Radiative transfer, interception and scattering in coniferous forests : models and applications for production ecology and remote sensing

This work develops methods to account for shoot structure in models of coniferous canopy radiative transfer. Shoot structure, as it varies along the light gradient inside canopy, affects the efficiency of light interception per unit needle area, foliage biomass, or foliage nitrogen. The clumping of needles in the shoot volume also causes a notable amount of multiple scattering of light within coniferous shoots. The effect of shoot structure on light interception is treated in the context of canopy level photosynthesis and resource use models, and the phenomenon of within-shoot multiple scattering in the context of physical canopy reflectance models for remote sensing purposes. Light interception. A method for estimating the amount of PAR (Photosynthetically Active Radiation) intercepted by a conifer shoot is presented. The method combines modelling of the directional distribution of radiation above canopy, fish-eye photographs taken at shoot locations to measure canopy gap fraction, and geometrical measurements of shoot orientation and structure. Data on light availability, shoot and needle structure and nitrogen content has been collected from canopies of Pacific silver fir (Abies amabilis (Dougl.) Forbes) and Norway spruce (Picea abies (L.) Karst.). Shoot structure acclimated to light gradient inside canopy so that more shaded shoots have better light interception efficiency. Light interception efficiency of shoots varied about two-fold per needle area, about four-fold per needle dry mass, and about five-fold per nitrogen content. Comparison of fertilized and control stands of Norway spruce indicated that light interception efficiency is not greatly affected by fertilization. Light scattering. Structure of coniferous shoots gives rise to multiple scattering of light between the needles of the shoot. Using geometric models of shoots, multiple scattering was studied by photon tracing simulations. Based on simulation results, the dependence of the scattering coefficient of shoot from the scattering coefficient of needles is shown to follow a simple one-parameter model. The single parameter, termed the recollision probability, describes the level of clumping of the needles in the shoot, is wavelength independent, and can be connected to previously used clumping indices. By using the recollision probability to correct for the within-shoot multiple scattering, canopy radiative transfer models which have used leaves as basic elements can use shoots as basic elements, and thus be applied for coniferous forests. Preliminary testing of this approach seems to explain, at least partially, why coniferous forests appear darker than broadleaved forests in satellite data.

Reconfiguring agriculture through the relocation of production systems for water, environment and food security under climate change

The prospect of climate change has revived both fears of food insecurity and its corollary, market opportunities for agricultural production. In Australia, with its long history of state-sponsored agricultural development, there is renewed interest in the agricultural development of tropical and sub-tropical northern regions. Climate projections suggest that there will be less water available to the main irrigation systems of the eastern central and southern regions of Australia, while net rainfall could be sustained or even increase in the northern areas. Hence, there could be more intensive use of northern agricultural areas, with the relocation of some production of economically important commodities such as vegetables, rice and cotton. The problem is that the expansion of cropping in northern Australia has been constrained by agronomic and economic considerations. The present paper examines the economics, at both farm and regional level, of relocating some cotton production from the east-central irrigation areas to the north where there is an existing irrigation scheme together with some industry and individual interest in such relocation. Integrated modelling and expert knowledge are used to examine this example of prospective climate change adaptation. Farm-level simulations show that without adaptation, overall gross margins will decrease under a combination of climate change and reduction in water availability. A dynamic regional Computable General Equilibrium model is used to explore two scenarios of relocating cotton production from south east Queensland, to sugar-dominated areas in northern Queensland. Overall, an increase in real economic output and real income was realized when some cotton production was relocated to sugar cane fallow land/new land. There were, however, large negative effects on regional economies where cotton production displaced sugar cane. It is concluded that even excluding the agronomic uncertainties, which are not examined here, there is unlikely to be significant market-driven relocation of cotton production.

