The biodiversity of micro-organisms is of paramount importance for the functioning of our biosphere. This basic component is however, often overlooked due to its microscopic size, and seems to obey the saying ‘Out of sight, out of mind'. To solve this shortcoming, novel molecular tools have been developed since two decades, and the DNA-chips are one of the most advanced methods that has been adapted for microbial diversity assessments and environmental monitorings. Because it was intractable to study the total bacterial diversity, we took a model system. We have studied the planktonic cyanobacteria in European freshwaters.

The cyanobacteria represent a well defined branch of the bacterial world, and play an important role in aquatic biotopes. They perform photosynthesis and produce oxygen, and are basic primary producers in the aquatic food chain. Moreover, planktonic cyanobacteria can form proliferations, called blooms, in summer and autumn. 30 to 50% of these blooms were shown to be toxic for animals and humans. Indeed, some planktonic cyanobacterial strains synthesize hepatotoxins and neurotoxins, of which the targets are the liver and the nervous system, respectively.

The DNA chip that we have designed allows to detect the presence of 25 kinds of cyanobacteria on the basis of a gene sequence that is currently used as taxonomic marker, the 16S ribosomal RNA gene. In addition, several probes were made on the basis of a gene involved in the synthesis of microcystin, the most frequent cyanotoxin in European waters. Not only the presence of the gene, but also the identity of 5 known toxin-producers can be determined. A patent was deposited in Finland, because we believe that this kind of novel tool can be used to monitor, in a fast and efficient manner, a large number of lakes and ponds.

As more people start using the chip and accumulate large data sets, it will be possible to map the diversity and toxicity of cyanobacteria in Europe with unprecedented precision. For the study of other micro-organisms, different probes should be designed. The format of the DNA chip (using the so-called universal chip with Zip codes) is very flexible and could accommodate more probes for different taxa.

Halting species loss by 2010 means that one knows which are the species present. For micro-organisms, the characterisation of alpha-diversity is still a challenge. This is the first step to determine which bacterial species are in risk of being lost.

Back to HOME.