Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments

Separation of fluorescence-labelled terminal restriction fragment DNA on a two-dimensional gel (T-RFs-2D) - an efficient approach for microbial consortium characterization

(2011) Shanquan Wang et al.   ENVIRONMENTAL MICROBIOLOGY

DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment

(2011) Marc G. Dumont et al.   ENVIRONMENTAL MICROBIOLOGY

Complete Debromination of Tetra- and Penta-Brominated Diphenyl Ethers by a Coculture Consisting ofDehalococcoidesandDesulfovibrioSpecies

(2011) Lip Kim Lee et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray

(2011) Patrick K H Lee et al.   ISME Journal

Development of an Environmental Functional Gene Microarray for Soil Microbial Communities

(2010) K. C. McGrath et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Detection of 2,4,6-Trinitrotoluene-Utilizing Anaerobic Bacteria by 15N and 13C Incorporation

(2010) E. M. Gallagher et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification and Characterization of a Novel CprA Reductive Dehalogenase Specific to Highly Chlorinated Phenols from Desulfitobacterium hafniense Strain PCP-1

(2010) A. Bisaillon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enzyme systems for biodegradation of polychlorinated dibenzo-p-dioxins

(2010) Toshiyuki Sakaki et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Characterization of microbial community structure and population dynamics of tetrachloroethene-dechlorinating tidal mudflat communities

(2010) Jaejin Lee et al.   BIODEGRADATION

Cloning of a Novel Dehalogenase from Environmental DNA

(2010) Hisashi KIMOTO et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

(2010) Ashish Agarwal et al.   BMC GENOMICS

Novel Hybrid Esterase-Haloacid Dehalogenase Enzyme

(2010) Ana Beloqui et al.   CHEMBIOCHEM

Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils

(2010) Audra Nemir et al.   CHEMOSPHERE

Metagenomic era for biocatalyst identification

(2010) Lucía Fernández-Arrojo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Beyond directed evolution—semi-rational protein engineering and design

(2010) Stefan Lutz   CURRENT OPINION IN BIOTECHNOLOGY

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

Comparing On-Site to Off-Site Biomass Collection forDehalococcoidesBiomarker Gene Quantification To Predict in Situ Chlorinated Ethene Detoxification Potential

(2010) Kirsti M. Ritalahti et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Effect of Dechlorination and Sulfate Reduction on the Microbial Community Structure in Denitrifying Membrane-Biofilm Reactors

(2010) Husen Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Field Evidence for Co-Metabolism of Trichloroethene Stimulated by Addition of Electron Donor to Groundwater

(2010) Mark E. Conrad et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Effects of Elevated Temperature onDehalococcoidesDechlorination Performance and DNA and RNA Biomarker Abundance

(2010) Kelly E. Fletcher et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2010) Danuta Cichocka et al.   FEMS MICROBIOLOGY ECOLOGY

Concurrent hexachlorobenzene and chloroethene transformation by endogenous dechlorinating microorganisms in the Ebro River sediment

(2010) Neslihan Taş et al.   FEMS MICROBIOLOGY ECOLOGY

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

(2010) Zhili He et al.   ISME Journal

Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species

(2010) Wai Ling Chow et al.   ISME Journal

A Dehaloccoides-like bacterium and a new reductive dehalogenase are responsible for PCB dechlorination in marine sediments under in situ biogeochemical conditions

(2010) G. Zanaroli et al.   JOURNAL OF BIOTECHNOLOGY

Protein-based stable isotope probing

(2010) Nico Jehmlich et al.   Nature Protocols

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

(2010) A. M. Smith et al.   NUCLEIC ACIDS RESEARCH

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

(2010) Terry C. Hazen et al.   SCIENCE

Tracking Functional Guilds: "Dehalococcoides" spp. in European River Basins Contaminated with Hexachlorobenzene

(2009) N. Tas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of a Dehalobacter Coculture That Dechlorinates 1,2-Dichloroethane to Ethene and Identification of the Putative Reductive Dehalogenase Gene

(2009) A. Grostern et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity and Distribution of Anaeromyxobacter Strains in a Uranium-Contaminated Subsurface Environment with a Nonuniform Groundwater Flow

(2009) S. H. Thomas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Isolation and Characterization of "Dehalococcoides" sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene

(2009) D. Cheng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Detection and Quantification of Dehalogenimonas and "Dehalococcoides" Populations via PCR-Based Protocols Targeting 16S rRNA Genes

(2009) J. Yan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evidence for Nitrogen Fixation by "Dehalococcoides ethenogenes" Strain 195

(2009) P. K. H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcription Analysis of Genes Encoding Homologues of Reductive Dehalogenases in "Dehalococcoides" sp. Strain CBDB1 by Using Terminal Restriction Fragment Length Polymorphism and Quantitative PCR

(2009) A. Wagner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment

(2009) W. J. Sul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities

(2009) A. Ramette   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Advances in molecular and “-omics” technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites

(2009) Chirayu Desai et al.   BIORESOURCE TECHNOLOGY

Absolute quantification ofDehalococcoidesproteins: enzyme bioindicators of chlorinated ethene dehalorespiration

(2009) Jeffrey J. Werner et al.   ENVIRONMENTAL MICROBIOLOGY

GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer

(2009) Joy D. Van Nostrand et al.   ENVIRONMENTAL MICROBIOLOGY

Reductive dehalogenation of brominated ethenes bySulfurospirillum multivoransandDesulfitobacterium hafniensePCE-S

(2009) Lidan Ye et al.   ENVIRONMENTAL MICROBIOLOGY

Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing

(2009) Steffi Herrmann et al.   ENVIRONMENTAL MICROBIOLOGY

Comparison of an assay for Dehalococcoides DNA and a microcosm study in predicting reductive dechlorination of chlorinated ethenes in the field

