Genome Sequence of the PCE-Dechlorinating Bacterium<i>Dehalococcoides ethenogenes</i>

Seshadri, Rekha; Adrian, Lorenz; Fouts, Derrick E.; Eisen, Jonathan A.; Phillippy, Adam M.; Methé, Barbara A.; Ward, Naomi; Nelson, William; DeBoy, Robert T.; Khouri, Hoda; Kolonay, James F.; Dodson, Robert J.; Daugherty, Sean C.; Brinkac, Lauren; Sullivan, Steven A.; Madupu, Ramana; Nelson, Karen E.; Kang, Katherine H.; Impraim, Marjorie; Tran, Kevin; Robinson, Jeffrey M.; Forberger, Heather A.; Fraser, Claire M.; Zinder, Stephen H.; Heidelberg, John F.

doi:10.1126/science.1102226

Cited by 399 publications

(504 citation statements)

References 36 publications

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“…Several rdh genes in this region seem to originate from recent duplication events as they show noticeable high sequence similarity to each other (cbdbA1550-cbdbA1570; cbdbA1546-cbdbA1575). Nine regions predicted previously as integrated elements 4 are present in strain 195 but not in strain CBDB1 (Fig. 1c, green boxes, regions I-IX).…”

Section: Comparison With D Ethenogenes Strain 195mentioning

confidence: 65%

“…Strain 195 has a complex nutrition, requiring acetate, vitamins and extracts from mixed cultures 5 and its genome annotation predicted an incomplete pathway to methionine, lesions in the tricarboxylic acid cycle leading to glutamate, as well as incomplete pathways for the synthesis of vitamin B 12 , biotin and quinones 4 . Strain CBDB1 is able to grow in a defined medium containing only acetate and vitamins, yet these same lesions are still predicted to be present.…”

Section: Discussionmentioning

confidence: 99%

“…1c and Supplementary Tables 1 and 2 online). In strain CBDB1, three regions contain large putative integrated elements (region 1: bp 58,790-108,048; region 3: bp 570,912-579,362; region 7: bp 1,166,180-1,213,880), which are characterized by exceptional di-and trinucleotide composition 4,9 (see Supplementary Fig. 3 online), deviation from the average GC content found across the entire genome ( Supplementary Fig.…”

Section: Comparison With D Ethenogenes Strain 195mentioning

confidence: 99%

“…The recently described genome sequence of D. ethenogenes, strain 195 (ref. 4), an organism that reductively dechlorinates the solvents tetrachloroethene and trichloroethene to vinyl chloride and ethene 5 , reflects this specialization: although only 1.47-megabases (Mb) long, the genome possesses 17 rdhAB pairs potentially encoding reductive dehalogenases and genes predicted to encode five different hydrogenase complexes. We describe here the genome sequence of Dehalococcoides sp.…”

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confidence: 99%

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Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1

et al. 2005

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Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most toxic and persistent chlorinated aromatics and aliphatics by reductive dechlorination and are used for in situ bioremediation of contaminated sites. Our sequencing of the complete 1,395,502 base pair genome of Dehalococcoides strain CBDB1 has revealed the presence of 32 reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the bacteria an immense dehalogenating potential. Most rdh genes were associated with genes encoding transcription regulators such as two-component regulatory systems or transcription regulators of the MarR-type. Four new paralog groups of rdh-associated genes without known function were detected. Comparison with the recently sequenced genome of Dehalococcoides ethenogenes strain 195 reveals a high degree of gene context conservation (synteny) but exceptionally high plasticity in all regions containing rdh genes, suggesting that these regions are under intense evolutionary pressure.In the past century, human activities have released large amounts of chlorinated organic compounds into the environment, and these compounds are among the most pervasive groundwater pollutants. Chloroorganics with fewer chlorines can usually be biodegraded by aerobic microorganisms, whereas more highly chlorinated ones can be reductively dechlorinated by organisms using them as electron acceptors for anaerobic respiration. Several microbial groups carry out respiratory reductive dechlorination 1 , but one genus, Dehalococcoides, seems particularly adapted to a unique niche, and the bacteria are only known to use chloroorganics as electron acceptors and hydrogen as an electron donor for growth. Several studies have now shown successful application of Dehalococcoides-containing cultures for in situ remediation of contaminated sites 2,3 . The recently described genome sequence of D. ethenogenes, strain 195 (ref. 4), an organism that reductively dechlorinates the solvents tetrachloroethene and trichloroethene to vinyl chloride and ethene 5 , reflects this specialization: although only 1.47-megabases (Mb) long, the genome possesses 17 rdhAB pairs potentially encoding reductive dehalogenases and genes predicted to encode five different hydrogenase complexes. We describe here the genome sequence of Dehalococcoides sp. strain CBDB1, a bacterium that has in many ways a different dechlorination spectrum from strain 195. For instance, strain CBDB1 (refs. 6,7) dechlorinated 1,2,3-trichlorobenzene, 1,2,4-trichlorobenzene, 2,3-dichloro-p-dibenzodioxin and the 'Seveso dioxin ' 2,3,7,8-tetrachloro-p-dibenzodioxin, but strain 195 (ref. 8) did not. In contrast to strain 195, strain CBDB1 did not dechlorinate tetrachloroethene past dichloroethene 6 . By sequencing a second Dehalococcoides genome, we can now show that strain CBDB1 has an even greater potential as a reductive dechlorinator than strain 195 and, in addition, the comparison of the two genomes with each other provides insights into the evolution of reductive dechlori...

