School of Agriculture, Food and Ecosystem Sciences - Theses
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ItemThe state of data sharing in oncology research: an examination of policies, practices and perspectives of key research stakeholders( 2023-08)Over the last decade or more, there have been increasing efforts to evaluate and improve the transparency of scholarly research across many fields of science. Part of these efforts include lobbying for greater investment in data stewardship, as well as increased public and private access to researchers’ data. In the context of cancer research, this would bring numerous benefits to the research community. For example, greater access to data provides researchers with opportunities to validate discovered findings, answer questions not originally considered by the data creators, and accelerate research through the synthesis of existing datasets. However, transparency also brings challenges, such as the navigation of privacy legislation, increased demands on time and resources, development of infrastructure and expertise, and substantial concerns among researchers such as fears about misinterpretation and misuse of shared data. In this thesis, I present research from five empirical studies that have explored the state of data sharing in oncology. These constitute Chapters 2 to 7. In Chapter 2, I report findings from a survey of journal editors, observing that journals report a wide variety of policies and practices on peer review and data sharing; even within different disciplines, norms are far from fixed. In Chapters 3 and 4, I present the protocol and the findings of a systematic review and individual participant data meta-analysis of over 2.1 million medical publications. At the end of these studies, I estimate that only 8% of medical articles published between 2016 and 2021 declared that the data were publicly available, and only 2% actually shared data. I also estimate that only a third of researchers comply with mandatory data sharing policies of journals, and even fewer – only a fifth – comply with policies requiring researchers to share with others on request. In Chapter 5, I narrow my focus down to data sharing in oncology research, and report that while one in five articles declare that data are publicly available, less than 1% share in accordance with the FAIR Guiding Principles. In this chapter, I also observed similar levels of non-compliance with mandatory data sharing policies of journals to Chapter 4. In Chapter 6, I report the results of a survey of cancer researchers, asking them about their experience with, and thoughts on data sharing. In my final empirical chapter, Chapter 7, I turn to individuals affected by cancer to ask their opinions about whether data from cancer research should be shared, and with whom. Together my work indicates that while both cancer researchers and patients support sharing data, the practice is still uncommon, and that current policies which aim to increase sharing are often wanting. A stronger commitment from key research policymakers such as publishers, funders, and research institutions are needed if we are to improve both the frequency and quality of data sharing in oncology.
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ItemMapping for Sustainable Livelihoods: using cultural mapping to clarify community shared visions and livelihood options in natural and cultural resource planning and development( 2023-04)Abstract The development of sustainable livelihoods and sustainable growth is a key challenge for society. While there is often the best of intent, many opportunities for sustainable development are not realised. The goal of this research was to understand the reasons for overlooked or lost opportunities for sustainable livelihoods and sustainable growth. The research was undertaken in the Kimberley region, a contested landscape in the north of Western Australia. This region includes a diverse range of industry, government and community stakeholders, all with vested interests in its natural and cultural resources. The region is rich in resources, and Indigenous people’s intergenerational knowledge of the area is keenly sought after from sectors such as tourism, mining, national parks, education, health and environment. However, despite the amount of private investment and government funding for development that is poured into the area, it results in little change for its at-risk Indigenous communities of the Kimberley despite the constant demand from academic, industry and government sectors to engage with them and address their needs. The intent was to learn their perspectives about the constraints when engaging with communities and to identify opportunities for improving interactions and more sustainable outcomes for all parties. The study explored research questions related to this goal using personal ethnography, interviews, a workshop and tailored cultural mapping practice, and engaged with a large range of sector leaders. Another focus was to explore an approach to sharing of knowledge between Indigenous communities and the many stakeholders they engage with, and the benefits that might come from this. A bespoke designed method of cultural mapping was refined and accredited and used as a research framework. Bespoke is when a training method is designed to address a real-world issue or concern. This method was used to design the research questions and a workshop involving interviewees. This method was also used to develop multi sector engagement scenarios that make sustainable livelihoods, and the constraints to achieving them, more visible. The study found livelihood and growth opportunities were missed because: 1. cultural knowledge was not specifically recognised to be of value in sustainable development; 2. time poor community leaders cannot fully evaluate potential opportunities arising from the huge amount of investment; 3. Kimberley Indigenous communities do not feel heard or included in culturally appropriate ways in the large-scale development being implemented by others; and 4. knowledge collected from communities rarely had any benefits for the communities, yet that knowledge benefited those collecting it. Further, the study found that development proponents from the public and private sectors predominantly work in silos. The consequence for communities is the effort expected when each stakeholder knocks on their door to ‘consult’ or gather information. This commitment takes time