Biological, Earth and Environmental Sciences - Doctoral Theses

Permanent URI for this collection

https://hdl.handle.net/10468/139

Browse

Now showing 1 - 5 of 123

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.
Exploring the microbial ecology and energetics of wild and domesticated Atlantic salmon (Salmo salar)
(University College Cork, 2023) Schaal, Patrick Daniel; McGinnity, Philip; Reed, Thomas; Llewellyn, Martin; Biotechnology and Biological Sciences Research Council; Science Foundation Ireland; Higher Education Authority
Since the inception of Atlantic salmon (Salmo salar) aquaculture in the 1970s, millions of domesticated fish have escaped from aquaculture facilities into the wild. This phenomenon raises concerns about the ecological and genetic consequences of farmed fish interbreeding with their wild counterparts. The fitness of hybrid offspring from such interactions has long been recognised as diminished compared to pure wild salmon populations, thereby posing a substantial threat to the overall health and robustness of Atlantic salmon populations. This study takes a comprehensive approach to investigate the impact of domestication on two vital aspects of Atlantic salmon biology: gut microbial communities and metabolism. Both traits have been identified as critical determinants of fish health and well-being. To disentangle the genetic effects from confounding environmental factors, this study employed common garden experiments. These experiments involved rearing fish with diverse genetic backgrounds, including wild, domesticated and reciprocal hybrids, together from the eyed-egg stage through both freshwater and marine phases. This design allowed us to simulate farmed escape and hybridisation events that naturally occur in the wild. The first data chapter examines the drivers and sources that shape gut microbial assembly over time in juvenile Atlantic salmon in a natural river system. The study shows that the major contributors to the salmon intestine's microbial taxa come from macroinvertebrates, a potential food source, rather than the water column. Moreover, results suggest a possible role of host genetics in driving inter-individual differences in gut microbial community composition, leading to distinct microbiota assemblages between farmed, wild and hybrid fish. Neutral modelling further revealed that the majority of gut taxa are transient, underscoring the dynamic nature of these microbial communities and emphasizing the need to distinguish between transient and resident taxa within the gut environment. The second data chapter examines the seasonal dynamics of gut microbial communities and energetics in juvenile Atlantic salmon, considering potential variations among farmed, wild and hybrid fish. The study unveils genetic factors as significant influencers of metabolic flexibility in Atlantic salmon. Wild fish exhibit lower metabolic rates in winter and higher rates in summer compared to farmed salmon, indicating their adaptability to seasonal environmental changes. This metabolic flexibility potentially enhances their chances of survival in variable wild environments compared to their farmed counterparts, which might exhibit less adaptability due to artificial selection for commercially favoured traits. Furthermore, our research unveils shifts in gut microbial communities during the winter months, particularly among the offspring of wild fish, possibly attributable to reduced feeding activity. This reduced activity, in turn, might be associated with their generally lower metabolic demands in winter. The third data chapter assesses whether survivability, gut microbial structure and metabolic rate of Atlantic salmon reared in marine sea pens are affected by amoebic gill disease (AGD), a parasitic infection that poses a significant challenge to Atlantic salmon reared in aquaculture facilities, and if those effects vary between fish from farmed, wild and hybrid origins. Wild fish exhibited substantially higher mortality rates compared to their farmed counterparts, while hybrids fell in between. All fish, regardless of genetic origin, showed significantly lower metabolic rates with increased AGD infection rates. In addition, gut microbial diversity significantly declined in AGD-infected fish. In summary, our study significantly contributes to our understanding of the complex interactions between host genetics, environmental factors and gut microbiota in Atlantic salmon. It offers indications that the domestication process in Atlantic salmon has influenced both host-associated microbiota and metabolism. As aquaculture continues to expand, these findings underscore the need for comprehensive conservation strategies to safeguard the ecological integrity of wild Atlantic salmon populations in the face of evolving aquaculture practices and the potential consequences of farmed fish escape events.
Practical new approaches to delivering biologically rational vector control in the context of conflict, displacement, extreme weather events and other natural disasters
(University College Cork, 2023) Allan, Richard James; Killeen, Gerry; Cunningham, Colette; BASF Construction Chemicals Italia
