School of Agriculture, Food and Ecosystem Sciences - Theses
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ItemImproving species distribution models using extreme value theory and climate dataset ensembles( 2020)The development of climate datasets at fine spatial and temporal scales has commonly been driven by the need to better understand vegetation distributions and ecological systems. While a wide range of global, national and regional climate datasets have been developed over the last two decades, they are rarely compared directly in the ecological literature. This thesis evaluates a range of climate interpolation techniques and investigates how the spatial and temporal characteristics of climate datasets may be utilised to improve the predictive performance of plant species distribution models (SDM). A series of spline-based and geostatistical methods for interpolating temperature variables are first compared across Victoria, southeast Australia. Secondary predictors (thermal remote sensing data and local topographic indices) which indirectly capture mesoscale microclimate and cold air drainage regimes were found to improve monthly mean minimum temperature interpolations by up to 39%. Thermal remote sensing data only reduced root mean square error (RMSE) by up to 6% for maximum temperature across Victoria and was most effective during the summer months. The interpolation methods used in southeast Australia were subsequently transferred to the Royal Himalayan Kingdom of Bhutan to validate their effectiveness in a novel climate. In Bhutan, the predictive performance of minimum temperature interpolations was also improved considerably (up to 23% reduction in RMSE) when using thermal remote sensing data and local topographic indices as spatial covariates. Thermal remote sensing data also reduced the RMSE for maximum temperature interpolations by up to 16% in Bhutan. Interannual variability of climate extremes were used to evaluate how the temporal characteristics of climate may be used to improve the predictive performance of SDMs. Generalised Extreme Value (GEV) distributions were fitted to monthly climate data to generate variables which account for the skewed distribution of extremes. Models incorporating interannual variability (drawn from a range of expected return intervals) improved predictive performance compared to models using seasonal extremes only for 28 of 37 species assessed. Iteratively fitting models using alternate expected return intervals typically acted on the leading and trailing edges of current distributions, indicating that such methods may be useful for model calibration and characterising climate-driven source-sink population dynamics. The impact of spatial disparities in climate on the predictive performance of plant SDMs was evaluated using three distinct datasets developed for Victoria as part of this research, in addition to two global datasets (WorldClim v1 and v2). Individual models were compared against one another and as ensembles to explore the potential for alternate predictions to complement one another. The Victorian datasets demonstrated a significant improvement over the original WorldClim dataset (up to 17.3% mean increase in D2) and trended towards an improvement relative to WorldClim v2; however, no significant differences were found when comparing the alternate Victorian datasets. Multi-model ensembles achieved a mean increase of up to 13.8% and 29.2% in D2 relative to individual models when using regional and global datasets, respectively. Ensembles provide a pragmatic method to improve the predictive performance of SDMs and allow a trade-off between the uncertainties and potential biases embedded in competing climate datasets.
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ItemMaking the connection between history, agricultural diversity and place: the story of Victorian apples( 2016)Apple growing practices are embedded in a productivist mentality aiming for ever higher efficiency and productivity. And while the climate change impacts are to a large extent known, there is little attention given to the coupling of the social and the ecological effects. I use apple growing as a case study to explore the relationship between place, biodiversity and rural change in Victoria. My research is based on historical research; including an analysis of the Museum Victoria’s collection of wax apple models, and in-depth interviews with orchardists. By drawing on environmental history, social-ecological systems thinking and Bourdieu's theory of practice, I highlight the importance of a systems perspective and inform it by emphasis on the critical role of underlying power structures and individual dispositions, or the habitus, of the growers. These dispositions have been shaped and internalised by the growers’ histories and their physical surroundings. Orchardists have been able to respond to intensifying production requirements by utilizing technologies and scientific nous to keep up with the continuous aim for efficiency. Growers are caught up in a self-reinforcing cycle of satisfying the demand for perfect apples by adopting expensive techno-scientific approaches to enable ever more intensive production. The symbolic violence and amplified biophysical pressure orchardists experience has driven many to despair; resulting in a significant decline in small scale apple growing businesses over the last decade. I offer some suggestions for government policy and support measures and argue that any services or support programs need to be tailored to the appropriate level and need of each orchard business and the individuals who are involved. My analysis shows that those growers, who engage more closely with their biophysical place as well as their history and identity as apple growers in that place are (re-)creating another version of what it means to be an apple grower. In some cases this is resulting in resistance to the vortex of agricultural productivism that has been the basis of their existence for many generations.
