School of Agriculture, Food and Ecosystem Sciences - Theses
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ItemThe physiology and functional genomics of the heat stress response in dairy cattle( 2017)Thermal stress experienced by dairy cattle, can be one of the greatest limitations on production efficiency and animal health. In the Australian climate the effects of heat stress causes millions of dollars in lost production every year. A correlated response to selection for improved milk production has facilitated an increase in metabolic heat and susceptibility to thermal stress. With the increase in the frequency and severity of heat events in the temperate climate dairying regions of Australia, the need to identify and breed heat tolerant dairy cattle is one of the most important traits. New information regarding the physiological responses to heat stress, will assist in determining the heat stress susceptibility of dairy cows in the Australian climates and reinforce the need to employ amelioration strategies. Amelioration strategies for heat stress in the Australian dairy industry, are often limited by the fact that the majority of dairy cows are exposed to the elements as they graze pasture. Techniques such as providing shade, sprinklers and fans becomes challenging and expensive for the producers. Another, perhaps more practical amelioration strategy is the identification of genetically heat tolerant dairy cows. The research presented in this thesis firstly examines the physiological and metabolic responses of Australian dairy cows to experimentally induced heat stress which replicates the moderate short-term heat events observed in the temperate climates of Australia. The experiment presented demonstrates the susceptibility to heat stress of dairy cows which are adapted to a temperate climate. The experiment also described the recovery period after exposure to a heat challenge, which identified that there was a delay between the return to normal feed intake and milk production. This indicates that there may be a period of metabolic recovery required post heat exposure. This thesis also presents an experiment validating genomic selection for heat tolerance within the Holstein Friesian breed. Genome wide DNA marker based prediction (genomic predictions) of heat tolerance from previous research were validated, as the genomically predicted heat tolerant cows during experimentally induced heat stress maintained milk production and feed intake to a higher level, and had lower core body temperature than genomically heat susceptible cows. The experiment also found that there are thermoregulatory differences between genomically heat tolerant and heat susceptible cows, as the heat tolerant cows displayed more efficient heat dissipation mechanisms via evaporative cooling. This validation of genomic selection technology is an important progression towards breeding heat tolerant dairy cows in the future. The cellular changes at the molecular level in response to heat stress were investigated using global gene expression changes derived from whole transcriptome mRNA sequencing. The thesis presents global gene expression changes in vivo in white blood cells and milk cells of dairy cows experiencing experimentally induced heat stress. This experiment identified that there is a verifiable link between the heat stress phenotypes and gene expression. The genes identified to be differentially expressed in the blood, suggest that fatty acid metabolism, immune responses, inflammation, and blood pressure regulation were affected by heat stress. The transcripts in the milk suggest that cholesterol metabolism and lipolysis, and antibody production were also impacted by the heat challenge. These findings provide new insights into molecular adaptations induced during moderate short-term heat stress. Novel differences in global gene expression changes in vivo in the blood of genomically selected heat tolerant and heat susceptible cows were identified. The genes differentially expressed between heat tolerant and heat susceptible cows, suggest that lactation, glycolysis, lipid metabolism and oxidative stress related gene regulation was affected differently in the heat tolerant cows compared to the heat susceptible cows. This investigation of the functional genomic responses in the white blood cells during heat stress demonstrated the depth of the cellular response to heat. Biological pathways that were consistently affected by heat stress throughout the thesis were lipid metabolism, carbohydrate metabolism, apoptosis and protein folding, and a candidate list of genes were identified for further targeted research.
