Science - November 9, 2009

Quick hunt for harmful worms via DNA test

Harmful worms can be identified at one go in soil samples with tens of thousands of these organisms. This can be done by the Dutch Plant Protection Service and analysis laboratory Blgg as a result of the phylogenetic tree with about 1,200 different nematode species published recently by the Laboratory of Nematology.

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Strict European legislations require flower bulbs, potatoes and vegetables, for example meant for export, to be constantly checked for the presence of harmful organisms. Even the soils on which they grow have to be free from harmful worms such as stem nematodes, potato cyst nematodes and carrot lesion nematodes. Screening laboratories for the agriculture and the horticulture sectors employ tens of analysts to look into such soil samples.
The work is difficult and time-consuming as Dutch soil is rich in nematodes (worms). Moreover, the harmful types are not easily distinguished from the useful ones. 'It was difficult to find staff who would stay on for this labour intensive and monotonous analysis work', says nematologist Hans Helder. 'This can now be done by a small number of trained general molecular analysts.'
Helder and his colleagues have charted the relationship of 1,200 nematodes in a phylogenetic tree. This is the first of its kind of such a magnitude which has ever been published. The tree is not yet complete but it covers a big part of the diversity found in northwest European soils. The major pathogenic organisms in agriculture and related species have been listed in detail. 'This is of great value in applications', says Helder.
Patents
The phylogenetic tree was already completed two years ago. In collaboration with technology organization STW, which financed the research, several work methods have been patented. 'These patents made it worthwhile for companies to invest in this detection technology', says Helder. In the meantime, Blgg has already introduced this knowledge as a new screening method in the market.
The method is based on a piece of genome which is responsible for the protein synthesis of nematodes. Helder can identify a nematode and whether it is harmful from reading its DNA sequence data.
The development of the phylogenetic tree has also given rise to some fundamental insight. 'We have tried to reconstruct evolution', says Helder. 'And in doing so, questions arise, such as: do the parasitic nematodes have ancestors? The answer seems to be: no, the plant and animal parasitic nematodes have all existed many times independently of one another during the course of evolution.'

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