A molecular strategy for the study of natural bacterial communities by PCR-based techniques

The microbial ecology studies on bacterial communities implies the analysis of their composition, structure and dynamic and so the identification and typing of its members. Many conventional and molecular methods are routinely used for this purpose, but in spite of the availability of so many techniques, it lacks of a sound experimental approach to study the composition, structure and dynamic of natural bacterial communities based on reliable, rapid and reproducible methods. Here we define a molecular approach to the study of bacterial populations isolated from natural environment which takes advantage of PCR-based techniques: ARDRA (Amplified Ribosomal DNA Restriction Analysis), direct sequencing of 16S rDNA for the identification of bacterial isolates, and the RAPD (Random Amplified Polymorphic DNA) for the discrimination of strains at intrasubspecific level. This strategy utilises these three techniques in a sequential manner in such a way as to obtain the characterisation and typing of the whole studied bacterial community strongly reducing efforts and time-consuming steps. This approach was utilised and tested for the study of bacterial communities isolated from three different environments: water soil and a coleopter. Results obtained suggested that the proposed strategy represents a reliable, rapid and relatively cheap method for the study of composition, structure and dynamic of natural bacterial community.