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Yan J, Im J, Yang Y, Löffler FE. Guided cobalamin biosynthesis supports Dehalococcoides mccartyi reductive dechlorination activity. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120320. [PMID: 23479750 DOI: 10.1098/rstb.2012.0320] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Dehalococcoides mccartyi strains are corrinoid-auxotrophic Bacteria and axenic cultures that require vitamin B12 (CN-Cbl) to conserve energy via organohalide respiration. Cultures of D. mccartyi strains BAV1, GT and FL2 grown with limiting amounts of 1 µg l(-1) CN-Cbl quickly depleted CN-Cbl, and reductive dechlorination of polychlorinated ethenes was incomplete leading to vinyl chloride (VC) accumulation. In contrast, the same cultures amended with 25 µg l(-1) CN-Cbl exhibited up to 2.3-fold higher dechlorination rates, 2.8-9.1-fold increased growth yields, and completely consumed growth-supporting chlorinated ethenes. To explore whether known cobamide-producing microbes supply Dehalococcoides with the required corrinoid cofactor, co-culture experiments were performed with the methanogen Methanosarcina barkeri strain Fusaro and two acetogens, Sporomusa ovata and Sporomusa sp. strain KB-1, as Dehalococcoides partner populations. During growth with H2/CO2, M. barkeri axenic cultures produced 4.2 ± 0.1 µg l(-1) extracellular cobamide (factor III), whereas the Sporomusa cultures produced phenolyl- and p-cresolyl-cobamides. Neither factor III nor the phenolic cobamides supported Dehalococcoides reductive dechlorination activity suggesting that M. barkeri and the Sporomusa sp. cannot fulfil Dehalococcoides' nutritional requirements. Dehalococcoides dechlorination activity and growth occurred in M. barkeri and Sporomusa sp. co-cultures amended with 10 µM 5',6'-dimethylbenzimidazole (DMB), indicating that a cobalamin is a preferred corrinoid cofactor of strains BAV1, GT and FL2 when grown with chlorinated ethenes as electron acceptors. Even though the methanogen and acetogen populations tested did not produce cobalamin, the addition of DMB enabled guided biosynthesis and generated a cobalamin that supported Dehalococcoides' activity and growth. Guided cobalamin biosynthesis may offer opportunities to sustain and enhance Dehalococcoides activity in contaminated subsurface environments.
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Affiliation(s)
- Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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52
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Schipp CJ, Marco-Urrea E, Kublik A, Seifert J, Adrian L. Organic cofactors in the metabolism of Dehalococcoides mccartyi strains. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120321. [PMID: 23479751 DOI: 10.1098/rstb.2012.0321] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Dehalococcoides mccartyi strains are strictly anaerobic organisms specialized to grow with halogenated compounds as electron acceptor via a respiratory process. Their genomes are among the smallest known for free-living organisms, and the embedded gene set reflects their strong specialization. Here, we briefly review main characteristics of published Dehalococcoides genomes and show how genome information together with cultivation and biochemical experiments have contributed to our understanding of Dehalococcoides physiology and biochemistry. We extend this approach by the detailed analysis of cofactor metabolism in Dehalococcoides strain CBDB1. Dehalococcoides genomes were screened for encoded proteins annotated to contain or interact with organic cofactors, and the expression of these proteins was analysed by shotgun proteomics to shed light on cofactor requirements. In parallel, cultivation experiments testing for vitamin requirements showed that cyanocobalamin (vitamin B12), thiamine and biotin were essential supplements and that cyanocobalamin could be substituted by dicyanocobinamide and dimethylbenzimidazole. Dehalococcoides genome analysis, detection of single enzymes by shotgun proteomics and inhibition studies confirmed the expression of the biosynthetic pathways for pyridoxal-5-phosphate, flavin nucleotides, folate, S-adenosylmethionine, pantothenate and nicotinic acids in strain CBDB1. Haem/cytochromes, quinones and lipoic acids were not necessary for cultivation or dechlorination activity and no biosynthetic pathways were identified in the genomes.