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Section: Comparison With D Ethenogenes Strain 195mentioning

confidence: 65%

Section: Discussionmentioning

confidence: 99%

Section: Comparison With D Ethenogenes Strain 195mentioning

confidence: 99%

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confidence: 99%

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Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1

et al. 2005

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“…(Dhc) (MaymoGatell et al, 1997). Dhc containing the gene tceA have been found to respire TCE and cis-DCE (Seshadri et al, 2005) whereas Dhc with the genes vcrA or bvcA respire cis-DCE and vinyl chloride (VC) (Muller et al, 2004;Sung et al, 2006). Several recent laboratory studies have also suggested that abiotic degradation pathways for chlorinated ethenes are of importance in the presence of iron minerals (Darlington et al, 2008;Ferrey et al, 2004;He et al, 2008He et al, , 2010Jeong et al, 2011;Lollar et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis

Damgaard

Bjerg

Bælum

et al. 2013

Journal of Contaminant Hydrology

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a b s t r a c tThe degradation of chlorinated ethenes and ethanes in clay till was investigated at a contaminated site (Vadsby, Denmark) by high resolution sampling of intact cores combined with groundwater sampling. Over decades of contamination, bioactive zones with degradation of trichloroethene (TCE) and 1,1,1-trichloroethane (1,1,1-TCA) to 1,2-cis-dichloroethene (cis-DCE) and 1,1-dichloroethane, respectively, had developed in most of the clay till matrix. Dehalobacter dominated over Dehalococcoides (Dhc) in the clay till matrix corresponding with stagnation of sequential dechlorination at cis-DCE. Sporadically distributed bioactive zones with partial degradation to ethene were identified in the clay till matrix (thickness from 0.10 to 0.22 m). In one sub-section profile the presence of Dhc with the vcrA gene supported the occurrence of degradation of cis-DCE and VC, and in another enriched δ 13 C for TCE, cis-DCE and VC documented degradation. Highly enriched δ 13 C for 1,1,1-TCA (25‰) and cis-DCE (−4‰) suggested the occurrence of abiotic degradation in a third sub-section profile. Due to fine scale heterogeneity the identification of active degradation zones in the clay till matrix depended on high resolution subsampling of the clay till cores. The study demonstrates that an integrated approach combining chemical analysis, molecular microbial tools and compound specific isotope analysis (CSIA) was required in order to document biotic and abiotic degradations in the clay till system.

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Thioredoxin‐Like [2Fe–2S] Ferredoxin

Meyer

Andrade

Einsle

2004

Handbook of Metalloproteins

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Putative electron transfer protein, may have regulatory function.The small size of the protein (3D structure) and the −300 mV reduction potential of its 2+,+ active site may suggest an electron transfer function among some of the more reducing redox reactions in microbial cells. In contrast, the dimeric structure and the protruding loop near the [2Fe-2S] cluster are more suggestive of a regulatory function, possibly in association with redox processes. O C C U R R E N C E

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Genome Sequence of the PCE-Dechlorinating BacteriumDehalococcoides ethenogenes

Cited by 399 publications

References 36 publications

Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1

Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1

Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis

Thioredoxin‐Like [2Fe–2S] Ferredoxin

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