chloroflexi

Summary

Summary: Phylum of green nonsulfur bacteria including the family Chloroflexaceae, among others.

Top Publications

  1. Miura Y, Watanabe Y, Okabe S. Significance of Chloroflexi in performance of submerged membrane bioreactors (MBR) treating municipal wastewater. Environ Sci Technol. 2007;41:7787-94 pubmed
    ..increased, which consequently resulted in membrane fouling, when relative abundance of the member of uncultured Chloroflexi decreased from over 30% of total Bacteria to less than 10%...
  2. Kragelund C, Levantesi C, Borger A, Thelen K, Eikelboom D, Tandoi V, et al. Identity, abundance and ecophysiology of filamentous Chloroflexi species present in activated sludge treatment plants. FEMS Microbiol Ecol. 2007;59:671-82 pubmed
    Filamentous Chloroflexi species are often present in activated sludge wastewater treatment plants in relatively low numbers, although bulking incidences caused by Chloroflexi filaments have been observed...
  3. Fennell D, Nijenhuis I, Wilson S, Zinder S, Häggblom M. Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. Environ Sci Technol. 2004;38:2075-81 pubmed
    ..Harnessing microorganisms such as Dehalococcoides spp. that detoxify these compounds via removal of halogens may lead to cost-effective biotechnological approaches for remediation. ..
  4. McMurdie P, Behrens S, Müller J, Goke J, Ritalahti K, Wagner R, et al. Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet. 2009;5:e1000714 pubmed publisher
    ..This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism. ..
  5. Kittelmann S, Friedrich M. Novel uncultured Chloroflexi dechlorinate perchloroethene to trans-dichloroethene in tidal flat sediments. Environ Microbiol. 2008;10:1557-70 pubmed publisher
    ..0%; 22.4% delta-, 12.1% gamma-, 6.9% alpha-, 6.9% beta- and 1.7% epsilon-subgroup) and Chloroflexi (29.3%)...
  6. Rowe A, Lazar B, Morris R, Richardson R. Characterization of the community structure of a dechlorinating mixed culture and comparisons of gene expression in planktonic and biofloc-associated "Dehalococcoides" and Methanospirillum species. Appl Environ Microbiol. 2008;74:6709-19 pubmed publisher
    ..This suggests that, unlike the comparable activity of D. ethenogenes from both enrichments, planktonic M. hungatei is responsible for only a small fraction of the hydrogenotrophic methanogenesis in this culture...
  7. He J, Holmes V, Lee P, Alvarez Cohen L. Influence of vitamin B12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl Environ Microbiol. 2007;73:2847-53 pubmed
  8. Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, et al. Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. J Bacteriol. 2006;188:2262-74 pubmed
    ..Our results provide further impetus to the use of desulfitobacteria as tools for bioremediation...
  9. Bunge M, Wagner A, Fischer M, Andreesen J, Lechner U. Enrichment of a dioxin-dehalogenating Dehalococcoides species in two-liquid phase cultures. Environ Microbiol. 2008;10:2670-83 pubmed publisher
    ..The novel Dehalococcoides strain DCMB5 was enriched up to 50% by the cultivation with organic acids, hydrogen and vancomycin, and was finally purified by conventional isolation techniques. ..

More Information

Publications86

  1. Krajmalnik Brown R, H lscher T, Thomson I, Saunders F, Ritalahti K, L ffler F. Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Appl Environ Microbiol. 2004;70:6347-51 pubmed publisher
    ..bvcA was absent in Dehalococcoides isolates that failed to respire VC, yet was detected in four of eight VC-respiring mixed cultures...
  2. Yan J, Rash B, Rainey F, Moe W. Isolation of novel bacteria within the Chloroflexi capable of reductive dechlorination of 1,2,3-trichloropropane. Environ Microbiol. 2009;11:833-43 pubmed
    ..analysis based on 16S rRNA gene sequence data showed these isolates to represent a new lineage within the Chloroflexi. Their closest previously cultured relatives are 'Dehalococcoides' strains, with 16S rRNA gene sequence ..
