Project number: 2001-102
Project Status:
Budget expenditure: $464,739.00
Principal Investigator: Maylene Loo
Organisation: SARDI Food Safety and Innovation
Project start/end date: 30 Jan 2002 - 27 Mar 2007


Cage-culture of marine finfish is an increasingly important economic activity in regional Australia however, the longer-term development of the industry requires that operations be undertaken in a manner that ensures the continued health of the marine environment and recognises the conservation values society places on its marine ecological assets. In particular, there is a need to better understand the relationship between farm management practices and the environmental effects of sea-cage aquaculture. Community concerns about tuna farming have focussed on impacts to marine ecosystems where the ability to quantify impacts and optimise farm management practices is of fundamental importance in securing tenure for licence holders. Importantly, because the health of the seabed also influences the water quality in and around farms, an understanding of the relationship between farm management and souring of the benthos will provide significant outcomes in terms of optimising productivity and product quality.

Traditional approaches to the assessment of ecosystem responses to cage-culture require detailed assessment and enumeration of benthic infaunal communities that are both expensive and time consuming (see eg Cheshire et al. 1996a, b). This severely limits the extent to which the conventional methods can used for monitoring and assessment. There is a need therefore, to develop tools which allow for the rapid assessment of ecosystems responses in order to provide for the cost-effective monitoring of farming systems as well as to test the effectiveness of new management practices or technologies. The resultant lack of information about these issues presents major risks to industry including uncertainty of tenure and a lack of any capacity to relate changes in farming practices to changes in ecosystems health, productivity or product quality.

To achieve these changes we need a scientifically defensible, rapid assessment system for predicting and evaluating the environmental impacts of sea-cage aquaculture. The PCR system detailed in this proposal will provide potential savings of >50% in the cost of processing samples and improve turn around times from (typically) 3-4 months to less than 1 week. This will enable industry to investigate a wide variety of issues including the relationship between farm management practices, cage technologies and the environmental outcomes of cage farming systems.


1. To identify a range of benthic infaunal species and possibly ecosystem processes (sulphur reduction / methanogenesis) which are variously characteristic of sites ranging from heavily impacted (organically polluted) tuna sea-cages through to non-impacted (pristine) environments.
2. To develop a system for the rapid detection of selected taxa in sediment samples using PCR techniques.
3. To evaluate the extent to which rapid detection systems can be routinely applied to provide quantitative estimates of the relative abundance of indicator taxa or processes in sediments (and therefore of the health of seabed systems).
4. To assess the generality of the technique to other forms of aquaculture (particularly salmon).
5. Improve the sensitivity of the assays to levels comparable with terrestrial systems.
6. Develop PCR assays for 3 additional taxa
7. Quantitatively calibrate all 5 assays (existing and new assays)
8. Demonstrate the "proof of application" of this methodology in comparison with traditional, manual enumeration methods.
9. Further clarify the phylogentic relationship in spionidae and evaluate the need for multiple spionidae assays.

Final report

Related research


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