Doctoral Theses
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The Doctoral Theses collection contains digital copies of AUT doctoral theses deposited with the Library since 2004 and made available open access. All theses for doctorates awarded from 2007 onwards are required to be deposited in Tuwhera Open Theses unless subject to an embargo.
For theses submitted prior to 2007, open access was not mandatory, so only those theses for which the author has given consent are available in Tuwhera Open Theses. Where consent for open access has not been provided, the thesis is usually recorded in the AUT Library catalogue where the full text, if available, may be accessed with an AUT password. Other people should request an Interlibrary Loan through their library.
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Browsing Doctoral Theses by Supervisor "Alfaro, Andrea"
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- ItemApplication of Omics Tools to Explore the Health of New Zealand Greenshell™ Mussels(Auckland University of Technology, 2023) Li, SiMingThe New Zealand Green-lipped mussel (Perna canaliculus) is an important corner stone of aquaculture and a major component of the country’s coastal habitat systems. However, unexpected mortalities in farm and wild settings, especially during summer times (summer mortality) present a major ecological and economical challenge. The complex interactions between host, environment, and pathogens during these mortality events are poorly understood and require innovative diagnostic tools. Multi-omics applications are rapidly emerging as powerful tools to accurately and effectively assess the organism’s stress and health condition, among others. This approach allows multi-faceted insights into complex biological processes and can provide insights into disease processes as well as the identification of molecular biomarkers for early warning systems. This thesis was designed to provide, for the first time, an integrative and multi-omics approach of the metabolic, protein and microbiome responses of Perna canaliculus to a range of stressors, such thermal, pathogenic and nutritional stress. The bioinformatic integration of metabolomic and proteomic data revealed strong evidence of alterations in energy and immune-related metabolic pathways in mussels suffering from heat induced mortality in a mussel farm. Our resulted revealed indication of oxidative stress in unhealthy mussels as a result of perturbations in glutathione metabolism and protein glutathione S-transferases. In addition, degradation in the cytoskeleton structure and regulation of cilia/flagellum gill tissues of unhealthy mussels may be a contributing factor to undesired changes in gill membrane fluidity, permeability, and lipid composition impairing function. The integrative metabolome and proteome profile data provides new insight into molecular interactions associated with incidences of summer mortality in this species. The application of microbiomics/microbiome analysis initially involved a baseline characterisation of bacteria and fungi within key wild Perna canaliculus tissues (gills, haemolymph, digestive gland, and stomach) using high-throughput amplicon sequencing of 16S rRNA gene and ITS1 region for bacteria and fungi, respectively. The study revealed that different mussel tissue types displayed distinctive bacterial profiles, which were dominated by phyla which reflected a fluid exchange between the circulatory system and surrounding aqueous environment, as well as a highly diverse digestive system microbiota. Along with a distinct pattern in microbiome structure, multiple significant phylum , including Gammaproteobacteria, Campylobacterota, Firmicutes, Cyanobacteria, and Bactroidota were identified in Perna canaliculus tissues. Among these biomarkers, Gammaproteobacteria, Bacteroidota and Cyanobacteria were shown to change in relative abundance when mussels were subjected to short term starvation periods in the laboratory. Further microbiome analysis of farmed mussels suffering from heat induced summer mortality revealed alterations in Gammaproteobacteria, Bacteroidota and Campilobacterota in the gill tissue and hepatopancreas tissue. Numerous significant bacterial genus signature was also identified in this thesis. The most interesting genus, Endozoicomonas, was found to be the most dominate member of the Phylum Proteobacteria in tissue types, such as gill tissue and haemolymph. Its variation in abundance within mussels exposed to different experimental conditions, suggests that this group may be a good biomarker for mussel condition and fitness. Specifically, changes in the relative abundances of Endozoicomonas bacteria were detected in the gill tissues of unhealthy mussels suffering from summer mortality. Endozoicomonas relative abundance was also altered in response to seasonal changes, potentially linked to temperature and salinity parameters. Based on these results, it is suggested that future studies focus on Endozoicomonas as a potential host health biomarker n P. canaliculus. In conclusion, this thesis has successfully demonstrated the application of multiple omic approaches for the study of Green-lipped mussels, which contributes novel information regarding the animal’s physiological and metabolic responses to stressors, such as temperature, pathogen and nutrition.