  3. Yamada M, Zhang H, Hanada S, Nagashima K, Shimada K, Matsuura K. Structural and spectroscopic properties of a reaction center complex from the chlorosome-lacking filamentous anoxygenic phototrophic bacterium Roseiflexus castenholzii. J Bacteriol. 2005;187:1702-9 pubmed
    ..castenholzii have intermediate characteristics between those of purple bacteria and C. aurantiacus, it is likely that they retain many features of the common ancestor of purple bacteria and filamentous anoxygenic phototrophic bacteria. ..
  4. Kube M, Beck A, Zinder S, Kuhl H, Reinhardt R, Adrian L. Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol. 2005;23:1269-73 pubmed
  5. Wagner A, Adrian L, Kleinsteuber S, Andreesen J, Lechner U. Transcription analysis of genes encoding homologues of reductive dehalogenases in "Dehalococcoides" sp. strain CBDB1 by using terminal restriction fragment length polymorphism and quantitative PCR. Appl Environ Microbiol. 2009;75:1876-84 pubmed publisher
    ..Finally, cbrA was transcribed to a level of 22 transcripts per cbrA gene, suggesting that cbrA mRNA could be an appropriate biomarker for the investigation of the natural dechlorination potential at chlorobenzene-contaminated sites. ..
  6. Maphosa F, Smidt H, de Vos W, Röling W. Microbial community- and metabolite dynamics of an anoxic dechlorinating bioreactor. Environ Sci Technol. 2010;44:4884-90 pubmed publisher
  7. Grégoire P, Fardeau M, Joseph M, Guasco S, Hamaide F, Biasutti S, et al. Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum "Chloroflexi", isolated from a deep hot aquifer in the Aquitaine Basin. Syst Appl Microbiol. 2011;34:494-7 pubmed publisher
    ..is proposed to be assigned to a novel species of a novel genus within the class Anaerolineae (subphylum I), phylum "Chloroflexi", Thermanaerothrix daxensis gen. nov., sp. nov. The GenBank accession number is HM596746.
  8. Yan J, Rash B, Rainey F, Moe W. Detection and quantification of Dehalogenimonas and "Dehalococcoides" populations via PCR-based protocols targeting 16S rRNA genes. Appl Environ Microbiol. 2009;75:7560-4 pubmed publisher
    ..Use of the genus-specific primers revealed the presence of both bacterial groups in groundwater at a Louisiana Superfund site. ..
  9. Ziv El M, Popat S, Cai K, Halden R, Krajmalnik Brown R, Rittmann B. Managing methanogens and homoacetogens to promote reductive dechlorination of trichloroethene with direct delivery of H2 in a membrane biofilm reactor. Biotechnol Bioeng. 2012;109:2200-10 pubmed publisher
  10. Lee P, Macbeth T, Sorenson K, Deeb R, Alvarez Cohen L. Quantifying genes and transcripts to assess the in situ physiology of "Dehalococcoides" spp. in a trichloroethene-contaminated groundwater site. Appl Environ Microbiol. 2008;74:2728-39 pubmed publisher
    ..Overall, results from this study demonstrate that quantification of biomarker dynamics at field sites can provide useful information about the in situ physiology of Dehalococcoides strains and their associated activity. ..
  11. Lau C, Aitchison J, Pointing S. Early colonization of thermal niches in a silica-depositing hot spring in central Tibet. Geobiology. 2008;6:136-46 pubmed publisher
    ..The thin surface layer of silicification-resistant cyanobacteria that developed on the surface of mature mats may play a role in preventing biomineralization of the susceptible R. castenholzii beneath within these communities. ..
  12. Duhamel M, Edwards E. Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. FEMS Microbiol Ecol. 2006;58:538-49 pubmed
    ..The Sulfurospirillum phylotype was estimated to comprise a minor fraction of 16S rRNA gene copies and did not appear to have an important role in dechlorination. ..
  13. Yan T, LaPara T, Novak P. The effect of varying levels of sodium bicarbonate on polychlorinated biphenyl dechlorination in Hudson River sediment cultures. Environ Microbiol. 2006;8:1288-98 pubmed
  14. Tang Y, Yi S, Zhuang W, Zinder S, Keasling J, Alvarez Cohen L. Investigation of carbon metabolism in "Dehalococcoides ethenogenes" strain 195 by use of isotopomer and transcriptomic analyses. J Bacteriol. 2009;191:5224-31 pubmed publisher
    ..e., a novel Re-citrate synthase that is apparently different from the one recently reported in Clostridium kluyveri. ..
