Mapping species differences for adventitious rooting in a Corymbia torelliana x Corymbia citriodora subspecies variegata hybrid

Quantitative trait loci (QTL) detection was carried out for adventitious rooting and associated propagation traits in a second-generation outbred Corymbia torelliana x Corymbia citriodora subspecies variegata hybrid family (n=186). The parental species of this cross are divergent in their capacity to develop roots adventitiously on stem cuttings and their propensity to form lignotubers. For the ten traits studied, there was one or two QTL detected, with some QTL explaining large amounts of phenotypic variation (e.g. 66% for one QTL for percentage rooting), suggesting that major effects influence rooting in this cross. Collocation of QTL for many strongly genetically correlated rooting traits to a single region on linkage group 12 suggested pleiotropy. A three locus model was most parsimonious for linkage group 12, however, as differences in QTL position and lower genetic correlations suggested separate loci for each of the traits of shoot production and root initiation. Species differences were thought to be the major source of phenotypic variation for some rooting rate and root quality traits because of the major QTL effects and up to 59-fold larger homospecific deviations (attributed to species differences) relative to heterospecific deviations (attributed to standing variation within species) evident at some QTL for these traits. A large homospecific/heterospecific ratio at major QTL suggested that the gene action evident in one cross may be indicative of gene action more broadly in hybrids between these species for some traits.

Methanotrophs from natural ecosystems for ruminant methane mitigation

Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane production. Methane produced in this manner is released to the atmosphere where it is highly efficient at absorbing thermal radiation, which consequently increases the global surface temperature. Although many different strategies to control ruminant methane emissions have been considered, few are currently considered viable. Obligate and acultative methane oxidising bacteria (MOB) and anaerobic methane oxidising archaea (ANME) play a fundamental role in the carbon cycle by metabolising methane before it is released into the atmosphere. Because of this, methanotrophic microorganisms represent a novel biological control agent in mitigating ruminant methane emissions. This project aims to characterise methanotrophic microorganisms from a range of environments, and to subsequently determine the metabolic activity of these microorganisms under in vitro rumen-like conditions.

Baseline and greenhouse-gas emissions in extensive livestock enterprises, with a case study of feeding lipid to beef cattle

For accurate calculation of reductions in greenhouse-gas (GHG) emissions, methodologies under the Australian Government's Carbon Farming Initiative (CFI) depend on a valid assessment of the baseline and project emissions. Life-cycle assessments (LCAs) clearly show that enteric methane emitted from the rumen of cattle and sheep is the major source of GHG emissions from livestock enterprises. Where a historic baseline for a CFI methodology for livestock is required, the use of simulated data for cow-calf enterprises at six sites in southern Australia demonstrated that a 5-year rolling emission average will provide an acceptable trade off in terms of accuracy and stability, but this is a much shorter time period than typically used for LCA. For many CFI livestock methodologies, comparative or pair-wise baselines are potentially more appropriate than historic baselines. A case study of lipid supplementation of beef cows over winter is presented. The case study of a control herd of 250 cows used a comparative baseline derived from simple data on livestock numbers and class of livestock to quantify the emission abatement. Compared with the control herd, lipid supplementation to cows over winter increased livestock productivity, total livestock production and enterprise GHG emissions from 990 t CO2-e to 1022 t CO2-e. Energy embodied in the supplement and extra diesel used in transporting the supplement diminished the enteric-methane abatement benefit of lipid supplementation. Reducing the cow herd to 238 cows maintained the level of livestock production of the control herd and reduced enterprise emissions to 938 t CO2-e, but was not cost effective under the assumptions of this case study.

Mapping the carriage of flaA-restriction fragment length polymorphism Campylobacter genotypes on poultry carcasses through the processing chain and comparison to clinical isolates

Poultry are considered a major source for campylobacteriosis in humans. A total of 1866 Campylobacter spp. isolates collected through the poultry processing chain were typed using flaA-restriction fragment length polymorphism to measure the impact of processing on the genotypes present. Temporally related human clinical isolates (n = 497) were also typed. Isolates were obtained from whole chicken carcass rinses of chickens collected before scalding, after scalding, before immersion chilling, after immersion chilling and after packaging as well as from individual caecal samples. A total of 32 genotypes comprising at least four isolates each were recognised. Simpson's Index of Diversity (D) was calculated for each sampling site within each flock, for each flock as a whole and for the clinical isolates. From caecal collection to after packaging samples the D value did not change in two flocks, decreased in one flock and increased in the fourth flock. Dominant genotypes occurred in each flock but their constitutive percentages changed through processing. There were 23 overlapping genotypes between clinical and chicken isolates. The diversity of Campylobacter is flock dependant and may alter through processing. This study confirms that poultry are a source of campylobacteriosis in the Australian population although other sources may contribute.