- ItemThe Ecophysiology of the New Zealand Mangrove, Avicennia marina (Forssk.) Vierh. subsp. australasica (Walp.) J. Everett(Auckland University of Technology, 2019) Ravi, SrideviThe availability of water is an important environmental factor determining plant growth, survival, and distribution globally. From a physiological viewpoint, non-structural carbohydrates (NSCs) are necessary for plants to cope with abiotic factors such as drought and may allow us to understand how plants like mangroves are able to survive in what is seemingly an inhospitable habitat. Furthermore, the metabolic profiles of these plants may also provide relevant information as to how routine metabolic processes contribute to their success in estuarine conditions. In this thesis, I studied the role of NSCs in species distribution and survival of the New Zealand mangrove, Avicennia marina subsp. australasica. In Chapter 2, I discuss the methods of NSC quantification used in this study. I also investigate latitudinal NSC dynamics in New Zealand mangroves. NSC quantification using enzymatic hydrolysis did not yield interpretable results for the species studied. So I show that near infrared spectroscopy is a useful method to estimate NSC content in the species. My results show that total carbon content was significantly affected by season (summer vs. winter) across the latitudinal gradient. Total carbon content was increased in the southernmost sites in summer. In summer, only leaf total NSC content was increased in the southernmost sites in comparison to the northern sites. Whereas in stem cores, total NSC content was neither affected by season nor latitude. In Chapter 3, I elucidate the role of different NSC levels in the physiological responses of the New Zealand mangroves to drought and salinity. Plants with different NSC levels were obtained through a light swapping treatment. Low NSC (L-NSC) plants were grown in low light conditions during the second half of the light swapping treatment, whereas high NSC (H-NSC) plants were those that were grown in high light conditions in the second half of the manipulation. I show that during drought and saline conditions, higher NSC levels help in maintenance of physiological functioning, however, growth parameters remained unaffected in both L-NSC and H-NSC plants. My results show that most variables such as stem water potential and hydraulic conductivity were affected by three-way or four-way interactions along with main effects of either initial NSC level, salinity, drought, and time. Plants with high initial NSC had higher water potential and conductivity under high drought and salinity. Plants with high NSC also had higher survival rates under drought and elevated salinity levels. In Chapter 4, when describing metabolomic responses to drought and salinity, I show that high NSC plants have lower abundance of α-ketoglutarate than the low NSC plants under high drought and salinity conditions. H-NSC plants also had higher abundance of soluble sugars under high drought and salinity aiding osmotic adjustment. In conclusion, this thesis contributes to our knowledge of NSCs in mangrove ecophysiology and improves our general understanding of NSC dynamics in plants. My work extends the established paradigms of plant physiological responses of terrestrial tropical and temperate tree species under abiotic stress, especially drought and salinity, to mangroves. The results from my work can be further explored and incorporated into vegetation modelling, useful in prediction of future mangrove or other tree species distribution.
