Policing environmental compliance at salmon farms could become cheaper and faster thanks to a new test using bacterial DNA.
New Zealand King Salmon's Clay Point salmon farm in the Tory Channel. Photo: LDR / Supplied
The Cawthron Institute has found analysing seabed samples from beneath fish farms by their bacterial DNA, and not by hand, will cut the cost of environmental monitoring in half, and shorten processing times from five months to four weeks.
Monitoring results help determine if farms in the Marlborough Sounds are sticking to best management practice guidelines laid down by the Government and Marlborough District Council.
Cawthron Institute marine phylogeneticist Xavier Pochon last week told the council that bacterial testing was a "very promising alternative" or a "very complementary method" to traditional methods, and ready to be "immediately integrated".
Salmon farm monitoring was currently "labour intensive" and involved taking samples from several points beneath a farm in the late spring, then identifying and counting invertebrates.
Results were reported back in early autumn, several months later, as identifying invertebrates caused a "major bottleneck".
But Pochon said tested environments could have changed during the "time lag", making it hard for the council to be sure if steps to fix problems were still necessary or appropriate.
"This is a huge problem. We need much faster and cost effective methods to give us a faster answer, essentially."
Cawthron Institute began studying "environmental DNA" left behind by marine organisms as an alternative solution in 2014, after it secured funding from industry, government and community heavyweights.
Cawthron Institute marine phylogeneticist Xavier Pochon presenting his report on using DNA to speed up environmental monitoring. Photo: LDR / Chloe Ranford
Instead of identifying and counting invertebrates, researchers "screen the environment" by extracting the DNA of fish farm samples and comparing them to a database of micro-organisms, which allowed them to see what they had found.
Mucus, sperm, eggs, full or partial body parts, and bacteria were all forms of environmental DNA, but bacteria had the strongest relationship with seabed enrichment, Pochon said.
"The simple fact that we can analyse hundreds of samples in the same round is quite fascinating, because you can really reduce the cost [and] reduce the turnaround time, effectively."
The study was done alongside traditional methods, so the two tactics could be compared, and researchers found DNA testing was "very effective" in capturing environment changes.
Results were presented to the Marlborough District Council in 2017 and to the Benthic Standards Working Group in 2018, which featured representatives from Cawthron Institute, NZ King Salmon, National Institute of Water and Atmospheric Research (NIWA), Fisheries New Zealand, and the council.
The group recommended a study on seven year's worth of samples from nine salmon farms, co-ordinated by Cawthron Institute, be run to ensure the new method was "robust".
This included samples from two Queen Charlotte Sound farms, two Tory Channel farms and two Pelorus Sound farms.
The study proved the method was affordable and versatile, but still had to be accepted by the working group on Friday.
If approved, Pochon suggested the council adopt a transition period where both the traditional monitoring method and new bacterial DNA method could be "analysed in parallel".
The council received his report, which had been referred onto next full council meeting on 27 February for adoption.
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