Biological, Earth and Environmental Sciences - Doctoral Theses

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Lead toxicity in Mute swans: Cygnus olor (Gmelin)
(University College Cork, 1987) O'Halloran, John; Myers, A. A.
Lead toxicity in Mute swans Cygnus olor (Gmelin) was investigated. Two methods for the assessment of lead exposure were used: (1) blood lead level and (2) free red blood cell protoporphyrin. An accurate estimation of haemoglobin was found to be a prerequisite to determining lead exposure. A measurement of haemoglobin based on converting all haem species to alkaline haematin was found to give accurate and reproducible results. Variation in blood lead during the diel cycle in caged birds was investigated. Blood lead levels in a flock of Mute swans at a coarse-fish angling site were examined over a two year period. Forty-two percent of blood samples (n = 870) from this site were shown to have elevated lead. X-ray examination of swans revealed the source of contamination to be ingested lead pellets. Post mortem examination showed that 68% (n = 101) of all Mute swans examined died from lead poisoning. Two sources of lead were identified: spent gunshot and lost or discarded anglers' weights. Biochemical and haematological aspects of swan blood were also investigated. Reference haematological and biochemical values were established from 'normal' healthy Mute swans. These reference values were used as a baseline against which changes in lead poisoned birds could be measured. Moulting and immaturity were identified as causing natural variation, while acute lead poisoning was found to increase protoporphyrin, cholesterol and two serum enzymes: lactate dehydrogenase and aspartate amino transferase. Hypochromic anaemia was noted in swans suffering from acute lead poisoning. The possible role of lead in causing other sub-lethal effects, for example collisions, is also discussed.
Monitoring mammals in airfield environments; a case study of the Irish hare at Dublin Airport
(University College Cork, 2022) Ball, Samantha; Butler, Fidelma; Caravaggi, Anthony; Irish Research Council for Science, Engineering and Technology; Dublin Airport
The number of reported wildlife-aircraft collisions (i.e., strikes) with mammal species is increasing globally with severe consequences for passenger safety, industry economics and wildlife populations. Despite this, little research has been conducted on the class Mammalia in airfield environments, with strike mitigation research efforts predominantly focused on avian species. This thesis addresses some of the wildlife hazard issues faced by the aviation industry, specifically looking to mammal species. The thesis focuses on developing ecological survey methods for mammals in airfields and exploring the role of ecological data in informing strike risk. The Irish hare (Lepus timidus hibernicus) population at Dublin airport is used as a population case study to assess survey methods in an airport environment, throughout. As little is known about mammal strikes on a global scale, strike records with mammals from available literature and national aviation authorities are collated in chapter 1. These data highlighted that mammal strikes are widespread and identify 42 mammal families involved in strike events in 47 countries and demonstrate that reported mammal strike events have been increasing by up to 68% annually. Looking to mammal management measures on a European scale for chapter 2, the most successful mammal mitigation measures were identified as: (i) the management of watercourses within the airfield; (ii) the implementation of specific grass cutting regimes (94.4%) and (iii) the management of waste products at the airfield so as not to attract or sustain wildlife (93.8%). Utilising historical strike data in chapter 3, it was demonstrated that hare strikes have been increasing by an average of 14% annually at Dublin Airport with over 340 recorded wildlife strikes since 1997. The kinetic energy of such an event (10,576 J) is substantial enough to inflict damage to the landing gear of an aircraft, although this has never been reported to have occurred. As the basis of effective wildlife management practices necessitates reliable estimates of the population size, design and model-based distance sampling methods were compared, alongside Random Encounter Modelling, to establish ecological survey methods suitable for monitoring mammals in airfields for chapter 5. Population estimates ranged from 29 (SE ± 9) to 133 (SE ± 19) individuals, with the most robust model (nocturnal line transects), estimating a population size of 118 (SE ± 21) hares at Dublin Airport. A concern regarding mammal strike events is not only the strike event itself, but the secondary strike risk with a predatory or scavenger species. Camera trap surveys were utilised to identify secondary strike risk in chapter 4. It was identified that birds take an average of 2 hours and 23 minutes to detect a mammal carcass following a replicated strike event at Dublin Airport and an average of 11 hours 40 minutes for mammal species to detect a carcass. These data indicate that current clean-up practices at Dublin Airport (i.e., immediate clean-up and closing of the runway to facilitate clean-up operations) are likely adequate for reducing the likelihood of a secondary strike event. This thesis presents some of the first data collected through remote monitoring methods (camera traps/ GPS trackers) to inform of airside wildlife hazard. These methods, in