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ItemThe effects of urban land use, riparian forest cover, and instream habitat complexity on macroinvertebrate assemblages( 2017)Urban land use changes natural catchment processes through deforestation and the construction of impervious surfaces and stormwater drainage systems, resulting in the degradation of instream habitat and biota. Despite these urban degraders occurring at the catchment-scale, most efforts to mitigate urban impacts involve stream restoration at smaller scales, along the riparian zone or within the channel. Restoration efforts often rest on the assumption that restoration of physical habitat at these smaller scales will lead to the restoration of biological communities. However, recent reviews of restoration attempts have concluded that mitigation of urban impacts via riparian and channel habitat restoration is rarely successful, and hence mitigation attempts may require management actions at larger scales which address the sources of stress in the catchment. Identifying the magnitude and spatial scales of urban influences throughout the catchment can aid in determining the best restoration practices. To date, relatively few studies have assessed the influence of riparian land cover changes on stream ecosystems influenced by different levels of catchment stormwater runoff. This project aims to assess responses to changes in habitat diversity and corresponding macroinvertebrate communities as a result of riparian deforestation and catchment urban land use, testing if the often-assumed relationship in restoration ecology between habitat complexity and biodiversity varies under different levels of urbanization. Changes in instream habitat associated with riparian deforestation and catchment urban land use were assessed using estimates of impervious area connected to the stream by stormwater drainage (attenuated imperviousness; AI), riparian forest cover weighted by flow-path distance to the stream (attenuated forest cover; AF), and riparian canopy cover lining a stream reach (canopy cover; CC). Three tributaries of the Yarra River, ~35 km east of Melbourne, Victoria, Australia, were selected for this study, which had catchment sizes ranging from 7.73 – 23.27 km2. Two of the tributaries ranged from 0.13 – 0.81% AI, with urban settlements in the lower reaches. The other tributary ranged from 2.23 – 4.16% AI, with urban settlements in 2.5 km2 of its uplands, and rural residential and low-intensity grazing agriculture downstream. Habitat variables measured were the ratio of channel width to depth (W/D), the ratio of bank height to catchment area, the proportion of clay, silt, sand, fine gravel, medium gravel, coarse gravel, and the amount of coarse particulate organic matter (CPOM), and large woody debris (LWD). Catchment urban land use had the greatest effect on instream habitat variables, as it was associated with major changes in sediment composition, larger bank heights, and lower amounts of CPOM and LWD. The presence of riparian vegetation was associated with a reduction in some, but not all of the effects of urban land use on instream habitat. Specifically, AF was associated with lower bank height and mobile sediments, and both CC and AF were associated with increased CPOM in the most urban stream. Responses of macroinvertebrate communities to urban degraders were also assessed using AI, AF, and CC. All macroinvertebrate samples were taken from submerged LWD within the three tributaries of the Yarra River that had varying levels of catchment urban land use and riparian vegetation. Total macroinvertebrate density and richness, Ephemeroptera, Plecoptera, and Trichoptera (EPT) density, and the densities of individual taxa that were abundant in each stream were determined. Higher levels of AI were associated with lower EPT density and richness, as well as a decrease in the density of sensitive taxa and increase in the density of tolerant taxa. Riparian vegetation had positive effect on EPT density, especially in 1 of the 2 less urban streams. These results lead to the conclusion that AF can increase the density of EPT taxa, especially in streams with low levels of urban land use, but more substantial increases in sensitive taxa density and richness are likely only if urban stormwater drainage impacts are mitigated or removed. To test whether the alteration of macroinvertebrate communities resulting from catchment-scale perturbations can be mitigated by direct manipulation of instream habitat complexity, the effect of manipulating surface complexity on macroinvertebrate assemblages in urban and non-urban streams was experimentally assessed. Experimental wood block substrates were used with two treatment types; smooth blocks with low surface complexity and grooved blocks with 4-mm x 2-mm grooves cut into them, and hence higher surface complexity. Blocks were cut to size so that regardless of complexity, surface areas of all wood substrates were held constant (1094 cm2) to eliminate the possibility of sampling effects. Macroinvertebrate assemblage composition differed strongly with urban land use, but not with surface complexity. EPT density was lower with urban land use, and higher with surface complexity. Total taxon and EPT richness was lower in urban sites, but did not show a difference in response to surface complexity. Of the 30 taxa analysed, 13 differed in density with catchment condition, but not with surface complexity. Only two taxa were affected by both catchment condition and surface complexity. The results suggest that EPT density in urban streams can be increased by increasing local habitat surface complexity, but improved stormwater management is needed to increase other aspects of macroinvertebrate communities, such as EPT and total taxon richness. Catchment factors were the main driver of instream habitat and macroinvertebrate communities in the streams used here. Hence the best chance of restoring streams such as these, is to mitigate the impacts of urban stormwater runoff. The influence of riparian and instream physical habitat was reduced in urban catchments, however they still provided some benefit to the streams used here, with low levels of stormwater impacts. Therefore, the protection and restoration of these habitats is not sufficient to establish instream biota similar to pre-urban conditions, but can aid in mitigating some of the impacts of urbanisation.
