title: Microbial community analysis at crude oil-contaminated soils targeting the 16S ribosomal RNA, xylM, C23O, and bcr genes.
abstract: OBJECTIVE
  The analyses targeting multiple functional genes were performed on the samples of crude oil-contaminated soil, to investigate community structures of organisms involved in monoaromatic hydrocarbon degradation.
  
  
  RESULTS
  Environmental samples were obtained from two sites that were contaminated with different components of crude oil. The analysis on 16S rRNA gene revealed that bacterial community structures were clearly different between the two sites. The cloning analyses were performed by using primers specific for the catabolic genes involved in the aerobic or anaerobic degradation of monoaromatic hydrocarbons, i.e. xylene monooxygenase (xylM), catechol 2,3-dioxygenase (C23O), and benzoyl-CoA reductase (bcr) genes. From the result of xylM gene, it was suggested that there are lineages specific to the respective sites, reflecting the differences of sampling sites. In the analysis of the C23O gene, the results obtained with two primer sets were distinct from each other. A comparison of these suggested that catabolic types of major bacteria carrying this gene were different between the two sites. As for the bcr gene, no amplicon was obtained from one sample. Phylogenetic analysis revealed that the sequences obtained from the other sample were distinct from the known sequences.
  
  
  CONCLUSIONS
  The differences between the two sites were demonstrated in the analyses of all tested genes. As for aerobic cleavage of the aromatic ring, it was also suggested that analysis using two primer sets provide more detailed information about microbial communities in the contaminated site.
  
  
  CONCLUSIONS
  The present study demonstrated that analysis targeting multiple functional genes as molecular markers is practical to examine microbial community in crude oil-contaminated environments.
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Higashioka
authors.forename: H
authors.initials: H
authors.lastname: Kojima
authors.forename: S
authors.initials: S
authors.lastname: Sato
authors.forename: M
authors.initials: M
authors.lastname: Fukui
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D015415:Biomarkers / Q000032:analysis; D050557:Catechol 2,3-Dioxygenase / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D004587:Electrophoresis, Agar Gel; D006838:Hydrocarbons / Q000378:metabolism*; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000235:genetics; D010105:Oxygenases / Q000235:genetics; D010578:Petroleum / Q000032:analysis / Q000382:microbiology*; D016133:Polymerase Chain Reaction; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D015415:Biomarkers; D017931:DNA Primers; D006838:Hydrocarbons; D010578:Petroleum; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D010105:Oxygenases; D050557:Catechol 2,3-Dioxygenase; C067624:xylene monooxygenase; D044925:Oxidoreductases Acting on CH-CH Group Donors; C109030:benzoyl-coenzyme A reductase (dearomatizing)