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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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Kato S, Tahara YO, Nishimura Y, Uematsu K, Arai T, Nakane D, Ihara A, Nishizaka T, Iwasaki W, Itoh T, Miyata M, Ohkuma M. Cell surface architecture of the cultivated DPANN archaeon Nanobdella aerobiophila. J Bacteriol 2024; 206:e0035123. [PMID: 38289045 PMCID: PMC10882981 DOI: 10.1128/jb.00351-23] [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: 10/27/2023] [Accepted: 12/22/2023] [Indexed: 02/23/2024] Open
Abstract
The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeon Nanobdella aerobiophila strain MJ1T and its host Metallosphaera sedula strain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy, quick-freeze deep-etch TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1T were different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1T gene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1T and MJ1HA were motile, but sole MJ1T cells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila.IMPORTANCEDPANN archaea are widely distributed in a variety of natural and artificial environments and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon, Nanobdella aerobiophila, using electron microscopy, live cell imaging, transcriptomics, and genomics, including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Yuki Nishimura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | | | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Ayaka Ihara
- Department of Physics, Gakushuin University, Tokyo, Japan
| | | | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
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Yamaguchi M, Takahashi-Nakaguchi A, Uematsu K, Yamada H, Sato-Okamoto M, Chibana H. Ultrastructural Examination of Mouse Glomerular Capillary Loop by Sandwich Freezing and Freeze-Substitution. Microscopy (Oxf) 2022; 71:289-296. [PMID: 35778971 DOI: 10.1093/jmicro/dfac031] [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] [Received: 03/10/2022] [Revised: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 11/12/2022] Open
Abstract
Sandwich freezing is a method of rapid freezing by sandwiching specimens between two metal disks, and has been used for observing exquisite close-to-native ultrastructure of living yeast and bacteria. Recently, this method has been found to be useful for preserving cell images of glutaraldehyde-fixed animal and human tissues. In the present study, this method was applied to observe fine structure of mouse glomerular capillary loops. Morphometry was then performed, and the results were compared with the data obtained by in vivo cryotechnique, which may provide the closest ultrastructure to the native state of living tissue. The results show that the ultrastructure of glomerular capillary loops obtained by sandwich freezing-freeze substitution after glutaraldehyde fixation was close to that of the ultrastructure obtained by in vivo cryotechnique, not only in quality of cell image but also in quantitative morphometry. They indicate that the ultrastructure obtained by sandwich freezing-freeze-substitution after glutaraldehyde fixation may more closely reflect the living state of cells and tissues than conventional chemical fixation and dehydration at room temperature and conventional rapid freezing freeze-substitution of excised tissues without glutaraldehyde fixation. Sandwich freezing-freeze substitution technique should be used routinely as a standard method for observing close-to-native ultrastructure of biological specimens.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | | | - Katsuyuki Uematsu
- Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24, Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Michiyo Sato-Okamoto
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
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Yamaguchi M, Takahashi-Nakaguchi A, Uematsu K, Naito K, Sato-Okamoto M, Ishiwata K, Naraoka S, Chibana H. Electron Microscopy of Mouse Tissues by Sandwich Freezing and Freeze-Substitution. CYTOLOGIA 2022. [DOI: 10.1508/cytologia.87.149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | - Kumiko Naito
- Department of Diabetes, Metabolism and Endocrinology, Chiba University Hospital
| | | | - Kazuki Ishiwata
- Department of Endocrinology, Hematology and Gerontology, Chiba University Hospital
| | - Sakino Naraoka
- Graduate School of Science and Engineering, Advanced Science and Engineering Biology, Chiba University
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Yamaguchi M, Takahashi-Nakaguchi A, Uematsu K, Taguchi M, Sato-Okamoto M, Chibana H. Rapid Freezing using Sandwich Freezing Device for Good Ultrastructural Preservation of Biological Specimens in Electron Microscopy. J Vis Exp 2021. [PMID: 34338682 DOI: 10.3791/62431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Chemical fixation has been used for observing the ultrastructure of cells and tissues. However, this method does not adequately preserve the ultrastructure of cells; artifacts and extraction of cell contents are usually observed. Rapid freezing is a better alternative for the preservation of cell structure. Sandwich freezing of living yeast or bacteria followed by freeze-substitution has been used for observing the exquisite natural ultrastructure of cells. Recently, sandwich freezing of glutaraldehyde-fixed cultured cells or human tissues has also been used to reveal the ultrastructure of cells and tissues. These studies have thus far been carried out with a handmade sandwich freezing device, and applications to studies in other laboratories have been limited. A new sandwich freezing device has recently been fabricated and is now commercially available. The present paper shows how to use the sandwich freezing device for rapid freezing of biological specimens, including bacteria, yeast, cultured cells, isolated cells, animal and human tissues, and viruses. Also shown is the preparation of specimens for ultrathin sectioning after rapid freezing and procedures for freeze-substitution, resin embedding, trimming of blocks, cutting of ultrathin sections, recovering of sections, staining, and covering of grids with support films.
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6
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Yamaguchi M, Taguchi M, Uematsu K, Takahashi-Nakaguchi A, Sato-Okamoto M, Chibana H. Sandwich freezing device for rapid freezing of viruses, bacteria, yeast, cultured cells and animal and human tissues in electron microscopy. Microscopy (Oxf) 2021; 70:215-223. [PMID: 33206169 DOI: 10.1093/jmicro/dfaa049] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/14/2022] Open
Abstract
We have been using sandwich freezing of living yeast and bacteria followed by freeze-substitution for observing close-to-native ultrastructure of cells. Recently, sandwich freezing of glutaraldehyde-fixed cultured cells and human tissues have been found to give excellent preservation of ultrastructure of cells and tissues. These studies, however, have been conducted using a handmade sandwich freezing device and have been limited in a few laboratories. To spread the use of this method to other laboratories, we fabricated and commercialized a new sandwich freezing device. The new device is inexpensive, portable and sterilizable. It can be used to rapid-freeze viruses, bacteria, yeast, cultured cells and animal and human tissues to a depth of 0.2 mm if tissues are prefixed with glutaraldehyde. The commercial availability of this device will expand application of rapid freezing to wide range of biological materials.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Masaki Taguchi
- Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
| | - Katsuyuki Uematsu
- Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
| | | | - Michiyo Sato-Okamoto
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
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Nomaki H, Chen C, Oda K, Tsuchiya M, Tame A, Uematsu K, Isobe N. Abundant Chitinous Structures in Chilostomella (Foraminifera, Rhizaria) and Their Potential Functions. J Eukaryot Microbiol 2021; 68:e12828. [PMID: 33128276 PMCID: PMC7894498 DOI: 10.1111/jeu.12828] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/28/2020] [Accepted: 10/20/2020] [Indexed: 12/01/2022]
Abstract
Benthic foraminifera, members of Rhizaria, inhabit a broad range of marine environments and are particularly common in hypoxic sediments. The biology of benthic foraminifera is key to understanding benthic ecosystems and relevant biogeochemical cycles, especially in hypoxic environments. Chilostomella is a foraminiferal genus commonly found in hypoxic deep-sea sediments and has poorly understood ecological characteristics. For example, the carbon isotopic compositions of their lipids are substantially different from other co-occurring genera, probably reflecting unique features of its metabolism. Here, we investigated the cytoplasmic and ultrastructural features of Chilostomella ovoidea from bathyal sediments of Sagami Bay, Japan, based on serial semi-thin sections examined using an optical microscope followed by a three-dimensional reconstruction, combined with TEM observations of ultra-thin sections. Observations by TEM revealed the presence of abundant electron-dense structures dividing the cytoplasm. Based on histochemical staining, these structures are shown to be composed of chitin. Our 3D reconstruction revealed chitinous structures in the final seven chambers. These exhibited a plate-like morphology in the final chambers but became rolled up in earlier chambers (toward the proloculus). These chitinous, plate-like structures may function to partition the cytoplasm in a chamber to increase the surface/volume ratio and/or act as a reactive site for some metabolic functions.