Conflicts and extreme weather events have multiplied since the 1960s, disproportionately affecting some regions and displacing escalating numbers of people annually. By 2022, 114 ongoing armed conflicts, mainly in countries with endemic vector borne diseases (VBD), left 274 million people dependent on humanitarian assistance, including 103 million forcibly displaced facing dreadful journeys, often without shelter, followed by years living in camps. The UN predict numbers needing humanitarian assistance will rise to 339 million during 2023. Extreme events often generate hazardous environmental conditions in which arthropod vectors thrive and human vulnerability to VBD increases. Related morbidity and mortality rates escalate in the early weeks of new humanitarian crises, remaining high until implementation of effective vector control (VC) measures. In the most challenging contexts, disease transmission may continue uncontrolled due to lack of suitable VC tools. Roll Back Malaria halved annual malaria deaths by 2015, and averted 2 billion malaria cases (2000 to 2021). Distribution of >2.5 billion insecticide treated nets (ITNs) and targeted indoor residual spraying were credited for 69% and 10% of cases averted, respectively. These tools exploit the specialized behaviours of just a few largely nocturnal mosquito species, together with humans’ night-time behaviour in houses, making these very efficient malaria vectors highly vulnerable to control. Mosquito species without this sterotypical behaviour may avoid control and continue to transmit malaria. For homeless displaced people sleeping outside or in flimsy temporary shelters in high malaria burden countries in Africa, standard VC house tools can be poorly adapted. Between 2015 and 2021, annual global malaria deaths rose by 41%; just eleven countries accounted for 80% of these, with eight affected by humanitarian crises. This thesis covers research investigating the feasibility, acceptability, durability, and effectiveness of existing and new VC measures for suppressing disease transmission throughout the hellish journeys of the forced displaced. The first study compared 12-month performance of Interceptor® LLIN and conventional ITNs amongst returnees to rural villages in Liberia. User-perceived effectiveness drove high (94%) retention and utilization, with 11 >50% reduction of malaria prevalence. Laboratory analysis revealed just 22% total insecticide loss in Interceptor® over 12 months. The durability of the LLINs most commonly distributed in 2000-2011 (Interceptor®, Olyset® and Permanet®) was investigated amongst displaced and host families living in grass and stick shelters and mud huts, during conflict in Chad. Fourteen months post-distribution, standard hole index (STI) categorisation classed 69.5% of LLIN in “poor” or “very poor” condition, with “poor” condition 4.2 times more likely in polyester compared to polyethylene LLINs. Performance of PermaNet® Dumuria, an innovative non-mesh polyester LLIN, with UV protectant, was assessed amongst nomadic people sleeping outdoors in north-east Kenya. Data analysis revealed 95.3% of respondents liked this LLIN at 12 months, with 98.0% retention at 22 months and 97.1% nets in “good” condition (STI); acceptable insecticide levels (WHO definition) were found in 100% and 66.7% of nets after 18 and 22 months outdoor usage, respectively. Studies exploring an alternative VC option for displaced populations confirmed that temporary shelters constructed fully with novel insecticide-treated plastic sheeting were safe and reduced malaria incidence among young refugee children by 61% in camps in Sierra Leone. Finally, a randomised cluster trial of durable wall lining (DWL) was carried out amongst Liberian returnees. The DWLs contained Abamectin and Fenpyroximate, never previously used for controlling malaria mosquitoes. DWL installed on internal walls and ceilings of houses in 20 villages resulted in a reduction of malaria 12 months later (p=0.022), although this effect was limited to upland villages. Rapid reduction of bioefficacy after 12 months indicates the need for further research and development. In conclusion, this thesis helps inform practical and biologically-rational VC planning in different humanitarian crises’ contexts. It provides insights into the overall effectiveness of conventional and practical technical variations on the deployment of insecticide-treated materials to physically shelter crisis victims and target the anthropophagic vectors responsible for most of their night-time malaria exposure. The thesis reviews published work on the need to integrate VC strategies and develop new tools, to control the wider range of 12 insects that then thrive among living conditions associated with newly settled human communities as populations emerge from crisis and either resettle back into their rural homes or move permanently into poor, overcrowded, informal urban settlements.
Nurturing blue growth: enabling sustainable development of emerging marine sectors