- ItemElemental Status and Dynamics in Temperate (New Zealand) and Semi-arid Mangroves (New Caledonia)(Auckland University of Technology, 2021) Bourgeois, CarineMangrove ecosystems demonstrate a high capacity to accumulate macronutrients and trace metals and play a significant role in global oceanic nutrient budget and water quality. With growing pressures from global change, this role is now at stake as mangroves experience increasing shifts in their biogeochemistry, distribution and productivity. In particular, the simultaneous influences of sea-level rise, increasing aridity and anthropogenic pressures worldwide are projected to have a significant impact on mangrove element cycles. The aim of this thesis was to improve our understanding of global change effects on macronutrient (C, N, P, K, Mg, Ca, S) and trace metal (Fe, Mn, Al, Ni, Cu, Zn, Cr, Co) dynamics and their transfers within the mangrove soil-plant continuum. In order to do so, this research focuses on the distribution of these elements and their interactions in situ, in contrasted climate conditions and in different physiographic contexts in temperate New Zealand and semi-arid New Caledonia. Worldwide data showed that despite a decrease in mangrove biomass with increasing latitude, the various elemental sources and biogeochemical processes in mangrove ecosystems lead to a strong heterogeneity in elemental concentrations in plants and soils at every spatial scale. This point is further demonstrated in a case study in temperate Avicennia marina (Forsk.) Vierh subsp. australasica (Walp.) J. Everett estuarine mangroves in New Zealand, where soils were found to be a significant sink of C, macronutrients and trace metals. Although this research highlights the role of temperate mangroves as an efficient filter for terrigenous materials, findings also showed that this capacity significantly decreases with increasing length of immersion, tidal energy and reduction-oxidation potential (Eh). Thus, there is cause for concern over sea-level rise and erosion subsequent to mangrove stand removal. As we move to a warmer and drier climate in New Caledonia, elevation measurements showed dramatic centimetre-scale variations of soil properties and elemental contents along a semi-arid toposequence. Strong evapotranspiration in landward areas results in a 200 and 400% increase in pore-water salinity and Eh compared to seaward areas. This difference in Eh was magnified during the dry season and coincided with a loss of trace metal content compared to mangrove soils at the lowest elevations. In addition, plant component analyses demonstrated the magnitude of the influence of soil Eh, salinity and total sodium variations on trace metal and macronutrient soil-plant transfers along semi-arid mangrove gradients. The effect of a recent increase in tidal range on elemental distribution was also investigated at the two extremities of that same toposequence. Increase in soil elevation and a depletion of trace metals in fringe mangrove stands suggest that while mangroves may partly mitigate sea-level rise by vertical accretion or root accumulation, the effect of tidal pumping, perturbation and weathering on the pool of nutrients and trace metals in soils may remain significant. At the highest elevations, soil surface analyses in salt-flats recently colonized by A. marina give an insight into the ability of this pioneer species to transform hypersaline soils in a substrate favourable for plant growth. These results together with total Na contents analyses in A. marina‘s tissues showed that the success of this species in colonizing arid mangrove soils is due as much to its capacity to modify soil structure, nutrient contents and water-holding capacity as to its ability to tolerate salinity stress. Further research in different study sites adjacent to mining and aquaculture activities showed how variations of physico-chemical properties and OM cycling lead to polarized responses to labile OM and trace metal loads in mangrove plants and soils along semi-arid intertidal gradients. Results suggest that increased pollution, aridity and sea-level rise are likely to increase P accumulation in mangrove soils and nutrient export from soil towards plant biomass and litterfall. This research also indicates a potential decline in mangrove ability to accumulate OM, N and K in soils in landward areas and trace metals in seaward areas. The findings of this work contribute significantly to the understanding of macronutrient and trace metal dynamics in temperate and semi-arid mangroves. This work also provides insights into the implications of drought intensification on plant nutrition and their response to salinity and metal stresses.
- ItemInvestigating the Social-ecological Trade-offs Between Removing and Preserving Mangroves in New Zealand(Auckland University of Technology, 2019) Dencer-Brown, AmritHow we perceive and interact with the natural world will govern our future in times of great environmental change. In New Zealand, the indigenous mangrove species Avicennia marina (subsp.) australasica has expanded within estuaries in the North Island at a rapid rate over the past few decades. This has led to polarity in public perceptions and attitudes towards mangrove preservation and removal. Although protected, removal of large areas of mangroves has occurred and continues to take place. This thesis investigates the social-ecological trade-offs between removing and preserving mangroves in New Zealand. The research approach employs a mixed methods Holistic Mangrove Framework, which explores gaps in the social-ecological monitoring of mangroves both nationwide and specifically at four sites of removal in the Manukau Harbour, Auckland. Chapter two’s review of the literature on mangrove social-ecology showed that prominent knowledge gaps remain in ecological monitoring of mammals, reptiles, insects and spiders, which is also true globally. In a social context, little is known about the cultural value of mangroves (manawa) to Māori or the intrinsic value of this ecosystem. Chapter three showed the creation of a novel framework to investigate the creeping environmental problem of mangrove expansion in New Zealand. This framework has the capacity to be applied to any social-ecological system for a holistic understanding of interactions between humans and nature. Chapter five’s integrated biodiversity assessments revealed that there is much heterogeneity in habitat complexity, species richness and abundance among sites. The study site adjacent to the largest mangrove removal area possesses the greatest abundance of bird species, and richness and abundance of arboreal arthropods compared to all other study sites. This highlights that a site- by-site management approach is required and generalisations about the i habitat value of mangroves for wildlife cannot be made in the New Zealand context. Chapter six’s exploration into perceptions and attitudes towards mangrove preservation and removal revealed significant disparity in attitude between community groups and conservation organisations. Sediment and nutrient retention properties of mangroves are the highest rated ecosystem services. The desire for reversion of estuaries to a pre-urban state is the greatest issue affecting mangroves. Iwi recommend monitoring of water quality and contaminants in mangrove soils. Based on the findings of this study, it is recommended to look beyond mangroves as an ecosystem which has expanded and replaced other adjacent habitats and start thinking about managing our coastal landscapes in a holistic manner. Embracing connectivity and complexity of coastal landscapes and addressing wider land-based issues of sedimentation and nutrient run-off is a necessity. It is advisable for us to work with and be part of our natural environment in order to create a more sustainable future in Aotearoa New Zealand. This is true for interactions with social-ecological systems globally. This study has added to baseline data on social and ecological information on New Zealand’s mangroves and contributes to the international body of work on this coastal ecosystem using a mixed methods approach.
