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

The arrival of chemicals in a soil or groundwater ecosystem could upset the natural balance of the microbial community. Since soil microorganisms are the first to be exposed to the chemicals released into the soil environment, we evaluated the use of a phylogenetic microarray as a bio-indicator of community perturbations due to the exposure to trichloroethylene (TCE). The phylogenetic microarray, which measures the presence of different members of the soil community, was used to evaluate unpolluted soils exposed to TCE as well as to samples from historically TCE polluted sites. We were able to determine an apparent threshold at which the microbial community structure was significantly affected (about 1ppm). In addition, the members of the microbial community most affected were identified. This approach could be useful for assessing environmental impact of chemicals on the biosphere as well as important members of the microbial community involved in TCE degradation.

[1]  Harald Meier,et al.  46. ARB: A Software Environment for Sequence Data , 2011 .

[2]  N. Stacey.  Toxicity of Mixtures of Trichloroethylene, Tetrachloroethylene and 1,1,1-Trichloroethane: Similarity of in Vitro to in Vivo Responses , 1989, Toxicology and industrial health.

[3]  H. D. Stensel,et al.  Analysis and comparison of the microbial community structures of two enrichment cultures capable of reductively dechlorinating TCE and cis-DCE. , 2003, Environmental microbiology.

[4]  J. Hobman,et al.  Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction , 1992, Applied and environmental microbiology.

[5]  S. Harayama,et al.  Bacterial populations occuring in a trichloroethylene-contaminated aquifer during methane injection. , 2001, Environmental microbiology.

[6]  F. Löffler,et al.  Comparative analysis of three tetrachloroethene to ethene halorespiring consortia suggests functional redundancy. , 2007, Environmental science & technology.

[7]  R. Vink,et al.  Degradation of chlorinated aliphatic hydrocarbons by Methylosinus trichosporium OB3b expressing soluble methane monooxygenase , 1989, Applied and environmental microbiology.

[8]  T. Leisinger,et al.  Isolation of an anaerobic bacterium which reductively dechlorinates tetrachloroethene and trichloroethene , 2004, Biodegradation.

[9]  T. Brüning,et al.  Renal carcinogenicity of trichloroethylene: update, mode of action, and fundamentals for occupational standard setting. , 2005, Reviews on environmental health.

[10]  A. Hooper,et al.  Degradation of trichloroethylene by the ammonia-oxidizing bacterium Nitrosomonas europaea. , 1989, Biochemical and biophysical research communications.

[11]  A. Konopka,et al.  Microbial Community Analysis of Soils Contaminated with Lead, Chromium and Petroleum Hydrocarbons , 2006, Microbial Ecology.

[12]  Dorothea K. Thompson,et al.  Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment , 2001, Applied and Environmental Microbiology.

[13]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[14]  N. Stralis-Pavese,et al.  Development and validation of a diagnostic microbial microarray for methanotrophs. , 2003, Environmental microbiology.

[15]  D. L. Song,et al.  Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques. , 2002, Environmental science & technology.

[16]  Jean Thioulouse,et al.  ADE-4: a multivariate analysis and graphical display software , 1997, Stat. Comput..

[17]  Jizhong Zhou,et al.  Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. , 2004, BioTechniques.

[18]  Frank Oliver Glöckner,et al.  Graphical representation of ribosomal RNA probe accessibility data using ARB software package , 2005, BMC Bioinformatics.

[19]  L. Alvarez-Cohen,et al.  Transcriptional Expression of the tceA Gene in a Dehalococcoides-Containing Microbial Enrichment , 2005, Applied and Environmental Microbiology.

[20]  S. Giovannoni,et al.  Bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethene-contaminated groundwater. , 2005, Environmental microbiology.

[21]  K. Nakamura,et al.  Constitutive trichloroethylene degradation led by tac promoter chromosomally integrated upstream of phenol hydroxylase genes of Ralstonia sp. KN1 and its nucleotide sequence analysis. , 2000, Journal of bioscience and bioengineering.