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Affiliation(s)
- Christian J Schipp
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
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53
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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. [PMID: 23378114 DOI: 10.1099/ijs.0.046532-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, chemoheterotrophic, Gram-negative-staining, multicellular filamentous bacterium, designated strain 110S(T), was isolated from an iron-rich coastal hydrothermal field in Japan. The isolate is facultatively aerobic and chemoheterotrophic. Phylogenetic analysis using 16S rRNA gene sequences nested strain 110S(T) in a novel class-level clone cluster of the phylum 'Chloroflexi'. The isolate grows by dissimilatory iron- and nitrate-reduction under anaerobic conditions, which is the first report of these abilities in the phylum 'Chloroflexi'. The organism is capable of growth with oxygen, ferric iron and nitrate as a possible electron acceptor, has a wide range of growth temperatures, and tolerates higher NaCl concentrations for growth compared to the other isolates in the phylum. Using phenotypic and phylogenetic data, strain 110S(T) (= JCM 17282(T) = NBRC 107679(T) = DSM 23922(T) = KCTC 23289(T) = ATCC BAA-2145(T)) is proposed as the type strain of a novel species in a new genus, Ardenticatena maritima gen. nov., sp. nov. In addition, as strain 110S(T) apparently constitutes a new class of the phylum 'Chloroflexi' with other related uncultivated clone sequences, we propose Ardenticatenia classis nov. and the subordinate taxa Ardenticatenales ord. nov. and Ardenticatenaceae fam. nov.
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Affiliation(s)
- Satoshi Kawaichi
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Norihiro Ito
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Ryoma Kamikawa
- Laboratory of Molecular Evolution of Microbes, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Tatsuya Sugawara
- Laboratory of Marine Bioproducts Technology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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54
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Krzmarzick MJ, McNamara PJ, Crary BB, Novak PJ. Abundance and diversity of organohalide-respiring bacteria in lake sediments across a geographical sulfur gradient. FEMS Microbiol Ecol 2013; 84:248-58. [DOI: 10.1111/1574-6941.12059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 12/04/2012] [Accepted: 12/07/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Mark J. Krzmarzick
- Department of Civil Engineering; University of Minnesota; Minneapolis; MN; USA
| | - Patrick J. McNamara
- Department of Civil Engineering; University of Minnesota; Minneapolis; MN; USA
| | - Benjamin B. Crary
- Department of Civil Engineering; University of Minnesota; Minneapolis; MN; USA
| | - Paige J. Novak
- Department of Civil Engineering; University of Minnesota; Minneapolis; MN; USA
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55
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CARD-FISH analysis of a TCE-dechlorinating biocathode operated at different set potentials. N Biotechnol 2012; 30:33-8. [DOI: 10.1016/j.nbt.2012.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/06/2012] [Accepted: 06/11/2012] [Indexed: 11/18/2022]
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56
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Maness AD, Bowman KS, Yan J, Rainey FA, Moe WM. Dehalogenimonas spp. can Reductively Dehalogenate High Concentrations of 1,2-Dichloroethane, 1,2-Dichloropropane, and 1,1,2-Trichloroethane. AMB Express 2012; 2:54. [PMID: 23046725 PMCID: PMC3492069 DOI: 10.1186/2191-0855-2-54] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 11/30/2022] Open
Abstract
The contaminant concentrations over which type strains of the species Dehalogenimonas alkenigignens and Dehalogenimonas lykanthroporepellens were able to reductively dechlorinate 1,2-dichloroethane (1,2-DCA), 1,2-dichloropropane (1,2-DCP), and 1,1,2-trichloroethane (1,1,2-TCA) were evaluated. Although initially isolated from an environment with much lower halogenated solvent concentrations, D. alkenigignens IP3-3T was found to reductively dehalogenate chlorinated alkanes at concentrations comparable to D. lykanthroporepellens BL-DC-9T. Both species dechlorinated 1,2-DCA, 1,2-DCP, and 1,1,2-TCA present at initial concentrations at least as high as 8.7, 4.0, and 3.5 mM, respectively. The ability of Dehalogenimonas spp. to carry out anaerobic reductive dechlorination even in the presence of high concentrations of chlorinated aliphatic alkanes has important implications for remediation of contaminated soil and groundwater.