Large-scale expansion of no-take closures within the Great Barrier Reef has not enhanced fishery production

A rare opportunity to test hypotheses about potential fishery benefits of large-scale closures was initiated in July 2004 when an additional 28.4% of the 348 000 km2 Great Barrier Reef (GBR) region of Queensland, Australia was closed to all fishing. Advice to the Australian and Queensland governments that supported this initiative predicted these additional closures would generate minimal (10%) initial reductions in both catch and landed value within the GBR area, with recovery of catches becoming apparent after three years. To test these predictions, commercial fisheries data from the GBR area and from the two adjacent (non-GBR) areas of Queensland were compared for the periods immediately before and after the closures were implemented. The observed means for total annual catch and value within the GBR declined from pre-closure (2000–2003) levels of 12 780 Mg and Australian $160 million, to initial post-closure (2005–2008) levels of 8143 Mg and $102 million; decreases of 35% and 36% respectively. Because the reference areas in the non-GBR had minimal changes in catch and value, the beyond-BACI (before, after, control, impact) analyses estimated initial net reductions within the GBR of 35% for both total catch and value. There was no evidence of recovery in total catch levels or any comparative improvement in catch rates within the GBR nine years after implementation. These results are not consistent with the advice to governments that the closures would have minimal initial impacts and rapidly generate benefits to fisheries in the GBR through increased juvenile recruitment and adult spillovers. Instead, the absence of evidence of recovery in catches to date currently supports an alternative hypothesis that where there is already effective fisheries management, the closing of areas to all fishing will generate reductions in overall catches similar to the percentage of the fished area that is closed.

Pre-emptive breeding to combine superior eating quality in tropical super sweet corn with resistance to major diseases

This report presents the process and outcomes of a five year project, which employed genetics and breeding approach for integrating disease resistance,agronomy and quality traits that enhances sustainable productivity improvement in sweet corn production. The report outlines a molecular markers based approach to introgress quantitative traits loci that are believed to contribute to resistance to downy mildew, a potentially devastating disease that threatens sweet corn and other similar crops. It also details the approach followed to integrate resistances for other major diseases such as southern rust (caused by Puccinia polysora Underw), Northern Corn Leaf Blight (Exserohilum turcicum) with improved agronomy and eating quality. The report explains the importance of heterosis (hybrid vigour) and combining ability in the development of useful sweet corn hybrids. It also explains the relevance of parental performance to predict its breeding value and the performance of its hybrids.

Production attributes of Merino sheep genetically divergent for wool growth are reflected in differing rumen microbiotas

Divergent genetic selection for wool growth as a single trait has led to major changes in sheep physiology and metabolism, including variations in rumen microbial protein production and uptake of α-amino nitrogen in portal blood. This study was conducted to determine if sheep with different genetic merit for wool growth exhibit distinct rumen bacterial diversity. Eighteen Merino wethers were separated into groups of contrasting genetic merit for clean fleece weight (CFW; low: WG− and high: WG+) and fed a blend of oaten and lucerne chaff diet at two levels of intake (LOI; 1 or 1.5 times maintenance energy requirements) for two seven-week periods in a crossover design. Bacterial diversity in rumen fluid collected by esophageal intubation was characterized using 454 amplicon pyrosequencing of the V3/V4 regions of the 16S rRNA gene. Bacterial diversity estimated by Phylogenetic distance, Chao1 and observed species did not differ significantly with CFW or LOI; however, the Shannon diversity index differed (P=0.04) between WG+ (7.67) and WG− sheep (8.02). WG+ animals had a higher (P=0.03) proportion of Bacteroidetes (71.9% vs 66.5%) and a lower (P=0.04) proportion of Firmicutes (26.6% vs 31.6%) than WG− animals. Twenty-four specific operational taxonomic units (OTUs), belonging to the Firmicutes and Bacteroidetes phyla, were shared among all the samples, whereas specific OTUs varied significantly in presence/abundance (P<0.05) between wool genotypes and 50 varied (P<0.05) with LOI. It appears that genetic selection for fleece weight is associated with differences in rumen bacterial diversity that persist across different feeding levels. Moderate correlations between seven continuous traits, such as methane production or microbial protein production, and the presence and abundance of 17 OTUs were found, indicating scope for targeted modification of the microbiome to improve the energetic efficiency of rumen microbial synthesis and reduce the greenhouse gas footprint of ruminants.

