First report of phytoplasma disease in capsicum, celery and chicory in Queensland, Australia

Tomato big bud phytoplasma (16SrII-E group), a widely distributed phytoplasma in Australia, was detected in celery, capsicum and chicory plants from southern Queensland, Australia in February 2002.

First report of Tomato spotted wilt virus in chickpea (Cicer arietinum) in Australia

Tomato spotted wilt virus (genus Tospovirus) is recorded on chickpea (Cicer arietinum) in Australia for the first time. It caused shoot tip symptoms of wilting, necrosis, bunching and chlorosis, followed by premature death of plants.

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.

Cyanide poisoning in cattle from Dysphania glomulifera (red crumbweed): Using the internet for rapid plant identification and diagnostic advice: Case Report

A 300-strong Angus-Brahman cattle herd near Springsure, central Queensland, was being fed Acacia shirleyi (lancewood) browse during drought and crossed a 5-hectare, previously burnt area with an almost pure growth of Dysphania glomulifera subspecies glomulifera (red crumbweed) on their way to drinking water. Forty cows died of cyanide poisoning over 2 days before further access to the plant was prevented. A digital image of a plant specimen made on a flat-bed scanner and transmitted by email was used to identify D glomulifera. Specific advice on the plant's poisonous properties and management of the case was then provided by email within 2 hours of an initial telephone call by the field veterinarian to the laboratory some 600 km away. The conventional method using physical transport of a pressed dried plant specimen to confirm the identification took 5 days. D glomulifera was identified in the rumen of one of two cows necropsied. The cyanogenic potential of D glomulifera measured 4 days after collection from the site of cattle deaths was 18,600 mg HCN/kg in dry matter. The lethal dose of D glomulifera for a 420 kg cow was estimated as 150 to 190 g wet weight. The plant also contained 4.8% KNO3 equivalent in dry matter, but nitrate-nitrite poisoning was not involved in the deaths.

Towards Ecologically Sustainable Management of the Torres Strait Prawn Fishery. CRC Torres Strait Task T1.5 – Final Report

This publication, which is the final report to the Torres Strait Cooperative Research Centre, provides an overview of all the research that was conducted as part of the Torres Strait CRC Task 1.5 - Towards Ecologically Sustainable Management of the Torres Strait Prawn Fishery The objectives of the task were: To develop cost-effective protocols to monitor and quantify the bycatch and environmental impacts of commercial prawn trawling. To monitor the status of target species using both fishery dependent and fishery independent data. To develop biological reference points for target species and undertake management strategy evaluation, in particular a risk assessment of fishing at various levels of fishing mortality. This report focuses on the second component of objective 1 and details a comparative analysis of bycatch samples collected from areas of the Torres Strait that were both closed and open to prawn trawl fishing. The report also reviews the research conducted in relation to objectives 2 and 3 which are detailed in a separate report, Stock Assessment of the Torres Strait Tiger Prawn Fishery (Penaeus esculentus).

Coastal Wetlands Resources Investigation of the Burdekin Delta for declaration as fisheries reserves. Report to Ocean Rescue 2000

A project to investigate the coastal wetland resources of the Burdekin Delta, north Queensland, was undertaken as part of the long-term assessment of the coastal fisheries resources of Queensland. Extending from November 1993 to May 1995, fieldwork was undertaken in November 1993 and August 1994. The scope of the coastal wetlands resources investigation of the Burdekin Delta for declaration as a Fish Habitat Area was: 1. To document and map the marine wetland vegetation communities in the Burdekin River delta. 2. To document levels of existing disturbance to wetlands, existing recreational and commercial fisheries resources, and existing fishing activities. 3. To evaluate the conservation values of the areas investigated from the viewpoint of fisheries productivity and as habitat for important/threatened species. 4. To initiate Fish Habitat Area declaration under Section 120 of the Queensland Fisheries Act 1994 with formal consultation to all stakeholders. This report concentrates on Points 1 and 3, the documentation of the marine wetland vegetation communities and the evaluation of conservation values from a fisheries viewpoint. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

First report of Colombian datura virus from Australia.