- ItemInvestigation of the Pathophysiology of the New Zealand Black-footed Abalone (Haliotis iris)(Auckland University of Technology, 2019) Grandiosa, RoffiThis study was conducted to improve the knowledge regarding the immunological aspects of the New Zealand Blackfooted abalone (H. iris), to anticipate future occurrence of disease and to establish environmental-friendly therapeutic strategies in regards to the H. iris immune system. An initial study to identify the immunological aspects were by conducting characterization upon haemocytes using a combination of classical and novel (flow cytometry with Sysmex XN-1000 and Muse® Cell analyser) techniques. Two types of haemocytes were identified in this study, including type I (monocyte-like) and type II (lymphocyte-like) cells. Monocyte-like cells showed higher phagocytic activity when encountering Zymosan A particles compared to lymphocyte-like cells. The ability to successfully prepare and preserve haemocyte cells for microscopy and flow cytometry is critical for further investigation of the abalone immune system. Therefore, the study to apply different antiaggregants and handling protocols was conducted upon New Zealand black-footed abalone (H. iris) haemocytes. Results showed that Alsever’s solution was an effective antiaggregant, whereas K2EDTA Microtainer® tubes was similarly as effective as Alsever’s solution. However, the influence of different mixing techniques of K2EDTA Microtainer® tubes should be noticed. Observation of the immune capacity in juvenile New Zealand Black-footed abalone (H. iris) was assessed by conducting an experiment with probiotic enriched diet. Two groups of abalone were fed over a four-month period with different diets: one control and the other a probiotic diet enriched with Exiguobacterium JHEb1), 7x105 (Vibrio JH1) and 4.10x108 (Enterococcus JHLDc) CFU g-1 feed. Results showed that in comparison to control abalone (fed with the same diet but no probiotics), the probiotic fed abalone had a significantly higher (p < 0.05) total haemocyte count (1.9x106 cells), higher viable cell counts (90.77%), higher reactive oxygen species (ROS) positive haemocyte cells (12.03%) and a higher amount of non-apoptotic cells (87.96%). Further, foot tissue samples were obtained for metabolomics GC-MS analysis. Six free amino acids (lysine, proline, asparagine, glutamine and serine), two fatty acid (adrenic acid and palmitoleic acid), three organic compounds (lactic acid, succinic acid and oxalic acid) were detected in a higher amount in the foot muscle tissue of the probiotic-fed abalone. In addition, probiotic-fed animals showed improved growth and survival compared to control fed abalone. The immune response of the probiotic-fed abalone to an intramuscular Vibrio splendidus challenge was also observed. Each abalone in this experiment were challenged by 109 cells mL−1 of pathogenic bacteria. Probiotic-fed abalone had a significantly higher survival rate post challenge compared to non-probiotic fed abalone. It was observed that the infected probiotic-fed abalone had higher THCs, slightly lower proportions of haemocytes undergoing early apoptosis, and lower percentages of ROS-producing haemocytes compared to infected control-fed abalone. These results indicate that the probiotic diet enhances immune capacity by stimulating haematopoietic processes, with a simultaneous low-level upregulation of ROS production, as a priming mechanism of the antibacterial defence system. In addition, metabolite profiles of muscle tissues generated via GC-MS provided suggestions of a perturbed ROS-regulatory system in infected abalone through changes in key metabolites associated with glutathione biosynthesis. This study suggests probiotics as an immunostimulant strategy since it potentially induce a protective effect against bacterial diseases leading to enhanced production and sustainability of the growing New Zealand abalone industry.