and effort that communities could invest into their own initiatives. More broadly, these findings indicate that community livelihood opportunities are not being realised because culture, and its complexity, are being ignored, which points to the need for including culture in a more practical and realistic way into the existing sustainable development paradigms. Culture remains ambiguous in these paradigms, indicating the lack of clarity that underpins efforts to incorporate it. As a result of this disconnection, decision makers and investors fail to acknowledge the urgency of reversing the loss of cultural knowledge. This knowledge is potentially critical to addressing major challenges such as climate change, language loss, and loss of biodiversity. These findings, and findings of prior studies underpinning this one, show that for communities to have the chance to achieve sustainable livelihoods, their single most important cultural asset, their practices and knowledge of their region and its natural environments, must be protected and acknowledged. These findings have wider implications for achieving sustainable livelihood and development objectives in Indigenous communities across Australia and in many other communities around the world. It is recommended that ‘culture’ be incorporated as the first pillar of the sustainable development paradigm, and become a standalone Sustainable Development Goal
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ItemIdentification of long non-coding RNAs in plant reproductive development( 2023-07)Linear and circular long non-coding RNAs (lncRNAs, and circRNAs) are regulatory RNA molecules that do not encode proteins but play critical roles in biological processes in responses to internal and external factors. These non-coding RNAs can originate from various genomic regions, including exonic, intronic, or intergenic regions and function based on their specific nucleotide sequences and structures. This thesis aims to advance our understanding of circRNA and lncRNA expression patterns and functional roles in plants during flowering, employing RNA sequencing and plant transformation techniques, with a focus on soybean flowering and Brassica rapa pollen development. Pollen development is a crucial process that plays a pivotal role in fertility and subsequent seed production. In-depth RNA sequencing investigations were conducted to examine circRNA expression during five distinct stages of pollen development in B. rapa. A total 1180 circRNAs were identified. These circRNAs were generally small, ranging from 100 to 600 nucleotides in length, comprised of one to two exons, and displayed an uneven distribution across all chromosomes. Further analysis demonstrated differential and stage-specific expression patterns of circRNAs, primarily showing an upregulation trend during pollen development. Comparative analysis using bioinformatics tools revealed that the identified circRNAs in B. rapa exhibited approximately 35% sequence conservation with circRNAs identified in Arabidopsis thaliana, while only about 3% sequence conservation was observed with circRNAs from other plant species. Functionally, the identified circRNAs in B. rapa were found to regulate pollen development by participating in diverse biological processes, including protein biosynthesis, meiotic and meiosis cell division processes, DNA processing, enzymatic activities, and carbohydrate metabolism. Moreover, the investigation identified 88 circRNAs containing binding sites for microRNAs (miRNAs), indicating their potential role as miRNA sponges in post-transcriptional gene regulation. Specifically, the circRNAs expressed in B. rapa pollen exhibited binding elements for various flowering miRNAs, such as miR156, miR164, and miR172, suggesting their potential involvement in pollen developmental processes. To validate the presence of circRNAs, nine circRNAs were selected and confirmed through experimental procedures, including the verification of back-splicing junctions using divergent primers and Sanger sequencing experiments. Soybean (Glycine max) is considered the world's major source of vegetable oil and protein. The transition from vegetative growth to flower development in soybean is triggered by exposure to short-day photoperiod, as it is a short-day plant. During floral transition in soybean, RNA sequencing data was generated from Shoot Apical Meristem (SAM) samples dissected from plants subjected to short-day treatment at four time points: 0, 2, 4, and 6 days after treatment. The expression profiling of circRNAs identified 384 circRNAs in soybean SAM, which were found to be predominantly short in length (300-600 nucleotides) and composed of two to four exons. Furthermore, an uneven distribution across the 20 chromosomes of soybean was observed. CircRNAs exhibiting short-day treatment-specific expression patterns were noted during the floral transition processes in soybean, with a greater number of circRNAs displaying upregulation following six days of short-day treatment. An analysis of circRNAs expressed in soybean SAM revealed that they possess longer flanking introns, which were significantly enriched with reverse complementary elements, potentially facilitating circRNA biogenesis. Additionally, circRNAs derived from genes involved in flowering-related hormones such as abscisic acid and auxin were also identified. The involvement of circRNAs in diverse biological processes, including SAM development, adaxial/abaxial axis specification, reproductive shoot system development, and the regulation of flower development, was unveiled through in-silico functional analysis. Furthermore, miRNA binding sites were found in 38 circRNAs, including those associated with development and flowering, such as miR156 and miR172, suggesting their potential function in circRNA-miRNA-mRNA networks that regulate gene expression during floral transition. The backsplicing of 26 selected circRNAs was validated through divergent primer amplifications or Sanger sequencing. The intricate gene regulatory network underlying the floral transition in soybean was illuminated by these findings, which highlighted the unique characteristics and potential functions of circRNAs during this process. To explore the role of lncRNAs in soybean flowering, a specific flowering-associated lncRNA known as NC_GMAXST00046315 was introduced into soybean via Agrobacterium-mediated transformation. PCR screening of the obtained transgenic lines was performed using