Tobacco Streak Virus (TSV) in Cotton - scoping study

This project aims to examine the possible impact of Tobacco Streak Virus (TSV) on the Australian cotton industry. TSV is transmitted by thrips, causes a disease which has had a significant impact on grain crops in Central Queensland and a preliminary study in 2007 has shown that cotton is also susceptible to field infection in this region, but many questions remain unanswered. This project aims to: • Determine the impact of TSV in “normal” seasons. • Survey New South Wales and Queensland crops and determine alternative weed and crop hosts. • Assess yield-loss in cotton due to TSV, and factors that lead to systemic infection. • Assess thrips vector species present in cotton • Provide extension material on the impact and management of TSV in cotton

Weed management strategies for farming systems with herbicide tolerant cotton.

The introduction of glyphosate tolerant cotton has significantly improved the flexibility and management of a number of problem weeds in cotton systems. However, reliance on glyphosate poses risks to the industry in term of glyphosate resistance and species shift. The aims of this project were to identify these risks, and determine strategies to prevent and mitigate the potential for resistance evolution. Field surveys identified fleabane as the most common weed now in both irrigated and dryland system. Sowthistle has also increased in prevalence, and bladder ketmia and peachvine remained common. The continued reliance on glyphosate has favoured small seeded, and glyphosate tolerant species. Fleabane is both of these, with populations confirmed resistant in grains systems in Queensland and NSW. When species were assessed for their resistance risk, fleabane, liverseed grass, feathertop Rhodes grass, sowthistle and barnyard grass were determined to have high risk ratings. Management practices were also determined to rely heavily on glyphosate and therefore be high risk in summer fallows, and dryland glyphosate tolerant and conventional cotton. Situations were these high risk species are present in high risk cropping phases need particular attention. The confirmation of a glyphosate resistance barnyard grass population in a dryland glyphosate tolerant cotton system means resistance is now a reality for the cotton industry. However, experiments have shown that resistant populations can be managed with other herbicide options currently available. However, the options for fleabane management in cotton are still limited. Although some selective residual herbicides are showing promise, the majority of fleabane control tactics can only be used in other phases of the cotton rotation. An online glyphosate resistance tool has been developed. This tool allows growers to assess their individual glyphosate resistance risks, and how they can adjust their practices to reduce their risks. It also provides researchers with current information on weed species present and practices used across the industry. This tool will be extremely useful in tailoring future research and extension efforts. Simulations from the expanded glyphosate resistance model have shown that glyphosate resistance can be prevented and managed in glyphosate-tolerant cotton farming systems. However, for strategies to be successful, some effort is required. Simulations have shown the importance of controlling survivors of glyphosate applications, using effective glyphosate alternatives in fallows, and combining several effective glyphosate alternatives in crop, and these are the key to the prevention and management of glyphosate resistance.

Agronomic indices, growth, yield-contributing traits, and yield of dry-seeded rice under varying herbicides

Dry-seeded rice (DSR) is an emerging resource-conserving technology in many Asian countries, but weeds remain the major threat to the production of DSR systems. A field study was conducted in 2012 and 2013 at the International Rice Research Institute (IRRI), Los Baños, Philippines, to evaluate the performance of sole and sequential applications of preemergence (oxadiazon and pendimethalin), early postemergence (butachlor + propanil and thiobencarb + 2,4-D), and late postemergence herbicides (bispyribac-sodium and fenoxaprop + ethoxysulfuron) with different modes of action in comparison to manual weeding in DSR. The sequential applications of all preemergence and postemergence herbicides reduced weed density and biomass by 80–100% compared to the nontreated plots. The sole application of postemergence herbicides reduced weed density by only 44–54% and weed biomass by 51–61%, whereas oxadiazon alone reduced weed density and biomass by 96–100%. All herbicide treatments and manual weeding significantly affected tiller number, biomass, crop growth rate, agronomic indices, yield-contributing parameters (panicle density and filled grains), and yield (biological and grain) of rice. The highest grain yield was obtained in the manually weeded plots (5.9–6.1 t ha−1) and the plots treated with oxadiazon alone (5.4–5.6 t ha−1) and oxadiazon followed by postemergence herbicides (5.2–5.8 t ha−1). The lowest paddy yield (0.22 t ha−1) was achieved in the nontreated plots followed by the plots treated with the sole application of bispyribac-sodium and fenoxaprop + ethoxysulfuron. The results suggest that oxadiazon is the best broad-spectrum and economically effective herbicide when applied alone or in combination with other effective postemergence herbicides with different modes of action, depending on the weed species present in the field.

