Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site

Barbara Hendrickx, Howard Junca, Jolana Vosahlova, Antje Lindner, Irene Rüegg, Margarete Bucheli-Witschel, Folkert Faber, Thomas Egli, Margit Mau, Michael Schlömann, Maria Brennerova, Vladimir Brenner, Dietmar H Pieper, Eva M Top, Winnie Dejonghe, Leen Bastiaens, Dirk Springael

Onderzoeksoutput: ArticleAcademicpeer review

Uittreksel

Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for meta-cleavage of the aromatic ring. The new primer sets allowed detection of the corresponding genotypes in soil with a detection limit of 10(3)-10(4) or 10(5)-10(6) gene copies g(-1) soil, assuming one copy of the gene per cell. The primer sets were used in PCR to assess the distribution of the catabolic genes in BTEX degrading bacterial strains and DNA extracts isolated from soils sampled from different locations and depths (vadose, capillary fringe and saturated zone) within a BTEX contaminated site. In both soil DNA and the isolates, tmoA-, xylM- and xylE1-like genes were the most frequently recovered BTEX catabolic genes. xylM and xylE1 were only recovered from material from the contaminated samples while tmoA was detected in material from both the contaminated and non-contaminated samples. The isolates, mainly obtained from the contaminated locations, belonged to the Actinobacteria or Proteobacteria (mainly Pseudomonas). The ability to degrade benzene was the most common BTEX degradation phenotype among them and its distribution was largely congruent with the distribution of the tmoA-like genotype. The presence of tmoA and xylM genes in phylogenetically distant strains indicated the occurrence of horizontal transfer of BTEX catabolic genes in the aquifer. Overall, these results show spatial variation in the composition of the BTEX degradation genes and hence in the type of BTEX degradation activity and pathway, at the examined site. They indicate that bacteria carrying specific pathways and primarily carrying tmoA/xylM/xylE1 genotypes, are being selected upon BTEX contamination.

Originele taal-2English
Pagina's (van-tot)250-265
TijdschriftJournal of microbiological methods
Volume64
Nummer van het tijdschrift2
DOI's
StatusPublished - feb 2006

Keywords

  • microbiologie

Citeer dit

Hendrickx, Barbara ; Junca, Howard ; Vosahlova, Jolana ; Lindner, Antje ; Rüegg, Irene ; Bucheli-Witschel, Margarete ; Faber, Folkert ; Egli, Thomas ; Mau, Margit ; Schlömann, Michael ; Brennerova, Maria ; Brenner, Vladimir ; Pieper, Dietmar H ; Top, Eva M ; Dejonghe, Winnie ; Bastiaens, Leen ; Springael, Dirk. / Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation : distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site. In: Journal of microbiological methods. 2006 ; Vol. 64, Nr. 2. blz. 250-265.
@article{54bbc97179c64ace835cb62b4867d37d,
title = "Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site",
abstract = "Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for meta-cleavage of the aromatic ring. The new primer sets allowed detection of the corresponding genotypes in soil with a detection limit of 10(3)-10(4) or 10(5)-10(6) gene copies g(-1) soil, assuming one copy of the gene per cell. The primer sets were used in PCR to assess the distribution of the catabolic genes in BTEX degrading bacterial strains and DNA extracts isolated from soils sampled from different locations and depths (vadose, capillary fringe and saturated zone) within a BTEX contaminated site. In both soil DNA and the isolates, tmoA-, xylM- and xylE1-like genes were the most frequently recovered BTEX catabolic genes. xylM and xylE1 were only recovered from material from the contaminated samples while tmoA was detected in material from both the contaminated and non-contaminated samples. The isolates, mainly obtained from the contaminated locations, belonged to the Actinobacteria or Proteobacteria (mainly Pseudomonas). The ability to degrade benzene was the most common BTEX degradation phenotype among them and its distribution was largely congruent with the distribution of the tmoA-like genotype. The presence of tmoA and xylM genes in phylogenetically distant strains indicated the occurrence of horizontal transfer of BTEX catabolic genes in the aquifer. Overall, these results show spatial variation in the composition of the BTEX degradation genes and hence in the type of BTEX degradation activity and pathway, at the examined site. They indicate that bacteria carrying specific pathways and primarily carrying tmoA/xylM/xylE1 genotypes, are being selected upon BTEX contamination.",
keywords = "Actinobacteria/genetics, Bacteria, Aerobic/genetics, Bacterial Proteins, Biodegradation, Environmental, Carbohydrate Epimerases, DNA Primers, Environmental Pollution, Gene Transfer, Horizontal, Genes, Bacterial/physiology, Hydrocarbons/metabolism, Industrial Waste, Polymerase Chain Reaction/methods, Proteobacteria/genetics, Soil Microbiology, Soil Pollutants/metabolism, Species Specificity, Substrate Specificity, microbiologie",
author = "Barbara Hendrickx and Howard Junca and Jolana Vosahlova and Antje Lindner and Irene R{\"u}egg and Margarete Bucheli-Witschel and Folkert Faber and Thomas Egli and Margit Mau and Michael Schl{\"o}mann and Maria Brennerova and Vladimir Brenner and Pieper, {Dietmar H} and Top, {Eva M} and Winnie Dejonghe and Leen Bastiaens and Dirk Springael",
year = "2006",
month = "2",
doi = "10.1016/j.mimet.2005.04.018",
language = "English",
volume = "64",
pages = "250--265",
journal = "Journal of microbiological methods",
issn = "0167-7012",
publisher = "Elsevier Science",
number = "2",