(2009) Xiaoxia Lu et al.   ENVIRONMENTAL POLLUTION

Spatial and Temporal Distributions of Geobacter lovleyi and Dehalococcoides spp. during Bioenhanced PCE-NAPL Dissolution

(2009) Benjamin K. Amos et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Spatial heterogeneity of dechlorinating bacteria and limiting factors forin situ trichloroethene dechlorination revealed by analyses of sediment cores from a polluted field site

(2009) Kerstin Dowideit et al.   FEMS MICROBIOLOGY ECOLOGY

Transcriptomic microarray analysis of corrinoid responsive genes inDehalococcoides ethenogenesstrain 195

(2009) David R. Johnson et al.   FEMS MICROBIOLOGY LETTERS

A Dehalococcoides-containing co-culture that dechlorinates tetrachloroethene to trans-1,2-dichloroethene

(2009) Dan Cheng et al.   ISME Journal

Investigation of Carbon Metabolism in "Dehalococcoides ethenogenes" Strain 195 by Use of Isotopomer and Transcriptomic Analyses

(2009) Y. J. Tang et al.   JOURNAL OF BACTERIOLOGY

Removal of polychlorinated dioxins by semi-aerobic fed-batch composting with biostimulation of “Dehalococcoides”

(2009) Takashi Narihiro et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Phylogenetic and Transcriptional Analyses of a Tetrachloroethene-Dechlorinating "Dehalococcoides" Enrichment Culture TUT2264 and Its Reductive-Dehalogenase Genes

(2009) Hiroyuki Futamata et al.   MICROBES AND ENVIRONMENTS

Quantitative detection of chloroethene-reductive bacteria Dehalococcoides spp. using alternately binding probe competitive polymerase chain reaction

(2009) Ryo Miyata et al.   MOLECULAR AND CELLULAR PROBES

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

(2009) Martina Pavlova et al.   Nature Chemical Biology

Next-generation DNA sequencing techniques

(2009) Wilhelm J. Ansorge   New Biotechnology

The little bacteria that can - diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments

(2009) Neslihan Taş et al.   Microbial Biotechnology

Sequence- and activity-based screening of microbial genomes for novel dehalogenases

(2009) Wing Yiu Chan et al.   Microbial Biotechnology

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Resolution of Culture Clostridium bifermentans DPH-1 into Two Populations, a Clostridium sp. and Tetrachloroethene-Dechlorinating Desulfitobacterium hafniense Strain JH1

(2008) K. E. Fletcher et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative Genomics of "Dehalococcoides ethenogenes" 195 and an Enrichment Culture Containing Unsequenced "Dehalococcoides" Strains

(2008) K. A. West et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Temporal Transcriptomic Microarray Analysis of "Dehalococcoides ethenogenes" Strain 195 during the Transition into Stationary Phase

(2008) D. R. Johnson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantifying Genes and Transcripts To Assess the In Situ Physiology of "Dehalococcoides" spp. in a Trichloroethene-Contaminated Groundwater Site

(2008) P. K. H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of the Community Structure of a Dechlorinating Mixed Culture and Comparisons of Gene Expression in Planktonic and Biofloc-Associated "Dehalococcoides" and Methanospirillum Species

(2008) A. R. Rowe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dehalorespiration with Polychlorinated Biphenyls by an Anaerobic Ultramicrobacterium

(2008) H. D. May et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system

(2008) Chunhong Mao et al.   BMC MICROBIOLOGY

Novel uncultured Chloroflexi dechlorinate perchloroethene to trans-dichloroethene in tidal flat sediments

(2008) Sandra Kittelmann et al.   ENVIRONMENTAL MICROBIOLOGY

Site-specific microbial communities in three PCB-impacted sediments are associated with different in situ dechlorinating activities

(2008) Birthe V. Kjellerup et al.   ENVIRONMENTAL MICROBIOLOGY

Enrichment of a dioxin-dehalogenating Dehalococcoides species in two-liquid phase cultures

(2008) Michael Bunge et al.   ENVIRONMENTAL MICROBIOLOGY

Isolation of novel bacteria within theChloroflexicapable of reductive dechlorination of 1,2,3-trichloropropane

(2008) J. Yan et al.   ENVIRONMENTAL MICROBIOLOGY

Oxygen Effect onDehalococcoidesViability and Biomarker Quantification

(2008) Benjamin K. Amos et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Development of Microbial Genome-Probing Microarrays Using Digital Multiple Displacement Amplification of Uncultivated Microbial Single Cells

(2008) Ho-Won Chang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Dehalococcoides’ Gene Transcripts As Quantitative Bioindicators of Tetrachloroethene, Trichloroethene, andcis-1,2-Dichloroethene Dehalorespiration Rates

(2008) Brian G. Rahm et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

(2008) A JUSTE et al.   FOOD MICROBIOLOGY

A novel and rapid method for synthesizing positive controls and standards for quantitative PCR

(2008) Maude M. David et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Statistical superiority of genome-probing microarrays as genomic DNA–DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods

(2008) Ho-Won Chang et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

(2008) Z. M.-P. Lee et al.   NUCLEIC ACIDS RESEARCH

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlation of Respiratory Gene Expression Levels and Pseudo-Steady-State PCE Respiration Rates inDehalococcoides ethenogenes

(2007) Brian G. Rahm et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Application of Clostridium-specific PCR primers on the analysis of dark fermentation hydrogen-producing bacterial community

(2007) C HUNG et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

Real-time PCR quantification of Dehalococcoides populations: Methods and applications

(2007) Alison M. Cupples   JOURNAL OF MICROBIOLOGICAL METHODS