title: Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence.
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 4.8 Mbp 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 T. ingrica in lake sediment.
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
authors.forename: Hisaya
authors.initials: H
authors.lastname: Kojima
authors.affiliation: 1] Division of Microbial Genomics, Department of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan [2] Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Yoshitoshi
authors.initials: Y
authors.lastname: Ogura
authors.affiliation: Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Nozomi
authors.initials: N
authors.lastname: Yamamoto
authors.affiliation: Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Togashi
authors.affiliation: Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Mori
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Watanabe
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
authors.forename: Fumiko
authors.initials: F
authors.lastname: Nemoto
authors.affiliation: 1] Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan [2] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Kurokawa
authors.affiliation: 1] Division of Microbial Genomics, Department of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan [2] Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Hayashi
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
authors.forename: Manabu
authors.initials: M
authors.lastname: Fukui
mesh_terms: D002244:Carbon / Q000737:chemistry; D017753:Ecosystem; D005618:Fresh Water / Q000382:microbiology; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D007564:Japan; D060106:Lakes; D056186:Metagenomics; D009566:Nitrates / Q000737:chemistry / Q000378:metabolism; D010802:Phylogeny; D020543:Proteome; D040901:Proteomics; D017422:Sequence Analysis, DNA; D013455:Sulfur / Q000737:chemistry; D041962:Thiotrichaceae / Q000235:genetics* / Q000502:physiology; D014871:Water Microbiology
chemical_list: D009566:Nitrates; D020543:Proteome; D013455:Sulfur; D002244:Carbon