Colombian datura virus was identified from the ornamental plant Brugmansia sp., showing leaf mosaic symptoms. The nucleotide sequence of the 3 untranslated region and the amino acid sequence of the 3 portion of the coat protein were 100% identical to those from a Hungarian isolate of the virus. This represents the first record of this virus in Australia.

Resource Assessment of the Tidal Wetland Vegetation of Western Cape York Peninsula, North Queensland, Report to Ocean Rescue 2000

A project to allow the resource assessment of tidal wetland vegetation of western Cape York Peninsula, in north Queensland, was undertaken as part of the longterm assessment of the coastal fisheries resources of Queensland. The project incorporated a littoral invertebrate fauna component. Extending from May 1993 to December 1994, fieldwork was undertaken in May 1993, November 1993 and April 1994. The aims of this project were to: • obtain baseline information on the distribution of marine plants of western Cape York Peninsula; • commence a preliminary assessment of the littoral invertebrate fauna and their habitat requirements with a view to extending knowledge of their biogeographic affinities; • perform biogeographic classification of the tidal wetlands at a meso and local scale for marine conservation planning; • evaluate the conservation values of the areas investigated from the viewpoint of fisheries productivity and as habitat for important/threatened species. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

Development of a DNA based aging technique for use in fisheries assessments. Final report, Australian Fisheries Research and Development Corporation Project 2007/033.

The productivity of a fisheries resource can be quantified from estimates of recruitment, individual growth and natural and fisheries-related mortality, assuming the spatial extent of the resource has been quantified and there is minimal immigration or emigration. The sustainability of a fisheries resource is facilitated by management controls such as minimum and maximum size limits and total allowable catch. Minimum size limits are often set to allow individuals the opportunity to reproduce at least once before the chance of capture. Total allowable catches are a proportion of the population biomass, which is estimated based on known reproduction, recruitment, mortality and growth rates. In some fisheries, however, management actions are put in place without quantification of the resource through the stock assessment process. This occurs because species-specific information, for example individual growth, may not be available. In these circumstances, management actions need to be precautionary to protect against future resource collapse, but this often means that the resource is lightly exploited. Consequently, the productivity of the resource is not fully realised. Australia’s most valuable fisheries are invertebrate fisheries (Australian Department of Agriculture Fisheries and Forestry, 2008). For example, Australian fisheries (i.e. excluding aquaculture) production of crustaceans (largely prawns, rock lobster and crab) was 41,000 tonnes in 2006/7, worth $778 million. Production from mollusc (largely abalone, scallops, oysters and squid) fisheries was 39,000 tonnes, worth $502 million. Together, in 2006/7 crustacean and mollusc fisheries represented 58% of the total value of Australian wild fisheries production. Sustainable management of Australia’s invertebrate fisheries is frustrated by the lack of data on species-specific growth rates. This project investigated a new method to estimate age, and hence individual growth rates, in invertebrate fisheries species. The principle behind the new aging method was that telomeres (i.e. DNA end-caps of chromosomes) get shorter as an individual gets older. We studied commercial crustacean and molluscan species. A vertebrate fish species (silver perch, Bidyanus bidyanus) was used as a control to standardise our work against the literature. We found a clear relationship between telomere length and shell size for temperate abalone (Haliotis rubra). Further research is recommended before the method can be implemented to assist management of wildharvested abalone populations. Age needs to be substituted for shell size in the relationship and it needs to be studied for abalone from several regions. This project showed that telomere length declined with increasing age in Sydney rock oysters (Saccostrea glomerata) and was affected by regional variation. A relationship was not apparent between telomere length and age (or size as a surrogate for age) for crustacean species (school prawns, Metapenaeus macleayi; eastern rock lobster, Sagmariasus verreauxi; southern rock lobster, Jasus edwardsii; and spanner crabs, Ranina ranina). For school prawns, there was no difference between telomere length in males and females. Further research is recommended, however, as telomeric DNA from crustaceans was difficult to analyse using the terminal restriction fragment (TRF) assay. Telomere lengths of spanner crabs and lobsters were at the upper limit of resolution of the assay used and results were affected by degradation and possible contamination of telomeric DNA. It is possible that telomere length is an indicator of remaining lifespan in molluscan and crustacean individuals, as suggested for some vertebrate species (e.g. Monaghan, 2010). Among abalone of similar shell size and among lobster pueruli, there was evidence of individuals having significantly longer or shorter telomeres than the group average. At a population level, this may be a surrogate for estimates of future natural mortality, which may have usefulness in the management of those populations. The method used to assay telomere length (terminal restriction fragment assay) performed adequately for most species, but it was too expensive and time-consuming to be considered a useful tool for gathering information for fisheries management. Research on alternative methods is strongly recommended.

