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Hirayama H, Takaki Y, Abe M, Miyazaki M, Uematsu K, Matsui Y, Takai K. Methylomarinovum tepidoasis sp. nov., a moderately thermophilic methanotroph of the family Methylothermaceae isolated from a deep-sea hydrothermal field. Int J Syst Evol Microbiol 2024; 74:006288. [PMID: 38478579 PMCID: PMC10950024 DOI: 10.1099/ijsem.0.006288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024] Open
Abstract
A novel aerobic methanotrophic bacterium, designated as strain IN45T, was isolated from in situ colonisation systems deployed at the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. IN45T was a moderately thermophilic obligate methanotroph that grew only on methane or methanol at temperatures between 25 and 56 °C (optimum 45-50 °C). It was an oval-shaped, Gram-reaction-negative, motile bacterium with a single polar flagellum and an intracytoplasmic membrane system. It required 1.5-4.0 % (w/v) NaCl (optimum 2-3 %) for growth. The major phospholipid fatty acids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The 16S rRNA gene sequence comparison revealed 99.1 % sequence identity with Methylomarinovum caldicuralii IT-9T, the only species of the genus Methylomarinovum with a validly published name within the family Methylothermaceae. The complete genome sequence of IN45T consisted of a 2.42-Mbp chromosome (DNA G+C content, 64.1 mol%) and a 20.5-kbp plasmid. The genome encodes genes for particulate methane monooxygenase and two types of methanol dehydrogenase (mxaFI and xoxF). Genes involved in the ribulose monophosphate pathway for carbon assimilation are encoded, but the transaldolase gene was not found. The genome indicated that IN45T performs partial denitrification of nitrate to N2O, and its occurrence was indirectly confirmed by N2O production in cultures grown with nitrate. Genomic relatedness indices between the complete genome sequences of IN45T and M. caldicuralii IT-9T, such as digital DNA-DNA hybridisation (51.2 %), average nucleotide identity (92.94 %) and average amino acid identity (93.21 %), indicated that these two methanotrophs should be separated at the species level. On the basis of these results, strain IN45T represents a novel species, for which we propose the name Methylomarinovum tepidoasis sp. nov. with IN45T (=JCM 35101T =DSM 113422T) as the type strain.
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Affiliation(s)
- Hisako Hirayama
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mariko Abe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | | | - Yohei Matsui
- Research Institute for Global Change (RIGC), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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Miyazaki U, Mizutani D, Hashimoto Y, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Helicovermis profundi gen. nov., sp. nov., a novel mesophilic, asporogenous bacterium within the Clostridia isolated from a deep-sea hydrothermal vent chimney. Antonie Van Leeuwenhoek 2024; 117:24. [PMID: 38217723 DOI: 10.1007/s10482-023-01919-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/12/2023] [Indexed: 01/15/2024]
Abstract
A novel mesophilic bacterial strain, designated S502T, was isolated from a deep-sea hydrothermal vent at Suiyo Seamount, Japan. Cells were Gram-positive, asporogenous, motile, and curved rods, measuring 1.6-5.6 µm in length. The strain was an obligate anaerobe that grew fermentatively on complex substrates such as yeast extract and Bacto peptone. Elemental sulfur stimulated the growth of the strain, and was reduced to hydrogen sulfide. The strain grew within a temperature range of 10-23 °C (optimum at 20 °C), pH range of 4.8-8.3 (optimum at 7.4), and a NaCl concentration range of 1.0-4.0% (w/v) (optimum at 3.0%, w/v). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the class Clostridia, with Fusibacter paucivorans strain SEBR 4211T (91.1% sequence identity) being its closest relative. The total size of the genome of the strain was 3.12 Mbp, and a G + C content was 28.2 mol%. The highest values for average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) value of strain S502T with relatives were 67.5% (with Marinisporobacter balticus strain 59.4MT), 51.5% (with M. balticus strain 59.4MT), and 40.9% (with Alkaliphilus serpentinus strain LacTT), respectively. Based on a combination of phylogenetic, genomic, and phenotypic characteristics, we propose strain S502T to represent a novel genus and species, Helicovermis profundi gen. nov., sp. nov., with the type strain S502T (= DSM 112048T = JCM 39167T).
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Affiliation(s)
- Urara Miyazaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Daiki Mizutani
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Akihiro Tame
- Depertment of Marine and Earth Sciences, Marine Works Japan Ltd, 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
- General Affairs Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Ken Takai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan.
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan.
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Zhang Y, Takaki Y, Yoshida-Takashima Y, Hiraoka S, Kurosawa K, Nunoura T, Takai K. A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems. mSystems 2023; 8:e0081723. [PMID: 37843256 PMCID: PMC10734518 DOI: 10.1128/msystems.00817-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE The elucidation of the molecular basis of virus-host coevolutionary interactions is boosted with state-of-the-art sequencing technologies. However, the sequence-only information is often insufficient to output a conclusive argument without biochemical characterizations. We proposed a 1-day and one-pot approach to confirm the exact function of putative restriction-modification (R-M) genes that presumably mediate microbial coevolution. The experiments mainly focused on a series of putative R-M enzymes from a deep-sea virus and its host bacterium. The results quickly unveiled unambiguous substrate specificities, superior catalytic performance, and unique sequence preferences for two new restriction enzymes (capable of cleaving DNA) and two new methyltransferases (capable of modifying DNA with methyl groups). The reality of the functional R-M system reinforced a model of mutually beneficial interactions with the virus in the deep-sea microbial ecosystem. The cell culture-independent approach also holds great potential for exploring novel and biotechnologically significant R-M enzymes from microbial dark matter.
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Affiliation(s)
- Yi Zhang
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yukari Yoshida-Takashima
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Kanako Kurosawa
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Miyazaki U, Sanari M, Tame A, Kitajima M, Okamoto A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Pyrofollis japonicus gen. nov. sp. nov., a novel member of the family Pyrodictiaceae isolated from the Iheya North hydrothermal field. Extremophiles 2023; 27:28. [PMID: 37843723 DOI: 10.1007/s00792-023-01316-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023]
Abstract
A novel hyperthermophilic, heterotrophic archaeon, strain YC29T, was isolated from a deep-sea hydrothermal vent in the Mid-Okinawa Trough, Japan. Cells of strain YC29T were non-motile, irregular cocci with diameters of 1.2-3.0 µm. The strain was an obligatory fermentative anaerobe capable of growth on complex proteinaceous substrates. Growth was observed between 85 and 100 °C (optimum 90-95 °C), pH 4.9-6.4 (optimum 5.1), and in the presence of 1.4-4.0% (w/v) NaCl (optimum 3.0%). Inorganic carbon was required as a carbon source. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the family Pyrodictiaceae. The genome size was 2.02 Mbp with a G+C content of 49.4%. The maximum values for average nucleotide identity (ANI), average amino acid identity (AAI), and in silico DNA-DNA hybridization (dDDH) value of strain YC29T with relatives were 67.9% (with Pyrodictium abyssi strain AV2T), 61.1% (with Pyrodictium occultum strain PL-19T), and 33.8% (with Pyrolobus fumarii strain 1AT), respectively. Based on the phylogenetic, genomic, and phenotypic characteristics, we propose that strain YC29T represents a novel genus and species, Pyrofollis japonicus gen. nov., sp. (type strain YC29T = DSM 113394T = JCM 39171T).
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Affiliation(s)
- Urara Miyazaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Kyoto, 606-8502, Japan
| | - Masaru Sanari
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Kyoto, 606-8502, Japan
| | - Akihiro Tame
- Department of Marine and Earth Sciences, Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
- General Affairs Department, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-Ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-Ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Kyoto, 606-8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Ken Takai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Kyoto, 606-8502, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan.
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan.
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Takahagi W, Okada S, Matsui Y, Ono S, Takai K, Takahashi Y, Kitadai N. Extreme accumulation of ammonia on electroreduced mackinawite: An abiotic ammonia storage mechanism in early ocean hydrothermal systems. Proc Natl Acad Sci U S A 2023; 120:e2303302120. [PMID: 37782799 PMCID: PMC10576140 DOI: 10.1073/pnas.2303302120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 08/14/2023] [Indexed: 10/04/2023] Open
Abstract
An increasing amount of evidence suggests that early ocean hydrothermal systems were sustained sources of ammonia, an essential nitrogen species for prebiotic synthesis of life's building blocks. However, it remains a riddle how the abiotically generated ammonia was retained at the vent-ocean interface for the subsequent chemical evolution. Here, we demonstrate that, under simulated geoelectrochemical conditions in early ocean hydrothermal systems ([Formula: see text][Formula: see text] V versus the standard hydrogen electrode), mackinawite gradually reduces to zero-valent iron ([Formula: see text]), generating interlayer [Formula: see text] sites. This reductive conversion leads to an up to 55-fold increase in the solid/liquid partition coefficient for ammonia, enabling over 90% adsorption of 1 mM ammonia in 1 M NaCl at neutral pH. A coordinative binding of ammonia on the interlayer [Formula: see text] sites was computed to be the major mechanism of selective ammonia adsorption. Mackinawite is a ubiquitous sulfide precipitate in submarine hydrothermal systems. Given its reported catalytic function in amination, the extreme accumulation of ammonia on electroreduced mackinawite should have been a crucial initial step for prebiotic nitrogen assimilation, paving the way to the origin of life.
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Affiliation(s)
- Wataru Takahagi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, (X-star), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka237-0061, Japan
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Satoshi Okada
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, (X-star), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka237-0061, Japan
| | - Yohei Matsui
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka237-0061, Japan
| | - Shigeaki Ono
- Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology, Yokosuka237-0061, Japan
| | - Ken Takai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, (X-star), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka237-0061, Japan
| | - Yoshio Takahashi
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
| | - Norio Kitadai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, (X-star), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo152-8550, Japan
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Miyazaki U, Tame A, Miyazaki J, Takai K, Sawayama S, Kitajima M, Okamoto A, Nakagawa S. Haliovirga abyssi gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from the Iheya North hydrothermal field, and proposal of Haliovirgaceae fam. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37540001 DOI: 10.1099/ijsem.0.006014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
A novel mesophilic, obligately anaerobic, facultatively sulphur-reducing bacterium, designated strain IC12T, was isolated from a deep-sea hydrothermal field in the Mid-Okinawa Trough, Japan. The cells were Gram-negative, motile, short rods with a single polar flagellum. The ranges and optima of the growth temperature, NaCl concentration and pH of strain IC12T were 15-40 °C (optimum, 30-35 °C), 10-60 g l-1 (optimum, 20-30 g l-1) and pH 4.9-6.7 (optimum, pH 5.8), respectively. Yeast extract was utilized as a sole carbon and energy source for fermentative growth. Major fatty acids of strain IC12T were C14 : 0, C16 : 0 and C16 : 1 ω7. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IC12T was affiliated to the phylum Fusobacteriota and was most closely related to Ilyobacter insuetus VenChi2T (86.5 % sequence similarity). Strain IC12T contained a chromosome of 2.43 Mbp and a large plasmid of 0.30 Mbp. The G+C content of the genomic DNA was 26.4 mol%. The maximum values for average nucleotide identity and in silico DNA-DNA hybridization between strain IC12T and related strains of the phylum Fusobacteriota were 71.4 and 26.4 %, respectively. Phylogenomic, physiological and chemotaxonomic analyses indicate that strain IC12T represents a novel genus and species within the phylum Fusobacteriota, for which the name Haliovirga abyssi gen. nov., sp. nov. is proposed, with strain IC12T (= DSM 112164T=JCM 39166T) as the type strain. We also propose the family Haliovirgaceae fam. nov. to accommodate this novel genus.