(University College Cork, 2024) Giannoumis, Jessica; Wheeler, Andrew; Dooley, Lawrence; Cummins, Valerie
Current marine resource exploitation practices and management are unsustainable as resource degradation is ongoing and coastal regions struggle to realise sustainable development of marine resources. The key topic of this research is expanding knowledge on the reconciliation of environmental and economic models regarding the sustainable development of marine resources through the EU-introduced concept of blue growth. In the context of this research, blue growth refers to the sustainable development of marine resources, generating livelihoods, and securing well-being from innovation in emerging marine sectors. Blue growth development attracted interest across Europe and beyond, as the utilisation of marine resources is viewed as an opportunity to meet climate change obligations, enable a transition away from finite resources, and creating employment opportunities, thereby enabling long-term regional economic development. Blue growth development initially focused on the development of five emerging marine sectors with economic growth potential including coastal tourism, aquaculture, ocean renewable energy including offshore wind development, seabed mining, and marine biotechnology. Yet, EU coastal regions struggle with the realisation of blue growth as they received limited guidance from the European Commission on what blue growth is and what successful blue growth development looks like. This highlights a need to investigate what nurtures blue growth to enable coastal regions to realise their blue growth potential. This qualitative and interdisciplinary research focuses on the potential of blue growth in coastal regions focusing on the development of emerging marine sectors. In the context of this research, a region refers to coastal regions with common economic activities and characteristics, such as access to regionally specific marine resources, and common administrative characteristics such as specific political and governmental functions, e.g., regional economic development policies. Within the scope of this research, emerging sectors refer to rapidly growing industries utilising innovative technologies to enable sustainable development of regions, job creation, and technological advancement. This research investigates the manifestation and effectiveness of an EU intervention, the ProtoAtlantic project which includes regions of Orkney (SCT), Cork (IRE), Brest (FR), Porto (PT), and Las Palmas (SP) and two in-depth cases in Norway and Scotland. ProtoAtlantic was a Interreg Atlantic Area project, initially funded from November 2017 to October 2020, due to Covid-19, the project was extended to October 2021. The study harnessed an opportunity to engage with a wide range of multiple stakeholders representing stakeholders from government, industry, and academia. Data collection from the ProtoAtlantic cases included extensive desktop research and policy analysis of marine and generic development strategies in each case, analysis of regional blue growth stakeholder workshops which were carried out in each region, as well as analysis of additional material provided through the ProtoAtlantic project such as the outcomes of the ProtoAtlantic accelerator programme, and semi-structured interviews with nine regional stakeholders. The two deep dive cases included the offshore wind sector development around the DeepWind cluster in Scotland and the Norwegian aquaculture sector. Data collection from the in-depth cases included extensive desktop research and policy analysis of marine development strategies with particular focus on offshore wind development in Scotland and aquaculture development in Norway, in addition to 32 semi-structured interviews. To date, limited scientific attention has been paid to blue growth realisation from a marine governance perspective. Even less research has been undertaken to understand blue growth development from a business perspective. The research aim was to expand on how economic opportunities can catalyse sustainable development in a marine context. By achieving economic sustainability, coastal communities may consequently be in a better position to achieve environmental and social sustainability. The findings of this research address this research gap and provide practical contributions on how decisionmakers in coastal regions can nurture and realise their regional blue growth potential. In-depth analysis found that blue growth requires a systems approach which enables the integration of blue growth antecedents, this has been lacking from current marine management approaches. Furthermore, the study found that economic development approaches to marine resource management can secure well-being of coastal communities and ensure sustainable practices to marine resource utilisation. This research offers a modification of Ostrom’s Social-Ecological Systems framework, the expansions of the framework provide insight into collective action, the role of technology development, and the need for bespoke regional approaches to identify and realise blue growth. This research examines the role of regional stakeholders, the need for entrepreneurial activity and clustering activities in driving blue growth development and offers recommendations for policymakers and decisionmakers in coastal regions to nurture blue growth adoption and development. This research also presents a Practitioner’s Guide to Blue Growth which offers relevant questions to enable practitioners and intermediaries in the identification and realisation of their regional blue growth potential.
