Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products

Separation of polymerase chain reaction (PCR)-amplified 16S rDNA products u sing denaturing gradient gel electrophoresis (DGGE) was tested as a means t o study microbial community composition in bulk soil samples. DNA was extra cted from six soils from agroecosystems in Norway and the USA under differe nt agronomic treatments (crop, rotation, and tillage); one soil is contamin ated with polyaromatic hydrocarbons (PAH, 700 mg kg(-1)). Two sets of prime rs 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 contributio n of each domain to the microbial community. Reproducible, characteristic p rofiles of the communities were obtained by DGGE separation of the PCR ampl ification products. The number of fragments resolved by DGGE indicated bact erial diversity was far greater than that of the Archaea in the agricultura l soils examined. Only the soil contaminated with PAHs had reduced bacteria l diversity, evidenced by a distinct DGGE profile. The results showed that the method is useful as an initial step to discriminate among communities b ecause it is rapid and multiple samples can be easily screened. There are s ome limitations, but under highly selective conditions it is possible to di stinguish communities from different soils and to indicate the presence of numerically dominant populations.