Herpesviral haematopoietic necrosis virus (CyHV-2) infection: case studies from commercial goldfish farms

Herpesviral haematopoietic necrosis is a disease of goldfish, Carassius auratus, caused by Cyprinid herpesvirus-2 (CyHV-2) infection. Quantitative PCR was carried out on tissue homogenates from healthy goldfish fingerlings, broodfish, eggs and fry directly sampled from commercial farms, from moribund fish submitted to our laboratory for disease diagnosis, and on naturally-infected CyHV-2 carriers subjected to experimental stress treatments. Healthy fish from 14 of 18 farms were positive with copy numbers ranging from tens to 10(7) copies mu g(-1) DNA extracted from infected fish. Of 118 pools of broodfish tested, 42 were positive. The CyHV-2 was detected in one lot of fry produced from disinfected eggs. Testing of moribund goldfish, in which we could not detect any other pathogens, produced 12 of 30 cases with 10(6)-10(8) copies of CyHV-2 mu g(-1) DNA extracted. Subjecting healthy CyHV-2 carriers to cold shock (22-10 degrees C) but not heat, ammonia or high pH, increased viral copy numbers from mean copy number (+/- SE) of 7.3 +/- 11 to 394 +/- 55 mu g(-1) DNA extracted after 24 h. CyHV-2 is widespread on commercial goldfish farms and outbreaks apparently occur when healthy carriers are subjected to a sharp temperature drop followed by holding at the permissive temperature for the disease.

Quantifying Transmission of Campylobacter jejuni in Commercial Broiler Flocks

Since meat from poultry colonized with Campylobacter spp. is a major cause of bacterial gastroenteritis, human exposure should be reduced by, among other things, prevention of colonization of broiler flocks. To obtain more insight into possible sources of introduction of Campylobacter into broiler flocks, it is essential to estimate the moment that the first bird in a flock is colonized. If the rate of transmission within a flock were known, such an estimate could be determined from the change in the prevalence of colonized birds in a flock over time. The aim of this study was to determine the rate of transmission of Campylobacter using field data gathered for 5 years for Australian broiler flocks. We used unique sampling data for 42 Campylobacter jejuni-colonized flocks and estimated the transmission rate, which is defined as the number of secondary infections caused by one colonized bird per day. The estimate was 2.37 +/- 0.295 infections per infectious bird per day, which implies that in our study population colonized flocks consisting of 20,000 broilers would have an increase in within-flock prevalence to 95% within 4.4 to 7.2 days after colonization of the first broiler. Using Bayesian analysis, the moment of colonization of the first bird in a flock was estimated to be from 21 days of age onward in all flocks in the study. This study provides an important quantitative estimate of the rate of transmission of Campylobacter in broiler flocks, which could be helpful in future studies on the epidemiology of Campylobacter in the field.

Development and testing of an evaluation procedure for commercial manure additive products.

Manure additive products can be used to reduce odour emissions (OE) from livestock farms. The standardised evaluation of these manure additive products under specific farm conditions is important. In this study, the efficacy of a manure additive (WonderTreat(TM), CKLS, Inc., Hong-Kong) was assessed under Australian conditions utilising a combination of laboratory and field-scale evaluation techniques. As a first step, the efficacy of the manure additive was assessed in a laboratory-scale trial using a series of uniformly managed digesters and standard odour, liquor ammonia and hydrogen sulphide concentration measurement procedures. This showed that the addition of WonderTreat(TM) at the 'low dose rate' (LDR) (102.6 g m-2) used during the trial significantly, but only marginally (30%; P = 0.02) reduced the OE rate (mean 13.9 OU m-2 s-1) of anaerobic pig liquor relative to an untreated control (UC) (19.9 OU m-2 s-1). However, the 'high dose rate' (HDR) (205.3 g m-2) also assessed during the trial preformed similarly (19.7 OU m-2 s-1) to the UC. No statistically significant difference in the concentrations of a range of measured water quality variables at the 5% level was observed between the treatments or controls digesters. As a second step, a field-scale assessment of the manure additive was undertaken at a commercial piggery. Two piggery manure lagoons (each with approximately 2500 m2 surface area) were included in the study; one was treated with WonderTreat(TM) while the other was used as control. The efficacy of the treatment was assessed using olfactometric evaluation of odour samples collected from the surface of the pond using a dynamic wind tunnel and ancillary equipment. No statistically significant reduction in OE rate could be demonstrated (P = 0.35), partially due to the limited number of samples taken during the assessment. However, there was a numerical reduction in the average OE rate of the treatment pond (29 OU m-2 s-1 at 1 m s-1) compared to the control lagoon (38 OU m-2 s-1 at 1 m s-1).