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Affiliation(s)
- Urara Miyazaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Akihiro Tame
- Depertment of Marine and Earth Sciences, Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
- General Affairs Department, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Junichi Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
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Takahagi W, Kitadai N, Okada S, Zhou H, Takai K, Yamada T. Quantification of polysulfide species in aqueous sulfur thermocell. CHEM LETT 2023. [DOI: 10.1246/cl.220486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Wataru Takahagi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
- Super-cutting-edge Grand and Advanced Research (SUGAR), Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061
| | - Norio Kitadai
- Super-cutting-edge Grand and Advanced Research (SUGAR), Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550
| | - Satoshi Okada
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
| | - Hongyao Zhou
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR), Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061
| | - Teppei Yamada
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
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Igisu M, Miyazaki M, Sakai S, Nakagawa S, Sakai HD, Takai K. Domain-level Identification of Single Prokaryotic Cells by Optical Photothermal Infrared Spectroscopy. Microbes Environ 2023; 38:ME23052. [PMID: 37853632 PMCID: PMC10728636 DOI: 10.1264/jsme2.me23052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/22/2023] [Indexed: 10/20/2023] Open
Abstract
Infrared spectroscopy is used for the chemical characterization of prokaryotes. However, its application has been limited to cell aggregates and lipid extracts because of the relatively low spatial resolution of diffraction. We herein report optical photothermal infrared (O-PTIR) spectroscopy of prokaryotes for a domain-level diagnosis at the single-cell level. The technique provided infrared spectra of individual bacterial as well as archaeal cells, and the resulting aliphatic CH3/CH2 intensity ratios showed domain-specific signatures, which may reflect distinctive cellular lipid compositions; however, there was interference by other cellular components. These results suggest the potential of O-PTIR for a domain-level diagnosis of single prokaryotic cells in natural environments.
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Affiliation(s)
- Motoko Igisu
- Super-cutting-edge Grand and Advanced Research (Sugar) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 237–0061, Japan
| | - Masayuki Miyazaki
- Super-cutting-edge Grand and Advanced Research (Sugar) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 237–0061, Japan
| | - Sanae Sakai
- Super-cutting-edge Grand and Advanced Research (Sugar) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 237–0061, Japan
| | - Satoshi Nakagawa
- Super-cutting-edge Grand and Advanced Research (Sugar) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 237–0061, Japan
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5–1 Higashiyama, Myodaiji, Okazaki, Aichi 444–8787, Japan
| | - Hiroyuki D. Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
- Present address: BioResource Research Center, Japan Collection of Microorganisms, RIKEN, Tsukuba, Ibaraki 305–0074, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (Sugar) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima, Yokosuka, Kanagawa 237–0061, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5–1 Higashiyama, Myodaiji, Okazaki, Aichi 444–8787, Japan
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9
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Muto H, Miyazaki J, Sawayama S, Takai K, Nakagawa S. A Simple and Effective Method for Solid Medium Cultivation of Strictly Hydrogen- and Sulfur-oxidizing Chemolithoautotrophs Predominant in Deep-sea Hydrothermal Fields. Microbes Environ 2023; 38:ME23072. [PMID: 38104970 PMCID: PMC10728628 DOI: 10.1264/jsme2.me23072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
Strictly hydrogen- and sulfur-oxidizing chemolithoautotrophic bacteria, particularly members of the phyla Campylobacterota and Aquificota, have a cosmopolitan distribution in deep-sea hydrothermal fields. The successful cultivation of these microorganisms in liquid media has provided insights into their physiological, evolutionary, and ecological characteristics. Notably, recent population genetic studies on Sulfurimonas (Campylobacterota) and Persephonella (Aquificota) revealed geographic separation in their populations. Advances in this field of research are largely dependent on the availability of pure cultures, which demand labor-intensive liquid cultivation procedures, such as dilution-to-extinction, given the longstanding assumption that many strictly or facultatively anaerobic chemolithoautotrophs cannot easily form colonies on solid media. We herein describe a simple and cost-effective approach for cultivating these chemolithoautotrophs on solid media. The results obtained suggest that not only the choice of gelling agent, but also the gas phase composition significantly affect the colony-forming ratio of diverse laboratory strains. The use of gellan gum as a gelling agent combined with high concentrations of H2 and CO2 in a pouch bag promoted the formation of colonies. This contrasted with the absence of colony formation on an agar-solidified medium, in which thiosulfate served as an electron donor, nitrate as an electron acceptor, and bicarbonate as a carbon source, placed in anaerobic jars under an N2 atmosphere. Our method efficiently isolated chemolithoautotrophs from a deep-sea vent sample, underscoring its potential value in research requiring pure cultures of hydrogen- and sulfur-oxidizing chemolithoautotrophs.
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Affiliation(s)
- Hisashi Muto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
- Deep-Sea and Deep Subsurface Life Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), 5–1 Higashiyama Myodaiji, Okazaki 444–8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
- Deep-Sea and Deep Subsurface Life Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), 5–1 Higashiyama Myodaiji, Okazaki 444–8787, Japan
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10
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Kawagucci S, Sakai S, Tasumi E, Hirai M, Takaki Y, Nunoura T, Saitoh M, Ueno Y, Yoshida N, Shibuya T, Clifford Sample J, Okumura T, Takai K. Deep Subseafloor Biogeochemical Processes and Microbial Populations Potentially Associated with the 2011 Tohoku-oki Earthquake at the Japan Trench Accretionary Wedge (IODP Expedition 343). Microbes Environ 2023; 38:n/a. [PMID: 37331792 DOI: 10.1264/jsme2.me22108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023] Open
Abstract
Post-mega-earthquake geochemical and microbiological properties in subseafloor sediments of the Japan Trench accretionary wedge were investigated using core samples from Hole C0019E, which was drilled down to 851 m below seafloor (mbsf) at a water depth of 6,890 m. Methane was abundant throughout accretionary prism sediments; however, its concentration decreased close to the plate boundary decollement. Methane isotope systematics indicated a biogenic origin. The content of mole-cular hydrogen (H2) was low throughout core samples, but markedly increased at specific depths that were close to potential faults predicted by logging-while-drilling ana-lyses. Based on isotopic systematics, H2 appeared to have been abundantly produced via a low-temperature interaction between pore water and the fresh surface of crushed rock induced by earthquakes. Subseafloor microbial cell density remained constant at approximately 105 cells mL-1. Amplicon sequences revealed that predominant members at the phylum level were common throughout the units tested, which also included members frequently found in anoxic subseafloor sediments. Metabolic potential assays using radioactive isotopes as tracers revealed homoacetogenic activity in H2-enriched core samples collected near the fault. Furthermore, homoacetogenic bacteria, including Acetobacterium carbinolicum, were isolated from similar samples. Therefore, post-earthquake subseafloor microbial communities in the Japan Trench accretionary prism appear to be episodically dominated by homoacetogenic populations and potentially function due to the earthquake-induced low-temperature generation of H2. These post-earthquake microbial communities may eventually return to the steady-state communities dominated by oligotrophic heterotrophs and hydrogenotrophic and methylotrophic methanogens that are dependent on refractory organic matter in the sediment.
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Affiliation(s)
- Shinsuke Kawagucci
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Sanae Sakai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Eiji Tasumi
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Yuichiro Ueno
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology
- Earth-Life Science Institute, Tokyo Institute of Technology
| | - Naohiro Yoshida
- Earth-Life Science Institute, Tokyo Institute of Technology
- National Institute of Information and Communications Technology
| | - Takazo Shibuya
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Tomoyo Okumura
- Center for Advanced Marine Core Research, Kochi University
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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11
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Hashimoto Y, Shimamura S, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Physiological and comparative proteomic characterization of Desulfolithobacter dissulfuricans gen. nov., sp. nov., a novel mesophilic, sulfur-disproportionating chemolithoautotroph from a deep-sea hydrothermal vent. Front Microbiol 2022; 13:1042116. [PMID: 36532468 PMCID: PMC9751629 DOI: 10.3389/fmicb.2022.1042116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
In deep-sea hydrothermal environments, inorganic sulfur compounds are important energy substrates for sulfur-oxidizing, -reducing, and -disproportionating microorganisms. Among these, sulfur-disproportionating bacteria have been poorly understood in terms of ecophysiology and phylogenetic diversity. Here, we isolated and characterized a novel mesophilic, strictly chemolithoautotrophic, diazotrophic sulfur-disproportionating bacterium, designated strain GF1T, from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. Strain GF1T disproportionated elemental sulfur, thiosulfate, and tetrathionate in the presence of ferrihydrite. The isolate also grew by respiratory hydrogen oxidation coupled to sulfate reduction. Phylogenetic and physiological analyses support that strain GF1T represents the type strain of a new genus and species in the family Desulfobulbaceae, for which the name Desulfolithobacter dissulfuricans gen. nov. sp. nov. is proposed. Proteomic analysis revealed that proteins related to tetrathionate reductase were specifically and abundantly produced when grown via thiosulfate disproportionation. In addition, several proteins possibly involved in thiosulfate disproportionation, including those encoded by the YTD gene cluster, were also found. The overall findings pointed to a possible diversity of sulfur-disproportionating bacteria in hydrothermal systems and provided a refined picture of microbial sulfur disproportionation.
