title: Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based-PCR and DGGE.
abstract: OBJECTIVE
  The aim of this study was to apply a group specific PCR system followed by denaturing gradient gel electrophoresis (DGGE) analysis to evaluate the effect of oil contamination and the biostimulation process on the diversity of Pseudomonas populations in soil ecosystems.
  
  
  RESULTS
  Direct DNA extraction from biostimulated- and oil-contaminated soil samples was performed. Primers specific for the genus Pseudomonas spp. were used to amplify 16S rRNA genes and then a semi-nested PCR reaction was applied to obtain smaller fragments for comparing the PCR products by DGGE. Whether in bulk, oil-contaminated or biostimulated soils, the DGGE profiles revealed little change in Pseudomonas community throughout the 270 days of experiment. The presence of a few additional bands observed only in treated samples indicated that a bacterial shift occurred with the addition of nutrients and with oil contamination.
  
  
  CONCLUSIONS
  The combination of semi-nested PCR and DGGE was found to be a rapid and sensitive technique to study the diversity within the genus Pseudomonas and may be suitable for further studies concerning the role of this bacterial group in large-scale oil-contaminated areas.
authors.affiliation: Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil.
authors.forename: F F
authors.initials: FF
authors.lastname: Evans
authors.forename: L
authors.initials: L
authors.lastname: Seldin
authors.forename: G V
authors.initials: GV
authors.lastname: Sebastian
authors.forename: S
authors.initials: S
authors.lastname: Kjelleberg
authors.forename: C
authors.initials: C
authors.lastname: Holmström
authors.forename: A S
authors.initials: AS
authors.lastname: Rosado
mesh_terms: D000645:Ammonium Sulfate / Q000378:metabolism; D044822:Biodiversity; D004269:DNA, Bacterial / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000032:analysis / Q000302:isolation & purification; D017753:Ecosystem; D004591:Electrophoresis, Polyacrylamide Gel; D020459:Genes, rRNA; D009691:Nucleic Acid Denaturation; D010578:Petroleum; D010710:Phosphates / Q000378:metabolism; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017680:Potassium Compounds / Q000378:metabolism; D011549:Pseudomonas / Q000145:classification / Q000502:physiology*; D012988:Soil Microbiology; D012989:Soil Pollutants
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D010578:Petroleum; D010710:Phosphates; D017680:Potassium Compounds; D012989:Soil Pollutants; C013216:potassium phosphate; D000645:Ammonium Sulfate