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).

Sustainable native forest management. Case studies in managing private native forest in southeast Queensland.

The introduction describes productive forest in Queensland and summaries the principles of native forest management that achieve optimum productivity. Case study 1 deals with thinning an even-aged regrowth forest. It shows how thinning the stand actively manages the future composition and structure to improve productivity in the best stems and increase the commercial value of the next harvest. Case study 2 describes restoring productivity in a high-graded spotted gum - ironbark forest. It shows that defective and non-saleable trees should be removed so they do not repress the future stand; and that regeneration should be thinned, retaining the best trees in adequate growing space. Case study 3 discusses on-farm value adding for hardwood forests. It shows how long-term viability and maximum productivity and returns depend on the best management practices and knowing how to obtain the best returns from a range of forest products. Case study 4 examines integrated harvesting in a eucalypt forest. It shows how integrating the harvest enables the full range of timber products are harvested and sold for their maximum value while reducing the amount of waste.

Queensland Coastal Wetland Resources: the Northern Territory Border to Flinders River

Protection of coastal wetland environments is an important prerequisite to effective and sustainable fisheries management and conservation of habitats for the use of future generations. Mangroves, saltmarshes and seagrasses directly support local and offshore fisheries through the provision of food, shelter, breeding and nursery grounds. As such, these vegetated wetland environments along with sandbars, mudflats, rocky foreshores and reefs have significant economic value as well as their intrinsic aesthetic and ecological values. This report summarises the results of the mapping undertaken in the Gulf of Carpentaria Region from the Queensland/Northern Territory border eastwards to the western bank of the Flinders River (hereafter called the Gulf Study Area). The study was undertaken in order to: 1. document and map coastal wetlands of the Gulf Study Area; 2. document levels of existing disturbance to and protection of these wetlands; 3. examine existing recreational, indigenous and commercial fisheries of the region; 4. evaluate the conservation values of the areas investigated from the viewpoint of fisheries productivity and as habitat for important and/or threatened species for future FHA/Marine Protected Area (MPA) declaration. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

Queensland Coastal Wetland Resources: Sand Bay to Keppel Bay.

Protection of coastal wetland environments is an important prerequisite to effective and sustainable inshore fisheries management and conservation of habitats for use by future generations. Mangroves, saltmarshes, seagrasses and non vegetated habitats directly support local and regional inshore and offshore fisheries through the provision of food, shelter, breeding and nursery grounds. As such, these wetland environments have significant economic value as well as their intrinsic aesthetic and ecological values. This report summarises the results of the mapping undertaken in the Central Queensland Coast from Sand Bay to Keppel Bay (hereafter referred to as the Study Area). The study was undertaken in order to: 1. document and map the coastal wetland communities along the Queensland coastline from Sand Bay (20.93°S, 149.04°E) to Keppel Bay (23.65°S, 151.07°E); 2. document levels of existing disturbance to and protection of the wetlands; 3. examine existing recreational and commercial fisheries in the region; and 4. evaluate the conservation values of the areas investigated from the viewpoint of fisheries productivity and as habitat for important and/or threatened species. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