Postharvest physiology and volatile production by flowers of Ptilotus nobilis

Ptilotus nobilis (Lindl.) F. Muell. has potential in the floriculture industries as a cut flower crop. Ethylene production and respiration rates, fresh weight changes and volatile scent production from cut inflorescences of P. nobilis cultivars Passion (dark pink flowers) and Purity (white-green flowers) were measured during vase life. Inflorescence weight loss was significant (P < 0.001) during vase life with wilting and colour loss being the primary reasons for loss of vase life. Inflorescences ready for the cut market stored and at 22 °C had vase lives of >12 d. Ethylene production by inflorescences was low to negligible. Treatment with silverthiosulphate (STS) and ethylene had no effects on vase life. Evidently, ethylene did not play a role in determining the postharvest longevity of cut P. nobilis flowers. Respiration rates of inflorescences were high at harvest (>700 mg CO2 kg−1 FW h−1) and declined gradually thereafter during vase life. Total volatile emissions followed a similar pattern. For Passion, respiration rates of immature florets were significantly greater (P = 0.02) than florets from other developmental stages while the calyx produced the most CO2. For Purity, respiration rates of florets of different maturities did not differ and the reproductive tissue produced the most CO2. Only fully opened mature florets with their stigma and anthers revealed, emitted significant quantities of volatiles (P < 0.001) and primarily from the calyx tissue for both cultivars. The individual volatiles differed somewhat for the two cultivars. However, both produced significant quantities of benzaldehyde, 3,5-dimethoxytoluene and benzyl alcohol. These compounds have previously been associated with desirable floral scent.

Postharvest physiology and volatile production by flowers of Ptilotus nobilis

Ptilotus nobilis (Lindl.) F. Muell. has potential in the floriculture industries as a cut flower crop. Ethylene production and respiration rates, fresh weight changes and volatile scent production from cut inflorescences of P. nobilis cultivars Passion (dark pink flowers) and Purity (white-green flowers) were measured during vase life. Inflorescence weight loss was significant (P < 0.001) during vase life with wilting and colour loss being the primary reasons for loss of vase life. Inflorescences ready for the cut market stored and at 22 °C had vase lives of >12 d. Ethylene production by inflorescences was low to negligible. Treatment with silverthiosulphate (STS) and ethylene had no effects on vase life. Evidently, ethylene did not play a role in determining the postharvest longevity of cut P. nobilis flowers. Respiration rates of inflorescences were high at harvest (>700 mg CO2 kg−1 FW h−1) and declined gradually thereafter during vase life. Total volatile emissions followed a similar pattern. For Passion, respiration rates of immature florets were significantly greater (P = 0.02) than florets from other developmental stages while the calyx produced the most CO2. For Purity, respiration rates of florets of different maturities did not differ and the reproductive tissue produced the most CO2. Only fully opened mature florets with their stigma and anthers revealed, emitted significant quantities of volatiles (P < 0.001) and primarily from the calyx tissue for both cultivars. The individual volatiles differed somewhat for the two cultivars. However, both produced significant quantities of benzaldehyde, 3,5-dimethoxytoluene and benzyl alcohol. These compounds have previously been associated with desirable floral scent.

Legumes or nitrification inhibitors to reduce N2O emissions from subtropical cereal cropping systems in Oxisols?

The DAYCENT biogeochemical model was used to investigate how the use of fertilizers coated with nitrification inhibitors and the introduction of legumes in the crop rotation can affect subtropical cereal production and N2O emissions. The model was validated using comprehensive multi-seasonal, high-frequency dataset from two field investigations conducted on an Oxisol, which is the most common soil type in subtropical regions. Different N fertilizer rates were tested for each N management strategy and simulated under varying weather conditions. DAYCENT was able to reliably predict soil N dynamics, seasonal N2O emissions and crop production, although some discrepancies were observed in the treatments with low or no added N inputs and in the simulation of daily N2O fluxes. Simulations highlighted that the high clay content and the relatively low C levels of the Oxisol analyzed in this study limit the chances for significant amounts of N to be lost via deep leaching or denitrification. The application of urea coated with a nitrification inhibitor was the most effective strategy to minimize N2O emissions. This strategy however did not increase yields since the nitrification inhibitor did not substantially decrease overall N losses compared to conventional urea. Simulations indicated that replacing part of crop N requirements with N mineralized by legume residues is the most effective strategy to reduce N2O emissions and support cereal productivity. The results of this study show that legumes have significant potential to enhance the sustainable and profitable intensification of subtropical cereal cropping systems in Oxisols.