A multi-method approach to understanding the ecology of harbour porpoise in Irish waters
(University College Cork, 2023) Todd, Nicole R. E.; Jessopp, Mark John; Rogan, Emer; Kavanagh, Ailbhe; Irish Research Council
Small coastal cetaceans are often some of the most threatened species by anthropogenic and climate change impacts. Distribution and behavioural patterns can be difficult to determine for these wide-ranging, cryptic species that spend a limited amount of time at the surface, making direct observation difficult. Harbour porpoise (Phocoena phocoena phocoena, Linnaeus, 1758) is protected across European waters, listed under Annex II of the EU Habitats Directive, requiring Special Areas of Conservation (SAC) for their conservation. Despite its protected status, harbour porpoise are a relatively understudied species. It is therefore important to determine long-term habitat use patterns to ensure effective conservation is put in place. This research uses long-term passive acoustic monitoring (PAM) to increase our understanding of harbour porpoise habitat use in Irish waters. Firstly, feeding buzzes and spatial-orientation echolocation clicks of harbour porpoise were differentiated within a 9-year PAM dataset from northwest Ireland (Chapter 2). The spatio-temporal distribution of foraging behaviour was investigated using Generalized Additive Models (GAMs), at multiple temporal scales. The research identified clear interannual and seasonal variation, with peak foraging buzzes detected in autumn, as well as highlighting a negative impact of construction related activities in the area. A new PAM monitoring network was also established in an SAC designated for harbour porpoise in southwest Ireland, over a 3-year period. GAMs were used to examine harbour porpoise occurrence and foraging behaviour in relation to intra-site differences in habitat use and environmental variables (Chapter 5). Harbour porpoise were detected year-round within the SAC, with seasonal trends in occurrence and foraging behaviour observed, with peak detections in the late autumn and winter reflecting similar trends from Broadhaven Bay (Chapter 2). Clear preferences in habitat use were identified, with porpoise occurrence and foraging varying across small spatial scales, as well as across diel, tidal, and lunar cycles. This research also noted an overall decline in acoustic detections across the monitoring period, reflecting wider population trends in Irish waters that bears further investigation. An in-field comparison of a widely used PAM tool, the C-POD (Cetacean POrpoise Detector) with its recently developed successor the F-POD (Full waveform capture POD) was conducted, providing timely insights into the integration of this new equipment into acoustic monitoring programmes (Chapter 3). The F-POD recorded twice the amount of harbour porpoise detections compared to a co-deployed C-POD. GAMs highlighted similar patterns of harbour porpoise occurrence, however, in contrast to the F-POD, the C-POD failed to detect sufficient foraging rates to identify temporal trends in foraging behaviour. This work suggests that the switch to F-PODs will likely have minimal effect on our understanding of seasonal patterns of occurrence but may improve our understanding of foraging. Following on from this finding, an in-field playback experiment was conducted to determine the detection probability and effective detection radius/area (EDR/EDA) of three commonly used PAM devices, the C-POD, the F-POD, along with a continuous recording hydrophone (SoundTrap) (Chapter 4). The SoundTrap detected porpoise playbacks at the greatest distance, followed by the F-POD. The C-POD detection range was considerably less than the other two PAM devices. The type of harbour porpoise echolocation (spatial orientation clicks versus buzzes) was also found to influence the detection range, with clicks detected at a closer range across all devices. Understanding how this range of PAM devices compare provides valuable information to enable robust comparison of studies and inform appropriate planning of acoustic monitoring programmes. Collectively, the research has significantly enhanced our knowledge of acoustic monitoring methodologies and identified key harbour porpoise habitat use patterns. The findings can inform more effective conservation management of harbour porpoise at a national and international level. Additionally, this research contributes valuable insights to inform the designation of protected areas to cover important feeding habitats, and ensure targeted protections are put in place in the future.

Browse

Recent Submissions