研究者データベース

渡邉 友浩(ワタナベ トモヒロ)
低温科学研究所 生物環境部門
助教

基本情報

所属

  • 低温科学研究所 生物環境部門

職名

  • 助教

学位

  • 博士(環境科学)(2014年03月 北海道大学)

科研費研究者番号

  • 80731968

ORCID ID

J-Global ID

職歴

  • 2020年04月 - 現在 北海道大学 低温科学研究所 生物環境部門 助教
  • 2018年08月 - 2020年03月 マックスプランク陸生微生物学研究所 Microbial Protein Structure 日本学術振興会海外特別研究員
  • 2016年08月 - 2018年07月 マックスプランク陸生微生物学研究所 Microbial protein structure アレクサンダーフォンフンボルト財団奨励研究員
  • 2016年04月 - 2016年07月 S + W speak + write アレクサンダーフォンフンボルト財団奨励研究員(ドイツ語語学研修)
  • 2014年04月 - 2016年03月 北海道大学 低温科学研究所 生物環境部門 非常勤研究員

学歴

  • 2011年04月 - 2014年03月   北海道大学   大学院環境科学研究院   生物圏科学専攻
  • 2009年04月 - 2011年03月   北里大学   獣医畜産学研究科   動物資源科学専攻
  • 2005年04月 - 2009年03月   北里大学   獣医畜産学部   動物資源科学科