Thrips incidence in green beans and the degree of damage caused

Green bean production accounts for 2.4% of the total value of Australian vegetable production and was Australia's tenth largest vegetable crop in 2008-2009 by value. Australian green bean production is concentrated in Queensland (51%) and Tasmania (34%) where lost productivity as a direct result of insect damage is recognised as a key threat to the industry (AUSVEG, 2011). Green beans attract a wide range of insect pests, with thrips causing the most damage to the harvestable product, the pod. Thrips populations were monitored in green bean crops in the Gatton Research Facility, Lockyer Valley, South-east Queensland, Australia from 2002-2011. Field trials were conducted to identify the thrips species present, to record fluctuation in abundance during the season and assess pod damage as a direct result of thrips. Thirteen species of thrips were recorded during this time on bean plantings, with six dominant species being collected during most of the growing season: Frankliniella occidentalis, F. schultzei, Megalurothrips usitatus, Pseudanaphothrips achaetus, Thrips imaginis and T. tabaci. Thrips numbers ranged from less than one thrips per flower to as high as 5.39 thrips per flower. The highest incidence of thrips presence found in October/November 2008, resulted in 10.74% unmarketable pods due to thrips damage, while the lowest number of thrips recorded in April 2008 caused a productivity loss of 36.65% of pods as a result of thrips damage.

Isolation and expression analysis of multiple isoforms of putative farnesoic acid O-methyltransferase in several crustacean species

Farnesoic acid O-methyltransferase (FaMeT) is the enzyme responsible for the conversion of farnesoic acid (FA) to methyl farnesoate (MF) in the final step of MF synthesis. Multiple isoforms of putative FaMeT were isolated from six crustacean species belonging to the families Portunidae, Penaeidae, Scyllaridae and Parastacidae. The portunid crabs Portunus pelagicus and Scylla serrata code for three forms: short, intermediate and long. Two isoforms (short and long) were isolated from the penaeid prawns Penaeus monodon and Fenneropenaeus merguiensis. Two isoforms were also identified in the scyllarid Thenus orientalis and parastacid Cherax quadricarinatus. Putative FaMeT sequences were also amplified from the genomic DNA of P. pelagicus and compared to the putative FaMeT transcripts expressed. Each putative FaMeT cDNA isoform was represented in the genomic DNA, indicative of a multi-gene family. Various tissues from P. pelagicus were individually screened for putative FaMeT expression using PCR and fragment analysis. Each tissue type expressed all three isoforms of putative FaMeT irrespective of sex or moult stage. Protein domain analysis revealed the presence of a deduced casein kinase II phosphorylation site present only in the long isoform of putative FaMeT.

Congruence in QTL for adventitious rooting in Pinus elliottii x Pinus caribaea hybrids resolves between and within-species effects

Targeting between-species effects for improvement in synthetic hybrid populations derived from outcrossing parental tree species may be one way to increase the efficacy and predictability of hybrid breeding. We present a comparative analysis of the quantitative trait loci (QTL) which resolved between from within-species effects for adventitious rooting in two populations of hybrids between Pinus elliottii and P. caribaea, an outbred F1 (n=287) and an inbred-like F2 family (n=357). Most small to moderate effect QTL (each explaining 2-5% of phenotypic variation, PV) were congruent (3 out of 4 QTL in each family) and therefore considered within-species effects as they segregated in both families. A single large effect QTL (40% PV) was detected uniquely in the F2 family and assumed to be due to a between-species effect, resulting from a genetic locus with contrasting alleles in each parental species. Oligogenic as opposed to polygenic architecture was supported in both families (60% and 20% PV explained by 4 QTL in the F 2 and F1 respectively). The importance of adventitious rooting for adaptation to survive water-logged environments was thought in part to explain oligogenic architecture of what is believed to be a complex trait controlled by many hundreds of genes.