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Affiliation(s)
- Hidetaka Nomaki
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Chong Chen
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Kaya Oda
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Masashi Tsuchiya
- Research Institute for Global Change (RIGC)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawa
237‐0061Japan
| | - Akihiro Tame
- Marine Works Japan Ltd.3‐54‐1 Oppamahigashi‐choYokosukaKanagawa237‐0063Japan
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd.3‐54‐1 Oppamahigashi‐choYokosukaKanagawa237‐0063Japan
| | - Noriyuki Isobe
- Research Institute for Marine Resources Utilization (MRU)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawa237‐0061Japan
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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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Uematsu K, Chen C, Hirayama H. SS1-4 3D reconstruction of intracytoplasmic membrane structure of methane-oxidizing bacteria by electron microscopy imaging. Microscopy (Oxf) 2019. [DOI: 10.1093/jmicro/dfz065] [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: 11/14/2022] Open
Affiliation(s)
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hisako Hirayama
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Kato S, Okumura T, Uematsu K, Hirai M, Iijima K, Usui A, Suzuki K. Heterogeneity of Microbial Communities on Deep-Sea Ferromanganese Crusts in the Takuyo-Daigo Seamount. Microbes Environ 2018; 33:366-377. [PMID: 30381615 PMCID: PMC6307992 DOI: 10.1264/jsme2.me18090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 11/12/2022] Open
Abstract
Rock outcrops of aged deep-sea seamounts are generally covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Although the presence of microorganisms in Fe-Mn crusts has been reported, limited information is currently available on intra- and inter-variations in crust microbial communities. Therefore, we collected several Fe-Mn crusts in bathyal and abyssal zones (water depths of 1,150-5,520 m) in the Takuyo-Daigo Seamount in the northwestern Pacific, and examined microbial communities on the crusts using culture-independent molecular and microscopic analyses. Quantitative PCR showed that microbial cells were abundant (106-108 cells g-1) on Fe-Mn crust surfaces through the water depths. A comparative 16S rRNA gene analysis revealed community differences among Fe-Mn crusts through the water depths, which may have been caused by changes in dissolved oxygen concentrations. Moreover, community differences were observed among positions within each Fe-Mn crust, and potentially depended on the availability of sinking particulate organic matter. Microscopic and elemental analyses of thin Fe-Mn crust sections revealed the accumulation of microbial cells accompanied by the depletion of Mn in valleys of bumpy crust surfaces. Our results suggest that heterogeneous and abundant microbial communities play a role in the biogeochemical cycling of Mn, in addition to C and N, on crusts and contribute to the extremely slow growth of Fe-Mn crusts.
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Affiliation(s)
- Shingo Kato
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Research and Development Center for Submarine Resources, JAMSTEC
| | - Tomoyo Okumura
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC.,Center for Advanced Marine Core Research, Kochi University
| | | | - Miho Hirai
- Research and Development Center for Marine Biosciences, JAMSTEC
| | - Koichi Iijima
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Research and Development Center for Submarine Resources, JAMSTEC
| | - Akira Usui
- Center for Advanced Marine Core Research, Kochi University
| | - Katsuhiko Suzuki
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Research and Development Center for Submarine Resources, JAMSTEC
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Sakai K, Inoue M, Nishimura H, Mikami S, Kuwabara Y, Kojima A, Toda M, Kobayashi Y, Kikuchi S, Hirata Y, Kyoyama H, Moriyama G, Gemma A, Uematsu K. P2.06-31 Inhibition of Heat Shock Protein 70 Function Suppresses Proliferation in Mesothelioma Cells. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1286] [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: 10/28/2022]
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12
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Yamaguchi M, Yamada H, Uematsu K, Horinouchi Y, Chibana H. Electron Microscopy and Structome Analysis of Unique Amorphous Bacteria from the Deep Sea in Japan. CYTOLOGIA 2018. [DOI: 10.1508/cytologia.83.337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association
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13
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Tsuchiya M, Chikaraishi Y, Nomaki H, Sasaki Y, Tame A, Uematsu K, Ohkouchi N. Compound-specific isotope analysis of benthic foraminifer amino acids suggests microhabitat variability in rocky-shore environments. Ecol Evol 2018; 8:8380-8395. [PMID: 30250710 PMCID: PMC6144965 DOI: 10.1002/ece3.4358] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 10/31/2017] [Revised: 04/19/2018] [Accepted: 06/20/2018] [Indexed: 01/13/2023] Open
Abstract
The abundance and biomass of benthic foraminifera are high in intertidal rocky-shore habitats. However, the availability of food to support their high biomass has been poorly studied in these habitats compared to those at seafloor covered by sediments. Previous field and laboratory observations have suggested that there is diversity in the food preferences and modes of life among rocky-shore benthic foraminifera. In this study, we used the stable nitrogen isotopic composition of amino acids to estimate the trophic position, trophic niche, and feeding strategy of individual foraminifera species. We also characterized the configuration and structure of the endobiotic microalgae in foraminifera using transmission electron microscopy, and we identified the origin of endobionts based on nucleotide sequences. Our results demonstrated a large variation in the trophic positions of different foraminifera from the same habitat, a reflection of endobiotic features and the different modes of life and food preferences of the foraminifera. Foraminifera did not rely solely on exogenous food sources. Some species effectively used organic matter derived from endobionts in the cell cytoplasm. The high biomass and species density of benthic foraminifera found in intertidal rocky-shore habitats are thus probably maintained by the use of multiple nitrogen resources and by microhabitat segregation among species as a consequence.
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Affiliation(s)
- Masashi Tsuchiya
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | - Yoshito Chikaraishi
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
| | - Hidetaka Nomaki
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | - Yoko Sasaki
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | | | | | - Naohiko Ohkouchi
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
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14
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Abstract
Life stages of some animals, including amphibians and insects, are so different that they have historically been seen as different species. 'Metamorphosis' broadly encompasses major changes in organism bodies and, importantly, concomitant shifts in trophic strategies. Many marine animals have a biphasic lifestyle, with small pelagic larvae undergoing one or more metamorphic transformations before settling into a permanent, adult morphology on the benthos. Post-settlement, the hydrothermal vent gastropod Gigantopelta chessoia experiences a further, cryptic metamorphosis at body sizes around 5-7 mm. The terminal adult stage is entirely dependent on chemoautotrophic symbionts; smaller individuals do not house symbionts and presumably depend on grazing. Using high-resolution X-ray microtomography to reconstruct the internal organs in a growth series, we show that this sudden transition in small but sexually mature individuals dramatically reconfigures the organs, but is in no way apparent from external morphology. We introduce the term 'cryptometamorphosis' to identify this novel phenomenon of a major body change and trophic shift, not related to sexual maturity, transforming only the internal anatomy. Understanding energy flow in ecosystems depends on the feeding ecology of species; the present study highlights the possibility for adult animals to make profound shifts in biology that influence energy dynamics.
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Affiliation(s)
- Chong Chen
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 2370061, Japan
| | - Katrin Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka, Kanagawa 2370063, Japan
| | - Julia D Sigwart
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry BT22 1PF, N. Ireland
- Museum of Paleontology, University of California, Berkeley, CA 94720, USA
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15
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Uematsu K, Noguchi K, Nakano K. Synthesis and properties of [7]helicene and [7]helicene-like compounds with a cyclopenta[1,2-b:4,3-b′]dithiophene or dithieno[2,3-b:3′,2′-d]heterole skeleton. Phys Chem Chem Phys 2018; 20:3286-3295. [DOI: 10.1039/c7cp06342c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of [7]helicene and [7]helicene-like compounds composed of a cyclopenta[1,2-b:4,3-b′]dithiophene or dithieno[2,3-b:3′,2′-d]heterole moiety and two naphthalene moieties were successfully synthesized from a common synthetic intermediate, 1,1′-binaphtho[2,1-b]thiophene.