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ItemUnravelling spatio-temporal water balance patterns in topographically complex landscapes( 2017)The Budyko framework for understanding how precipitation (P) is partitioned into evapotranspiration (ET) and streamflow has been shown to be remarkably robust at large spatial scales. The Budyko model simply uses P and potential ET as variables. However, at smaller spatial scales additional predictor variables are required to partition precipitation. In steep uplands, topography appears to exert strong control on the water balance at the hillslope scale. Organization of vegetation suggest heterogeneity in the water balance at these scales. This topographic control though is poorly characterized in most environments and therefore not well represented in models. The aim of this thesis is to quantify the effect of local topography (aspect and drainage position) on forest water balance as a first step towards a down-scaling of the Budyko model in steep upland terrain. Six intensively instrumented sited were established on three drainage positions and two aspects in mixed species eucalypt forests (MSEF), with all other variables remaining constant. Continuously monitored water balances were extrapolated across a ~70 ha catchment using a Random Forest model and LiDAR characterization of stand density and structure. The study demonstrated that spatial vegetation patterns emerged in response to topographic control on water-availability via soil depth, water redistribution and sub-canopy radiation loads. Moreover, short-term variations of overstory transpiration (To) were driven by atmospheric forcing, whereas seasonal and annual To patterns were explained by sapwood area index (As, R^2:0.89). Understory and forest floor evapotranspiration (ETu) was controlled by sub-canopy short-wave radiation. Further, the combined effect of aspect and drainage position on water balance partitioning markedly diverged along the south and north-facing transect. All plots on northern aspects had a positive water balance (P> ET), whereas only the ridge plot on the south-facing slope had a positive water balance, while the lower hillslope had higher ET rates than rainfall inputs.ET measurements from the distributed plots could be up-scaled using terrain and vegetation information derived from LiDAR and unveiled strong spatial variability of To (4.5-fold), ETu (3.5-fold) and total ET rates (2-fold) over as little as 200 m distance. The observed ET range corresponds to eucalypt forests typically located >100s of kilometers apart, with the lower end similar to arid open woodlands in Western Australia and the upper end to tall mountain ash forests in the Victorian highlands. Predicting ET using the Budyko framework revealed strongly biased ET estimates in relation to landscape position, where ~18% of the catchment area plotted above the theoretical water limit, confirming the importance of topographic water redistribution. Further, model residuals were explained well by As and terrain patterns. My thesis presented strong links between vegetation patterns, topography, soil depth and energy and water fluxes in upland MSEF. Ultimately, the study demonstrated the potential of remotely sensed vegetation and terrain patterns to infer and scale water-balance patterns in heterogeneous upland forests.
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ItemAn evaluation of fast processed urban food waste as a soil amendment( 2017)With the fast development of urbanization, an increased demand for natural resources and manufactured consumer goods has put pressure on the environment. At least one third of municipal solid waste is food waste (urban food waste, UFW). On one hand, the huge quantity of food waste being generated each year results in a direct economic loss, and also an indirect loss of natural resources, human resources and environmental sustainability. On the other hand, we are facing the challenge to produce more food to feed the growing population in the next century while the world population projected to grow to 9.7 billion by 2050. At the same time known phosphorus reserves, required to feed this population, are dwindling. Additionally, one in nine of the global population, are suffering from food hunger problems. Therefore, we are now facing the dilemma between food over-consumption, food hunger and food and nutrient waste. In Australia, more than 4 million tonnes of food waste are disposed to landfill every year, generating greenhouse gases, accumulating toxins, and pollution from leachate. Other than landfill, UFW could potentially be reused or recycled as a value-added soil organic amendment. This work aims to evaluate the potential of processed urban food waste (PUFW) as a soil organic amendment with recovery of nutrients back to soils. In order to achieve this goal, this work uses a new technology for managing UFW namely, the Fast Composting Unit (FCU). The FCU technique claims a “ready-to-use” organic product in only 24 hours. These claims have not been scientifically tested and the suitability of the output for land application is unknown. This thesis is the first attempt to characterize different sources of PUFW (restaurant waste (RW), canteen waste (CW) and bistro waste(BW), and their suitability for agriculture use, interactions with soils, and nutrients recovery potential for plants. The PUFW samples were collected over five samplings, and assessed by the Australian Standards for compost, mulch and organic amendments. The result suggested that PUFW had a modest nutrient value with 2-3% N and 0.5-1% P. However, some properties, such as pH, EC and volatile organic acid content were failed to meet the requirement of the mature compost. PUFW was immature and this was reflected in a low grade of composting for the FCU. An incubation experiment was conducted to understand the mineralization rate, potential nutrient release characterises (primary N and P) in different agricultural soils (a fine sandy clay loam, clay loam and sandy soil). RW had the highest N mineralization rate on sand soil and this was significantly affected by the rate of waste addition with 7.5 mg/kg of N per day at rate 6%, 4.2 mg/kg of N per day at rate 3%, 1.6 mg/kg of N per day at rate 1% and only 0.7 mg/kg of N per day at rate 0.5%. In contrast, with a higher C:N ratio, CW and BW showed strong immobilization of N across all soils. Phosphorus availability, as measured by Olsen P was in agreement with this. Additionally, a pre-incubation of PUFW with these soils saw additional available P. However, it was the immaturity of PUFW that limited the agricultural potential and caused phytotoxicity as assessed by seed germination and root elongation.There was a clear phytotoxic effect on seed germination index with 48% for RW, 27% for CW and 51% for BW. In order to redress this phytotoxicity further composting of PUFW was carried out with sawdust, coal ash, and/or combinations of both. Coal ash is another problematic waste stream in Victoria state and the utilization to PUFW co-composting can be a win-win strategy. Co-composting was found to eliminate the phytotoxicity problem of RW. A glasshouse experiment evaluated the agronomic value of cocomposted food waste and confirmed that increasing levels of un-amended RW significantly decreased the sorghum plant shoot biomass from 17.5 g/pot at control to 12.2 g/pot at the 3% application rate. A simple framework was used to integrate these findings in regard to urban food waste in Australia. Based on these calculations, significant savings could be made when the urban food waste is properly recycled to agriculture soils.