Recruitment dynamics of invasive species in rainforest habitats following Cyclone Larry

In tropical forests, natural disturbance creates opportunities for species to claim previously utilized space and resources and is considered an important mechanism in the maintenance of species diversity. However, ecologists have long recognized that disturbance also promotes exotic plant invasions. Cyclones cause extensive defoliation, loss of major branches and multiple tree falls, resulting in a significantly more open canopy and increased light and heat levels in the understorey. The widespread and massive disturbance caused by cyclones provides ideal conditions for rapid recruitment and spread of invasive species. The ecological roles of invasive species in rainforest habitats following such a severe disturbance are poorly understood. Severe category 4 Cyclone Larry crossed the North Queensland coast in March 2006 causing massive disturbance to rainforest habitats from Tully to Cairns and west to the Atherton Tablelands. We established 10 plots in an area extensively damaged by this cyclone near El Arish in North Queensland. On each plot nine 2 × 2 m quadrats were established with three quadrats per plot in each of the following treatments: (i) complete debris removal down to the soil layer, (ii) removal of coarse woody debris only, and (iii) uncleared. We monitored recruitment, growth and mortality of all native and invasive species in the 90 quadrats every 3 months since the cyclone. Here we present the recruitment dynamics of invasive species across the study area in relation to the level of disturbance, the type of quadrat treatment, and the diversity and abundance of the native recruiting flora over the first 12 months post-cyclone. Our results suggest that invasive species will mostly comprise a transient component of the flora in the early stages of the successional response. However, some species may have longer-term effects on the successional trajectory of the rainforest and future forest composition and structure.

Phylogenetic relationships of unclassified, satellitic Pasteurellaceae obtained from different species of birds as demonstrated by 16S rRNA gene sequence comparison

Avian haemophili demonstrating in vitro satellitic growth, also referred to as the V-factor or NAD requirement, have mainly been classified with Avibacterium paragallinarum (Haemophilus paragallinarum), Avibacterium avium (Pasteurella avium), Avibacterium volantium (Pasteurella volantium) and Avibacterium sp. A (Pasteurella species A). The aim of the present study was to assess the taxonomic position of 18 V-factor-requiring isolates of unclassified Haemophilus-like organisms isolated from galliforme, anseriforme, columbiforme and gruiforme birds as well as kestrels and psittacine birds including budgerigars by conventional phenotypic tests and 16S rRNA gene sequencing. All isolates shared phenotypical characteristics which allowed classification with Pasteurellaceae. Haemolysis of bovine red blood cells was negative. Haemin (X-factor) was not required for growth. Maximum-likelihood phylogenetic analysis including bootstrap analysis showed that six isolates were related to the avian 16S rRNA group and were classified as Avibacterium according to 16S rRNA sequence analysis. Surprisingly, the other 12 isolates were unrelated to Avibacterium. Two isolates were unrelated to any of the known 16S rRNA groups of Pasteurellaceae. Two isolates were related to Volucribacter of the avian 16S rRNA group. Seven isolates belonged to the Testudinis 16S rRNA group and out of these, two isolates were closely related to taxa 14 and 32 of Bisgaard, whereas four other isolates were found to form a genus-like group distantly related to taxon 40 and one isolated remained distantly related to other members of the Testudinis group. One isolate was closely related to taxon 26 (a member of Actinobacillus sensu stricto). The study documented major genetic diversity among V-factor-requiring avian isolates beyond the traditional interpretation that they only belong to Avibacterium, underlining the limited value of satellitic growth for identification of avian members of Pasteurellaceae. Our study also emphasized that these organisms will never be isolated without the use of special media satisfying the V-factor requirement.

Comparative seed and dispersal ecology of three exotic subtropical Asparagus species

The genus Asparagus includes at least six invasive species in Australia. Asparagus aethiopicus and A. africanus are invasive in subtropical Australia, and a third species, A. virgatus is naturalized and demonstrates localized spread in south east Queensland. To better understand how the attributes of these species contribute to their invasiveness, we compared fruit and seed traits, germination, seedling emergence, seed survival, and time-to-maturity. We further investigated dispersal ecology of A. africanus, examining the diet of a local frugivore, the figbird (Sphecotheres viridis) and the effect of gut passage on seedling emergence. Overall, A. aethiopicus was superior in germination and emergence, with the highest mean germination (98.8%) and emergence (94.5%) under optimal conditions and higher emergence (mean of 73.3%) across all treatments. In contrast, A. africanus had the lowest germination under optimal conditions (71.7%) and low mean seedling emergence (49.5%), but had fruits with the highest relative yield (ratio of dry pulp to fruit fresh weight) that were favored by a local frugivore. Figbirds consumed large numbers of A. africanus fruits (~30% of all non-Ficus fruits), and seedling germination was not significantly affected by gut passage compared to unprocessed fruits. Asparagus virgatus germinated poorly under cool, light conditions (1.4%) despite a high optimum mean (95.0%) and had low mean performance across emergence treatments (36.3%). The species also had fruits with a low pulp return for frugivores. For all species, seed survival declined rapidly in the first 12 mo and fell to < 3.2% viability at 36 mo. On the basis of the traits considered, A. virgatus is unlikely to have the invasive potential of its congeners. Uniformly short seed survival times suggest that weed managers do not have to contend with a substantial persistent soil-stored seed bank, but frugivore-mediated dispersal beyond existing infestations will present a considerable management challenge.

