Protecting Europe's crops and woodland from pests and pathogens
In the UK, Plant Health Officials are approving a newly developed portable DNA testing device for disease diagnosis. They are checking for ash dieback, the spore-borne disease caused by the fungus Chalara fraxinea which, according to the UK Forestry Commission, has infected more than 330 sites in the UK and resulted in the destruction of tens of thousands of young trees. A sample of infected bark is taken from an ash tree and prepared in a manner which can amplify and detect DNA from the organism. The result is available within minutes - rather than the days it would have taken if the sample had been sent for laboratory analysis. Since speed is of critical importance in diagnosing such disease outbreaks, this is a major step forward.
The development of the Genie II portable DNA device was one of the several advances achieved by Q-DETECT, a three-year research project which started in 2010 with the support of European Union (EU) funding, to pioneer simple, user-friendly methods of detecting and monitoring a wide range of plant pests and pathogens that threaten European crop and forestry output.
European rules currently list some hundreds organisms that are subject to quarantine control. They include, for example, viruses, bacteria, fungi, insects and nematodes (roundworms) – and they are estimated to cost Europe billions of Euros every year. Given a chance, these pests and pathogens spread rapidly, so speedy detection and response are vital. Bringing together 15 partner organisations - not only from Europe but also, reflecting the international significance and scope of the issue, Peru and China as well - the Q-DETECT project faced a complex challenge. Not only did it have to develop detection methods which were easy to use in situ, capable of providing reliable and quick results, but it also had to confront the reality that the sheer variety of quarantine plant pests or pathogens to be guarded against meant that no single detection method would be sufficient. A whole arsenal of weapons was required.
In addition to the portable DNA testing, one of the areas the Q-DETECT researchers focused on was using the sense of smell to ‘sniff out’ contamination by plant pests, developing devices such as electronic noses or laser-based spectroscopes to detect the volatile compounds known to be emitted by plants in response to infection.
Remote imaging provided another productive avenue of research for Q-DETECT. Seen through the near infrared part of the spectrum, for example, diseased or damaged vegetation is much less reflective than healthy crops. As Q-DETECT’s project coordinator, Dr Neil Boonham of the UK’s Food and Environment Research Agency points out, this approach has been made all the more relevant as a result of the emerging availability of unmanned high-altitude vehicles, such as one recently developed by Rutherford Appleton Laboratory, one of the Q-DETECT partners.
Acoustic detection was a third method investigated by the project, with the development of devices carefully tuned to identify the distinctive sounds made by various wood-boring insects - including the Asian Longhorn Beetle. Finally, Q-DETECT also developed the use of physical traps to capture and monitor pests – including ‘smart traps’ able to remotely record and transmit images of what is caught.
Some of the techniques developed by Q-DETECT are already available for use or close to being so, such as portable DNA testing. Others, such as laser spectroscopy, require further research. But the ultimate aim of Q-DETECT was not just to develop the tools, says Dr Boonham. It was also to model the inspection processes themselves in order to provide detailed guidance on how the new techniques could practically be used by inspectors in their day-to-day work. “If sniffing techniques were used, for example, how would they be used? At what point in the chain? This was an important part of the work, moving from blue-sky thought to real application,” Dr Boonham emphasises.