School of BioSciences - Theses
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ItemThe role of lipids in the formation of beneficial interactions between plant roots and soil microbiota under heat stress( 2022-11)Climate change, which is characterized by the rise of global atmospheric temperatures known as global warming, has serious detrimental effects on crop production because of the direct influence of elevated temperature on plant development. One novel strategy to increase crop productivity while mitigating heat stress is the use of soil microbes, which is slowly gaining popularity because of its low-cost approach, availability, sustainability, and quick turnover. Specific soil microbes can form symbiotic relationships with the roots, whose beneficial effects on plant growth and development, as well as on plant responses to biotic and abiotic stresses, lead to improved plant performance. The plant-microbe interaction is complex and involves below-ground communication, followed by modifications of molecular, biochemical, and morphological processes in the plant. Plant roots display extreme plasticity in adapting to a range of environmental stimuli and are therefore important indicators of plant-level responses to microbial colonization, via changes in architecture and metabolic processes. Lipids, which are essential constituents of the plasma membrane with diverse functions in cellular processes and homeostasis, have been proposed to play significant roles in the rhizosphere. Because heat stresses have a profound effect on membrane stability and lipid composition, rising global temperatures are likely to impact the formation of plant-microbe symbiosis. This study aimed to characterize and quantify the bacteria-induced growth promotion and heat tolerance in plants, and to investigate how plant root lipid profiles are altered under both bacteria and high-temperature conditions. For that, advanced phenotyping and lipidomics technology were employed to monitor plant responses to developmental and environmental changes. By using the high-resolution, high-throughput phenotyping platform GrowScreen-Agar II, an open-top plant-bacteria co-cultivation system was optimized utilizing the model plant Arabidopsis thaliana and the plant-growth-promoting rhizobacteria (PGPR) Paraburkholderia phytofirmans PsJN. This allowed for in-depth, tissue- and time-specific root-and-shoot morphological trait characterization, which elucidated the dynamics of bacterial promotion on plant growth. We have quantified the magnitude of bacterial-induced plant stimulation between ambient and elevated temperatures, confirming the excellent benefit of the PGPR in ameliorating the adverse effects of heat stress. These morphological traits were also associated with the root lipid profile using state-of-the-art lipidomics technology, which revealed specific lipid species and their functions in this tripartite interaction. Knowledge gained from this study, besides being fundamental in the understanding of plant-microbe interactions, can also inform research agenda of future directions for microbial studies as potential agricultural and biotechnological solutions in the endeavor to address global food security under climate change.
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ItemQuaternary diversity dynamics of Australian reptiles( 2022)Predicting the outcomes of anthropogenic impacts on ecosystems is an essential step to counteract the recent biodiversity crisis. The Quaternary fossil record offers a unique opportunity to formulate such predictions by testing how ecological communities and / or species distributions change through time, e.g., in response to the repeated and intensifying shifts in global climate during the glacial-interglacial cycles. Such paleoecological information is particularly critical for ectothermic vertebrates, such as reptiles and amphibians collectively known as herpetofauna, as these groups comprise a high number of threatened species and are particularly sensitive to changing climates. Yet, in most cases, the investigation of long-term faunal dynamics requires a morphology-based taxonomic or ecological identification of fossilized elements. For herpetofauna this has been notoriously difficult, due to a lack of comparative knowledge about the osteological variation in modern taxa, underdeveloped osteological museum collections, and the prevalence of cryptic diversity. These difficulties pose a major challenge when paleontological data are intended to inform conservation, because applied conservation measures fundamentally rely on (species-level) taxonomy (e.g., the IUCN Red List). In this thesis, I test the recognizability of herpetofaunal species in the Quaternary Australian fossil record and apply alternative methods for inferring climate-related faunal dynamics, through a combination of quantitative paleontological and neontological methods. Australia is ideal for such an analysis as the continent comprises an exceptionally high herpetofaunal diversity as well as numerous Quaternary fossil sites, preserving a relatively continuous temporal sequence of reptile and amphibian