Publication

PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites

Hendrickx, B., Dejonghe, W., Faber, F., Boenne, W., Bastiaens, L., Verstraete, W., Top, EM. & Springael, D., Feb-2006, In : FEMS Microbial Ecology. 55, 2, p. 262-273 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

APA

Hendrickx, B., Dejonghe, W., Faber, F., Boenne, W., Bastiaens, L., Verstraete, W., ... Springael, D. (2006). PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. FEMS Microbial Ecology, 55(2), 262-273. https://doi.org/10.1111/j.1574-6941.2005.00018.x

Author

Hendrickx, B ; Dejonghe, W ; Faber, F ; Boenne, W ; Bastiaens, L ; Verstraete, W ; Top, EM ; Springael, D. / PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. In: FEMS Microbial Ecology. 2006 ; Vol. 55, No. 2. pp. 262-273.

Harvard

Hendrickx, B, Dejonghe, W, Faber, F, Boenne, W, Bastiaens, L, Verstraete, W, Top, EM & Springael, D 2006, 'PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites', FEMS Microbial Ecology, vol. 55, no. 2, pp. 262-273. https://doi.org/10.1111/j.1574-6941.2005.00018.x

Standard

PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. / Hendrickx, B; Dejonghe, W; Faber, F; Boenne, W; Bastiaens, L; Verstraete, W; Top, EM; Springael, D.

In: FEMS Microbial Ecology, Vol. 55, No. 2, 02.2006, p. 262-273.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Hendrickx B, Dejonghe W, Faber F, Boenne W, Bastiaens L, Verstraete W et al. PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. FEMS Microbial Ecology. 2006 Feb;55(2):262-273. https://doi.org/10.1111/j.1574-6941.2005.00018.x


BibTeX

@article{4c3472dc942e48409e03d2a2c1aaef5c,
title = "PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites",
abstract = "tmoA and related genes encode the alpha-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent mono-oxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoA-analogues in the environment is larger than suggested from described TmoA-analogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence.",
keywords = "BTEX biodegradation, catabolic gene, tmoA, PCR detection, DGGE analysis, GRADIENT GEL-ELECTROPHORESIS, 16S RIBOSOMAL-RNA, CATECHOL 2,3-DIOXYGENASE GENE, AROMATIC-HYDROCARBONS, ENVIRONMENTAL-SAMPLES, TOLUENE DEGRADATION, FUNCTIONAL-ANALYSIS, PHENOL HYDROXYLASE, OXIDIZING BACTERIA, SOIL",
author = "B Hendrickx and W Dejonghe and F Faber and W Boenne and L Bastiaens and W Verstraete and EM Top and D Springael",
year = "2006",
month = "2",
doi = "10.1111/j.1574-6941.2005.00018.x",
language = "English",
volume = "55",
pages = "262--273",
journal = "FEMS Microbial Ecology",
issn = "0168-6496",
publisher = "Oxford University Press",
number = "2",

}

RIS

TY - JOUR

T1 - PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites

AU - Hendrickx, B

AU - Dejonghe, W

AU - Faber, F

AU - Boenne, W

AU - Bastiaens, L

AU - Verstraete, W

AU - Top, EM

AU - Springael, D

PY - 2006/2

Y1 - 2006/2

N2 - tmoA and related genes encode the alpha-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent mono-oxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoA-analogues in the environment is larger than suggested from described TmoA-analogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence.

AB - tmoA and related genes encode the alpha-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent mono-oxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoA-analogues in the environment is larger than suggested from described TmoA-analogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence.

KW - BTEX biodegradation

KW - catabolic gene

KW - tmoA

KW - PCR detection

KW - DGGE analysis

KW - GRADIENT GEL-ELECTROPHORESIS

KW - 16S RIBOSOMAL-RNA

KW - CATECHOL 2,3-DIOXYGENASE GENE

KW - AROMATIC-HYDROCARBONS

KW - ENVIRONMENTAL-SAMPLES

KW - TOLUENE DEGRADATION

KW - FUNCTIONAL-ANALYSIS

KW - PHENOL HYDROXYLASE

KW - OXIDIZING BACTERIA

KW - SOIL

U2 - 10.1111/j.1574-6941.2005.00018.x

DO - 10.1111/j.1574-6941.2005.00018.x

M3 - Article

VL - 55

SP - 262

EP - 273

JO - FEMS Microbial Ecology

JF - FEMS Microbial Ecology

SN - 0168-6496

IS - 2

ER -

ID: 4404205