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Affiliation(s)
- K. Uematsu
- Department of Organic and Polymer Materials Chemistry, Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - K. Noguchi
- Instrumentation Analysis Center, Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - K. Nakano
- Department of Organic and Polymer Materials Chemistry, Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
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16
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Uematsu K, Chen C, Kimoto K. 2S-B1-3Three-dimensional Analysis of the Whole Cytoplasm of Foraminifera Using Array Tomography Method. Microscopy (Oxf) 2017. [DOI: 10.1093/jmicro/dfx056] [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: 11/12/2022] Open
Affiliation(s)
| | - Chong Chen
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Katsunori Kimoto
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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17
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Chen C, Uematsu K, Linse K, Sigwart JD. By more ways than one: Rapid convergence at hydrothermal vents shown by 3D anatomical reconstruction of Gigantopelta (Mollusca: Neomphalina). BMC Evol Biol 2017; 17:62. [PMID: 28249568 PMCID: PMC5333402 DOI: 10.1186/s12862-017-0917-z] [Citation(s) in RCA: 21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/17/2017] [Indexed: 02/03/2023] Open
Abstract
Background Extreme environments prompt the evolution of characteristic adaptations. Yet questions remain about whether radiations in extreme environments originate from a single lineage that masters a key adaptive pathway, or if the same features can arise in parallel through convergence. Species endemic to deep-sea hydrothermal vents must accommodate high temperature and low pH. The most successful vent species share a constrained pathway to successful energy exploitation: hosting symbionts. The vent-endemic gastropod genus Gigantopelta, from the Southern and Indian Oceans, shares unusual features with a co-occurring peltospirid, the ‘scaly-foot gastropod’ Chrysomallon squamiferum. Both are unusually large for the clade and share other adaptive features such as a prominent enlarged trophosome-like oesophageal gland, not found in any other vent molluscs. Results Transmission electron microscopy confirmed endosymbiont bacteria in the oesophageal gland of Gigantopelta, as also seen in Chrysomallon. They are the only known members of their phylum in vent ecosystems hosting internal endosymbionts; other vent molluscs host endosymbionts in or on their gills, or in the mantle cavity. A five-gene phylogenetic reconstruction demonstrated that Gigantopelta and Chrysomallon are not phylogenetically sister-taxa, despite their superficial similarity. Both genera have specialist adaptations to accommodate internalised endosymbionts, but with anatomical differences that indicate separate evolutionary origins. Hosting endosymbionts in an internal organ within the host means that all resources required by the bacteria must be supplied by the animal, rather than directly by the vent fluid. Unlike Chrysomallon, which has an enlarged oesophageal gland throughout post-settlement life, the oesophageal gland in Gigantopelta is proportionally much smaller in juveniles and the animals likely undergo a trophic shift during ontogeny. The circulatory system is hypertrophied in both but the overall size is smaller in Gigantopelta. In contrast with Chrysomallon, Gigantopelta possesses true ganglia and is gonochoristic. Conclusions Key anatomical differences between Gigantopelta and Chrysomallon demonstrate these two genera acquired a similar way of life through independent and convergent adaptive pathways. What appear to be the holobiont’s adaptations to an extreme environment, are driven by optimising bacteria’s access to vent nutrients. By comparing Gigantopelta and Chrysomallon, we show that metazoans are capable of rapidly and repeatedly evolving equivalent anatomical adaptations and close-knit relationships with chemoautotrophic bacteria, achieving the same end-product through parallel evolutionary trajectories. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0917-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chong Chen
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry, Northern Ireland. .,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
| | - Katrin Linse
- British Antarctic Survey, High Cross, Cambridge, UK
| | - Julia D Sigwart
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry, Northern Ireland.,Berkeley, Museum of Paleontology, University of California, VLSB 1101, Berkeley, CA, 94720, USA
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18
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Nakagawa H, Kim SW, Hasegawa T, Hasegawa S, Ishigaki T, Uematsu K, Toda K, Takaba H, Sato M. Stabilization of novel high temperature phase yellow-emitting σ-type (Ba1−x−yEuxMgy)2P2O7 phosphors using a melt synthesis technique. Inorg Chem Front 2017. [DOI: 10.1039/c7qi00359e] [Citation(s) in RCA: 5] [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: 02/05/2023]
Abstract
Novel high-temperature phase σ-type (Ba1−x−yEuxMgy)2P2O7 phosphors were synthesized for the first time by a melt synthesis technique using an arc-imaging furnace.
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Affiliation(s)
- H. Nakagawa
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - S. W. Kim
- Electronic Convergence Materials Division
- Optic & Display Materials Center
- Korea Institute of Ceramic Engineering and Technology
- Jinju-si
- Republic of Korea
| | - T. Hasegawa
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
- Department of Marine Resource Science
| | - S. Hasegawa
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - T. Ishigaki
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - K. Uematsu
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - K. Toda
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - H. Takaba
- Department of Environmental and Energy Chemistry
- Faculty of Engineering
- Kogakuin University
- Hachioji
- Japan
| | - M. Sato
- Department of Chemistry and Chemical Engineering
- Niigata University
- Niigata 950-2181
- Japan
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19
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Kim SW, Hasegawa T, Muto M, Toda A, Kaneko T, Sugimoto K, Uematsu K, Ishigaki T, Toda K, Sato M, Koide J, Toda M, Kudo Y. Improvement of luminescence properties of rubidium vanadate, RbVO3, phosphors by erbium doping in the crystal lattice. NEW J CHEM 2017. [DOI: 10.1039/c6nj03823a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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
The thermal quenching effect of RbVO3 phosphor was effectively improved by Er3+ doping into the lattice, as a result, the emission intensity of the phosphor was successfully enhanced.
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20
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Makita H, Tanaka E, Mitsunobu S, Miyazaki M, Nunoura T, Uematsu K, Takaki Y, Nishi S, Shimamura S, Takai K. Mariprofundus micogutta sp. nov., a novel iron-oxidizing zetaproteobacterium isolated from a deep-sea hydrothermal field at the Bayonnaise knoll of the Izu-Ogasawara arc, and a description of Mariprofundales ord. nov. and Zetaproteobacteria classis nov. Arch Microbiol 2016; 199:335-346. [PMID: 27766355 DOI: 10.1007/s00203-016-1307-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 06/10/2016] [Revised: 09/20/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
Abstract
A novel iron-oxidizing chemolithoautotrophic bacterium, strain ET2T, was isolated from a deep-sea sediment in a hydrothermal field of the Bayonnaise knoll of the Izu-Ogasawara arc. Cells were bean-shaped, curved short rods. Growth was observed at a temperature range of 15-30 °C (optimum 25 °C, doubling time 24 h) and a pH range of 5.8-7.0 (optimum pH 6.4) in the presence of NaCl at a range of 1.0-4.0 % (optimum 2.75 %). The isolate was a microaerophilic, strict chemolithoautotroph capable of growing using ferrous iron and molecular oxygen (O2) as the sole electron donor and acceptor, respectively; carbon dioxide as the sole carbon source; and either ammonium or nitrate as the sole nitrogen source. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the new isolate was related to the only previously isolated Mariprofundus species, M. ferrooxydans. Although relatively high 16S rRNA gene similarity (95 %) was found between the new isolate and M. ferrooxydans, the isolate was distinct in terms of cellular fatty acid composition, genomic DNA G+C content and cell morphology. Furthermore, genomic comparison between ET2T and M. ferrooxydans PV-1 indicated that the genomic dissimilarity of these strains met the standard for species-level differentiation. On the basis of its physiological and molecular characteristics, strain ET2T (= KCTC 15556T = JCM 30585 T) represents a novel species of Mariprofundus, for which the name Mariprofundus micogutta is proposed. We also propose the subordinate taxa Mariprofundales ord. nov. and Zetaproteobacteria classis nov. in the phylum Proteobacteria.
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Affiliation(s)
- Hiroko Makita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan. .,Department of Applied Chemistry, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa, 243-0292, Japan.
| | - Emiko Tanaka
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Department of Applied Chemistry, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa, 243-0292, Japan
| | - Satoshi Mitsunobu
- Department of Environmental Conservation, Graduate School of Agriculture, Ehime University, Tarumi, Matsuyama, 790-8566, Japan
| | - Masayuki Miyazaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Takuro Nunoura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Katsuyuki Uematsu
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd., Yokosuka, 237-0061, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Shinro Nishi
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Shigeru Shimamura
- 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
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21
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Ohishi K, Yamamoto M, Tame A, Kusaka C, Nagai Y, Sugimura M, Inoue K, Uematsu K, Yoshida T, Ikuta T, Toyofuku T, Maruyama T. Long-term Cultivation of the Deep-Sea Clam Calyptogena okutanii: Changes in the Abundance of Chemoautotrophic Symbiont, Elemental Sulfur, and Mucus. Biol Bull 2016; 230:257-267. [PMID: 27365420 DOI: 10.1086/bblv230n3p257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Survival of deep-sea Calyptogena clams depends on organic carbon produced by symbiotic, sulfur-oxidizing, autotrophic bacteria present in the epithelial cells of the gill. To understand the mechanism underlying this symbiosis, the development of a long-term cultivation system is essential. We cultivated specimens of Calyptogena okutanii in an artificial chemosynthetic aquarium with a hydrogen sulfide (H2S) supply system provided by the sulfate reduction of dog food buried in the sediment. We studied morphological and histochemical changes in the clams' gills by immunohistochemical and energy-dispersive X-ray analyses. The freshly collected clams contained a high amount of elemental sulfur in the gill epithelial cells, as well as densely packed symbiotic bacteria. Neither elemental sulfur nor symbiotic bacteria was detected in any other organs except the ovaries, where symbiotic bacteria, but not sulfur, was detected. The longest survival of an individual clam in this aquarium was 151 days. In the 3 clams dissected on Days 57 and 91 of the experiment, no elemental sulfur was detected in the gills. The symbiotic bacteria content had significantly decreased by Day 57, and was absent by Day 91. For comparison, we also studied the deep-sea mussel Bathymodiolus septemdierum, which harbors a phylogenetically close, sulfur-oxidizing, symbiotic bacterium with similar sulfur oxidation pathways. Sulfur particles were not detected, even in the gills of the freshly collected mussels. We discuss the importance of the proportion of available H2S and oxygen to the bivalves for elemental sulfur accumulation. Storage of nontoxic elemental sulfur, an energy source, seems to be an adaptive strategy of C. okutanii.
