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

Abstract 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 chlori...

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Autores principales:	Masafumi Yohda, Kentaro Ikegami, Yuto Aita, Mizuki Kitajima, Ayane Takechi, Megumi Iwamoto, Tomomi Fukuda, Noriyoshi Tamura, Junji Shibasaki, Seiji Koike, Daisuke Komatsu, Sakari Miyagi, Minoru Nishimura, Yoshihito Uchino, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Misuzu Shinzato, Shun Ohki, Kazuma Nakano, Kuniko Teruya, Kazuhito Satou, Takashi Hirano, Osami Yagi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/93e81ab37d8440769b64ca6966a5e68a
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spelling	oai:doaj.org-article:93e81ab37d8440769b64ca6966a5e68a2021-12-02T16:07:00ZIsolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture10.1038/s41598-017-02381-02045-2322https://doaj.org/article/93e81ab37d8440769b64ca6966a5e68a2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02381-0https://doaj.org/toc/2045-2322Abstract 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.Masafumi YohdaKentaro IkegamiYuto AitaMizuki KitajimaAyane TakechiMegumi IwamotoTomomi FukudaNoriyoshi TamuraJunji ShibasakiSeiji KoikeDaisuke KomatsuSakari MiyagiMinoru NishimuraYoshihito UchinoAkino ShiromaMakiko ShimojiHinako TamotsuNoriko AshimineMisuzu ShinzatoShun OhkiKazuma NakanoKuniko TeruyaKazuhito SatouTakashi HiranoOsami YagiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Masafumi Yohda Kentaro Ikegami Yuto Aita Mizuki Kitajima Ayane Takechi Megumi Iwamoto Tomomi Fukuda Noriyoshi Tamura Junji Shibasaki Seiji Koike Daisuke Komatsu Sakari Miyagi Minoru Nishimura Yoshihito Uchino Akino Shiroma Makiko Shimoji Hinako Tamotsu Noriko Ashimine Misuzu Shinzato Shun Ohki Kazuma Nakano Kuniko Teruya Kazuhito Satou Takashi Hirano Osami Yagi Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture
description	Abstract 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.
format	article
author	Masafumi Yohda Kentaro Ikegami Yuto Aita Mizuki Kitajima Ayane Takechi Megumi Iwamoto Tomomi Fukuda Noriyoshi Tamura Junji Shibasaki Seiji Koike Daisuke Komatsu Sakari Miyagi Minoru Nishimura Yoshihito Uchino Akino Shiroma Makiko Shimoji Hinako Tamotsu Noriko Ashimine Misuzu Shinzato Shun Ohki Kazuma Nakano Kuniko Teruya Kazuhito Satou Takashi Hirano Osami Yagi
author_facet	Masafumi Yohda Kentaro Ikegami Yuto Aita Mizuki Kitajima Ayane Takechi Megumi Iwamoto Tomomi Fukuda Noriyoshi Tamura Junji Shibasaki Seiji Koike Daisuke Komatsu Sakari Miyagi Minoru Nishimura Yoshihito Uchino Akino Shiroma Makiko Shimoji Hinako Tamotsu Noriko Ashimine Misuzu Shinzato Shun Ohki Kazuma Nakano Kuniko Teruya Kazuhito Satou Takashi Hirano Osami Yagi
author_sort	Masafumi Yohda
title	Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture
title_short	Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture
title_full	Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture
title_fullStr	Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture
title_full_unstemmed	Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture
title_sort	isolation and genomic characterization of a dehalococcoides strain suggests genomic rearrangement during culture
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/93e81ab37d8440769b64ca6966a5e68a
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_version_	1718384790767403008

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

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