Current practices for slaughter of farmed Barramundi use ice slurry. The sector has undertaken preliminary research to understand impacts of harvest and slaughter methods on stress, product quality and fish welfare.
Further investigation is needed into practical and cost-effective application of rested harvest on farms, together with understanding how practices can be improved, for example understanding optimal ice slurry amount, timing, and crowding; and determining impact on flesh quality indicators (e.g. flesh pH, blood glucose and lactate and blood pH). Complementary to harvest method protocols, is the need to investigate the impact on stress of direct transfer of fish into ice slurry as a slaughter method.

The project focus contributes directly to the National priority of:
Improving productivity and profitability of fishing and aquaculture, by increasing profitability through better supply-chain connections (FRDC RD&E plan, 2015-20).
Similarly, the project addresses the NPIRDEF, Working together: the National fishing and aquaculture RD&E Strategy, 2010 value chain outcome of:
Fisheries and aquaculture are prosperous and viable; strategic research themes – growth and profitability; maximising value from aquatic resources.

Estimates of the age structure of fish populations are central to assessing the status of fished stocks, evaluating management strategies and the impact of fishing. Determining fish age is usually done by counting growth checks in fish otoliths. This is generally a laborious, time-consuming process involving considerable preparation of the otoliths (resin-embedding, cutting and polishing) prior to ring-counting. This proposal aims to develop and validate a rapid innovative method for ageing fish based on an analysis of otoliths by NIRS. With increasing costs and, in some jurisdictions, diminishing R&D budgets, collection and ageing of representative fish samples becomes increasingly difficult. If NIRS is as efficient at determining fish age as the preliminary study suggests, it will be a breakthrough of global significance.

Commonwealth and State legislation requires that fishery resources be managed sustainably. Age-based stock assessment methods are one of the most informative tools available for assessing Australia’s fisheries. The collection of otoliths from recreational and commercial catches is undertaken across a wide range of fisheries as part of fishery monitoring and assessment programs.

This proposal addresses the need and QFRAB priority for:

• Developing innovative tools and technologies for managing Australian fisheries

• Developing more efficient, cost-effective ways of obtaining the information needed to undertake age-based fishery assessments

• More reliable fishery assessments by improving the availability and quality of age information from fish population samples

Recreational fish stocking is widely practiced throughout Australia and has delivered considerable benefits to anglers and substantial economic flow-on effects have been previously documented in some fisheries (Rutledge et al. 1991). The long-term “success” of freshwater fish stocking in Queensland and other States is, however, contingent on demonstrating that it is an ecologically sustainable practice having no detrimental effects on wild populations and ecosystems. Some environmental groups and government agencies (e.g. Wet Tropics Management Authority) are now questioning if freshwater fish stocking is a sustainable activity and the Threatened Species Scientific Committee considered a nomination to list the introduction of live native or non-native fish into Australian watercourses that are outside their natural geographic distribution as a key threatening process. One of the criteria that fisheries managers now use for assessing freshwater fish stocking applications is the risk that they pose to local aquatic communities, although there is very little real information on the likely ecological and genetic impacts of native freshwater fish stocking activities to support this decision making process. This type of information is therefore urgently needed if our stocking industry is to adopt “world’s best practice” to ensure future sustainability.
These same concerns were expressed at a recent FRDC national expert workshop “Towards responsible native freshwater fish stocking” where the potential ecological and genetic impacts of fish stocking, particularly for barramundi and Murray cod, were nominated as the most pressing research and management issues. This proposed project and another being developed on Murray cod, are part of a coordinated national response to these critical issues.

Nodavirus in wild barramundi populations

* There is a need to address concerns about the effect of stocking hatchery-reared barramundi on the level of unapparent nodavirus infections (that is, the prevalence) in wild barramundi.
* The first step is to determine the prevalence of nodavirus in wild populations of barramundi (that is to say the natural level of nodavirus-carrier status – an infection without disease).
* The baseline nodavirus prevalence data will permit:
- comparison of barramundi populations in areas where stocking has or has not occurred,
- assessment of changes in prevalence of nodavirus in future years,
- effective decisions about appropriate sources of replacement broodstock for breeding programs.

Nodavirus in freshwater fishes

* There is a need to address concerns about the risk of possible lethal transmission of barramundi nodavirus to freshwater fishes.
* Recent investigations have shown a possible susceptibility of freshwater fishes to barramundi nodavirus and that nodaviruses naturally occur in species other than barramundi in Australia, including the freshwater species, sleepy cod.
* There is a need to determine if there are nodaviruses in freshwater fishes as a risk analysis for translocation should include disease-status information in the receiving population.

Are the nodaviruses found in freshwater fishes related to barramundi nodavirus?

* If nodaviruses are detected in freshwater fish an analysis of relatedness (sequence analysis of PCR products) could indicate an association to previous stocking in that area of hatchery-reared barramundi. This information would support effective risk analysis for future translocation considerations.

A testing protocol for hatchery production of nodavirus-free fish fry.

* Broodstock screening protocols to identify nodavirus-free broodstock have been described from overseas but the detection tests used then are not as sensitive as the two-step or nested RT-PCR, and the protocols include a requirement for egg/water disinfection and repeat testing of larvae.
* There is a need to evaluate and validate the sensitivity of the two-step or nested RT-PCR to identify nodavirus-free broodstock and to determine if one or more tests are required to confirm the nodavirus-free status.
* There is a need to confirm in barramundi that larvae/fry become infected by nodavirus through the vertical transmission route (ie., from their parent(s)).
* There is a need to determine if fry can become infected via nodavirus-contaminated water once they are stocked into nursery systems.
* If the vertical infection route is the same for all fish species, the information on the testing protocol required to produce nodavirus-free barramundi fry will be a model testing protocol applicable to all fish species in breeding programs in Australia.

Freshwater allocations to sustain fisheries

The 1994 COAG Water Reform Agreement and various state legislation (e.g. Water Act 2000 in Queensland) requires managers to allocate water to maintain downstream ecosystem health. One aspect of ecosystem health is estuarine and coastal fisheries production. Information on the role of freshwater in maintaining the productivity of commercial and recreational fisheries is needed to ensure that estuaries and their stakeholders are duly represented in the water allocation processes. Natural resource managers (fisheries and water) need to be made aware of the fishing industry’s vulnerability to the impacts of non-fishing activities, such as water regulation. This issue has been identified as a challenge for the fishing industry in reaching sustainable production (see Challenge 1 of FRDC’s R&D Plan 2000, page 59).

Logical frameworks for research leading to new procedures and methods

A logical framework needs to be developed for investigating the role of freshwater flows in estuaries. Procedures to assess the impacts of current and proposed water infrastructure in Australian coastal rivers on estuarine fisheries need to be developed. Methods for monitoring biological responses to environmental flows are needed to provide feedback to managers as to whether desired fisheries-related outcomes are being achieved under current water allocations.

Enhancing the research outcomes - integrating across research disciplines

An integrated research program is needed to develop a robust sampling proceedures that can investigate the role of freshwater flows in estuaries and the impacts of modified flows on fisheries production. The CZCRC offers the opportunity to integrate flow-influenced fisheries data with other hydrological (i.e. costal modelling) and primary productivity (i.e. nutrient cycling) research projects that will provide greater insight into ecosystems processes.