Soybean rotation and crop residue management to reduce nitrous oxide emissions from sugarcane soils

NITROUS OXIDE (N2O) IS a potent greenhouse gas and the predominant ozone-depleting substance in the atmosphere. Agricultural nitrogenous fertiliser use is the major source of human-induced N2O emissions. A field experiment was conducted at Bundaberg from October 2012 to September 2014 to examine the impacts of legume crop (soybean) rotation as an alternative nitrogen (N) source on N2O emissions during the fallow period and to investigate low-emission soybean residue management practices. An automatic monitoring system and manual gas sampling chambers were used to measure greenhouse gas emissions from soil. Soybean cropping during the fallow period reduced N2O emissions compared to the bare fallow. Based on the N content in the soybean crop residues, the fertiliser N application rate was reduced by about 120 kg N/ha for the subsequent sugarcane crop. Consequently, emissions of N2O during the sugarcane cropping season were significantly lower from the soybean cropped soil than those from the conventionally fertilised (145 kg N/ha) soil following bare fallow. However, tillage that incorporated the soybean crop residues into soil promoted N2O emissions in the first two months. Spraying a nitrification inhibitor (DMPP) onto the soybean crop residues before tillage effectively prevented the N2O emission spikes. Compared to conventional tillage, practising no-till with or without growing a nitrogen catch crop during the time after soybean harvest and before cane planting also reduced N2O emissions substantially. These results demonstrated that soybean rotation during the fallow period followed with N conservation management practices could offer a promising N2O mitigation strategy in sugarcane farming. Further investigation is required to provide guidance on N and water management following soybean fallow to maintain sugar productivity.

Natural Hendra Virus Infection in Flying-Foxes - Tissue Tropism and Risk Factors

Hendra virus (HeV) is a lethal zoonotic agent that emerged in 1994 in Australia. Pteropid bats (flying-foxes) are the natural reservoir. To date, HeV has spilled over from flying-foxes to horses on 51 known occasions, and from infected horses to close-contact humans on seven occasions. We undertook screening of archived bat tissues for HeV by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Tissues were tested from 310 bats including 295 Pteropodiformes and 15 Vespertilioniformes. HeV was detected in 20 individual flying-foxes (6.4%) from various tissues including spleen, kidney, liver, lung, placenta and blood components. Detection was significantly higher in Pteropus Alecto and Pconspicillatus, identifying species as a risk factor for infection. Further, our findings indicate that HeV has a predilection for the spleen, suggesting this organ plays an important role in HeV infection. The lack of detections in the foetal tissues of HeV-positive females suggests that vertical transmission is not a regular mode of transmission in naturally infected flying-foxes, and that placental and foetal tissues are not a major source of infection for horses. A better understanding of HeV tissue tropism will strengthen management of the risk of spillover from flying-foxes to horses and ultimately humans.

A new data source for fisheries resource assessment: genetic estimates of the effective number of spawners. Final Report to the Fisheries Research and Development Corporation.

