The intrinsic plasticity of farm businesses and their resilience to change. An Australian example.

This paper examines the idea that plasticity in farm management introduces resilience to change and allows farm businesses to perform when operating in highly variable environments. We also argue for the need to develop and apply more integrative assessments of farm performance that combine the use of modelling tools with deliberative processes involving farmers and researchers in a co-learning process, to more effectively identify and implement more productive and resilient farm businesses. In a plastic farming system, farm management is highly contingent on environmental conditions. In plastic farming systems farm managers constantly vary crops and inputs based on the availability of limited and variable resources (e.g. land, water, finances, labour, machinery, etc.), and signals from its operating environment (e.g. climate, markets), with the objective of maximising a number of, often competing, objectives (e.g. maximise profits, minimise risks, etc.). In contrast in more rigid farming systems farm management is more calendar driven and relatively fixed sequences of crops are regularly followed over time and across the farm. Here we describe the application of a whole farm simulation model to (i) compare, in silico, the sensitivity of two farming systems designs of contrasting levels of plasticity, operating in two contrasting environments, when exposed to a stressor in the form of climate change scenarios;(ii) investigate the presence of interactions and feedbacks at the field and farm levels capable of modifying the intensity and direction of the responses to climate signals; and (iii) discuss the need for the development and application of more integrative assessments in the analysis of impacts and adaptation options to climate change. In both environments, the more plastic farm management strategy had higher median profits and was less risky for the baseline and less intensive climate change scenarios (2030). However, for the more severe climate change scenarios (2070), the benefit of plastic strategies tended to disappear. These results suggest that, to a point, farming systems having higher levels of plasticity would enable farmers to more effectively respond to climate shifts, thus ensuring the economic viability of the farm business. Though, as the intensity of the stress increases (e.g. 2070 climate change scenario) more significant changes in the farming system might be required to adapt. We also found that in the case studies analysed here, most of the impacts from the climate change scenarios on farm profit and economic risk originated from important reductions in cropping intensity and changes in crop mix rather than from changes in the yields of individual crops. Changes in cropping intensity and crop mix were explained by the combination of reductions in the number of sowing opportunities around critical times in the cropping calendar, and to operational constraints at the whole farm level i.e. limited work capacity in an environment having fewer and more concentrated sowing opportunities. This indicates that indirect impacts from shifts in climate on farm operations can be more important than direct impacts from climate on the yield of individual crops. The results suggest that due to the complexity of farm businesses, impact assessments and opportunities for adaptation to climate change might also need to be pursued at higher integration levels than the crop or the field. We conclude that plasticity can be a desirable characteristic in farming systems operating in highly variable environments, and that integrated whole farm systems analyses of impacts and adaptation to climate change are required to identify important interactions between farm management decision rules, availability of resources, and farmer's preference.

A morphological and genetic description of pentastomid infective nymphs belonging to the family Sebekidae Sambon, 1922 in fish in Australian waters

Infective nymphal stages of the family Sebekidae Sambon, 1922 are reported from four species of fish in Australian waters for the first time. Infected fish were collected from locations in Western Australia, the Northern Territory and north Queensland. The infective nymphs of Alofia merki Giglioli in Sambon, 1922 and Sebekia purdieae Riley, Spratt et Winch, 1990 are reported and described for the first time. The remaining specimens were identified as belonging to the genus Sebekia Sambon, 1922 based on the combination of buccal cadre shape, shape and size of hooks, and overall body size, but could not be attributed to any of the other species of Sebekia already reported due to missing required morphological features. DNA sequences of members of the family Sebekidae are presented for the first time. The lack of knowledge on the pentastome fauna of wild crocodiles, and any potential intermediate hosts, in northern Australia, is also outlined.

Potential Human Exposure to Australian Bat Lyssavirus, Queensland, 1996-1999

Two human deaths caused by Australian bat lyssavirus (ABL) infection have been reported since 1996. Information was obtained from 205 persons (mostly adults from south Brisbane and the South Coast of Queensland), who reported potential ABL exposure to the Brisbane Southside Public Health Unit from November 1,1996, to January 31, 1999. Volunteer animal handlers accounted for 39% of potential exposures, their family members for 12%, professional animal handlers for 14%, community members who intentionally handled bats for 31%, and community members with contacts initiated by bats for 4%. The prevalence of Lyssavirus detected by fluorescent antibody test in 366 sick, injured, or orphaned bats from the area was 6%. Sequelae of exposure, including the requirement for expensive postexposure prophylaxis, may be reduced by educating bat handlers and the public of the risks involved in handling Australian bats.

