title: Use of rpoB gene analysis for identification of nitrogen-fixing Paenibacillus species as an alternative to the 16S rRNA gene.
abstract: OBJECTIVE
  To avoid the limitations of 16S rRNA-based phylogenetic analysis for Paenibacillus species, the usefulness of the RNA polymerase beta-subunit encoding gene (rpoB) was investigated as an alternative to the 16S rRNA gene for taxonomic studies.
  
  
  RESULTS
  Partial rpoB sequences were generated for the type strains of eight nitrogen-fixing Paenibacillus species. The presence of only one copy of rpoB in the genome of P. graminis strain RSA19(T) was demonstrated by denaturing gradient gel electrophoresis and hybridization assays. A comparative analysis of the sequences of the 16S rRNA and rpoB genes was performed and the eight species showed between 91.6-99.1% (16S rRNA) and 77.9-97.3% (rpoB) similarity, allowing a more accurate discrimination between the different species using the rpoB gene. Finally, 24 isolates from the rhizosphere of different cultivars of maize previously identified as Paenibacillus spp. were assigned correctly to one of the nitrogen-fixing species.
  
  
  CONCLUSIONS
  The data obtained in this study indicate that rpoB is a powerful identification tool, which can be used for the correct discrimination of the nitrogen-fixing species of agricultural and industrial importance within the genus Paenibacillus.
authors.affiliation: Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Rio de Janeiro, Brasil.
authors.forename: F F
authors.initials: FF
authors.lastname: da Mota
authors.forename: E A
authors.initials: EA
authors.lastname: Gomes
authors.forename: E
authors.initials: E
authors.lastname: Paiva
authors.forename: A S
authors.initials: AS
authors.lastname: Rosado
authors.forename: L
authors.initials: L
authors.lastname: Seldin
mesh_terms: D001406:Bacillaceae / Q000145:classification* / Q000235:genetics; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000032:analysis; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D020459:Genes, rRNA; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D003313:Zea mays
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit