Biological, Earth and Environmental Sciences - Doctoral Theses

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The role of biofluorescence in the health and welfare of integrated multi-trophic aquaculture species
(University College Cork, 2024) Juhasz-Dora, Thomas; Doyle, Thomas; Maguire, Julie; Horizon 2020
Biofluorescence in marine organisms is emitted as a lower wavelength light by the fluorophore compounds present within their bodies after excitation by the blue-shifted light of the water column. Biofluorescence produced in healthy scleractinian coral tissue has been applied as a non-invasive monitoring tool for gauging the physiological response of corals to environmental stress and disease outbreaks. By measuring shifting levels of fluorescent emissions in tissue, changes in the physiological status can be identified. However, the presence of and responsiveness of biofluorescence to stress in higher order marine organisms used in aquaculture operations is unknown. The first phase of this thesis assessed whether biofluorescence was produced in seven economically valued species present within the northeast Atlantic Ocean: the commercially valued macroalgal species Laminaria digitata, Palmaria palmata, and Saccharina latissima, the green sea urchin Strongylocentrotus droebachiensis, the European black sea cucumber Holothuria forskali, the red king crab Paralithodes camtschaticus, and the lumpfish Cyclopterus lumpus. Biofluorescence was documented in all species, with the complex emissions produced from physical damage or released exudates in sea urchins, while the lumpfish biofluorescence differed according to life stage and sex. The second phase of this study assessed whether biofluorescence responded to stressors typically experienced in aquaculture. Green sea urchins exposed to three environmental variables (out of water transport, in water transport at elevated temperatures, and in water transport at ambient temperature) produced fluorescent emissions in response to all treatments in their external anatomy but varied in intensity according to treatment type, time interval sampled, and in their coelomic fluid fluorescence. Furthermore, the fluorescence emissions in the red king crab were responsive when subjected to the out of water shipping methodology used for market transport, increasing in both the external anatomy and the haemolymph after exposure. Likewise, lumpfish subjected to a freshwater therapeutic bath used to control parasites increased fluorescent emissions in the green spectra, while the control group placed back into saltwater did not increase in intensity. The identification of reproductive development stages in macroalgae was tested using fluorescence. The exploration of fluorescent emission within the blades found differences in intensity according to whether reproductive sori were present in the blade. Biofluorescence has been found through these studies to be an effective alternative method(s) to non-invasively assess subclinical stress, wounds, and even reproductive status in marine organisms on a real-time basis. The third phase of this thesis was a pharmacokinetic study of European black sea cucumber Holothuria forskali tissue after the animals ingested salmon pellets simultaneously treated with the recommended dosages for the Atlantic salmon therapeutants emamectin benzoate and oxytetracycline. Liquid chromatography with tandem mass spectrometry detected greater bioavailability of oxytetracycline in sea cucumber tissue, requiring 18-34 days for elimination in comparison to the 9-14 days for emamectin benzoate. These results reflect a more realistic scenario of how sea cucumbers react to feeding on organic matter containing veterinary therapeutants, helping to define a baseline for the withdrawal period for the two compounds in sea cucumber tissue as well as for further studies on the dynamics within actual field conditions.
The taphonomy of anurans from the Eocene Geiseltal Konservat-Lagerstätte
(University College Cork, 2024) Falk, Daniel; McNamara, Maria; Wings, Oliver; Irish Research Council for Science, Engineering and Technology
The Eocene Geiseltal fossil site is represented by ca. 50,000 fossil specimens that were recovered from open-cast lignite mines in central Germany in the early to mid-20th century. The fossils were excavated primarily from organic-rich sediments of lacustrine and fluvial deposits and are curated in the Geiseltal Collection of the Natural Sciences Collections of the Martin Luther University Halle-Wittenberg in Halle (Saale). The fossil collection includes vertebrates, invertebrates, plants and trace fossils. Despite its rich fauna and flora, the taphonomy of the biota is poorly understood. This is because the primary fossil collections, studied extensively in the early 20th century, were not accessible for study using modern techniques. The Geiseltal biota is famous for reports of three dimensionally preserved soft tissues; the subcellular anatomical details described for various soft tissues in different vertebrate groups and in the anurans in particular, represent a fidelity of preservation that is among the highest known for any Konservat-Lagerstätte. Intriguingly, the proposed mode of preservation, direct replication in silica, is not known in other fossils, but has not been verified using modern approaches. This thesis addresses these issues using quantitative taphonomic approaches, microbeam techniques (scanning electron microscopy, micro-Fourier transform infrared spectroscopy, micro-Raman spectroscopy, X-ray diffraction and synchrotron rapid scanning-X-ray fluorescence) and statistical analysis to elucidate the taphonomy of the Geiseltal anurans (i.e., frogs and toads). Critical assessment of trends in the articulation and completeness of the fossil anurans reveals a hierarchy of taphonomic controls, whereby preservation is controlled at the specimen level by the size and location of bones, by the three-dimensional configuration of joints, by the impact of predators and scavengers, by the duration of pre-depositional transport and the impact of bottom currents on the lake floor. The studied Geiseltal anurans lack most of the soft tissues reported originally; there is no evidence for preservation in silica. Instead, the only soft tissue features present are melanosome films and the anuran-specific mid-dermal Eberth-Katschenko (E-K) layer, preserved as sulfurised organic remains and as a phosphatised replacement, respectively. Multivariate analysis of geometry data of melanosomes preserved in anurans from Geiseltal, other fossil