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Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing.

Jiang L, Song M, Luo C, Zhang D, Zhang G - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.

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.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of the isolated phenanthrene degraders.Phylogenetic tree for the taxonomic location of Pseudomonas sp. PHE-1, Pseudomonas sp. PHE-2 and Staphylococcus sp. PHE-3. This tree based on 16S rRNA sequence was produced by MEGA 5.0.
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pone.0130846.g003: Phylogenetic tree of the isolated phenanthrene degraders.Phylogenetic tree for the taxonomic location of Pseudomonas sp. PHE-1, Pseudomonas sp. PHE-2 and Staphylococcus sp. PHE-3. This tree based on 16S rRNA sequence was produced by MEGA 5.0.

Mentions: Among the phenanthrene-degrading bacteria using MSM with 1 mg/L and 10 mg/L (w/v) phenanthrene as the sole carbon source, three colonies were selected based on the size of the clear zone in the phenanthrene layer, respectively. DNA sequence analysis identified these three isolates as Pseudomonas sp. PHE-1, Pseudomonas sp. PHE-2, and Staphylococcus sp. PHE-3 (Fig 3). As shown in S1 Table, for the degradation of 1 mg/kg phenanthrene, the most efficient strain was Pseudomonas sp. PHE-1 (98.5% degradation within three days), followed by Pseudomonas sp. PHE-2 and Staphylococcus sp. PHE-3, with 82.3% and 75.6% degradation in the same time period, respectively. At 10 mg/kg phenanthrene, a 51.2% degradation performance was evident in the presence of Pseudomonas sp. PHE-1.


Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing.

Jiang L, Song M, Luo C, Zhang D, Zhang G - PLoS ONE (2015)

Phylogenetic tree of the isolated phenanthrene degraders.Phylogenetic tree for the taxonomic location of Pseudomonas sp. PHE-1, Pseudomonas sp. PHE-2 and Staphylococcus sp. PHE-3. This tree based on 16S rRNA sequence was produced by MEGA 5.0.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4476716&req=5

pone.0130846.g003: Phylogenetic tree of the isolated phenanthrene degraders.Phylogenetic tree for the taxonomic location of Pseudomonas sp. PHE-1, Pseudomonas sp. PHE-2 and Staphylococcus sp. PHE-3. This tree based on 16S rRNA sequence was produced by MEGA 5.0.
Mentions: Among the phenanthrene-degrading bacteria using MSM with 1 mg/L and 10 mg/L (w/v) phenanthrene as the sole carbon source, three colonies were selected based on the size of the clear zone in the phenanthrene layer, respectively. DNA sequence analysis identified these three isolates as Pseudomonas sp. PHE-1, Pseudomonas sp. PHE-2, and Staphylococcus sp. PHE-3 (Fig 3). As shown in S1 Table, for the degradation of 1 mg/kg phenanthrene, the most efficient strain was Pseudomonas sp. PHE-1 (98.5% degradation within three days), followed by Pseudomonas sp. PHE-2 and Staphylococcus sp. PHE-3, with 82.3% and 75.6% degradation in the same time period, respectively. At 10 mg/kg phenanthrene, a 51.2% degradation performance was evident in the presence of Pseudomonas sp. PHE-1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.

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.

No MeSH data available.


Related in: MedlinePlus