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Affiliation(s)
| | - Masahiro Yamamoto
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Department of Technical Services, Marine Works Japan, Ltd., Oppama higashi-cho, Yokosuka, Kanagawa 237-0063, Japan
| | - Chiho Kusaka
- Department of Marine Biodiversity Research, JAMSTEC, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, JAMSTEC, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Makoto Sugimura
- Enoshima Aquarium, 2-19-1 Katasekaigan, Fujisawa, Kanagawa 251-0035, Japan
| | - Koji Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan; and
| | - Katsuyuki Uematsu
- Department of Technical Services, Marine Works Japan, Ltd., Oppama higashi-cho, Yokosuka, Kanagawa 237-0063, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, JAMSTEC, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Tetsuro Ikuta
- Department of Marine Biodiversity Research, JAMSTEC, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Takashi Toyofuku
- Department of Marine Biodiversity Research, JAMSTEC, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Marine Biodiversity Research Program, and Research and Development Center for Marine Biosciences, JAMSTEC, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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22
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Nomaki H, Bernhard JM, Ishida A, Tsuchiya M, Uematsu K, Tame A, Kitahashi T, Takahata N, Sano Y, Toyofuku T. Intracellular Isotope Localization in Ammonia sp. (Foraminifera) of Oxygen-Depleted Environments: Results of Nitrate and Sulfate Labeling Experiments. Front Microbiol 2016; 7:163. [PMID: 26925038 PMCID: PMC4759270 DOI: 10.3389/fmicb.2016.00163] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 11/02/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much (15)N or (34)S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200-500 nm in diameter and co-occurred with possible endobionts, were labeled with (15)N originated from (15)N-labeled nitrate under anoxia and were labeled with both (15)N and (34)S under dysoxia. The labeling with (15)N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.
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Affiliation(s)
- Hidetaka Nomaki
- Department of Biogeochemistry, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Joan M Bernhard
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Akizumi Ishida
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Masashi Tsuchiya
- Department of Marine Biodiversity, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | | | | | - Tomo Kitahashi
- Project Team for Research and Development of Next-generation Technology for Ocean Resources Exploration, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Naoto Takahata
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Yuji Sano
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Takashi Toyofuku
- Department of Marine Biodiversity, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
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23
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Kim SW, Hasegawa T, Hasegawa S, Yamanashi R, Nakagawa H, Toda K, Ishigaki T, Uematsu K, Sato M. Improved synthesis of SrLiAl3N4:Eu2+ phosphor using complex nitride raw material. RSC Adv 2016. [DOI: 10.1039/c6ra14107b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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] Open
Abstract
Narrow band deep-red emission SrLiAl3N4:Eu2+ phosphor was effectively synthesized using complex nitride Sr3Al2N4 and Li3AlN2 as raw materials. The phosphor exhibited strong deep-red emission peaking at 654 nm under excitation at 450 nm.
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Affiliation(s)
- S. W. Kim
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
- Department of Nanotechnology and Advanced Material Engineering
| | - T. Hasegawa
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - S. Hasegawa
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - R. Yamanashi
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - H. Nakagawa
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - K. Toda
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - T. Ishigaki
- Graduate School of Science and Technology
- Niigata University
- Niigata 950-2181
- Japan
| | - K. Uematsu
- Department of Chemistry and Chemical Engineering
- Niigata University
- Niigata 950-2181
- Japan
| | - M. Sato
- Department of Chemistry and Chemical Engineering
- Niigata University
- Niigata 950-2181
- Japan
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24
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Koyama S, Tsubouchi T, Usui K, Uematsu K, Tame A, Nogi Y, Ohta Y, Hatada Y, Kato C, Miwa T, Toyofuku T, Nagahama T, Konishi M, Nagano Y, Abe F. Involvement of flocculin in negative potential-applied ITO electrode adhesion of yeast cells. FEMS Yeast Res 2015; 15:fov064. [PMID: 26187908 PMCID: PMC4629795 DOI: 10.1093/femsyr/fov064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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] [Accepted: 07/10/2015] [Indexed: 12/13/2022] Open
Abstract
The purpose of this study was to develop novel methods for attachment and cultivation of specifically positioned single yeast cells on a microelectrode surface with the application of a weak electrical potential. Saccharomyces cerevisiae diploid strains attached to an indium tin oxide/glass (ITO) electrode to which a negative potential between −0.2 and −0.4 V vs. Ag/AgCl was applied, while they did not adhere to a gallium-doped zinc oxide/glass electrode surface. The yeast cells attached to the negative potential-applied ITO electrodes showed normal cell proliferation. We found that the flocculin FLO10 gene-disrupted diploid BY4743 mutant strain (flo10Δ /flo10Δ) almost completely lost the ability to adhere to the negative potential-applied ITO electrode. Our results indicate that the mechanisms of diploid BY4743 S. cerevisiae adhesion involve interaction between the negative potential-applied ITO electrode and the Flo10 protein on the cell wall surface. A combination of micropatterning techniques of living single yeast cell on the ITO electrode and omics technologies holds potential of novel, highly parallelized, microchip-based single-cell analysis that will contribute to new screening concepts and applications. Yeast Saccharomyces cerevisiae were selectively attached on the negative potential-applied indium tin oxide/glass electrode. Mechanisms of the yeast cell attachment involve Flocculin Flo10 proteins.
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Affiliation(s)
- Sumihiro Koyama
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Taishi Tsubouchi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Department of Marine Science, Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
| | - Akihiro Tame
- Department of Marine Science, Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Yukari Ohta
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Tetsuya Miwa
- Marine Technology and Engineering Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Takashi Toyofuku
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Takehiko Nagahama
- Department of Foods and Human Nutrition, Notre Dame Seishin University, 2-16-9 Ifuku-cho, Kita-ku, Okayama 700-8516, Japan
| | - Masaaki Konishi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yuriko Nagano
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Fumiyoshi Abe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
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Shigeno S, Tame A, Uematsu K, Miura T, Tsuchida S, Fujikura K. Dual Cellular Supporters: Multi-Layer Glial Wrapping and the Penetrative Matrix Specialized in Deep-Sea Hydrothermal Vent Endemic Scale-Worms. Biol Bull 2015; 228:217-226. [PMID: 26124448 DOI: 10.1086/bblv228n3p217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hydrothermal vent organisms undergo extreme environments that may require unique innovations. The present study reports a distinct case of cellular supportive systems in the nervous systems of a scale-worm, Branchinotogluma japonica, endemic to deep-sea hydrothermal vents. We found two organizations in the tissues of these animals. First, multi-layers of glia ensheath the ventral cell bodies of the brain and ventral nerve cord, in a manner similar to that of myelin or lamellar ensheathments. Second, matrices of numerous penetrative fibers, or tonofilaments, composed of bundles of ca. 20-nm fibers, are directly connected with the basal parts of epidermal cuticles and run into the diffuse intercellular spaces of the brain neuropils and peripheral nerves. Both types of tissue might be mechanical supportive structures for the neuronal cell bodies. In addition, as a glial function, the multi-layer membranes and the epithelial support cells may be required for physicochemical homeostatic regulation to filter toxic heavy metals and for inhibiting breakdown of glial membrane integrity under strong oxidative stress imposed by hypoxia in the hydrothermal vent environment. Similar functions are known in the well-studied cases of the blood-brain barrier in mammalian brains, including in human stroke.
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Affiliation(s)
- Shuichi Shigeno
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan;
| | - Akihiro Tame
- Marine Works Japan LTD., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan; and
| | - Katsuyuki Uematsu
- Marine Works Japan LTD., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan; and
| | - Tomoyuki Miura
- Faculty of Agriculture, University of Miyazaki, Gakuen-kibanadai-nishi-1-1, Miyazaki 889-2192, Japan
| | - Shinji Tsuchida
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Katsunori Fujikura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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Tsubouchi T, Mori K, Miyamoto N, Fujiwara Y, Kawato M, Shimane Y, Usui K, Tokuda M, Uemura M, Tame A, Uematsu K, Maruyama T, Hatada Y. Aneurinibacillus tyrosinisolvens sp. nov., a tyrosine-dissolving bacterium isolated from organics- and methane-rich seafloor sediment. Int J Syst Evol Microbiol 2015; 65:1999-2005. [PMID: 25813364 DOI: 10.1099/ijs.0.000213] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-positive-staining, strictly aerobic and heterotrophic bacterium, designated strain LL-002T, was isolated from organics- and methane-rich seafloor sediment at a depth of 100 m in Kagoshima Bay, Kagoshima, Japan. Colonies were lustreless and translucent white in colour. The temperature, pH and salt concentration ranges for growth were 10-30 °C, pH 6.0-6.5 and 0-1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain LL-002T belongs to the genus Aneurinibacillus of the family Paenibacillaceae. 16S rRNA gene sequence similarities between strain LL-002T and the type strains of species of the genus Aneurinibacillus were 92.8-95.7 %; the highest sequence identity was with the type strain of Aneurinibacillus migulanus. The DNA G+C content of strain LL-002T was 46.2 mol%. MK-7 was the predominant menaquinone. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and the cell-wall peptidoglycan contained meso-diaminopimelic acid and glutamic acid, glycine and alanine in addition to muramic acid and glucosamine. The peptidoglycan type was A1γ. In DNA-DNA hybridization assays between strain LL-002T and the type strains of the other species of the genus Aneurinibacillus, the level of hybridization was 6.3-30.1 %. On the basis of its biological features and the 16S rRNA gene sequence comparison presented here, strain LL-002T is considered to represent a novel species of the genus Aneurinibacillus, for which the name Aneurinibacillus tyrosinisolvens sp. nov. is proposed; the type strain is LL-002T ( = NBRC 110097T = CECT 8536T).