Queensland Coastal Wetland Resources: Cape Tribulation to Bowling Green Bay

This report provides key resource data for the ongoing assessment of the requirement for additional Marine Protected Areas (e.g. FHAs under the Queensland Fisheries Act 1994) in regions of high fish habitat value in northern Queensland from Cape Tribulation to Bowling Green Bay (hereafter referred to as the Study Area). The study also provides baseline information on the coastal wetlands within this Study Area for consideration in the Ramsar site nomination process. The Study Area extends from Cape Tribulation (16o 6’S, 145o 24’E) to Bowling Green Bay (19o 30’S, 147o 24’E) in tropical north Queensland. The project aimed to: 1. document and map the coastal wetland communities of the Study Area; 2. document levels of existing disturbance to and protection of the wetlands; 3. examine existing recreational, indigenous and commercial fisheries resources in the region; 4. evaluate the conservation values of the areas investigated from the viewpoint of fisheries productivity and as habitat for important and/or threatened species for future FHA/MPA declaration. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

Queensland Coastal Wetland Resource Investigation of the Bowen Region: Cape Upstart to Gloucester Island

The wetland resources of the Queensland coastline have been mapped as a baseline dataset for Marine Protected Area investigation and particularly Fish Habitat Area (FHA) declaration, Ramsar site nomination and continued monitoring of these important fish habitats. This report summarises the results of the mapping undertaken in the Bowen region from the East Coast of Cape Upstart (Abbot Bay) to Gloucester Island (encompassing Edgecumbe Bay). The study was undertaken in order to: 1. document and map the coastal wetland communities within the Bowen region; 2. document levels of existing disturbance to and protection of the wetlands; 3. examine existing recreational and commercial fisheries in the region; and 4. evaluate the significance of the coastal wetlands in the region. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

Great Barrier Reef Fish Biological Data

Biological measurements on fish sampled during the course of FRDC funded project Growth, Reproduction and Recruitment of Great Barrier Reef Food Fish Stocks (FRDC 90/18). The comma-delimited ascii file comprises the following fields: 1. Cruise number 2. Date (d-m-y) 3, Region (descriptor of part of Queensland coast or Great Barrier Reef system) 4. Reef (name or number) 5. Data source (Res=research, Rec=recreational fisher, Com=commercial fisher) 6. Capture method 7. Trap number (where appropriate) 8. Species name 9. LthStd (standard length, cm) 10. LthFrk (fork length, cm) 11. LthTot (total length, cm) 12. WtTot (approx total weight, g; weighed at sea) 13. FrameWt (weight of frame [after filleting, with viscera], g; weighed in lab) 14. Sex (macroscopic examination only) 15. GonadWt (g) Data obtained by the Department Employment, Economic Development and Innovation (formerly Primary Industries and Fisheries) between 1988 and 1993, primarily in the southern Great Barrier Reef (Capricorn-Bunker and Swain Groups), with fish traps and handlining.

Survival of graded scallops amusium balloti in Queensland's (Australia) trawl fishery.

In the Queensland, Australia, scallop fishery, the scallop catch is graded at sea using a specially designed grading machine called a "tumbler." Experiments were conducted to determine the effect of repeated trawl capture, grading, and discarding on the survival of sublegal saucer scallops Amusium balloti. Scallops were caught within an area closed to commercial fishing and known to contain dense scallop beds. The trawled scallops were randomly divided into 2 groups, tumbled and control, and subjected to up to 4 tumbles and/or trawls before being caged for 2.5 days adjacent to the trawl grounds. Increased levels of both trawling and tumbling were found to decrease significantly the survival of sublegal scallops. Although 83% of scallops survived repeated intensive trawling (4 consecutive tows), survival fell to 64% when scallops were also graded using a commercial tumbler. Survival was high for both tumbled and control sublegal scallops after 1 trawl (97% and 98%, respectively).