An investigation of migration and possible stock structuring by the stout whiting, Sillago robusta, in southern Queensland waters, and its impact on managing the fishery. Final Report on the Pilot Program

A highly polymorphic genetic locus of Stout Whiting was examined for evidence of geographical subdivision amongst samples collected from three locales in southern Queensland waters. Statistical indicators of subdivision were not significantly different from zero, suggesting that it is unlikely that the Stout Whiting resource in southern Queensland is genetically subdivided into separate stocks. It is recommended that the full-scale genetic program not proceed and that the resource be managed as a single stock.

Determination of management units for grey mackerel fisheries in northern Australia.

The requirement for Queensland, Northern Territory and Western Australian jurisdictions to ensure sustainable harvest of fish resources and their optimal use relies on robust information on the resource status. For grey mackerel (Scomberomorus semifasciatus) fisheries, each of these jurisdictions has their own management regime in their corresponding waters. The lack of information on stock structure of grey mackerel, however, means that the appropriate spatial scale of management is not known. As well, fishers require assurance of future sustainability to encourage investment and long-term involvement in a fishery that supplies lucrative overseas markets. These management and fisher-unfriendly circumstances must be viewed in the context of recent 3-fold increases in catches of grey mackerel along the Queensland east coast, combined with significant and increasing catches in other parts of the species' northern Australian range. Establishing the stock structure of grey mackerel would also immensely improve the relevance of resource assessments for fishery management of grey mackerel across northern Australia. This highlighted the urgent need for stock structure information for this species. The impetus for this project came from the strategic recommendations of the FRDC review by Ward and Rogers (2003), "Northern mackerel (Scombridae: Scomberomorus): current and future research needs" (Project No. 2002/096), which promoted the urgency for information on the stock structure of grey mackerel. In following these recommendations this project adopted a multi-technique and phased sampling approach as carried out by Buckworth et al (2007), who examined the stock structure of Spanish mackerel, Scomberomorus commerson, across northern Australia. The project objectives were to determine the stock structure of grey mackerel across their northern Australian range, and use this information to define management units and their appropriate spatial scales. We used multiple techniques concurrently to determine the stock structure of grey mackerel. These techniques were: genetic analyses (mitochondrial DNA and microsatellite DNA), otolith (ear bones) isotope ratios, parasite abundances, and growth parameters. The advantage of using this type of multi-technique approach was that each of the different methods is informative about the fish’s life history at different spatial and temporal scales. Genetics can inform about the evolutionary patterns as well as rates of mixing of fish from adjacent areas, while parasites and otolith microchemistry are directly influenced by the environment and so will inform about the patterns of movement during the fishes lifetime. Growth patterns are influenced by both genetic and environmental factors. Due to these differences the use of these techniques concurrently increases the likelihood of detecting different stocks where they exist. We adopted a phased sampling approach whereby sampling was carried out at broad spatial scales in the first year: east coast, eastern Gulf of Carpentaria (GoC), western GoC, and the NW Northern Territory (NW NT). By comparing the fish samples from each of these locations, and using each of the techniques, we tested