Assessment of the survival rate of microorganisms in the soil and assessment of the soil microbial biodiversity with the use of the DGGE technique

Only a small proportion of microorganisms living in the soil environment start growing on nutrient media in the laboratory. For this reason, molecular techniques based on the analysis of DNA extracted directly from the soil are used to study the microbial diversity of soils. These techniques include the DGGE (Denaturating Gradient Gel Electrophoresis) technique based on the separation of PCR products in acrylamide gels. The DGGE technique consists in separating single amplicons of the same length, but differing in sequence, in a polyacrylamide gel, in a chemical gradient. This technique allows assessment of microbial diversity of soils, as well as precise identification of strains of microorganisms, which can be done by extracting DNA from individual bands in the gel and obtaining DNA sequences. Identification of bacteria by means of this technique is most often based on the analysis of the 16S rRNA gene, while the identification of fungi is based on the 18S rRNA gene.