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Affiliation(s)
- Andrew D Maness
- Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA
| | - Kimberly S Bowman
- Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Jun Yan
- Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA
- Present address: Jun Yan, Department of Microbiology and Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Fred A Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
| | - William M Moe
- Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA
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57
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Jiang L, Ni J, Liu Q. Evolution of selenoproteins in the metazoan. BMC Genomics 2012; 13:446. [PMID: 22943432 PMCID: PMC3473315 DOI: 10.1186/1471-2164-13-446] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 08/20/2012] [Indexed: 11/10/2022] Open
Abstract
Background The selenocysteine (Sec) containing proteins, selenoproteins, are an important group of proteins present throughout all 3 kingdoms of life. With the rapid progression of selenoprotein research in the post-genomic era, application of bioinformatics methods to the identification of selenoproteins in newly sequenced species has become increasingly important. Although selenoproteins in human and other vertebrates have been investigated, studies of primitive invertebrate selenoproteomes are rarely reported outside of insects and nematodes. Result A more integrated view of selenoprotein evolution was constructed using several representative species from different evolutionary eras. Using a SelGenAmic-based selenoprotein identification method, 178 selenoprotein genes were identified in 6 invertebrates: Amphimedon queenslandica, Trichoplax adhaerens, Nematostella vectensis, Lottia gigantean, Capitella teleta, and Branchiostoma floridae. Amphioxus was found to have the most abundant and variant selenoproteins of any animal currently characterized, including a special selenoprotein P (SelP) possessing 3 repeated Trx-like domains and Sec residues in the N-terminal and 2 Sec residues in the C-terminal. This gene structure suggests the existence of two different strategies for extension of Sec numbers in SelP for the preservation and transportation of selenium. In addition, novel eukaryotic AphC-like selenoproteins were identified in sponges. Conclusion Comparison of various animal species suggests that even the most primitive animals possess a selenoproteome range and variety similar to humans. During evolutionary history, only a few new selenoproteins have emerged and few were lost. Furthermore, the massive loss of selenoproteins in nematodes and insects likely occurred independently in isolated partial evolutionary branches.
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Affiliation(s)
- Liang Jiang
- College of Life Sciences, Shenzhen University, Shenzhen, 518060, Guangdong Province, PR, China
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58
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Samin G, Janssen DB. Transformation and biodegradation of 1,2,3-trichloropropane (TCP). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2012; 19:3067-78. [PMID: 22875418 PMCID: PMC3414701 DOI: 10.1007/s11356-012-0859-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 03/09/2012] [Indexed: 05/04/2023]
Abstract
PURPOSE 1,2,3-Trichloropropane (TCP) is a persistent groundwater pollutant and a suspected human carcinogen. It is also is an industrial chemical waste that has been formed in large amounts during epichlorohydrin manufacture. In view of the spread of TCP via groundwater and its toxicity, there is a need for cheap and efficient technologies for the cleanup of TCP-contaminated sites. In situ or on-site bioremediation of TCP is an option if biodegradation can be achieved and stimulated. This paper presents an overview of methods for the remediation of TCP-contaminated water with an emphasis on the possibilities of biodegradation. CONCLUSIONS Although TCP is a xenobiotic chlorinated compound of high chemical stability, a number of abiotic and biotic conversions have been demonstrated, including abiotic oxidative conversion in the presence of a strong oxidant and reductive conversion by zero-valent zinc. Biotransformations that have been observed include reductive dechlorination, monooxygenase-mediated cometabolism, and enzymatic hydrolysis. No natural organisms are known that can use TCP as a carbon source for growth under aerobic conditions, but anaerobically TCP may serve as electron acceptor. The application of biodegradation is hindered by low degradation rates and incomplete mineralization. Protein engineering and genetic modification can be used to obtain microorganisms with enhanced TCP degradation potential.
