title: Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene.
abstract: A Dehalococcoides-containing bacterial consortium that performed dechlorination of 0.20 mM cis-1,2-dichloroethene to ethene in 14 days was obtained from the sediment mud of the lotus field. To obtain detailed information of the consortium, the metagenome was analyzed using the short-read next-generation sequencer SOLiD 3. Matching the obtained sequence tags with the reference genome sequences indicated that the Dehalococcoides sp. in the consortium was highly homologous to Dehalococcoides mccartyi CBDB1 and BAV1. Sequence comparison with the reference sequence constructed from 16S rRNA gene sequences in a public database showed the presence of Sedimentibacter, Sulfurospirillum, Clostridium, Desulfovibrio, Parabacteroides, Alistipes, Eubacterium, Peptostreptococcus and Proteocatella in addition to Dehalococcoides sp. After further enrichment, the members of the consortium were narrowed down to almost three species. Finally, the full-length circular genome sequence of the Dehalococcoides sp. in the consortium, D. mccartyi IBARAKI, was determined by analyzing the metagenome with the single-molecule DNA sequencer PacBio RS. The accuracy of the sequence was confirmed by matching it to the tag sequences obtained by SOLiD 3. The genome is 1,451,062 nt and the number of CDS is 1566, which includes 3 rRNA genes and 47 tRNA genes. There exist twenty-eight RDase genes that are accompanied by the genes for anchor proteins. The genome exhibits significant sequence identity with other Dehalococcoides spp. throughout the genome, but there exists significant difference in the distribution RDase genes. The combination of a short-read next-generation DNA sequencer and a long-read single-molecule DNA sequencer gives detailed information of a bacterial consortium.
authors.affiliation: Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. Electronic address: yohda@cc.tuat.ac.jp.
authors.forename: Masafumi
authors.initials: M
authors.lastname: Yohda
authors.affiliation: Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, 1-2-1 Izumi-cho, Narashino, Chiba 275-8575, Japan.
authors.forename: Osami
authors.initials: O
authors.lastname: Yagi
authors.affiliation: Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
authors.forename: Ayane
authors.initials: A
authors.lastname: Takechi
authors.affiliation: Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
authors.forename: Mizuki
authors.initials: M
authors.lastname: Kitajima
authors.affiliation: Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan.
authors.forename: Hisashi
authors.initials: H
authors.lastname: Matsuda
authors.affiliation: Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan.
authors.forename: Naoaki
authors.initials: N
authors.lastname: Miyamura
authors.affiliation: Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Aizawa
authors.affiliation: Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan.
authors.forename: Mutsuyasu
authors.initials: M
authors.lastname: Nakajima
authors.affiliation: Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan.
authors.forename: Michio
authors.initials: M
authors.lastname: Sunairi
authors.affiliation: Accelrys, 3-7-1 Kasumigaseki, Chiyoda-ku, Tokyo 100-0013, Japan.
authors.forename: Akito
authors.initials: A
authors.lastname: Daiba
authors.affiliation: TM Software, PMB 282, 713 W. Duarte Rd., #G, Arcadia, CA 91007, USA.
authors.forename: Takashi
authors.initials: T
authors.lastname: Miyajima
authors.affiliation: Okinawa Industrial Technology Center, 12-2 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Morimi
authors.initials: M
authors.lastname: Teruya
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Kuniko
authors.initials: K
authors.lastname: Teruya
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Akino
authors.initials: A
authors.lastname: Shiroma
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Makiko
authors.initials: M
authors.lastname: Shimoji
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Hinako
authors.initials: H
authors.lastname: Tamotsu
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Ayaka
authors.initials: A
authors.lastname: Juan
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Kazuma
authors.initials: K
authors.lastname: Nakano
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Misako
authors.initials: M
authors.lastname: Aoyama
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Yasunobu
authors.initials: Y
authors.lastname: Terabayashi
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Kazuhito
authors.initials: K
authors.lastname: Satou
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-8 Suzaki, Uruma, Okinawa 904-2234, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Hirano
mesh_terms: D001483:Base Sequence; D001673:Biodegradation, Environmental; D002713:Chlorine / Q000378:metabolism; D041862:Chloroflexi / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification / Q000378:metabolism*; D004000:Dichloroethylenes / Q000378:metabolism*; D005030:Ethylenes / Q000378:metabolism; D020459:Genes, rRNA / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D054879:Halogenation; D056186:Metagenomics; D059013:Microbial Consortia / Q000235:genetics* / Q000502:physiology; D010084:Oxidation-Reduction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004000:Dichloroethylenes; D005030:Ethylenes; D012336:RNA, Ribosomal, 16S; D002713:Chlorine; C036216:ethylene; C035384:1,2-dichloroethylene
keywords: Bioremediation; Chloroethene; Dehalococcoides; Metagenome; Reductive dehalogenase