Molecular genetic tools to detect didymo earlier
Drift net used for collecting samples
Once didymo has really taken hold in a river system, the thick and unsightly clumps of algae are all too obvious. An incursion can take a long time to reach this stage, however, and it can be present for some time before being noticed – even under a microscope.
Early detection of didymo in a waterway is vital for two reasons: it gives an opportunity to warn river users so steps can be taken earlier not to spread it further; and just as importantly, it provides a better opportunity to contain or suppress the alga in a river system should a suitable control tool become available.
Work carried out by Professor Craig Cary, Associate Professor Brendan Hicks and their team at the University of Waikato’s Centre for Biodiversity and Ecology Research for MAF Biosecurity New Zealand has made significant progress in the development of a reliable, specific and highly sensitive test for didymo at very low levels.
Craig Cary updated guests at the didymo science seminar, held in Wellington on 24 July, on progress with the research programme.
Highly sensitive tools
He explained that microscopy, the current detection method used to confirm the presence of didymo in a sample, is not able to detect didymo at levels as low as can been done using DNA techniques. The Waikato research team has been using highly sensitive molecular genetic tools to develop a reliable method for identifying didymo – a cost-effective analysis method that can be used in surveillance programmes and that can cope with high volumes of samples.
Specifically, the new methodology required:
- robust field capabilities
- specificity for Didymosphenia geminata
- extreme sensitivity for low-level detections
- a broad dynamic range of detection levels
- reproducibility
- efficient, cost-effective, rapid, high-throughput laboratory capability.
This is new scientific territory, and the researchers had to develop a system from the ground up, starting with the way samples were collected (a drift net proved the most reliable). Reliable DNA preservation and extraction methods also had to be developed.
That achieved, the scientists could then turn their attention to the real challenge: identifying a fragment of DNA from Didymosphenia geminata that could be used to reliably identify the alga, and clearly distinguish it from other freshwater diatoms. The key gene – 18S rDNA – was found to have the distinctiveness from other known species they needed, and using quantitative polymerase chain reaction (QPCR) to amplify this sequence, the researchers have laid the foundations for a reliable didymo analysis method.
Craig said rigorous laboratory validation was applied to the test, using three separate methods to confirm the DNA test was specific to didymo. It is also effective across a very broad range of cell concentrations, being able to detect didymo at levels of anything from 1 to 10,000 cells per millilitre.
The research team initially worked with field samples from eight locations in the South Island’s Buller, Gowan and Owen Rivers. Validation work also went international, including didymo samples from North America and Europe being used in the development of the analysis method.
The technology being used also has great potential to identify and distinguish genetically distinct populations of didymo, Craig said. This would assist greatly in tracing the movements of didymo and understanding how it may have been transported from place to place.
Looking ahead, Craig said the team will be refining their phylogeographic work to find out more about the origins of New Zealand’s didymo, and perhaps revealing whether it came from a single introduction or was introduced from multiple sources.
Beneficial for surveillance
A major strength of DNA analysis is in confirming a negative didymo status, and thus the method could be beneficial for use in didymo surveillance programmes in the North Island, where didymo has not been detected. Noting the importance of increased sampling pressure, he quoted invasive species specialist Daniel Simberloff, who has said that control at the earliest possible stage of invasion is much easier and cheaper than at any later stage. (See Biosecurity 78:6 for an interview with Dr Simberloff.)
Research team – Centre for Biodiversity and Ecology Research University of Waikato:
- Craig Cary, Brendan Hicks, Catherine Barnett, Chrissen Gemmill, Andreas Rueckert, Kathryn Coyne1
1University of Delaware, College of Marine and Earth Sciences
To download the research report (select Research Reports > Distribution):
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Page last updated: 24 June 2008