Limits...
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 PAH-RHDα gene.Phylogenetic relationship of PAH-RHDα gene cloned from soil treated by 1 mg/kg phenanthrene. PAH-RHD1 and PAH-RHD2 showed 97% and 92% similarity with genes from Mycobacterium_rhodesiaee and uncultured organism, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4476716&req=5

pone.0130846.g002: Phylogenetic tree of PAH-RHDα gene.Phylogenetic relationship of PAH-RHDα gene cloned from soil treated by 1 mg/kg phenanthrene. PAH-RHD1 and PAH-RHD2 showed 97% and 92% similarity with genes from Mycobacterium_rhodesiaee and uncultured organism, respectively.

Mentions: PAH-RHDα genes from Gram-positive (GP) and Gram-negative (GN) bacteria were analyzed in heavy DNA fractions. On the global scale, the proportion of PAH-RHDα GN tends to be higher than that of the PAH-RHDα GP [31]. However, in the present study only two types of PAH-RHDα GP gene were detected in the heavy DNA, and were affiliated to PAH-RHDα genes from Mycobacterium rhodesiae NBB3 (CP003169) and an uncultured organism (EF128730.1) (Fig 2). These may be the functional genes associated with the phenanthrene-degrading strains of Acidobacterium and Collimonas identified by SIP. It should be noted that the active phenanthrene degrading bacteria might contain other functional genes that could not be targeted by the primer used in the present study.


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 PAH-RHDα gene.Phylogenetic relationship of PAH-RHDα gene cloned from soil treated by 1 mg/kg phenanthrene. PAH-RHD1 and PAH-RHD2 showed 97% and 92% similarity with genes from Mycobacterium_rhodesiaee and uncultured organism, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0130846.g002: Phylogenetic tree of PAH-RHDα gene.Phylogenetic relationship of PAH-RHDα gene cloned from soil treated by 1 mg/kg phenanthrene. PAH-RHD1 and PAH-RHD2 showed 97% and 92% similarity with genes from Mycobacterium_rhodesiaee and uncultured organism, respectively.
Mentions: PAH-RHDα genes from Gram-positive (GP) and Gram-negative (GN) bacteria were analyzed in heavy DNA fractions. On the global scale, the proportion of PAH-RHDα GN tends to be higher than that of the PAH-RHDα GP [31]. However, in the present study only two types of PAH-RHDα GP gene were detected in the heavy DNA, and were affiliated to PAH-RHDα genes from Mycobacterium rhodesiae NBB3 (CP003169) and an uncultured organism (EF128730.1) (Fig 2). These may be the functional genes associated with the phenanthrene-degrading strains of Acidobacterium and Collimonas identified by SIP. It should be noted that the active phenanthrene degrading bacteria might contain other functional genes that could not be targeted by the primer used in the present study.

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