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Affiliation(s)
- Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Shimamura
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Akihiro Tame
- General Affairs Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Department of Marine and Earth Sciences, Marine Works Japan Ltd., Yokosuka, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junichi Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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12
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Yoshida-Takashima Y, Takaki Y, Yoshida M, Zhang Y, Nunoura T, Takai K. Genomic insights into phage-host interaction in the deep-sea chemolithoautotrophic Campylobacterota, Nitratiruptor. ISME Commun 2022; 2:108. [PMID: 37938718 PMCID: PMC9723563 DOI: 10.1038/s43705-022-00194-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2023]
Abstract
The genus Nitratiruptor represents one of the most numerically abundant chemolithoautotrophic Campylobacterota populations in the mixing zones of habitats between hydrothermal fluids and ambient seawater in deep-sea hydrothermal environments. We isolated and characterized four novel temperate phages (NrS-2, NrS-3, NrS-4, and NrS-5) having a siphoviral morphology, infecting Nitratiruptor strains from the Hatoma Knoll hydrothermal field in the southern-Okinawa Trough, Japan, and conducted comparative genomic analyses among Nitratiruptor strains and their phages. The Nitratiruptor temperate phages shared many potential core genes (e.g., integrase, Cro, two structural proteins, lysozyme, and MazG) with each other despite their diverse morphological and genetic features. Some homologs of coding sequences (CDSs) of the temperate phages were dispersed throughout the non-prophage regions of the Nitratiruptor genomes. In addition, several regions of the phage genome sequences matched to spacer sequences within clustered regularly interspaced short palindromic repeats (CRISPR) in Nitratiruptor genomes. Moreover, a restriction-modification system found in a temperate phage affected an epigenetic feature of its host. These results strongly suggested a coevolution of temperate phages and their host genomes via the acquisition of temperate phages, the CRISPR systems, the nucleotide substitution, and the epigenetic regulation during multiple phage infections in the deep-sea environments.
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Affiliation(s)
- Yukari Yoshida-Takashima
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mitsuhiro Yoshida
- Deep-Sea Bioresource Research Group, Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yi Zhang
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takuro Nunoura
- Deep-Sea Bioresource Research Group, Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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13
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Imachi H, Nobu MK, Miyazaki M, Tasumi E, Saito Y, Sakai S, Ogawara M, Ohashi A, Takai K. Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study. Nat Protoc 2022; 17:2784-2814. [DOI: 10.1038/s41596-022-00735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
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14
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Lan Y, Sun J, Chen C, Wang H, Xiao Y, Perez M, Yang Y, Kwan YH, Sun Y, Zhou Y, Han X, Miyazaki J, Watsuji TO, Bissessur D, Qiu JW, Takai K, Qian PY. Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont. ISME J 2022; 16:2132-2143. [PMID: 35715703 PMCID: PMC9381778 DOI: 10.1038/s41396-022-01261-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022]
Abstract
The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host’s cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.
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Affiliation(s)
- Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Prefecture, Japan
| | - Hao Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yao Xiao
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Maeva Perez
- Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Yi Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yick Hang Kwan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanan Sun
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Xiqiu Han
- Key Laboratory of Submarine Geosciences & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Junichi Miyazaki
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Prefecture, Japan
| | - Tomo-O Watsuji
- Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kitakyusyu, 803-0846, Japan
| | - Dass Bissessur
- Department for Continental Shelf, Maritime Zones Administration & Exploration, Prime Minister's Office, 2nd Floor, Belmont House, 12 Intendance Street, Port Louis, 11328, Mauritius
| | - Jian-Wen Qiu
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ken Takai
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Prefecture, Japan
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China. .,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
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15
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Okada S, Chen C, Watanabe HK, Isobe N, Takai K. Unusual bromine enrichment in the gastric mill and setae of the hadal amphipod Hirondellea gigas. PLoS One 2022; 17:e0272032. [PMID: 35925928 PMCID: PMC9352070 DOI: 10.1371/journal.pone.0272032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
The hadal amphipod Hirondellea gigas is an emblematic animal of the Pacific trenches, and has a number of special adaptations to thrive in this ‘extreme’ environment, which includes the deepest part of the Earth’s ocean. One such adaptation that has been suggested is the presence of an ‘aluminum gel shield’ on the surface of its body in order to prevent the dissolution of calcitic exoskeleton below the carbonate compensation depth. However, this has not been investigated under experimental conditions that sufficiently prevent aluminum artefacts, and the possibility of other elements with similar characteristic X-ray energy as aluminum (such as bromine) has not been considered. Here, we show with new electron microscopy data gathered under optimized conditions to minimize aluminum artefacts that H. gigas actually does not have an aluminum shield–instead many parts of its body are enriched in bromine, particularly gastric ossicles and setae. Results from elemental analyses pointed to the use of calcite partially substituted with magnesium by H. gigas in its exoskeleton, in order to suppress dissolution. Our results exemplify the necessity of careful sample preparation and analysis of the signals in energy-dispersive X-ray spectroscopic analysis, and the importance of analyses at different electron energies.
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Affiliation(s)
- Satoshi Okada
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
- * E-mail:
| | - Chong Chen
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Hiromi Kayama Watanabe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Noriyuki Isobe
- Biogeochemistry Research Center, Research Institute for Marine Resources Utilization (MRU), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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16
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Isobe N, Chen C, Daicho K, Saito T, Bissessur D, Takai K, Okada S. Uniaxial orientation of β-chitin nanofibres used as an organic framework in the scales of a hot vent snail. J R Soc Interface 2022; 19:20220120. [PMID: 35642424 PMCID: PMC9156901 DOI: 10.1098/rsif.2022.0120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Organisms use various forms and orientations of chitin nanofibres to make structures with a wide range of functions, from insect wings to mussel shells. Lophotrochozoan animals such as snails and annelid worms possess an ancient ‘biomineralization toolkit’, enabling them to flexibly and rapidly evolve unique hard parts. The scaly-foot snail is a gastropod endemic to deep-sea hydrothermal vents, unique in producing dermal sclerites used as sites of sulfur detoxification. Once considered to be strictly proteinaceous, recent data pointed to the presence of chitin in these sclerites, but direct evidence is still lacking. Here, we show that β-chitin fibres (approx. 5% of native weight) are indeed the building framework, through a combination of solid-state nuclear magnetic resonance spectroscopy, wide-angle X-ray diffraction, and electron microscopy. The fibres are uniaxially oriented, likely forming a structural basis for column-like channels into which the scaly-foot snail is known to actively secrete sulfur waste—expanding the known function of chitinous hard parts in animals. Our results add to the existing evidence that animals are capable of modifying and co-opting chitin synthesis pathways flexibly and rapidly, in order to serve novel functions during their evolution.
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Affiliation(s)
- Noriyuki Isobe
- Biogeochemistry Research Center, Research Institute for Marine Resources Utilization (MRU), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Chong Chen
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Kazuho Daicho
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tsuguyuki Saito
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Dass Bissessur
- Department for Continental Shelf, Maritime Zones Administration and Exploration, Prime Minister's Office, 2nd Floor, Belmont House, 12 Intendance Street, Port Louis 11328, Mauritius
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Satoshi Okada
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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17
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Hashimoto Y, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Desulfomarina profundi gen. nov., sp. nov., a novel mesophilic, hydrogen-oxidizing, sulphate-reducing chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 2021; 71. [PMID: 34739365 DOI: 10.1099/ijsem.0.005083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic, strictly anaerobic, chemolithoautotrophic sulphate-reducing bacterium, designated strain KT2T, was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc. Strain KT2T grew at 25-40 °C (optimum 35 °C) and pH 5.5-7.0 (optimum 6.6) in the presence of 25-45 g l-1 NaCl (optimum 30 g l-1). Growth occurred with molecular hydrogen as the electron donor and sulphate, thiosulphate, and sulphite as the electron acceptors. The isolate utilized CO2 as the sole carbon source for chemolithoautotrophic growth on H2. Glycerol, succinate, fumarate, malate, glutamate, or casamino acids could serve as an alternative electron donor in the presence of CO2. Malate, citrate, glutamate, and casamino acids were used as fermentative substrates for weak growth. The G+C content of genomic DNA was 46.1 %. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain KT2T is a member of the family Desulfobulbaceae, showing a sequence similarity of 94.3 % with Desulforhopalus singaporensis. Phylogenomic analysis based on concatenated 156 single-copy marker genes confirmed the same topology as the 16S rRNA gene phylogeny. The ANI and AAI values between strain KT2T and related genera of the family Desulfobulbaceae were 65.6-68.6 % and 53.1-62.9 %. Based on the genomic, molecular, and physiological characteristics, strain KT2T represents a novel genus and species within the family Desulfobulbaceae, for which the name Desulfomarina profundi gen. nov., sp. nov. is proposed, with KT2T (=JCM 34118T = DSM 111364T) as the type strain.
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Affiliation(s)
- Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Akihiro Tame
- Department of Technical Services, Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan.,General Affairs Department, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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18
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D W B, Osipov VY, Takai K. Long range interactions and related carbon-carbon bond reconstruction between interior and surface defects in nanodiamonds. Phys Chem Chem Phys 2021; 23:14592-14600. [PMID: 34164634 DOI: 10.1039/d0cp05914e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interactions between interior substitutional nitrogen defects and surface unsaturated dangling bonds in synthetic nanodiamonds of ∼25 nm size were explored experimentally and theoretically. The experimental results demonstrate the disappearance of the specific paramagnetism of nitrogen centers in the smallest nanoparticles isolated after processing large micron diamonds in a ball mill, accompanied by the formation of unsaturated surface dangling bonds and internal defects. First principles modelling confirms the vanishing of the magnetic moments related with nitrogen centers even for distances from the surface defects greater than 1 nm. To understand this effect, we consider a bond reconstruction scheme with the formation of several carbon-carbon double bonds in the area between the interior and surface point defects. The scheme is in agreement with the changes in electron density through the distance between the two defects. The developed approach can be used to describe the interactions between various defects in carbon-based systems.
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Affiliation(s)
- Boukhvalov D W
- College of Science, Institute of Materials Physics and Chemistry, Nanjing Forestry University, Nanjing 210037, P. R. China. and Institute of Physics and Technology, Ural Federal University, Mira 19 Str., 620002, Yekaterinburg, Russia
| | - V Yu Osipov
- Ioffe Institute, Polytechnicheskaya 26, St. Petersburg 194021, Russia
| | - K Takai
- Department of Chemical Science and Technology, Hosei University, 3-7-2, Kajino, Koganei, Tokyo 184-8584, Japan
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19
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Kitadai N, Nakamura R, Yamamoto M, Okada S, Takahagi W, Nakano Y, Takahashi Y, Takai K, Oono Y. Thioester synthesis through geoelectrochemical CO 2 fixation on Ni sulfides. Commun Chem 2021; 4:37. [PMID: 36697522 PMCID: PMC9814748 DOI: 10.1038/s42004-021-00475-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023] Open
Abstract
A prevailing scenario of the origin of life postulates thioesters as key intermediates in protometabolism, but there is no experimental support for the prebiotic CO2 fixation routes to thioesters. Here we demonstrate that, under a simulated geoelectrochemical condition in primordial ocean hydrothermal systems (-0.6 to -1.0 V versus the standard hydrogen electrode), nickel sulfide (NiS) gradually reduces to Ni0, while accumulating surface-bound carbon monoxide (CO) due to CO2 electroreduction. The resultant partially reduced NiS realizes thioester (S-methyl thioacetate) formation from CO and methanethiol even at room temperature and neutral pH with the yield up to 35% based on CO. This thioester formation is not inhibited, or even improved, by 50:50 coprecipitation of NiS with FeS or CoS (the maximum yields; 27 or 56%, respectively). Such a simple thioester synthesis likely occurred in Hadean deep-sea vent environments, setting a stage for the autotrophic origin of life.
