Micro-Arrays for the Detection of the Abundance and Distribution of Pathogenic Protozoa, Flagellated Algae and Diatoms (EU project MICROPAD)

The environment is experiencing rapid and accelerating changes, largely originating from human activity, whether coming from local impacts or from the more dispersed effects of global climate change. Widespread realisation that biodiversity is strongly modified by these changes has generated plans to conserve and protect biodiversity in many parts of the world. Adequate ecosystem functioning and the continued use of the goods and services that ecosystems provide to humans depend on maintaining biodiversity. Thus, it follows that recognising and documenting biodiversity at all levels is essential for preserving biodiversity. Generalisations concerning biodiversity patterns on all scales, the mechanisms that determine these patterns, and the consequences of biodiversity loss, are largely derived from the terrestrial ecosystems and may not be applicable to all aquatic ecosystems. Only now we are developing the tools required to adequately document the microbial diversity on routine basis. These tools are arising from the combination three powerful techniques, namely analytical flow cytometry, artificial neural nets and molecular probes. The latter coupled with mircorarray construction provides a novel technique to quantify the abundance and distribution of microorganisms in a rapid and sensitive method.
 
DNA microarray technology allows the parallel analysis of a large number of hybridisations in one experiment. A DNA microarray consists of a glass-slide with spots of nucleic acids in the form of oligonucleotides, PCR-products, cDNA etc. Currently DNA microarrays exist with numbers of spots as high as 100.000 spots cm^-2. The detection of a hybridisation occurs via a fluorecent label attached to the target-DNA, that is hybridised to the DNA microarray.
 
The main focus of project is the design of phylogenetic DNA microarrays with oligonucleotide probes specific for the identification of selected protozoa and algal species in order to evaluate waterquality, ecosystem dynamics and augment the understanding of biodiversity.
 
The project is done in collaboration with the University of Camerino (Italy) and the University of Delft (Netherlands). At the University of Camerino, microarrays are designed for the detection of diatoms in the assessment of water quality in freshwater systems, whereas the microarrays which are developed at the University of Delft are supposed to be used for the detection of pathogenic protozoans in aquatic ecosystems. The work at the AWI is dedicated to the development of a DNA-microarray for the detection of flagellated microalgae in long time series data for costal marine phytoplankton.