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Affiliation(s)
- Ghufrana Samin
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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59
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Bowman KS, Nobre MF, da Costa MS, Rainey FA, Moe WM. Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater. Int J Syst Evol Microbiol 2012; 63:1492-1498. [PMID: 22888191 DOI: 10.1099/ijs.0.045054-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strictly anaerobic bacterial strains, designated IP3-3(T) and SBP-1, were isolated from groundwater contaminated by chlorinated alkanes and alkenes at a Superfund Site located near Baton Rouge, Louisiana (USA). Both strains reductively dehalogenate a variety of polychlorinated aliphatic alkanes, including 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2,3-trichloropropane, when provided with hydrogen as the electron donor. To clarify their taxonomic position, strains IP3-3(T) and SBP-1 were characterized using a polyphasic approach. Both IP3-3(T) and SBP-1 are mesophilic, non-spore-forming, non-motile and Gram-stain-negative. Cells of both strains are irregular cocci with diameters of 0.4-1.1 µm. Both are resistant to ampicillin and vancomycin. The genomic DNA G+C contents of strains IP3-3(T) and SBP-1 are 55.5±0.4 and 56.2±0.2 mol% (HPLC), respectively. Major cellular fatty acids include C18 : 1ω9c, C16 : 0, C14 : 0 and C16 : 1ω9c. 16S rRNA gene sequence based phylogenetic analyses indicated that the strains cluster within the phylum Chloroflexi most closely related to but distinct from the species Dehalogenimonas lykanthroporepellens (96.2 % pairwise similarity) and Dehalococcoides mccartyi (90.6 % pairwise similarity). Physiological and chemotaxonomic traits as well as phylogenetic analysis support the conclusion that these strains represent a novel species within the genus Dehalogenimonas for which the name Dehalogenimonas alkenigignens sp. nov. is proposed. The type strain is IP3-3(T) ( = JCM 17062(T) = NRRL B-59545(T)).
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Affiliation(s)
- Kimberly S Bowman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.,Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Milton S da Costa
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Fred A Rainey
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, Alaska 99508, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - William M Moe
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
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60
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Moe WM, Stebbing RE, Rao JU, Bowman KS, Nobre MF, da Costa MS, Rainey FA. Pelosinus
defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus
Pelosinus
and transfer of
Sporotalea propionica
to Pelosinus
propionicus comb. nov. Int J Syst Evol Microbiol 2012; 62:1369-1376. [DOI: 10.1099/ijs.0.033753-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two anaerobic bacterial strains, designated SHI-1T and SHI-2, were isolated from chlorinated solvent-contaminated groundwater. They were found to be identical in phenotypic properties and shared high (98.5–99.8 %) pairwise 16S rRNA gene sequence similarity. Multiple 16S rRNA genes were found to be present in the isolates as well as
Pelosinus fermentans
DSM 17108T and
Sporotalea propionica
DSM 13327T. Strains SHI-1T and SHI-2 could be differentiated from their closest phylogenetic relatives,
P. fermentans
DSM 17108T and
S. propionica
DSM 13327T, on the basis of their phenotypic and phylogenetic properties. The isolates were Gram-negative, spore-forming, motile rods with peritrichous flagella. Growth occurred at 10–42 °C and pH 5.5–8.5. Fermentative growth was observed on Casamino acids, fructose, fumarate, glucose, glycerol, pyruvate and yeast extract. The major organic acids produced from glucose and glycerol fermentation were propionate and acetate. The major organic acids produced from fermentation of fumarate were propionate, acetate and succinate. The major cellular fatty acids were summed feature 4 (consisting of C15 : 1ω8c and/or C15 : 2), summed feature 8 (consisting of C17 : 1ω8c and/or C17 : 2) and C14 : 0 dimethyl aldehyde. The polar lipids comprised aminophospholipids, including phosphatidylethanolamine and phosphatidylserine, and an unknown phospholipid. The genomic DNA G+C content was 39.2 mol%. We propose that strains SHI-1T and SHI-2 are assigned to a novel species of the genus
Pelosinus
, with the name Pelosinus
defluvii sp. nov. (type strain SHI-1T = NRRL Y-59407T = LMG 25549T). The description of the genus
Pelosinus
is emended. We also propose the transfer of
S. propionica
to the genus
Pelosinus
as Pelosinus
propionicus comb. nov. (type strain TmPN3T = DSM 13327T = ATCC BAA-626T), on the basis of phylogenetic, chemotaxonomic and phenotypic properties.