fossils. I show in Chapter 1 that faunal change can be detected at higher taxonomic levels (above the species-level) and that changes in relative abundance of different reptile subfamilies over time correspond to changing aridity throughout a fossil deposit in western Victoria. This suggests that historical baselines for evaluating the stability of modern ecosystems may be established even in the absence of species-level taxonomic resolutions. The central aspect of this thesis is addressed in Chapters 2 and 3. Using a quantitative approach based on 3D geometric morphometrics, I leverage digital morphological data (CT scans) to test how reliable individual bones of agamids (Chapter 2) and varanids (Chapter 3) can be assigned to (modern) lower-level taxonomic or ecological categories. My results show that genus- or subgenus-level as well as ecological identifications can be confidently achieved in most cases (> 90%). Thus, these categories constitute appropriate groupings for the investigation of temporal diversity dynamics. In contrast, species-level identifications were generally less reliable and sensitive to incompleteness of the bones or sample size. These results add to the long-standing question of transferability of modern species boundaries to the fossil record and imply that a comparison of modern and past (species-level) biodiversity may be prone to identification errors, at least within these groups. Finally, in Chapter 4, I integrated fossil occurrences, generated through the quantitative identification framework developed in the previous chapters, with (paleo-)species-distribution modelling, population genomics and osteological data of modern specimens to examine the decline of the threatened Mountain Dragon (Rankinia diemensis). This integrative approach revealed a strong link between Quaternary climate change and ongoing habitat loss and fragmentation in this temperate-adapted agamid lizard. My results suggest that increasing temperatures will likely force R. diemensis to further shift its distribution to higher altitudes, leading to a reduction of suitable habitat and increasing fragmentation of populations as global warming proceeds. Overall, my thesis provides new insights into the possibilities and limitations of the Quaternary Australian herpetofaunal fossil record in a conservation-paleobiological context, as well as an extensive resource of virtual morphological data and a quantitative methodological framework for future research.
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ItemEffects of fishing and climate change on the Chondrichthyan species in the Gulf of California region( 2019)This thesis is composed of three data chapters and a general introduction and discussion. Each chapter, except for the general introduction and the general discussion is composed of an introduction, materials and methods, results, discussion, and conclusions. The aim of this study was to assess the vulnerability risk to fishing and climate change stressors of 106 species of chondrichthyans with ≥10% of their distribution within the EEZ off western Mexico. For my analysis, I determine the vulnerability of the chondrichthyan species inside the Gulf (GCI) and compare these results with those for two other contiguous broad regions with different oceanographic conditions, the region around the entrance to the Gulf of California (GCE) and Mexico’s remaining Pacific waters (MPW). I have built on existing approaches to provide, in a single framework, a vulnerability analysis and risk assessment of the Mexican chondrichthyan (sharks, rays, skates and chimaeras) fauna by combining three components of vulnerability risk to climate change (exposure, sensitivity and adaptive capacity) (ESA), together with three components of vulnerability risk to fishing stressors (exposure, productivity, and susceptibility) (EPS). Here, vulnerability is expressed as the risk of marked reduction of the population of chondrichthyans based on the knowledge of its biology and its exposure to stressors associated with fishing and climate change. For fishing stressors, I use the productivity of the chondrichthyan species, which is related to the maximum age of the species, and susceptibility, which derives from four parameters; availability, encounterability, selectivity, and post-encounter mortality. For climate change stressors, I use sensitivity, which has two parameters; rarity and habitat specificity as species attributes that contribute to this, and adaptive capacity. Adaptive capacity involves distributional flexibility and trophic level as relevant attributes. I assigned each species to one of six ecological groups (EGs), which is a flexible and novel way to allocate a large number of species based on habitat use, depth strata (shelf-inshore and shelf-offshore), habitat dependence (freshwater, reef substrate, and sandy substrate), and lifestyle (demersal or pelagic). For fishing stressors, I analyzed data sets from 2006 to 2017 for the prawn trawl fishery, the elasmobranch fishery (artisanal and semi-industrial) and for the sardine fishery, and published information on the sport-recreational