The development of innovative methods of stock assessment is a priority for State and Commonwealth fisheries agencies. It is driven by the need to facilitate sustainable exploitation of naturally occurring fisheries resources for the current and future economic, social and environmental well being of Australia. This project was initiated in this context and took advantage of considerable recent achievements in genomics that are shaping our comprehension of the DNA of humans and animals. The basic idea behind this project was that genetic estimates of effective population size, which can be made from empirical measurements of genetic drift, were equivalent to estimates of the successful number of spawners that is an important parameter in process of fisheries stock assessment. The broad objectives of this study were to 1. Critically evaluate a variety of mathematical methods of calculating effective spawner numbers (Ne) by a. conducting comprehensive computer simulations, and by b. analysis of empirical data collected from the Moreton Bay population of tiger prawns (P. esculentus). 2. Lay the groundwork for the application of the technology in the northern prawn fishery (NPF). 3. Produce software for the calculation of Ne, and to make it widely available. The project pulled together a range of mathematical models for estimating current effective population size from diverse sources. Some of them had been recently implemented with the latest statistical methods (eg. Bayesian framework Berthier, Beaumont et al. 2002), while others had lower profiles (eg. Pudovkin, Zaykin et al. 1996; Rousset and Raymond 1995). Computer code and later software with a user-friendly interface (NeEstimator) was produced to implement the methods. This was used as a basis for simulation experiments to evaluate the performance of the methods with an individual-based model of a prawn population. Following the guidelines suggested by computer simulations, the tiger prawn population in Moreton Bay (south-east Queensland) was sampled for genetic analysis with eight microsatellite loci in three successive spring spawning seasons in 2001, 2002 and 2003. As predicted by the simulations, the estimates had non-infinite upper confidence limits, which is a major achievement for the application of the method to a naturally-occurring, short generation, highly fecund invertebrate species. The genetic estimate of the number of successful spawners was around 1000 individuals in two consecutive years. This contrasts with about 500,000 prawns participating in spawning. It is not possible to distinguish successful from non-successful spawners so we suggest a high level of protection for the entire spawning population. We interpret the difference in numbers between successful and non-successful spawners as a large variation in the number of offspring per family that survive – a large number of families have no surviving offspring, while a few have a large number. We explored various ways in which Ne can be useful in fisheries management. It can be a surrogate for spawning population size, assuming the ratio between Ne and spawning population size has been previously calculated for that species. Alternatively, it can be a surrogate for recruitment, again assuming that the ratio between Ne and recruitment has been previously determined. The number of species that can be analysed in this way, however, is likely to be small because of species-specific life history requirements that need to be satisfied for accuracy. The most universal approach would be to integrate Ne with spawning stock-recruitment models, so that these models are more accurate when applied to fisheries populations. A pathway to achieve this was established in this project, which we predict will significantly improve fisheries sustainability in the future. Regardless of the success of integrating Ne into spawning stock-recruitment models, Ne could be used as a fisheries monitoring tool. Declines in spawning stock size or increases in natural or harvest mortality would be reflected by a decline in Ne. This would be good for data-poor fisheries and provides fishery independent information, however, we suggest a species-by-species approach. Some species may be too numerous or experiencing too much migration for the method to work. During the project two important theoretical studies of the simultaneous estimation of effective population size and migration were published (Vitalis and Couvet 2001b; Wang and Whitlock 2003). These methods, combined with collection of preliminary genetic data from the tiger prawn population in southern Gulf of Carpentaria population and a computer simulation study that evaluated the effect of differing reproductive strategies on genetic estimates, suggest that this technology could make an important contribution to the stock assessment process in the northern prawn fishery (NPF). Advances in the genomics world are rapid and already a cheaper, more reliable substitute for microsatellite loci in this technology is available. Digital data from single nucleotide polymorphisms (SNPs) are likely to super cede ‘analogue’ microsatellite data, making it cheaper and easier to apply the method to species with large population sizes.

Biological control of bellyache bush (Jatropha gossypiifolia) in Australia: South America as a possible source of natural enemies

Bellyache bush (Jatropha gossypiifolia, Euphorbiaceae), a deciduous shrub introduced as an ornamental from tropical America, is a major and expanding weed of rangelands and riparian zones in northern Australia. Biological control is the most economically viable and long-term management solution for this weed. Surveys for potential biological control agents for J gossypiifolia in Mexico,Central America and the Caribbean resulted in release of the seed-feeding jewel bug Agonosoma trilineatum (Hemiptera: Scutelleridae), which failed to establish, and prioritisation of a leaf-rust Phakopsora arthuriana (Puccineales: Phakopsoraceae) for host-specificity testing, which is ongoing. With poor prospects for new agents from Mexico and Central America and the Caribbean, the search for candidate agents on J gossypiifolia shifted to localities south of the equator. Surveys were conducted on the purple-leaf form of J gossypiifolia, Jatropha excisa, Jatropha clavuligera and Jatropha curcas in Peru, Bolivia and Paraguay in 2012 and 2013. A total of 11 insect species, one mite species and the leaf-rust (P. arthuriana) were observed. These include a yet to be described leafmining moth (Stomphastis sp.) (Lepidoptera: Gracillaridae), a shoot and leaf-galling midge Prodiplosis longifila, and leaf-feeding midge Prodiplosis sp. near longifila (both Diptera:Cecidomyiidae) and an unidentified leaf-feeding moth larva (Lepidoptera: Notodontidae). The leafminer is widespread and damaging and has a field host range restricted to the genus Jatropha in Peru and Bolivia, holds the greatest promise as a biological control agent in Australia. Phakopsora arthuriana was recorded for the first time ever from Bolivia and Peru. Further exploration will be conducted in Peru and Bolivia during the wet season to confirm the field host range of collected agents,and to look for more new agents. Promising agents with field host-range restricted to Jatropha spp. will be imported into a quarantine facility in Australia for host-specificity testing.