The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus)

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.

Evidence of a latitudinal gradient in spider diversity in Australian cotton

The most common explanation for species diversity increasing towards the tropics is the corresponding increase in habitats (spatial heterogeneity). Consequently, a monoculture (like cotton in Australia) which is grown along a latitudinal gradient, should have the same degree of species diversity throughout its range. We tested to see if diversity in a dominant cotton community (spiders) changed with latitude, and if the community was structurally identical in different parts of Australia. We sampled seven sites extending over 20 degrees of latitude. At each site we sampled 1-3 fields 3-5 times during the cotton growing season using pitfall traps and beatsheets, recording all the spiders collected to family. We found that spider communities in cotton are diverse, including a large range of foraging guilds, making them suitable for a conservation biological control programme. We also found that spider diversity increased from high to low latitudes, and the communities were different, even though the spiders were in the same monocultural habitat. Spider beatsheet communities around Australia were dominated by different families, and responded differently to seasonal changes, indicating that different pest groups would be targeted at different locations. These results show that diversity can increase from high to low latitudes, even if spatial heterogeneity is held constant, and that other factors external to the cotton crop are influencing spider species composition. Other models which may account for the latitudinal gradient, such as non-equilibrium regional processes, are discussed.

Sulfur-associated polioencephalomalacia in cattle grazing plants in the Family Brassicaceae

Polioencephalomalacia was diagnosed histologically in cattle from two herds on the Darling Downs, Queensland, during July-August 2007. In the first incident, 8 of 20 18-month-old Aberdeen Angus steers died while grazing pastures comprising 60% Sisymbrium irio (London rocket) and 40% Capsella bursapastoris (shepherd's purse). In the second incident, 2 of 150 mixed-breed adult cattle died, and another was successfully treated with thiamine, while grazing a pasture comprising almost 100% Raphanus raphanistrum (wild radish). Affected cattle were either found dead or comatose or were seen apparently blind and head-pressing in some cases. For both incidents, plant and water assays were used to calculate the total dietary sulfur content in dry matter as 0.62% and 1.01% respectively, both exceeding the recommended 0.5% for cattle eating more than 40% forage. Blood and tissue assays for lead were negative in both cases. No access to thiaminase, concentrated sodium ion or extrinsic hydrogen sulfide sources were identified in either incident. Below-median late summer and autumn rainfall followed by above-median unseasonal winter rainfall promoted weed growth at the expense of wholesome pasture species before these incidents.

Choosing a fishery's governance structure using data poor methods

Multi-species fisheries are complex to manage and the ability to develop an appropriate governance structure is often seriously impeded because trading between sustainability objectives at the species level, economic objectives at the fleet level, and social objectives at the community scale, is complex. Many of these fisheries also tend to have a mix of information, with stock assessments available for some species and almost no information on other species. The fleets themselves comprise fishers from small family enterprises to large vertically integrated businesses. The Queensland trawl fishery in Australia is used as a case study for this kind of fishery. It has the added complexity that a large part of the fishery is within a World Heritage Area, the Great Barrier Reef Marine Park, which is managed by an agency of the Australian Commonwealth Government whereas the fishery itself is managed by the Queensland State Government. A stakeholder elicitation process was used to develop social, governance, economic and ecological objectives, and then weight the relative importance of these. An expert group was used to develop different governance strawmen (or management strategies) and these were assessed by a group of industry stakeholders and experts using multi-criteria decision analysis techniques against the different objectives. One strawman clearly provided the best overall set of outcomes given the multiple objectives, but was not optimal in terms of every objective, demonstrating that even the "best" strawman may be less than perfect. © 2012.

Australian monocot-infecting mastrevirus diversity rivals that in Africa

Monocotyledonous plant infecting mastreviruses (family Geminiviridae) have been found in the Old World. The greatest diversity of these viruses has been found in Africa but this may simply reflect the more extensive sampling that has been done there. To provide a better understanding of mastrevirus diversity in Australia. we have sequenced the genomes of 41 virus isolates found in naturalised and native grasses and identified four new species in addition to the four previously characterised species. Two of these species, which were recovered from a single Sporobolus plant, are highly divergent and are most closely related to the African streak viruses. This, coupled with the discovery of divergent dicotyledonous plant infecting mastreviruses in Australia brings into question the hypothesis that mastreviruses may have originated in Africa. We found that the patterns of inter- and intra-species recombination and the recombination hotspots mirror those found in both their African monocot-infecting counterparts and dicot-infecting mastrevirus. (C) 2012 Elsevier B.V. All rights reserved.

