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421 results on '"Tamaki, Hideyuki"'

3. Atrimonas thermophila gen. nov., sp. nov., a novel anaerobic thermophilic bacterium of the phylum Atribacterota isolated from deep subsurface gas field and proposal of Atrimonadaceae fam. nov. within the class Atribacteria in the phylum Atribacterota

Author

Kawamoto, Hiroki, Watanabe, Miho, Mochimaru, Hanako, Nakahara, Nozomi, Meng, Xiang-Ying, Sakamoto, Sachiko, Morinaga, Kana, Katayama, Taiki, Yoshioka, Hideyoshi, Nomura, Nobuhiko, and Tamaki, Hideyuki

Published
2024
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10. Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

Author

Browne, Patrick, Tamaki, Hideyuki, Kyrpides, Nikos, Woyke, Tanja, Goodwin, Lynne, Imachi, Hiroyuki, Bräuer, Suzanna, Yavitt, Joseph B, Liu, Wen-Tso, Zinder, Stephen, and Cadillo-Quiroz, Hinsby

Subjects
Microbiology, Biological Sciences, Environmental Sciences, Human Genome, Genetics, Climate Action, Acclimatization, Adaptation, Physiological, Ecosystem, Genome, Archaeal, Genomics, Methane, Methanomicrobiales, Phylogeny, Soil, Soil Microbiology, Technology, Biological sciences, Environmental sciences
Abstract

Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H2-CO2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H+ rather than Na+ transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na+ and H+ chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.

Published
2017

12. Isolation of an archaeon at the prokaryote–eukaryote interface

Author

Imachi, Hiroyuki, Nobu, Masaru K., Nakahara, Nozomi, Morono, Yuki, Ogawara, Miyuki, Takaki, Yoshihiro, Takano, Yoshinori, Uematsu, Katsuyuki, Ikuta, Tetsuro, Ito, Motoo, Matsui, Yohei, Miyazaki, Masayuki, Murata, Kazuyoshi, Saito, Yumi, Sakai, Sanae, Song, Chihong, Tasumi, Eiji, Yamanaka, Yuko, Yamaguchi, Takashi, Kamagata, Yoichi, Tamaki, Hideyuki, and Takai, Ken

Published
2020
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15. Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge Blanket Reactor

Author

Yamamoto, Kyosuke, Tamaki, Hideyuki, Cadillo-Quiroz, Hinsby, Imachi, Hiroyuki, Kyrpides, Nikos, Woyke, Tanja, Goodwin, Lynne, Zinder, Stephen H, Kamagata, Yoichi, and Liu, Wen-Tso

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Biotechnology
Abstract

Methanoregula formicica SMSP(T) is a mesophilic H2/formate-utilizing methanogenic archaeon and a representative of the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales. Here, we report a 2.8-Mb complete genome sequence of this methanogenic archaeon.

Published
2014

16. Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge

Author

Yamamoto, Kyosuke, Tamaki, Hideyuki, Cadillo-Quiroz, Hinsby, Imachi, Hiroyuki, Kyrpides, Nikos, Woyke, Tanja, Goodwin, Lynne, Zinder, Stephen H, Kamagata, Yoichi, and Liu, Wen-Tso

Subjects
Microbiology, Biological Sciences, Genetics, Biotechnology, Human Genome
Abstract

Here, we report a 2.0-Mb complete genome sequence of Methanolinea tarda NOBI-1(T), a methanogenic archaeon isolated from an anaerobic digested sludge. This is the first genome report of the genus Methanolinea isolate belonging to the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales.

Published
2014

17. Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph

Author

Nobu, Masaru K, Narihiro, Takashi, Tamaki, Hideyuki, Qiu, Yan-Ling, Sekiguchi, Yuji, Woyke, Tanja, Goodwin, Lynne, Davenport, Karen W, Kamagata, Yoichi, and Liu, Wen-Tso

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Biotechnology
Abstract

Syntrophorhabdus aromaticivorans strain UI is a mesophilic bacterium capable of degrading aromatic substrates in syntrophic cooperation with a partner methanogen. The draft genome sequence is 3.7 Mb, with a G+C content of 52.0%.