  15. Morris R, Fung J, Rahm B, Zhang S, Freedman D, Zinder S, et al. Comparative proteomics of Dehalococcoides spp. reveals strain-specific peptides associated with activity. Appl Environ Microbiol. 2007;73:320-6 pubmed
    ..Several additional proteins, including a formate dehydrogenase-like protein (Fdh), had high coverage in all strains and under all growth conditions. ..
  16. Podosokorskaya O, Bonch Osmolovskaya E, Novikov A, Kolganova T, Kublanov I. Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae. Int J Syst Evol Microbiol. 2013;63:86-92 pubmed publisher
    ..nov., sp. nov. is proposed; the type strain of O. apprima is P3M-1(T) (= DSM 23815(T)=VKM B-2669(T))...
  17. Rahm B, Richardson R. Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes. Environ Sci Technol. 2008;42:416-21 pubmed
    ..2 micromol/L/hr did not necessarily lead to corresponding increases in transcript levels...
  18. Tas N, van Eekert M, de Vos W, Smidt H. The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments. Microb Biotechnol. 2010;3:389-402 pubmed publisher
    ..Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments...
  19. Chung J, Krajmalnik Brown R, Rittmann B. Bioreduction of trichloroethene using a hydrogen-based membrane biofilm reactor. Environ Sci Technol. 2008;42:477-83 pubmed
    ..One of them seems to be a new strain that is unique for having tceA and bvcA reductive dehalogenases...
  20. Futamata H, Yoshida N, Kurogi T, Kaiya S, Hiraishi A. Reductive dechlorination of chloroethenes by Dehalococcoides-containing cultures enriched from a polychlorinated-dioxin-contaminated microcosm. ISME J. 2007;1:471-9 pubmed
  21. Yamada T, Imachi H, Ohashi A, Harada H, Hanada S, Kamagata Y, et al. Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. Int J Syst Evol Microbiol. 2007;57:2299-306 pubmed
    ..the strains were placed in different phylogenetic positions in the class Anaerolineae of the bacterial phylum Chloroflexi. Their phenotypic and genetic traits strongly supported the conclusion that the strains should be described as ..
  22. van der Zaan B, Hannes F, Hoekstra N, Rijnaarts H, de Vos W, Smidt H, et al. Correlation of Dehalococcoides 16S rRNA and chloroethene-reductive dehalogenase genes with geochemical conditions in chloroethene-contaminated groundwater. Appl Environ Microbiol. 2010;76:843-50 pubmed publisher
    ..Because the variation in VC-reductase gene numbers was not directly correlated to variation in Dehalococcoides spp., VC-reductase genes are better monitoring parameters for VC dechlorination capacity than Dehalococcoides spp...
  23. Nijenhuis I, Zinder S. Characterization of hydrogenase and reductive dehalogenase activities of Dehalococcoides ethenogenes strain 195. Appl Environ Microbiol. 2005;71:1664-7 pubmed
    ..Benzyl viologen or diquat (Eo' approximately -360 mV) supported reductive dechlorination of PCE or TCE at rates comparable to MV (-450 mV) in cell extracts...
  24. McMurdie P, Behrens S, Holmes S, Spormann A. Unusual codon bias in vinyl chloride reductase genes of Dehalococcoides species. Appl Environ Microbiol. 2007;73:2744-7 pubmed
    ..The comparatively high level of abnormality in the codon usage of VC-RDase genes suggests an evolutionary history that is different from that of most other Dehalococcoides genes...
  25. H lscher T, Krajmalnik Brown R, Ritalahti K, Von Wintzingerode F, G risch H, L ffler F, et al. Multiple nonidentical reductive-dehalogenase-homologous genes are common in Dehalococcoides. Appl Environ Microbiol. 2004;70:5290-7 pubmed publisher
    ..In conclusion, this study demonstrates that the presence of multiple nonidentical RDH genes is characteristic of Dehalococcoides strains...
  26. Müller J, Rosner B, von Abendroth G, Meshulam Simon G, McCarty P, Spormann A. Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution. Appl Environ Microbiol. 2004;70:4880-8 pubmed
    ..Therefore, the vcrA gene identified here may be a useful molecular target for evaluating, predicting, and monitoring in situ reductive VC dehalogenation...