研究活動情報

論文

  • Tomohiro Watanabe, Kyoko Kubo, Yoshiharu Kamei, Hisaya Kojima, Manabu Fukui
    Systematic and Applied Microbiology 45 3 126320 - 126320 2022年05月
  • Tomohiro Watanabe, Olivia Pfeil-Gardiner, Jörg Kahnt, Jürgen Koch, Seigo Shima, Bonnie J. Murphy
    Science 373 6559 1151 - 1156 2021年09月03日
  • Tomohiro Watanabe, Seigo Shima
    Chemistry Letters 2020年11月18日
  • Tomohiro Watanabe, Tristan Wagner, Gangfeng Huang, Jörg Kahnt, Kenichi Ataka, Ulrich Ermler, Seigo Shima
    Angewandte Chemie International Edition 58 11 3506 - 3510 2019年03月11日 
    [Fe]-hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyl-tetrahydromethanopterin (methenyl-H4MPT+) with H-2. H4MPT is a C1-carrier of methanogenic archaea. One bacterial genus, Desulfurobacterium, contains putative genes for the Hmd paralog, termed HmdII, and the HcgA-G proteins. The latter are required for the biosynthesis of the prosthetic group of Hmd, the iron-guanylylpyridinol (FeGP) cofactor. This finding is intriguing because Hmd and HmdII strictly use H4MPT derivatives that are absent in most bacteria. We identified the presence of the FeGP cofactor in D. thermolithotrophum. The bacterial HmdII reconstituted with the FeGP cofactor catalyzed the hydrogenation of derivatives of tetrahydrofolate, the bacterial C1-carrier, albeit with low enzymatic activities. The crystal structures show how Hmd recognizes tetrahydrofolate derivatives. These findings have an impact on future biotechnology by identifying a bacterial Hmd paralog.
  • Tomohiro Watanabe, Hisaya Kojima, Kazuhiro Umezawa, Chiaki Hori, Taichi E. Takasuka, Yukako Kato, Manabu Fukui
    FRONTIERS IN MICROBIOLOGY 10 2019年02月 
    Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family 'Sulfuricellaceae'. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterohbacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.
  • Melody Cabrera Ospino, Hisaya Kojima, Tomohiro Watanabe, Tomoya Iwata, Manabu Fukui
    Limnology 19 2 177 - 183 2018年04月 
    Anaerobic arsenite oxidation is potentially important but the least understood process in the arsenic cycle. The catalytic subunit of the key enzyme for anaerobic arsenite oxidation is encoded by the arxA gene. In this study, a novel primer pair for the arxA gene was designed to detect diverse sequences of this notable gene. Further modification of the designed primer was made by adding extra bases to its 5'- end. This modification made it possible to analyze the PCR products with TA cloning, which provides higher throughput of investigations. With the combination of modified primer pair and TA cloning, diverse arxA gene sequences were effectively obtained from samples of lake water, spring water, and hot spring microbial mat. The sequences detected in the samples characterized by low salinity and nearly neutral pH were phylogenetically distinct from the majority of previously known arxA genes, found in the genome of alkaliphiles and halophiles.
  • Tomohiro Watanabe, Aya Miura, Tomoya Iwata, Hisaya Kojima, Manabu Fukui
    Environmental Microbiology Reports 9 5 522 - 527 2017年10月 
