Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene

Yohda, Masafumi; Yagi, Osami; Takechi, Ayane; Kitajima, Mizuki; Matsuda, Hisashi; Miyamura, Naoaki; Aizawa, Takuya; Nakajima, Mizuki; Sunairi, Michio; Daiba, Akito; Miyajima, Takashi; Teruya, Morimi; Teruya, Kuniko; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Juan, Ayaka; Nakano, Kazuma; Aoyama, Misako; Terabayashi, Yasunobu; Satou, Kazuhito; Hirano, Takashi

doi:10.1016/j.jbiosc.2014.12.001

Cited by 15 publications

(10 citation statements)

References 26 publications

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“…Comparison against 16S rRNA gene sequences in the public database was performed as described previously 19 . We compared the obtained tag sequences with the reference sequences constructed from 357,656 bacterial 16S rRNA gene sequences.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, we tried to obtain bacteria that support the growth of D. mccartyi UCH-ATV1. As the constructed consortium contained various species, we isolated Dehalococcoides -supporting bacteria from the consortium obtained in our previous study 19 . DGGE analysis showed that only three bacterial species including D. mccartyi IBARAKI dominantly existed in the Ibaraki consortium.…”

Section: Resultsmentioning

confidence: 99%

“…The PCR cycling conditions were as described above. The PCR products were purified and sequenced as described previously 19 . The PCR products were purified using the Wizard SV Gel and PCR Clean-Up System (Promega).…”

Section: Methodsmentioning

confidence: 99%

“…is hampered by their very slow growth rates. As Dehalococcoides is commonly found in microbial communities that contain other anaerobes, such as Desulfovibrio , Eubacterium , Acetobacterium , Citrobacter , Spirochetes and Clostridium 16–19 , and it is suggested that symbiotic interactions are indispensable for the growth of Dehalococcoides spp. The growth of D. mccartyi 195 is sustained by Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense 20 .…”

Section: Introductionmentioning

confidence: 99%

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Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture

Yohda

Ikegami

Aita

et al. 2017

Sci Rep

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We have developed and characterized a bacterial consortium that reductively dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA and reductive dehalogenase genes showed that the consortium is highly enriched with Dehalococcoides spp. that have two vinyl chloride reductive dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase gene, tceA. The metagenome analysis of the consortium by the next generation sequencer SOLiD 3 Plus suggests that a Dehalococcoides sp. that is highly homologous to D. mccartyi 195 and equipped with vcrA and tceA exists in the consortium. We isolated this Dehalococcoides sp. and designated it as D. mccartyi UCH-ATV1. As the growth of D. mccartyi UCH-ATV1 is too slow under isolated conditions, we constructed a consortium by mixing D. mccartyi UCH-ATV1 with several other bacteria and performed metagenomic sequencing using the single molecule DNA sequencer PacBio RS II. We successfully determined the complete genome sequence of D. mccartyi UCH-ATV1. The strain is equipped with vcrA and tceA, but lacks bvcA. Comparison with tag sequences of SOLiD 3 Plus from the original consortium shows a few differences between the sequences. This suggests that a genome rearrangement of Dehalococcoides sp. occurred during culture.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture

Yohda

Ikegami

Aita

et al. 2017

Sci Rep

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“…indica ATCC 53714, flv gene clusterPacBioNot openedNot openedNot openedNot openedLC0955922015 [31] Lactobacillus curvatus FBA2PacBioChromosome1,848,75642.143 sets of >1000-bp identical sequence pairs (3118-bp maximum), G+C content of 26.9% regionCP0160282016 [32] Dehalococcoides. mccartyi IBARAKIPacBio, SOLiD3Chromosome1,451,06247.0039 sets of >1000-bp identical sequence pairsNZ-AP0145632014 [33]Endosymbiont of Bathymodiolus septemdierum str. Myojin KnollPacBio, 454, Sanger, IlluminaChromosome1,469,43438.70SubpopulationAP0130422015 [34]Bacterial symbiont “TC1” of Trimyema compressum PacBioChromosome1,586,45332.8207 sets of >1000-bp identical sequence pairs, G+C content of 23.5% regionCP0146062016 [36]Plasmid35,79529.7CP014607 Vigna.…”

Section: Noted Studies Using Pacbio Rs IImentioning

confidence: 99%

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

et al. 2017

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PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II’s sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

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Microbial degradation of chloroethenes: a review

Dolinová

Štrojsová

Černík

et al. 2017

Environ Sci Pollut Res

115

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Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.

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Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene

Cited by 15 publications

References 26 publications

Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture

Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

Microbial degradation of chloroethenes: a review

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