Investigation of an emerging bacterial disease in wild Queensland groper, marine fish and stingrays with production of diagnostic tools to reduce the spread of disease to other states of Australia : final report

This project describes how Streptococcus agalactiae can be transmitted experimentally in Queensland grouper. The implications of this research furthers the relatedness between Australian S. agalactiae strains from animals and humans. Additionally, this research has developed diagnostic tools for Australian State Veterinary Laboratories and Universities, which will assist in State and National aquatic animal disease detection, surveillance, disease monitoring and reporting

Benzyl isothiocyanate: maximising production in papaya tissue extracts

Abstract: Although mainly grown for its sweet flavoured fruit, papaya (Carica papaya) has also been used for pharmacological purposes for many years. The reasons for use are varied with one of the best known being its anti-fungal action. Benzyl isothiocyanate (BITC) is the constituent most often implicated in this activity. Isothiocyanates are formed when the enzyme myrosinase catalyses the hydrolysis of the non-bioactive glucosinolates. This occurs when cellular contents come into contact through chewing, cutting or during extraction processes in the laboratory. While this is common in Brassica vegetables, the glucosinolate-myrosinase system is rare in fruit, papaya being a notable exception. It contains benzyl glucosinolate (BG), the glucosinolate precursor of BITC, in significant quantities. Parameters that determine the amount of BITC formed are duration of hydrolysis, presence/absence of nitrile-specifier proteins and BG content of different cultivars and tissues. We experimented with differing BITC extraction solvents, with the intention of developing a low cost, natural anti-fungal extract based on under-utilised papaya tissues. The findings suggest that papaya seeds, particularly from quarter-ripe fruit, have the potential to produce the highest levels of BITC necessary. Furthermore, they compare well with the nitrile-specifier protein-containing garden cress seeds (Lepidium sativum). To utilise the papaya seeds as a BITC source, an organic solvent such as ethanol is required to extract the largely water-insoluble BITC from the hydrolysed papaya seed mixture.

Characterization of maize growing environments in eastern and southern Africa using the APSIM model

Maize grown in eastern and southern Africa experiences random occurrences of drought. This uncertainty creates difficulty in developing superior varieties and their agronomy. Characterisation of drought types and their frequencies could help in better defining selection environments for improving resistance to drought. We used the well tested APSIM maize model to characterise major drought stress patterns and their frequencies across six countries of the region including Ethiopia, Kenya, Tanzania, Malawi, Mozambique and Zimbabwe. The database thus generated covered 35 sites, 17 to 86 years of daily climate records, 3 varieties and 3 planting densities from a total of 11,174 simulations. The analysis identified four major drought environment types including those characterised by low-stress which occurred in 42% of the years, mid-season drought occurring in 15% of the years, late-terminal stress which occurred in 22% of the years and early-terminal drought occurring in 21% of the years. These frequencies varied in relation to sites, genotypes and management. The simulations showed that early terminal stress could result in a yield reduction of 70% compared with low-stress environmental types. The study presents the importance of environmental characterization in contributing to maize improvement in eastern and southern Africa.

