Biological, Earth and Environmental Sciences - Doctoral Theses

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    The impact of UV radiation on the health and pathogen development of the Pacific oyster (Crassostrea gigas)
    (University College Cork, 2022-10-07) Kett, Gary; Culloty, Sarah C.; Lynch, Sharon A.; Jansen, Marcel A. K.; Horizon 2020 Framework Programme; European Regional Development Fund
    Pacific oysters Crassostrea gigas are cultured worldwide and play an important role in global food supply and the sustainable blue economy. Oyster culture sites in Europe, USA, Australasia, and Asia have been experiencing episodic summer mass mortality events. These mortality events can be severely damaging with significant impacts on stock reliability and profitability. Summer mass mortality events are believed to have a multifactorial aetiology driven by high water temperatures and the presence of pathogens, particularly Ostreid herpesvirus-1 and variants (OsHV-1 Var) and bacteria of the genus Vibrio such as V. aestuarianus. UV radiation (UVR) is an intertidal stressor which functions as an ecosystem regulator. UVR has disinfectant properties with the energetic potential to damage nucleic acids of microbes inhabiting surface waters. UVR can also have both positive and negative impacts on animal immune functioning by the activation or inactivation of certain biochemical pathways. Climate model predictions show UV levels changing globally due to changes in cloud cover, aerosols, ozone, and precipitation patterns. This study aimed to investigate the impact of UV radiation (UVR) on oyster health and pathogen performance. Firstly, a desk-based literature review study found that UVR predominantly hinders pathogens, although with varying efficacy, has mixed effects on aquatic invertebrates and has mixed effects on host-pathogen relationships. A clear knowledge gap was identified in that no study could be found which investigated the impact of UVR on bivalve health and survival. Vibrio bacteria are reported to be highly sensitive to UVR while herpesviruses either have high tolerance or can even be activated by solar UVR. UVR can be additive, synergistic, antagonistic, or neutral in outcomes of host-pathogen dynamics. Secondly, novel diagnostic methods for the detection and localisation of Vibrio bacteria within oyster tissues were designed, a generic conventional polymerase chain reaction PCR and a DIG-labelled in situ hybridisation (ISH) assay. These tools were designed to complement existing PCR and qPCR tools and allow for improved understanding of pathogen behaviour inside a C. gigas host exposed to UVR. Primers (VibF3/VibR3) were designed to amplify a 286 bp product from the 16S ribosomal RNA gene common to all Vibrio spp. and to form the ISH probe. ISH was carried out on C. gigas seed sourced from a V. aestuarianus endemic bay (n = 17) and on C. gigas juveniles sourced from a V. aestuarianus naive site (n = 12). Positive ISH signals were observed in PCR and qPCR positive C. gigas while no ISH signal was observed in uninfected samples from the naïve site. Direct Sangar sequencing of PCR products (n = 30), Blastn analysis and Clustal Omega alignments were used to confirm Vibrio sp. detection and assess similarity. Next, to examine the effect of supplemental UV-B on C. gigas seed, a set of laboratory-based experiments were constructed. Various size classes of C. gigas seed were exposed to two conditions: i) a short duration, high intensity UV-B exposure while immersed underwater or ii) a longer duration, low intensity UV-B exposure while emersed out of water. These experimental conditions were chosen to mimic tidal immersion and emersion. The intensity of exposure was lowered in the second trial in order to carry out the treatment over the length of a typical solar peak (midday) during low tide, with the total dose typical of what would be experienced in the south coast of Ireland on a clear summer day. The impact of UV exposure on oyster health was measured by monitoring survival daily, gill tissue DNA samples were used to monitor pathogen prevalence and intensity, and histological tissue cross-sections were examined for pathological damage. Results showed that UV-B exposure negatively impacted oyster survival, most notable in the smallest seed, reducing survival by up to 35%. UV-B also impeded the development of V. aestuarianus, although most effects were transitory and returned to pre-exposure infection levels within 1 - 3 days. Moribund oysters exposed to UV-B had significantly weaker V. aestuarianus infection intensities than moribund oysters in the control group. OsHV-1 Var was not detected in any sample throughout the experiment. These findings indicate that oyster mortality was caused by UV-B exposure rather than by pathogen infection. These data are the first reported impacts of UV-B on C. gigas health and the host-pathogen dynamic with V. aestuarianus. Results from this study suggest that UVR is likely to be a causative factor in C. gigas summer mass mortality episodes. Lastly, to bridge the prior findings to the natural environment, a field trial was designed on a commercial oyster culture cite to investigate the impact of shore grow-out height and the resulting emersion conditions including solar UVR on C. gigas and pathogen performance. Emersion has been shown to have mixed