- ItemLeiopelma hochstetteri Fitzinger 1861 (Anura: Leiopelmatidae) habitat ecology in the Waitakere Ranges, New Zealand(Auckland University of Technology, 2009) Najera-Hillman, EduardoDeclines and extinctions of amphibian populations are a global dilemma with complex local causes, which should be viewed in the context of a much larger biodiversity crisis. As other animal groups, amphibians with restricted distributions, such as island endemics, are thought to be more vulnerable to environmental change and susceptible to population declines. In the New Zealand archipelago, the only four native species of frogs (Leiopelma hochstetteri, L. archeyi, L. hamiltoni and L. pakeka) are classified as threatened. In particular Leiopelma hochstetteri, the most widespread and abundant endemic frog species in New Zealand, now survives only in spatially fragmented populations as a result of direct or indirect human activity. Hence, it is recognised as threatened and fully protected by legislation. In the last fifty years, some L. hochstetteri populations have been studied, providing descriptive information, which may be used to assess the current status (increasing, stable or declining) of previously or never monitored populations. This thesis examines the diet and trophic level, the effects ship rats (Rattus rattus) as well as the distribution and abundance of L. hochstetteri on a habitat-use context, to provide a basis for evaluating conceivable decline-agents, and to establish a platform to design directed conservation strategies. The Waitakere Ranges are considered a Leiopelma hochstetteri conservation management unit, on which L. hochstetteri has been previously studied. This area consists of a series of hills that run roughly north–south, which are mostly covered in regenerating indigenous vegetation. Today, 60% of the Waitakere Ranges fall within a Regional Park, which together with its surrounding residential areas is afforded protection to minimise the effects of development on the region. The accessibility and conservation character of this area makes it an ideal area for the study of L. hochstetteri populations. As a first step to characterise the diet and trophic level of L. hochstetteri within streams in the Waitakere Ranges, Auckland, stable carbon and nitrogen isotope analyses were undertaken on a variety of sympatric terrestrial and aquatic plant and animal species, including adult frogs. These results showed that: 1) aquatic and terrestrial food webs were linked by terrestrial inputs into the stream; 2) invertebrate and vertebrate predators separated well into distinct trophic groups; and 3) L. hochstetteri occupied an intermediate trophic position among predators, with a diet, at least as an adult, comprising terrestrial invertebrates. Shortfin eels and banded kokopu were identified as potential predators of L. hochstetteri, but data for rats were inconclusive. The inconclusiveness of these trophic studies, with regard to the effects of ship rats on L. hochstetteri populations, lead me to evaluate the influence of a seven-year ship rat management operation on frog abundance. To achieve a reliable evaluation, the habitat characteristics that had significant influence on frog abundance were identified. Then, it was confirmed that the study areas represented similar habitats in terms of those variables, and finally the effect of the pest-management activities was evaluated. Presence/absence of pest-management operations did not have a significant effect on frog abundance. These results, together with the results of the diet and trophic level analyses, suggested that ship rats do not represent a significant threat for this frog species, at least in the Waitakere Ranges. The results of distribution and abundance investigations indicated that in the Waitakere Ranges frogs are currently widely distributed, relatively abundant and that recruitment has occurred at least in the last ten years. Additionally, in order to identify associations between habitat characteristics and frog distribution and abundance, reliable and specifically designed monitoring methodologies were developed. Although this frog is known to occur in wet areas adjacent to shaded streams in forested catchments, quantitative ecological data previously did not exist to enable characterisation of its habitat. Here, novel data were reported on the current distribution and habitat requirements of this species in the Waitakere Ranges. Statistical modelling demonstrates frogs most likely occur in small, erosive streams with coarse substrates and cold waters, surrounded by mature or undisturbed riparian vegetation, where higher abundances of frogs may be found in steep areas with stable patches of cobbles and boulders lying against larger stream bed elements within the stream channel. Anthropogenic activities, such as clearing or logging, and upstream disturbances that potentially increase silt input into streams were identified as threats to these frog species. Finally, the habitat-use information gathered during this investigation was utilised to develop a spatial decision support system (SDSS) as a tool to assess the quality and quantity of habitat available to L. hochstetteri populations associated with the Auckland Region. These results have important implications for the conservation of New Zealand native frog species and riparian stream habitat.