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Affiliation(s)
- William M. Moe
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Rachael E. Stebbing
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jyoti U. Rao
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kimberly S. Bowman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M. Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Milton S. da Costa
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Fred A. Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, Detter C, Tapia R, Han S, Goodwin L, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Land M, Chang YJ, Kyrpides NC, Ovchinnikova G, Hauser L, Lapidus A, Yan J, Bowman KS, da Costa MS, Rainey FA, Moe WM. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to "Dehalococcoides" strains. Stand Genomic Sci 2012; 6:251-64. [PMID: 22768368 PMCID: PMC3387798 DOI: 10.4056/sigs.2806097] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which belongs to a deeply branching lineage within the phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore-forming, Gram-negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana, USA. D. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) an unusual ability to couple growth with reductive dechlorination of environmentally important polychlorinated aliphatic alkanes and (b) a phylogenetic position that is distant from previously sequenced bacteria. The 1,686,510 bp circular chromosome of strain BL-DC-9(T) contains 1,720 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small subunit rRNA (16S) locus.
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Ding C, He J. Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments. Microb Biotechnol 2012; 5:347-67. [PMID: 22070763 PMCID: PMC3821678 DOI: 10.1111/j.1751-7915.2011.00313.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 09/24/2011] [Accepted: 09/28/2011] [Indexed: 11/28/2022] Open
Abstract
Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction-based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next-generation sequencing, provide unsurpassed detection ability, which has enabled large-scale comparative genomic and whole-genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic-acid-based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions.
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Affiliation(s)
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
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63
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Löffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Müller JA, Fullerton H, Zinder SH, Spormann AM. Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 2012; 63:625-635. [PMID: 22544797 DOI: 10.1099/ijs.0.034926-0] [Citation(s) in RCA: 365] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Six obligately anaerobic bacterial isolates (195(T), CBDB1, BAV1, VS, FL2 and GT) with strictly organohalide-respiring metabolisms were obtained from chlorinated solvent-contaminated aquifers, contaminated and uncontaminated river sediments or anoxic digester sludge. Cells were non-motile with a disc-shaped morphology, 0.3-1 µm in diameter and 0.1-0.2 µm thick, and characteristic indentations on opposite flat sides of the cell. Growth occurred in completely synthetic, reduced medium amended with a haloorganic electron acceptor (mostly chlorinated but also some brominated compounds), hydrogen as electron donor, acetate as carbon source, and vitamins. No other growth-supporting redox couples were identified. Aqueous hydrogen consumption threshold concentrations were <1 nM. Growth ceased when vitamin B(12) was omitted from the medium. Addition of sterile cell-free supernatant of Dehalococcoides-containing enrichment cultures enhanced dechlorination and growth of strains 195 and FL2, suggesting the existence of so-far unidentified stimulants. Dechlorination occurred between pH 6.5 and 8.0 and over a temperature range of 15-35 °C, with an optimum growth temperature between 25 and 30 °C. The major phospholipid fatty acids were 14 : 0 (15.7 mol%), br15 : 0 (6.2 mol%), 16 : 0 (22.7 mol%), 10-methyl 16 : 0 (25.8 mol%) and 18 : 0 (16.6 mol%). Unusual furan fatty acids including 9-(5-pentyl-2-furyl)-nonanoate and 8-(5-hexyl-2-furyl)-octanoate were detected in strains FL2, BAV1 and GT, but not in strains 195(T) and CBDB1. The 16S rRNA gene sequences of the six isolates shared more than 98 % identity, and phylogenetic analysis revealed an affiliation with the phylum Chloroflexi and more than 10 % sequence divergence from other described isolates. The genome sizes and G+C contents ranged from 1.34 to 1.47 Mbp and 47 to 48.9 mol% G+C, respectively. Based on 16S rRNA gene sequence comparisons, genome-wide average nucleotide identity and phenotypic characteristics, the organohalide-respiring isolates represent a new genus and species, for which the name Dehalococcoides mccartyi gen. nov., sp. nov. is proposed. Isolates BAV1 ( = ATCC BAA-2100 = JCM 16839 = KCTC 5957), FL2 ( = ATCC BAA-2098 = DSM 23585 = JCM 16840 = KCTC 5959), GT ( = ATCC BAA-2099 = JCM 16841 = KCTC 5958), CBDB1, 195(T) ( = ATCC BAA-2266(T) = KCTC 15142(T)) and VS are considered strains of Dehalococcoides mccartyi, with strain 195(T) as the type strain. The new class Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov. are described to accommodate the new taxon.