fishing. These fisheries have the potential to reduce the size of the population of a chondrichthyan species by altering the mortality rate in the regions where the fisheries operate. I then characterised the fishing stressors in terms of fishing methods and the bathymetric range of deployment of the fishing gear (Chapters 1, 3 and 4). For climate change stressors, I obtained data sets from several sources to show trends in the past oceanographic conditions and how they may vary in response to climate change. I then characterised the oceanography of the Gulf of California and adjacent waters. My assessment is based on observed changes from 1960 to 2017, and projected changes. In the period from 1960 to 2017 two important phenomena that warm the sea surface water occurred; “El Nino” and “El Blob”. The latter is a phenomenon related to a warm mass of water as a result of high levels of atmospheric pressure and of which origin is detected in the Gulf of Alaska in 2013. The name “Blob” echos the 1958 horror film which describes a character that keeps growing as it consumes everything in its path just as this warming event did (Cornwall, 2019). The “El Blob” was detected until several months later 2013, so it is unknown whether “El Blob” can occur again with the same or higher intensity. The other timescales are based on projected changes by 2055 and by 2099 using low (2.6), medium (4.5) and high (8.5) emissions scenarios from the RCP (representative concentration pathway) family. Because of a temperature gradient in coastal waters increasing from north-western Mexico to southwestern Mexico (Chapter 2), I established ten contiguous ‘subregions’ in these waters (Chapter 4). This allowed me to evaluate the risk associated with the attribute 'distributional flexibility' of the chondrichthyan species and to determine thermal tolerance range categories as follows: all waters (AW), cool waters (CW), warm waters (WW) or Gulf of California water (GoCw). These categories provided a basis for projecting how chondrichthyan distributions might change in response to climate change. I identified a total of 54 species of sharks, 48 species of rays and 4 species of chimaeras, which belong to 3 superorders, 12 orders, and 33 families. Based on the thermal tolerance range indicated by the current presence-absence of each species in the subregions, a total of 35 chondrichthyan species are distributed in all Mexican waters (AW), suggesting the species are adapted to the full range of temperatures currently occurring in Mexican waters. The majority of these are commercial shark species and these are the least likely species to redistribute out of Mexican waters as waters warm progressively northward as climate change progresses. A total of 31 species were classed CW (i.e., favouring cooler waters) and likely to reduce their distributional range northwards as Mexican waters warm in response to climate change. The majority of these are also commercial shark species. On the other hand, 34 species of chondrichthyans were classed WW (i.e., favouring warm waters), and are likely to expand their distribution northwards within Mexican waters. The majority of these are ray species, some of them of commercial importance. One species of shark, one species of ray and one species of chimaera are distributed only in the GoC waters, and another species of shark and two species of rays are distributed in only inside and outside the GoC in the adjacent MP-C subregion. The ecological groups (developed for all three regions) are shelf-inshore, shelf-reef, shelf-sand (<75 m), shelf-sand (75–150 m), pelagic waters and bathyal (>150 m). A total of 46 species were allocated to the ecological group ‘shelf-sand (<75m)’, 14 species were allocated to the ecological group ‘shelf-sand (75–150 m)’, and 22 species to the ecological group ‘pelagic waters’. Some of these species are demersal and others swim near the bottom or may swim up in the water column. A total of 19 species of chondrichthyans are in the ecological group ‘bathyal (>150 m)’, one species is in the ecological group ‘shelfinshore’, and 4 species were allocated to the ecological group ‘shelf-reef’. Vulnerability risk varies among the current chondrichthyan species, among ecological groups and among fishing and climate change stressors. For total vulnerability to fishing stressors, there were 10 species in the GCI and GCE regions, and 40 species in the MPW region at medium vulnerability risk. I determined 33 species in the GCI and GCE regions, and one species in the MPW region were at high vulnerability risk. For climate change (CC) stressors in the whole of western Mexico, a total of 15 and 10 species were at medium vulnerability risk under the medium and high emissions scenarios, respectively, and 10 species were at high vulnerability risk under the high emission scenario. The species allocated in the EG shelf-sand (<75 m) are highly vulnerable to the combination of fishing and CC stressors in all three regions for all the CC scenarios. In contrast, the species allocated in the EG bathyal (>150 m) are at low vulnerability but varies for species allocated to the other EGs.
