Biological, Earth and Environmental Sciences - Doctoral Theses

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    Gelatinous zooplankton in a marine reserve and surrounding waters: diversity, seasonal dynamics, oceanography and trophic importance
    (University College Cork, 2024) McGuinness, Maria; Doyle, Thomas; Haberlin, Damien; Science Foundation Ireland
    The marine area off the southwest coast of Ireland is dynamic, highly productive and contains a rich and diverse marine ecosystem. The oceanography of the region, such as the Celtic Sea front and the Irish coastal current, heavily influence the distribution of plankton, often creating abrupt boundaries which separate plankton communities. The area is considered biologically sensitive and has recently been proposed as a potential marine protected area. Lough Hyne (Europe and Ireland’s first marine reserve) is located in the southwest of Ireland and is known for its remarkable biodiversity. Despite over 100 years of research conducted in Lough Hyne and surrounding waters, limited studies have focused on gelatinous zooplankton and several knowledge gaps remain. Firstly, while the influence of the coastal current on the distribution of phytoplankton has been assessed, no study has investigated how this current may influence the abundance of zooplankton or gelatinous zooplankton. Secondly, gelatinous zooplankton was last monitored in Lough Hyne 30 years ago, and in the intervening years, numerous ecosystem changes have taken place in the urchin, algal and sponge communities among others in this marine reserve. It is not known how gelatinous zooplankton have responded to these changes but given that there is global concern that altered and perturbed ecosystems give rise to increases in gelatinous zooplankton, this needs to be addressed. Thirdly, no study has investigated the trophic ecology of plankton using molecular tools such as fatty acid analysis. Lastly, limited knowledge exists globally on the larval stage of phoronid worms which are known to occur in Lough Hyne. To address these questions, a 7-day research survey was carried out around southwest Ireland to investigate the Irish coastal current and the vertical and horizontal distribution of gelatinous zooplankton in this current. In situ measurements (temperature, salinity, density) were used to identify the coastal current and a multinet with mesh size 300 µm was used to collect zooplankton samples. A key finding was that the current was acting as a boundary to offshore waters and was involved in moving coastal neritic species around the southwest of Ireland. From an aquaculture perspective, the coastal current had higher abundances of the harmful jellyfish Muggiaea atlantica than the offshore waters and supports the hypothesis that M. atlantica is advected around the south and southwest coast of Ireland by the coastal current into aquaculturally sensitive areas. This study also carried out a detailed examination of gelatinous zooplankton abundance, diversity and seasonality over 3 years in Lough Hyne. Zooplankton samples from 58 sampling dates from January 2021 to December 2023 were collected using a 200 µm HydroBios ring net every month from November to March and fortnightly from April to October. The abundance of gelatinous zooplankton was exceptional (six times higher than other nearby coastal locations) and was dominated by four taxa: the appendicularians Oikopleura sp. and Fritillaria sp. and the hydrozoans Lizzia blondina and Obelia sp. It was noteworthy that the species richness of gelatinous zooplankton (n=32) in Lough Hyne was similar to other areas in southwest Ireland, contrary to previous reports. This indicates that southwest Ireland in general and not Lough Hyne specifically, has a high species richness of gelatinous zooplankton. Fatty acid analysis was conducted on phytoplankton and zooplankton samples from Lough Hyne over a 6-month period. This study found evidence for two phytoplankton communities, each of which had distinct fatty acid signatures. The first community was dominated by a single genus, Chaetoceros sp. and had low fatty acid content (5.05 ± 2.26 (µg/mg DW), while the second community was more diverse and had a much higher fatty acid content (19.26 ± 0.26 (µg/mg DW). This may have a significant bottom-up effect on the food web as fatty acids can regulate growth and reproduction rates in higher trophic levels, such as planktivorous fish. From a gelatinous zooplankton perspective, the study suggested that appendicularians may be far more important to the food web in Lough Hyne at the start of the year in February and March than previously thought. It was found that appendicularians may contain high levels of important fatty acids, which would benefit predators such as fish. Finally, two species of phoronid worms were recorded in Lough Hyne, Phoronis muelleri and P. hippocrepia. Their larvae were present in plankton samples from April to October with abundances in the same range as echinoderm and fish larvae. In summary, this thesis demonstrated that the southwest of Ireland has a high diversity of gelatinous zooplankton, very high abundances of gelatinous zooplankton (making up on average 16.5% of zooplankton communities in Lough Hyne) and that gelatinous zooplankton may be distributed by the coastal current. It also demonstrated that gelatinous zooplankton may be rich in essential nutrients, such as fatty acids, and thus play a more significant role in the food web of southwest Ireland than previously thought. Gelatinous zooplankton is therefore very important in southwest Ireland and requires regular monitoring.