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Affiliation(s)
- Taishi Tsubouchi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kozue Mori
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Norio Miyamoto
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yoshihiro Fujiwara
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Masaru Kawato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yasuhiro Shimane
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Maki Tokuda
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Moeka Uemura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Section1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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27
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Tsuchiya M, Toyofuku T, Uematsu K, Brüchert V, Collen J, Yamamoto H, Kitazato H. Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera). J Eukaryot Microbiol 2015; 62:454-69. [PMID: 25510528 DOI: 10.1111/jeu.12200] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 11/10/2014] [Accepted: 12/01/2014] [Indexed: 11/30/2022]
Abstract
The benthic foraminifer Virgulinella fragilis Grindell and Collen 1976 has multiple putative symbioses with both bacterial and kleptoplast endobionts, possibly aiding its survival in environments from dysoxia (5-45 μmol-O2 /L) to microxia (0-5 μmol-O2 /L) and in the dark. To clarify the origin and function of V. fragilis endobionts, we used genetic analyses and transmission electron microscope observations. Virgulinella fragilis retained δ-proteobacteria concentrated at its cell periphery just beneath the cell membranes. Unlike another foraminifer Stainforthia spp., which retains many bacterial species, V. fragilis has a less variable bacterial community. This suggests that V. fragilis maintains a specific intracellular bacterial flora. Unlike the endobiotic bacteria, V. fragilis klepto-plasts originated from various diatom species and are found in the interior cytoplasm. We found evidence of both retention and digestion of kleptoplasts, and of fragmentation of the kleptoplastid outer membrane that likely facilitates transport of kleptoplastid products to the host. Accumulations of mitochondria were observed encircling endobiotic bacteria. It is likely that the bacteria use host organic material for carbon oxidation. The mitochondria may use oxygen available around the δ-proteobacteria and synthesize adenosine triphosphate, perhaps for sulfide oxidation.
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Affiliation(s)
- Masashi Tsuchiya
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Takashi Toyofuku
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Katsuyuki Uematsu
- Marine Works Japan, Ltd, 3-54-1 Oppamahigashi-cho, Yokosuka, Kanagawa, 237-0036, Japan
| | - Volker Brüchert
- Department of Geology and Geochemistry, Stockholm University, Svante Arrhenius väg 8C, 10691, Stockholm, Sweden
| | - John Collen
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Hiroyuki Yamamoto
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Hiroshi Kitazato
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
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Tsubouchi T, Koyama S, Mori K, Shimane Y, Usui K, Tokuda M, Tame A, Uematsu K, Maruyama T, Hatada Y. Brevundimonas denitrificans sp. nov., a denitrifying bacterium isolated from deep subseafloor sediment. Int J Syst Evol Microbiol 2014; 64:3709-3716. [DOI: 10.1099/ijs.0.067199-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, heterotrophic, stalked and capsulated bacterium with potential denitrification ability, designated strain TAR-002T, was isolated from deep seafloor sediment in Japan. Colonies lacked lustre, and were viscous and translucent white. The ranges of temperature, pH and salt concentration for growth were 8–30 °C, pH 6.0–10.0 and 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-002T belongs to the genus
Brevundimonas
of the class
Alphaproteobacteria
. Levels of similarity between the 16S rRNA gene sequence of strain TAR-002T and those of the type strains of species of the genus
Brevundimonas
were 93.5–98.9 %; the most closely related species was
Brevundimonas basaltis
. In DNA–DNA hybridization assays between strain TAR-002T and its phylogenetic neighbours,
Brevundimonas lenta
DS-18T,
B. basaltis
J22T,
Brevundimonas subvibrioides
ATCC 15264T and
Brevundimonas alba
DSM 4736T, mean hybridization levels were 6.4–27.7 %. The G+C content of strain TAR-002T was 70.3 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18 : 1ω7c and C16 : 0, and the presence of 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol (DGL) indicates the affiliation of strain TAR-002T with the genus
Brevundimonas
. On the basis of biological characteristics and 16S rRNA gene sequence comparisons, strain TAR-002T is considered to represent a novel species of the genus
Brevundimonas
, for which the name Brevundimonas denitrificans sp. nov. is proposed; the type strain is TAR-002T ( = NBRC 110107T = CECT 8537T).
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Affiliation(s)
- Taishi Tsubouchi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Sumihiro Koyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kozue Mori
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Maki Tokuda
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Section1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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29
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Miyazaki M, Sakai S, Ritalahti KM, Saito Y, Yamanaka Y, Saito Y, Tame A, Uematsu K, Löffler FE, Takai K, Imachi H. Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta. Int J Syst Evol Microbiol 2014; 64:4147-4154. [PMID: 25249566 DOI: 10.1099/ijs.0.068148-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anaerobic, psychrophilic bacterium, strain MO-SPC2(T), was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediments collected from off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. Cells were pleomorphic: spherical, annular, curved rod, helical and coccoid cell morphologies were observed. Motility only occurred in helical cells. Strain MO-SPC2(T) grew at 0-17 °C (optimally at 9 °C), at pH 6.0-8.0 (optimally at pH 6.8-7.2) and in 20-40 g NaCl l(-1) (optimally at 20-30 NaCl l(-1)). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC2(T) were phosphatidylglycolipids, phospholipids and glycolipids. The major cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9. Isoprenoid quinones were not detected. The G+C content of the DNA was 32.3 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-SPC2(T) was affiliated with the genus Sphaerochaeta within the phylum Spirochaetes, and its closest relatives were Sphaerochaeta pleomorpha Grapes(T) (88.4 % sequence identity), Sphaerochaeta globosa Buddy(T) (86.7 %) and Sphaerochaeta coccoides SPN1(T) (85.4 %). Based on phenotypic characteristics and phylogenetic traits, strain MO-SPC2(T) is considered to represent a novel species of the genus Sphaerochaeta, for which the name Sphaerochaeta multiformis sp. nov. is proposed. The type strain is MO-SPC2(T) ( = JCM 17281(T) = DSM 23952(T)). An emended description of the genus Sphaerochaeta is also proposed.
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Affiliation(s)
- Masayuki Miyazaki
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Sanae Sakai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Kirsti M Ritalahti
- Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Yayoi Saito
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.,Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Yuko Yamanaka
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Yumi Saito
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Akihiko Tame
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, Yokosuka, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, Yokosuka, Kanagawa 237-0061, Japan
| | - Frank E Löffler
- Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Ken Takai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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30
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Matsui K, Terada M, Tominaga K, Shigenobu Y, Nishigami T, Uematsu K, Hada T. A case of malignant fibrous histiocytoma on the knee joint in a patient with rheumatoid arthritis. Mod Rheumatol 2014; 11:242-5. [DOI: 10.3109/s101650170012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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31
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Tsubouchi T, Ohta Y, Haga T, Usui K, Shimane Y, Mori K, Tanizaki A, Adachi A, Kobayashi K, Yukawa K, Takagi E, Tame A, Uematsu K, Maruyama T, Hatada Y. Thalassospira alkalitolerans sp. nov. and Thalassospira mesophila sp. nov., isolated from a decaying bamboo sunken in the marine environment, and emended description of the genus Thalassospira. Int J Syst Evol Microbiol 2014; 64:107-115. [DOI: 10.1099/ijs.0.056028-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two marine bacteria, designated strains MBE#61T and MBE#74T, were isolated from a piece of sunken bamboo in the marine environment in Japan. Both of these strains were Gram-stain-negative, but had different cell shapes: MBE#61T was spiral, whereas MBE#74T was rod-shaped. The temperature, pH and salt concentration ranges for growth of strain MBE#61T were 4–38 °C (optimal at 32 °C), pH 4.5–11.0 (optimal at pH 7.0–8.0) and 1–11 % (optimal at 2 %) NaCl, whereas those of strain MBE#74T were 4–36 °C (optimal at 30 °C), pH 4.0–10.5 (optimal at pH 7.0–8.0) and 1–12 % (optimal at 4 %) NaCl. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that both strains belong to the genus
Thalassospira
within the class
Alphaproteobacteria
. Similarity between the 16S rRNA gene sequence of strain MBE#61T and those of the type strains of species of the genus
Thalassospira
was 97.5–99.0 %, and that of strain MBE#74T was 96.9–98.6 %; these two isolates were most closely related to
Thalassospira lucentensis
QMT2T. However, the DNA–DNA hybridization values between
T. lucentensis
QMT2T and strain MBE#61T or MBE#74T were only 16.0 % and 7.1 %, respectively. The DNA G+C content of strain MBE#61T was 54.4 mol%, and that of strain MBE#74T was 55.9 mol%. The predominant isoprenoid quinone of the two strains was Q-10 (MBE#61T, 97.3 %; MBE#74T, 93.5 %). The major cellular fatty acids of strain MBE#61T were C18 : 1ω7c (31.1 %), summed feature 3 comprising C16 : 0ω7c/iso-C15 : 0 2-OH (26.1 %) and C16 : 0 (20.9 %); those of strain MBE#74T were C16 : 0 (26.2 %), C17 : 0 cyclo (19.9 %) and C18 : 1ω7c (12.1 %). On the basis of these results, strain MBE#61T and strain MBE#74T are considered to represent novel species of the genus
Thalassospira
, for which names Thalassospira alkalitolerans sp. nov. and Thalassospira mesophila sp. nov. are proposed. The type strains are MBE#61T ( = JCM 18968T = CECT 8273T) and MBE#74T ( = JCM 18969T = CECT 8274T), respectively. An emended description of the genus
Thalassospira
is also proposed.