A novel species of mastrevirus (family Geminiviridae) isolated from Digitaria didactyla grass from Australia.

Mastreviruses (family Geminiviridae) that infect monocotyledonous plants occur throughout the temperate and tropical regions of Asia, Africa, Europe and Australia. Despite the identification of a very diverse array of mastrevirus species whose members infect African monocots, few such species have been discovered in other parts of the world. For example, the sequence of only a single monocot-infecting mastrevirus, Chloris striate mosaic virus (CSMV), has been reported so far from Australia, even though earlier biological and serological studies suggested that other distinct mastreviruses were present. Here, we have obtained the complete nucleotide sequence of a virus from the grass Digitaria didactyla originating from Australia. Analysis of the sequence shows the virus to be a typical mastrevirus, with four open reading frames, two in each orientation, separated by two non-coding intergenic regions. Although it showed the highest levels of sequence identity to CSMV (68.7%), their sequences are sufficiently diverse for the virus to be considered a member of a new species in the genus Mastrevirus, based on the present species demarcation criteria. We propose that the name first used during the 1980s be used for this species, Digitaria didactyla striate mosaic virus (DDSMV).

Quambalaria species: increasing threat to eucalypt plantations in Australia

Spotted gum (Corymbia citriodora subsp. variegata and C. maculata) is a valuable source of commercial timber and suitable for a wide range of different soil types in eastern Australia. The main biological constraint to further expansion of spotted gum plantations is Quambalaria shoot blight caused by the fungus Quambalaria pitereka. Surveys conducted to evaluate the impact of Quambalaria shoot blight have shown that the disease is present in all spotted gum plantations and on a range of Corymbia species and hybrids in subtropical and tropical regions surveyed in eastern Australia. More recently, Q. eucalypti has also been identified from a range of Eucalyptus species in these regions. Both pathogens have also been found associated with foliage blight and die-back of amenity trees and Q. pitereka in native stands of Corymbia species, which is the probable initial infection source for plantations. Infection by Q. pitereka commonly results in the repeated destruction of the growing tips and the subsequent formation of a bushy crown or death of trees in severe cases. In comparison, Q. eucalypti causes small, limited lesions and has in some cases been associated with insect feeding. It has not been recorded as causing severe shoot and stem blight. A better understanding of factors influencing disease development and host-pathogen interactions is essential in the development of a disease management strategy for these poorly understood but important pathogens in the rapidly expanding eucalypt (Corymbia and Eucalyptus spp.) plantation industry in subtropical and tropical eastern Australia.

The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago

Background: The territorial fishing zones of Australia and Indonesia are contiguous to the north of Australia in the Timor and Arafura Seas and in the Indian Ocean to the north of Christmas Island. The area surrounding the shared boundary consists of a variety of bio-diverse marine habitats including shallow continental shelf waters, oceanic trenches and numerous offshore islands. Both countries exploit a variety of fisheries species, including whaler (Carcharhinus spp.) and hammerhead sharks (Sphyrna spp.). Despite their differences in social and financial arrangements, the two countries are motivated to develop complementary co-management practices to achieve resource sustainability. An essential starting point is knowledge of the degree of population subdivision, and hence fisheries stock status, in exploited species. Results: Populations of four commercially harvested shark species (Carcharhinus obscurus, Carcharhinus sorrah, Prionace glauca, Sphyrna lewini) were sampled from northern Australia and central Indonesia. Neutral genetic markers (mitochondrial DNA control region sequence and allelic variation at co-dominant microsatellite loci) revealed genetic subdivision between Australian and Indonesian populations of C. sorrah. Further research is needed to address the possibility of genetic subdivision among C. obscurus populations. There was no evidence of genetic subdivision for P. glauca and S. lewini populations, but the sampling represented a relatively small part of their distributional range. For these species, more detailed analyses of population genetic structure is recommended in the future. Conclusion: Cooperative management between Australia and Indonesia is the best option at present for P. glauca and S. lewini, while C. sorrah and C. obscurus should be managed independently. On-going research on these and other exploited shark and ray species is strongly recommended. Biological and ecological similarity between species may not be a predictor of population genetic structure, so species-specific studies are recommended to provide new data to assist with sustainable fisheries management.