effects on C. gigas performance, though little is known about the impact of UVR in this host-pathogen-environment model. The field experiment in this study was carried out over 5 months, in July C. gigas seed (n = 570) were relayed in 6 replicate mesh bags split across two shore heights equating to a +4-hour emersion time in High Shore (HS) groups compared to the Low Shore (LS) cohort. Mortality (%) was counted in the field and samples (n = 30/shore height) were returned to the lab for pathogen screening for OsHV-1 Var and V. aestuarianus using PCR and qPCR. Increased oyster mortality was associated with emersion, particularly in periods of high UV exposure (>2.4 kJ/m2) and high air temperatures (>21 oC). Pathogen partitioning was observed, OsHV-1 Var was detected more in high shore cohorts while a higher prevalence of V. aestuarianus was detected in low shore C. gigas. Results indicate that environmental conditions impacted spat survival more so than pathogen infection. These findings further demonstrate that oyster mortality and infection levels are influenced by shore height and emersion time. Results from this study can be applied in husbandry practices to reduce losses during summer mass mortality events. Research outcomes are discussed in terms of the wider framework of theoretical knowledge and global development goals, future research questions are posed and recommendations for experimental design are offered. In terms of commercial application, specific husbandry practices are suggested based on the findings of this study, however additional research should be carried out to support or improve upon these recommendations.
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    The application of object-based image analysis to geomorphological seabed mapping
    (University College Cork, 2023-02) Summers, Gerard; Wheeler, Andrew; Lim, Aaron; European Commission; Interreg; Irish Research Council; Geological Survey of Ireland
    Increasing anthropogenic pressures on marine ecosystems due to the reliance on marine resources and the intense development of the marine realm within the last 10 years has threatened the effective functioning of many unique and fragile marine habitats. These environmental stresses warrant effective monitoring and management practices to ensure the preservation of good environmental status. In situ monitoring of marine environmental processes, such as current flow analysis through Acoustic Doppler Current Profilers, provide data with a high temporal resolution at distinct points on the seafloor. However, extensive spatial coverage of seafloor environmental requires a more efficient strategy to quantify these processes. Seabed mapping has long been established as an essential implement in the effective administration of marine ecosystems. Furthermore, in recognition of the significance of seabed mapping in the successful governance of the marine realm, several international seabed mapping initiatives and national seabed mapping programmes have been established with the goal to achieve complete mapping coverage of the seafloor by 2030. Such a significant volume of data evokes the necessity for an objective and repeatable approach to extract meaningful information from the seabed. Geomorphological seafloor features, including current induced seabed sedimentary bedforms (SSBs), are important indicators of habitat, and are readily apparent in seabed mapping data. Moreover, SSBs are common to many marine habitats and spatial scales and are the physical expression of seafloor hydrodynamics, thus these features are appropriate for a standardised approach designed to ascertain objective information on seabed hydrodynamics. This thesis develops a scale robust object-based image analysis (OBIA) approach that is created to classify SSBs as depicted in multibeam echosounder (MBES) bathymetry and derive hydrodynamic information from their morphometrics. This OBIA approach was applied to SSBs occurring in two spatial resolutions of MBES data. Here, four machine learning classifiers support vector machines, two multi-layer perceptrons, and voting ensemble were assessed on their ability to classify SSBs in these two resolutions of data. The results show that the voting ensemble classifier provided the most accurate results for both datasets. The OBIA framework was applied to SSBs depicted in MBES data acquired in a cold-water coral (CWC) habitat in the “downslope Moira Mounds” in the Porcupine Seabight. The SSB attributes of wave height and wavelength were derived from the SSBs classified in these data were used as an input to a multiple linear regression that predicted the seabed current velocity. These predictions illustrated the variable influence of topographic steering occurring at regional-, local-, and micro-spatial scales on regional hydrodynamics. This workflow presented the first estimation of current flow velocity and direction from SSBs in MBES data. Finally, this OBIA approach was used to assess SSBs occurring in multiple resolutions of data within the same region, altering the resolution of observation to evaluate the effect of spatial resolution on the temporal resolution of seabed current hydrodynamics. Moreover, this study determined that the coarse spatial resolution MBES data prevented the assessment of short-term variations in seabed benthic habitat hydrodynamics.