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Affiliation(s)
- Norio Kitadai
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan ,grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, Meguroku, Tokyo Japan
| | - Ryuhei Nakamura
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, Meguroku, Tokyo Japan ,grid.7597.c0000000094465255Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama Japan
| | - Masahiro Yamamoto
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Okada
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Wataru Takahagi
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo Japan
| | - Yuko Nakano
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, Meguroku, Tokyo Japan
| | - Yoshio Takahashi
- grid.26999.3d0000 0001 2151 536XDepartment of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo Japan
| | - Ken Takai
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshi Oono
- grid.35403.310000 0004 1936 9991Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL USA
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20
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Osipov VY, Boukhvalov DW, Takai K. Structure and Magnetic Properties of Superoxide Radical Anion Complexes with Low Binding Energy at the Graphene Edges. RUSS J COORD CHEM+ 2020. [DOI: 10.1134/s107032842011007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Takahashi S, Mine T, Kawai H, Takai K, Yoshikawa F, Takada M, Fujita K, Nishibori Y, Maruyama T. Conduction gaps after pulmonary vein isolation due to high contact force ablation in patients with atrial fibrillation. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.0444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Catheter ablation for atrial fibrillation (AF) with high contact force (CF) has been reported to lead to the gaps after pulmonary vein isolation (PVI), and the appearance of the gaps depends on the site in the left atrium (LA).
Purpose
The aim of this study is to clarify the relationship between the gaps appearance and high CF.
Methods
In the clinical study, 74 consecutive patients (39 males, age 71±9, 46 with paroxysmal AF) underwent conventional PVI with a point-by-point radiofrequency (RF) ablation using a CF sensing catheter (TactiCath SETM). RF energy (J), number of RF point, Lesion index (LSI), force-time integral (FTI), average CF (g), and the degree of LA depression with high CF were evaluated. In the experimental study (figure), the relationship between the ablation area and the degree of depression with high CF using bovine left ventricular wall.
Results
In the clinical study, the gaps were found in 175 of 1182 sites after first path PVI ablation. The CF in the gap sites was higher than without the gap sites in RPV roof, anterior RSPV and anterior RPV carina (18.9±6.8 vs 15.0±5.7g p=0.0262, 26.4±11.6 vs 19.5±6.0g p=0.0029, 22.7±6.4 vs 19.1±5.5g, p=0.0161). Meanwhile, there were no differences in RF energy, number of RF point, LSI, FTI. High CF (≥30g) showed a depression of 3 mm or more in only RPV roof and anterior RPV (figure). In the experimental study, the ablation range narrowed as the indentation deepened with more than 30g CF (r=0.6417, p=0.0625).
Conclusion
Catheter ablation for AF with high contact force might lead to the gaps in RPV roof and anterior RPV site by the reduction of the ablation area due to depression caused by the pressure.
Extension of each contact force
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
| | - T Mine
- Hyogo College of Medicine, cardiovascular division, Hyogo, Japan
| | - H Kawai
- Kawasaki Hospital, Kobe, Japan
| | - K Takai
- Kawasaki Hospital, Kobe, Japan
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22
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Enomoto S, Shimane Y, Ihara K, Kamekura M, Itoh T, Ohkuma M, Takahashi-Ando N, Fukushima Y, Yoshida Y, Usami R, Takai K, Minegishi H. Haloarcula mannanilytica sp. nov., a galactomannan-degrading haloarchaeon isolated from commercial salt. Int J Syst Evol Microbiol 2020; 70:6331-6337. [PMID: 33095133 DOI: 10.1099/ijsem.0.004535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mannan-degrading halophilic archaeal strain, MD130-1T, was isolated from a commercial salt sample. Cells were motile, rod-shaped, and stained Gram-negative. Colonies were pink pigmented. Strain MD130-1T was able to grow at 1.5-4.6 M NaCl (optimum, 3.6 M) at pH 6.0-8.0 (optimum, pH 7.0) and at 25-50 °C (optimum, 40 °C). The DNA G+C content was 62.1 mol% (genome). The orthologous 16S rRNA gene sequence showed the highest similarity (99.4 %) to those of Haloarcula japonica JCM 7785T and Haloarcula hispanica JCM 8911T. The values of genome relatedness between strain MD130-1T and Haloarcula species were 84.33-85.96 % in ANIb and 30.4-32.9 % using GGDC formula 2. The polar lipids of strain MD130-1T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and triglycosyl diether-2. Based on the results of phenotypic and phylogenetic analyses, the strain represents a new species of the genus Haloarcula, for which the name Haloarcula mannanilytica sp. nov. is proposed. The type strain is MD130-1T (=JCM 33835T=KCTC 4287T) isolated from commercial salt made in Ishikawa prefecture, Japan.
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Affiliation(s)
- Shigeaki Enomoto
- Graduate School of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Kawagoe-shi, Saitama 350-8585, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Masahiro Kamekura
- Halophiles Research Institute, 677-1 Shimizu, Noda-shi, Chiba 278-0043, Japan
| | - Takashi Itoh
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, Japan
| | - Naoko Takahashi-Ando
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Graduate School of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Kawagoe-shi, Saitama 350-8585, Japan
| | - Yasumasa Fukushima
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Graduate School of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Kawagoe-shi, Saitama 350-8585, Japan
| | - Yasuhiko Yoshida
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Graduate School of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Kawagoe-shi, Saitama 350-8585, Japan
| | - Ron Usami
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Hiroaki Minegishi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan.,Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Graduate School of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Kawagoe-shi, Saitama 350-8585, Japan
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23
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Fukushi M, Mino S, Tanaka H, Nakagawa S, Takai K, Sawabe T. Biogeochemical Implications of N 2O-Reducing Thermophilic Campylobacteria in Deep-Sea Vent Fields, and the Description of Nitratiruptor labii sp. nov. iScience 2020; 23:101462. [PMID: 32866828 PMCID: PMC7476070 DOI: 10.1016/j.isci.2020.101462] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/21/2020] [Accepted: 08/12/2020] [Indexed: 01/02/2023] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and has significantly increased in the atmosphere. Deep-sea hydrothermal fields are representative environments dominated by mesophilic to thermophilic members of the class Campylobacteria that possess clade II nosZ encoding nitrous oxide reductase. Here, we report a strain HRV44T representing the first thermophilic campylobacterium capable of growth by H2 oxidation coupled to N2O reduction. On the basis of physiological and genomic properties, it is proposed that strain HRV44T (=JCM 34002 = DSM 111345) represents a novel species of the genus Nitratiruptor, Nitratiruptor labii sp. nov. The comparison of the N2O consumption ability of strain HRV44T with those of additional Nitratiruptor and other campylobacterial strains revealed the highest level in strain HRV44T and suggests the N2O-respiring metabolism might be the common physiological trait for the genus Nitratiruptor. Our findings provide insights into contributions of thermophilic Campylobacteria to the N2O sink in deep-sea hydrothermal environments.
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Affiliation(s)
- Muneyuki Fukushi
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Hirohisa Tanaka
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
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24
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Chiba Y, Shitara M, Takai K. Fragmentation of acetate-CoA ligase gives a clue to understand domain rearrangement history of NDP-forming acyl-CoA synthetase superfamily proteins. Biosci Biotechnol Biochem 2020; 84:2045-2053. [PMID: 32538302 DOI: 10.1080/09168451.2020.1779581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
NDP-forming type acyl-CoA synthetase superfamily proteins are known to have six essential subdomains (1, 2, 3, a, b, c) of which partition and order are varied, suggesting yet-to-be-defined subdomain rearrangement happened in its evolution. Comparison in physicochemical and biochemical characteristics between the recombinant proteins which we made from fragmented subdomains and wild-type protein, acetate-CoA ligase in a hyperthermophilic archaeon, consisting of two distinct subunits (α1-2-3 and βa-b-c) provided a clue to the mystery of its molecular evolutionary passage. Although solubility and thermostability of each fragmented subdomain turned out to be lower than that of wild-type, mixture of the three synthetic subunits of α1-2, α3, and βa-b-c had quaternary structure, thermostability, and enzymatic activity comparable to those of the wild-type. This suggests that substantial independence and mobility of subdomain 3 have enabled rearrangement of the subdomains; and thermostability of the subdomains has constrained the composition of the subunits.
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Affiliation(s)
- Yoko Chiba
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science (CSRS) , Wako, Saitama, Japan.,Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka, Kanagawa, Japan
| | - Mariko Shitara
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka, Kanagawa, Japan
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25
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Affiliation(s)
- Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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26
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Sun J, Chen C, Miyamoto N, Li R, Sigwart JD, Xu T, Sun Y, Wong WC, Ip JCH, Zhang W, Lan Y, Bissessur D, Watsuji TO, Watanabe HK, Takaki Y, Ikeo K, Fujii N, Yoshitake K, Qiu JW, Takai K, Qian PY. The Scaly-foot Snail genome and implications for the origins of biomineralised armour. Nat Commun 2020; 11:1657. [PMID: 32269225 PMCID: PMC7142155 DOI: 10.1038/s41467-020-15522-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 03/13/2020] [Indexed: 12/22/2022] Open
Abstract
The Scaly-foot Snail, Chrysomallon squamiferum, presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused hard parts. Thus the Scaly-foot Snail is an ideal model to study the genomic mechanisms underlying the evolutionary diversification of biomineralised armour. Here, we present a high-quality whole-genome assembly and tissue-specific transcriptomic data, and show that scale and shell formation in the Scaly-foot Snail employ independent subsets of 25 highly-expressed transcription factors. Comparisons with other lophotrochozoan genomes imply that this biomineralisation toolkit is ancient, though expression patterns differ across major lineages. We suggest that the ability of lophotrochozoan lineages to generate a wide range of hard parts, exemplified by the remarkable morphological disparity in Mollusca, draws on a capacity for dynamic modification of the expression and positioning of toolkit elements across the genome.
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Affiliation(s)
- Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Julia D Sigwart
- Marine Laboratory, Queen's University Belfast, Portaferry, N. Ireland
- Senckenberg Museum, Frankfurt, Germany
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yanan Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jack C H Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Weipeng Zhang
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yi Lan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Dass Bissessur
- Department for Continental Shelf, Maritime Zones Administration & Exploration, Ministry of Defence and Rodrigues, 2nd Floor, Belmont House, 12 Intendance Street, Port-Louis, 11328, Mauritius
| | - Tomo-O Watsuji
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
- Department of Food and Nutrition, Higashi-Chikushi Junior College, Kitakyusyu, Japan
| | - Hiromi Kayama Watanabe
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Takaki
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Kazuho Ikeo
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
| | - Nobuyuki Fujii
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ken Takai
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China.