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    Gelatinous zooplankton dynamics in Bantry Bay and the development of a harmful jellyfish forecast for the salmon aquaculture industry
    (University College Cork, 2024) Brownlow, Hannah; Doyle, Thomas; Haberlin, Damien; Irish Research Council
    It is well recognised that gelatinous zooplankton can have negative socioeconomic impacts in areas where they interact with human activities. However, knowledge gaps on the ecology of gelatinous zooplankton and the influence of physical oceanographic processes on their distribution are substantial barriers to successfully mitigating these impacts. Therefore, this thesis sought to review the current state of the art on modelling jellyfish, develop an early warning system for a harmful jellyfish species, Muggiaea atlantica, which has been implicated in high mortality events of farmed salmon, and investigate the ecology of gelatinous zooplankton in detail. A literature review was carried out to determine the scope and applications of modelling jellyfish. The models identified could be broadly categorised into two different types: empirical and mechanistic. A distinct geographic bias was displayed with the majority of models developed in Europe (n = 15), Asia (n = 7) and the USA (n = 6). A common approach used was Lagrangian particle tracking coupled with regional hydrodynamic models. However, challenges to modelling jellyfish were identified including a lack of quantitative abundance data and the coarse resolution of many hydrodynamic models, which fail to capture the fine scale processes that influence jellyfish distribution, especially near the coast. High resolution sampling revealed further insights into the seasonality of M. atlantica and other gelatinous zooplankton. The seasonality of M. atlantica exhibited a distinct pattern, likely driven by local oceanographic processes and wind exchange events, with maximum abundances recorded in September or October each year. Abundances of M. atlantica showed considerable differences between years with maximum abundances of 322 ± 9.1, 39.3 ± 2.2 and 3105.4 ± 71.5 individuals m-3 in 2020, 2021 and 2022 respectively. Since the mechanism transporting aggregations of M. atlantica into the bay is likely wind driven coastal/shelf exchange, correlations with oceanic species (chaetognaths and Tomopteris spp.) were examined which revealed strong positive relationships in each year of the study. This further highlights that intrusions of oceanic water masses are influencing the composition and abundance of zooplankton in Bantry Bay. This project sought to test an early warning system for harmful jellyfish in Bantry Bay, which is based on a successful Harmful Algal Bloom (HABs) model. To do this we carried out high temporal resolution zooplankton sampling and measured environmental parameters over three and a half years at a site in proximity to a salmon farm in southwest Ireland. The hindcast model successfully predicted all M. atlantica events (n = 3) over the three and a half year study. An important finding was that the model did not generate any false positives and each M. atlantica event (defined as the first substantial increase of at least 100 individuals m-3 within a two-week period) was hindcast by the model. This suggests that wind driven exchanges between the bay and adjacent shelf waters is the likely mechanism advecting aggregations of harmful gelatinous zooplankton into Bantry Bay. A research cruise in 2021, CoCoJel, enabled a targeted study of vertical distribution in the bay. Differences in the abundance of gelatinous zooplankton species were observed between the inshore and offshore stations, with a higher mean abundance inside the bay (30.8 ± 10.9 indiv. m-3) compared to outside the bay (16.9 ± 9.7 indiv. m-3). The abundance of M. atlantica was similar outside and inside the bay, however, it was notably absent from the surface strata (0 – 10 m) for all inshore stations, with highest abundances at 20 – 30 m. The presence of a well-defined thermocline during the study indicates that species such as M. atlantica and Nanomia cara are likely targeting populations of prey species which are known to aggregate at these depths. The potential impact these findings have on mitigating harmful impacts on salmon aquaculture are discussed.