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    From genotype to phenotype: characterising intraspecific variation in the three-spined stickleback (Gasterosteus aculeatus) in the Burrishoole aquatic ecosystem complex in western Ireland
    (University College Cork, 2022-07) Leseur, Floriane; McGinnity, Philip; Reed, Thomas; Marine Institute
    The stickleback Gasterosteus aculeatus is a resident of coastal marine and freshwaters throughout the temperate Holarctic and is a model species for evolutionary biology, particularly due to its recolonization events of freshwaters in previously glaciated catchments. This study concentrates on the species in Ireland, particularly in the Burrishoole system in the west coast of Ireland. The latter is an extensively studied catchment with freshwater streams and lakes running into a brackish lake over waterfalls largely impassable upstream to sticklebacks; then connecting to coastal waters. Previous genetic (using microsatellites), morphological and meristic studies in the Burrishoole catchment identified four statistically distinct populations; one in the major freshwater lake and three (completely-, partially- and low-plated forms) in the brackish lake. Here, a more extensive study was undertaken extending the geographic and temporal analyses of genetic aspects (using neutral and adaptive SNPs) and phenotypic traits including morphological and metabolic characters, and gut microbiome composition. Neutral SNPs showed largely the same population composition as previously suggested using microsatellites (i.e. isolation-by-adaptation reflective of time of divergence), though the partially-plated group in the brackish lake was not supported. This composition being temporarily stable and supported by morphological analysis. The confirmed adaptive SNPs suggest a different scenario with isolation-by-environment in relation to the two populations differentiated by ecomorph (plates, body shape, gill rakers and migratory behaviour) co-existing in Lough Furnace. Analysis of traits associated with metabolism and gut microbiome did not extend population differentiation, but yielded novel results individually. The individual results are discussed in four separate chapters, and the thesis then concludes with an overview chapter. Similarity or differences with other stickleback studies around the North Atlantic and Pacific are explored, and possible isolating mechanisms between the completely- and low-plated forms co-occurring during the spawning season in the brackish lake identified (migratory behaviour – anadromy - in the completely-plated form, absence of evidence of hybridisation in co-habitation, wash out from the freshwater population into the brackish lake). The rare physical characteristics observed in the Burrishoole system may allow clarification of the process of recolonization of freshwaters in this species.
