title: Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing.
abstract: Microorganisms responsible for the degradation of phenanthrene in a clean forest soil sample were identified by DNA-based stable isotope probing (SIP). The soil was artificially amended with either 12C- or 13C-labeled phenanthrene, and soil DNA was extracted on days 3, 6 and 9. Terminal restriction fragment length polymorphism (TRFLP) results revealed that the fragments of 219- and 241-bp in HaeIII digests were distributed throughout the gradient profile at three different sampling time points, and both fragments were more dominant in the heavy fractions of the samples exposed to the 13C-labeled contaminant. 16S rRNA sequencing of the 13C-enriched fraction suggested that Acidobacterium spp. within the class Acidobacteria, and Collimonas spp. within the class Betaproteobacteria, were directly involved in the uptake and degradation of phenanthrene at different times. To our knowledge, this is the first report that the genus Collimonas has the ability to degrade PAHs. Two PAH-RHDα genes were identified in 13C-labeled DNA. However, isolation of pure cultures indicated that strains of Staphylococcus sp. PHE-3, Pseudomonas sp. PHE-1, and Pseudomonas sp. PHE-2 in the soil had high phenanthrene-degrading ability. This emphasizes the role of a culture-independent method in the functional understanding of microbial communities in situ.
authors.affiliation: State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
authors.forename: Longfei
authors.initials: L
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; Graduate University of Chinese Academy of Sciences, Beijing, 100039, China.
authors.forename: Mengke
authors.initials: M
authors.lastname: Song
authors.affiliation: State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
authors.forename: Chunling
authors.initials: C
authors.lastname: Luo
authors.affiliation: Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom.
authors.forename: Dayi
authors.initials: D
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
authors.forename: Gan
authors.initials: G
authors.lastname: Zhang
mesh_terms: D061271:Acidobacteria / Q000378:metabolism*; D001483:Base Sequence; D020562:Betaproteobacteria / Q000378:metabolism*; D002247:Carbon Isotopes / Q000378:metabolism; D015342:DNA Probes; D052918:Environmental Restoration and Remediation / Q000379:methods*; D007553:Isotope Labeling; D008969:Molecular Sequence Data; D010616:Phenanthrenes / Q000032:analysis / Q000378:metabolism*; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017423:Sequence Analysis, RNA; D012987:Soil / Q000737:chemistry*
chemical_list: D002247:Carbon Isotopes; D015342:DNA Probes; D010616:Phenanthrenes; D012336:RNA, Ribosomal, 16S; D012987:Soil; C031181:phenanthrene