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    Biology & ecology of a killer whale (Orcinus orca) community that interacts with pelagic trawlers in the Northeast Atlantic
    (University College Cork, 2024) Pinfield, Róisín; Rogan, Emer; Reed, Thomas; Reid, David; Irish Research Council; Marine Science Institute, University of the Philippines
    Observations of killer whales (Orcinus orca) aggregating around pelagic fishing vessels operating offshore during the autumn/winter Northeast Atlantic mackerel (Scomber scrombrus) fishery, have been documented in the literature since the 1970s. However, baseline information on the biology and ecology of these killer whales is lacking. To bridge the gap, this PhD thesis aims to address key questions in relation to the behaviour, abundance, site fidelity, population structure, diet and PCB contaminant levels of this killer whale community. The research involved the utilisation of Irish pelagic trawl vessels as platforms of opportunity for obtaining killer whale behavioural and photo-identification data, skin biopsies, fish and seawater (eDNA) samples. Data collection was carried out in four separate fishing seasons between 2016 and 2018. In the first scientific chapter (chapter 2), killer whale interactions with the mackerel fishery are shown to occur annually, along the mackerel spawning migration route from the North Sea into the Northeast (NE) Atlantic, with killer whale sightings ceasing northwest of Ireland. Information on killer whale group size, composition and behaviour are provided along with an insight into the range of quantities of fish dropouts that can become available to the killer whales during hauling operations. Furthermore, Poisson general linear models were used to investigate if the number of sightings on the fishing grounds per week were explained by either the percentage fat or protein in the sampled mackerel. In chapter 3, insights into the abundance, geographical range and site fidelity of the killer whales are presented based on photo-identification analyses. The results suggest that this killer whale community may be relatively small in comparison to neighbouring communities in the NE Atlantic and show strong seasonal fishery/site fidelity. Photo-ID image matches with several sources indicate that the geographical range of these killer whales includes the NE Atlantic, North Sea, Norwegian Sea and possibly includes the Skagerrak strait. In chapter 4, genetic, stable isotope and polychlorinated biphenyl (PCB) analyses were used to infer population structure, foraging ecology, and PCB contaminant exposure of killer whales sampled around Scotland and Ireland. This large multi-disciplinary study involved the utilisation of epithelial samples collected from killer whale strandings around Scotland and Ireland, and from biopsies taken from the mackerel fishery killer whales. As part of the genetic analysis, individuals that were successfully genotyped, were entered into a large pre-existing North Atlantic killer whale genotype database, to examine relatedness, and to determine if the addition of these samples changed the inference of population structure in the North Atlantic. The results indicate at least five genetic clusters (populations) exist in the North Atlantic, three of which include individuals sampled around Scotland and Ireland. Subsequently, the link between the foraging ecology and PCB contaminant loads in the identified populations are examined and discussed. In the final scientific chapter (Chapter 5), the use of eDNA (seawater sampling) to effectively capture killer whale DNA from the fishing vessels and from a small boat around Icelandic killer whales was tested. Both targeted quantitative PCR (qPCR) and whole-genome enrichment capture followed by shotgun sequencing were carried out on the samples separately, however, none returned strongly positive detections. Possible explanations for the lack of positive killer whale detections, potential pitfalls, and the apparent limitations of eDNA for genetic research on cetaceans are provided. To conclude, the findings provided within this thesis have substantially increased the knowledge of the mackerel fishery associating killer whale community and on a wider scale, have provided updated information on the population structure of North Atlantic killer whale populations. The results herein will ultimately aid in critically assessing the conservation status of killer whales in this region and affording adequate protection under the EU Habitats Directive.
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    Determining the impact of global warming on Atlantic salmon populations
    (University College Cork, 2024) Rinaldo, Adrian; McGinnity, Philip; Reed, Thomas; de Eyto, Elvira; HORIZON EUROPE Marie Sklodowska-Curie Actions
    Climate change poses a significant threat to anadromous fish species such as the Atlantic salmon (Salmo salar), whose life history is tightly coupled with environmental conditions in freshwater ecosystems. In this thesis, I investigate how rising river temperatures and other human-induced pressures reshapes juvenile growth, life-history scheduling, and demographic patterns in Atlantic salmon populations across Europe. Using a combination of long-term datasets, climate model projections, statistical modelling and individual-based models, I explore the phenotypic and demographic responses of salmon to changing thermal regimes and other environmental pressures. My first study focuses on the Atlantic salmon population native to the Burrishoole catchment on the west coast of Ireland, using decades of climate and biological data to model the relationships between atmospheric conditions, water temperature, and growth in juvenile Atlantic salmon. Projections of future climate change suggests a shift towards earlier smoltification, with an increasing proportion of juveniles migrating as one-year-old smolts. These changes are expected to have a cascading effect throughout the life-cycle and ultimately impact the population dynamics of the Atlantic salmon population native to the Burrishoole catchment. Expanding the spatial scope, my second study investigates temperature-dependent growth rates across 15 European populations using the modelling framework developed in my first study. The analysis indicates latitudinal differences in growth rates despite accounting for temperature differences using a degree-day approach. I find that population-specific growth rates are important for the accurate estimation of climate change impact on life-history scheduling, which underpins the importance of regional adaptations in shaping climate resilience. My third study examines how gene flow from farm escaped Atlantic salmon alters growth responses and life-history timing in wild populations. Through common garden experiments and growth simulations, I demonstrate that fish with farm ancestry exhibits faster growth and earlier smoltification than their wild conspecifics, which may potentially reduce life-history diversity and increase vulnerability to climate change. Finally, my fourth paper investigates the ecological implications of reproductive behaviour in Atlantic salmon, specifically the spatial clustering of offspring in redds. Using a spatially explicit, individual-based foraging model supported by empirical data, I show how early-life density-dependent mortality in clustered spatial distributions may be compensatory, which may entail better growth conditions and potentially higher smolt production compared to dispersed spatial distributions. This finding suggests that the protective spawning strategy which has evolved in salmonids of clustering eggs in gravel substrates rather than dispersing them is not ecologically disadvantageous. Collectively, this thesis provides new insights into how climate change and other anthropogenic impacts may interact in the future to shape the biology of Atlantic salmon. By integrating long-term monitoring, climate projections, statistical models, it highlights the vulnerabilities of salmon populations in the face of climate change.