specific primers for the reporter gene beta-glucuronidase (GUS), which successfully confirmed the presence of the transgene in the transgenic lines. The quantitative PCR (qPCR) analysis revealed that the inserted lncRNA in the soybean genome exists in a copy number ranging from one to three copies. Moreover, qPCR analysis validated successful overexpression in selected transgenic lines, with expression levels ranging from 1.8- to 2.35-fold higher compared to non-transgenic plants. Since lncRNAs typically regulate the expression of their neighbouring genes in cis or trans, further investigations were undertaken to assess whether the expression of neighbouring genes was influenced by overexpression of the lncRNA. Specifically, the impact of lncRNA overexpression was compared between non-stress and heat stress conditions, as the BAG gene (heat-responsive gene) is located downstream of the lncRNA. The results indicated a significant decrease in the expression of BAG in transgenic lines compared to WT plants (non-transgenic Bragg) under non-stress condition. During heat stress, a noteworthy increase in lncRNA expression was observed in WT plants, implying its involvement in stress-responsive pathways in soybean. The expression of the BAG gene exhibited a 270-fold increase in WT plants and up to 680-fold increase in transgenic lines, indicating the potential regulatory effect of the overexpressed lncRNA on BAG gene. The transgenic soybean lines also exhibited notable improvements in seed characteristics, resulting in significantly higher yields compared to WT plants. Specifically, the transgenic lines displayed enhanced seed weight and a higher percentage of undamaged seed coat, while WT plants produced smaller seeds with wrinkled discoloured seed coat. The seed weight of transgenic lines increased by approximately 15%, and the occurrence of intact seed coat increased by 6-9% compared to WT plants. These findings highlight the positive impact of lncRNA overexpression on soybean yield, particularly under heat stress conditions. In summary, the significance of circRNAs and lncRNAs in plant flowering and reproduction is emphasized by this research. The identification of critical regulatory circRNAs and lncRNAs in this study contributes to a deeper understanding of the regulatory mechanisms that control flower development in crop plants. Furthermore, this knowledge has the potential to facilitate the advancement of more efficient and higher yielding seed-producing crops.
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ItemCharacterization of phenolic compounds from the selected native Australian flora, their bioaccessibility, bioactivities, safety evaluation, and their reciprocal interactions with the gut microbiota( 2023-08)Plants have formed the basis of a traditional medicine system that has existed for thousands of years. The growing interest in phytochemicals for general health to prevent chronic disease and aging fueled nutritionists and other scientists to explore the nature, composition, and presence of bioactive metabolites in plants. Phenolic compounds are diverse bioactive metabolites, including phenolic acids, flavonoids, lignans, stilbenes, coumarins, phenolic terpenes, tyrosols, and other polyphenols. Phenolic metabolites have attracted much interest due to their wide range of proven biological properties. Australian native plants offer a substantial potential source of new antioxidant chemicals for medicinal or functional products. The emerging interest in the food supply required detailed analytical characterization and quantification of antioxidants to collectively understand their role in food and human health. Previously, a few studies were conducted to characterize and identify phenolic compounds from native Australian fruits, herbs, and medicinal plants. However, comprehensive profiling of these plants still needs to be improved due to the complex nature of phenolic and non-phenolic compounds and the expense and non-availability of commercial standards. Considering the potential of phenolic compounds, I comprehensively characterized 19 selected native Australian flora (Kakadu plum, Davidson plum, muntries, quandong peaches, rosella, strawberry gum, lemon aspen, mountain pepper berries, river mint, bush mint, sea parsley, bush tomatoes, lemongrass, wattle seeds, Oldman saltbush, sandalwood nuts, aniseed myrtle, lemon myrtle and cinnamon myrtle were studied for in-depth screening of phenolic compounds and their biological activities. The highest total phenolic content (TPC) was measured in Kakadu plum (74.84 mg GAE/g), while the lowest TPC was quantified in lemon aspen (4.40 mg GAE/g). The other selected plants (bush mint, river mint, quandong peach, strawberry gum, Davidson plum, bush tomatoes, muntries, and lemongrass) were quantified with the TPC (57.70, 46.59, 42.85, 36.57, 32.49, 26.78, 23.04 and 15.09) mg GAE/g, respectively. Kakadu plum, Davidson plum, muntries, and quandong peaches contain diverse phenolic compounds, particularly flavonoids (condensed tannins and anthocyanins). For example, the Kakadu plum contains condensed tannins like ellagic acid, punicafolin, pedunculagin, punicalin, and kurilagin corilagin, potent phenolic compounds. Davidson plums and quandong peaches were measured with higher amounts of anthocyanins than blueberries and blackberries, highlighting that these fruits are highly beneficial for human health. Delphinidin 3-O-sambubioside, delphinidin 3-O-glucoside, cyanidin 3-glucoside, and ellagic acid were measured with a higher concentration in Davidson plum, while isorhamnetin, delphinidin 3-O-glucoside, and cyanidin 3-rutinoside were found with a higher concentration in quandong peach. Moreover, higher concentrations of rosmarinic acid, chlorogenic acid, sagerinic acid, quinic acid, and caffeic acid were measured in bush mint, river mint, bush tomatoes, and mountain pepper berries. Chlorogenic acid, myricetin 3-O-rhamnoside, quercetin 3-O-arabnoside, quercetin 3-(2-galloylglucoside), and epicatechin had higher concentrations than other quantified phenolic compounds in strawberry gum; and delphinidin 3-O-sambubioside, cyanidin 3-rutinoside, cyanidin 3-glucoside, cyanidin-3-sambubioside, cyanidin, epicatechin, and chlorogenic acid had higher concentrations in rosella. In this study, I identified and quantified many new compounds in all studied plants and explained their chemistry. Antioxidant, anti-diabetic, and anti-Alzheimer activities were also measured for