Characterization of commercial cultivars and naturalized genotypes of Stenotaphrum secundatum (Walter) Kuntze in Australia

Stenotaphrum secundatum (Walter) Kuntze, known as "St Augustinegrass" in the USA and "buffalo grass" in Australia, is a widely used turfgrass species in subtropical and warm temperate regions of the world. Throughout its range, S. secundatum encompasses a great deal of genetic diversity, which can be exploited in future breeding programs. To understand better the range of genetic variation in Australia, morphological-agronomic classification and DNA profiling were used to characterize and group 17 commercial cultivars and 18 naturalized genotypes collected from across Australia. Historically, there have been two main sources of S. secundatum in Austalia: one a reputedly sterile triploid race (the so-called Cape deme) from South Africa now represented by the Australian Common group naturalized in all Australian states; and the other a "normal" fertile diploid race naturalized north from Sydney along the NSW coast, which is referred to here as the Australian Commercial group because it has been the source of most of the new cultivars recently developed in Australia. Over the past 30 years, some US cultivars have also been introduced and commercialized; these are again "normal" fertile diploids, but from a group distinclty different from the Australian Commercial genotypes as shown by both DNA analysis and grouping based on 28 morphological-agronomic characteristics. The implications for future breeding within S. secundatum in Australia are discussed.

Raw data for project "Development of a DNA based aging technique for use in fisheries assessments" Fisheries and Development Corporation project 2007/033

The primary aim of this study was to determine the relationship between telomere length and age in a range of marine invertebrates including abalone (Haliotis spp) oysters (Saccostrea glomerata), spiny lobsters (Sagmariasus verreauxi formerly Jasus verreauxi and Jasus edwardsii) and school prawns (Metapenaeus macleayi). Additionally, this relationship was studied in a vertebrate organism using the freshwater fish Silver perch (Bidyanus bidyanus). Telomere length differences between tissues were also examined in some species such as Saccostrea glomerata, Sagmariasus verreauxi and Bidyanus bidyanus. In some cases cultured specimens of known age were used and this is quoted in the spreadsheets. For other wild-caught specimens where age was not known, size was used as a proxy for age. This may be a broad size class, or be determined by shell size or carapace length depending on the organism. Each spreadsheet contains raw data of telomere length estimates from Terminal Restriction Fragment Assays (TRF) for various individuals of each species including appropriate details such as age or size and tissue. Telomere length estimates are given in base pairs (bp). In most cases replicate experiments were conducted on groups of samples three times but on a small number of occasions only two replicate experiments were conducted. Further description of the samples can be found in final report of FRDC 2007/033. The arithmetic average for each individual (sample ID) across the two or three replicate experiments is also given. Bidyanus bidyanus (SilverPerch) Two sheets are contained within. a) Comparison of telomere length between different tissues (heart, liver and muscle) within the three year old age class - two replicate experiments were conducted. b) Comparison of telomere length between fish of different but known ages (0.25, 1, 2, and 3 years old) in each of three tissues, heart, liver and muscle – three replicate experiments were conducted per tissue. Haliotis spp (Abalone species) Three species were tested. H. asinina Telomere length was compared in two age classes-11 month and 18 month old abalone using muscle tissue from the foot. Within gel-variation was also estimated using a single sample run three times on one gel (replicate experiment). H. laevigata x H. rubra hybrids Telomere length was compared in three known age classes – two, three and four years old using muscle tissue from the foot. H. rubra Telomere length was compared in a range of different sized abalone using muscle tissue from the foot. Shell size is also given for each abalone Saccostrea glomerata Three sheets are contained within the file. a) Samples came from Moreton Bay Queensland in 2007. Telomere length was compared in two tissues (gill and mantle) of oysters in three age groups (1, 3 and 4 years) b) Samples came from Moreton Bay Queensland in 2009. Telomere length was compared in three age classes using DNA from gill tissue only c) Samples came from Wallis Lake, New South Wales. Telomere length was estimated from whole body minus the shell from 1 year old oysters, gill tissue of 3 age classes (1.5 years, 3 and 4 years), mantle tissue of two age classes (3 and 4 years). Sagmariasus verreauxi (formerly Jasus verreauxi) Telomere length was estimated from abdomen tissue of puerulus, gill and muscle tissue of 3 year old, large and very large size classes of lobsters. Jasus edwardsii Telomere length was measured in two size classes of lobsters- adults of varying sizes using muscle tissue and puerulus using tissues from the abdomen minus the exoskeleton. Metapenaeus macleayi Telomere length was measured in three size classes of school prawns adults. Muscle tissue was used, minus the exoskeleton.