    Facultative autotrophs of the genus Sulfuritalea within the class Betaproteobacteria have been predicted to be an important bacterial population in stratified freshwater lakes based on previous PCR-based studies. Here, we designed a new probe specific for the genus Sulfuritalea and performed catalysed reporter deposition-fluorescence in situ hybridisation to enumerate cells of Sulfuritalea species throughout the water column in a stratified freshwater lake. The cells stained with the Sulfuritalea-specific probe were detected in all hypoxic water samples collected in different seasons and years. Their abundance ranged from 1.4 × 104 to 2.1 × 105 cells ml-1 , corresponding to 0.5-5.5% of the total DAPI-stained cells and 2.3-15% of the total bacterial cells. A high abundance of Sulfuritalea species was recorded in hypoxic water samples without nitrate, which is the only known anaerobic electron acceptor for Sulfuritalea. Nitrate-independent anaerobic respiration was further investigated using a single cultured representative of this genus, and its growth via arsenate respiration was experimentally demonstrated. In conclusion, Sulfuritalea species were found to be a major component of the planktonic bacterial community in nitrate-depleted hypoxic water, where arsenate respiration is one of the possible energy metabolisms of Sulfuritalea.
  • Kazuhiro Umezawa, Tomohiro Watanabe, Aya Miura, Hisaya Kojima, Manabu Fukui
    Standards in Genomic Sciences 11 1 2016年12月 
    Sulfurifustis variabilis and Sulfuricaulis limicola are autotrophic sulfur-oxidizing bacteria belonging to the family Acidiferrobacteraceae in the order Acidiferrobacterales. The type strains of these species, strain skN76(T) and strain HA5(T), were isolated from lakes in Japan. Here we describe the complete genome sequences of Sulfurifustis variabilis skN76T and Sulfuricaulis limicola HA5T. The genome of Sulfurifustis variabilis skN76T consists of one circular chromosome with size of 4.0 Mbp including 3864 protein-coding sequences. The genome of Sulfuricaulis limicola HA5T is 2.9 Mbp chromosome with 2763 protein-coding sequences. In both genomes, 46 transfer RNA-coding genes and one ribosomal RNA operon were identified. In the genomes, redundancies of the genes involved in sulfur oxidation and inorganic carbon fixation pathways were observed. This is the first report to show the complete genome sequences of bacteria belonging to the order Acidiferrobacterales in the class Gammaproteobacteria.
  • Tomohiro Watanabe, Hisaya Kojima, Manabu Fukui
    Scientific Reports 6 1 2016年12月 
    Adenylylsulfate reductase is a heterodimeric complex of two subunits, AprB and AprA, and is a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. Common use of aprA as a functional marker gene has revealed the diversity of sulfur-cycle prokaryotes in diverse environments. In this study, we established a comprehensive sequence set of apr genes and employed it to reanalyze apr phylogeny, evaluate the coverage of a widely used primer set (AprA-1-FW/AprA-5-RV), and categorize environmental aprA sequences. Phylogenetic tree construction revealed new members of Apr lineage II and several previously unrecognized lateral gene transfer events. Using the established phylogenetic tree, we classified all previously reported aprA sequences amplified from freshwater lakes with the primer pair AprA-1-FW/AprA-5-RV in addition to the aprA sequences newly retrieved from freshwater lakes; the obtained results were complemented by 16S rRNA clone library analysis. Apr-based classifications of some of operational taxonomic units were supported by 16S rRNA-based analysis. This study updates our knowledge on the phylogeny of aprBA and shows the identities of several sulfur-cycle bacteria, which could not be classified to a known taxa until now. The established apr sequence set is publicly available and can be applied to assign environmental sequences to known lineages.
  • Tomohiro Watanabe, Aya Miura, Arisa Shinohara, Hisaya Kojima, Manabu Fukui
    International Journal of Systematic and Evolutionary Microbiology 66 5 1986 - 1989 2016年05月01日 