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27
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Fryer P, Wheat CG, Williams T, Kelley C, Johnson K, Ryan J, Kurz W, Shervais J, Albers E, Bekins B, Debret B, Deng J, Dong Y, Eickenbusch P, Frery E, Ichiyama Y, Johnston R, Kevorkian R, Magalhaes V, Mantovanelli S, Menapace W, Menzies C, Michibayashi K, Moyer C, Mullane K, Park JW, Price R, Sissmann O, Suzuki S, Takai K, Walter B, Zhang R, Amon D, Glickson D, Pomponi S. Mariana serpentinite mud volcanism exhumes subducted seamount materials: implications for the origin of life. Philos Trans A Math Phys Eng Sci 2020; 378:20180425. [PMID: 31902339 PMCID: PMC7015305 DOI: 10.1098/rsta.2018.0425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
The subduction of seamounts and ridge features at convergent plate boundaries plays an important role in the deformation of the overriding plate and influences geochemical cycling and associated biological processes. Active serpentinization of forearc mantle and serpentinite mud volcanism on the Mariana forearc (between the trench and active volcanic arc) provides windows on subduction processes. Here, we present (1) the first observation of an extensive exposure of an undeformed Cretaceous seamount currently being subducted at the Mariana Trench inner slope; (2) vertical deformation of the forearc region related to subduction of Pacific Plate seamounts and thickened crust; (3) recovered Ocean Drilling Program and International Ocean Discovery Program cores of serpentinite mudflows that confirm exhumation of various Pacific Plate lithologies, including subducted reef limestone; (4) petrologic, geochemical and paleontological data from the cores that show that Pacific Plate seamount exhumation covers greater spatial and temporal extents; (5) the inference that microbial communities associated with serpentinite mud volcanism may also be exhumed from the subducted plate seafloor and/or seamounts; and (6) the implications for effects of these processes with regard to evolution of life. This article is part of a discussion meeting issue 'Serpentine in the Earth system'.
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Affiliation(s)
- Patricia Fryer
- School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, HI, USA
| | | | - Trevor Williams
- International Ocean Discovery Program, Texas A&M University, College Station, TX, USA
| | - Christopher Kelley
- School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Kevin Johnson
- School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jeffrey Ryan
- School of Geosciences, University of South Florida, Tampa, FL, USA
| | - Walter Kurz
- Institute of Earth Sciences, University of Graz, NAWI Graz Geocenter, Institute of Earth Sciences, Graz, Austria
| | - John Shervais
- Department of Geology, Utah State University, Logan, UT, USA
| | - Elmar Albers
- Department of Geosciences, University of Bremen, Bremen, Germany
| | - Barbara Bekins
- United States Geological Survey, NASA Ames, Mountain View, CA, USA
| | | | - Jianghong Deng
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui Province, People's Republic of China
| | - Yanhui Dong
- Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, Zhejiang Province, People's Republic of China
| | - Philip Eickenbusch
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Emanuelle Frery
- Commonwealth Scientific and Industrial Research Organisation, Kensington, Western Australia, Australia
| | - Yuji Ichiyama
- Department of Earth Sciences, Chiba University, Chiba, Chiba Prefecture, Japan
| | - Raymond Johnston
- School of Geosciences, University of South Florida, Tampa, FL, USA
| | - Richard Kevorkian
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Vitor Magalhaes
- Por Portuguese Institute for Sea and Atmosphere (IPMA), Rua C ao Aeroporto, Lisbon, Portugal
| | | | - Walter Menapace
- MARUM - Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Catriona Menzies
- Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, UK
| | - Katsuyoshi Michibayashi
- Department of Earth and Planetary Sciences, Graduate School of Environmental Studies, Nagoya University, Nagoya, Aichi Prefecture, Japan
| | - Craig Moyer
- Biology Department, Western Washington University, Bellingham, WA, USA
| | - Kelli Mullane
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Jung-Woo Park
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Roy Price
- School of Marine and Atmospheric Sciences, State University of New York, Stony Brook, NY, USA
| | - Olivier Sissmann
- IFP Energies Nouvelles, 92500 Rueil-Malmaison, Ile-de-France, France
| | - Shino Suzuki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi Prefecture, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa Prefecture, Japan
| | - Bastien Walter
- GeoResources, Universite de Lorraine, Vandoeuvre-les-Nancy, Cedex, France
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Sciences, Institute of Marine Microbes and Exospheres, Xiamen University, Xiang'an Campus, Xiamen, Fujian Province, People's Republic of China
| | - Diva Amon
- Life Sciences Department, Natural History Museum, London, Cromwell Road, London, UK
| | - Deborah Glickson
- Board on Earth Sciences and Resources, National Academies of Sciences, Engineering, and Medicine, Washington, DC, USA
| | - Shirley Pomponi
- NOAA Cooperative Institute for Ocean Exploration, Research, and Technology, Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
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28
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Miyazaki J, Ikuta T, Watsuji TO, Abe M, Yamamoto M, Nakagawa S, Takaki Y, Nakamura K, Takai K. Dual energy metabolism of the Campylobacterota endosymbiont in the chemosynthetic snail Alviniconcha marisindica. ISME J 2020; 14:1273-1289. [PMID: 32051527 PMCID: PMC7174374 DOI: 10.1038/s41396-020-0605-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Some deep-sea chemosynthetic invertebrates and their symbiotic bacteria can use molecular hydrogen (H2) as their energy source. However, how much the chemosynthetic holobiont (endosymbiont-host association) physiologically depends on H2 oxidation has not yet been determined. Here, we demonstrate that the Campylobacterota endosymbionts of the gastropod Alviniconcha marisindica in the Kairei and Edmond fields (kAlv and eAlv populations, respectively) of the Indian Ocean, utilize H2 in response to their physical and environmental H2 conditions, although the 16S rRNA gene sequence of both the endosymbionts shared 99.6% identity. A thermodynamic calculation using in situ H2 and hydrogen sulfide (H2S) concentrations indicated that chemosynthetic symbiosis could be supported by metabolic energy via H2 oxidation, particularly for the kAlv holobiont. Metabolic activity measurements showed that both the living individuals and the gill tissues consumed H2 and H2S at similar levels. Moreover, a combination of fluorescence in situ hybridization, quantitative transcript analyses, and enzymatic activity measurements showed that the kAlv endosymbiont expressed the genes and enzymes for both H2- and sulfur-oxidations. These results suggest that both H2 and H2S could serve as the primary energy sources for the kAlv holobiont. The eAlv holobiont had the ability to utilize H2, but the gene expression and enzyme activity for hydrogenases were much lower than for sulfur-oxidation enzymes. These results suggest that the energy acquisitions of A. marisindica holobionts are dependent on H2- and sulfur-oxidation in the H2-enriched Kairei field and that the mechanism of dual metabolism is controlled by the in situ H2 concentration.
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Affiliation(s)
- Junichi Miyazaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Tetsuro Ikuta
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Tomo-O Watsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kitakyusyu, 803-0846, Japan
| | - Mariko Abe
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Masahiro Yamamoto
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Satoshi Nakagawa
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Kentaro Nakamura
- Department of Systems Innovation, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
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29
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Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 2020; 577:519-525. [PMID: 31942073 PMCID: PMC7015854 DOI: 10.1038/s41586-019-1916-6] [Citation(s) in RCA: 313] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022]
Abstract
The origin of eukaryotes remains unclear1-4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3) model.
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Affiliation(s)
- Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
| | - Nozomi Nakahara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yuki Morono
- Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan
| | - Miyuki Ogawara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshinori Takano
- Biogeochemistry Program, Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan
| | - Katsuyuki Uematsu
- Department of Marine and Earth Sciences, Marine Work Japan, Yokosuka, Japan
| | - Tetsuro Ikuta
- Research Institute for Global Change, JAMSTEC, Yokosuka, Japan
| | - Motoo Ito
- Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan
| | - Yohei Matsui
- Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Yumi Saito
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sanae Sakai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Japan
| | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yuko Yamanaka
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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30
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Affiliation(s)
- Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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31
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Hiraoka S, Hirai M, Matsui Y, Makabe A, Minegishi H, Tsuda M, Juliarni, Rastelli E, Danovaro R, Corinaldesi C, Kitahashi T, Tasumi E, Nishizawa M, Takai K, Nomaki H, Nunoura T. Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments. ISME J 2019; 14:740-756. [PMID: 31827245 PMCID: PMC7031335 DOI: 10.1038/s41396-019-0564-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/20/2019] [Accepted: 11/28/2019] [Indexed: 12/28/2022]
Abstract
Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.
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Affiliation(s)
- Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.
| | - Miho Hirai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Yohei Matsui
- Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Akiko Makabe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Hiroaki Minegishi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.,Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe, 350-8585, Saitama, Japan
| | - Miwako Tsuda
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Juliarni
- Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Eugenio Rastelli
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Tomo Kitahashi
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Manabu Nishizawa
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Hidetaka Nomaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.
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32
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Chiba Y, Miyakawa T, Shimane Y, Takai K, Tanokura M, Nozaki T. Structural comparisons of phosphoenolpyruvate carboxykinases reveal the evolutionary trajectories of these phosphodiester energy conversion enzymes. J Biol Chem 2019; 294:19269-19278. [PMID: 31662435 DOI: 10.1074/jbc.ra119.010920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/24/2019] [Indexed: 11/06/2022] Open
Abstract
Inorganic pyrophosphate (PPi) consists of two phosphate molecules and can act as an energy and phosphate donor in cellular reactions, similar to ATP. Several kinases use PPi as a substrate, and these kinases have recently been suggested to have evolved from ATP-dependent functional homologs, which have significant amino acid sequence similarity to PPi-utilizing enzymes. In contrast, phosphoenolpyruvate carboxykinase (PEPCK) can be divided into three types according to the phosphate donor (ATP, GTP, or PPi), and the amino acid sequence similarity of these PEPCKs is too low to confirm that they share a common ancestor. Here we solved the crystal structure of a PPi-PEPCK homolog from the bacterium Actinomyces israelii at 2.6 Å resolution and compared it with previously reported structures from ATP- and GTP-specific PEPCKs to assess the degrees of similarities and divergences among these PEPCKs. These comparisons revealed that they share a tertiary structure with significant value and that amino acid residues directly contributing to substrate recognition, except for those that recognize purine moieties, are conserved. Furthermore, the order of secondary structural elements between PPi-, ATP-, and GTP-specific PEPCKs was strictly conserved. The structure-based comparisons of the three PEPCK types provide key insights into the structural basis of PPi specificity and suggest that all of these PEPCKs are derived from a common ancestor.