addition to overlap analysis and cross correlation functions have demonstrated that recorded strike times are closely associated with hares’ circadian activity and largely dissociated with aircraft movements (chapter 6). Additionally, data collected via GPS tracking devices in chapter 7 demonstrated that the hares at Dublin Airport have an average home range size of 0.28 km2 (±SD 0.1 km2), based on 95% Kernal Density Utilisation Distribution. What’s more, it is demonstrated that the hares incorporate active area habitat types (i.e., runways and taxiways) into their home ranges with up to 13% of one individual’s movements incorporating these areas. These data have fed directly into the Wildlife Hazard Management Plan at Dublin Airport and instigated targeted strike mitigation measures. Throughout this thesis, the importance of ecological data for informing strike risk and mammal management in airfield environments is highlighted. While the Irish hare is used as a case study for ecological field methods in airfield environments, this thesis also broadly demonstrates the extent of mammal related issued at airfields worldwide. Thus, although here the focus is on a specific species at a specific airport, the developed methodologies are suitable for cohort of terrestrial mammals inhabiting airfield environments worldwide.
Genetic basis and fitness consequences of migration in facultatively anadromous brown trout Salmo trutta
(University College Cork, 2023) Wynne, Robert; Reed, Thomas; McGinnity, Philip; European Research Council; Science Foundation Ireland
Animal migration is a widespread, but complex phenomenon, that evolves in response to spatial, temporal or ontogenetic separation of optimal feeding and breeding habitats. Considerable diversity in migratory behaviours and associated physiological, morphological and life-history traits can occur even within a single species, making it challenging to understand the various evolutionary and ecological processes involved. This thesis focuses on brown trout (Salmo trutta) as an excellent model species to study the drivers and consequences of alternative migratory tactics, as they display a vast continuum of migratory life histories, even within one population. Until recently, relatively little was known about the genetic mechanisms and selective pressures shaping the huge variation in migratory life histories in brown trout and other salmonids. Advances in molecular biology (the ‘omics revolution’), coupled with increasingly sophisticated telemetry techniques for studying movement behaviours in the wild, are now facilitating improved understanding of how migratory phenotypes are shaped by complex interactions between genes and environment. This, in turn, informs conservation and management of facultatively anadromous species in rapidly changing environments. The overarching aims of this thesis are to provide a deeper understanding of the genetic/evolutionary basis of migration in brown trout, but also to use genetics as a tool to gain insights into basic aspects of brown trout biology. The first data chapter (Chapter Two of the thesis) involved a common garden experiment undertaken in the Burrishoole catchment (northwest Ireland), which tested for heritable differences in migratory life history among geographically proximate, partially reproductively isolated, brown trout populations. Six different types of genetic crosses were made using wild-sourced broodstock. The progeny were then released into an experimental section of the Srahrevagh River (Burrishoole catchment) and their subsequent fates and movements tracked across three years using electrofishing surveys, trapping facilities and passive integrated transponder (PIT) telemetry, coupled with genetic parentage assignment (microsatellite markers) to assign sampled juveniles back to genetic cross types. The key findings of this chapter were that early movement behaviours (emigration from the river) and smolting rates (emigration to sea) differed among cross types, consistent with there being a quantifiable genetic basis to alternative migratory tactics. The contemporary sea trout run in the Burrishoole system is a remnant of what it once was, yet the numbers of resident/potamodromous brown trout remain apparently healthy. The results of Chapter Two imply that rapid evolutionary responses to anthropogenic environmental change could partially explain this switch away from anadromy towards residency. Although it has long been known that migrants and residents can co-occur within the same trout population, the underlying molecular mechanisms driving alternative life histories has remained poorly understood. Therefore, in Chapter Three, I performed transcriptional profiling (RNA sequencing or “RNA-seq”) of brain and liver tissues collected from immature brown trout smolts (migrants) and mature residents, in the context of a tank-based laboratory experiment. The results stated in chapter three provide new insights into tissue - and sex-specific gene expression patterns and associated molecular processes (particularly metabolism-associated pathways within the liver) that underlie the production of alternate migratory life histories and physiologies. In Chapter Four I then examined a different but related aspect of phenotypic diversity in brown trout, namely the long-recognised yet poorly understood phenomenon of autumn versus spring outmigration (from the river into sea), using genetic identity analysis complemented with physical tagging (PIT telemetry) within a