biotas and extant anurans reveals that the evolution of melanosomes in the skin is decoupled from that of melanosomes in the eyes and internal tissues. This most likely reflects disparate physiological constraints on melanosome function since the Middle Eocene. In summary, comparison of the taphonomy of the Geiseltal anurans with fossils from other lacustrine Konservat-Lagerstätten reveals that the skeletal and soft tissue features of the Geiseltal anurans are not unique. The mode of preservation of the Geiseltal anurans also applies to anurans from other lacustrine Konservat-Lagerstätten, revealing high-level controls on the preservation of anurans in the fossil record. The major controls on skeletal taphonomy are the broad palaeoclimatic setting, which controls lake water temperature, lake physiography, which controls the lake depth and lake size and anatomy, which control the size and location, respectively, of bones. These results potentially apply to other vertebrate groups. The major controls on the preservation of anuran soft tissues are the availability of phosphate ions and reduced sulfur species, the development of microenvironments during decay and the tissue chemistry. This thesis highlights the power of combining quantitative, analytical and comparative approaches to assess the skeletal and soft tissue taphonomy of fossil vertebrates in order to develop models for the preservation of fossil vertebrates in lacustrine environments. This thesis also demonstrates that comparative analysis of melanosome data from fossil and extant specimens in a single vertebrate group can inform on the evolution of melanin in that group. Finally, scientific investigation of fossil collections using modern analytical techniques is essential to critically re-evaluate both historical fossil interpretations and established scientific paradigms.
The spatial ecology and conservation of an important game bird in Ireland: the Eurasian woodcock
(University College Cork, 2024) O'Neill, James B.; Quinn, John; Holloway, Paul; Hoodless, Andrew; Irish Research Council; National Association of Regional Game Councils; Game and Wildlife Conservation Trust; National Parks and Wildlife Service
A wide range of species are targeted by human hunters, including those with uncertain or poor conservation status. However, the direct and indirect effects of this exploitation can be complex and are often poorly understood. The Eurasian woodcock (hereon woodcock) is a largely migratory ground-nesting bird in the family Scolopacidae associated with forested habitat, and is commonly hunted by humans across its European range. The direct and indirect effects of hunting on this species are generally poorly known, and it can be difficult to study owing to its elusive and crepuscular habits. On the island of Ireland, the woodcock population comprises both resident breeding birds and migratory overwintering birds which originate from areas such as Fennoscandia, the Baltic States and Russia. The breeding population is thought to have declined in recent decades, with available evidence suggesting a range contraction of over 70% between 1968 and 2011, whilst trends for migratory birds are unknown. However, the species is popular among hunters in Ireland, and no information exists as to how hunting activity affects its population or ecology. To address these knowledge gaps, this research had four main objectives: i. Establish an understanding of the current distribution and abundance of breeding woodcock in Ireland, and the environmental drivers that influence these, through a nationwide ‘roding’ survey from 2017 to 2021 and a two-step species distribution modelling (SDM) method. ii. Explore whether hunting and bird age affected the survival of non-breeding woodcock using radiotelemetry to monitor the fates and activity of 168 tagged birds across three hunted and three not hunted sites. iii. Explore whether hunting and bird age affected the use of space and movement ecology of non-breeding woodcock using global positioning system (GPS) tracking of 42 birds across three hunted and three not hunted sites. iv. Assess woodcock habitat preferences in the context of heterogenous Irish landscapes, and explore whether hunting affects habitat preferences using GPS tracking of 42 birds across three hunted and three not hunted sites. These objectives produced the following key results: i. National roding survey results and SDM outputs estimated that breeding woodcock are more widespread in Ireland than recently reported, with a population estimate of 27,434 males (95% CL: 16,947 - 36,288). Bioclimatic variables, including precipitation and temperature seasonality and mean winter temperature, were important determinants of woodcock distribution, whilst forest habitat availability and composition at different landscape scales significantly influenced their abundance. ii. Survival of overwinter woodcock across the six sites was high relative to the findings of comparative studies, with an estimated monthly survival rate during the hunting open season of 98.0%. The predominant cause of recorded mortality was hunting, followed by natural predation. Too few mortalities were recorded to meaningfully investigate the effect of hunting and bird age on mortality rates. iii. Both hunting and bird age affected the use of space and movement ecology of non-breeding woodcock. Hunted and juvenile birds recorded larger diurnal and nocturnal home ranges than not hunted and adult birds, respectively, and hunting disproportionately affected adult woodcock commuting movements. Juveniles showed a slightly higher level of localised exploratory movement than adults. iv. Diurnal and nocturnal habitat preferences of non-breeding woodcock were ranked. Hunting affected habitat preference, with hunted birds showing greater preference for broadleaved forest and less preference for hedgerows and scrub; these three habitats were of equal importance to not hunted birds. Nocturnally, hunted birds showed greater preference for grassland habitats at night and lower preference for closed habitats. The results are discussed in the context of wider knowledge of woodcock and other species, and the scope for further research and species monitoring effort is explored. This research provides novel information and methodology with international appeal on the spatial ecology and impacts of human activity on this species. It is hoped that this work will contribute to the implementation of sustainable landscape and species management practices with a view to reducing human impacts on the natural world.