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Affiliation(s)
- Frank E Löffler
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jun Yan
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Kirsti M Ritalahti
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, D-04318 Leipzig, Germany
| | - Elizabeth A Edwards
- Department of Chemical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jochen A Müller
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, D-04318 Leipzig, Germany
| | - Heather Fullerton
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Stephen H Zinder
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Alfred M Spormann
- Departments of Civil and Environmental Engineering and of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
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Abstract
The phylum Chloroflexi contains several isolated bacteria that have been found to respire a diverse array of halogenated anthropogenic chemicals. The distribution and role of these Chloroflexi in uncontaminated terrestrial environments, where abundant natural organohalogens could function as potential electron acceptors, have not been studied. Soil samples (116 total, including 6 sectioned cores) from a range of uncontaminated sites were analyzed for the number of Dehalococcoides-like Chloroflexi 16S rRNA genes present. Dehalococcoides-like Chloroflexi populations were detected in all but 13 samples. The concentrations of organochlorine ([organochlorine]), inorganic chloride, and total organic carbon (TOC) were obtained for 67 soil core sections. The number of Dehalococcoides-like Chloroflexi 16S rRNA genes positively correlated with [organochlorine]/TOC while the number of Bacteria 16S rRNA genes did not. Dehalococcoides-like Chloroflexi were also observed to increase in number with a concomitant accumulation of chloride when cultured with an enzymatically produced mixture of organochlorines. This research provides evidence that organohalide-respiring Chloroflexi are widely distributed as part of uncontaminated terrestrial ecosystems, they are correlated with the fraction of TOC present as organochlorines, and they increase in abundance while dechlorinating organochlorines. These findings suggest that organohalide-respiring Chloroflexi may play an integral role in the biogeochemical chlorine cycle.
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Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria. Trends Biotechnol 2010; 28:308-16. [DOI: 10.1016/j.tibtech.2010.03.005] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 03/23/2010] [Accepted: 03/26/2010] [Indexed: 11/20/2022]
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66
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Ye L, Schilhabel A, Bartram S, Boland W, Diekert G. Reductive dehalogenation of brominated ethenes bySulfurospirillum multivoransandDesulfitobacterium hafniensePCE-S. Environ Microbiol 2010; 12:501-9. [DOI: 10.1111/j.1462-2920.2009.02093.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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67
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Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., hydrogen-producing bacteria from chlorinated solvent-contaminated groundwater. Int J Syst Evol Microbiol 2010; 60:358-363. [DOI: 10.1099/ijs.0.013169-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four hydrogen-producing, aerotolerant, anaerobic bacterial strains isolated from chlorinated solvent-contaminated groundwater were characterized using a polyphasic approach. Three of the strains, designated BL-18, BL-19 and BL-20T, were found to be identical in 16S rRNA gene sequences and in phenotypic properties. Cells of these strains are Gram-positive-staining, spore-forming, motile rods with peritrichous flagella. Growth occurred at 15–40 °C, pH 5.0–10.0 and at NaCl concentrations up to 5 % (w/v). Acid was produced in fermentation of cellobiose, fructose, galactose (weak), glucose, maltose and salicin. Products of fermentation in PYG medium were acetate, butyrate, ethanol, formate, carbon dioxide and hydrogen. Dominant cellular fatty acids when grown in PYG medium were C13 : 0 iso, C16 : 0, C13 : 0 anteiso, C15 : 0 iso and C15 : 0 anteiso. The genomic DNA G+C content was 30.4 mol%. These isolates can be differentiated from their closest phylogenetic relative, the cluster I Clostridium species Clostridium frigidicarnis (97.2 % similar to the type strain in 16S rRNA gene sequence), on the basis of phenotypic and chemotaxonomic properties. The other strain characterized in this study, BL-28T, was Gram-positive-staining with spore-forming, rod-shaped cells. Growth occurred at 15–46 °C, pH 6.0–8.5 and at NaCl concentrations up to 3 % (w/v). Acid was produced from cellobiose, dextran, fructose (weak), glucose, maltose, salicin and trehalose. End products of PYG fermentation included acetate, butyrate, pyruvate, carbon dioxide and hydrogen. Dominant cellular fatty acids from cells grown in PYG medium at 30 °C were C14 : 0, C14 : 0 dimethyl aldehyde, C16 : 0 and C12 : 0. The DNA G+C content was 28.