selected plants. These fruits provide a potential source of natural antioxidants for various health applications (anti-diabetic and anti-Alzheimer). The function-structure relationship is also described using in-silico molecular docking and simulated pharmacokinetics models. Native Australian fruits have remarkable pharmacological and medicinal values. The effective utilization of native Australian fruits and herbs could help to detoxify reactive oxygen species in antioxidants-deficient individuals and fulfill the antioxidants and nutritional sufficiency in the population. Based on the higher value of the Kakadu plum, Davidson peaches, muntries, and quandong peaches were further analyzed for bioaccessibility of phenolic compounds, their reciprocal interactions with the gut microbiota, and safety evaluation using a zebrafish model. The safety of phytochemical extracts from these selected fruits was evaluated using an embryonic zebrafish model to effectively utilize these plants in drug discovery effectively. Muntries were quantified with the least LC50 value (169 mg/L) compared to Davidson plum (376 mg/L), Kakadu plum (>480 mg/L), and Quandong peach (>480 mg/L), which indicates that muntries extract was more toxic than other fruit extracts. Importantly, we found that adverse effects were not correlated to the total phenolic content and antioxidant potential of these native Australian fruits and cannot simply be predicted from the in vitro analysis. According to the Organization for Economic Cooperation and Development (OECD) guidelines, native Australian fruit extracts are included in the safe category. Additionally, the bioaccessibility and biotransformation of phenolic compounds, the production of short-chain fatty acids, and the impact of native Australian fruits on gut microbiota composition during in-vitro digestion and colonic fermentation were also investigated in this thesis. Quandong peaches were measured with a higher amount of total bioaccessible phenolic compounds than other selected fruits. Native Australian fruits significantly affect the diversity of microbial composition and production of short-chain fatty acids. Kakadu plum and muntries have significantly higher total short-chain fatty acids production than Davidson plum and quandong peaches. These native fruits are beneficial for maintaining gut health by regulating microbial composition. This could also be due to the higher concentration of dietary fiber in these fruits, condensed tannins, anthocyanins, and other flavonoids, which are highly beneficial for gut microbiota. This study addressed many gaps in the selected native Australian flora and added value for native Australian fruits and herbs commercialization. It broadened the knowledge of the complex metabolomic profiling of the selected fruits, their bioactive functions, safety evaluation, and their impact on the gut microbiota. This study will develop further research to explore the phytopharmaceutical potential of these native Australian fruits, herbs, and spices in drug discovery using different in-vivo models.
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ItemEvaluating biochar to enhance hydrological benefits of green roofs( 2023-02)Urbanisation increases imperviousness which alters natural hydrological cycles with adverse effects on the environment and human well-being. Impervious surfaces convert rainfall into stormwater and reduce infiltration into soil which limits urban vegetation for cooling through evapotranspiration and shade. Re-introducing plant-soil systems in cities, commonly referred to as green infrastructure, can partially restore hydrologic function by increasing rainfall infiltration and water provision for plant uptake, which in turn reduces stormwater runoff and inner-city temperatures. However, the uptake of ground-based green infrastructure is challenged by pressure to develop higher density cities. Consequently, on-structure engineered green infrastructure such as green roofs are highly desirable as roof space makes up to 50% of a cities impervious surface. Modern green roofs are installed in layers on top of a building’s water proofing with plants growing in a substrate (growing media). Green roofs can provide multiple ecosystem services including reduced stormwater runoff, lowered ambient and inner-building temperatures and increased recreational space and habitat for flora and fauna. However, their widespread implementation is hindered by the considerable weight of the green roof substrate, particularly on existing buildings with limited weight-loading capacity. Moreover, climates with hot and dry summers challenge the balance of green roof function for stormwater management, which is best achieved by dry substrates at the onset of a rain event, and plant survival, which requires water availability for plant uptake, thus continuously moist substrates. Attempting to balance the contrasting demands of green roof weight, water retention, and plant survival, this thesis aimed to develop light-weight green roof substrates with high water retention capacity to reduce stormwater runoff and improve plant survival. To achieve this, I evaluated whether biochar, a light-weight and porous type of charcoal that can be locally produced from organic waste materials, could be added to green roof substrates to improve water retention and make them lighter. However, biochars differ in their properties depending on the raw material (feedstock), process conditions (pyrolysis) and post-pyrolysis processing (grading), and their effect on water retention depends on the substrate they are added to and local climate conditions. In Chapter 1, I identified potentially beneficial properties, feedstock types and process conditions of biochar for green roof substrate amendment through a review of the literature. In Chapter 2, I explored the relationship between feedstock properties (density and cell structure) and biochar properties (water retention and weight). Chapter 3 investigated the mechanistic effects of biochar amendment (feedstock type, particle size and amendment rate) on green roof substrate properties (water retention, infiltration and weight). In Chapter 4, I evaluated how biochar amendment (30% v/v) and planting density influence green roof hydrologic performance (rainfall retention, evapotranspiration), plant growth (dry shoot biomass, leaf area) and weight (dry and saturated bulk density) under a simulated rainfall regime in a south-eastern Australian