Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community

BackgroundThe Dehalococcoides are strictly anaerobic bacteria that gain metabolic energy via the oxidation of H2 coupled to the reduction of halogenated organic compounds. Dehalococcoides spp. grow best in mixed microbial consortia, relying on non-dechlorinating members to provide essential nutrients and maintain anaerobic conditions.A metagenome sequence was generated for the dechlorinating mixed microbial consortium KB-1. A comparative metagenomic study utilizing two additional metagenome sequences for Dehalococcoides-containing dechlorinating microbial consortia was undertaken to identify common features that are provided by the non-dechlorinating community and are potentially essential to Dehalococcoides growth.ResultsThe KB-1 metagenome contained eighteen novel homologs to reductive dehalogenase genes. The metagenomes obtained from the three consortia were automatically annotated using the MG-RAST server, from which statistically significant differences in community composition and metabolic profiles were determined. Examination of specific metabolic pathways, including corrinoid synthesis, methionine synthesis, oxygen scavenging, and electron-donor metabolism identified the Firmicutes, methanogenic Archaea, and the ∂-Proteobacteria as key organisms encoding these pathways, and thus potentially producing metabolites required for Dehalococcoides growth.ConclusionsComparative metagenomics of the three Dehalococcoides-containing consortia identified that similarities across the three consortia are more apparent at the functional level than at the taxonomic level, indicating the non-dechlorinating organisms’ identities can vary provided they fill the same niche within a consortium. Functional redundancy was identified in each metabolic pathway of interest, with key processes encoded by multiple taxonomic groups. This redundancy likely contributes to the robust growth and dechlorination rates in dechlorinating enrichment cultures.

[1]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[2]  Robert G. Beiko,et al.  Classifying short genomic fragments from novel lineages using composition and homology , 2011, BMC Bioinformatics.

[3]  Itai Sharon,et al.  Comparative metagenomics of microbial traits within oceanic viral communities , 2011, The ISME Journal.

[4]  L. Alvarez-Cohen,et al.  Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses , 2011, The ISME Journal.

[5]  Michaye L. McMaster,et al.  Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene. , 2002, Environmental science & technology.

[6]  E. Edwards,et al.  Anaerobic degradation of toluene and o-xylene by a methanogenic consortium , 1994, Applied and environmental microbiology.

[7]  Alla Lapidus,et al.  The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens , 2009, BMC Microbiology.

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

[9]  K. Wilson.  Preparation of Genomic DNA from Bacteria , 2001, Current protocols in molecular biology.

[10]  M. Gelfand,et al.  Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes* , 2003, Journal of Biological Chemistry.

[11]  E. Edwards,et al.  Growth and yields of dechlorinators, acetogens, and methanogens during reductive dechlorination of chlorinated ethenes and dihaloelimination of 1 ,2-dichloroethane. , 2007, Environmental science & technology.

[12]  Benjamin J. Raphael,et al.  The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families , 2007, PLoS biology.

[13]  M. Adams,et al.  Biological Hydrogen Production: Not So Elementary , 1998, Science.

[14]  Eoin L. Brodie,et al.  Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray , 2011, The ISME Journal.

[15]  Alison S. Waller.  Molecular Investigation of Chloroethene Reductive Dehalogenation by the Mixed Microbial Community KB1 , 2010 .

[16]  Radhakrishnan Mahadevan,et al.  Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model , 2010, PLoS Comput. Biol..

[17]  G. Zellner,et al.  Degradation of lactate by an anaerobic mixed culture in a fluidized-bed reactor , 1994 .

[18]  A. Spormann,et al.  Molecular Identification of the Catabolic Vinyl Chloride Reductase from Dehalococcoides sp. Strain VS and Its Environmental Distribution , 2004, Applied and Environmental Microbiology.

[19]  Howard Ochman,et al.  Comparative Metagenomics and Population Dynamics of the Gut Microbiota in Mother and Infant , 2010, Genome biology and evolution.

[20]  A. Xu,et al.  Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries , 2011, The ISME Journal.

[21]  Robert G. Beiko,et al.  Rapid identification of high-confidence taxonomic assignments for metagenomic data , 2012, Nucleic acids research.

[22]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[23]  J. Gossett,et al.  Reductive Dechlorination of Tetrachloroethene to Ethene by a Two-Component Enzyme Pathway , 1998, Applied and Environmental Microbiology.

[24]  W. Hagen,et al.  Characterization of the Corrinoid Iron-Sulfur Protein Tetrachloroethene Reductive Dehalogenase of Dehalobacter restrictus , 2003, Applied and Environmental Microbiology.

[25]  D. Shultis,et al.  Outer Membrane Active Transport: Structure of the BtuB:TonB Complex , 2006, Science.

[26]  Hui-Hsien Chou,et al.  DNA sequence quality trimming and vector removal , 2001, Bioinform..

[27]  Hiroshi Mori,et al.  Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes , 2007, DNA research : an international journal for rapid publication of reports on genes and genomes.

[28]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[29]  Alison S. Waller,et al.  Transcriptional Analysis of a Dehalococcoides-Containing Microbial Consortium Reveals Prophage Activation , 2011, Applied and Environmental Microbiology.

[30]  S. Kravitz,et al.  CAMERA: A Community Resource for Metagenomics , 2007, PLoS biology.

[31]  J. Meyer,et al.  Classification and phylogeny of hydrogenases. , 2001, FEMS microbiology reviews.

[32]  Jianzhong He,et al.  Isolation and Characterization of “Dehalococcoides” sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene , 2009, Applied and Environmental Microbiology.