wild population of brown trout located in northwest Ireland (Burrishoole catchment). Both autumn and spring migrants exhibited a sex bias towards females, but was stronger in spring than in autumn outmigrants, implying that the fitness costs and benefits of adopting either strategy may differ between the sexes. Crucially, I also found that autumn outmigrants returned to freshwater at a similar rate and only slightly smaller size than spring outmigrants, despite the former category being much smaller on leaving freshwater and spending longer away overall than the latter category. These findings suggest that autumn outmigrants are not a demographic dead-end and may be key contributors to the overall gene pool. There is a brackish lagoon (Lough Furnace) at the freshwater-marine interface in this catchment that may support the maintenance of these evolutionarily important alternative migratory tactics. My results emphasise how autumn outmigrating trout, and the transitional habitats that support their existence, should not be overlooked in the context of evolutionarily enlightened fisheries management. Collectively, the body of work presented in this thesis has shed new light on the molecular mechanisms and ecological/evolutionary processes involved in facultative animal migration and the maintenance of intraspecific phenotypic diversity in a culturally and economically important fish species. It is increasingly apparent that a “one size fits all” approach to management and conservation is suboptimal for species exhibiting complex life history patterns where a single population may express multiple life histories concurrently including for example as observed here partial migration and run time variation. Future genomics, transcriptomics and epigenomic work, coupled with detailed behavioural and physiological investigations, will aid progress towards a more holistic understanding of the evolutionary ecology of migration.
How seabirds respond to a changing oceanic environment: a biologging approach
(University College Cork, 2023) Darby, Jamie; Jessopp, Mark John; Quinn, John; Irish Research Council; Petroleum Infrastructure Program
Marine habitats are undergoing rapid change due to human influences. The intensity and diversity of human impacts on oceanic habitats are increasing with rising demand for energy and resources. For example, fisheries operate in over 90% of the ocean, harvesting marine life and directly affecting ecosystem functions and resilience. Climate change is also changing the physical and chemical properties of the ocean and altering storm frequency and intensity at a global scale. Seabirds are a group of marine predators that are sensitive to such changes, with impacts contributing to global population declines. We broadly understand how stressors affect different species through effects on life histories and physiological traits, and where seabirds are most impacted based on spatiotemporal overlap of seabirds with human activities. However, finer scale behavioural data are required to understand the functional response of seabirds to different stressors. Biologging devices are continuously improving and miniaturising, being applied to collect fine-scale behavioural information for smaller species and for more protracted durations. In this thesis, biotelemetry is used to investigate the at-sea behaviour of three North Atlantic seabird species in order to understand the drivers of distribution. A better understanding of such drivers sheds light on the challenges facing seabird species when far from land, susceptibility to stressors, and provides insights into more effective monitoring and conservation efforts. Chapter 1 provides a broad introduction to seabird ecology, the application of biologging, and identifies model species for investigating seabird responses to a range of environmental stressors. Chapter 2 investigates the diving behaviour of Manx shearwaters (Puffinus puffinus) and how this correlates with water clarity, which is predicted to deteriorate with increasing urbanisation, eutrophication, and climate impacts. Chapter 3 highlights the relative importance of commercial fisheries compared to other environmental variables in driving the foraging distribution and behaviour of northern fulmars (Fulmarus glacialis) during the breeding season. Chapter 4 expands on this by identifying fulmar-vessel encounters in the non-breeding season, showing how nocturnal vessel attendance is increasing over time, and the apparent relationship with migration effort and time-activity budgets. Chapter 5 identifies unusual levels of variability in the moult period of Atlantic puffins (Fratercula arctica), when they are flightless and more susceptible to climate impacts that may prevent them from foraging. Variability in moult strategy is tied to susceptibility of populations to risks posed by severe winter storms. Chapter 6 provides a synthesis of findings from previous chapters, highlighting how the methods and principles developed may be built upon to further improve our knowledge of seabird ecology and design appropriate conservation measures. Building on insights from previous chapters, I discuss how seabirds are likely to functionally respond to several stressors in the marine environment, including fisheries practices, climate change, and shifting prey availability. Several recommendations are made for further research, including exploring mitigative measures that can be employed to tackle the negative effects of changes to their environment.