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ItemBreeding for processing peach yield from a diel fruit growth perspective( 2017)Yield in terms of fruit size and fruit number is an essential breeding criteria for the majority of fruit breeding programs, for without threshold levels of yield the commercial production of a cultivar becomes non-viable. Yet there is relatively little research on the inheritance of yield traits in tree fruit crops and their phenotypic and genetic assessment. Fruit growth potential is governed by both cell division and cell expansion that determine cell number and cell size respectively. The contribution of expansive fruit growth to fruit size and yield can be compared between genotypes by analysis of their fruit growth on a 24 hour (diel) scale. Continuous monitoring of fruit growth can provide a link between the genotype and the phenotype to visualise how different genotypes react to changes in the environment to produce larger fruit sizes and higher yields. Narrow-sense heritability of yield in peach (Prunus persica L. Batch) is low and labour intensive to measure. This makes rapid genetic gain in processing yield difficult and time-consuming to achieve. More efficient evaluation of yield traits is desirable to facilitate rapid release of new cultivars in the processing peach industry. A rapid three year evaluation system was investigated where trees were cropped at successively higher crop loads as the trees increased in size to align with their natural cropping behaviour. Fruit density is typically low in the first cropping year as the tree directs assimilates into development of the tree structure. Thus genotypes were evaluated at an ultra-low crop load to determine their maximum fruit growth potential in terms of fruit size. A standard crop load was applied in the second year. In the third year, genotypes were evaluated at an ultra-high crop load, to confirm which genotypes could continue to size fruit under intense competition for resources to produce high processing yields. The productivity experiment included 280 genotypes laid out in a nearest neighbour incomplete block design with eight replicates. All trees were assessed on a whole-tree basis for fruit density, fruit weight, gross and processing yield and percentage smalls (proportion of fruit < 60.3 mm in diameter). Variance components, heritability, and phenotypic and genotypic correlations were estimated using repeated measures over three years of evaluation. The first aim of the productivity experiment was to determine if promising genotypes could be reliably selected for yield traits early in the evaluation cycle. For the first year to be a reliable indicator of future performance, the narrow sense heritability in the first year and later years, and the additive genetic correlations between these years needs to be high. The results showed that mean fruit weight at an ultra-low crop load was a good indicator of later performance at an ultra-high crop load. Heritability estimates for processing yield (0.03 to 0.16) were low in all years of evaluation compared to other yield traits. However, breeding values for processing yield and other secondary yield traits showed strong correlations across years to facilitate reliable selection. The second aim of the productivity experiment was to investigate methods to improve the selection of processing yield by either derived expression of yield based on tree size, or by indirect correlation with secondary yield traits. The expression of yield in terms of tree size (trunk cross sectional area [TCSA], fraction of above-canopy photosynthetically active radiation [PARf] or 1 to 7 point-scale rating), did not improve the size of the heritability estimates for processing yield. Genetic correlations between processing yield and fruit weight were greatest in the first year at an ultra-low crop load (r = 0.996) but decreased in later years. The % small’s trait had higher genetic correlations with processing yield than either fruit weight or fruit density alone. It also showed strong correlations with both fruit weight and fruit density at higher crop loads to facilitate selection for processing yield. Principal components (PC) analysis of yield traits at the standard crop load showed the majority of variance between genotypes could be explained by PC1 (44.8 %) and PC2 (38.6 %) that encompassed fruit density, fruit weight, gross and processing yields and tree size (TCSA) traits. There was a strong trend for recent cultivar releases from the Australian processing peach breeding program to cluster along the processing yield line in the PC analysis bi-plot compared to older cultivars. This indirectly demonstrated that selection for high processing yield was facilitated by evaluations at ultra-low and ultra-high crop loads. As a new avenue for genetic improvement in processing yield, diel growth data of peach fruit were monitored in a series of experiments to determine which diel traits contribute to phenotypic and genotypic differences in fruit size. The daily phases of fruit growth were determined from the points of inflection on fruit growth curves generated from 20 minute readings. These phases were the cessation of growth/start of shrinkage (G-stop); cessation of shrinkage (S-stop); start of rehydration (R-start); and start of growth (G-start). They were then used to determine the amplitude, period and rates of shrinkage, rehydration and growth. A simulation study on peach indicated a sample size of at least 10 fruit was required to minimise variance in the points of inflection on the diel fruit growth curves. An initial fruit size experiment showed that larger fruit had both a significantly higher growth rate and a longer period of diel growth than medium-sized fruit. Under a thinning treatment there was a significant increase in growth rate but no alteration in the phases of growth compared to fruit on unthinned trees. Both the commencement and cessation time of growth phases (G-start and G-stop) were important determinants of the diel growth period under non-water stressed conditions. The diel fruit growth components (amplitude, period and phase of