title: Stable-isotope probing of the polycyclic aromatic hydrocarbon-degrading bacterial guild in a contaminated soil.
abstract: The bacteria responsible for the degradation of naphthalene, phenanthrene, pyrene, fluoranthene or benz[a]anthracene in a polycyclic aromatic hydrocarbon (PAH)-contaminated soil were investigated by DNA-based stable-isotope probing (SIP). Clone libraries of 16S rRNA genes were generated from the (13) C-enriched ('heavy') DNA recovered from each SIP experiment, and quantitative PCR primers targeting the 16S rRNA gene were developed to measure the abundances of many of the SIP-identified sequences. Clone libraries from the SIP experiments with naphthalene, phenanthrene and fluoranthene primarily contained sequences related to bacteria previously associated with the degradation of those compounds. However, Pigmentiphaga-related sequences were newly associated with naphthalene and phenanthrene degradation, and sequences from a group of uncultivated γ-Proteobacteria known as Pyrene Group 2 were newly associated with fluoranthene and benz[a]anthracene degradation. Pyrene Group 2-related sequences were the only sequences recovered from the clone library generated from SIP with pyrene, and they were 82% of the sequences recovered from the clone library generated from SIP with benz[a]anthracene. In time-course experiments with each substrate in unlabelled form, the abundance of each of the measured groups increased in response to the corresponding substrate. These results provide a comprehensive description of the microbial ecology of a PAH-contaminated soil as it relates to the biodegradation of PAHs from two to four rings, and they underscore that bacteria in Pyrene Group 2 are well-suited for the degradation of four-ring PAHs.
authors.affiliation: Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, CB #7431 Chapel Hill, NC 27599-7431, USA. maiyshajones@unc.edu
authors.forename: Maiysha D
authors.initials: MD
authors.lastname: Jones
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Crandell
authors.forename: David R
authors.initials: DR
authors.lastname: Singleton
authors.forename: Michael D
authors.initials: MD
authors.lastname: Aitken
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D001551:Benz(a)Anthracenes / Q000378:metabolism; D001673:Biodegradation, Environmental; D002247:Carbon Isotopes / Q000032:analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005449:Fluorenes / Q000378:metabolism; D015723:Gene Library; D008969:Molecular Sequence Data; D009281:Naphthalenes / Q000378:metabolism; D010616:Phenanthrenes / Q000378:metabolism; D011084:Polycyclic Aromatic Hydrocarbons / Q000378:metabolism*; D011721:Pyrenes / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism*
chemical_list: D001551:Benz(a)Anthracenes; D002247:Carbon Isotopes; D004269:DNA, Bacterial; D005449:Fluorenes; D009281:Naphthalenes; D010616:Phenanthrenes; D011084:Polycyclic Aromatic Hydrocarbons; D011721:Pyrenes; D012336:RNA, Ribosomal, 16S; D012987:Soil; D012989:Soil Pollutants; C031721:naphthalene; C007738:fluoranthene; C031181:phenanthrene; C030984:pyrene; C030935:benz(a)anthracene