the null hypothesis that grey mackerel were comprised of a single homogeneous population across northern Australia. Having rejected the null hypothesis we re-sampled the 1st year locations to test for temporal stability in stock structure, and to assess stock structure at finer spatial scales. This included increased spatial coverage on the east coast, the GoC, and WA. From genetic approaches we determined that there at least four genetic stocks of grey mackerel across northern Australia: WA, NW NT (Timor/Arafura), the GoC and the east Grey mackerel management units in northern Australia ix coast. All markers revealed concordant patterns showing WA and NW NT to be clearly divergent stocks. The mtDNA D-loop fragment appeared to have more power to resolve stock boundaries because it was able to show that the GoC and east coast QLD stocks were genetically differentiated. Patterns of stock structure on a finer scale, or where stock boundaries are located, were less clear. From otolith stable isotope analyses four major groups of S. semifasciatus were identified: WA, NT/GoC, northern east coast and central east coast. Differences in the isotopic composition of whole otoliths indicate that these groups must have spent their life history in different locations. The magnitude of the difference between the groups suggests a prolonged separation period at least equal to the fish’s life span. The parasite abundance analyses, although did not include samples from WA, suggest the existence of at least four stocks of grey mackerel in northern Australia: NW NT, the GoC, northern east coast and central east coast. Grey mackerel parasite fauna on the east coast suggests a separation somewhere between Townsville and Mackay. The NW NT region also appears to comprise a separate stock while within the GoC there exists a high degree of variability in parasite faunas among the regions sampled. This may be due to 1. natural variation within the GoC and there is one grey mackerel stock, or 2. the existence of multiple localised adult sub-stocks (metapopulations) within the GoC. Growth parameter comparisons were only possible from four major locations and identified the NW NT, the GoC, and the east coast as having different population growth characteristics. Through the use of multiple techniques, and by integrating the results from each, we were able to determine that there exist at least five stocks of grey mackerel across northern Australia, with some likelihood of additional stock structuring within the GoC. The major management units determined from this study therefore were Western Australia, NW Northern Territory (Timor/Arafura), the Gulf of Carpentaria, northern east Queensland coast and central east Queensland coast. The management implications of these results indicate the possible need for management of grey mackerel fisheries in Australia to be carried out on regional scales finer than are currently in place. In some regions the spatial scales of management might continue as is currently (e.g. WA), while in other regions, such as the GoC and the east coast, managers should at least monitor fisheries on a more local scale dictated by fishing effort and assess accordingly. Stock assessments should also consider the stock divisions identified, particularly on the east coast and for the GoC, and use life history parameters particular to each stock. We also emphasise that where we have not identified different stocks does not preclude the possibility of the occurrence of further stock division. Further, this study did not, nor did it set out to, assess the status of each of the stocks identified. This we identify as a high priority action for research and development of grey mackerel fisheries, as well as a management strategy evaluation that incorporates the conclusions of this work. Until such time that these priorities are addressed, management of grey mackerel fisheries should be cognisant of these uncertainties, particularly for the GoC and the Queensland east coast.