growth, shrinkage and rehydration) were then analysed on the standard Australian processing cultivar ‘T204’ and four related peach accessions (‘SAB66’, ‘SAB176’, ‘SAB441’ and ‘SAB461’) from the initial productivity experiment to determine how diel traits contribute to differences in processing yields between genotypes. In the third year of the productivity experiment, three single tree replicates of each genotype were evenly thinned to an average crop load of 5.3 ± 0.2 fruit/TCSA four to five weeks after full bloom. An exception was ‘SAB461’ which had a lower fruit density and was set to 2.2 ± 0.5 fruit/TCSA. Ten fruit/tree were selected with fruit diameters of 25.5 ± 2.1 mm 64 DAFB of ‘T204’ and their fruit diameter continuously measured over three stages of fruit development using linear potentiometers. Our results showed the differences in diel growth between the higher productive (‘T204’, ‘SAB176’, ‘SAB441’) and lower productive genotypes (‘SAB66’, ‘SAB461’) were reflected in changes in both the periods and rates of growth, shrinkage and rehydration and were dependent upon the stage of fruit development. We concluded that fruit growth potential of peach trees are most limited by their diel period of growth due to high day-to-day variation. Lastly, diel growth traits of these genotypes were analysed across two generations of breeding for estimated breeding values (EBV). Genetic analysis of diel traits were undertaken across three stages of fruit development using restricted maximum likelihood (Reml) to create linear mixed models that took into account all their pedigree relationships. Our results showed that diel growth and its components diel growth rate and diel growth period were moderately heritable in stage 1 of fruit development, but not in latter stages. The genotypes with the highest processing yields were characterised by high EBV for diel growth rates and/or diel growth periods, but were dependent upon the stage of fruit development. This research highlights the importance of changes in both the phase and periods of diel growth on fruit size and yield traits in addition to any changes in growth rates. It has previously been proposed that yield could be improved in new cultivars by cross-pollinating between cultivars with high growth rates in stage 1 and stage 3 of seasonal fruit development. This research indicates that processing yields can also be enhanced through selection of genotypes with longer periods and higher rates of diel growth and that resultant fruit size differences selected for early in the breeding cycle.
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ItemThe effect of urbanization on butterfly assemblages in Melbourne, Australia( 2017)Urbanization is the fastest expanding land-use conversion in the world. Alteration or loss of habitats in urban areas often results in overall biodiversity decline. Insects are integral components of ecosystems, providing important services such as decomposition and pollination. Despite this, we know little about the ecology of insects within urban settings. Butterflies are well suited for study in urban areas because they are conspicuous components of any landscape and play an important role within the ecosystem. To date, there has been a lack of understanding of the interplay between the ability of urban areas to provide necessary butterfly habitat resources (e.g., adult and larval food plants) and how the presence of those resources affects the butterfly community. Urban ecology studies are often entrenched in patch-matrix theory, but the use of a gradient paradigm allows for a more mechanistic understanding of the response of species and higher taxa to increasing urbanization. Therefore, this thesis uses a continuous gradient of imperviousness (percent cover of impervious surfaces) to assess how the urban landscape may support the local butterfly community through the availability of their required resources. This PhD first aimed to quantify the spatial variation in butterfly community structure across a gradient of imperviousness using two measures of habitat quality for adult butterflies and larval stages: native and non-native floral abundance and the availability of remnant vegetation. Approximately 21% of the region’s butterfly species were detected within the study area. Butterfly species richness and abundance and floral abundance declined with increasing imperviousness. The effects of total and native floral abundance measures on butterfly richness and abundance were small, but positive. The availability of remnant vegetation had a small, but positive influence on butterfly species richness. The second aim was to assess the response of larval host plants (LHPs) over the same imperviousness gradient. Laval host plant richness and cover decreased with increasing imperviousness, but LHP richness in particular had a significant, positive influence on butterfly richness and abundance. Larval host plant cover explained 57% of the variation within part of the butterfly community. Common butterflies within the matrix had a significant relationship with some of their specific LHPs. The third aim was to determine if the local butterfly community derived any benefit from wildlife gardening (resource supplementation or management decisions to benefit wildlife) within urban areas. Comparisons of the butterfly communities across gardens managed for wildlife versus those that are not, revealed that garden type did not influence butterfly responses, but instead led to increased native floral resources in wildlife gardens. This study suggests the landscape context of wildlife gardens may play a role in their effectiveness. This work demonstrates that the landscape-scale alterations imposed by urbanization have a negative impact upon butterfly communities, and the adult and larval food resources they require. Increases in these resources had some positive effects, but these were mostly small and in some cases only benefitted common butterflies. Management programs aiming to increase habitat for butterflies in urban areas need to consider species-specific requirements and urban context in order to support urban butterfly communities.