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Affiliation(s)
- Taishi Tsubouchi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yukari Ohta
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Takuma Haga
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kozue Mori
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akiko Tanizaki
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akiko Adachi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kiwa Kobayashi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kiyotaka Yukawa
- Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0027, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Emiko Takagi
- Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0027, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Section1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0027, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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32
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Hongo Y, Nakamura Y, Shimamura S, Takaki Y, Uematsu K, Toyofuku T, Hirayama H, Takai K, Nakazawa M, Maruyama T, Yoshida T. Exclusive localization of carbonic anhydrase in bacteriocytes of the deep-sea clam Calyptogena okutanii with thioautotrophic symbiotic bacteria. ACTA ACUST UNITED AC 2013; 216:4403-14. [PMID: 24031050 DOI: 10.1242/jeb.092809] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 11/20/2022]
Abstract
Deep-sea Calyptogena clams harbor thioautotrophic intracellular symbiotic bacteria in their gill epithelial cells. The symbiont fixes CO2 to synthesize organic compounds. Carbonic anhydrase (CA) from the host catalyzes the reaction CO2 + H2O ↔ HCO3(-) + H(+), and is assumed to facilitate inorganic carbon (Ci) uptake and transport to the symbiont. However, the localization of CA in gill tissue remains unknown. We therefore analyzed mRNA sequences, proteins and CA activity in Calyptogena okutanii using expression sequence tag, SDS-PAGE and LC-MS/MS. We found that acetazolamide-sensitive soluble CA was abundantly expressed in the gill tissue of C. okutanii, and the enzyme was purified by affinity chromatography. Mouse monoclonal antibodies against the CA of C. okutanii were used in western blot analysis and immunofluorescence staining of the gill tissues of C. okutanii, which showed that CA was exclusively localized in the symbiont-harboring cells (bacteriocytes) in gill epithelial cells. Western blot analysis and measurement of activity showed that CA was abundantly (26-72% of total soluble protein) detected in the gill tissues of not only Calyptogena clams but also deep-sea Bathymodiolus mussels that harbor thioautotrophic or methanotrophic symbiotic bacteria, but was not detected in a non-symbiotic mussel, Mytilus sp. The present study showed that CA is abundant in the gill tissues of deep-sea symbiotic bivalves and specifically localizes in the cytoplasm of bacteriocytes of C. okutanii. This indicates that the Ci supply process to symbionts in the vacuole (symbiosome) in bacteriocytes is essential for symbiosis.
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Affiliation(s)
- Yuki Hongo
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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33
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Tsubouchi T, Shimane Y, Usui K, Shimamura S, Mori K, Hiraki T, Tame A, Uematsu K, Maruyama T, Hatada Y. Brevundimonas
abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment. Int J Syst Evol Microbiol 2013; 63:1987-1994. [DOI: 10.1099/ijs.0.043364-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, aerobic, psychrotolerant, alkali-tolerant, heterotrophic and dimorphic prosthecate bacterium, designated strain TAR-001T, was isolated from deep-sea floor sediment in Japan. Cells of this strain had a dimorphic life cycle and developed an adhesive stalk at a site not coincident with the centre of the cell pole, and the other type of cell, a swarm cell, had a polar flagellum. Colonies were glossy, viscous and yellowish-white in colour. The temperature, pH and salt concentration range for growth were 2–41 °C, pH 6.5–10.0 and 1–4 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-001T belongs to the family
Caulobacteraceae
of the class
Alphaproteobacteria
, and lies between the genus
Brevundimonas
and the genus
Caulobacter
. Levels of similarity between the 16S rRNA gene sequence of strain TAR-001T and those of the type strains of
Brevundimonas
species were 93.3–95.7 %; highest sequence similarity was with the type strain of
Brevundimonas diminuta
. Levels of sequence similarity between those of the type strains of
Caulobacter
species were 94.9–96.0 %; highest sequence similarity was with the type strain of
Caulobacter mirabilis
. The G+C content of strain TAR-001T was 67.6 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18 : 1ω7c and C16 : 0, and the presence of 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol suggests strain TAR-001T is more closely to the genus
Brevundimonas
than to the genus
Caulobacter
. The mean DNA–DNA hybridization levels between strain TAR-001T and the type strains of two species of the genus
Brevundimonas
were higher than that of the genus
Caulobacter
. On the basis of polyphasic biological features and the 16S rRNA gene sequence comparison presented here, strain TAR-001T is considered to represent a novel species of the genus
Brevundimonas
, for which the name
Brevundimonas
abyssalis sp. nov. is proposed; the type strain is TAR-001T ( = JCM 18150T = CECT 8073T).
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Affiliation(s)
- Taishi Tsubouchi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Shigeru Shimamura
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kozue Mori
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Toshiki Hiraki
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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34
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Tsubouchi T, Shimane Y, Mori K, Usui K, Hiraki T, Tame A, Uematsu K, Maruyama T, Hatada Y. Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment. Int J Syst Evol Microbiol 2013; 63:1972-1981. [DOI: 10.1099/ijs.0.043596-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel filamentous bacterium, designated strain JIR-001T, was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55–73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family
Thermoactinomycetaceae
. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001T belongs to the family
Thermoactinomycetaceae
within the class
Bacilli
. Similarity levels between the 16S rRNA gene sequence of strain JIR-001T and those of the type strains of
Thermoactinomycetaceae
species were 85.5–93.5 %; highest sequence similarity was with
Melghirimyces algeriensis
NariEXT. In the DNA–DNA hybridization assays between strain JIR-001T and its phylogenetic neighbours the mean hybridization levels with
Melghirimyces algeriensis
NariEXT,
Planifilum fimeticola
H0165T,
Planifilum fulgidum
500275T and
Planifilum yunnanense
LA5T were 5.3–7.5, 2.3–4.7, 2.1–4.8 and 2.5–4.9 %, respectively. The DNA G+C content of strain JIR-001T was 55.1 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001T is considered to represent a novel species in a new genus of the family
Thermoactinomycetaceae
, for which the name Polycladomyces abyssicola gen. nov., sp. nov. is proposed. The type strain of Polycladomyces abyssicola is JIR-001T ( = JCM 18147T = CECT 8074T).
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Affiliation(s)
- Taishi Tsubouchi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kozue Mori
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Toshiki Hiraki
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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35
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Tsubouchi T, Shimane Y, Mori K, Miyazaki M, Tame A, Uematsu K, Maruyama T, Hatada Y. Loktanella cinnabarina sp. nov., isolated from a deep subseafloor sediment, and emended description of the genus
Loktanella. Int J Syst Evol Microbiol 2013; 63:1390-1395. [DOI: 10.1099/ijs.0.043174-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, heterotrophic and salt-tolerant bacterium, designated strain LL-001T, was isolated from a deep subseafloor sediment in Japanese waters. Cells were non-motile rods and colonies were smooth, convex, circular and vermilion. The conditions for growth were 15–35 °C, pH 5.5–7.5 and 1–8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain LL-001T belonged to the genus
Loktanella
within the family
Rhodobacteraceae
of the class
Alphaproteobacteria
. 16S rRNA gene sequence similarity between strain LL-001T and members of the genus
Loktanella
was 94.5–98.5 %; the highest sequence similarity was with
Loktanella hongkongensis
UST950701-009PT. DNA–DNA relatedness between strain LL-001T and
L. hongkongensis
UST950701-009PT was 41.5–43.6 %. The DNA G+C content of strain LL-001T was 69.3 mol%. On the basis of biochemical features and 16S rRNA gene sequence comparison, strain LL-001T is considered to represent a novel species of the genus
Loktanella
, for which the name Loktanella cinnabarina sp. nov. is proposed. The type strain is LL-001T ( = JCM 18161T = CECT 8072T). The description of the genus
Loktanella
is also emended.