Productivity of plantation hardwood tree species in north-eastern Australia: A report from the Forest Adaptation and Sequestration Alliance

The report summarises data from a large number of trials of species with potential for use by the plantation forest industry in north-eastern Australia and provides information aimed at improving the understanding of growth rates, pest and disease risks and carbon sequestration. Data is summarised and presented at a regional level as opposed to individual trial or plot level. As well, nutritional impediments to tree growth and impacts on forest health are also reported. This report is intended to contribute to policy deliberations about developing forestry opportunities that can that can be integrated into the landscape, with particular consideration given to lower rainfall regions. There are several examples in north-eastern Australia where production forests have developed sub-optimally; this has often been due to poor selection of tree species as little information has been available. This report helps address this deficiency.

Tertiary Treatment of Ayr Municipal Wastewater using Bioremediation: A Pilot-Scale Study. A Report Prepared for the Burdekin Shire Council and the Burdekin Rangeland Reef Initiative

This joint DPI/Burdekin Shire Council project assessed the efficacy of a pilot-scale biological remediation system to recover Nitrogen (N) and Phosphorous (P) nutrients from secondary treated municipal wastewater at the Ayr Sewage Treatment Plant. Additionally, this study considered potential commercial uses for by-products from the treatment system. Knowledge gained from this study can provide directions for implementing a larger-scale final effluent treatment protocol on site at the Ayr plant. Trials were conducted over 10 months and assessed nutrient removal from duckweed-based treatments and an algae/fish treatment – both as sequential and as stand-alone treatment systems. A 42.3% reduction in Total N was found through the sequential treatment system (duckweed followed by algae/fish treatment) after 6.6 days Effluent Retention Time (E.R.T.). However, duckweed treatment was responsible for the majority of this nutrient recovery (7.8 times more effective than algae/fish treatment). Likewise, Total P reduction (15.75% reduction after 6.6 days E.R.T.) was twice as great in the duckweed treatment. A phytoplankton bloom, which developed in the algae/fish tanks, reduced nutrient recovery in this treatment. A second trial tested whether the addition of fish enhanced duckweed treatment by evaluating systems with and without fish. After four weeks operation, low DO under the duckweed blanket caused fish mortalities. Decomposition of these fish led to an additional organic load and this was reflected in a breakdown of nitrogen species that showed an increase in organic nitrogen. However, the Dissolved Inorganic Nitrogen (DIN: ammonia, nitrite and nitrate) removal was similar between treatments with and without fish (57% and 59% DIN removal from incoming, respectively). Overall, three effluent residence times were evaluated using duckweed-based treatments; i.e. 3.5 days, 5.5 days and 10.4 days. Total N removal was 37.5%, 55.7% and 70.3%, respectively. The 10.4-day E.R.T. trial, however, was evaluated by sequential nutrient removal through the duckweed-minus-fish treatment followed by the duckweed-plus-fish treatment. Therefore, the 70.3% Total N removal was lower than could have been achieved at this retention time due to the abovementioned fish mortalities. Phosphorous removal from duckweed treatments was greatest after 10.4-days E.R.T. (13.6%). Plant uptake was considered the most important mechanism for this P removal since there was no clay substrate in the plastic tanks that could have contributed to P absorption as part of the natural phosphorous cycle. Duckweed inhibited phytoplankton production (therefore reducing T.S.S) and maintained pH close to neutral. DO beneath the duckweed blanket fell to below 1ppm; however, this did not limit plant production. If fish are to be used as part of the duckweed treatment, air-uplifts can be installed that maintain DO levels without disturbing surface waters. Duckweed grown in the treatments doubled its biomass on average every 5.7 days. On a per-surface area basis, 1.23kg/m2 was harvested weekly. Moisture content of duckweed was 92%, equating to a total dry weight harvest of 0.098kg/m2/week. Nutrient analysis of dried duckweed gave an N content of 6.67% and a P content of 1.27%. According to semi-quantitative analyses, harvested duckweed contained no residual elements from the effluent stream that were greater than ANZECC toxicant guidelines proposed for aquaculture. In addition, jade perch, a local aquaculture species, actively consumed and gained weight on harvested duckweed, suggesting potential for large-scale fish production using by-products from the effluent treatment process. This suggests that a duckweed-based system may be one viable option for tertiary treatment of Ayr municipal wastewater. The tertiary detention lagoon proposed by the Burdekin Shire Council, consisting of six bays approximately 290 x 35 metres (x 1.5 metres deep), would be suitable for duckweed culture with minor modification to facilitate the efficient distribution of duckweed plants across the entire available growing surface (such as floating containment grids). The effluent residence time resulting from this proposed configuration (~30 days) should be adequate to recover most effluent nutrients (certainly N) based on the current trial. Duckweed harvest techniques on this scale, however, need to be further investigated. Based on duckweed production in the current trial (1.23kg/m2/week), a weekly harvest of approximately 75 000kg (wet weight) could be expected from the proposed lagoon configuration under full duckweed production. A benefit of the proposed multi-bay lagoon is that full lagoon production of duckweed may not be needed to restore effluent to a desirable standard under the present nutrient load, and duckweed treatment may be restricted to certain bays. Restored effluent could be released without risk of contaminating the receiving waterway with duckweed by evacuating water through an internal standpipe located mid-way in the water column.

Coordinator's report: descriptions of barley genetic stocks for 2010.

In this volume, 64 new and revised barley genetic stock (BGS) descriptions for 2010 are presented. The current lists of new and revised BGS descriptions are presented by BGS number order and by locus symbol in alphabetical order. Information on the description location, recommended locus name, chromosomal location, previous gene symbols, and the primary genetic stock (GSHO number and/or NGB number) are included in these lists.

Coordinator's report: rules for nomenclature and gene symbolization in barley.

In this volume, the recommended rules for nomenclature and gene symbolization in barley are reprinted. The current lists of new and revised barley genetic stock descriptions are presented by BGS number order and by locus symbol in alphabetical order.