  27. Watts J, Fagervold S, May H, Sowers K. A PCR-based specific assay reveals a population of bacteria within the Chloroflexi associated with the reductive dehalogenation of polychlorinated biphenyls. Microbiology. 2005;151:2039-46 pubmed
    ..detected 16S rRNA gene sequences revealed a relatively diverse group of organisms within the dehalogenating Chloroflexi that are distinct from the Dehalococcoides spp...
  28. Botero L, Brown K, Brumefield S, Burr M, Castenholz R, Young M, et al. Thermobaculum terrenum gen. nov., sp. nov.: a non-phototrophic gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green non-sulfur bacteria) and Thermomicrobia. Arch Microbiol. 2004;181:269-77 pubmed
    ..placed this organism in a clade composed entirely of environmental clones most closely related to the phyla Chloroflexi and Thermomicrobia...
  29. Klatt C, Liu Z, Ludwig M, Kuhl M, Jensen S, Bryant D, et al. Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring. ISME J. 2013;7:1775-89 pubmed publisher
    ..It further proposes that, in daytime, polyhydroxyalkanoates and wax esters are degraded and used as carbon and electron reserves to support photomixotrophy via the 3-OHP bi-cycle. ..
  30. Cheng D, He J. Isolation and characterization of "Dehalococcoides" sp. strain MB, which dechlorinates tetrachloroethene to trans-1,2-dichloroethene. Appl Environ Microbiol. 2009;75:5910-8 pubmed publisher
    ..It also enhances our understanding of the evolution of this unusual microbial group, Dehalococcoides species...
  31. Adrian L, Dudková V, Demnerová K, Bedard D. "Dehalococcoides" sp. strain CBDB1 extensively dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260. Appl Environ Microbiol. 2009;75:4516-24 pubmed publisher
    ..This is the first time that a complex naturally occurring PCB dechlorination pattern has been reproduced in the laboratory using a single bacterial strain...
  32. Seshadri R, Adrian L, Fouts D, Eisen J, Phillippy A, Methe B, et al. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science. 2005;307:105-8 pubmed
    ..Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph...
  33. Kawaichi S, Ito N, Kamikawa R, Sugawara T, Yoshida T, Sako Y. Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov. Int J Syst Evol Microbiol. 2013;63:2992-3002 pubmed publisher
    ..using 16S rRNA gene sequences nested strain 110S(T) in a novel class-level clone cluster of the phylum 'Chloroflexi'...
  34. Gupta R, Chander P, George S. Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] into the suborder Chloroflexineae subord. nov., consisting of the emended fami. Antonie Van Leeuwenhoek. 2013;103:99-119 pubmed publisher
    The phylum "Chloroflexi" contains highly divergent groups of bacteria...
  35. Grostern A, Edwards E. Growth of Dehalobacter and Dehalococcoides spp. during degradation of chlorinated ethanes. Appl Environ Microbiol. 2006;72:428-36 pubmed
    ..This demonstrated that in mixed cultures containing multiple dechlorinating microorganisms, these organisms can have either competitive or complementary dechlorination activities, depending on the chloro-organic substrate...
  36. Morris R, Sowell S, Barofsky D, Zinder S, Richardson R. Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes. Environ Microbiol. 2006;8:1499-509 pubmed
    ..Overall, genomic and proteomic approaches have provided novel insights into the metabolism of this difficult to culture organism...
  37. Holmes V, He J, Lee P, Alvarez Cohen L. Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl Environ Microbiol. 2006;72:5877-83 pubmed
  38. Adrian L, Hansen S, Fung J, Görisch H, Zinder S. Growth of Dehalococcoides strains with chlorophenols as electron acceptors. Environ Sci Technol. 2007;41:2318-23 pubmed
    ..Because chlorinated phenolic compounds are widely distributed as natural components in anaerobic environments, our results reveal one mode in which the Dehalococcoides species could have survived through earth history...
  39. Fung J, Morris R, Adrian L, Zinder S. Expression of reductive dehalogenase genes in Dehalococcoides ethenogenes strain 195 growing on tetrachloroethene, trichloroethene, or 2,3-dichlorophenol. Appl Environ Microbiol. 2007;73:4439-45 pubmed
    ..Chlorophenols naturally occur in soils and are good candidates for the original substrates for PceA...
