The European Community produces every year 200 million tonnes of biodegradable wastes, which have to be diverted from land-filling according to European laws. Biological digestion, either aerobic or anaerobic, is the most environmentally favourable option f or the recycling of biowastes. Composts resulting from these processes are used as soil improvers, which, among other benefits, exert plant disease supressiveness due to the presence of microorganisms that are antagonists to pathogens. However, improperly treated composts may spread pathogenic microorganisms, thus damaging the environment and posing risks to human health. This causes concern among the general public, especially after the food alerts during the last decade, and constitutes a priority issue within the European Research Area.
Therefore, a tool that allows the quick analysis of compost microbiota is needed to safeguarde its agronomic value. DNA biochip technology offers the possibility to simultaneously detect an entire array of micro-organisms. The host group has recently designed a micro-array addressed towards compost microbiota. This proposal aims to design an oligonucleotide micro-array to detect signature microorganisms in composts from anaerobic digestion. Micro-organisms that will be isolated from compost will be targeted. Additional probes will be selected on basis of sequences determined from bands in DGGE gels run with compost DNA. Oligonucleotide probes will be designed using sequence differences in the 16S rDNA gene and printed onto the arrays.
Fluorescently labelled DNA will be prepared and hybridised, and the arrays analysed by fluorescent screening. The validation of the micro-array will be mainly conducted through spiking experiments and through their wide application to already characterised compost samples. If successful, the micro-array might permit assessing whether soil improvers meet hygiene demands, thus increasing their marketability and promoting confidence among European consumers
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