Grey Mackerel (Scomberomorus semifasciatus) microsatellite genotypes (nine loci) representing twelve regions along Australia's northern coastline from the eastern coast of Queensland to the western coast of Western Australia.

Scomberomorus semifasciatus is an Australian endemic found in tropical, coastal waters from eastern to western Australia. Commercial and recreational exploitation is common and regulated by state-based authorities. This study used mitochondrial DNA sequence and microsatellite markers to elucidate the population structure of Scomberomorus semifasciatus collected from twelve, equidistant sampling locations. Samples (n=544) were genotyped with nine microsatellite loci, and 353 were sequenced for d-loop (384 bp) and ATP (800bp) mitochondrial DNA gene regions. Combined interpretation of microsatellite and mtDNA data identified four genetic stocks of S. semifasciatus: Western Australia, northwest coast of the Northern Territory, Gulf of Carpentaria and the east coast of Queensland. Connectivity among stocks across northern Australia from the Northern Territory to the east coast of Queensland was high, but in contrast, there was a clear genetic break between populations in Western Australia compared to the rest of northern Australia. This indicates a restriction to gene flow possibly associated with suboptimal habitat along the Kimberley coast (northwestern Australia). The appropriate scale of management for this species corresponds to the jurisdictions of the three Australian states, except that the Gulf of Carpentaria stock should be co-managed by authorities in Queensland and Northern Territory.

Spatial subdivision among assemblages of Spanish mackerel, Scomberomorus commerson (Pisces: Scombridae) across northern Australia: implications for fisheries management

Aim: This study investigated the use of stable δ13C and δ18O isotopes in the sagittal otolith carbonate of narrow-barred Spanish mackerel, Scomberomorus commerson, as indicators of population structure across Australia. Location: Samples were collected from 25 locations extending from the lower west coast of Western Australia (30°), across northern Australian waters, and to the east coast of Australia (18°) covering a coastline length of approximately 9500 km, including samples from Indonesia. Methods: The stable δ13C and δ18O isotopes in the sagittal otolith carbonate of S. commerson were analysed using standard mass spectrometric techniques. The isotope ratios across northern Australian subregions were subjected to an agglomerative hierarchical cluster analysis to define subregions. Isotope ratios within each of the subregions were compared to assess population structure across Australia. Results: Cluster analysis separated samples into four subregions: central Western Australia, north Western Australia, northern Australia and the Gulf of Carpentaria and eastern Australia. Isotope signatures for fish from a number of sampling sites from across Australia and Indonesia were significantly different, indicating population separation. No significant differences were found in otolith isotope ratios between sampling times (no temporal variation). Main conclusions: Significant differences in the isotopic signatures of S. commerson demonstrate that there is unlikely to be any substantial movement of fish among these spatially discrete adult assemblages. The lack of temporal variation among otolith isotope ratios indicates that S. commerson populations do not undergo longshore spatial shifts in distribution during their life history. The temporal persistence of spatially explicit stable isotopic signatures indicates that, at these spatial scales, the population units sampled comprise functionally distinct management units or separate ‘stocks’ for many of the purposes of fisheries management. The spatial subdivision evident among populations of S. commerson across northern and western Australia indicates that it may be advantageous to consider S. commerson population dynamics and fisheries management from a metapopulation perspective (at least at the regional level).