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ItemEffects of adding nutrients on soil chemistry and tree growth in native Eucalyptus forests of south-eastern Australia( 2007)The decreasing area available for timber extraction in south-eastern Australia, due largely to social pressure to reserve greater areas of forest, has led to the consideration of fertiliser-application to increase wood output from the remaining available forest. Potentially deleterious effects of fertilising on water quality must be assessed before implementation on a wide scale. This is in accordance with relevant forest management policies. This study examined the effects of applying fertilisers containing nitrogen and phosphorus, on soil and soil-water chemistry in two pole-sized stands of mixed Eucalyptus spp in the Wombat Forest, in the Midlands Forest Management Area, Victoria, Australia. The findings are synthesised and discussed in relation to management of regenerating mixed-eucalypt forests in south-eastern Australia. Fertiliser treatments were none (R); 400 kg N ha-1 as ammonium-sulphate (N); or 400 kg ha-1 plus 202 kg P ha-1 as triple superphosphate coated with 10% sulphur (NP). It was calculated that incidental additions of S were 1371 kg ha -1 (N treatments), and 1696 kg ha-1 (NP treatments). It was expected that P would be principally adsorbed on soil surfaces; N immobilised in the soil organic pool and that metallic cations would enter the soil solution to varying degrees. Fertiliser-addition increased both plot-basal-area (BA) growth and the rate of stand self-thinning. In 3.8 years, BA in reference (R) plots at two sites increased by 7.3% and 23.4%. Where N alone was added, BA increased by 14.2% and 27.1%, while in NP plots BA increased by 17.1% and 42.7% respectively. Mortality was 9% in untreated plots compared to 14% in NP plots. Estimated increases in biomass growth equated to additional above-ground nutrient accumulation of 0.4 to 1.5 kg ha-1 of P, and 5.5 to 20.8 kg ha-1 of N. This represented only 0.2 to 0.7% of added P, and 1.4 to 5.2% of added N. Soil solution was extracted from 10 and 50 cm with porous-ceramic-cup tension-lysimeters (-0.6 kPa). Concentrations of P and N were low both before and after adding fertiliser. Across all treatments the maximum median PO43- concentration in soil-water at 50 cm was 0.12 ppm (mean 0.28 ppm). Typically PO43- concentrations were not higher than 0.03 ppm. The 400 kg ha-1 of added N was rapidly immobilised in the soil organic pool. The greatest mean NH4' concentration from a single sampling occasion was 1.1 ppm. The mean NO3 concentration at 50 cm was never higher than 0.26 ppm. After adding N in fertiliser the proportion of NO3- relative to NH4* in soil-water increased and was correlated with decreasing soil-water pH. Less than 1% of added P and N was recovered from soil solution at 50 cm. The largest pool of added P recovered was PO43- adsorbed to soil between 0 and 20 cm, due to the soil adsorption capacity being well in excess of the applied 202 kg P ha-1. Phosphate desorption using sequential extractions with a mild acid extractant (0.3M NH4F, 0.1M HCI) recovered between 25% and 116% of added P. Differences were attributed to both the amount of P added and the effect of time since treatment at different sites. Soil disturbance during sampler installation was found to be more likely to raise soil-water P concentrations at 50 cm than would adding up to 202 kg P ha-1. Among the ions in solution. SO42- and CI' were the dominant anions while Cat+ dominated the cation chemistry. In untreated forest 5042- in soil-water ranged from 7.7 to 16.0 ppm at 10 cm and 7.9 to 12.2 ppm at 50 cm. In fertilised plots up to 100.5 ppm SO42 was measured in soil-water at 50 cm depth. In the N treatment at 50 cm, SO42- in soil-water accounted for 9.4 % of applied S. compared to 14.0 % in NP. In untreated forest, soil-water Cl- and SO42- accounted for over 98% of the total soil-water anions, in roughly equal proportions at 10 cm, and CI- slightly higher at 50 cm. Following fertiliser-application soil-water pH at 10 cm fell from 6.3 in R to as low as 4.81 (N) and 4.45 (NP). At 50 cm pH never dropped below 6 and there were no visible departures from reference concentrations. Relative activities of K+ and Mg2+ in solution increased with decreasing pH, indicating increased leaching potential. Sulphate in soil-water increased total anion charge further in NP than in N. Total charge (cmolc L-1) for cations followed anions. A slight deficit in anion charge was likely due to the unquantified contribution of organic anions. These results confirm that despite the quantity of fertilisers added in this trial being double likely operational quantities, the forest and associated soils had the capacity to retain these nutrients through a variety of processes. The study validates the environmental sustainability of proposed intensive management practices including fertiliser-application in this forest type. It also emphasises the importance of understanding fundamental forest nutrient cycling processes when aiming to carry out intensive forest management practices in an environmentally sensitive manner.