[22]  J. Trevors,et al.  Methods of studying soil microbial diversity. , 2004, Journal of microbiological methods.

[23]  M. Lidstrom,et al.  Trichloroethylene Biodegradation by a Methane-Oxidizing Bacterium , 1988, Applied and environmental microbiology.

[24]  L. Alvarez-Cohen,et al.  Evaluation of Toxic Effects of Aeration and Trichloroethylene Oxidation on Methanotrophic Bacteria Grown with Different Nitrogen Sources , 1999, Applied and Environmental Microbiology.

[25]  L. Alvarez-Cohen,et al.  Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors. , 2005, Environmental science & technology.

[26]  R. Fulthorpe,et al.  Monitoring Gene Expression in Mixed Microbial Communities by Using DNA Microarrays , 2003, Applied and Environmental Microbiology.

[27]  T. Vogel,et al.  Thematic Issue on Horizontal Gene Transfer Detection of potential transgenic plant DNA recipients among soil bacteria , 2007 .

[28]  P. Brown,et al.  Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[29]  J. Humphries,et al.  Microbial community structure and trichloroethylene degradation in groundwater. , 2005, Canadian journal of microbiology.

[30]  S. Penn,et al.  Applications of gene arrays in environmental toxicology: fingerprints of gene regulation associated with cadmium chloride, benzo(a)pyrene, and trichloroethylene. , 2000, Environmental health perspectives.

[31]  H. Wolf,et al.  Genetic effects of chlorinated ethylenes in the yeast Saccharomyces cerevisiae. , 1988, Mutation research.

[32]  T. Vogel,et al.  Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities , 2006, Applied and Environmental Microbiology.

[33]  T. Fan,et al.  Relationships between Sediment Microbial Communities and Pollutants in Two California Salt Marshes , 2006, Microbial Ecology.

[34]  C. Piccoli,et al.  The study of gap junctional intercellular communication in keratinocytes as screening of promoter effect induced by industrial and environmental toxic substances. , 2005, La Medicina del lavoro.

[35]  J. Tiedje,et al.  Quantitative Detection of Microbial Genes by Using DNA Microarrays , 2002, Applied and Environmental Microbiology.

[36]  V. de Lorenzo,et al.  Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. , 2006, Environmental microbiology.

[37]  P. H. Pritchard,et al.  Aerobic Metabolism of Trichloroethylene by a Bacterial Isolate , 1986, Applied and environmental microbiology.

[38]  D. E. Ellis,et al.  Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe , 2002, Applied and Environmental Microbiology.

[39]  T. Vogel,et al.  High molecular weight DNA recovery from soils prerequisite for biotechnological metagenomic library construction. , 2005, Journal of microbiological methods.

[40]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[41]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[42]  P. Sharma,et al.  Isolation and Characterization of a Facultatively Aerobic Bacterium That Reductively Dehalogenates Tetrachloroethene to cis-1,2-Dichloroethene , 1996, Applied and environmental microbiology.

[43]  J. Gossett,et al.  Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. , 1997, Science.

[44]  Roland Brousseau,et al.  Molecular Biology and DNA Microarray Technology for Microbial Quality Monitoring of Water , 2004, Critical reviews in microbiology.

[45]  P. Brown,et al.  A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. , 1996, Genome research.

[46]  T. Vogel,et al.  Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditions , 1985, Applied and environmental microbiology.

[47]  P. Chiu,et al.  2-Bromoethanesulfonate Affects Bacteria in a Trichloroethene-Dechlorinating Culture , 2001, Applied and Environmental Microbiology.

[48]  C. Tyson,et al.  Rat Liver Foci and in Vitro Assays to Detect Initiating and Promoting Effects of Chlorinated Ethanes and Ethylenes a , 1988, Annals of the New York Academy of Sciences.

[49]  Pascal Simonet,et al.  Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. , 2006, Environmental microbiology.