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    The application of machine learning and 3D photogrammetry for cold-water coral habitat classification in the NE Atlantic
    (University College Cork, 2023) de Oliveira, Larissa Macêdo Cruz; Wheeler, Andrew; Lim, Aaron; Conti, Luis Americo; Irish Research Council; Science Foundation Ireland; Marine Institute
    Cold-water coral reefs are complex structural habitats that represent one of the most important deep marine ecosystems. As three-dimensional habitats with high structural complexity, they provide ecosystem services that influence species abundance and biodiversity, being indicators of ecosystem health. These habitats are considered hotspots of biodiversity around the globe, especially in cold and deep waters between 50 and 4000 metres depth. Similar to their tropical counterparts, these habitats are subject to several climate and anthropogenic threats. Over the last two decades, research efforts to identify, map and manage these environments have increased along with the advances in data acquisition. Technologies such as remotely underwater vehicles are equipped with high-resolution sensors that generate gigabytes to terabytes of data. However, data analysis methods are being outpaced by acquisition technologies and there is a latency in the extraction of meaningful information from large datasets. Furthermore, the fine-scale heterogeneity promoted by the three-dimensional scleractinian coral branching structure is often overlooked, being reduced to a two-dimensional scale. This thesis explores methods that can advance seabed mapping to further understand cold-water coral reef habitat features in the deep sea considering their natural, three-dimensional structure and posed data analysis demands given the current technologies. The key aims of the research were to: i) develop an unprecedented 3D imaging classification workflow for CWC habitats of Ireland whilst analysing the suitability and transferability of 2D and 3D data to represent these habitats in high-resolution; ii) quantify facies distribution and spatial variability; iii) link image data to processes driving CWC reef development; iv) develop new forms of visualisation of 3D data of underwater environments; v) derive meaningful information from dense optical datasets. Here, CWC reef habitats in the Porcupine Bank Canyon and the Belgica Mound Province, in the Porcupine Seabight, SW of Ireland were reconstructed in 3D using Structure-from-Motion (SfM) photogrammetry. Point clouds, meshes, orthomosaics and digital elevation models (DEMs) were produced at sub-centimetric resolution. Four different classification workflows were developed and analysed, namely: Multiscale Geometrical Classification (MGC); Colour and Geometrical Classification (CGC); Object-Based Image Classification (OBIA) and; Machine Learning Multiclass classification (MLMC). These first three workflows provided a binary (coral, seabed) classification with accuracy ranging 56 to 74% and provided the analysis of the percentage class distribution for each habitat in 2D and 3D. Results show that there is an impact in mapping CWC in 3D and 2D of at least a tenth of order of magnitude. The MLMC method provided a multiclass (live coral, dead coral, coral rubble, and sediments and dropstones) classification of the 3D point cloud which achieved f1 scores of up to 95.1%. DEMs and classification results were used to assess local and regional CWC patterns in relation to terrain features, facies size and facies distribution. Further investigation revealed that CWC are not randomly distributed within CWC reefs, instead their distribution may be driven by local geomorphometric properties. Aiming to raise awareness and facilitate the interaction of humans with deep-water environments, an application for visualisation of 3D models of CWC in mobile phones was developed. This thesis demonstrates how SfM and machine learning can be used to quantify CWC facies and understand CWC reef habitats.