- ItemMetabolomics Applications in Immunological Studies of Marine Molluscs(Auckland University of Technology, 2020) Nguyen, Van ThaoMolluscs form an important group in aquaculture as well as in coastal wild systems. However, high mortalities in molluscan species, specifically marine bivalves, have been encountered in the wild during summer times (summer mortality) as well as in aquaculture settings, which present a major economical challenge in many parts of the world. The complex interactions between host, environment and pathogens during these mortality events require new diagnostic tools and integrated approaches. Metabolomics is one of the newest and fastest growing omics. The sensitivity and specificity of metabolomics approaches make this a powerful tool for immunological studies, where it can provide insights into disease processes as well as the identification of metabolite biomarkers for early warning systems. This thesis was designed to provide, for the first time, a comprehensive understanding of the metabolic responses of mussel haemocytes and other tissues (e.g., gills, hepatopancreas, mantle) to external stimuli (Vibrio sp., lipopolysaccharides [LPS], Cu²⁺) using gas chromatography-mass spectrometry (GC-MS)-based metabolomics approach. Along with the core metabolomics tool, novel flow cytometry (FCM) protocols were developed in order to assess immunological parameters of the host upon stimulation. The combined method allows characterization of the mussel immune responses at both cellular and molecular levels and expands the number of biomarkers used to understand the animal’s response. Initially, tissue-specific metabolic responses of gill, haemolymph and hepatopancreas were observed in mussels challenged with Vibrio sp. Then, haemolymph was chosen as the target tissue/organ for the rest of the experiments in the thesis (Chapter 4). FCM revealed sex-based differences in immune responses of mussels to Vibrio sp. challenge. In this case, female mussels had lower haemocyte mortality, production of reactive oxygen species (ROS) and apoptotic cells after pathogen exposure compared to male mussels (Chapter 5). This suggests that female mussels have more efficient defence system than male mussels. However, metabolite profiles of haemolymph showed no significant difference between males and females. Subsequently, metabolic profiles of mussel haemolymph were intensively investigated in response to Vibrio sp. challenge, LPS and copper exposure (Chapter 6, 7 & 8). The alterations of metabolite profiles along with changes in immune characteristics due to stimulation provided insights into a number of pathways involved in immune responses of the host to Vibrio sp. infection and copper exposure. The study also identified a number of candidate biomarkers involved in mussel immune processes. Among these metabolites, the presence of itaconic acid (ITA) and its accumulation were observed in different tissues of mussels following Vibrio sp. challenges, suggesting the important role of this metabolite as an antimicrobial compound in the innate immune system of bivalves (Chapter 4, 5 & 6). In fact, the challenge experiment (Chapter 9) revealed the complete inhibition of ITA on Vibiro sp. growth at 6 mM, and Vibrio growth was partially inhibited at 3 mM ITA. This confirmed, for the first time, the antibacterial activity of ITA against marine Vibiro sp. and suggests that ITA could be used as an antimicrobial compound for antibiotic resistant bacteria in aquaculture. Subsequently, the ITA concentrations in different tissues of mussels challenged with Vibrio sp. were quantitatively measured (Chapter 10). Interestingly, the results revealed that mussels are able to produce an effective amount of ITA to support the internal defence system, suggesting that ITA could be a valuable biomarker for health assessment of bivalves. In addition, ITA may also involve in anti-inflammation activities and other unknown functions in the bivalve innate immune system, which need further studies to reveal. In conclusion, this thesis has successfully demonstrated the use of novel metabolomics approaches for aquaculture and marine science, which contribute new information regarding the molluscan immune system. It is envisaged that metabolomics will continue to grow as a tool of choice in studies of marine molluscs, as well as the broader field of marine science.