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Affiliation(s)
- Taishi Tsubouchi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kozue Mori
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Masayuki Miyazaki
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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36
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Kawase T, Uematsu K, Nagata M, Okuda K, Burns D, Yoshie H. Biological and biomechanical characterization of highly self-multilayered human periosteal sheets as an osteogenic grafting material. Cytotherapy 2013. [DOI: 10.1016/j.jcyt.2013.01.174] [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: 11/28/2022]
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37
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Yamaguchi M, Mori Y, Kozuka Y, Okada H, Uematsu K, Tame A, Furukawa H, Maruyama T, Worman CO, Yokoyama K. Prokaryote or eukaryote? A unique microorganism from the deep sea. Microscopy (Oxf) 2012; 61:423-431. [PMID: 23024290 DOI: 10.1093/jmicro/dfs062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
There are only two kinds of organisms on the Earth: prokaryotes and eukaryotes. Although eukaryotes are considered to have evolved from prokaryotes, there were no previously known intermediate forms between them. The differences in their cellular structures are so vast that the problem of how eukaryotes could have evolved from prokaryotes is one of the greatest enigmas in biology. Here, we report a unique organism with cellular structures appearing to have intermediate features between prokaryotes and eukaryotes, which was discovered in the deep sea off the coast of Japan using electron microscopy and structome analysis. The organism was 10 µm long and 3 µm in diameter, having >100 times the volume of Escherichia coli. It had a large 'nucleoid', consisting of naked DNA fibers, with a single nucleoid membrane and endosymbionts that resemble bacteria, but no mitochondria. Because this organism appears to be a life form distinct from both prokaryotes and eukaryotes but similar to eukaryotes, we named this unique microorganism the 'Myojin parakaryote' with the scientific name of Parakaryon myojinensis ('next to (eu)karyote from Myojin') after the discovery location and its intermediate morphology. The existence of this organism is an indication of a potential evolutionary path between prokaryotes and eukaryotes.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
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38
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Yashima M, Tagami N, Taniguchi S, Unemori T, Uematsu K, Mukuda H, Kitaoka Y, Ota Y, Honda F, Settai R, Onuki Y. Possibility of valence-fluctuatsion-mediated superconductivity in Cd-doped CeIrIn(5) probed by In NQR. Phys Rev Lett 2012; 109:117001. [PMID: 23005666 DOI: 10.1103/physrevlett.109.117001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 06/12/2012] [Indexed: 06/01/2023]
Abstract
We report on a pressure-induced evolution of exotic superconductivity and spin correlations in CeIr(In(1-x)Cd(x))(5) by means of in-nuclear-quadrupole-resonance (NQR) studies. Measurements of an NQR spectrum and nuclear-spin-lattice-relaxation rate 1/T(1) have revealed that antiferromagnetism induced by Cd doping emerges locally around Cd dopants, but superconductivity is suddenly induced at T(c)=0.7 and 0.9 K at 2.34 and 2.75 GPa, respectively. The unique superconducting characteristics with a large fraction of the residual density of state at the Fermi level which increases with T(c) differ from those for anisotropic superconductivity mediated by antiferromagnetic correlations. By incorporating the pressure dependence of the NQR frequency pointing to the valence change of Ce, we suggest that unconventional superconductivity in the CeIr(In(1-x)Cd(x))(5) system may be mediated by valence fluctuations.
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Affiliation(s)
- M Yashima
- Department of Materials Engineering Science, Osaka University, Osaka 560-8531, Japan
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39
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Hirayama H, Suzuki Y, Abe M, Miyazaki M, Makita H, Inagaki F, Uematsu K, Takai K. Methylothermus subterraneus sp. nov., a moderately thermophilic methanotroph isolated from a terrestrial subsurface hot aquifer. Int J Syst Evol Microbiol 2011; 61:2646-2653. [DOI: 10.1099/ijs.0.028092-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel methane-oxidizing bacterium, strain HTM55T, was isolated from subsurface hot aquifer water from a Japanese gold mine. Strain HTM55T was a Gram-negative, aerobic, motile, coccoid bacterium with a single polar flagellum and the distinctive intracytoplasmic membrane arrangement of a type I methanotroph. Strain HTM55T was a moderately thermophilic, obligate methanotroph that grew on methane and methanol at 37–65 °C (optimum 55–60 °C). The isolate grew at pH 5.2–7.5 (optimum 5.8–6.3) and with 0–1 % NaCl (optimum 0–0.3 %). The ribulose monophosphate pathway was operative for carbon assimilation. The DNA G+C content was 54.4 mol% and the major fatty acids were C16 : 0 (52.0 %) and C18 : 1ω7c (34.8 %). Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HTM55T was closely related to Methylothermus thermalis MYHTT (99.2 % 16S rRNA gene sequence similarity), which is within the class Gammaproteobacteria. However, DNA–DNA relatedness between strain HTM55T and Methylothermus thermalis MYHTT was ≤39 %. On the basis of distinct phylogenetic, chemotaxonomic and physiological characteristics, strain HTM55T represents a novel species of the genus Methylothermus, for which the name Methylothermus subterraneus sp. nov. is proposed. The type strain is HTM55T ( = JCM 13664T = DSM 19750T).
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Affiliation(s)
- Hisako Hirayama
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Yohey Suzuki
- Institute for Geo-Resources & Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, 305-8567, Japan
| | - Mariko Abe
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Masayuki Miyazaki
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Hiroko Makita
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Monobe B200, Nankoku, Kochi, 783-8502, Japan
| | - Katsuyuki Uematsu
- Department of Technical Services, Marine Works Japan Ltd, 2-16-32 Kamariyahigashi, Kanazawa-ku, Yokohama, 236-0042, Japan
| | - Ken Takai
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
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40
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Sakamoto T, Kousaka S, Uematsu K, Ishigaki T, Toda K, Sato M. Synthesis and properties of Na3
YSi2
O7
:Eu3+
phosphor for fluorescent lamp. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/pssc.201084125] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Yamaguchi M, Namiki Y, Okada H, Uematsu K, Tame A, Maruyama T, Kozuka Y. Improved preservation of fine structure of deep-sea microorganisms by freeze-substitution after glutaraldehyde fixation. J Electron Microsc (Tokyo) 2011; 60:283-287. [PMID: 21571752 DOI: 10.1093/jmicro/dfr032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A method was proposed for improving preservation of ultrastructures of deep-sea microorganisms by using rapid-freeze freeze-substitution after glutaraldehyde fixation. This method produced clear high-resolution images of cells appearing in their natural state, close to the quality of images obtained by rapidly freezing freeze-substituted specimens of living cells. The method may be useful for observing any microorganism when rapid freezing of living samples is difficult and only glutaraldehyde fixation can be carried out.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan.
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42
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Uematsu K, Saika T, Kanbara D, Kobayashi Y, Gobara H, Hiraki T, Mimura H, Kanazawa S, Nasu Y, Kumon H. Percutaneous radiofrequency ablation therapy as a first choice for renal tumor in patients with von Hippel-Lindau disease. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.7_suppl.375] [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: 11/20/2022] Open
Abstract
375 Background: Forty percent of patients with von Hippel-Lindau (VHL) disease have multifocal, bilateral renal cell carcinoma (RCC). The advent of ablative therapy has allowed many of these tumors to be approached percutaneously. Probe-based radiofrequency ablation (RFA) have recently been shown to be feasible nephron-sparing therapies for RCC, and have been proposed as first-line treatments for patients with VHL. We evaluated the feasibility, safety and therapeutic effects of RFA for VHL patients. Methods: We reviewed the outcomes of VHL patients with RCC treated by RFA from 2003 to 2010. Follow-up consisted of serum creatinine measurement, physical examination and serial contrast enhanced computerized tomography or magnetic resonance imaging. Results: The 42 tumors of 15 patients (23-70 years old, median 40) received a total of 43 RFA treatments to a 7 to 28 mm renal tumor (median 16). Seven of the patients had bilateral renal tumors. Tumor enhancement was eliminated and the renal function was preserved after the treatment in all tumors. There were no major complications related to the procedures though eight of small subcapsular hematomas, one of hematuria, one of small urine overflow, and one of nausea were seen after RFA. There was no recurrence after RFA during a mean follow-up period of 28.9 months (range 4.0-89.0, median 20.0 months). The overall recurrence-free survival rate was 100%. There was also a 100% metastasis-free and disease specific survival rate in the cohort. Conclusions: The result of the present study showed percutaneous RFA was a feasible, safe, and promising therapy for the treatment of VHL patients with RCC. No significant financial relationships to disclose.
