Sean Kelly

Marine Institute Cullen Fellow

Project Title: Hydrographic control of deep anoxia in a tidally influenced saline lagoon and associated ecological implications

Low dissolved oxygen concentrations are of increasing concern in aquatic ecosystems, particularly those located at the interface between freshwater and marine environments. Hydrographic conditions, specifically vertical stratification of the water column and restricted horizontal exchange flow with adjacent oxygenated basins, can create hypoxic deep water conditions, with total anoxia developing in the extreme case. With climate change modifying these controlling hydrographic factors in coastal and estuarine systems, it remains to be seen what impacts the resulting changes to dissolved oxygen dynamics will be.

This project uses Lough Furnace, a protected, ecologically important coastal lagoon with naturally occurring deep anoxia, as a small scale test bed for studying the hydrodynamic processes that govern dissolved oxygen dynamics and to assess the ecological implications of anoxia. Specifically, it will look at how saline stratification and restricted input of oxygenated tidal water can lead to the isolation and long residence time of the deep basin water, with stagnant and oxygen deplete conditions persisting for years at a time. The study will assess the necessary combination of hydrographical and meteorological conditions that can lead to a renewal of this stagnant basin water and what the biological consequences are of these rare, dynamic renewal events. In addition, effects of the stratified structure of the lough on resident ecological communities will be investigated, primarily the importance of wind-driven upwelling of deep anoxic water into shallower, productive nearshore zones. It is anticipated that the overall results of this project will have wide application to aquatic systems susceptible to developing low dissolved oxygen zones, an increasingly common issue due climate and anthropogenic impacts.


Brian Doyle M.Sc. B.Sc.

Marine Institute Cullen Fellow


Project Title:  Resolving the organic carbon budget of a humic oligotrophic lake in the west of Ireland

Waters draining peat catchments are generally coloured due to high levels of dissolved organic carbon.  This carbon can represent the main carbon source to downstream lakes and therefore fuel the lake food-web.  Human activities have greatly modified global carbon exchange between the atmosphere, land and freshwater bodies in recent decades, including in peatland catchments.  Knowledge about the redistribution of this carbon is crucial, not only to understand global cycling, but for mitigation and management in affected catchments.  This project is investigating the carbon cycle in Burrishoole, Co Mayo, which is a humic catchment, building on work that has already been undertaken in recent years.  Specifically it is using high frequency monitoring data from in-situ platforms in Lough Feeagh, and in its main inflows and outflows to:

  1. Quantify the dissolved organic carbon and particulate organic carbon loads to Lough Feeagh.
  2. Collect new data to measure the atmospheric carbon fluxes from Lough Feeagh.
  3. Use these and other available historical data to resolve the carbon budget for the lake.

The information and insights gained from this project will help to inform on the main sources of carbon for the Burrishoole fish populations and on the carbon loading to down-stream ecosystems.


Aisling Doogan

Marine Institute Cullen Fellow

Project title: Investigation into the causes of early migration mortality in Atlantic salmon (Salmo salar) and sea trout (Salmo trutta) from the Burrishoole National Index River using acoustic telemetry in freshwater & coastal areas

As anadromous species, Atlantic salmon and sea trout are dispersed across different habitat types which can make it difficult to identify the various pressures affecting the fish during their life cycle.  This project involves the use of acoustic telemetry in order to describe and map the migration routes taken by smolts during their seaward migration from the Burrishoole catchment and through Clew Bay, Co. Mayo.   In particular survival will be estimated, partitioning of mortality during this early seaward migration and the influence of factors such as predation, obstacles, habitat features and body size will be evaluated.

In addition, annual survival rates of tagged fish will be obtained from coded wire tag returns.  In 1980 the Irish National Coded Wire Tag (CWT) and Recovery Programme was introduced in order to increase the understanding of salmon populations and determine the exploitation rates of various fisheries (Hansen et al and Brown 1982).  This programme provides an extended time series of return rates for hatchery and wild fish that can be used to investigate regional and annual trends in survival and to evaluate the effectiveness of management interventions.  Effects of the drift net fishery closures (in 2007) on survival will be examined.  Changes in fish size over time and migration routes will also be investigated using catches from the drift net fisheries.

Finally, an extensive archive of salmon scales is held by the Marine Institute.  Potential relationships between local and global environmental drivers and changes in growth and survival will be investigated.

Ross Finlay  MSc.

Marine Institute Cullen Fellow

Project Title:  Investigation of the early migration of salmon and brown trout from the Burrishoole National Index River using PIT tag technology in freshwater and brackish areas.

It has been shown that salmonid performance and ultimately survival depend on close synchrony between onset of key phenological events, such as smoltification or the commencement of marine migration, and the environmental conditions subsequently encountered (i.e. sea surface temperature). The timing of these events is influenced by local environmental conditions such as water temperature and river height which may vary significantly between years. Consequently, the effects of predicted climate change are likely to impact salmonid phenology, potentially leading to a disruption of the synchrony between key life history events and the optimum environmental conditions for these events. Ultimately, such disruptions may lead to reduced fitness and, in the absence of rapid phenological adaptation, declining salmonid populations.

This project aims to examine the role of local freshwater environmental conditions in determining the phenological behaviour, growth and survival of salmon and brown trout with the ultimate goal of anticipating the effects of predicted climate change on these species. To this end, long term data on migration phenology, survival and concurrent climatic variables will be used in conjunction with modern PIT telemetry methods, facilitating an investigation at the individual and the population level.


Sian Egerton MSc.

IRC’s Enterprise Partnership Fund with Biomarine Ingredients Ltd

APC Microbiome Institute

Project title: Investigating the effects of fish protein hydrolysate supplementation of plant protein-based diets in juvenile freshwater Atlantic salmon (Salmo salar)

There are two major challenges that the aquaculture industry is currently facing; 1.) how to reduce disease among farmed fish, and 2.) the manufacture of nutritionally balanced and sustainable compound diets that will produce healthy, high quality fish. These challenges are not mutually exclusive, and it is expected that optimum feed formulation will play a role in the reduction of infectious disease through improving animal health and immunity.

This project aims to address these industry challenges by developing a high-quality natural supplemental nutritional ingredient (fish protein hydrolysate) that can be added to a high plant protein diet to enhance the health, nutrition, growth and stress-tolerance of Atlantic salmon (Salmo salar).  Reducing the amount of fishmeal used in aquafeeds and replacing it with plant-protein is currently being researched. One proposed method by which this is achievable is the use of smaller quantities of appropriately balanced, highly absorbable and convertible protein. With the aim of reducing the consumption of valuable fish sources, while meeting the nutritional needs of aquaculture stock, fish by-products and low-value fish sources can be converted into high-quality protein sources such as protein hydrolysates. This study will investigate the effect of dietary protein hydrolysates on the immune levels, growth rates and body composition to juvenile Atlantic salmon in the freshwater developmental stage.