  40. Bedard D, Ritalahti K, Löffler F. The Dehalococcoides population in sediment-free mixed cultures metabolically dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260. Appl Environ Microbiol. 2007;73:2513-21 pubmed
    ..Dehalobacter, Desulfuromonas, Sulfurospirillum, Anaeromyxobacter, Geobacter, and o-17/DF-1-type Chloroflexi organisms) ruled out any involvement of these bacterial groups in the dechlorination...
  41. Friis A, Heimann A, Jakobsen R, Albrechtsen H, Cox E, Bjerg P. Temperature dependence of anaerobic TCE-dechlorination in a highly enriched Dehalococcoides-containing culture. Water Res. 2007;41:355-64 pubmed
    ..This study demonstrates that bioaugmentation of chlorinated ethene sites may be more efficient at elevated temperatures...
  42. Lee P, Cheng D, Hu P, West K, Dick G, Brodie E, et al. Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J. 2011;5:1014-24 pubmed publisher
    ..Overall, the microarrays are a valuable high-throughput tool for comparative genomics of unsequenced Dehalococcoides-containing samples to provide insights into their gene content and dechlorination functions...
  43. Vainberg S, Condee C, Steffan R. Large-scale production of bacterial consortia for remediation of chlorinated solvent-contaminated groundwater. J Ind Microbiol Biotechnol. 2009;36:1189-97 pubmed publisher
    ..Dehalogenation of PCE by the fermented cultures was affected by pH with no measurable activity at pH <5.0...
  44. Liu Z, Klatt C, Wood J, Rusch D, Ludwig M, Wittekindt N, et al. Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J. 2011;5:1279-90 pubmed publisher
    ..composition, which showed that ~84% of the rRNA was derived from members of four kingdoms Cyanobacteria, Chloroflexi, Chlorobi and Acidobacteria...
  45. Scheutz C, Durant N, Dennis P, Hansen M, Jørgensen T, Jakobsen R, et al. Concurrent ethene generation and growth of Dehalococcoides containing vinyl chloride reductive dehalogenase genes during an enhanced reductive dechlorination field demonstration. Environ Sci Technol. 2008;42:9302-9 pubmed
    ..The quantitative increase in concentrations of Dehalococcoides containing vcrA at this site provides further evidence that the vcrA gene is an effective biomarker for field-scale ERD systems...
  46. Schmitt S, Deines P, Behnam F, Wagner M, Taylor M. Chloroflexi bacteria are more diverse, abundant, and similar in high than in low microbial abundance sponges. FEMS Microbiol Ecol. 2011;78:497-510 pubmed publisher
    ..We focused on the phylum Chloroflexi that frequently occurs in sponges to investigate the different associations with three HMA and three LMA ..
  47. Schaefer C, Condee C, Vainberg S, Steffan R. Bioaugmentation for chlorinated ethenes using Dehalococcoides sp.: comparison between batch and column experiments. Chemosphere. 2009;75:141-8 pubmed publisher
  48. Krajmalnik Brown R, Sung Y, Ritalahti K, Saunders F, Löffler F. Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides. FEMS Microbiol Ecol. 2007;59:206-14 pubmed
    ..Sequence identity was interrupted downstream of tceB and upstream or downstream of the PTE, suggesting that intrachromosomal or interchromosomal transfer of tceAB had occurred...
  49. Griebler C, Adrian L, Meckenstock R, Richnow H. Stable carbon isotope fractionation during aerobic and anaerobic transformation of trichlorobenzene. FEMS Microbiol Ecol. 2004;48:313-21 pubmed publisher
  50. Adrian L, Rahnenführer J, Gobom J, Hölscher T. Identification of a chlorobenzene reductive dehalogenase in Dehalococcoides sp. strain CBDB1. Appl Environ Microbiol. 2007;73:7717-24 pubmed
    ..Other highly expressed proteins identified with our approach included the major subunit of a protein annotated as formate dehydrogenase, transporter subunits, and a putative S-layer protein...