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Affiliation(s)
- Yoko Chiba
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka-city, Kanagawa, 237-0061, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuhiro Shimane
- Super-Cutting-Edge Grand and Advanced Research Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka-city, Kanagawa, 237-0061, Japan
| | - Ken Takai
- Super-Cutting-Edge Grand and Advanced Research Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka-city, Kanagawa, 237-0061, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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33
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Eickenbusch P, Takai K, Sissman O, Suzuki S, Menzies C, Sakai S, Sansjofre P, Tasumi E, Bernasconi SM, Glombitza C, Jørgensen BB, Morono Y, Lever MA. Origin of Short-Chain Organic Acids in Serpentinite Mud Volcanoes of the Mariana Convergent Margin. Front Microbiol 2019; 10:1729. [PMID: 31404165 PMCID: PMC6677109 DOI: 10.3389/fmicb.2019.01729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/12/2019] [Indexed: 11/17/2022] Open
Abstract
Serpentinitic systems are potential habitats for microbial life due to frequently high concentrations of microbial energy substrates, such as hydrogen (H2), methane (CH4), and short-chain organic acids (SCOAs). Yet, many serpentinitic systems are also physiologically challenging environments due to highly alkaline conditions (pH > 10) and elevated temperatures (>80°C). To elucidate the possibility of microbial life in deep serpentinitic crustal environments, International Ocean Discovery Program (IODP) Expedition 366 drilled into the Yinazao, Fantangisña, and Asùt Tesoru serpentinite mud volcanoes on the Mariana Forearc. These mud volcanoes differ in temperature (80, 150, 250°C, respectively) of the underlying subducting slab, and in the porewater pH (11.0, 11.2, 12.5, respectively) of the serpentinite mud. Increases in formate and acetate concentrations across the three mud volcanoes, which are positively correlated with temperature in the subducting slab and coincide with strong increases in H2 concentrations, indicate a serpentinization-related origin. Thermodynamic calculations suggest that formate is produced by equilibrium reactions with dissolved inorganic carbon (DIC) + H2, and that equilibration continues during fluid ascent at temperatures below 80°C. By contrast, the mechanism(s) of acetate production are not clear. Besides formate, acetate, and H2 data, we present concentrations of other SCOAs, methane, carbon monoxide, and sulfate, δ13C-data on bulk carbon pools, and microbial cell counts. Even though calculations indicate a wide range of microbial catabolic reactions to be thermodynamically favorable, concentration profiles of potential energy substrates, and very low cell numbers suggest that microbial life is scarce or absent. We discuss the potential roles of temperature, pH, pressure, and dispersal in limiting the occurrence of microbial life in deep serpentinitic environments.
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Affiliation(s)
- Philip Eickenbusch
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Ken Takai
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | | | - Shino Suzuki
- Geomicrobiology Research Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan
| | - Catriona Menzies
- Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton, United Kingdom.,Department of Geology and Petroleum Geology, University of Aberdeen, Aberdeen, United Kingdom
| | - Sanae Sakai
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | - Pierre Sansjofre
- Laboratoire Géosciences Océan UMR 6538, Université de Bretagne Occidentale, Brest, France
| | - Eiji Tasumi
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | | | - Clemens Glombitza
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland.,NASA Ames Research Center, Moffett Field, CA, United States
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Yuki Morono
- Geomicrobiology Research Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan
| | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
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Kitadai N, Nakamura R, Yamamoto M, Takai K, Yoshida N, Oono Y. Metals likely promoted protometabolism in early ocean alkaline hydrothermal systems. Sci Adv 2019; 5:eaav7848. [PMID: 31223650 PMCID: PMC6584212 DOI: 10.1126/sciadv.aav7848] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/15/2019] [Indexed: 06/01/2023]
Abstract
One of the most plausible scenarios of the origin of life assumes the preceding prebiotic autotrophic metabolism in sulfide-rich hydrothermal vent environments. However, geochemical mechanisms to harness the reductive power provided by hydrothermal systems remain to be elucidated. Here, we show that, under a geoelectrochemical condition realizable in the early ocean hydrothermal systems, several metal sulfides (FeS, Ag2S, CuS, and PbS) undergo hour- to day-scale conversion to the corresponding metals at ≤-0.7 V (versus the standard hydrogen electrode). The electrochemically produced FeS-Fe0 assemblage promoted various reactions including certain steps in the reductive tricarboxylic acid cycle with efficiencies far superior to those due to pure FeS. The threshold potential is readily generated in the H2-rich alkaline hydrothermal systems that were probably ubiquitous on the Hadean seafloor. Thus, widespread metal production and metal-sustained primordial metabolism were likely to occur as a natural consequence of the active hydrothermal processes on the Hadean Earth.
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Affiliation(s)
- Norio Kitadai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Ryuhei Nakamura
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masahiro Yamamoto
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Naohiro Yoshida
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanazawa 226-8503, Japan
| | - Yoshi Oono
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801-3080, USA
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Pan D, Morono Y, Inagaki F, Takai K. An Improved Method for Extracting Viruses From Sediment: Detection of Far More Viruses in the Subseafloor Than Previously Reported. Front Microbiol 2019; 10:878. [PMID: 31110497 PMCID: PMC6501758 DOI: 10.3389/fmicb.2019.00878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/05/2019] [Indexed: 01/21/2023] Open
Abstract
Viruses are the most abundant biological entities on Earth and perform essential ecological functions in aquatic environments by mediating biogeochemical cycling and lateral gene transfer. Cellular life as well as viruses have been found in deep subseafloor sediment. However, the study of deep sediment viruses has been hampered by the complexities involved in efficiently extracting viruses from a sediment matrix. Here, we developed a new method for the extraction of viruses from sediment based on density separation using a Nycodenz density step gradient. The density separation method resulted in up to 2 orders of magnitude greater recovery of viruses from diverse subseafloor sediments compared to conventional methods. The density separation method also showed more consistent performance between samples of different sediment lithology, whereas conventional virus extraction methods were highly inconsistent. Using this new method, we show that previously published virus counts have underestimated viral abundances by up to 2 orders of magnitude. These improvements suggest that the carbon contained within viral biomass in the subseafloor environment may potentially be revised upward to 0.8-3.7 Gt from current estimates of 0.2 Gt. The vastly improved recovery of viruses indicate that viruses represent a far larger pool of organic carbon in subseafloor environments than previously estimated.
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Affiliation(s)
- Donald Pan
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and Technology, Yokohama, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
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Sakai S, Takaki Y, Miyazaki M, Ogawara M, Yanagawa K, Miyazaki J, Takai K. Methanofervidicoccus abyssi gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a hydrothermal vent chimney in the Mid-Cayman Spreading Center, the Caribbean Sea. Int J Syst Evol Microbiol 2019; 69:1225-1230. [PMID: 30843780 DOI: 10.1099/ijsem.0.003297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A novel hydrogenotrophic methanogen, strain HHBT, was isolated from a deep-sea hydrothermal vent chimney sample collected from Beebe Vent Field at the Mid-Cayman Spreading Center, Caribbean Sea. The cells were non-motile regular to irregular cocci possessing several flagella. The novel isolate grew at 60-80 °C, pH 5.0-7.4 and with 1-4 % of NaCl (w/v). The isolate utilized H2/CO2 as the only substrates for growth and methane production. The results of phylogenetic analyses of both 16S rRNA and mcrA gene sequences and comparative genome analysis indicated that HHBT represented a member of the order Methanococcales, and was closely related to the members of the genera Methanothermococcus and Methanotorris. The most closely related species were Methanothermococcus okinawensis IH1T and Methanotorris igneus Kol 5T in comparison of 16S rRNA gene sequences (each with 93 % identity), and Methanotorris formicicus Mc-S-70T in the case of deduced amino acid sequence similarity of mcrA genes (92 % similarity). The ANI and AAI values between HHBT and the members of the genera Methanothermococcus and Methanotorris were 69-72 % and 66-70 %, respectively. Although many of the morphological and physiological characteristics were quite similar between HHBT and the species of the genera Methanothermococcus and Methanotorris, they were distinguishable by the differences in susceptibility to antibiotics, formate utilization, growth temperature and NaCl ranges. On the basis of these phenotypic, phylogenetic and genomic properties, we propose that strain HHBT represents a novel species, of a novel genus, Methanofervidicoccus abyssi gen. nov., sp. nov. The type strain is HHBT (=JCM 32161T=DSM 105918T).
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Affiliation(s)
- Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Miyuki Ogawara
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Katsunori Yanagawa
- Department of Life and Environmental Engineering, Faculty of Environmental Engineering, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Junichi Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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Imachi H, Tasumi E, Takaki Y, Hoshino T, Schubotz F, Gan S, Tu TH, Saito Y, Yamanaka Y, Ijiri A, Matsui Y, Miyazaki M, Morono Y, Takai K, Hinrichs KU, Inagaki F. Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation. Sci Rep 2019; 9:2305. [PMID: 30783143 PMCID: PMC6381156 DOI: 10.1038/s41598-019-38754-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/09/2019] [Indexed: 11/08/2022] Open
Abstract
Recent explorations of scientific ocean drilling have revealed the presence of microbial communities persisting in sediments down to ~2.5 km below the ocean floor. However, our knowledge of these microbial populations in the deep subseafloor sedimentary biosphere remains limited. Here, we present a cultivation experiment of 2-km-deep subseafloor microbial communities in 20-million-year-old lignite coalbeds using a continuous-flow bioreactor operating at 40 °C for 1029 days with lignite particles as the major energy source. Chemical monitoring of effluent samples via fluorescence emission-excitation matrices spectroscopy and stable isotope analyses traced the transformation of coalbed-derived organic matter in the dissolved phase. Hereby, the production of acetate and 13C-depleted methane together with the increase and transformation of high molecular weight humics point to an active lignite-degrading methanogenic community present within the bioreactor. Electron microscopy revealed abundant microbial cells growing on the surface of lignite particles. Small subunit rRNA gene sequence analysis revealed that diverse microorganisms grew in the bioreactor (e.g., phyla Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Bacteroidetes, Spirochaetes, Tenericutes, Ignavibacteriae, and SBR1093). These results indicate that activation and adaptive growth of 2-km-deep microbes was successfully accomplished using a continuous-flow bioreactor, which lays the groundwork to explore networks of microbial communities of the deep biosphere and their physiologies.
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Affiliation(s)
- Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan.
