Soil Community Analysis Using DGGE of 16S rDNA Polymerase Chain Reaction Products

Abstract

Separation of polymerase chain reaction (PCR)–amplified 16S rDNA products using denaturing gradient gel electrophoresis (DGGE) was tested as a means to study microbial community composition in bulk soil samples. DNA was extracted from six soils from agroecosystems in Norway and the USA under different agronomic treatments (crop, rotation, and tillage); one soil is contaminated with polyaromatic hydrocarbons (PAH, 700 mg kg −1 ). Two sets of primers specific for Bacteria (V3 and the V6/V9 regions of 16S rRNA) and another for Archaea (V3 region of 16S rRNA) were used to determine the contribution of each domain to the microbial community. Reproducible, characteristic profiles of the communities were obtained by DGGE separation of the PCR amplification products. The number of fragments resolved by DGGE indicated bacterial diversity was far greater than that of the Archaea in the agricultural soils examined. Only the soil contaminated with PAHs had reduced bacterial diversity, evidenced by a distinct DGGE profile. The results showed that the method is useful as an initial step to discriminate among communities because it is rapid and multiple samples can be easily screened. There are some limitations, but under highly selective conditions it is possible to distinguish communities from different soils and to indicate the presence of numerically dominant populations.