    A novel sulfur oxidizer, strain wk12T, was isolated from an industrially synthesized lead (II) sulfide. The G+C content of the genomic DNA was around 58.5 mol%. The major components in the cellular fatty acid profile were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The strain oxidized lead sulfide, thiosulfate and tetrathionate as electron donors to support autotrophic growth. Cells of strain wk12T were motile, rod-shaped (0.5-1.0 × 0.7-2.2 μm), and Gram-stain-negative. For growth, the temperature range was 5-37 °C, and optimum growth was observed at 28-32 °C. The pH range for growth was 5.8-8.7, with optimum growth at pH 6.4-7.1. Optimum growth of the isolate was observed in medium without NaCl, and no growth was observed in the medium containing 0.5 M or more NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the class Acidithiobacillia. The closest relative with a validly published name was Thermithiobacillus tepidarius DSM 3134T, with a 16S rRNA gene sequence similarity of 96 %. On the basis of phylogenetic and phenotypic properties, strain wk12T represents a novel species of the genus Thermithiobacillus, for which the name Thermithiobacillus plumbiphilus sp. nov. is proposed. The type strain is wk12T ( = NBRC 111508T = DSM 101799T).
  • Watanabe Tomohiro, Kojima Hisaya, Fukui Manabu
    International journal of systematic and evolutionary microbiology 66 5 2041 - 2045 Society for General Microbiology 2016年05月01日 
    A novel sulfur-oxidizing bacterium designated strain mst6(T) was isolated from spring water of Masutomi hot spring in Japan. The cells were rod-shaped (1.2-4.0 x 0.5-0.7 mm) and Gram-stain-negative. The G+C content of genomic DNA was around 52.6 mol%. The isolate possessed summed feature 3 (C-16 : 1 omega 7c and/or C-16 : 1 omega 6c), C-16 : 0 and C-12 : 0 as major cellular fatty acids. Strain mst6(T) grew by inorganic carbon fixation and oxidation of inorganic sulfur compounds with oxygen as an electron acceptor. The isolate grew over a temperature range of 5-34 degrees C, a NaCl concentration range of 0-110 mM and a pH range of 4.6-8.1. Optimum growth occurred at 32 degrees C, in the absence of NaCl and at pH 5.9-6.2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain mst6(T) belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relative was Sulfuriferula multivorans TTNT with a 16S rRNA gene sequence similarity of 97.0 %. On the basis of the data obtained in this study, strain mst6(T) represents a novel species of the genus Sulfuriferula, for which the name Sulfuriferula thiophila sp. nov. is proposed. The type strain is mst6(T) (=NBRC 111150(T) =DSM 101871(T)). In addition, we propose correcting the name Sulfuriferula plumbophilus Watanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig. based on Rule 12c, Rule 61 and Appendix 9 of the International Code of Nomenclature of Prokaryotes.
  • Tomohiro Watanabe, Hisaya Kojima, Arisa Shinohara, Manabu Fukui
    International Journal of Systematic and Evolutionary Microbiology 66 1 113 - 117 2016年01月01日
  • Hisaya Kojima, Tomohiro Watanabe, Manabu Fukui
    International Journal of Systematic and Evolutionary Microbiology 66 1 266 - 270 2016年01月01日
  • Y. Higashioka, H. Kojima, T. Watanabe, M. Fukui
    Genome Announcements 3 6 2015年11月12日 
    Desulfatitalea tepidiphila S28bF(T) is a sulfate-reducing bacterium closely related to Desulfosarcina species. Here, the draft genome sequence of strain S28bF(T) is reported.
  • Tomohiro Watanabe, Hisaya Kojima, Manabu Fukui
    MICROBIOLOGY RESOURCE ANNOUNCEMENTS 3 5 2015年09月 [査読有り][通常論文]
     
