Sustainable finfish aquaculture is dependent on a benthic environment that can assimilate and process farm particulate wastes. As outlined above, in MH, bottom and mid water DO levels have reached very low levels and we have observed an associated increase in the presence of bacterial mats and a significant decline in the abundance and diversity of benthic fauna. As a consequence, multiple cage sites across the harbour are now subject to mandatory fallowing. The challenge facing farmers and regulators is understanding and predicting the length of fallowing required for benthic recovery; this has major implications for future stocking plans in the harbour. FRDC project 2014/038 and 2015/024 provide the benthic baseline over the past 2 years of farming; repeating these surveys following the observed decline in oxygen levels and fauna is needed to understand benthic recovery following fallowing. It is clear that DO levels have been, and will be, a major determinant of the benthic response over the coming months and years. Thus, it is imperative that real time observations of DO levels are coupled with the benthic observations. However, it is also extremely important to improve our understanding of the drivers of oxygen drawdown and recharge, including identifying the flushing rates of the various bays and basins in the harbour as it is not just how low the oxygen levels get, but also how long they stay low that will influence ecological outcomes. The existing CSIRO Hydrodynamic and Oxygen Transport Model can help to address these critical questions.

The future of salmon farming in Macquarie Harbour depends on its long term environmental sustainability. This project will help inform the likely effectiveness and duration of any given fallowing or remediation strategy, and as such is essential for both operational management of farming activities and the long-term management of the harbour.

Whirling Disease is a chronic, debilitating wasting disease caused by Myxobolus cerebralis, a protozoan parasite. While the intermediate host of the parasite, a tubifex worm, is present in Australia, the parasite has never been detected in this country. It is however present in New Zealand where the bulk of salmonid imports into this country currently originate from. It is difficult to detect in imported fish. Infective spores can survive for considerable periods in fresh and frozen fillets.
Overseas it is a disease of salmonids; non salmonids have also been reported to be hosts.
There is a significant population of salmonids in Australia that would be susceptible to this disease were an outbreak to occur. These populations are valuable both commercially and recreationally.
It is extremely important to have in place options for dealing with an outbreak of the disease to minimize the impact of such an outbreak should it occur. It is also highly beneficial that such options have been considered and agreed to by relevant stakeholders before the emergency occurs. Such options would acknowledge this disease may be insidious in its onset so may go undetected for a long time. Spores can also survive the passage through the gut of birds.
While the Federal Government encourages a detection and eradication culture based on constant vigilance and a readiness to tackle any emergency, there are currently no accepted national guidelines for dealing with an outbreak of an exotic parasitic disease in finfish in Australia.
Hence there is a need to have a Disease Strategy Manual for Whirling Disease that describes details about the disease, response options and the preferred, nationally agreed-upon approach to its control. This is supported by the FRDC’s Subprogram’s Steering Committee who, through consultation with stakeholders from industry and governments have determined as a priority the need for this Manual.