NEW ZEALAND - DNA technology a 'game changer' for monitoring environmental impacts

New technology will deliver results in real-time so marine fish farms can know instantly if anything is changing in the ecosystems around their operations
August 14, 2014

Cawthron scientists have proved DNA technology can be used accurately and effectively to assess changes in the environment around marine-based operations.

Their findings have generated international interest – in particular from aquaculture, where there is huge potential for the technology. It will enable them to undertake environmental monitoring in near real-time.

\"This revolutionary DNA technology, while still in its infancy, will eventually deliver results in real-time so industries can know instantly if anything is changing in the marine ecosystems around their operations, and if necessary, they can respond and adapt their practices immediately – it\'s a game changer,\" Cawthron Institute Chief Executive Charles Eason said.

Marine-based industries such as aquaculture and off-shore and oil and gas operations are legally required to undertake regular monitoring to assess the effect their operations are having on marine organisms living in the seabed. Currently, environmental monitoring world-wide relies on either chemical analysis or identification of organisms using a microscope. It can take up to eight months to deliver results.

\"Current monitoring relies heavily on traditional taxonomy to analyse the ecological changes of thousands of organisms, which is time consuming, expensive and an area of shrinking capability worldwide,\" Cawthron Institute scientist and lead researcher Xavier Pochon says.

\"It can take decades to develop the skills to successfully identify microscopic organisms and, for organisms at the larval life stage, it\'s often impossible without the right expertise.\"

After two years of research, Dr Pochon and fellow Cawthron scientists Dr Susie Wood and Dr Nigel Keeley, in collaboration with Professor Jan Pawlowski from the University of Geneva, Switzerland, have proved that the health of the marine environment near aquaculture farms can be assessed by rapidly analysing the DNA of a group of microscopic single-celled organisms called foraminifera. These are abundant, diverse and highly responsive to environmental disturbance.

By extracting DNA from sediment samples they were able to determine simultaneously the unique signature of thousands of individual foraminifera. This technology, referred to as Next-Generation Sequencing (NGS), is a cheaper and faster way to monitor the impacts of changes to a natural environment.

For the past two years, the project has been in a \'proof of concept\' phase with the scientists trialling the technology for monitoring around salmon farms. They tested the new tool by analysing hundreds of sediment samples from aquaculture operations in New Zealand\'s Marlborough Sounds and from Stewart Island, in parallel with traditional monitoring methods.

The scientists found that the new system returned similar results as traditional methods, but in a fraction of the time and with potential to analyse many hundreds of species simultaneously.

The hope is that eventually, NGS will allow scientists to discover exactly what is living in an area via an automated process within days; by providing faster results, industry will be able to respond much faster and environmental impacts may be minimised.

\"Worldwide, it currently takes between three and eight months to get results, that means these operations could have been breaching guidelines for months before they know about it, or they could have made costly and unnecessary adjustments only to find out that there was no problem,\" Dr Pochon says.

\"NGS will make a huge difference. In terms of speed, it\'ll be like going from dial up internet to ultra-fast broadband.\"

Their findings have already attracted interest from salmon farming industries in Scotland, Norway and the United Kingdom, where the sector is much bigger than New Zealand. Norway for example has 1200 salmon farms, whereas New Zealand has around ten currently in operation.

\"Marine industries are very excited about this – they need a tool that allows them to affordably increase the frequency of their monitoring, while providing an almost real-time result, reducing the cost and demonstrating environmental sustainability.\"

The researchers are now working on phase two of the project, which involves comparing year to year results from the same locations in the Marlborough Sounds, Stewart Island, Norway, Scotland and the Faroe Islands over a three year period.

They will also expand their method from finfish aquaculture, to mussel aquaculture and the oil and gas sectors, while investigating the benefits of including other potential indicator organisms in samples.

\"In addition to the exciting commercial potential of the method, the research has led to the discovery of several new species of foraminifera, contributing to a better understanding of New Zealand\'s biodiversity,\" Dr Pochon says.

Their research has so far received funding from the Ministry of Business, Innovation and Employment, and in-kind support from New Zealand King Salmon Ltd, while Cawthron itself has invested around $80,000 in a liquid workstation \'robot\' which enables rapid processing of hundreds of samples simultaneously.

The results of their research will be published in two international peer-reviewed journals at the end of the year.