Use of rpoB and 16S rRNA genes to analyse bacterial diversity of a tropical soil using PCR and DGGE.
OBJECTIVE
To evaluate the rpoB gene as a biomarker for PCR-DGGE microbial analyses using soil DNA from the Cerrado, Brazil.


METHODS
DNA extraction from soil was followed by Polymerase Chain Reaction (PCR) amplification of rpoB and 16S rRNA genes. PCR products were compared by Denaturing Gradient Gel Electrophoresis (DGGE) to compare gene/community profiles.


RESULTS
The rpoB DGGE profiles comprised fewer bands than the 16S rDNA profiles and were easier to delineate and therefore to analyse. Comparison of the community profiles revealed that the methods were complementary.


CONCLUSIONS
The gene for the beta subunit of the RNA polymerase, rpoB, is a single copy gene unlike 16S rDNA. Multiple copies of 16S rRNA genes in bacterial genomes complicate diversity assessments made from DGGE profiles. Using the rpoB gene offers a better alternative to the commonly used 16S rRNA gene for microbial community analyses based on DGGE.
D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D015415:Biomarkers; D004269:DNA, Bacterial / Q000032:analysis; D012321:DNA-Directed RNA Polymerases; D017753:Ecosystem; D004591:Electrophoresis, Polyacrylamide Gel; D014644:Genetic Variation; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012988:Soil Microbiology
D015415:Biomarkers; D004269:DNA, Bacterial; D010940:Plant Proteins; D012336:RNA, Ribosomal, 16S; C101305:RpoB protein, Oryza sativa; D012321:DNA-Directed RNA Polymerases