Design and development of the ANAEROCHIP microarray for investigation of methanogenic communities

The aim of this study was to design a microarray targeting methanogens found in anaerobic digesters, and to apply this chip together with a cloning approach to investigate the methanogenic community present in an anaerobic digester. Oligonucleotide probes were designed based on sequence differences in the 16S rRNA genes in order to target microorganisms in situ. For microarray hybridisations, DNA was subjected to PCR amplification of the 16S rRNA gene and Cy5-labeled. The microarray was tested with pure cultures, and of the 1854 individual probe-target hybridisation reactions performed, there were only 28 false positive (1.5%) and 16 false negative signals (0.86%). The sensitivity of the array was also tested, and it was found that when 0.4pg of DNA from a pure culture was subjected to PCR amplification, signals above the detection limit were obtained. Also, the application of 25ng of PCR product from a pure culture to an array resulted in detectable signals. The ANAEROCHIP was hybridised with DNA from an anaerobic sludge. Strong hybridisation signals were obtained for Methanoculleus, and weaker signals, in decreasing order, were obtained for Methanosarcina, Methanobacterium, Methanobrevibacter, and Methanosphaera. In order to check the results obtained with the microarray, the archaeal community structure of the same digester was analysed by 16S rRNA gene cloning and sequencing. Community structure was determined by restriction digestion of almost 200 clones and by sequencing of the 15 different resulting patterns. Methanoculleus was the dominant (84.1%) microorganism in the anaerobic sludge, and Methanobrevibacter (5.8%), Methanobacterium (3.7%), Methanosarcina (2.1%), Methanosphaera (1.6%), an uncultured archaeon (1.6%) and Methanothermobacter (1%) were also detected. These results showed the microarray to be a suitable tool for studying methanogenic communities in sludge.