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ItemThe role of fire in the coevolution of vegetation, soil and landscapes in south eastern Australia( 2017)Fire is an important process in the earth system, with biological, ecological, hydrological and geomorphological consequences varying from negligible to severe. The short-term effect of fire on earth system processes had been studied in detail, however, its role in the coevolution of soil and vegetation within the critical zone has never been addressed. In South Eastern (SE) Australia, local studies have shown that post fire runoff and erosion rates increase with aridity (the ratio between potential evapotranspiration and precipitation). The systematic variation in forest type, fire frequency and post fire response make SE Australian uplands an excellent natural laboratory to study the role of fire in coevolution of the critical zone. The aim of this study was to explore the role of fire in coevolution and to identify the key mechanisms, processes and feedbacks involved. Observations in which drier forests burn more frequently and yield more post-fire runoff and erosion, were used to hypothesize that in SE Australian uplands, fire has a critical role in the coevolution of the critical zone, and that its contribution increases systematically with aridity. Three different methods were used to address the presented aim. The first method focused on the long-term fingerprints of coevolution, soil depth and landform. By considering the observed climate-related differences in forest type, fire frequency and erosion rates, I hypothesised that soil depth and hillslope gradient are north-south asymmetric, and that the magnitude of that asymmetry varies systematically with climate. I addressed these hypotheses by analysing data from soil depth measurements and topographic analysis of digital elevation models. Results showed that soil depth decreased non-linearly with aridity, and that south facing hillslopes were on average steeper and their soils deeper than those facing north. Indices of asymmetry in soil depth (SAI) and hillslope gradient (HAI) expressed a humped-type relationship with aridity, with a peak close to the water-energy limit boundary, pointing to the key role of climate and possibly fire in controlling differential hillslope-scale coevolution across pedomorphic and geomorphic timescales. In the second method, I used a new numerical model in order to: (i) test the hypothesis that fire related processes and feedbacks are critical to explain observed patterns and magnitude of differences in system states across the landscape, and that their effect increases with aridity; and (if the hypothesis was supported), (ii) evaluate the role of fire related mechanisms in the coevolution process. The model was formulated and parameterised to express processes typical to SE Australian systems, and was evaluated with literature and empirical data. Simulations with stochastic fire controlled by soil moisture deficit replicated the observed pattern and magnitude of difference in system states. The net effect of fire on soil depth increased non-linearly with aridity when results from these simulations were compared to those without fire (i.e., coevolution only controlled by climate). Analysis of simulations designed to isolate the key processes affected by fire indicated that model outputs are sensitive to fire frequency and the effect of individual fires on infiltration capacity (Ic), and less so to the effect of fire on forest cover. Using model simulations, a fire-related eco-hydro-geomorphic feedback was identified in which a long-term increase in post-fire erosion might contribute to more frequent fires and more erosion. The aim of the third approach was to evaluate and quantify, using intensive field measurements, the way in which contemporary vegetation and soil depth affect the partitioning of rainfall and solar radiation, and to estimate the implications of this on processes in the coevolution of the critical zone. Sub-canopy microclimate (and open reference sites) was measured at sites across an aridity gradient, and the effect of partitioning of rainfall and solar radiation on coevolution was addressed by analysing soil moisture and temperature data, which are central to several processes in coevolution: productivity, flammability and weathering. Results showed that throughfall decrease and net shortwave radiation under the canopy increase with aridity due to the lower rainfall and higher canopy openness (respectively). On wet (dry) sites, the closed (open) canopy and the deep (shallow) soils partition water and energy in a way that resulted in wetter (drier) soils throughout the year, pointing to lower (higher) flammability and higher (lower) productivity. Mean annual soil water stores decreased non-linearly with aridity, and were more than 5 times higher on wet sites, despite annual rainfall only differing by a factor of ~2. Soil weathering is affected by soil moisture, and the results indicates that the differences between the system states may be amplified by weathering rate differences. The results points to a coevolutionary feedback between weathering, productivity, erosion and fire, which is controlled by the partitioning of water and energy across the vegetation and soil. Overall, results show that fire can play a significant role in the coevolution of soil, vegetation and landscapes in SE Australia. This work is the first to show the importance of fire related eco-hydro-geomorphic feedbacks in coevolution, controlled by soil moisture. Fire was found to operate within feedback loops between its effects on system properties and consequential changes in fire frequency. Two feedback loops were identified: between fire frequency and erosion, and between soil development and fire frequency. By its effect on infiltration capacity and the corresponding reduction in soil depth in direr forests, fire was found to exaggerate the effect of climate on coevolution, and helps to explain the extreme differences in observed system states across an aridity gradient.
