New Primers for Denaturing Gradient Gel Electrophoresis Analysis of Nitrate-Reducing Bacterial Community in Soil

The narG gene is frequently used as a molecular marker for bacterial nitrate-reducing community analysis. In this study, a new set of primers targeting the narG gene was designed and applied to semi-nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay. The potential of the new primers was verified on DNA directly extracted from soils from five different experimental sites distributed in Central and Southern Italy. Specificity of the primers was determined by excision, amplification, and sequencing of bands resolved by DGGE. A phylogenetic analysis showed the correlation between the sequences retrieved from the soils studied and the narG sequences from β and γ-Proteobacteria. These primers expanded the existing molecular tools for ecological study on the size and diversity of nitrate-reducing bacterial community in soil.