  51. Krzmarzick M, Crary B, Harding J, Oyerinde O, Leri A, Myneni S, et al. Natural niche for organohalide-respiring Chloroflexi. Appl Environ Microbiol. 2012;78:393-401 pubmed publisher
    The phylum Chloroflexi contains several isolated bacteria that have been found to respire a diverse array of halogenated anthropogenic chemicals...
  52. Zhuang W, Yi S, Feng X, Zinder S, Tang Y, Alvarez Cohen L. Selective utilization of exogenous amino acids by Dehalococcoides ethenogenes strain 195 and its effects on growth and dechlorination activity. Appl Environ Microbiol. 2011;77:7797-803 pubmed publisher
    ..This study also demonstrates that using isotopomer-based metabolite analysis can be an efficient strategy for optimizing nutritional conditions for slow-growing microorganisms...
  53. Moe W, Yan J, Nobre M, da Costa M, Rainey F. Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater. Int J Syst Evol Microbiol. 2009;59:2692-7 pubmed publisher
    ..Phylogenetic analyses based on 16S rRNA gene sequences indicated that the strains cluster within the phylum Chloroflexi, but are related only distantly to all recognized taxa in the phylum...
  54. Amos B, Ritalahti K, Cruz Garcia C, Padilla Crespo E, Löffler F. Oxygen effect on Dehalococcoides viability and biomarker quantification. Environ Sci Technol. 2008;42:5718-26 pubmed
    ..Enhanced molecular tools that complement existing protocols and provide quantitative information on the viability and activity of the Dehalococcoides population are desirable...
  55. Sung Y, Ritalahti K, Apkarian R, Löffler F. Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate. Appl Environ Microbiol. 2006;72:1980-7 pubmed
  56. Rahm B, Morris R, Richardson R. Temporal expression of respiratory genes in an enrichment culture containing Dehalococcoides ethenogenes. Appl Environ Microbiol. 2006;72:5486-91 pubmed
  57. Kuznetsov B, Ivanovsky R, Keppen O, Sukhacheva M, Bumazhkin B, Patutina E, et al. Draft genome sequence of the anoxygenic filamentous phototrophic bacterium Oscillochloris trichoides subsp. DG-6. J Bacteriol. 2011;193:321-2 pubmed publisher
    ..Here, we present the draft genome sequence of Oscillochloris trichoides subsp. DG-6, the type strain of the species, which has permitted the prediction of genes for carbon and nitrogen metabolism and for the light-harvesting apparatus...
  58. Johnson D, Brodie E, Hubbard A, Andersen G, Zinder S, Alvarez Cohen L. Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase. Appl Environ Microbiol. 2008;74:2864-72 pubmed publisher
  59. Morris R, Rappe M, Urbach E, Connon S, Giovannoni S. Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean. Appl Environ Microbiol. 2004;70:2836-42 pubmed
    ..Together, these clones form a major, monophyletic subgroup of the phylum Chloroflexi: While members of this diverse group are consistently identified in the marine environment, there are currently ..
  60. West K, Johnson D, Hu P, DeSantis T, Brodie E, Lee P, et al. Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains. Appl Environ Microbiol. 2008;74:3533-40 pubmed publisher
  61. Klatt C, Bryant D, Ward D. Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ Microbiol. 2007;9:2067-78 pubmed
    ..The genomes of three filamentous anoxygenic phototrophic Chloroflexi isolates (Roseiflexus sp...
  62. Yim L, Hongmei J, Aitchison J, Pointing S. Highly diverse community structure in a remote central Tibetan geothermal spring does not display monotonic variation to thermal stress. FEMS Microbiol Ecol. 2006;57:80-91 pubmed
    ..Moreover, new phylogeographic and thermally defined lineages among the Cyanobacteria, Chloroflexi, Eubacterium and Thermus are identified...
  63. Popat S, Deshusses M. Reductive dehalogenation of trichloroethene vapors in an anaerobic biotrickling filter. Environ Sci Technol. 2009;43:7856-61 pubmed publisher
    ..Overall, the study shows that sustained anaerobic biotreatment of TCE vapors in biotrickling filters is possible...