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ItemPredicting the eating quality of pork( 2017)Reducing the variability in eating quality of Australian fresh pork remains a significant issue that needs to be addressed to improve consumer demand and satisfaction and drive increased consumption frequency. The differentiation of Australian pork as a niche, high quality product within a largely global commodity pork market will be supported through the implementation of an eating quality system by industry to manage, and carefully control, key production, processing, post-slaughter and cooking factors that can influence pork eating quality. Unlike the red meat sector, the Australian pork industry has not yet developed a non-prescriptive, pathway based eating quality model that can be accurately applied to different cut and cooking method combinations to improve its acceptability and consistency. Extensive knowledge of individual factors that influence both the meat and eating quality of pork has been generated over many years, both in Australia and overseas. These have primarily involved sensory evaluations of loin (M. longissimus thoracis et lumborum) cooked as a steak, either grilled or roasted. This information has been utilised and incorporated into industry quality assurance programs with standards in place to enable good agricultural practices or good manufacturing practices to be followed, rather than being used to inform the development of integrated predictive models for eating quality. Where eating quality guidelines and checklists have been developed, these have been used to support individual company brands. An objective of this thesis was to determine whether data compiled from mainly published studies fitting selection criteria could be used to estimate the size and effect of various pathway factors and their interactions on pork eating quality of different cuts and use this information to develop an eating quality predictive model for pork. Both Monte Carlo simulation techniques (Chapter 3) and random effects meta-regression analyses (Chapter 4) were applied to the constructed datasets that included data for the loin muscle due to lack of data for other cuts. From this, positive effects of moisture infusion, ageing for more than 2 days post-slaughter and hanging from the aitchbone on tenderness were found, whilst cooking to an endpoint temperature of greater than 80˚C negatively affected tenderness and juiciness. Due to a lack of eligible studies (including those presenting eating quality data for treatment interactions) as well as differences in study designs and methodologies used, it was not possible to establish algorithms to reliably estimate the effects of multiple factors on pork eating quality. For immunocastrated males, estimated means for tenderness, juiciness and flavour were determined on limited studies compared with those for pork from females, physical castrate and entire male pigs. Further studies were needed to generate datasets for different cut type and cooking method combinations, in addition to the loin, so that the system will truly be cuts-based. A series of multifactorial studies were designed and conducted involving consumer evaluations of pork to address these knowledge gaps. These datasets are to be used to inform statistical approaches associated with the development of algorithms to predict consumer eating quality scores of different cut type and cooking method combinations. The effects of ageing period (2 or 7 days), endpoint temperature (70 or 75˚C), cut type (loin, silverside, shoulder) and cooking method (roast and stir fry (all cuts) and steak (loin only)) on the eating quality of pork from female, physical castrate and entire male pigs (Chapter 5) and entire male and immunocastrated males (Chapter 6) from major supply chain were investigated. Across both studies, neither endpoint temperature nor ageing period, as main effects, influenced the eating quality of the seven cut type x cooking method treatments evaluated. Cooking loin steaks and stir fry cuts to an endpoint temperature of 75°C lowered juiciness scores and increased cooking losses compared to cooking to 70°C, whilst endpoint temperature did not influence sensory scores for roasts. As the boar taint prevalence of 15% and 10% in entire males were identified in studies reported in Chapters 5 and 6, respectively, the inclusion of entire males in any eating quality program for pork was questioned due to risks of poor eating experience by consumers. The effect size on eating quality scores due to cut type x cooking method were larger than those of the other pathway interventions investigated; only the shoulder stir fry and roast cuts met the fail rate target of <10% (defined as the percentage of pork rated as either unsatisfactory or below average by consumers) and were also more preferred by consumers than those from the loin and silverside. Alternate interventions to optimise the eating quality performance of different cuts prepared from the loin and silverside muscles, when cooked using different methods need to be identified and trialled. Further investigation to determine why ageing for 7 days post-slaughter was not an effective intervention was also recommended; longer ageing periods were investigated in Chapters 7 and 8. A simulation study to investigate the effects of age at slaughter from 20 to 24 weeks, (combined with dietary composition) and ageing period (7 or 28 days) on the eating quality of loin steaks and silverside roasts from female pigs cooked to 70 and 75˚C, respectively, was then conducted (Chapter 7). Finishing female pigs on a corn/soy diet and slaughtering at 24 weeks of age did not increase intramuscular fat concentrations in either loin steaks or silverside roasts compared with those fed a wheat/sorghum diet and slaughtered at 20 weeks of age. Based on these findings, pigs grown to 24 weeks of age could be eligible for inclusion in an eating quality system for pork. Proteolysis plateaued before 7 days post-slaughter as no differences in mean sensory scores were found for cuts aged for 7 and 28 days post-slaughter. Continuing efforts to improve sensory attributes of both cuts, particularly the silverside, are required as the fail rate target of <10% was not achieved for either cut. Further work to validate additional processing interventions, ascertained from Chapters 3 and 4, to improve eating quality performance of cuts from the loin and silverside muscles was then conducted (Chapters 8 and 9) to address the observed lack of shift in eating quality means of treatments already imposed. Two commercial validation studies involving immunocastrated and female pigs aimed to evaluate whether ageing period, moisture infusion and either hanging method or electrical stimulation and their interactions were effective in improving mean sensory scores and reducing fail rates to <10% of five