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    Understanding cold-water corals’ health and ecosystems on the Irish margin, NE Atlantic; a critical look into the ecology, geology, hydrodynamic processes and human impacts
    (University College Cork, 2022-08) Appah, John; Wheeler, Andrew; Ramsay, Ruth; Lim, Aaron; Science Foundation Ireland
    Cold-water corals (CWCs) have come under threat from climate change and anthropogenic activities such as fishing and marine litter pollution despite, being ecological engineers that support high biodiversity, and as a result are protected in Europe under the EU Habitats Directive with some designated as Special Areas of Conservation (SACs). Abiotic (low pH, macro and microplastics) and biotic (pathogens and harmful microbes) factors, due to climate change and human activities, can stress CWCs, disrupting the coral holobiont with dire consequences on the energy allocation processes, coral health and diseases, growth and survival, resilience as well as biodiversity in deep sea corals. CWCs are azooxanthellate, filter feed and exist withing temperature limits of 4-13 °C. Using a habitat mapping approach, coupled with CWC histology and studies of the coral microbiome, this PhD research investigates the CWCs’ ecosystem health and environmental processes that influence biodiversity in the two SACs, upper Porcupine Bank Canyon (uPBC) and the western Belgica Mound Province (wBMP), on the Irish continental margin, northeast Atlantic. Chapter one provides a general introduction to cold-water corals, the objectives of the research and the threats to ocean environmental health and consequent organismal health, while chapter two maps the spatial distribution of CWCs within one of the largest submarine canyons on the Irish margin, the uPBC, highlighting importantly habitat heterogeneity in reef habitats and the hydrographic factors that influence the pattern of CWCs distribution in the canyon. Chapter three mapped the distribution of marine litter in two special areas of conservation (PBC and BMP) on the Irish margin and its impact on CWCs’ distribution as well as to determine if the SACs are serving their purpose and their usefulness against litter entry. In chapter four, the study assessed the distribution and roles of the coral holobiont in the uPBC using molecular techniques whilst chapter five uses a combination of histological and molecular techniques to assess Haplosporidia and Vibrio spp. in main framework-forming corals in the uPBC. Chapter six synthesizes the data obtained and concludes on the distribution and status of the cold-water corals in the uPBC in the face of climate change and anthropogenic pressures. In the analysis, five different substrates were characterized in the uPBC and resolved into non-reef (sediment, sediment & dropstones and bedrock) and reef and rubble (live/dead coral and coral rubble) habitats, including the terrain features observed in the canyon, and these generally contributed to the high biodiversity. High benthic megafaunal diversity (higher number of taxa identified), although not significantly different from the Shannon’s diversity observed in reef and rubble habitats, was detected in the non-coral habitats compared to the reef and rubble habitats in the upper PBC. Percentage estimates of Shannon’s diversity for non-coral and reef and rubble habitats were (H’non-reef =2.38; H’reef and ruble = 2.16) and Pielou’s evenness (J’non--reef =0.71; J’ reef and ruble = 0.65) respectively whilst density estimates of Shannon’s diversity for non-coral and reef and rubble habitats were (H’non-reef =1.72; H’reef and ruble = 1.14) and Pielou’s evenness (J’non--reef =0.54; J’ reef and ruble = 0.43) respectively. Geomorphology and hydrography were noted to affect the distribution of litter in the SACs. Another striking finding was that fishing gear (uPBC=80.7%, wBMP = 14.3% buoys) and plastics (uPBC = 11.3%, wBMP = 55.1%) were detected in relatively high abundance, suggesting that anthropogenic activities such as fishing (>60% vessels) are ongoing in the PBC and BMP despite being a SACs. It is unclear, however, if the observed fishing gear in the uPBC and wBMP may have drifted into them by deep-sea currents or were dumped before they were designated an SAC, as the SACs are closed to fishing. Additionally, the results reveal the upper canyon as a high energy environment with sufficient mixing of materials and community composition among the corals, water and sediment samples. Shannon’s index (H = 2.19, P = 0.33) and species evenness (J’ = 1.66, P = 0.43) among the groups of samples, respectively, were not significantly different. A positive note is that the corals generally appear to be in good health with low Haplosporidia (0.03%) and Vibrio (0.03%) infections in a single L. pertusa individual from the canyon head respectively, although we risk losing the corals due to bottom fishing and the current trend of climate change. A total of 40% Rickettsiales-like organisms (RLOs), with 26.7% observed in the south branch and 13.3% observed in the canyon head were detected. Despite the many threats and pressures such as marine litter pollution, changing pH, sedimentation and bottom trawling, the CWCs on the Irish margin, are associated with high biodiversity and appear to be resilient, well adapted to the deep-sea environment. However, regular monitoring campaigns and health screening studies are advocated. Although continuous monitoring through research and management activities would be the way forward, it is recognised that the cost of such deep-sea surveys/expeditions are huge and require sufficient funding from the various funding bodies. It is believed that the findings of this research will inform policy makers and management on how to effectively protect the vulnerable ecosystems of these deep seas.