summer. Finally, Chapter 5 synthesises results from Chapters 1 – 4 and provides future implications for the use of biochar on green roofs and in other green infrastructure applications. The literature review suggests that low-density woody feedstocks, pyrolysed at temperatures between 450 – 550 degree Celsius in slow pyrolysis are best suited for producing beneficial biochar for green roof substrate amendment. Biochar properties were strongly correlated with feedstock wood density, with lower density hardwood resulting in biochar that had greater water retention, plant available water and lower weight when compared with biochar from higher density hardwood (Chapter 2). When adding biochar to green roof substrates (Chapter 3), particle size distribution and amendment rate had the most impact on substrate physical properties (i.e., water retention, infiltration rate, weight), outweighing differences between contrasting feedstock types of biochars used. In the rainfall simulation experiment (Chapter 4), amending green roof substrates with biochar did not increase rainfall retention and plant growth but did reduce green roof weight. While biochar increased water retention in green roof substrates (Chapter 3), the lack of an effect on rainfall retention in the rainfall simulation experiment (Chapter 4) was likely caused by fine particles of either the parent substrate or the biochar itself clogging pores of larger biochar particles, thereby limiting water storage within the substrate. This thesis demonstrated that biochar is a sustainable and viable option to reduce green roof weight without compromising green roof function for stormwater management and plant survival in hot and dry summer climates.
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ItemProductivity, methane emissions and carbon footprint of smallholder cattle fed improved diets in Kenya( 2023-05)Livestock production and its related activities account for about 18% of global anthropogenic greenhouse gas (GHG) emissions on a life cycle basis. Despite this, the sector also supports the livelihood of millions of the world’s most vulnerable populations living in the developed world. In Sub-Saharan Africa, cattle production is characterised by low productivity that is attributed to poor nutrition, especially during the dry season because of the drop in both feed quality and availability. Because of the suboptimal feeding, this has also been associated with increased enteric methane (CH4) emissions. To date, animal studies from East Africa quantifying actual animal productivity and enteric CH4 from local cattle breeds fed on local feed resources are very limited and inconclusive. As a result, East African countries continue to rely on CH4 default emission factors recommended by the Intergovernmental Panel on Climate Change (IPCC) that are extrapolated from other regions of the world, which results in high uncertainty in estimating GHG emissions from the livestock sector. The present thesis aimed at accurately establishing actual animal performance and enteric CH4 emissions from cattle fed commonly used feed resources in East African smallholder setup. This thesis also sought to quantify the effect of advancing from using IPCC Tier 1 to IPCC Tier 2 methodology in estimating total farmgate emissions and emission intensities (EIs) of animal products. Two controlled animal experiments were conducted, and animal productivity (milk and weight gain) and enteric CH4 were measured using respiration chambers. A partial life cycle assessment (LCA) was also conducted using data inputs collected at the farm level in two counties in western Kenya, together with the output from the two animal experiments. This thesis reports some of the pioneering respiration chamber measurements from East African cattle fed on local feed resources at production levels of feed intake. Feeding grass-based diets consisting of either Cenchrus purpureus, Chloris gayana or Urochloa brizantha to growing Boran steers (Bos taurus indicus) on ad libitum basis resulted in methane yields (MY; CH4 g DMI kg) ranging from 26.7-28.5, which was about 20% higher than the current IPCC recommendation for cattle fed on similar diets in East Africa. When lactating crossbred cattle also provided on a grass-based basal diet and supplemented with either commercial dairy concentrate or leguminous fodder; Desmodium intortum hay, this resulted in a 7% and 14% reduction in MY, respectively, compared to the control (27.6 CH4 g DMI kg). From the LCA, using IPCC Tier 2 instead of Tier 1 methodology total farmgate GHG calculation resulted in about 23% lower, while substituting regional MY defaults recommended by IPCC with locally generated values resulted in about 18% higher total emissions. Thus, there is a need for developing countries to invest in moving to a higher tier in calculating their national livestock GHG inventory for more accurate reporting and to be able to test suitable mitigation interventions that are suitable for their local cattle production systems. With the increasing urgency to reduce GHG emissions from all sectors of the economy globally to cap the harmful effects of climate change on the environment, all nations have a role to play in this. Countries, therefore, need to accurately quantify their emissions for accurate inventory reporting and to be able to identify and test suitable mitigation strategies for their local production systems. Most East African countries continue to use IPCC Tier 1 to report the emissions from their livestock sector. The present thesis indicates that this substantially overestimates the sectoral emissions, hence a need to move to a more country-specific methodology, i.e., Tier 2. In tandem with the need to reduce GHG emissions, East African countries also need to feed the rapidly growing population by increasing their food systems' productivity. This increase in food production is likely to inevitably increase absolute GHG emissions, with the implementation of mitigation strategies targeted at enteric CH4 emissions likely only to reduce EIs. These developing countries could explore a synergy between animal and whole-farm level mitigation interventions such as soil carbon sequestration to develop an environmentally sustainable food system that adequately feeds the growing population. More ambitious mitigation options, however, need to be researched and adopted in SSA to achieve a reduction in absolute GHG emissions from the present and future food production system.
