Catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH) detection of Dehalococcoides

Dijk, Johan; Breugelmans, Philip; Philips, Jo; Haest, Pieter Jan; Smolders, Erik; Springael, Dirk

doi:10.1016/j.mimet.2008.01.012

Cited by 18 publications

(8 citation statements)

References 27 publications

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“…The 16S rRNA gene copy numbers of Dehalococcoides were determined according to Dijk et al . (), while Geobacter and bacterial 16S rRNA gene copy numbers were quantified as described by Haest et al . ().…”

Section: Methodsmentioning

confidence: 97%

Distribution of a dechlorinating community in relation to the distance from a trichloroethene dense nonaqueous phase liquid in a model aquifer

Philips

Hamels

Smolders

et al. 2012

FEMS Microbiol Ecol

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The toxicity of trichloroethene (TCE) likely restricts microbial activity in close vicinity of a TCE dense nonaqueous phase liquid (DNAPL). This study examined the distribution of a dechlorinating community in relation to the distance from a TCE DNAPL using a diffusion-cell set-up. Subcultures of the KB-1(™) culture dechlorinating TCE to cis-dichloroethene and grown with either formate or lactate as electron donor were used to inoculate the diffusion-cells. 16S rRNA gene clone library analysis showed that both inocula consisted of dechlorinating bacteria similar to Geobacter lovleyi SZ and fermentative microorganisms related to Clostridium and Clostridiales. qPCR and RFLP analyses of pore water and sand samples showed a stratified microbial community composition in the diffusion-cells. Geobacter dominated where TCE was present, that is, in the lower 3 cm of the 5.5-cm-thick sand layer. Even at 0.5 cm distance from the DNAPL layer, Geobacter densities were two orders of magnitude higher than at inoculation, despite the expected TCE toxicity. In the upper 2.5 cm of the sand layer, where TCE was depleted, apparently fermenting populations prevailed, corresponding to Clostridium in some diffusion-cells. This analysis demonstrates that the microbial community composition in a source zone is related to the distance from the DNAPL.

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Section: Methodsmentioning

confidence: 97%

Distribution of a dechlorinating community in relation to the distance from a trichloroethene dense nonaqueous phase liquid in a model aquifer

Philips

Hamels

Smolders

et al. 2012

FEMS Microbiol Ecol

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“…DNA was extracted from 400 µL of liquid sample or 400 µg of wet solid phase as described by Uyttebroek et al (2006). Quantification of Dehalococcoides numbers was performed using real-time PCR as described previously (Dijk et al 2008) with a detection limit of 1.6×10 6 16S rDNA copies L -1 . Following the same protocol, Geobacter and Bacteria numbers were quantified in duplicate using the ABsolute TM QPCR SYBR Green Mix (ABgene) and primer sets Geo73f/Geo485r (Duhamel and Edwards, 2006) and Eub341F/Eub534r (Muyzer et al 1993), respectively (see supporting information).…”

Section: Analytical Methods and Data Analysis Tcementioning

confidence: 99%

The reactive transport of trichloroethene is influenced by residence time and microbial numbers

Haest

Philips

Springael

et al. 2011

Journal of Contaminant Hydrology

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The dechlorination rate in a flow-through porous matrix can be described by the species specific dechlorination rate observed in a liquid batch unless mass transport limitations prevail. This hypothesis was examined by comparing dechlorination rates in liquid batch with that in column experiments at various flow rates (3 -9 -12 cm d -1 ). Columns were loaded with an inoculated sand and eluted with a medium containing 1 mM trichloroethene (TCE) for 247 days. Dechlorination in the column treatments increased with decreasing flow rate, illustrating the effect of the longer residence time. Zero th order TCE or cis-DCE degradation rates were 4-7 fold larger in columns than in corresponding batch systems which could be explained by the higher measured Geobacter and Dehalococcoides numbers per unit pore volume in the columns. The microbial numbers also explained the variability in dechlorination rate among flow rate treatments marked by a large elution of the dechlorinating species' yield as flow increased. Stop flow events did not reveal mass transport limitations for dechlorination. We conclude that flow rate effects on reactive transport of TCE in this coarse sand are explained by residence time and by microbial transport and that mass transport limitations in this porous matrix are limited.

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“…The qPCR was performed in 15‐μL reaction volumes in duplicate. Calibration of the qPCR was performed as described by Dijk et al (2008). Previously cloned 16S rRNA gene PCR amplicons of D. ethenogenes strain 195 served as a template for the preparation of the standard curve.…”

Section: Methodsmentioning

confidence: 99%

Tetrachloroethene conversion to ethene by aDehalococcoides-containing enrichment culture from Bitterfeld

Cichocka

Nikolausz

Haest

et al. 2010

FEMS Microbiology Ecology

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A Dehalococcoides-dominated culture coupling reductive dechlorination of tetrachloroethene (PCE) to ethene to growth was enriched from a European field site for the first time. Microcosms were set up using groundwater from a chlorinated ethene-contaminated anaerobic aquifer in Bitterfeld (Germany). Active, lactate-amended microcosms capable of PCE dechlorination to ethene without the accumulation of intermediates were used for further enrichment. After three transfers on lactate as an electron donor and PCE as an electron acceptor, the enrichment was transferred to parallel cultures with one of the chlorinated ethenes as an electron acceptor and acetate and hydrogen as the carbon and energy source, respectively. After three more transfers, a highly purified culture was derived that was capable of dechlorinating PCE with hydrogen and acetate as the electron donor and carbon source, respectively. PCR, followed by denaturing gradient gel electrophoresis, cloning and sequencing revealed that this culture was dominated by a Dehalococcoides sp. belonging to the Pinellas group. Investigation of substrate specificity in the parallel cultures suggested the presence of a novel Dehalococcoides that can couple all dechlorination steps, from PCE to ethene, to energy conservation. Quantitative real-time PCR confirmed growth with PCE, cis-dichloroethene, 1,1-dichloroethene or vinyl chloride as electron acceptors. The culture was designated BTF08 due to its origin in Bitterfeld.

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Catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH) detection of Dehalococcoides

Cited by 18 publications

References 27 publications

Distribution of a dechlorinating community in relation to the distance from a trichloroethene dense nonaqueous phase liquid in a model aquifer

Distribution of a dechlorinating community in relation to the distance from a trichloroethene dense nonaqueous phase liquid in a model aquifer

The reactive transport of trichloroethene is influenced by residence time and microbial numbers

Tetrachloroethene conversion to ethene by aDehalococcoides-containing enrichment culture from Bitterfeld

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