different pork cuts produced from the loin and silverside. Pork cuts from immunocastrated males and females were comparable in eating quality across both supply chains. Ageing for either 7 or 14 days post-slaughter did not influence eating quality or lower fail rates for quality grade and re-purchase intention compared with pork aged for 2 days. Treatments imposed did not enable fail rates of <10% to be consistently achieved across all cut type x cooking method combinations. Moisture infusion was effective in reducing the fail rate of pork to <10%, particularly for stir fry and roast from the loin. A fail rate for quality grade of 9% was achieved for loin stir fry through aitchbone hanging compared with 21% for Achilles hung carcases. Chapter 10 presents a review of eating quality research conducted over the past sixteen years in Australia, including work presented in this thesis, to support the development of an eating quality system for pork. Chapter 11 presents the main conclusions obtained from the studies presented in this thesis, provides recommendations for future work to gain industry support and involvement commercial implementation and opportunities for further studies to refine the system over time. Overall, additional mechanistic understanding of factors influencing the ageing potential of Australian pork is needed to determine why it was not effective as a main effect across any of the studies conducted as part of this thesis. This is needed to utilise ageing as a reliable intervention to improve pork eating quality consistency; ageing period is a critical control point in the sheepmeat and beef MSA systems. Different processing interventions imposed to improve pork eating quality consistency also varied between supply chains and between cuts. This highlights that the eating quality models that will be developed for the Australian pork industry utilising data generated in this thesis must be non-prescriptive and include multiple factors to enable individual supply chains to use different interventions to deliver high quality pork to their customers. It is envisioned that the adoption of a cost-effective industry system to guarantee eating quality consistency of Australian pork, on a cut type x cooking method basis, will be used to underpin differentiation and integrity claims made by the commercial owners of branded Australian pork products.
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ItemProfitable sheep farming in south west Victoria: future options under volatile prices, costs and climate( 2017)Changes in seasonal and market conditions and the cost-price squeeze have implications for farm business profitability. A case study and whole farm systems modelling approach was used to examine the biophysical and economic performance of two sheep farms located in south west Victoria and possible development options to overcome the impacts of such changes. Under an historical climate, improvements in farm productivity offered attractive profits relative to risk; if purchasing land, productivity needs to be improved to compensate for the higher financial costs. Farming multiple enterprises offered modest profits relative to risk; while farming only prime lamb offered higher profits, but with greater risk. Under a future 2020 and 2050 climate, profits may be higher because of warmer winters enabling higher production, compensating for the higher supplementary feeding in summer and autumn. Under a 2080 climate, greater change will reduce profits and increase risk.
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ItemThe influence of urbanization on stream temperature regimes( 2017)Streams draining urban catchments are relatively warmer than non-urban streams. Catchment urbanization and subsequent stormwater drainage systems are likely a primary cause of this warming of urban streams, however, the extent of these causes and their relative contribution to the degradation of thermal regimes still remain unclear. Addressing this knowledge gap is important to provide guidelines for thermal regime restoration measures. Stream temperature data were collected continuously at a 15 minute time step from temperature loggers deployed across 82 sites around the city of Melbourne (population ~5 million people), in south-eastern Australia, over a 3 year period. After screening for periods with zero flow and removing logger errors, 53 sites with >80% of good quality data over a >30 month period were selected to calculate a set of temperature metrics that indicate the spatial patterns of thermal regimes (mean, mean daily maximum, mean daily minimum, mean diel change, maximum weekly average temperature, mean summer, mean winter, summer maxima and number of days exceeding threshold levels of 24, and 29C per year). To indicate temporal dynamics, the maximum amplitude of temperature surges during storm events was calculated (a surge was defined as >1 C temperature change recorded over 30 minute intervals). All temperature metrics were then linearly regressed with catchment and climatic variables to identify the main drivers of surges in temperature. The thermal regime of the study streams was also examined with reference to the thermal tolerances of native fish occurring in the region. The majority of streams in the study were unlikely to exceed tolerable temperature limits for most Australian native fish species. Spatial variation in temperature (~88%) were most plausibly predicted by models that included attenuated impervious cover (a measure of urban drainage systems), attenuated forest cover (a measure of riparian deforestation), mean annual discharge volume and mean annual air temperature. Stream temperature surges were observed most commonly after rain events and depending on the antecedent weather, the amplitude of surges was either positive or negative. Positive surges (i.e. increases in temperature) were most commonly observed in autumn, with fewer positive surges in summer than in winter. Negative surges (i.e. decreases in temperature) were most common in spring and summer, and least common in winter and autumn. The variations in the amplitude of negative surges (~74%) were explained by the attenuated imperious cover; however, the drivers of spatial variations in positive surges remained unclear. Surges are small and less common and thus, the potential degradation of stream ecosystem cannot be expected from temperature surges. Therefore, temperature surges were appeared not to be an important aspect of urban stormwater impacts on stream ecosystems in Melbourne water region. The temperature models suggest that increasing the extent of drainage systems and riparian deforestation in future climate change would have a potential to limit thermal habitats suitable for temperature-sensitive fish species. Moreover, riparian reforestation was shown not to be able to overcome the influence of drainage systems.