Characterization of a Polycyclic Aromatic Hydrocarbon Degradation Gene Cluster in a Phenanthrene-Degrading
            <i>Acidovorax</i>
            Strain

Singleton, David R.; Ramirez, Liza Guzmán; Aitken, Michael D.

doi:10.1128/aem.01955-08

Cited by 125 publications

(73 citation statements)

References 53 publications

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“…naphthalene, n-dod. n-dodecane (Skowasch et al 2002;Erikson et al 2003;Pannu et al 2003;Singleton et al 2009). T-RFs of 72 bp (39.59 %), 147 bp (14.87 %) and 153 bp (20.36 bp) represented 74.75 % of the total relative abundance in highly PAH impacted sample SCS.…”

Section: Discussionmentioning

confidence: 99%

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Benedek

Vajna

Táncsics

et al. 2013

World J Microbiol Biotechnol

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Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the longterm impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the a-, b-, c-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the b-, cProteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria.

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Section: Discussionmentioning

confidence: 99%

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Benedek

Vajna

Táncsics

et al. 2013

World J Microbiol Biotechnol

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“…The only Pseudomonadales genus isolated, Pseudomonas, is often found to possess the nah-type gene, which is involved in the breakdown of aromatic compounds (Singleton et al 2009) and is associated with alkane degradation (Saul et al 2005). Other root endophytic bacteria isolates have shown close association with hydrocarbon degradation, such as Brevundimonas (Caulobacterales), which was revealed to increase PAH degradation potential and activity (Phillips et al 2008).…”

Section: Identification Of Culturable Bacteriamentioning

confidence: 99%

Endophytic root bacteria associated with the natural vegetation growing at the hydrocarbon-contaminated Bitumount Provincial Historic site

2017

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Abstract:The Bitumount Provincial Historic site is the location of 2 of the world's first oil-extracting and -refining operations. Despite hydrocarbon levels ranging from 330 to 24 700 mg·(kg soil) −1 , plants have been able to recolonize the site through means of natural revegetation. This study was designed to achieve a better understanding of the plant-root-associated bacterial partnerships occurring within naturally revegetated hydrocarboncontaminated soils. Root endophytic bacterial communities were characterized from representative plant species throughout the site by both high-throughput sequencing and culturing techniques. Population abundance of rhizosphere and root endosphere bacteria was significantly influenced (p < 0.05) by plant species and sampling location. In general, members of the Actinomycetales, Rhizobiales, Pseudomonadales, Burkholderiales, and Sphingomonadales orders were the most commonly identified orders. Community structure of root-associated bacteria was influenced by both plant species and sampling location. Quantitative real-time polymerase chain reaction was used to determine the potential functional diversity of the root endophytic bacteria. The gene copy numbers of 16S rRNA and 2 hydrocarbon-degrading genes (CYP153 and alkB) were significantly affected (p < 0.05) by the interaction of plant species and sampling location. Our findings suggest that some of the bacterial communities detected are known to exhibit plant growth promotion characteristics.Key words: reclamation-remediation, endophytic root bacteria, petroleum hydrocarbons, microbial community.

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“…Earlier SIP studies of pyrenedegrading bacteria conducted in our lab revealed members of previously uncultivated beta-and gammaproteobacterial groups, neither of which is related to any cultivated genus (16,35). SIP investigations have also facilitated the isolation of ecologically relevant organisms (15,19,36) and have been used to reduce the complexity of community DNA slated for metagenomic analysis (4). To date, SIP of anthracene-degrading bacteria has not been reported.…”

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confidence: 99%

Multiple DNA Extractions Coupled with Stable-Isotope Probing of Anthracene-Degrading Bacteria in Contaminated Soil

Jones

Singleton

Sun

et al. 2011

Appl Environ Microbiol

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In many of the DNA-based stable-isotope probing (SIP) studies published to date in which soil communities were investigated, a single DNA extraction was performed on the soil sample, usually using a commercial DNA extraction kit, prior to recovering the 13 C-labeled (heavy) DNA by density-gradient ultracentrifugation. Recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of DNA from all of the organisms in the sample. To determine whether multiple DNA extractions would affect the DNA yield, the eubacterial 16S rRNA gene copy number, or the identification of anthracene-degrading bacteria, we performed seven successive DNA extractions on the same aliquot of contaminated soil either untreated or enriched with [U-13 C]anthracene. Multiple extractions were necessary to maximize the DNA yield and 16S rRNA gene copy number from both untreated and anthracene-enriched soil samples. Sequences within the order Sphingomonadales, but unrelated to any previously described genus, dominated the 16S rRNA gene clone libraries derived from 13 C-enriched DNA and were designated "anthracene group 1." Sequences clustering with Variovorax spp., which were also highly represented, and sequences related to the genus Pigmentiphaga were newly associated with anthracene degradation. The bacterial groups collectively identified across all seven extracts were all recovered in the first extract, although quantitative PCR analysis of SIP-identified groups revealed quantitative differences in extraction patterns. These results suggest that performing multiple DNA extractions on soil samples improves the extractable DNA yield and the number of quantifiable eubacterial 16S rRNA gene copies but have little qualitative effect on the identification of the bacterial groups associated with the degradation of a given carbon source by SIP.

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Characterization of a Polycyclic Aromatic Hydrocarbon Degradation Gene Cluster in a Phenanthrene-Degrading Acidovorax Strain

Cited by 125 publications

References 53 publications

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Endophytic root bacteria associated with the natural vegetation growing at the hydrocarbon-contaminated Bitumount Provincial Historic site

Multiple DNA Extractions Coupled with Stable-Isotope Probing of Anthracene-Degrading Bacteria in Contaminated Soil

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