Methodological constraints in the molecular biodiversity study of a thermomineral spring cyanobacterial mat: a case study.

The biodiversity of a specific cyanobacterial mat associated to a thermomineral spring from the Western Plain of Romania was investigated. Light and electron microscopy, together with molecular tools (denaturing gradient gel electrophoresis-DGGE, automated ribosomal intergenic spacer analysis-ARISA and amplified ribosomal DNA restriction analysis-ARDRA), based on 16S rDNA and 16S-23S internal transcribed spacer markers were used. Based on the partial 16S rRNA fragments sequenced, eight cyanobacterial taxons were identified, all belonging to the Oscillatoriales order, Phormidium and Leptolyngbya being dominant. A significant difference was observed, in comparison with the morphological approach. In certain conditions, DGGE can provide misleading information due to multiple melting domains in the same sequence, to multiple rrn operons in the same genome and due to unspecific hybridization among closely related sequences. This can lead to an overestimated species abundance which can cause incorrect description of the microbial community investigated. Additional techniques, such as ARISA and ARDRA, can improve the microbial biodiversity studies, thus providing optimal results.