[33]  R. Reinhardt,et al.  Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1 , 2005, Nature Biotechnology.

[34]  K. M. Ritalahti,et al.  Isolation and characterization of Dehalococcoides sp. strain FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe. , 2005, Environmental microbiology.

[35]  Alexander F. Auch,et al.  MEGAN analysis of metagenomic data. , 2007, Genome research.

[36]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[37]  J. Gobom,et al.  Identification of a Chlorobenzene Reductive Dehalogenase in Dehalococcoides sp. Strain CBDB1 , 2007, Applied and Environmental Microbiology.

[38]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[39]  E. Delong,et al.  Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre , 2009, Applied and Environmental Microbiology.

[40]  Andreas Wilke,et al.  phylogenetic and functional analysis of metagenomes , 2022 .

[41]  Alison S. Waller,et al.  Multiple Reductive-Dehalogenase-Homologous Genes Are Simultaneously Transcribed during Dechlorination by Dehalococcoides-Containing Cultures , 2005, Applied and Environmental Microbiology.

[42]  Paul J. McMurdie,et al.  Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides , 2011, BMC Genomics.

[43]  E. Edwards,et al.  Growth of Dehalobacter and Dehalococcoides spp. during Degradation of Chlorinated Ethanes , 2006, Applied and Environmental Microbiology.

[44]  C. Cruz-García,et al.  Oxygen effect on Dehalococcoides viability and biomarker quantification. , 2008, Environmental science & technology.

[45]  J A Eisen,et al.  Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments , 2003, Science.

[46]  H. Görisch,et al.  Reductive Dehalogenation of Chlorobenzene Congeners in Cell Extracts of Dehalococcoides sp. Strain CBDB1 , 2003, Applied and Environmental Microbiology.

[47]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[48]  S. Zinder,et al.  Characterization of Hydrogenase and Reductive Dehalogenase Activities of Dehalococcoides ethenogenes Strain 195 , 2005, Applied and Environmental Microbiology.

[49]  Daniel H. Huson,et al.  Visual and statistical comparison of metagenomes , 2009, Bioinform..

[50]  N. A. F R E E B O R N,et al.  Phylogenetic Analysis of TCE-Dechlorinating Consortia Enriched on a Variety of Electron Donors , 2022 .

[51]  R. Morris,et al.  Temporal Expression of Respiratory Genes in an Enrichment Culture Containing Dehalococcoides ethenogenes , 2006, Applied and Environmental Microbiology.

[52]  Katherine H. Kang,et al.  Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes , 2005, Science.

[53]  E. Edwards,et al.  Comparison of anaerobic dechlorinating enrichment cultures maintained on tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride. , 2002, Water Research.

[54]  L. Alvarez-Cohen,et al.  Influence of Vitamin B12 and Cocultures on the Growth of Dehalococcoides Isolates in Defined Medium , 2007, Applied and Environmental Microbiology.

[55]  Paul J. McMurdie,et al.  Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides , 2009, PLoS genetics.

[56]  Yinjie J. Tang,et al.  Investigation of Carbon Metabolism in “Dehalococcoides ethenogenes” Strain 195 by Use of Isotopomer and Transcriptomic Analyses , 2009, Journal of bacteriology.

[57]  D. Bedard,et al.  “Dehalococcoides” sp. Strain CBDB1 Extensively Dechlorinates the Commercial Polychlorinated Biphenyl Mixture Aroclor 1260 , 2009, Applied and Environmental Microbiology.

[58]  D. P. McCarty.  Phylogenetic Characterization of Microbial Communities That Reductively Dechlorinate TCE Based upon a Combination of Molecular Techniques , 2022 .

[59]  J. Paquet,et al.  The Ton System, an ABC Transporter, and a Universally Conserved GTPase Are Involved in Iron Utilization by Brucella melitensis 16M , 2004, Infection and Immunity.

[60]  James M. Gossett,et al.  Modeling the Production of and Competition for Hydrogen in a Dechlorinating Culture , 1998 .

[61]  Yinjie J. Tang,et al.  Selective Utilization of Exogenous Amino Acids by Dehalococcoides ethenogenes Strain 195 and Its Effects on Growth and Dechlorination Activity , 2011, Applied and Environmental Microbiology.

[62]  E. Edwards,et al.  Characterization of a Highly Enriched Dehalococcoides-Containing Culture That Grows on Vinyl Chloride and Trichloroethene , 2004, Applied and Environmental Microbiology.

[63]  E. Edwards,et al.  Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. , 2006, FEMS microbiology ecology.

[64]  Florent E. Angly,et al.  Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome , 2008, PloS one.

[65]  Y. Toyoshima,et al.  Isolation and Characterization of pos Mutants Defective in Correct Positioning of Septum in Schizosaccharomyces pombe , 1996, Zoological science.

[66]  R. Morris,et al.  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, Applied and Environmental Microbiology.

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

[68]  L. Alvarez-Cohen,et al.  Discrimination of Multiple Dehalococcoides Strains in a Trichloroethene Enrichment by Quantification of Their Reductive Dehalogenase Genes , 2006, Applied and Environmental Microbiology.

[69]  Forest Rohwer,et al.  An application of statistics to comparative metagenomics , 2006, BMC Bioinformatics.

[70]  Robert G. Beiko,et al.  Identifying biologically relevant differences between metagenomic communities , 2010, Bioinform..

[71]  D. Livermore.  beta-Lactamases in laboratory and clinical resistance , 1995, Clinical microbiology reviews.