Estimating daily methane production in individual cattle with irregular feed intake patterns from short-term methane emission measurements

Spot measurements of methane emission rate (n = 18 700) by 24 Angus steers fed mixed rations from GrowSafe feeders were made over 3- to 6-min periods by a GreenFeed emission monitoring (GEM) unit. The data were analysed to estimate daily methane production (DMP; g/day) and derived methane yield (MY; g/kg dry matter intake (DMI)). A one-compartment dose model of spot emission rate v. time since the preceding meal was compared with the models of Wood (1967) and Dijkstra et al. (1997) and the average of spot measures. Fitted values for DMP were calculated from the area under the curves. Two methods of relating methane and feed intakes were then studied: the classical calculation of MY as DMP/DMI (kg/day); and a novel method of estimating DMP from time and size of preceding meals using either the data for only the two meals preceding a spot measurement, or all meals for 3 days prior. Two approaches were also used to estimate DMP from spot measurements: fitting of splines on a 'per-animal per-day' basis and an alternate approach of modelling DMP after each feed event by least squares (using Solver), summing (for each animal) the contributions from each feed event by best-fitting a one-compartment model. Time since the preceding meal was of limited value in estimating DMP. Even when the meal sizes and time intervals between a spot measurement and all feeding events in the previous 72 h were assessed, only 16.9% of the variance in spot emission rate measured by GEM was explained by this feeding information. While using the preceding meal alone gave a biased (underestimate) of DMP, allowing for a longer feed history removed this bias. A power analysis taking into account the sources of variation in DMP indicated that to obtain an estimate of DMP with a 95% confidence interval within 5% of the observed 64 days mean of spot measures would require 40 animals measured over 45 days (two spot measurements per day) or 30 animals measured over 55 days. These numbers suggest that spot measurements could be made in association with feed efficiency tests made over 70 days. Spot measurements of enteric emissions can be used to define DMP but the number of animals and samples are larger than are needed when day-long measures are made.

Exotic plant pests–a threat to the sustainability of Australia’s grains industry

Exotic plant pests (EPPs) threaten production, market access and sustainability of Australian plant production systems. For the grains industry there are over 600 identified EPPs of which 54 are considered high priority, posing a significant threat. Despite Australia’s geographical isolation and strong quarantine systems, the threat from EPPs has never been higher with the increasing levels of travel and trade, emphasising the need for improving our efforts in prevention, preparedness and surveillance for EPPs.

Semantic Classes in Topic Detection and Tracking

Topic detection and tracking (TDT) is an area of information retrieval research the focus of which revolves around news events. The problems TDT deals with relate to segmenting news text into cohesive stories, detecting something new, previously unreported, tracking the development of a previously reported event, and grouping together news that discuss the same event. The performance of the traditional information retrieval techniques based on full-text similarity has remained inadequate for online production systems. It has been difficult to make the distinction between same and similar events. In this work, we explore ways of representing and comparing news documents in order to detect new events and track their development. First, however, we put forward a conceptual analysis of the notions of topic and event. The purpose is to clarify the terminology and align it with the process of news-making and the tradition of story-telling. Second, we present a framework for document similarity that is based on semantic classes, i.e., groups of words with similar meaning. We adopt people, organizations, and locations as semantic classes in addition to general terms. As each semantic class can be assigned its own similarity measure, document similarity can make use of ontologies, e.g., geographical taxonomies. The documents are compared class-wise, and the outcome is a weighted combination of class-wise similarities. Third, we incorporate temporal information into document similarity. We formalize the natural language temporal expressions occurring in the text, and use them to anchor the rest of the terms onto the time-line. Upon comparing documents for event-based similarity, we look not only at matching terms, but also how near their anchors are on the time-line. Fourth, we experiment with an adaptive variant of the semantic class similarity system. The news reflect changes in the real world, and in order to keep up, the system has to change its behavior based on the contents of the news stream. We put forward two strategies for rebuilding the topic representations and report experiment results. We run experiments with three annotated TDT corpora. The use of semantic classes increased the effectiveness of topic tracking by 10-30\% depending on the experimental setup. The gain in spotting new events remained lower, around 3-4\%. The anchoring the text to a time-line based on the temporal expressions gave a further 10\% increase the effectiveness of topic tracking. The gains in detecting new events, again, remained smaller. The adaptive systems did not improve the tracking results.