    Strain skMP5(T) is a moderately thermophilic and facultatively anaerobic bacterium, described as a representative of Mizugakiibacter sediminis. Here, we report the annotated draft genome sequence of strain skMP5(T).
  • Tomohiro Watanabe, Hisaya Kojima, Manabu Fukui
    International Journal of Systematic and Evolutionary Microbiology 65 5 1504 - 1508 2015年06月27日 
    A sulfur-oxidizing bacterium, strain TTN< sup> T< /sup> , was isolated from a Thioploca sample obtained from a freshwater lake in Japan. The isolate shared 97.1 % 16S rRNA gene sequence similarity with an obligately aerobic chemolithoautotroph, ‘Thiobacillus plumbophilus’ Gro7< sup> T< /sup> . Cells were rods, motile, and Gram-stain-negative. The G+C content of the genomic DNA was approximately 66 mol%. Strain TTN< sup> T< /sup> grew over a temperature range of 8-32 °C (optimum 22-25 °C), an NaCl concentration range of 0-133.3 mM (optimum 0-3.3 mM) and a pH range of 5.3-8.6 (optimum pH 6.4-7.0). Strain TTN< sup> T< /sup> was facultatively anaerobic and could utilize nitrate as an electron acceptor. The isolate oxidized tetrathionate, thiosulfate and elemental sulfur as the sole energy sources for autotrophic growth, and could also grow heterotrophically on a number of organic substrates. Based on its phylogenetic and phenotypic properties, strain TTN< sup> T< /sup> represents a novel species of a novel genus, for which the name Sulfuriferula multivorans gen. nov., sp. nov. is proposed. The type strain is TTN< sup> T< /sup> (=NBRC 110683< sup> T< /sup> =DSM 29343< sup> T< /sup> ). Along with this, the reclassification of ‘Thiobacillus plumbophilus’ asSulfuriferula plumbophilus sp. nov. (type strain Gro7< sup> T< /sup> =NBRC 107929< sup> T< /sup> =DSM 6690< sup> T< /sup> ) is proposed. Based on the data obtained in this study, we describe the designations Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.
  • Hisaya Kojima, Yoshitoshi Ogura, Nozomi Yamamoto, Tomoaki Togashi, Hiroshi Mori, Tomohiro Watanabe, Fumiko Nemoto, Ken Kurokawa, Tetsuya Hayashi, Manabu Fukui
    The ISME Journal 9 5 1166 - 1176 2015年05月 
    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.
  • Tomohiro Watanabe, Hisaya Kojima, Manabu Fukui
    MICROBIOLOGY RESOURCE ANNOUNCEMENTS 3 3 2015年05月 
    Sulfuricella sp. strain T08 is a sulfur-oxidizing autotroph newly isolated from a freshwater lake in Japan. Strain T08 is the second isolate of the genus Sulfuricella. Here, we report the annotated draft genome sequence of the isolate.
  • Tomohiro Watanabe, Hisaya Kojima, Manabu Fukui
    Genome Announcements 3 5 2015年 
    Strain skMP5T is a moderately thermophilic and facultatively anaerobic bacterium, described as a representative of Mizugakiibacter sediminis. Here, we report the annotated draft genome sequence of strain skMP5T.
  • Hisaya Kojima, Tomohiro Watanabe, Tomoya Iwata, Manabu Fukui
    PLoS ONE 9 4 2014年04月02日 
    Planktonic sulfur oxidizers are important constituents of ecosystems in stratified water bodies, and contribute to sulfide detoxification. In contrast to marine environments, taxonomic identities of major planktonic sulfur oxidizers in freshwater lakes still remain largely unknown. Bacterioplankton community structure was analyzed in a stratified freshwater lake, Lake Mizugaki in Japan. In the clone libraries of 16S rRNA gene, clones very closely related to a sulfur oxidizer isolated from this lake, Sulfuritalea hydrogenivorans, were detected in deep anoxic water, and occupied up to 12.5% in each library of different water depth. Assemblages of planktonic sulfur oxidizers were specifically analyzed by constructing clone libraries of genes involved in sulfur oxidation, aprA, dsrA, soxB and sqr. In the libraries, clones related to betaproteobacteria were detected with high frequencies, including the close relatives of Sulfuritalea hydrogenivorans. © 2014 Kojima et al.
  • Tomohiro Watanabe, Hisaya Kojima, Yoshinori Takano, Manabu Fukui
    Systematic and Applied Microbiology 36 6 436 - 443 2013年09月 
    The diversity of sulfate-reducing prokaryotes (SRPs) and sulfur-oxidizing prokaryotes (SOPs) in freshwater lake ecosystems was investigated by cloning and sequencing of the aprA gene, which encodes for a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. To understand their diversity better, the spatial distribution of aprA genes was investigated in sediments collected from six geographically distant lakes in Antarctica and Japan, including a hypersaline lake for comparison. The microbial community compositions of freshwater sediments and a hypersaline sediment showed notable differences. The clones affiliated with Desulfobacteraceae and Desulfobulbaceae were frequently detected in all freshwater lake sediments. The SOP community was mainly composed of four major phylogenetic groups. One of them formed a monophyletic cluster with a sulfur-oxidizing betaproteobacterium, Sulfuricella denitrificans, but the others were not assigned to specific genera. In addition, the AprA sequences, which were not clearly affiliated to either SRP or SOP lineages, dominated the libraries from four freshwater lake sediments. The results showed the wide distribution of some sulfur-cycle prokaryotes across geographical distances and supported the idea that metabolic flexibility is an important feature for SRP survival in low-sulfate environments. (C) 2013 Elsevier GmbH. All rights reserved.
  • Tomohiro Watanabe, Hisaya Kojima, Manabu Fukui
    Applied and Environmental Microbiology 78 18 6545 - 6549 2012年09月15日 
    ABSTRACTExcept for several conspicuous cases, very little is known about sulfur oxidizers living in natural freshwater environments.Sulfuricella denitrificansskB26 is a psychrotolerant sulfur oxidizer recently isolated from a freshwater lake as a representative of a new genus in the classBetaproteobacteria. In this study, an approximately 3.2-Mb draft genome sequence of strain skB26 was obtained. In the draft genome, consisting of 23 contigs, a single rRNA operon, 43 tRNA genes, and 3,133 coding sequences were identified. The identified genes include those required for sulfur oxidation, denitrification, and carbon fixation. Comparative proteomic analysis was conducted to assess cold adaptation mechanisms of this organism. From cells grown at 22°C and 5°C, proteins were extracted for analysis by nano-liquid chromatography–electrospray ionization–tandem mass spectrometry. In the cells cultured at 5°C, relative abundances of ribosomal proteins, cold shock proteins, and DEAD/DEAH box RNA helicases were increased in comparison to those at 22°C. These results suggest that maintenance of proper translation is critical for growth under low-temperature conditions, similar to the case for other cold-adapted prokaryotes.

その他活動・業績



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