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Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence

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Title: Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence
Authors: Kojima, Hisaya Browse this author →KAKEN DB
Ogura, Yoshitoshi Browse this author
Yamamoto, Nozomi Browse this author
Togashi, Tomoaki Browse this author
Mori, Hiroshi Browse this author
Watanabe, Tomohiro Browse this author
Nemoto, Fumiko Browse this author
Kurokawa, Ken Browse this author
Hayashi, Tetsuya Browse this author
Fukui, Manabu Browse this author
Issue Date: May-2015
Publisher: Nature Publishing Group
Journal Title: ISME journal
Volume: 9
Issue: 5
Start Page: 1166
End Page: 1176
Publisher DOI: 10.1038/ismej.2014.209
Abstract: Large sulfur-oxidizing bacteria, which accumulate a high concentration of nitrate, are important constituents of aquatic sediment ecosystems. No representative of this group has been isolated in pure culture, and only fragmented draft genome sequences are available for these microorganisms. In this study, we successfully reconstituted the genome of Thioploca ingrica from metagenomic sequences, thereby generating the first complete genome sequence from this group. The Thioploca samples for the metagenomic analysis were obtained from a freshwater lake in Japan. A PCR-free paired-end library was constructed from the DNA extracted from the samples and was sequenced on the Illumina MiSeq platform. By closing gaps within and between the scaffolds, we obtained a circular chromosome and a plasmid-like element. The reconstituted chromosome was 4.8Mbp in length with a 41.2% GC content. A sulfur oxidation pathway identical to that suggested for the closest relatives of Thioploca was deduced from the reconstituted genome. A full set of genes required for respiratory nitrate reduction to dinitrogen gas was also identified. We further performed a proteomic analysis of the Thioploca sample and detected many enzymes/proteins involved in sulfur oxidation, nitrate respiration and inorganic carbon fixation as major components of the protein extracts from the sample, suggesting that these metabolic activities are strongly associated with the physiology of Thioploca ingrica in lake sediment.
Type: article (author version)
URI: http://hdl.handle.net/2115/60178
Appears in Collections:低温科学研究所 (Institute of Low Temperature Science) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 小島 久弥

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