano is a PhD student with the
Aquaculture Research Group. Ashlie’s research
investigates the effect of prebiotics and probiotics
on marine invertebrates in aquaculture.
Milaja Nykanen is a PhD student with the Marine
Mammals and Fisheries Research Group.
Milaja’s research investigates coastal bottlenose
dolphins in Western Ireland.
Elaine Brennan is conducting an MSc by research
with the Shellfish Health Research Group.
Grainne Darmody is Research Assistant with the
Shellfish Health Research Group. Grainne is
working on the EU FP7 funded project, BEADS
project.
Jeanette (Nettan) Carlsson is Research
Assistant with the Shellfish Health Research
Group. Jeanette is working on the EU FP7
funded OYSTERECOVER project.
Gema Hernandez-Milian is the Beaufort EAFM
PhD student with the Marine Mammals and
Fisheries Research Group.
Amy O’Reilly is a PhD student with the Shellfish
Health Research Group. Amy ‘s research is part
of the EU FP7 funded BIVALIFE project.
Ana Santos is a PhD student with the Marine
Mammals and Fisheries Research Group working
on the ecology of Black Scabbardfish
(Aphanopus carbo).
Daryl Gunning is a PhD student with the
Aquaculture Research Group. Daryl’s research is
based on IMTA.
Amy Geraghty is a PhD student with the Shellfish
Health Research Group. Amy is researching the
health status of Irish waters in marine reserve and
non-marine reserve areas.
Aquaculture & Fisheries Development Centre Annual Report 2013
23
CONTACT:
The Aquaculture & Fisheries Development Centre
School of Biological, Earth & Environmental Sciences
Distillery Fields, North Mall
Cork, Ireland
Director: Dr Sarah Culloty
Manager: Dr Maria O’Mahoney
Email: [email protected]; [email protected]
http://afdc.ucc.ie