title: Application of denaturing high-performance liquid chromatography for monitoring sulfate-reducing bacteria in oil fields.
abstract: Sulfate-reducing bacteria (SRB) participate in microbially induced corrosion (MIC) of equipment and H2S-driven reservoir souring in oil field sites. Successful management of industrial processes requires methods that allow robust monitoring of microbial communities. This study investigated the applicability of denaturing high-performance liquid chromatography (DHPLC) targeting the dissimilatory sulfite reductase ß-subunit (dsrB) gene for monitoring SRB communities in oil field samples from the North Sea, the United States, and Brazil. Fifteen of the 28 screened samples gave a positive result in real-time PCR assays, containing 9 × 10(1) to 6 × 10(5) dsrB gene copies ml(-1). DHPLC and denaturing gradient gel electrophoresis (DGGE) community profiles of the PCR-positive samples shared an overall similarity; both methods revealed the same samples to have the lowest and highest diversity. The SRB communities were diverse, and different dsrB compositions were detected at different geographical locations. The identified dsrB gene sequences belonged to several phylogenetic groups, such as Desulfovibrio, Desulfococcus, Desulfomicrobium, Desulfobulbus, Desulfotignum, Desulfonatronovibrio, and Desulfonauticus. DHPLC showed an advantage over DGGE in that the community profiles were very reproducible from run to run, and the resolved gene fragments could be collected using an automated fraction collector and sequenced without a further purification step. DGGE, on the other hand, included casting of gradient gels, and several rounds of rerunning, excising, and reamplification of bands were needed for successful sequencing. In summary, DHPLC proved to be a suitable tool for routine monitoring of the diversity of SRB communities in oil field samples.
authors.affiliation: VTT Technical Research Centre of Finland, Espoo, Finland. outi.priha@vtt.fi
authors.forename: Outi
authors.initials: O
authors.lastname: Priha
authors.forename: Mari
authors.initials: M
authors.lastname: Nyyssönen
authors.forename: Malin
authors.initials: M
authors.lastname: Bomberg
authors.forename: Arja
authors.initials: A
authors.lastname: Laitila
authors.forename: Jaakko
authors.initials: J
authors.lastname: Simell
authors.forename: Anu
authors.initials: A
authors.lastname: Kapanen
authors.forename: Riikka
authors.initials: R
authors.lastname: Juvonen
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D058448:Biota; D001938:Brazil; D002853:Chromatography, Liquid / Q000379:methods*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D050885:Hydrogensulfite Reductase / Q000235:genetics*; D008969:Molecular Sequence Data; D009659:North Sea; D061329:Oil and Gas Fields / Q000382:microbiology*; D010084:Oxidation-Reduction; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA; D013431:Sulfates / Q000378:metabolism*; D014481:United States
chemical_list: D004269:DNA, Bacterial; D013431:Sulfates; D050885:Hydrogensulfite Reductase