  64. Behrens S, Azizian M, McMurdie P, Sabalowsky A, Dolan M, Semprini L, et al. Monitoring abundance and expression of "Dehalococcoides" species chloroethene-reductive dehalogenases in a tetrachloroethene-dechlorinating flow column. Appl Environ Microbiol. 2008;74:5695-703 pubmed publisher
    ..The results presented have implications for our understanding of the ecophysiology of reductively dehalogenating Dehalococcoides spp. and their role in bioremediation of chloroethenes...
  65. Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y. Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol. 2003;53:1843-51 pubmed
    ..sequences revealed that both strains belong to an uncultured, previously recognized clone lineage of the phylum Chloroflexi (formerly known as green non-sulfur bacteria)...
  66. Fagervold S, May H, Sowers K. Microbial reductive dechlorination of aroclor 1260 in Baltimore harbor sediment microcosms is catalyzed by three phylotypes within the phylum Chloroflexi. Appl Environ Microbiol. 2007;73:3009-18 pubmed
  67. Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, et al. Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in. Int J Syst Evol Microbiol. 2006;56:1331-40 pubmed
    ..which were previously isolated as members of the tentatively named class 'Anaerolineae' of the phylum Chloroflexi, were characterized. All isolates were strictly anaerobic micro-organisms...
  68. Waller A, Krajmalnik Brown R, Löffler F, Edwards E. Multiple reductive-dehalogenase-homologous genes are simultaneously transcribed during dechlorination by Dehalococcoides-containing cultures. Appl Environ Microbiol. 2005;71:8257-64 pubmed
    ..strain BAV1. These findings suggest that multiple RDH genes are induced by a single chlorinated substrate and that multiple reductive dehalogenases contribute to chloroethene degradation in KB1...
  69. Fagervold S, Watts J, May H, Sowers K. Sequential reductive dechlorination of meta-chlorinated polychlorinated biphenyl congeners in sediment microcosms by two different Chloroflexi phylotypes. Appl Environ Microbiol. 2005;71:8085-90 pubmed
    Three species within a deeply branching cluster of the Chloroflexi are the only microorganisms currently known to anaerobically transform polychlorinated biphenyls (PCBs) by the mechanism of reductive dechlorination...
  70. Sorokin D, Lücker S, Vejmelkova D, Kostrikina N, Kleerebezem R, Rijpstra W, et al. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J. 2012;6:2245-56 pubmed publisher
    ..we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism...
  71. Yamada T, Sekiguchi Y, Imachi H, Kamagata Y, Ohashi A, Harada H. Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl Environ Microbiol. 2005;71:7493-503 pubmed
    ..Anaerolinea thermophila, which is the first cultured representative of subphylum I of the bacterial phylum Chloroflexi, not only was one of the predominant constituents of thermophilic sludge granules but also was a causative ..
  72. Wasmund K, Schreiber L, Lloyd K, Petersen D, Schramm A, Stepanauskas R, et al. Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi. ISME J. 2014;8:383-97 pubmed publisher
    Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown...
  73. Blazejak A, Schippers A. High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiol Ecol. 2010;72:198-207 pubmed publisher
    ..of members of the bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi are frequently found in 16S rRNA gene clone libraries obtained from marine sediments...
  74. Regeard C, Maillard J, Dufraigne C, Deschavanne P, Holliger C. Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195. Appl Environ Microbiol. 2005;71:2955-61 pubmed
    ..A hierarchical classification of the atypical regions containing the reductive dehalogenase genes indicated that these regions were probably acquired by several gene transfer events...
  75. McMurdie P, Hug L, Edwards E, Holmes S, Spormann A. Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides. BMC Genomics. 2011;12:287 pubmed publisher
    ..strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene, ssrA...
  76. Bedard D. A case study for microbial biodegradation: anaerobic bacterial reductive dechlorination of polychlorinated biphenyls-from sediment to defined medium. Annu Rev Microbiol. 2008;62:253-70 pubmed publisher
    ..of several PCB congeners belong to a novel clade of putative dechlorinating bacteria within the phylum Chloroflexi. Dehalococcoides ethenogenes strain 195 also dechlorinates several PCB congeners when grown on chlorinated ..
  77. Chow W, Cheng D, Wang S, He J. Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species. ISME J. 2010;4:1020-30 pubmed publisher
    ..The new mbrA gene identified in this study may serve as an important biomarker for evaluating, predicting and elucidating the biological production of trans-DCE in the chloroethene-contaminated sites...