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CSI science benefits AN UPDATE FROM THE CAWTHRON INSTITUTE wo young Cawthron Institute scientists are involved in a ground-breaking research programme with significant implications for the aquaculture industry and the environment. Drs Xavier Pochon and Susie Wood, along with a scientist in Switzerland, are developing DNA-based techniques for use in environmental monitoring. "A decade ago this advanced detection method would have been considered science fiction, but now this CSI type research is available in the real world," Xavier says. "The science is developing at an incredibly fast rate, with new instruments with even greater sensitivities available every six months." The methods Xavier and Susie are using involve taking sediment, soil and water samples and through a detailed process, identifying biological communities within the sample based on its DNA or RNA. The ecological impact of any human-induced activity, including mining, sewerage disposal and aquaculture, in the natural environment is currently assessed by identifying the diversity of life around operation sites. As not all organisms respond equally to pollution, their distribution and abundance can be used to assess the degree of environmental disturbance, and thus help activate appropriate remedial actions. Traditionally, environmental monitoring has been in the form of chemical analysis or identification of organisms using a microscope. For example, the ecological impact of finfish farming such as with salmon, is currently assessed by identifying and enumerating a wide array of marine organisms living in the sediment of the seabed under farm structures. Although very effective, this approach can be timeconsuming, expensive, and reliant on expert taxonomists to identify each species. "It can take decades to develop the skills to identify microscopic organism successfully and for some organisms, such as planktonic larvae, it's impossible.The techniques we're developing will overcome these challenges and ultimately allow faster, cheaper and more sensitive detection of these critters," says Susie. Xaiver and Susie are currently collaborating with Cawthron Institute marine biologist Nigel Keeley and Professor Jan T NIGHT VISION ¥ THERMAL IMAGING Chosen by M.P.I. Fisheries, and Dunedin Marine Search & Rescue. $6,699.00 $1,447.00 Prices EXCLUDE GST. Contact us for more information. Archetype Precision Systems Phone 03 9700 570 Email: ant@acad.co.nz 8 ■ NZ AQUACULTURE ■ Thermal Imaging. See in 100% darkness, through fog and rain. Ideal for man-overboard emergencies. $16,900.00 MAY/JUNE 2013 Pawlowski, from the University of Geneva, Switzerland, on a project to evaluate whether 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 organisms are known to be abundant, diverse and highly responsive to environmental disturbance. The method used involves extracting DNA from sediment samples and the unique signature of thousands of individual foraminifera is determined simultaneously. This technology, referred to as Next-Generation Sequencing, will provide a cheaper and faster way to monitor the environmental impacts of changes to a natural environment and support environmental sustainability. "Eventually NGS will allow scientists to discover exactly what is existing within an area via an automated process within hours," says Susie. "By providing faster results, industry will be able to respond much faster and environmental impacts may be considerably reduced." There are other benefits too. Currently biosecurity monitoring in the marine environment does not include water column sampling but NGS has the potential to resolve this. Many marine pests have at least one part of their life cycle in which they inhabit the water column, and Xavier and Susie are also researching the potential of NGS to detect single marine invasive larva directly from complex environmental samples. Other Cawthron Institute scientists, including Drs Kirsty Smith and Jonathan Banks, are also developing similar NGS methods for the monitoring of harmful algal blooms and harmful microbes with important ramifications in seafood safety. NGS technology has tremendous potential for the early detection, management, and prevention of various pathogens and invasive species worldwide. So will science fiction becoming a reality mean that the skills of the likes of the taxonomist no longer be necessary? "Quite the contrary," Xavier says. "We have to have a catalogue of each organism and its DNA code, there are thousands of organisms that are yet to be morphologicaly identified and labelled with their genetic code, so they're definitely not able to relax for a long time yet!"