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Tatsuhiko Hoshino
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Shuchai Gan
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Tzu-Hsuan Tu
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Institute of Oceanography, National Taiwan University, Taipei, 106, Taiwan
| | - Yumi Saito
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yuko Yamanaka
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Akira Ijiri
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yohei Matsui
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yuki Morono
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Fumio Inagaki
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama, Kanagawa, 236-0001, Japan
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Nakahara N, Nobu MK, Takaki Y, Miyazaki M, Tasumi E, Sakai S, Ogawara M, Yoshida N, Tamaki H, Yamanaka Y, Katayama A, Yamaguchi T, Takai K, Imachi H. Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi. Int J Syst Evol Microbiol 2019; 69:1185-1194. [PMID: 30775966 DOI: 10.1099/ijsem.0.003291] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filaments were generally more than 20 µm (up to approximately 200 µm) long and 0.5-0.6 µm wide. Cells possessed pili-like structures on the cell surface and a multilayer structure in the cytoplasm. Growth of the strain was observed at 20-37 °C (optimum, 30 °C), pH 5.5-8.0 (pH 6.5-7.0), and 0-30 g l-1 NaCl (5 g l-1 NaCl). Under optimum growth conditions, doubling time and maximum cell density were estimated to be approximately 19 days and ~105 cells ml-1, respectively. Strain MO-CFX2T grew chemoorganotrophically on a limited range of organic substrates in anaerobic conditions. The major cellular fatty acids were saturated C16 : 0 (47.9 %) and C18 : 0 (36.9 %), and unsaturated C18 : 1ω9c (6.0 %) and C16 : 1ω7 (5.1 %). The G+C content of genomic DNA was 63.2 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-CFX2T shares a notably low sequence identity with its closest relatives, which were Thermanaerothrix daxensis GNS-1T and Thermomarinilinea lacunifontana SW7T (both 85.8 % sequence identity). Based on these phenotypic and genomic properties, we propose the name Aggregatilinea lenta gen. nov., sp. nov. for strain MO-CFX2T (=KCTC 15625T, =JCM 32065T). In addition, we also propose the associated family and order as Aggregatilineaceae fam. nov. and Aggregatilineales ord. nov., respectively.
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Affiliation(s)
- Nozomi Nakahara
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan.,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa 237-0061, Japan
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Miyuki Ogawara
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Naoko Yoshida
- Department of Civil and Environmental Engineering, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Yuko Yamanaka
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Arata Katayama
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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Tozuka K, Nagai SE, Matsumoto H, Hayashi Y, Kubo K, Tsuboi M, Sato A, Takai K, Wang X, Yamada Y, Inoue K. Abstract P5-12-17: Prognostic and predictive value of serum level of vascular endothelial growth factor-A in metastatic breast cancer patients treated with bevacizumab plus paclitaxel. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-12-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Several studies showed that first-line bevacizumab plus chemotherapy for HER2-negative metastatic breast cancer improves progression-free survival and tumor response rate but not overall survival. MERiDiAN trial evaluated plasma vascular endothelial growth factor-A (VEGF-A) prospectively as a predictive biomarker for bevacizumab efficacy in metastatic breast cancer. However, results of this trial do not support using baseline plasma VEGF-A to identify patients benefitting most from bevacizumab. We measured baseline serum VEGF-A level from stored blood samples of metastatic breast cancer patient with treated bevacizumab plus paclitaxel as fist-line and later line therapy, and evaluated a correlation between serum VEGF-A level and efficacy of bevacizumab and prognosis of breast cancer patients tread with bevacizumab, retrospectively.
Patients and methods
We examined blood samples from 57 metastatic breast cancer patients treated with bevacizumab and paclitaxel, after obtaining written informed consent. And, we evaluated a correlation between baseline serum VEGF-A level and time to treatment failure (TTF) and overall survival (OS). We also compared the serum VEGF-A level of response group (CR and PR) and that of non-response group (SD and PD).
Results
Baseline serum level of VEGF-A ranged from 80 to 2079 pg/ml. Cases of treatment line were as follows: first-line, 22 cases (38.6%); second line, 11 cases (19.3%) and third-line and the later line, 24 cases (42.1%). The cutoff identified by ROC curve analysis that was able to differentiate response group and non-response group in first-line setting was 360pg/ml for serum VEGF-A. And, we separated high serum VGEF-A group and low serum VEGF-A group of patients treated with bevacizumab plus paclitaxel.
In patients treated as first line therapy, median TTF was 4.0 months with high serum VGEF-A group versus 5.0 months with low serum VEGF-A group, and median OS was 12 months with high serum VGEF-A group versus 11months with low serum VEGF-A group. There were no significant differences in both TTF and OS in first line setting. In patients treated as second line and later line therapy, median TTF was 2.8 months with high serum VGEF-A group versus 7.1 months with low serum VEGF-A group, and median OS was 6.4 months with high serum VGEF-A group versus 12.7 months with low serum VEGF-A group. The prognosis of high serum VEGF-A group was significantly worse than that of low serum group in both TTF and OS.
The serum VEGF-A level of response group was tend to be higher than that of non-response group in first line setting, and was lower in second and later line setting. However, there were no significant differences.
Conclusion
In this study, serum VEGF-A cannot be a predictor for efficacy of bevacizumab plus paclitaxel as first line therapy for metastatic breast cancer patients. On the other hand, there was a possibility that high serum level of VEGF-A can be a poor prognostic factor in late line therapy setting of bevacizumab.
Citation Format: Tozuka K, Nagai SE, Matsumoto H, Hayashi Y, Kubo K, Tsuboi M, Sato A, Takai K, Wang X, Yamada Y, Inoue K. Prognostic and predictive value of serum level of vascular endothelial growth factor-A in metastatic breast cancer patients treated with bevacizumab plus paclitaxel [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-12-17.
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Affiliation(s)
- K Tozuka
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - SE Nagai
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - H Matsumoto
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - Y Hayashi
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - K Kubo
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - M Tsuboi
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - A Sato
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - K Takai
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - X Wang
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - Y Yamada
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
| | - K Inoue
- Saitama Cancer Center, Ina, Kita-adachi-gun, Saitama-Ken, Japan
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40
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Wang Y, Huang JM, Cui GJ, Nunoura T, Takaki Y, Li WL, Li J, Gao ZM, Takai K, Zhang AQ, Stepanauskas R. Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean. Environ Microbiol 2019; 21:716-729. [PMID: 30592124 DOI: 10.1111/1462-2920.14518] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/18/2018] [Accepted: 12/26/2018] [Indexed: 02/05/2023]
Abstract
Various lineages of ammonia-oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high-quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B (polB) and methyladenine DNA glycosylase (tag) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin-like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B12 -independent MetE and B12 -dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co-occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.
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Affiliation(s)
- Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Jiao-Mei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Guo-Jie Cui
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Wen-Li Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jun Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Zhao-Ming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Ai-Qun Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
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41
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Chiba Y, Yoshida A, Shimamura S, Kameya M, Tomita T, Nishiyama M, Takai K. Discovery and analysis of a novel type of the serine biosynthetic enzyme phosphoserine phosphatase in Thermus thermophilus. FEBS J 2018; 286:726-736. [PMID: 30430741 DOI: 10.1111/febs.14703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/11/2018] [Accepted: 11/13/2018] [Indexed: 11/26/2022]
Abstract
Studying the diversity of extant metabolisms and enzymes, especially those involved in the biosynthesis of primary metabolites including amino acids, is important to shed light on the evolution of life. Many organisms synthesize serine from phosphoserine via a reaction catalyzed by phosphoserine phosphatase (PSP). Two types of PSP, belonging to distinct protein superfamilies, have been reported. Genomic analyses have revealed that the thermophilic bacterium Thermus thermophilus lacks both homologs while still having the ability to synthesize serine. Here, we purified a protein from T. thermophilus which we biochemically identified as a PSP. A knockout mutant of the responsible gene (TT_C1695) was constructed, which showed serine auxotrophy. These results indicated the involvement of this gene in serine biosynthesis in T. thermophilus. TT_C1695 was originally annotated as a protein with unknown function belonging to the haloacid dehalogenase-like hydrolase (HAD) superfamily. The HAD superfamily, which comprises phosphatases against a variety of substrates, includes also the classical PSP as a member. However, the amino acid sequence of the TT_C1695 was more similar to phosphatases acting on non-phosphoserine substrates than classical PSP; therefore, a BLASTP search and phylogenetic analysis failed to predict TT_C1695 as a PSP. Our results strongly suggest that the T. thermophilus PSP and classical PSP evolved specificity for phosphoserine independently. ENZYMES: Phosphoserine phosphatase (PSP; EC 3.1.3.3); serine hydroxymethyltransferase (EC 2.1.2.1); 3-phosphoglycerate dehydrogenase (EC 1.1.1.95); 3-phosphoserine aminotransferase (EC 2.6.1.52).
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Affiliation(s)
- Yoko Chiba
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
| | - Ayako Yoshida
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
| | - Masafumi Kameya
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
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42
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Mino S, Yoneyama N, Nakagawa S, Takai K, Sawabe T. Enrichment and Genomic Characterization of a N 2O-Reducing Chemolithoautotroph From a Deep-Sea Hydrothermal Vent. Front Bioeng Biotechnol 2018; 6:184. [PMID: 30547029 PMCID: PMC6279868 DOI: 10.3389/fbioe.2018.00184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/13/2018] [Indexed: 01/24/2023] Open
Abstract
Nitrous oxide (N2O) is a greenhouse gas and also leads to stratospheric ozone depletion. In natural environments, only a single N2O sink process is the microbial reduction of N2O to N2, which is mediated by nitrous oxide reductase (NosZ) encoded by nosZ gene. The nosZ phylogeny has two distinct clades, clade I and formerly overlooked clade II. In deep-sea hydrothermal environments, several members of the class Campylobacteria are shown to harbor clade II nosZ gene and perform the complete denitrification of nitrate to N2; however, little is known about their ability to grow on exogenous N2O as the sole electron acceptor. Here, we obtained an enrichment culture from a deep-sea hydrothermal vent in the Southern Mariana Trough, which showed a respiratory N2O reduction with H2 as an electron donor. The single amplicon sequence variant (ASV) presenting 90% similarity to Hydrogenimonas species within the class Campylobacteria was predominant throughout the cultivation period. Metagenomic analyses using a combination of short-read and long-read sequence data succeeded in reconstructing a complete genome of the dominant ASV, which encoded clade II nosZ gene. This study represents the first cultivation analysis that shows the occurrence of N2O-respiring microorganisms in a deep-sea hydrothermal vent and provides the opportunity to assess their capability to reduce N2O emission from the environments.
