PMID- 26098417
OWN - NLM
STAT- MEDLINE
DCOM- 20160321
LR  - 20181113
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 10
IP  - 6
DP  - 2015
TI  - Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing.
PG  - e0130846
LID - 10.1371/journal.pone.0130846 [doi]
LID - e0130846
AB  - 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-RHDalpha 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.
FAU - Jiang, Longfei
AU  - Jiang L
AD  - State Key Laboratory of Organic Geochemistry, Guangzhou Institute of 
      Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
FAU - Song, Mengke
AU  - Song M
AD  - 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.
FAU - Luo, Chunling
AU  - Luo C
AD  - State Key Laboratory of Organic Geochemistry, Guangzhou Institute of 
      Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
FAU - Zhang, Dayi
AU  - Zhang D
AD  - Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United 
      Kingdom.
FAU - Zhang, Gan
AU  - Zhang G
AD  - State Key Laboratory of Organic Geochemistry, Guangzhou Institute of 
      Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20150622
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Carbon Isotopes)
RN  - 0 (DNA Probes)
RN  - 0 (Phenanthrenes)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 0 (Soil)
RN  - 448J8E5BST (phenanthrene)
SB  - IM
MH  - Acidobacteria/*metabolism
MH  - Base Sequence
MH  - Betaproteobacteria/*metabolism
MH  - Carbon Isotopes/metabolism
MH  - DNA Probes
MH  - Environmental Restoration and Remediation/*methods
MH  - Isotope Labeling
MH  - Molecular Sequence Data
MH  - Phenanthrenes/analysis/*metabolism
MH  - Polymorphism, Restriction Fragment Length
MH  - RNA, Ribosomal, 16S/genetics
MH  - Sequence Analysis, RNA
MH  - Soil/*chemistry
PMC - PMC4476716
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2015/06/23 06:00
MHDA- 2016/03/22 06:00
PMCR- 2015/06/22
CRDT- 2015/06/23 06:00
PHST- 2015/05/06 00:00 [received]
PHST- 2015/05/13 00:00 [accepted]
PHST- 2015/06/23 06:00 [entrez]
PHST- 2015/06/23 06:00 [pubmed]
PHST- 2016/03/22 06:00 [medline]
PHST- 2015/06/22 00:00 [pmc-release]
AID - PONE-D-15-19645 [pii]
AID - 10.1371/journal.pone.0130846 [doi]
PST - epublish
SO  - PLoS One. 2015 Jun 22;10(6):e0130846. doi: 10.1371/journal.pone.0130846. 
      eCollection 2015.