Detection of known and novel genes encoding aromatic ring-hydroxylating dioxygenases in soils and in aromatic hydrocarbon-degrading bacteria

Taylor, Paul Michael

doi:10.1016/s0378-1097(02)00971-0

Cited by 14 publications

(24 citation statements)

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“…However, we also amplified gene fragments that showed little or no homology to the known dioxygenase genes (38% for α subunit and 14% for β subunit). Previous studies also reported the presence of dioxygenase genes, which showed low or no homology to that available in the database (Taylor et al. 2002; Kahng and Oh 2005; Taylor and Janssen, 2005; Gomes et al.…”

Section: Discussionmentioning

confidence: 97%

Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

Kumar

Khanna

2010

Journal of Applied Microbiology

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Aims: In order to develop effective bioremediation strategies for polyaromatic hydrocarbons (PAHs) degradation, the composition and metabolic potential of microbial communities need to be better understood, especially in highly PAH contaminated sites in which little information on the cultivation‐independent communities is available. Methods and Results: Coal‐tar‐contaminated soil was collected, which consisted of 122·5 mg g−1 total extractable PAH compounds. Biodegradation studies with this soil indicated the presence of microbial community that is capable of degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene at 50 ppm each. PCR clone libraries were established from the DNA of the coal‐tar‐contaminated soil, targeting the 16S rRNA to characterize (i) the microbial communities, (ii) partial gene fragment encoding the Rieske iron sulfur center (α‐subunit) common to all PAH dioxygenase enzymes and (iii) β‐subunit of dioxygenase. Phylotypes related to Proteobacteria (Alpha‐, Epsilon‐ and Gammaproteobacteria), Acidobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA derived clone libraries. Many of the gene fragment sequences of α‐subunit and β‐subunit of dioxygenase obtained from the respective clone libraries fell into clades that are distinct from the reference dioxygenase gene sequences. Presence of consensus sequence of the Rieske type [2Fe‐2S] cluster binding site suggested that these gene fragments encode for α‐subunit of dioxygenase gene. Conclusions: Sequencing of the cloned libraries representing α‐subunit gene fragments (Rf1) and β‐subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal‐tar‐contaminated soil. Significance and Impact of the Study: The combination of the Rieske primers and bacterial community profiling represents a powerful tool for both assessing bioremediation potential and the exploration of novel dioxygenase genes in a contaminated environment.

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Section: Discussionmentioning

confidence: 97%

Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

Kumar

Khanna

2010

Journal of Applied Microbiology

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“…Having gained knowledge on metabolic properties of isolates, it is a logical step forward to define those genes, which may serve as markers to assess biodegradation potential at a given site. Typically, in respect to aromatic metabolism, these studies use primers designed based on conserved gene regions and focus on Rieske non‐haem iron oxygenases (Taylor et al ., 2002; Witzig et al ., 2006) or soluble diiron monooxygenases (Hendrickx et al ., 2006) as targets for activities initiating degradation or on extradiol dioxygenases cleaving the aromatic ring (Chandler and Brockman, 1996; Junca and Pieper, 2004). These studies range from those searching for a narrow window of genes similar or identical to those observed in type strains using non‐degenerated primers (Salminen et al ., 2008) or on subfamilies of homologous genes using degenerated primers (Witzig et al ., 2006).…”

Section: Basic Knowledge On Key Reactions For Aerobic Degradation Of mentioning

confidence: 99%

Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes

Vílchez-Vargas

Junca

Pieper

2010

Environmental Microbiology

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SummaryMicrobial degradation is the main mechanism responsible for the recovery of contaminated sites, where a huge body of investigations is available in which most concentrate on single isolates from soils capable of mineralizing pollutants. The rapid development of molecular techniques in recent years allows immense insights into the processes in situ, including identification of organisms active in target sites, community member interactions and catabolic gene structures. Only a detailed understanding of the functioning and interactions within microbial communities will allow their rational manipulation for the purpose of optimizing bioremediation efforts. We will present the status of the current capabilities to assess and predict catabolic potential of environmental sites by applying gene fingerprinting, catabolome arrays, metagenomics and complementary 'omics' technologies. Collectively, this will allow tracking regulation and evolution within microbial communities ultimately aiming to understand the mechanisms taking place in large scale bioremediation treatments for aromatic decontamination.

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“…For the past decade, PCR amplification using genespecific primers or degenerate primers has been used to study the diversity of aromatic-dioxygenase genes in PAHdegrading bacterial isolates and environmental samples (Hedlund et al, 1999;Lloyd-Jones et al, 1999;Wilson et al, 1999;Marlowe et al, 2002;Stach & Burns, 2002;Widada et al, 2002a, b;Brezna et al, 2003). The primers were designed based on the dioxygenase genes including nahAc (Hedlund et al, 1999;Wilson et al, 1999;Marlowe et al, 2002), phnAc (Lloyd-Jones et al, 1999;Widada et al, 2002a, b), nidA (Stach & Burns, 2002;Brezna et al, 2003), and the conserved segments of ring-hydroxylating dioxygenases (Yeates et al, 2000;Taylor et al, 2002;Kahl & Hofer, 2003). Their use has resulted in the detection of novel dioxygenase genes from environmental samples; however they have not been able to detect the PAH-degrading gene from some species, particularly from Sphingomonas strains (Hamann et al, 1999;Meyer et al, 1999;Widada et al, 2002a, b).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments

Hong

Guo

Wong

et al. 2006

FEMS Microbiology Letters

118

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To investigate the diversity of dioxygenase genes involved in polycyclic aromatic hydrocarbon (PAH)-degradation, a total of 32 bacterial strains were isolated from surface mangrove sediments, from the genera Mycobacterium, Sphingomonas, Terrabacter, Sphingopyxis, Sphingobium and Rhodococcus. Two sets of PCR primers were constructed to detect the nidA-like and nahAc-like sequences of the alpha subunit of the PAH ring-hydroxylating dioxygenase. PCR amplified the DNA fragments from all Gram-positive bacteria by using nidA-like primers and from all Gram-negative bacteria, except two, by using nahAc-like primers. The nidA-like primers showed three subtypes of nidA-like gene: (i) fadA1, clustering with nidA3 from M. vanbaalenii PYR-1, (ii) nidA, clustering with nidA from PYR-1, and (iii) fadA2 clustering with dioxygenase from Arthrobacter sp. FB24. The amplicons detected by nahAc-like primers had high sequence homologies to phnA1a from Sphingomonas sp. CHY-1 and were amplifiable from 8 of the 16 Gram-negative isolates. The primer also generated amplicons that had a 32-36% similarity to phnA1a and 53-93% identity to p-cumate dioxygenase. These results suggest that the nidA-like and nahAc-like genes are prevalent in the PAH-degrading bacteria and that they are useful for determining the presence of PAH-dioxygenase genes in environmental samples.

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Detection of known and novel genes encoding aromatic ring-hydroxylating dioxygenases in soils and in aromatic hydrocarbon-degrading bacteria

Cited by 14 publications

References 14 publications

Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes

Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments

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