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    Evaluating localized electrochlorination systems as a low-cost means of producing potable water
    (University College Cork, 2024) Campos Nogueira, Renata; Sullivan, Timothy; O'Dwyer, Jean; European Commission
    Research Aim: The thesis investigates the scalability and adaptability of electro-chlorinator devices in African rural communities seeking decentralized sodium hypochlorite production for water treatment. Methods: Investigations on operational parameters, usability, cost-effectiveness, and impact on water quality were conducted within diverse settings, encompassing hospitals, community water tanks, and schools in Sub-Saharan African countries. A range of devices adapted and scaled to the needs of school classrooms, community water tanks, and hospitals from remote areas were investigated. A pilot evaluation in 26 Healthcare facilities (HCF) from Burkina Faso focusing on usability, cost-effectiveness, and sodium hypochlorite concentration compared outcomes with a control group. At a later stage, in 68 HCFs from Chad, impacts on Water, Sanitation, and Hygiene (WASH) indicators, device usability, and performance were evaluated. An innovation allowing sodium hypochlorite production coupled into the dosing pump was tested in 31 Decentralized Water Systems (DWS) from Benin. In Congo, a DWS that serves up to 55.000 people was renewed. The Network water samples (boreholes, fountains at different locations) and household containers were tested for free residual chlorine (FRC) and microbiology (E. coli). A socio-economic study was conducted on the population collecting water from the DWS. For school settings, small-size electro-chlorinators and adapted teaching tools were tested in 20 schools from Burkina Faso. Drinking water was analyzed before commencement and 2 years post-programme. In Saint-Marie Island, Madagascar, a longitudinal study was performed on the programme’s sustainability over 2016-2021, assessing point-of-use water chlorination, safe water storage, and hand washing practices in 20 schools. Health center files on the diarrhea cases of children were consulted. Results: Health Care Facilities (HCFs): In Burkina Faso, 90% of HCFs implemented essential hygiene practices within 11 months, compared to 20% in the control group. Chlorine concentrations improved to an average of 5.1 g/L (control: 2.1 g/L), with daily cost savings ranging from 2.7 to 53 euros compared to purchasing chlorine tablets. In rural Chad, chlorine was used for surface disinfection in HCFs, but only 50% practiced water treatment due to barriers such as chlorine shortages, insufficient staff training, and the smell of chlorine. After installing sodium hypochlorite generators, 61% of HCFs produced it daily, and 97% of operators were trained; however, water treatment practices remained limited. Decentralized Water Systems (DWS): In Benin, structural issues were identified in 30% of water tanks, and 60% of borehole samples tested positive for microbiological contamination. Despite these challenges, Free Residual Chlorine (FRC) levels at distant fountains met national standards (0.1–0.8 mg/L), ensuring safe water in operational systems. In Congo, before intervention, only 16.6% of households treated water effectively, resulting in 73% of stored water being unsafe for consumption. Post-intervention, household water quality improved significantly, with 93% of water samples classified as low health risk, regardless of FRC fluctuations. Schools: In Burkina Faso, untreated water in schools led to 50% of samples being contaminated with fecal coliforms before intervention. Following the program, daily water treatment practices were implemented, and contamination was limited to schools in the control group. On Saint-Marie Island, 40% of water sources were replaced, 60% were improved, and student-led water clubs, supervised by teachers, managed water treatment. In health centers near participating schools, diarrhea cases decreased by 58% between 2018 and 2021. Conclusions: This research examines the practicality of electro-chlorinator devices regarding usability, cost-effectiveness, and the quality of sodium hypochlorite produced. This research confirms that these devices could be successfully scaled and adapted to various applications and conditions in rural Africa, contributing to local chlorine production. However, water source quality, pre-existing structures, local leadership, and financing are crucial for water treatment programmes in resource-limited settings.