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ItemEffects of organic applicants in a southern Victorian vineyard( 2007)Mulch is a material applied to the surface of the soil to reduce weed growth and reduce soil moisture loss through evaporation from the soil surface. The use of organic mulches will alter the soil environment. This alteration may include reducing soil temperature fluctuations, increasing soil organic matter, increasing soil microflora populations modifying soil chemical properties and increasing soil moisture retention. An experiment was conducted to compare composted green waste mulch and barley straw mulch with herbicide as alternative means of maintaining the undervine strip in a cool climate vineyard. Plant and soil responses to the different undervine treatments were monitored. Grapevine budburst was retarded, however, by the fourth week of vine growth there were no observable differences in grapevine growth stage. Both mulches stimulated grapevine growth and increased yield, with the compost mulch increasing vegetative growth with respect to fruit yield. The fruit quality parameters juice pH and titratable acidity were not significantly altered by the different undervine treatments. In the second year of the experiment the juice soluble solids were lower on the straw mulched grapevines. The compost mulch increased soil pH and carbon levels. The straw mulch improved soil water retention and the mass of soil fungal hyphae. Both mulches increased soil cation exchange capacity. The straw mulch increased soil exchangeable Mg to a greater extent than was predicted from straw nutrient content. The significant variations seen in soil cation content under the mulch treatments were not observed in the tissue analysis. Mulch can be used in a cool climate vineyard to increased yield without deleterious side effects.
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ItemIdentification of boron tolerance in Brassica rapa( 2006)There has been increasing interest in developing canola quality B. juncea for low rainfall areas across Australia over the past two decades. However, B. juncea genotypes are susceptible to high levels of boron in Western Victorian soils. An understanding of the genetics and the molecular basis of boron tolerance may enable fast and accurate tolerance selection and lead to improved boron tolerance. Being an allotetraploid species, B. juncea is difficult to understand at the genetic level because of chromosomal duplication and the potential presence of multiple copies of the loci of interest. Therefore, once the tolerance genes or chromosomal loci governing tolerance are identified in the diploid progenitor genomes, B. rapa and B. nigra, boron tolerant B. juncea lines may be resynthesized. Thus, as an initial step in this process, this thesis aimed to understand the physiological, genomic and molecular mechanisms involved in boron tolerance in B. rapa. Initially, B. rapa genotypes were screened for tolerance to boron toxicity using hydroponic and soil assays. On the basis of primary root length, severity of leaf toxicity symptoms, dry matter accumulation and shoot boron uptake, the B. rapa genotypes WWY Sarson and Local were identified as the most tolerant and the B. rapa genotypes Shillong and Kaga the most susceptible to toxic boron concentrations (1000 ?M B in hydroponic assay; 54 mg B kg-1 soil in soil assay). The main mechanism of tolerance to boron toxicity in B. rapa involved reduced net boron uptake by roots, with some boron accumulation in the tap roots and partial exclusion of boron from shoots. Furthermore, boron uptake was much lower in the WWY Sarson and Local genotypes than in the Shillong genotype, despite higher rates of transpiration. This implied that an active boron efflux mechanism may be operating in the tolerant genotypes. The inheritance pattern of tolerance to boron toxicity in B. rapa genotype, WWY Sarson best fitted a Mendelian model of two major dominant and epistatic genes. A B. rapa linkage map was constructed from an intraspecific F2 population (WWY Sarson X Shillong) with ISSR, RAPD, SRAP and SSR marker loci. The linkage map spanned a total length of 874.1 cM and contained 12 linkage groups. Chisquare analysis (P < 0.05) revealed 25 dominant markers that showed segregation distortion in the F2 progeny. QTL analysis using composite interval analysis identified three significant peaks on LG2 and LG8 that were associated with primary root length and which accounted for 17% of the trait variation. Differential transcript analysis of SRAP markers following exposure to a toxic boron concentration identified up-regulation of me4+em2570bp, me2+em2650bp, me2+em1 1600bp, me2+em1800bp and me4+em2500bp genes in Shillong and Kaga and down-regulation of me2+em2650bp, me2+em1 1600bp, me2+em1800bp and me1+em21200bp genes in WWY Sarson and Local. Of these, a UDP-glycosyltransferase gene (sharing 80% similarity to the Arabidopsis thaliana homolog) was highly transcribed only in the sensitive genotype, Shillong, and may be involved in excessive boron cross-linking to the glycosyl groups present in the cell walls and/or membranes eventually causing the observed reductions in shoot and root growth.
