Much to be learned from creative solutions

5 Feb 2009 Unit: Plant Research International The soil is een black box. We hardly know anything about the bacteria and fungi living in the soil. Metagenomics, which studies all DNA from an ecosystem at the same time, helps to increase our knowledge. Together with European colleagues Leo van Overbeek of Plant Research International worked on the optimisation of this still relatively unknown technique. The group of scientists studies agricultural soils that are known to be disease-suppressing. Antibiotics, capable of killing plant-pathogenic fungi, are expected to be present in the soil. Of all soil bacteria 99 per cent cannot be cultured in the lab; this makes DNA analysis of the species that are present impossible. The simultaneous analysis of all DNA from an ecosystem in any case reveals which DNA is present in the soil although it is not known from which organism it originates. The microbiologists have combined some well-known methods for extracting DNA from a soil sample, for cloning an undamaged DNA string, and for culturing the modified bacterium in the lab. This procedure means that the bacterium does not need to be alive provided that the DNA is intact. Development of this method was not an easy job. The team came across lots of problems while experimenting. Those problems have now been described in two publications: A procedure for the metagenomics exploration of disease-suppressive soils and The metagenomics of disease-suppressive soils – experiences from the METACONTROL project. “Problems are usually left undiscussed in publications. But precisely finding solutions and discussions about problems are important roads to learning more”, says Van Overbeek. The researchers have already discovered much news but direct applications have not yet been forthcoming. The DNA order of the micro-organisms found are in a worldwide database compared with other genetic material. But a match could not yet be found for many samples. The material of which it is unknown from which organism it originates is for the time being also stored in the database. The scientists can use this material if similar material would be found in the future.

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