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

Abstract

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. Coal-tar-contaminated soil was collected, which consisted of 122-122.5 mg g{sup -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 {alpha}-subunit) common to all PAH dioxygenase enzymes and (iii) {beta}-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 alpha-subunit and beta-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 (2Fe2S) cluster binding site suggested that these gene fragments encode for  More>>
Authors:
Kumar, M; Khanna, S [1] 
  1. NIIT Univ, Neemrana (India). Dept. of Biotechnology & Bioinformation
Publication Date:
Apr 15, 2010
Product Type:
Journal Article
Reference Number:
CLA-10:050303
Resource Relation:
Journal Name: Journal of Applied Microbiology; Journal Volume: 108; Journal Issue: 4
Subject:
01 COAL, LIGNITE, AND PEAT; COAL TAR; GENES; REMEDIAL ACTION; SOILS; POLYCYCLIC AROMATIC HYDROCARBONS; BIODEGRADATION; DECONTAMINATION; BACTERIA; EVALUATION; REMOVAL; OXYGENASES
OSTI ID:
21305890
Country of Origin:
United Kingdom
Language:
English
Other Identifying Numbers:
Journal ID: ISSN 1364-5072; JAMIFK; TRN: 100500303
Submitting Site:
CLA
Size:
page(s) 1252-1262
Announcement Date:
May 24, 2010

Citation Formats

Kumar, M, and Khanna, S. Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation. United Kingdom: N. p., 2010. Web. doi:10.1111/j.1365-2672.2009.04523.x.
Kumar, M, & Khanna, S. Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation. United Kingdom. doi:10.1111/j.1365-2672.2009.04523.x.
Kumar, M, and Khanna, S. 2010. "Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation." United Kingdom. doi:10.1111/j.1365-2672.2009.04523.x. https://www.osti.gov/servlets/purl/10.1111/j.1365-2672.2009.04523.x.
@misc{etde_21305890,
title = {Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation}
author = {Kumar, M, and Khanna, S}
abstractNote = {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. Coal-tar-contaminated soil was collected, which consisted of 122-122.5 mg g{sup -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 {alpha}-subunit) common to all PAH dioxygenase enzymes and (iii) {beta}-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 alpha-subunit and beta-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 (2Fe2S) cluster binding site suggested that these gene fragments encode for {alpha}-subunit of dioxygenase gene. Sequencing of the cloned libraries representing {alpha}-subunit gene fragments (Rf1) and beta-subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal-tar-contaminated soil.}
doi = {10.1111/j.1365-2672.2009.04523.x}
journal = {Journal of Applied Microbiology}
issue = {4}
volume = {108}
place = {United Kingdom}
year = {2010}
month = {Apr}
}