Spatiotemporal modelling of antimicrobial resistance in the Irish subsurface environment
(University College Cork, 2023-01-31) Albuquerque de Andrade, Luisa; O'Dwyer, Jean; Weatherill, John; Hynds, Paul; Science Foundation Ireland; Geological Survey of Ireland
Antimicrobial resistance represents a significant public health risk, with global estimates indicating that as many as 1.27 million deaths were directly attributable to antimicrobial resistant infections in 2019. The adverse human health effects attributed to the continuous rapid spread of antimicrobial resistance are particularly pressing in the aftermath of the COVID-19 pandemic, which highlighted societies’ acute susceptibility to infectious diseases in the absence of effective treatment options. The proliferation of antimicrobial resistant bacteria (ARB) was also acknowledged as the key emerging issue of environmental concern by the United Nations Environmental Programme in 2017. Despite this, the natural environment’s role in the spread of ARB-related infections remains unclear. In this context, ARB presence in groundwater resources represents a noteworthy concern, as these can act as prospective reservoirs, while offering a direct exposure route to the over 2.2 billion groundwater consumers worldwide. In the Republic of Ireland (RoI), private groundwater wells supply approximately 11% of the population, with these users already associated with increased incidence rates of waterborne infections. Indeed, Irish private wells have been linked to persistent microbiological contamination attributable to inadequate on-site domestic wastewater treatment systems and the widespread agricultural activities associated with the Irish rural landscape; both of which are also potential sources of ARB. Thus, and in combination with a diverse (hydro)geological profile and a temperate climate characterised by the absence of a dry season, the RoI may present the ‘perfect storm’ for groundwater contamination by ARB and subsequent adverse human health effects. To-date, however, just one spatiotemporally limited study exists which investigates this issue within the RoI, leading to significant knowledge gaps regarding the spatial and temporal dynamics of ARB contamination in Irish groundwater environments. Accordingly, the current research blends systematic literature review and pooled analyses, traditional hydrogeological fieldwork, geo-referencing, molecular microbiology, analytical chemistry, genome sequencing, and statistical modelling to quantify occurrence rates and elucidate the potential drivers of ARB contamination in groundwater resources. The overarching aim of this research is to better understand ARB presence in Irish groundwater supplies and inform appropriate source-protection strategies, in line with Sustainable Development Goals 3 ("good health and well-being") and 6 ("clean water and sanitation for all”). Research findings indicate that groundwater resources may represent a global reservoir/pathway for ARB, with 80.2% ± 29.0 of groundwater-derived bacteria from studies in the systematic review exhibiting resistance/intermediate resistance to at least one antimicrobial. In the RoI specifically, the analyses of monitoring data from a 10-year period showed Escherichia coli contamination in 66.7% of monitored (regulated) water supplies nationwide at least once, with pastoral agriculture (a well-known potential source of ARB in addition to faecal bacteria contamination) identified as a key risk factor. Additionally, fieldwork data identified antimicrobial resistance in 16.7% of Escherichia coli (8/48) but none of the Pseudomonas aeruginosa (0/6) collected from 132 geographically dispersed (unregulated) private wells in the RoI sampled during autumn 2019 and summer 2021. Fieldwork results also revealed that the presence of resistant E. coli was significantly associated with increased local cattle density (OR = 1.028; p = 0.037), having likely been transported into wells via surface run-off followed by direct wellhead ingress. Moreover, lack of statistical significance (p ≥ 0.084) between overarchingly low concentrations of co-selective (i.e., metal/metalloid) parameters and antimicrobial resistance gene abundance in E. coli isolates lead to the hypothesis that E. coli may have acquired resistance prior to entering these groundwater supply environments. With that, findings suggest contamination of rural groundwater resources with ARB in the RoI as being highly preventable by ensuring appropriate source protection measures. Research results bridge the gap between hydrology, geoscience, and heath, promote capacity building, and inform the development of effective policy for groundwater management and antimicrobial resistance action plans into the future.

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