The role of tillage, fertiliser and forage species in sustaining dairying based on crops in southern Queensland 1. Winter-dominant forage systems.

Field studies were conducted over 5 years on two dairy farms in southern Queensland to evaluate the impacts of zero-tillage, nitrogen (N) fertiliser and legumes on a winter-dominant forage system based on raingrown oats. Oats was able to be successfully established using zero-tillage methods, with no yield penalties and potential benefits in stubble retention over the summer fallow. N fertiliser, applied at above industry-standard rates (140 vs. 55 kg/ha.crop) in the first 3 years, increased forage N concentration significantly and had residual effects on soil nitrate-N at both sites. At one site, crop yield was increased by 10 kg DM/ha. kg fertiliser N applied above industry-standard rates. The difference between sites in fertiliser response reflected contrasting soil and fertiliser history. There was no evidence that modifications to oats cropping practices (zero-tillage and increased N fertiliser) increased surface soil organic carbon (0-10 cm) in the time frame of the present study. When oats was substituted with annual legumes, there were benefits in improved forage N content of the oat crop immediately following, but legume yield was significantly inferior to oats. In contrast, the perennial legume Medicago sativa was competitive in biomass production and forage quality with oats at both sites and increased soil nitrate-N levels following termination. However, its contribution to winter forage was low at 10% of total production, compared with 40% for oats, and soil water reserves were significantly reduced at one site, which had an impact on the following oat production. The study demonstrated that productive grazed oat crops can be grown using zero tillage and that increased N fertiliser is more consistent in its effect on N concentration than on forage yield. A lucerne ley provides a strategy for raising soil nitrate-N concentration and increasing overall forage productivity, although winter forage production is reduced.

Round scallops and square meshes: a comparison of four codend types on the catch rates of target species and by-catch in the Queensland (Australia) saucer scallop (Amusium balloti) trawl fishery

Concern over the amount of by-catch from benthic trawl fisheries and research into the problem have increased in recent years. The present paper demonstrated that by-catch rates in the Queensland (Australia) saucer scallop (Amusium balloti) trawl fishery can be reduced by 77% (by weight) using nets fitted with a turtle excluder device (TED) and a square-mesh codend, compared with a standard diamond-mesh codend with no TED. This large reduction was achieved with no significant effect on the legal size scallop catch rate and 39% fewer undersize scallops were caught. In total, 382 taxa were recorded in the by-catch, which was dominated by sponges, portunid crabs, small demersal and benthic fish (e.g. leatherjackets, stingerfish, bearded ghouls, nemipterids, longspine emperors, lizard fish, triggerfish, flounders and rabbitfish), elasmobranchs (e.g. mainly rays) and invertebrates (e.g. sea stars, sea urchins, sea cucumbers and bivalve molluscs). Extremely high reductions in catch rate (i.e. ≥85%) were demonstrated for several by-catch species owing to the square-mesh codend. Square-mesh codends show potential as a means of greatly reducing by-catch and lowering the incidental capture and mortality of undersize scallops and Moreton Bay bugs (Thenus australiensis) in this fishery

Virus species polemics: 14 senior virologists oppose a proposed change to the ICTV definition of virus species

The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) has recently decided to modify the current definition of virus species (Code of Virus Classification and Nomenclature Rule 3.21) and will soon ask the full ICTV membership (189 voting members) to ratify the proposed controversial change. In this discussion paper, 14 senior virologists, including six Life members of the ICTV, compare the present and proposed new definition and recommend that the existing definition of virus species should be retained. Since the pros and cons of the proposal posted on the ICTV website are not widely consulted, the arguments are summarized here in order to reach a wider audience.