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Experimental catchment

The Burrishoole river system (53º55’N 9º34’W) in the west coast of Ireland is home to the Marine Institute’s Newport Facility.  This freshwater catchment consists of a total area of 8949 ha drained into two lakes by 45 km of small shallow streams. before eventually discharging into the north east corner of Clew Bay.

The Marine Institute is situated between these two lakes; a freshwater lake (Lough Feeagh) and a tidal, brackish lake (Lough Furnace).  These lakes are connected by two channels at which sea entry traps are located (known locally as the Mill-Race and Salmon Leap traps), the traps have monitored the downstream and upstream movements of fish since the 1970s.  Census data on Salmon (Salmo salar)Sea trout (Salmo trutta) and eels (Anguilla anguilla) has been crucial for the conservation of these species as well as informing fishery targets.

Data collection is used extensively by ICES (International Council for the Exploration of the Seas) to monitor the overall status of Irish stocks on an annual basis and as such Burrishoole is utilised as one of the key index systems for Salmon, Sea trout and eel populations in the North Atlantic.


Another fish trap also exists on one of the many tributaries of the river system called the Srahrevagh river.  This trap allows for the monitoring of juvenile salmonid life phases and is capable of capturing all downstream movements.

The Institute also records environmental data; two Automatic water quality monitoring stations (AWQMS) are maintained on both lakes.  These systems are moored on buoys to the middle of each lake transmitting data back to base on temperature, conductivity, salinity, turbidity and pH every two minutes via an electronic sensor and telemetry system.

Rearing and Hatchery

The Marine Institute in Newport runs a comprehensive range of freshwater salmonid fish rearing facilities.  This includes two isolated hatchery units with egg incubation structures and indoor and outdoor pond rearing facilities with state of the art effluent treatments.  The Institute collects and holds broodstock returning to Newport as part of a captive breeding programme started in the 1960s.  Ranched fish are then released into the wild each year during the smolt-run.

(All images are accredited to the Marine Institute)

Molecular laboratory facilities

We undertake genetics/genomics work at our molecular laboratories in both UCC and QUB.  Both laboratories are well equipped for basic DNA/RNA extraction, PCR, gel electrophoresis and microsatellite genotyping work.  QUB has an Applied Biosystems 3500xL Genetic Analyzer 24-Capillary Array for sequencing fragment analysis, which is used mainly for microsatellite genotyping purposes.  UCC has recently acquired the same instrument, thus doubling our overall throughput potential in this regard. The UCC molecular lab also has a real-time qPCR machine, which can be used for targeted gene expression work and we are moving towards establishing a medium throughput single nucleotide polymorphism (SNP) platform at UCC also.
Through links with the recently established Genomics Core Technology Unit (CTU) suite at QUB, Prof. Paulo Prodohl and colleagues are developing a range of genomic pipelines using Next Generation Sequencing (NGS) technology. This includes SNP discovery, genotyping by sequencing protocols, RADseq, shotgun sequencing, transcriptomics via RNAseq, epigenomics via busulfite sequencing, and more.

 Experimental aquaculture facilities

At UCC we have constructed a state-of-the-art recirculation system that can run on freshwater or saltwater (housed in the Cooperage Building, as part of the Aquaculture and Fisheries Development Centre (AFDC)).  Currently there are 18 tanks in this set-up in a 14,000 litre system and each tank can experience one of two different water temperature regimes (see schematic below). Automated feeders on each tank, connected to a controlling unit, allow for precise control of feed levels. The system is also set up with an automated oxygen and temperature monitoring and alarm system. 
This system was designed and constructed by  Luke Harman and Steve Hutton.
 At the AFDC in UCC we also have the capacity to measure fish metabolic rates using an intermittent flow respirometry system.

Fish Eye Research Group