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ItemGrazing ecology and high producing dairy cows( 2005)This body of work (82 papers in scientific journals and 2 books) encompasses two broad areas of work. They are 1) growth, nutritive value and management of pastures grazed by dairy cows (40 publications), and 2) supplements for grazing dairy cows, with a particular focus on responses associated with supplement use and digestion in the rumen (44 publications). These two areas of research are inextricably linked and, taken together, have been termed `Grazing Ecology'. Of the 84 publications included, the candidate was the senior or sole author of 67% of them. The chronological development of the work reported includes research on stocking rates reported in the early 1980's through to the development of Diet Check, a decision support tool incorporating much of the information generated during the previous two decades, in the early 2000's. The publications cover aspects of grazing management to optimise growth, persistence and nutritive value of irrigated annual and perennial pastures for dairy cows. Most of this research has incorporated some aspect of stocking rate, whether it be stocking rate per se in long term experiments or frequency and/or intensity of defoliation in shorter term experiments. The aim was to establish optimum grazing strategies that best effected the compromise of maximum intake of pasture of high nutritive value while satisfying the requirements for maintenance of pasture growth and persistence of a balance of desirable pasture species. The research allowed the definition of the intake and nutritive characteristics of pasture grazed by lactating dairy cows under a range of management conditions. At the same time, strategies to effectively feed supplements were investigated. When more than one feed is offered to dairy cows, associative effects play an important role in the eventual responses achieved. Balance of nutrients, particularly in the rumen, and substitution of supplement for pasture in the diet of grazing dairy cows, were the main aspects of the associative effect between feeds considered in the research reported here. Substitution can have a huge effect on the responses obtained from supplements, and the type of supplement, by influencing the balance of nutrients ingested into the rumen, affects the composition of the milk produced. Finally, some attempt has been made to draw much of the information on pasture management and supplementation of grazing dairy cows together for use by dairy farmers and their advisers, and to define gaps in knowledge. This has been done by reviewing the scientific literature, and by the use of modelling to provide simple tools for tactical decision making. Although the research was undertaken in northern Victoria, many of the results apply equally in other areas of the world where pasture constitutes a major proportion of the diet of dairy cows. Victoria currently produces more than 60% of Australia's milk, with northern Victoria producing more than 40% of that. The development of dairying in Victoria mirrors much of the progress of the research reported in this collection of scientific publications. Before 1982, dairy farming was almost totally based on grazed pastures and the use of pasture supplements (hay and silage). A severe drought occurred in 1982, which prompted a serious consideration of the use of supplements for lactating cows grazing pasture. Today, dairy systems in Victoria vary to a huge extent, with the energy provided by pasture ranging from 0 to 100%. Over this period, average milk production has increased, from about 3000L/cow per lactation to more than 5000L/cow. With a fine line separating profit and loss in dairy businesses that basically depend on the price received for manufactured products on overseas markets, both grazed pasture and supplements need to be used optimally. The challenge has been to provide information and tools to allow dairy farmers to achieve this objective. I believe that my research, particularly in relation to pasture intake, substitution and associative effects, has been instrumental in allowing pasture-based dairy farmers to continue to remain viable in Australia, and that many of the principles developed apply wherever pasture constitutes a significant proportion of a cow's diet.
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