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ItemMulti-scale effects of landscape structure, fire and habitat on reptiles in fragmented landscapes( 2023-06)Changes to landscape structure and fire regimes are major drivers of biodiversity loss, influencing habitat availability and ecosystem functioning. Reptiles are considered sensitive to both processes due to their traits, including their reliance on native vegetation and limited dispersal ability. However, identifying the extent to which fire regimes and landscape structure influence distributions and diversity is challenging when 1) species respond to their environment at multiple spatial scales, and 2) fire and landscape structure may have interactive effects. To address this, I examined how drivers such as landscape structure and fire influence reptiles at multiple spatial scales. Victoria, Australia, is an ideal location to study the effects of these processes as large parts of the state have been fragmented, and fire (both prescribed burning and wildfire) is a regular disturbance. First, I examined the influence of landscape structure on reptiles by modelling the distributions of 40 species within Victoria and comparing the influence of biophysical and landscape structure variables. While climate variables were generally found to be the most important drivers of species distributions, the majority of species were also influenced by landscape structure variables. Of the five landscape structure variables examined, extent of native vegetation had the greatest influence, followed by measures of habitat configuration. Next, I investigated the responses of seven reptile species to site-scale variables (fire and several measures of habitat structure) and landscape-scale variables (native vegetation, plantation, and pasture cover) to 1) identify whether species’ responses to fire and habitat depended on landscape structure, and 2) examine the relative influence of time since fire, habitat structure and landscape structure on reptile responses. Reptile species were sampled at 107 sites within fire-prone heathy woodland, interspersed with plantation forestry and agriculture in south-west Victoria. For three species there was evidence that their responses to site-scale variables depended on landscape structure. While site-scale variables were the strongest predictors of reptiles overall, most species responded at both scales. Finally, I investigated potential drivers of reptile functional diversity at multiple scales within the fire-prone heathy woodland in south-west Victoria. I examined effects of fire history, habitat and landscape structure on functional diversity and species richness. At the site-scale, species richness and most measures of functional diversity were influenced by habitat structure, though one functional diversity measure was influenced by time since fire. At the landscape scale, functional diversity was influenced by presence of pasture, while species richness was influenced by extent of native vegetation. Results from all investigations indicate that maintaining and expanding native vegetation is key to promoting conservation of reptiles in modified landscapes. Further, my thesis demonstrates that reptile species and communities respond to drivers acting at a range of scales, including habitat, fire, and landscape structure; and also provides evidence that species responses to site-scale factors, including fire, may depend on landscape structure. Consequently, approaches to ecological management which consider multiple drivers at multiple scales are necessary to identify how reptiles respond to disturbance, and to identify the scale at which management actions are most likely to promote conservation.
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ItemApplication of New and Emerging Technologies to Assess Rice Quality and Sensory Perception by Consumers( 2023-07)Rice is a staple food for over half of the world's population. The selections of commercial rice in the market resulted from the diversity of rice quality preferences by consumers. Besides, demographic factors such as cultural background, urbanisation, and socioeconomic status may change rice quality preferences over time. Hence, rice breeders and producers need to actively assess the best rice quality attributes that suit the demands. However, the traditional methods to evaluate rice quality are commonly tedious, time-consuming, costly and non-portable. Besides, the conventional descriptive and consumer acceptance tests based on conscious responses are likely prone to bias, expensive, time-consuming and require a dedicated laboratory sensory to conduct the sensory sessions. Therefore, new methods to assess rice quality and sensory perceptions using artificial intelligence (AI) subdivision technologies might be beneficial to overcome these disadvantages. Integrating digital sensors, computer vision, biometrics, and machine learning technologies could offer new approaches to assess rice quality and consumer perception of rice using rapid methods. This research aimed to develop rice quality assessment methods using digital sensors, computer vision, biometrics and machine learning to assess the aromas, physicochemical quality and consumer perceptions towards different types of rice. The project was divided into three main scopes to assess raw and cooked rice physicochemical quality, consumer perception of uncooked rice, cooked rice and packaging and detection of rice adulteration. This study used different types of commercial rice bought from the local markets in Australia. The rice samples consisted of regular white rice (e.g., long, medium and short-grain rice), organic, and unpolished rice from different market segments and provenances. The wide selection of rice is essential to the study since various types of rice are consumed by diverse cultural backgrounds to cook different kinds of dishes worldwide. In this study, digital, chemical and aroma fingerprints of rice were obtained using digital sensing devices such as the smartphone camera, near-infrared (NIR) spectrometer and electronic nose (e-nose). The fingerprints were used as inputs to develop machine learning models to classify different types of rice and predict the aromas, physicochemical quality, consumer perceptions, and rice adulteration levels. Furthermore, biometrics responses were used to obtain subconscious responses to assess their relationship with self-reported responses and different types of rice samples. Findings from this research are expected to contribute to the scientific knowledge of the relationship between digital, chemical and aroma fingerprinting with consumer perceptions towards different types of rice quality. Besides, the proposed method to classify different kinds of rice quality and predict rice quality attributes, consumer perceptions and adulteration levels using the integration of digital sensors, computer vision and machine learning showed high prediction accuracy (classification model: accuracy > 90%; regression model: R > 0.94). The proposed methods using the new and emerging technologies described in this study will lead the rice industry towards applying the rapid technique at a lower cost to assess rice quality compared to the traditional method.