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BL-28T falls within cluster I of the genus Clostridium, but with ≤95.2 % identity with previously described species. On the basis of results presented here, strains BL-20T (=NRRL B-51348T =DSM 21757T) and BL-28T (=NRRL B-51352T =DSM 21758T) are proposed as the type strains of novel species of the genus Clostridium with the names Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., respectively.
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68
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Detection and quantification of Dehalogenimonas and "Dehalococcoides" populations via PCR-based protocols targeting 16S rRNA genes. Appl Environ Microbiol 2009; 75:7560-4. [PMID: 19820163 DOI: 10.1128/aem.01938-09] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the haloalkane dechlorinating genus Dehalogenimonas are distantly related to "Dehalococcoides" but share high homology in some variable regions of their 16S rRNA gene sequences. In this study, primers and PCR protocols intended to uniquely target Dehalococcoides were reevaluated, and primers and PCR protocols intended to uniquely target Dehalogenimonas were developed and tested. Use of the genus-specific primers revealed the presence of both bacterial groups in groundwater at a Louisiana Superfund site.
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Fletcher KE, Löffler FE, Richnow HH, Nijenhuis I. Stable carbon isotope fractionation of 1,2-dichloropropane during dichloroelimination by Dehalococcoides populations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:6915-6919. [PMID: 19806720 DOI: 10.1021/es900365x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The isotope fractionation of 1,2-dichloropropane (1,2-D) during dichloroelimination to propene by Dehalococcoides populations was explored in laboratory experiments in order to provide data for the characterization of the fate of 1,2-D in heterogeneous subsurface systems. Compound specific stable carbon isotope analysis (CSIA) was used to determine the bulk enrichment factors (epsilonbulk), reactive position specific enrichment factors (epsilonreactive), and apparent kinetic isotope effect (AKIE) values for 1,2-D dichloroelimination in two distinct Dehalococcoides-containing cultures. The epsilonbulk factors calculated in the two cultures were statistically identical, -10.8 +/- 0.9 and -11.3 +/- 0.8 per thousand, even though the cultures were derived from geographically distinct locations. AKIE values for 1,2-D dichloroelimination assuming stepwise and concerted reaction mechanisms were approximately 1.033 and 1.017, respectively. These values are within the range of previously reported values for dichloroelimination reactions and were equivalent to values reported for biotic 1,2-dichloroethane and abiotic 1,1,2,2,-tetrachloroethane and pentachloroethane dichloroelimination reactions.
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Affiliation(s)
- Kelly E Fletcher
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30332, USA
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Taş N, van Eekert MHA, de Vos WM, Smidt H. The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments. Microb Biotechnol 2009; 3:389-402. [PMID: 21255338 PMCID: PMC3815806 DOI: 10.1111/j.1751-7915.2009.00147.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely ‘Dehalococcoides’ spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase‐encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. 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.
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Affiliation(s)
- Neslihan Taş
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands
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71
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Moe WM, Yan J, Nobre MF, da Costa MS, Rainey FA. 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. [DOI: 10.1099/ijs.0.011502-0] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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