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ItemEffects of elevated atmospheric carbon dioxide on iron metabolism in bread wheat (Tritium aestivum L.)( 2019)Atmospheric carbon dioxide concentrations have increased from pre-industrial levels of 280 ppm to a current level of 406 ppm and are predicted to reach 550 ppm by the year 2050. The rise in atmospheric carbon dioxide is known to directly alter the photosynthetic activity of C3 crops resulting in enhanced photosynthetic carbon fixation and, as a consequence, an increase in water use efficiency, biomass and grain yield. Yet, there is considerable evidence indicating a concomitant reduction in the content of essential mineral micronutrients such as iron in cereal grain. Wheat is the second most consumed staple crop in the world and it is an important source of calories for the human population, however it contains low grain iron concentration. Under rising levels of carbon dioxide wheat grain will likely contain even lower iron concentration and thus, intensify the already existing acute problem of human iron malnutrition, which currently affects over two billion people worldwide. This project aims to study the reasons underlying decreased iron concentration in wheat grain under elevated carbon dioxide concentrations by investigating wheat iron metabolism in relation to its uptake and remobilisation in field settings and to assess the feasibility of lessening the decreased iron concentration in wheat grain using a transgenic biofortification approach. Field trials were conducted over two growing seasons at the Australian Grains Free Air Carbon Dioxide Enrichment facility to investigate changes in iron distribution of bread wheat grown under ambient and elevated carbon dioxide concentration. At maturity, grain iron concentration decreased under elevated carbon dioxide concentration by 25% in the first season and by 26% in the second season. Iron distribution analysis revealed that an increased proportion of iron remained in the lower leaf, flag leaf and bracts during grain filling under elevated carbon dioxide concentration, resulting in a decrease in the iron remobilisation from those organs to the grain. Iron is an essential micronutrient, not only for humans, but for all plants and is involved in several important biological processes, including photosynthesis, respiration and chlorophyll biosynthesis. Iron possesses chemical properties that make it suitable to associate with proteins as a cofactor in the form of heme and iron-sulphur cluster. In order to decipher whether altered iron distribution between organs under elevated carbon dioxide concentration was related to changes in metabolic processes, in which iron is involved, an untargeted and targeted metabolite analysis was performed in flag leaf, bracts and grain at grain filling under ambient and elevated carbon dioxide concentration. In addition, the expression of genes involved in iron long-distance transport, iron influx and efflux transport, iron chelation biosynthesis and iron storage were investigated. The results showed decreases in the levels of compounds involved in most metabolic processes related to iron, including those involved in photosynthesis, nitrogen assimilation and oxidative stress in all three organs under elevated carbon dioxide concentration, with increases in the compartmentalisation of iron in chloroplasts and vacuoles. The iron chelators nicotianamine and deoxymugineic acid; showed decreased concentration in the grain under elevated carbon dioxide concentration, with a decreased expression of the genes involved in their biosynthesis. Furthermore, a decreased expression of genes involved in iron long-distance transport from flag leaf and bracts into the grain was shown. Biofortification is the enrichment of staple crops with essential micronutrients through agricultural practices, conventional breeding and/or genetic engineering. Constitutive expression of nicotianamine synthase genes has been an effective genetic engineering strategy to increase iron concentration in cereals such as wheat. In order to investigate the effects of elevated carbon dioxide concentration on a transgenic iron biofortification trait in wheat, transgenic wheat constitutively overexpressing the nicotianamine synthase gene and corresponding null segregants were grown under ambient and elevated carbon dioxide concentration in a glasshouse setting. The analysis revealed that the transgenic iron biofortified wheat plants grown under elevated carbon dioxide concentration increased grain iron concentration as well as nicotianamine and deoxymugineic acid chelators compared to the null segregants. Overall the results of this PhD project indicate that the decreased iron concentration in wheat grain under elevated carbon dioxide concentration is associated with altered disruption of iron within the plant during grain filling, with a greater proportion of iron remaining in flag leaf and bracts at the expense of the grain. This study suggests that the iron surplus in flag leaf and bracts under elevated carbon dioxide concentration is related to a decreased expression of the long-distance iron transporters and chelator genes responsible for the loading of iron from flag leaf and bracts into the grain, where the iron is compartmentalised in chloroplasts and vacuoles to avoid toxicity. Iron biofortified wheat plants constitutively expressing the OsNAS gene show potential to counteract low grain iron concentration under elevated carbon dioxide concentration.