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ItemEffect of green roof design configuration and climate on rainfall retention, evapotranspiration, and plant drought stress( 2023-04)Urbanisation significantly alters the hydrological cycle through creation of impervious surfaces and removal of vegetation. Besides creating large volumes of stormwater runoff which degrades urban stream ecosystems and water sources, impervious surfaces reduce infiltration of rainfall and therefore water availability for remaining vegetation. Sustainable and resilient stormwater management techniques are required to mitigate the impacts of stormwater runoff and compensate for the loss of vegetation in cities. Green roofs are a promising green infrastructure technology with the potential to deliver these ecosystem services, however, gaps in our understanding of how they should be designed is preventing widespread uptake. Green roof substrates are typically shallow due to building weight-loading restrictions and therefore have limited water storage for reducing runoff and sustaining vegetation. Species typically used on green roofs are limited to those with the ability to survive harsh environmental conditions, such as succulent species. However, selecting plants with high water use, combined with drought resistance, such as non-succulent species, and planting at higher density in deeper substrates may improve green roof rainfall retention without substantially increasing plant drought stress. Where substrate depth cannot be increased, mimicking processes we observe in natural systems, such as redirecting rainfall towards vegetation in semi-arid banded systems, has significant potential to both increase rainfall retention and reduce plant drought stress. Climate is the primary driver of green roof performance, specifically the supply of and demand for water from the atmosphere, which in turn determines evapotranspiration, rainfall retention and plant drought stress. Ideally, by understanding the interaction of substrate depth, plant density (water use) and redistribution of water resources on green roofs, it should be possible to determine the most suitable green roof configuration for different climates, and therefore remove the key barrier to widespread green roof installation. In this thesis, I aimed to achieve this understanding through a combination of controlled experiments and water balance modelling. Firstly, a glasshouse experiment was used to understand how increasing substrate depth and plant density, as well as their interaction, impacted plant water use, drought stress and rainfall retention. Due to COVID-19 disruptions, only the first well-watered phase could be completed, after which the experiment had to be terminated without measuring water use and drought stress under water-deficit. Therefore, I used an established green roof water balance model to simulate performance under water deficit conditions. Pre-existing functions describing the plant species’ drought response were combined with well-watered plant crop factors (Kc) calculated from ET measured during the experiment, to estimate rainfall retention and the incidence of plant drought stress. Contrary to my initial hypotheses, increasing plant density did not result in a proportional increase in plant water use, even when substrate depth was doubled. Importantly, this indicated little gain in retention performance by increasing plant density. Using a water balance model to extend these findings to include performance under water deficit, I showed that rainfall retention was very high, regardless of substrate depth and plant density, as plants in the glasshouse had a very high crop factor and therefore rates of water use. With a high crop factor, all treatments from the glasshouse simulated in the model depleted the substrate water quickly, resulting in greater retention, but also significant plant drought stress. In this model, the indicator of drought stress in plants on each day of the rainfall simulation was when the depth of water (millimeter) in the substrate at the end of any given day reached zero. Importantly, increasing substrate depth showed no significant benefit to either rainfall retention or plant drought stress. Overall, planting in shallower substrates at a lower density optimised green roof performance when measured and simulated in a temperate climate. Secondly, a rainfall simulation experiment using green roof modules was conducted to understand the effect of plant density and redistribution of rainfall (runoff zones) on rainfall retention, plant water use and drought stress. In this experiment, drought stress in plants was indicated by midday leaf water potential (MegaPascal). Again, planting at a lower density (10 plants per module, approximately half the module area planted) achieved high rainfall retention and most importantly, plants experienced lower drought stress than fully-planted modules (18 plants per module). Furthermore, using runoff zones to direct rainfall towards plants also reduced plant drought stress. However, the runoff zones also created preferential flow pathways and shaded the substrate surface, both of which were the likely cause of lower rainfall retention, despite the observed reduction in plant drought stress. Although, reducing plant density showed the most effective way of achieving high rainfall retention and lower drought stress, there are other ways of increasing substrates' water retention and holding capacity, such as using water retention additives to increase water available for more densely planted green roofs which would improve the ecological, environmental, and social benefits of a green roofs. While redirecting rainfall showed promising approach, further work is required to improve their design to find the optimal method to redirect more water to plants and improve the coverage of plants on green roofs. Finally, using results from both experiments, I developed and validated a new green roof water balance model to simulate long-term green roof rainfall retention and plant performance in two contrasting climates (temperate vs semi-arid climates). Green roofs showed high rainfall retention in both temperate and semi-arid climates, regardless of substrate depth, plant density and presence/ absence of runoff zones. Even unplanted roofs showed high retention in