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Affiliation(s)
- Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Naoki Yoneyama
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.,Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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Watsuji TO, Motoki K, Hada E, Nagai Y, Takaki Y, Yamamoto A, Ueda K, Toyofuku T, Yamamoto H, Takai K. Compositional and Functional Shifts in the Epibiotic Bacterial Community of Shinkaia crosnieri Baba & Williams (a Squat Lobster from Hydrothermal Vents) during Methane-Fed Rearing. Microbes Environ 2018; 33:348-356. [PMID: 30333383 PMCID: PMC6308002 DOI: 10.1264/jsme2.me18072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The hydrothermal vent squat lobster Shinkaia crosnieri Baba & Williams harbors an epibiotic bacterial community, which is numerically and functionally dominated by methanotrophs affiliated with Methylococcaceae and thioautotrophs affiliated with Sulfurovum and Thiotrichaceae. In the present study, shifts in the phylogenetic composition and metabolic function of the epibiont community were investigated using S. crosnieri individuals, which were reared for one year in a tank fed with methane as the energy and carbon source. The results obtained indicated that indigenous predominant thioautotrophic populations, such as Sulfurovum and Thiotrichaceae members, became absent, possibly due to the lack of an energy source, and epibiotic communities were dominated by indigenous Methylococcaceae and betaproteobacterial methylotrophic members that adapted to the conditions present during rearing for 12 months with a supply of methane. Furthermore, the overall phylogenetic composition of the epibiotic community markedly changed from a composition dominated by chemolithotrophs to one enriched with cross-feeding heterotrophs in addition to methanotrophs and methylotrophs. Thus, the composition and function of the S. crosnieri epibiotic bacterial community were strongly affected by the balance between the energy and carbon sources supplied for chemosynthetic production as well as that between the production and consumption of organic compounds.
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Affiliation(s)
- Tomo-O Watsuji
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Kaori Motoki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Life Science Research Center, College of Bioresource Sciences, Nihon University.,Present Address: Department of Biological Sciences, Graduate School of Science, the University of Tokyo
| | - Emi Hada
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yukiko Nagai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Asami Yamamoto
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Life Science Research Center, College of Bioresource Sciences, Nihon University
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University
| | | | | | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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44
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Urayama SI, Takaki Y, Nishi S, Yoshida-Takashima Y, Deguchi S, Takai K, Nunoura T. Unveiling the RNA virosphere associated with marine microorganisms. Mol Ecol Resour 2018; 18:1444-1455. [PMID: 30256532 DOI: 10.1111/1755-0998.12936] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/28/2018] [Indexed: 01/01/2023]
Abstract
The study of extracellular DNA viral particles in the ocean is currently one of the most advanced fields of research in viral metagenomic analysis. However, even though the intracellular viruses of marine microorganisms might be the major source of extracellular virus particles in the ocean, the diversity of these intracellular viruses is not well understood. Here, our newly developed method, referred to herein as fragmented and primer ligated dsRNA sequencing (flds) version 2, identified considerable genetic diversity of marine RNA viruses in cell fractions obtained from surface seawater. The RNA virus community appears to cover genome sequences related to more than half of the established positive-sense ssRNA and dsRNA virus families, in addition to a number of unidentified viral lineages, and such diversity had not been previously observed in floating viral particles. In this study, more dsRNA viral contigs were detected in host cells than in extracellular viral particles. This illustrates the magnitude of the previously unknown marine RNA virus population in cell fractions, which has only been partially assessed by cellular metatranscriptomics and not by contemporary viral metagenomic studies. These results reveal the importance of studying cell fractions to illuminate the full spectrum of viral diversity on Earth.
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Affiliation(s)
- Syun-Ichi Urayama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.,Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.,Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka, Kanagawa, Japan.,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Japan
| | - Shinro Nishi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Japan
| | - Yukari Yoshida-Takashima
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Shigeru Deguchi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Japan
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45
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Drain AP, Takai K, Lawson DA, Littlepage LE, Karpuj M, Kessenbrock K, Le A, Inoue K, Weaver VM, Werb Z. Abstract LB-055: Discoidin domain receptor 1 (DDR1) ablation promotes tissue fibrosis and hypoxia to induce aggressive, basal-like breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancer studies implicate the discoidin domain receptor 1 (DDR1) in both pro- and anti-tumor roles. DDR1 is often overexpressed in breast tumors and its activation by collagen promotes tumor cell invasion and potentiates metastatic colonization by cell lines. However, DDR1 transfection into low DDR1 expressing tumor cells hinders cell migration. Moreover, low expression of DDR1 correlates with higher grade human tumors and associates with worse prognosis. To better understand the role of DDR1 in breast tumor progression and metastasis, we established a DDR1 knockout and crossed it into the MMTV-PyMT mouse. DDR1 loss compromised luminal cell adhesion and expanded the basal/myoepithelial population in adult mice. PyMT DDR1-/- tumors grew faster and had increased lung metastasis both in size and number of metastatic colonies. The DDR1-/- tumors broadly exhibited a more basal-like phenotype with enhanced fibrosis and were more hypoxic. Furthermore, these tumors contained more CD90+ CD24+ tumor cells and more K8+ K14+ cells surrounding necrotic regions. Taken together these data suggest DDR1 loss confers a growth advantage favoring basal cell expansion via impaired luminal adhesion and enhanced basal differentiation leading to more aggressive, basal-like disease.
Citation Format: Allison P. Drain, Ken Takai, Devon A. Lawson, Laurie E. Littlepage, Marcela Karpuj, Kai Kessenbrock, Annie Le, Kenichi Inoue, Valerie M. Weaver, Zena Werb. Discoidin domain receptor 1 (DDR1) ablation promotes tissue fibrosis and hypoxia to induce aggressive, basal-like breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-055.
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Affiliation(s)
| | - Ken Takai
- 2Saitama Cancer Center, Saitama, Japan
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46
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Affiliation(s)
- Masahiro Yamamoto
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR); Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka 273-0061 Japan
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research Team; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute; Tokyo Institute of Technology; 2-12-1-IE-1, Ookayama, Meguro-ku Tokyo 152-8550 Japan
| | - Ken Takai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR); Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka 273-0061 Japan
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47
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Ijiri A, Inagaki F, Kubo Y, Adhikari RR, Hattori S, Hoshino T, Imachi H, Kawagucci S, Morono Y, Ohtomo Y, Ono S, Sakai S, Takai K, Toki T, Wang DT, Yoshinaga MY, Arnold GL, Ashi J, Case DH, Feseker T, Hinrichs KU, Ikegawa Y, Ikehara M, Kallmeyer J, Kumagai H, Lever MA, Morita S, Nakamura KI, Nakamura Y, Nishizawa M, Orphan VJ, Røy H, Schmidt F, Tani A, Tanikawa W, Terada T, Tomaru H, Tsuji T, Tsunogai U, Yamaguchi YT, Yoshida N. Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex. Sci Adv 2018; 4:eaao4631. [PMID: 29928689 PMCID: PMC6007163 DOI: 10.1126/sciadv.aao4631] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
Microbial life inhabiting subseafloor sediments plays an important role in Earth's carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90% of methane is microbially produced at 16° to 30°C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (102 to 103 cells cm-3) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated.
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Affiliation(s)
- Akira Ijiri
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan
| | - Yusuke Kubo
- Center for Deep Earth Exploration, JAMSTEC, Yokohama 236-0001, Japan
| | - Rishi R. Adhikari
- Department of Earth and Environmental Sciences, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Shohei Hattori
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Hiroyuki Imachi
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Shinsuke Kawagucci
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Yoko Ohtomo
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Shuhei Ono
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Ken Takai
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
| | - Tomohiro Toki
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - David T. Wang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marcos Y. Yoshinaga
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Gail L. Arnold
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Juichiro Ashi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - David H. Case
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tomas Feseker
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Yojiro Ikegawa
- Civil Engineering Research Laboratory, Central Research Institute of Electric Power Industry, Abiko, Chiba 270-1194, Japan
| | - Minoru Ikehara
- Center for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Jens Kallmeyer
- Department of Earth and Environmental Sciences, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Hidenori Kumagai
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | - Mark A. Lever
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Sumito Morita
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | | | - Yuki Nakamura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hans Røy
- Center for Geomicrobiology, Department of Biological Sciences, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Frauke Schmidt
- MARUM and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Atsushi Tani
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Wataru Tanikawa
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka 237-0061, Japan
| | | | - Hitoshi Tomaru
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Takeshi Tsuji
- Department of Earth Resources Engineering, Kyushu University, Fukuoka 819-0395, Japan
- International Institute for Carbon-Neutral Energy Research, Department of Earth Resources Engineering, Kyushu University, 744 Motooka, Fukuoka-shi, Fukuoka 819-0395, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8601, Japan
| | - Yasuhiko T. Yamaguchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Naohiro Yoshida
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan
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48
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Nunoura T, Nishizawa M, Hirai M, Shimamura S, Harnvoravongchai P, Koide O, Morono Y, Fukui T, Inagaki F, Miyazaki J, Takaki Y, Takai K. Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench. Microbes Environ 2018; 33:186-194. [PMID: 29806625 PMCID: PMC6031389 DOI: 10.1264/jsme2.me17194] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, "Ca. Marinimicrobia" (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and "Ca. Woesearchaeota" (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.
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Affiliation(s)
- Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Osamu Koide
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Junichi Miyazaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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Vokhmintcev K, Linkov P, Samokhvalov P, Takai K, Baranov A, Fedorov A, Nabiev I. Large-scale Synthesis of Monodisperse PbS Quantum Dots. ACTA ACUST UNITED AC 2018. [DOI: 10.18502/ken.v3i3.2007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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50
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Satomura T, Hayashi J, Sakamoto H, Nunoura T, Takaki Y, Takai K, Takami H, Ohshima T, Sakuraba H, Suye SI. d-Lactate electrochemical biosensor prepared by immobilization of thermostable dye-linked d-lactate dehydrogenase from Candidatus Caldiarchaeum subterraneum. J Biosci Bioeng 2018; 126:425-430. [PMID: 29691195 DOI: 10.1016/j.jbiosc.2018.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
A stable d-lactate electrochemical sensing system was developed using a dye-linked d-lactate dehydrogenase (Dye-DLDH) from an uncultivated thermophilic archaeon, Candidatus Caldiarchaeum subterraneum. To develop the system, the putative gene encoding the Dye-DLDH from Ca. Caldiarchaeum subterraneum was overexpressed in Escherichia coli, and the expressed product was purified. The recombinant enzyme was a highly thermostable Dye-DLDH that retained full activity after incubation for 10 min at 70°C. The electrode for detection of d-lactate was prepared by immobilizing the thermostable Dye-DLDH and multi-walled carbon nanotube (MWCNT) within Nafion membrane. The electrocatalytic response of the electrode was clearly observed upon exposure to d-lactate. The electrode response to d-lactate was linear within the concentration range of 0.03-2.5 mM, and it showed little reduction in responsiveness after 50 days. This is the first report describing a d-lactate sensing system using a thermostable Dye-DLDH.
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Affiliation(s)
- Takenori Satomura
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan.
| | - Junji Hayashi
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Hiroaki Sakamoto
- Tenure-Track Program for Innovative Research, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Takuro Nunoura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hideto Takami
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technoligy, Ohmiya, 5-16-1 Asahi-ku, Ohsaka 535-8585 Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Shin-Ichiro Suye
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
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