}

Hendrickx, B, Junca, H, Vosahlova, J, Lindner, A, Rüegg, I, Bucheli-Witschel, M, Faber, F, Egli, T, Mau, M, Schlömann, M, Brennerova, M, Brenner, V, Pieper, DH, Top, EM, Dejonghe, W, Bastiaens, L & Springael, D 2006, 'Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site' Journal of microbiological methods, vol. 64, nr. 2, blz. 250-265. https://doi.org/10.1016/j.mimet.2005.04.018

Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation : distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site. / Hendrickx, Barbara; Junca, Howard; Vosahlova, Jolana; Lindner, Antje; Rüegg, Irene; Bucheli-Witschel, Margarete; Faber, Folkert; Egli, Thomas; Mau, Margit; Schlömann, Michael; Brennerova, Maria; Brenner, Vladimir; Pieper, Dietmar H; Top, Eva M; Dejonghe, Winnie; Bastiaens, Leen; Springael, Dirk.

In: Journal of microbiological methods, Vol. 64, Nr. 2, 02.2006, blz. 250-265.

Onderzoeksoutput: ArticleAcademicpeer review

TY - JOUR

T1 - Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation

T2 - distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site

AU - Hendrickx, Barbara

AU - Junca, Howard

AU - Vosahlova, Jolana

AU - Lindner, Antje

AU - Rüegg, Irene

AU - Bucheli-Witschel, Margarete

AU - Faber, Folkert

AU - Egli, Thomas

AU - Mau, Margit

AU - Schlömann, Michael

AU - Brennerova, Maria

AU - Brenner, Vladimir

AU - Pieper, Dietmar H

AU - Top, Eva M

AU - Dejonghe, Winnie

AU - Bastiaens, Leen

AU - Springael, Dirk

PY - 2006/2

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N2 - Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for meta-cleavage of the aromatic ring. The new primer sets allowed detection of the corresponding genotypes in soil with a detection limit of 10(3)-10(4) or 10(5)-10(6) gene copies g(-1) soil, assuming one copy of the gene per cell. The primer sets were used in PCR to assess the distribution of the catabolic genes in BTEX degrading bacterial strains and DNA extracts isolated from soils sampled from different locations and depths (vadose, capillary fringe and saturated zone) within a BTEX contaminated site. In both soil DNA and the isolates, tmoA-, xylM- and xylE1-like genes were the most frequently recovered BTEX catabolic genes. xylM and xylE1 were only recovered from material from the contaminated samples while tmoA was detected in material from both the contaminated and non-contaminated samples. The isolates, mainly obtained from the contaminated locations, belonged to the Actinobacteria or Proteobacteria (mainly Pseudomonas). The ability to degrade benzene was the most common BTEX degradation phenotype among them and its distribution was largely congruent with the distribution of the tmoA-like genotype. The presence of tmoA and xylM genes in phylogenetically distant strains indicated the occurrence of horizontal transfer of BTEX catabolic genes in the aquifer. Overall, these results show spatial variation in the composition of the BTEX degradation genes and hence in the type of BTEX degradation activity and pathway, at the examined site. They indicate that bacteria carrying specific pathways and primarily carrying tmoA/xylM/xylE1 genotypes, are being selected upon BTEX contamination.

AB - Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for meta-cleavage of the aromatic ring. The new primer sets allowed detection of the corresponding genotypes in soil with a detection limit of 10(3)-10(4) or 10(5)-10(6) gene copies g(-1) soil, assuming one copy of the gene per cell. The primer sets were used in PCR to assess the distribution of the catabolic genes in BTEX degrading bacterial strains and DNA extracts isolated from soils sampled from different locations and depths (vadose, capillary fringe and saturated zone) within a BTEX contaminated site. In both soil DNA and the isolates, tmoA-, xylM- and xylE1-like genes were the most frequently recovered BTEX catabolic genes. xylM and xylE1 were only recovered from material from the contaminated samples while tmoA was detected in material from both the contaminated and non-contaminated samples. The isolates, mainly obtained from the contaminated locations, belonged to the Actinobacteria or Proteobacteria (mainly Pseudomonas). The ability to degrade benzene was the most common BTEX degradation phenotype among them and its distribution was largely congruent with the distribution of the tmoA-like genotype. The presence of tmoA and xylM genes in phylogenetically distant strains indicated the occurrence of horizontal transfer of BTEX catabolic genes in the aquifer. Overall, these results show spatial variation in the composition of the BTEX degradation genes and hence in the type of BTEX degradation activity and pathway, at the examined site. They indicate that bacteria carrying specific pathways and primarily carrying tmoA/xylM/xylE1 genotypes, are being selected upon BTEX contamination.

KW - Actinobacteria/genetics

KW - Bacteria, Aerobic/genetics

KW - Bacterial Proteins

KW - Biodegradation, Environmental

KW - Carbohydrate Epimerases

KW - DNA Primers

KW - Environmental Pollution

KW - Gene Transfer, Horizontal

KW - Genes, Bacterial/physiology

KW - Hydrocarbons/metabolism

KW - Industrial Waste

KW - Polymerase Chain Reaction/methods

KW - Proteobacteria/genetics

KW - Soil Microbiology

KW - Soil Pollutants/metabolism

KW - Species Specificity

KW - Substrate Specificity

KW - microbiologie

UR - http://www.mendeley.com/research/alternative-primer-sets-pcr-detection-genotypes-involved-bacterial-aerobic-btex-degradation-distribu

U2 - 10.1016/j.mimet.2005.04.018

DO - 10.1016/j.mimet.2005.04.018

M3 - Article

VL - 64

SP - 250

EP - 265

JO - Journal of microbiological methods

JF - Journal of microbiological methods

SN - 0167-7012

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