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Affiliation(s)
- K. Uematsu
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - T. Saika
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - D. Kanbara
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Y. Kobayashi
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - H. Gobara
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - T. Hiraki
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - H. Mimura
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - S. Kanazawa
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Y. Nasu
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - H. Kumon
- Department of Radiology, Okayama University Graduate School of Medicine; Department of Urology, Okayama University Graduate School of Medicine, Okayama, Japan; Department of Radiology, Okayama University Graduate School of Medicine, Okayama, Japan
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Iwamoto Y, Nomura H, Sugiura I, Tsubaki J, Takahashi H, Ishikawa K, Shinohara N, Okumiya M, Yamada Y, Kamiya H, Uematsu K. Direct Observation of Microstructure Change During Densification of Silicon Nitride Ceramics with A Novel Characterization Method. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-287-435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ABSTRACTA novel characterization method is applied to study the evolution of microstructures during densification of silicon nitride ceramics. This characterization method involves an immersion liquid for making green and sintered bodies transparent, and a subsequent direct optical microscopic examination. Granules were prepared with the spray drying processand formed into green bodies by CIP. After sintering at various temperatures, the specimens were examined for microstructural evolution. Large pores were located at the center and boundary regions of granules left in the green bodies; they were not removed by densification and resulted in large pores in the sintered body, possibly forming fracture origin in ceramics.
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Sekiguchi T, Sato T, Enoki M, Kanehiro H, Uematsu K, Kato C. Isolation and characterization of biodegradable plastic degrading bacteria from deep-sea environments. ACTA ACUST UNITED AC 2011. [DOI: 10.5918/jamstecr.11.33] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Reynolds KC, Watanabe H, Strong EE, Sasaki T, Uematsu K, Miyake H, Kojima S, Suzuki Y, Fujikura K, Kim S, Young CM. New molluscan larval form: brooding and development in a hydrothermal vent gastropod, Ifremeria nautilei (Provannidae). Biol Bull 2010; 219:7-11. [PMID: 20813984 DOI: 10.1086/bblv219n1p7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Despite extreme differences between some shallow and deep-sea habitats, the developmental modes and larval forms of deep-sea animals are typically similar to those of their shallow-water relatives. Here we report one of the first documented exceptions to this general rule. The hydrothermal vent snail Ifremeria nautilei displays two novel life-history traits: (1) an unusual uniformly ciliated larva that we here name Warén's larva, and (2) internal brood protection in a modified metapodial pedal gland. Warén's larva emerges from the internal brood pouch as a fully ciliated lecithotrophic larva with a unique external cuticle. The larvae swim with their posterior end forward and metamorphose into typical veliger larvae after 15 days at room temperature. Warén's larva is the only known example of a free-swimming pre-veliger larval stage in the higher gastropods and is the first new gastropod larval form to be described in more than 100 years.
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Affiliation(s)
- Kyle C Reynolds
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing, California 95039, USA.
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Ishimoto Y, Hattori K, Ohgushi H, Uematsu K, Tanikake Y, Tanaka Y, Takakura Y. Spectrocolorimetric evaluation of human articular cartilage. Osteoarthritis Cartilage 2009; 17:1204-8. [PMID: 19328879 DOI: 10.1016/j.joca.2009.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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] [Received: 08/04/2008] [Revised: 01/08/2009] [Accepted: 02/02/2009] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The aim of this study was to investigate whether human articular cartilage can be quantitatively evaluated using a spectrocolorimeter. MATERIALS AND METHODS Human articular cartilage specimens were analyzed using a spectrocolorimeter after macroscopic evaluation using the Outerbridge classification. The cartilage characteristics were examined, the L*, a*, b* colorimetric system, the spectral reflectance distribution and the yellow/red spectral reflectance percentage (Y/R SRP). Moreover, the results of the spectrocolorimetric evaluation were compared with the histological score described by Mankin et al. RESULTS There were significant differences among the macroscopic four grades in the L*, a* and Y/R SRP values. The spectral reflectance distribution of grade 1 cartilage exhibited a gradual increase in the spectral reflectance ratio as the wavelength increased. The spectral reflectance curves of grades 2 to 4 cartilage had dips at a wavelength of around 580 nm. Across all the measured wavelengths, there were lower reflectance ratios with the progression of cartilage degeneration. Moreover, correlations were observed between the spectrocolorimetric values and Mankin score. A strong relationship existed between Mankin score and he Y/R SRP values. CONCLUSIONS The present study is the first to clearly demonstrate the relationship between spectrocolorimetric evaluation and the degeneration of human articular cartilage. The spectrocolorimeter may be a new quantitative evaluation tool for articular cartilage with clinical potential.
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Affiliation(s)
- Y Ishimoto
- Department of Orthopedic Surgery, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
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Nagahama T, Abdel-Wahab MA, Nogi Y, Miyazaki M, Uematsu K, Hamamoto M, Horikoshi K. Dipodascus tetrasporeus sp. nov., an ascosporogenous yeast isolated from deep-sea sediments in the Japan Trench. Int J Syst Evol Microbiol 2008; 58:1040-6. [PMID: 18398216 DOI: 10.1099/ijs.0.65471-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dipodascus tetrasporeus sp. nov. is described as a novel yeast species in the family Dipodascaceae to accommodate an isolate recovered from sediments collected on the deep-sea floor in the north-western Pacific Ocean. In the clade comprising the genera Dipodascus, Galactomyces and Geotrichum, this is the only species that forms asci that bear four ascospores. The ascospore is surrounded by an irregular exosporium wall, similar to what is observed in the genus Galactomyces, but they are released by rupture, which is characteristic of Dipodascus and not Galactomyces. D. tetrasporeus is remarkably divergent (>10 % difference) in its D1/D2 26S rDNA sequence from any other known species. Although maximum-likelihood analysis of combined 18S rDNA and D1/D2 26S rDNA sequences cannot elucidate a reliable position for this species, it was placed among Geotrichum carabidarum, Geotrichum cucujoidarum, Geotrichum fermentans and Geotrichum histeridarum, which also have morphological and physiological affinity with the species. The species is homothallic. The type strain of Dipodascus tetrasporeus sp. nov. is strain SY-277T (=NBRC 103136T =CBS 10071T).
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Affiliation(s)
- Takahiko Nagahama
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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Kuwahara H, Yoshida T, Takaki Y, Shimamura S, Nishi S, Harada M, Matsuyama K, Takishita K, Kawato M, Uematsu K, Fujiwara Y, Sato T, Kato C, Kitagawa M, Kato I, Maruyama T. Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii. Curr Biol 2007; 17:881-6. [PMID: 17493812 DOI: 10.1016/j.cub.2007.04.039] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 04/03/2007] [Accepted: 04/04/2007] [Indexed: 10/23/2022]
Abstract
Although dense animal communities at hydrothermal vents and cold seeps rely on symbioses with chemoautotrophic bacteria [1, 2], knowledge of the mechanisms underlying these chemosynthetic symbioses is still fragmentary because of the difficulty in culturing the symbionts and the hosts in the laboratory. Deep-sea Calyptogena clams harbor thioautotrophic bacterial symbionts in their gill epithelial cells [1, 2]. They have vestigial digestive tracts and nutritionally depend on their symbionts [3], which are vertically transmitted via eggs [4]. To clarify the symbionts' metabolic roles in the symbiosis and adaptations to intracellular conditions, we present the complete genome sequence of the symbiont of Calyptogena okutanii. The genome is a circular chromosome of 1,022,154 bp with 31.6% guanine + cytosine (G + C) content, and is the smallest reported genome in autotrophic bacteria. It encodes 939 protein-coding genes, including those for thioautotrophy and for the syntheses of almost all amino acids and various cofactors. However, transporters for these substances to the host cell are apparently absent. Genes that are unnecessary for an intracellular lifestyle, as well as some essential genes (e.g., ftsZ for cytokinesis), appear to have been lost from the symbiont genome. Reductive evolution of the genome might be ongoing in the vertically transmitted Calyptogena symbionts.
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Affiliation(s)
- Hirokazu Kuwahara
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Yokosuka 237-0061, Japan
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Hirano H, Okimura A, Nakasho K, Nishigami T, Uematsu K, Tamura K. Familial adenomatous polyposis associated with colon carcinoma, desmoid tumour, gallbladder carcinoma, and endometrioid carcinoma: a case report. Histopathology 2004; 45:642-3. [PMID: 15569058 DOI: 10.1111/j.1365-2559.2004.01888.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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