Modelling interactions between farm-level structural adjustment and a regional economy: A case of the Australian rice industry

Climate change and on-going water policy reforms will likely contribute to on-farm and regional structural adjustment in Australia. This paper gathers empirical evidence of farm-level structural adjustments and integrates these with a regional equilibrium model to investigate sectoral and regional impacts of climate change and recent water use policy on rice industry. We find strong evidence of adjustments to the farming system, enabled by existing diversity in on-farm production. A further loss of water with additional pressures to adopt less intensive and larger-scale farming, will however reduce the net number of farm businesses, which may affect regional rice production. The results from a regional CGE model show impacts on the regional economy over and above the direct cost of the environmental water, although a net reduction in real economic output and real income is partially offset by gains in rest of the Australia through the reallocation or resources. There is some interest within the industry and from potential new corporate entrants in the relocation of some rice production to the north. However, strong government support would be crucial to implement such relocation.

Gut-inhabiting yeasts from the gut of Australian passalid beetles

Passalidae (Polyphaga, Coleoptera) is a family of beetles with approximately 960 species that are distributed worldwide. Preliminary studies that characterized ascomycete and basidiomycete yeasts in the gut of these wood-eating beetles from the USA, Guatemala, and Thailand, demonstrated associations between certain yeast taxa and passalids. We extended the study to include yeasts and beetles from tropical forests near Cairns and Brisbane, Queensland, Australia. We isolated more than 1000 yeast strains from about 150 beetles belonging to 10 species. LSU and ITS rRNA markers were used to identify a subset of 250 yeast strains, which revealed that the gut of Australian passalids contained undescribed ascomycetes in the Debaryomyces, Dipodascus, Kazachstania, Ogataea, Scheffersomyces, Sugiyamaella, Spathaspora, Torulaspora, and Zygowilliopsis clades, as well as basidiomycetes in the genera Cryptococcus and Trichosporon. A close relative of Candida subhashii (Spathaspora clade) and the xylose-fermenting yeast Scheffersomyces stipitis were the most common species isolated in Queensland. These results agree with those of previous studies that showed a common association of xylose-fermenting yeasts in the gut of lignicolous insects. Species and higher taxa of yeasts, however, vary between Queensland passalids and those previously collected in distant regions.

Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

Key message “To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants.” Abstract Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.

Rhipicephalus microplus serine protease inhibitor family: annotation, expression and functional characterisation assessment

Background: Rhipicephalus (Boophilus) microplus evades the host's haemostatic system through a complex protein array secreted into tick saliva. Serine protease inhibitors (serpins) conform an important component of saliva which are represented by a large protease inhibitor family in Ixodidae. These secreted and non-secreted inhibitors modulate diverse and essential proteases involved in different physiological processes. Methods: The identification of R. microplus serpin sequences was performed through a web-based bioinformatics environment called Yabi. The database search was conducted on BmiGi V1, BmiGi V2.1, five SSH libraries, Australian tick transcriptome libraries and RmiTR V1 using bioinformatics methods. Semi quantitative PCR was carried out using different adult tissues and tick development stages. The cDNA of four identified R. microplus serpins were cloned and expressed in Pichia pastoris in order to determine biological targets of these serpins utilising protease inhibition assays. Results: A total of four out of twenty-two serpins identified in our analysis are new R. microplus serpins which were named as RmS-19 to RmS-22. The analyses of DNA and predicted amino acid sequences showed high conservation of the R. microplus serpin sequences. The expression data suggested ubiquitous expression of RmS except for RmS-6 and RmS-14 that were expressed only in nymphs and adult female ovaries, respectively. RmS-19, and -20 were expressed in all tissues samples analysed showing their important role in both parasitic and non-parasitic stages of R. microplus development. RmS-21 was not detected in ovaries and RmS-22 was not identified in ovary and nymph samples but were expressed in the rest of the samples analysed. A total of four expressed recombinant serpins showed protease specific inhibition for Chymotrypsin (RmS-1 and RmS-6), Chymotrypsin / Elastase (RmS-3) and Thrombin (RmS-15). Conclusion: This study constitutes an important contribution and improvement to the knowledge about the physiologic role of R. microplus serpins during the host-tick interaction.