Specific detection of rhizobia in root nodules and soil using the polymerase chain reaction

The polymerase chain reaction (PCR) amplification of specific DNA sequences, allows specific and sensitive detection of bacteria at the genus, species or strain level depending on the design of the oligonucleotide primers. In this study we utilized 20 mer primers that flanked a 300 bp region of the npt II gene of the transposon Tn5 thus allowing for the amplification of this region. Insertion of the Tn 5 element into rhizobia allowed for detection of these cells using PCR amplification. Using the npt II-specific primers and Tn5 insertion mutants of Rhizobium leguminosarum bv. phaseoli we were able to detect these specific rhizobia strains in root nodules of bean plants and in inoculated soils. Utilization of genus-specific gene sequences would allow for estimates of cells of that genus in environmental samples. Conversely, use of gene sequences common to rhizobia, e.g. nif and nod sequences, would give estimates of the population of rhizobia. This paper serves to illustrate the use of PCR, for detecting gene sequences in an environmental sample such as a root nodule.