both climates, showing that evaporation is the major component of evapotranspiration and therefore a primary driver of rainfall retention. In this experiment, midday leaf water potential was used to indicate the maximum water stress experienced by plants during the day and therefore plant drought stress. Therefore, I modified the water balance model used in the first experiment, by using the relationship between midday leaf water potential (MegaPascal) and substrate water content (S) to estimate plant drought stress. As expected, green roofs in semi-arid climates had significantly greater plant drought stress (more negative water potential) as compared with those in temperate climates, with no observed benefit in rainfall retention, despite increased substrate depth. Hence, a substrate depth of 150 millimeter could achieve optimal retention in both temperate and semi-arid climates. Increasing substrate depth, plant density and the use of runoff zones was less important for improving rainfall retention than climate. The modeled results also highlight that an unplanted roof is equally good for stormwater management alone, as it can achieve similar rates of rainfall retention as compared to a planted roof. However, keeping in mind the ecological, environmental, and social benefits of vegetated green roofs with good plant coverage, it is not recommended that practitioners install non-vegetated green roofs. Overall, the results showed that green roofs perform very well for rainfall retention, in both temperate climates with a large proportion of small rainfall events, and semi-arid climates with an annually low rainfall depth. However, only one plant species was evaluated in my thesis, which would have impacted on these results as the plants were high-water using species that could effectively dry out substrates after rainfall and also tolerate drought stress in dry substrates. The design of green roofs for good plant coverage and survival in semi-arid climates is likely to be more challenging than constructing in temperate climates in real conditions due to the risk of plant death where drought periods are more severe and prolonged. In this case, it is likely to be preferrable to plant low water using succulent species. In both temperate and semi-arid climates, green roof substrate depth did not necessarily need to be deeper than 150 mm, as the increase in rainfall retention was minimal and plant drought stress could not alleviate beyond this depth. Installing runoff zones is a promising approach to changing how water is distributed on green roofs and have the capacity to reduce plant drought stress. However, they can also promote preferential flow pathways minimising the water storage capacity of substrates and decreasing the evaporation from surface of substrates underneath their structure and therefore, reducing rainfall retention. Hence, reconsideration the design for such runoff zones could be a potential avenue of future research. In the end, the practical output of this research suggests that green roofs with lower plant density such as 1 plant per 0.1 square meter and substrate depth such as 150 millimeter can effectively retain rainfall in temperate and semi-arid climates. While in temperate climates, higher water using plant species can be used, it is recommended that in semi-arid climates, green roofs are planted with low water using species such as succulents to support vegetation cover on green roofs. This means that even when green roof plant cover reduces over time, green roofs will still have high performance for rainfall retention.
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ItemThe effects of fire and landscape structure on animal communities, species, and connectivity( 2023-04)The loss and fragmentation of habitat associated with land use change is the primary driver of global biodiversity declines. Changes to fire regimes that alter habitat suitability also threaten a range of animal taxa. Fire has been increasingly recognised as an important ecological process and is now used to manage fire-prone landscapes around the world, but important questions remain about the effects of fire regimes on animals, especially in fragmented landscapes. The aim of this thesis is to determine the influence of landscape structure (the composition and configuration of landscape elements) on animals in heathy woodlands in southern Australia in terms of fire, fragmentation, and interactions between them. First, I explored post-fire growth stage and land use together as components of landscape structure and assessed their relative and interacting effects on mammal communities. I used camera traps to collect mammal presence-absence data in 2019-20 and analysed it using ordination and linear modelling. I found that land cover composition was the primary influence on community composition. The composition of the fire mosaic had a secondary, weaker effect and one that may change depending on land cover composition. Second, I explored habitat structure as a mechanism by which fire regimes may affect mammal species, using a species activity index derived from the same camera trap data. Post-fire growth stage (a categorical representation of time since fire) was not a direct predictor of any species’ activity levels, but some habitat structure attributes were linked to certain growth stages and were therefore a mediating influence on animals. Finally, I assessed how the growth stages influence functional connectivity for a litter-dwelling skink. I used genetic data, landscape resistance modelling, and circuit theory-based mapping to find the relative connectivity of land use types and growth stages. Functional connectivity varied little with growth stage, with the primary influence on connectivity being the matrix of pasture and forestry plantation. Overall, I did not find direct effects of growth stage on animal communities, species, or connectivity. However, less obvious effects such as the composition of the fire mosaic beyond the site-scale and indirect effects through habitat structure are important to consider in future fire management. The extent of native heathy woodland was also vital for native mammal communities and functional connectivity; remaining native vegetation must be protected and expanded for the best outcomes for native diversity and species persistence.