The impacts of a suite of Nature-based Solutions on hydrology and water quality in an agricultural landscape
(University College Cork, 2024) Murphy, Darragh; Harrison, Simon; Weatherill, John; Bourke, Mary; Environmental Protection Agency
Across much of the world, rural catchments have been substantially modified by human activity to meet the demand for greater production of a limited number of crops for human and livestock consumption. Much of the expansion of tillage and pasture areas has been at the expense of transitional zones such as wetlands, floodplains and riparian zones, and of hydraulically and geomorphologically complex stream environments which can mediate the flux of water and nutrients through catchments. Modifications to rural catchments to limit over-bank flooding may bring about more severe flooding downstream as flood peaks are conveyed more quickly through straightened channels. In Ireland, as agricultural activity has increased over the past 70 years, the impacts of agriculture on water quality have increased in kind, with a current estimate of 50% of rivers in Ireland being in satisfactory ecological condition. Field surfaces, farm drains and hard-standing areas can harbor high loadings of organic and mineral nutrients and sediment which are mobilized by rainfall to adjacent water ways. In the relative absence natural sites of retention and processing of these water quality pressures, large fluxes may be conveyed downstream during high-flow events, harming aquatic communities and affecting drinking water supplies. Nature-based Solutions (NbS) are applied in landscapes which have been modified by human activities, with the goals of reinstating and supporting natural processes which mediate and mitigate the flux of pressures such as high stream discharges and agricultural pollution. NbS features may operate passively within landscapes, requiring low initial and ongoing costs and are therefore advocated to complement or replace traditional engineering solutions to anthropogenic pressures. In Ireland, however, empirical data on the potential to of NbS features to mitigate target pressures is lacking. This is especially true in agricultural catchments where flood peak mitigation and water quality management are affected by complex biological and geo-chemical cycling of nutrients, as well as the cultural and social constraints imposed by modern farming practices. This thesis investigates the performance of four NbS features reduction of flood peaks discharges and the flux of agricultural water quality pressures on a farm in Ireland. In addition to examination of key biological (sediment retention, nutrient uptake, sward health) and hydrological (peak discharge reduction) effects of NbS features, the success of these features was contingent on bringing no harm to the farming enterprise or channel morphology within the study area. We found that the four studied NbS features - a flood detention basin, a runoff-treatment woodland swale, in-stream boulder weirs and leaky wooden dams – brought about notable improvements to water quality and/or reduced stream discharges during high-flow events. Specifically, this research has demonstrated that the storage of stream water on farm pastures during peak discharge periods may bring about reductions in downstream discharge, and nutrients and sediment concentrations; and that such short-term (12-24hours) inundation of pasture during winter does not impair summer growth of the sward. In-stream features were also shown to reduce stream discharges during high-flow periods but their scouring effects on stream and channel sediments were cause for concern. The study also found that modest, yet scientifically led, modifications to open farm drains may improve water quality and reduce the risk of contamination of downstream water courses. Importantly, however, the effects of all NbS features were strongly influenced by antecedent hydrological conditions, upstream nutrient loading and the stoichiometry of nutrient-enriched water flowing through the features. In summary, NbS features may be utilized for targeted mitigation of anthropogenic and natural issues, but they require careful, context-specific management to ensure they do not cause more harm than good.
Elucidating the dynamic effects of UV on Mentha spicata L.: from the laboratory to innovative horticulture
(University College Cork, 2024) Crestani, Gaia; Jansen, Marcel A. K.; Science Foundation Ireland
Indoor farming provides a novel opportunity to manipulate crops in order to improve their architecture, nutritional value, and stress resistance. Moreover, indoor farming allows the control of key environmental parameters such as light, temperature, and water availability, which normally depend on the local season. Light quantity and quality are particularly critical parameters as these play a major role in determining the yield, architecture, and quality of produce. In particular, low doses of UV radiation can induce small, regulatory adjustments in plant physiology and morphology, which in many cases can be valuable from a horticultural perspective. The general aim of this thesis was to conduct a comprehensive study of UV effects on Mentha spicata L., a valuable commercial crop. This was achieved by exploring the effects of broadband and narrowband UV radiation on mint plants, with a focus on morphological responses, UV-priming, resistance against stressors, and variations in secondary metabolites. The accumulation of these metabolites is crucial for the plant's acclimatory response and holds significance for human health. Investigating the metabolic responses following UV exposure revealed a strategy to enhance plant quality and resistance. Additionally, the study delves into the content and composition of essential oils, particularly monoterpene and sesquiterpene content, under different narrowband UV wavelengths. Based on these findings, it is proposed that UV LEDs could play a significant role in shaping the future of agriculture for a more efficient, sustainable way to produce quality food.

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