Published
2014

26. Spontaneous Cell Lysis by Pelomonas saccharophila MRB3 Provides Plant-Available Macronutrients in Hydroponic Growth Media and Accelerates Biomass Production of Duckweed

Author

Ishizawa, Hidehiro, primary, Kaji, Yukiko, additional, Shimizu, Yuki, additional, Kuroda, Masashi, additional, Inoue, Daisuke, additional, Makino, Ayaka, additional, Nakai, Ryosuke, additional, Tamaki, Hideyuki, additional, Morikawa, Masaaki, additional, and Ike, Michihiko, additional

Published
2023
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28. Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae

Author

Morinaga, Kana, primary, Kusada, Hiroyuki, additional, Sakamoto, Sachiko, additional, Murakami, Takumi, additional, Toyoda, Atsushi, additional, Mori, Hiroshi, additional, Meng, Xian-Ying, additional, Takashino, Motoko, additional, Murotomi, Kazutoshi, additional, and Tamaki, Hideyuki, additional

Published
2022
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29. Unique H2-utilizing lithotrophy in serpentinite-hosted systems

Author

Nobu, Masaru Konishi, primary, Nakai, Ryosuke, additional, Tamazawa, Satoshi, additional, Mori, Hiroshi, additional, Toyoda, Atsushi, additional, Ijiri, Akira, additional, Suzuki, Shino, additional, Kurokawa, Ken, additional, Kamagata, Yoichi, additional, and Tamaki, Hideyuki, additional

Published
2022
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33. Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes

Author

40823745, 50270723, Okazaki, Yusuke, Nakano, Shin-ichi, Toyoda, Atsushi, Tamaki, Hideyuki, 40823745, 50270723, Okazaki, Yusuke, Nakano, Shin-ichi, Toyoda, Atsushi, and Tamaki, Hideyuki

Abstract

Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101, 781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck.

Published
2022

35. The origin of methane in serpentinite-hosted hyperalkaline hot spring at Hakuba Happo, Japan: Radiocarbon, methane isotopologue and noble gas isotope approaches

Author

Suda, Konomi, primary, Aze, Takahiro, additional, Miyairi, Yosuke, additional, Yokoyama, Yusuke, additional, Matsui, Yohei, additional, Ueda, Hisahiro, additional, Saito, Takuya, additional, Sato, Tomohiko, additional, Sawaki, Yusuke, additional, Nakai, Ryosuke, additional, Tamaki, Hideyuki, additional, Takahashi, Hiroshi A., additional, Morikawa, Noritoshi, additional, and Ono, Shuhei, additional

Published
2022
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37. Complete Genome Sequence of Luteitalea sp. Strain TBR-22

Author

Yamamoto, Kyosuke, primary, Yoneda, Yasuko, additional, Makino, Ayaka, additional, Tanaka, Yasuhiro, additional, Meng, Xian-Ying, additional, Hashimoto, Junko, additional, Shin-ya, Kazuo, additional, Satoh, Noriyuki, additional, Fujie, Manabu, additional, Toyama, Tadashi, additional, Mori, Kazuhiro, additional, Ike, Michihiko, additional, Morikawa, Masaaki, additional, Kamagata, Yoichi, additional, and Tamaki, Hideyuki, additional

Published
2022
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39. Draft Genome Sequence of Bryobacteraceae Strain F-183

Author

Yamamoto, Kyosuke, primary, Yoneda, Yasuko, additional, Makino, Ayaka, additional, Tanaka, Yasuhiro, additional, Meng, Xian-Ying, additional, Hashimoto, Junko, additional, Shin-ya, Kazuo, additional, Satoh, Noriyuki, additional, Fujie, Manabu, additional, Toyama, Tadashi, additional, Mori, Kazuhiro, additional, Ike, Michihiko, additional, Morikawa, Masaaki, additional, Kamagata, Yoichi, additional, and Tamaki, Hideyuki, additional

Published
2022
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41. Elioraea tepida, sp. nov., a Moderately Thermophilic Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Mat Community of an Alkaline Siliceous Hot Spring in Yellowstone National Park, WY, USA

Author

Saini, Mohit Kumar, primary, Yoshida, Shohei, additional, Sebastian, Aswathy, additional, Hara, Eri, additional, Tamaki, Hideyuki, additional, Soulier, Nathan T., additional, Albert, Istvan, additional, Hanada, Satoshi, additional, Tank, Marcus, additional, and Bryant, Donald A., additional

Published
2021
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47. Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Author

40823745, 50270723, Okazaki, Yusuke, Fujinaga, Shohei, Salcher, Michaela M., Callieri, Cristiana, Tanaka, Atsushi, Kohzu, Ayato, Oyagi, Hideo, Tamaki, Hideyuki, Nakano, Shin-ichi, 40823745, 50270723, Okazaki, Yusuke, Fujinaga, Shohei, Salcher, Michaela M., Callieri, Cristiana, Tanaka, Atsushi, Kohzu, Ayato, Oyagi, Hideo, Tamaki, Hideyuki, and Nakano, Shin-ichi

Abstract

[Background] Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. [Results] Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. [Conclusions] Our novel ap

Published
2021

50. Pantothenate kinase from the Thermoacidophilic archaeon Picrophilus torridus

Author

Takagi, Masakazu, Tamaki, Hideyuki, Miyamoto, Yukiko, Leonardi, Roberta, Hanada, Satoshi, Jackowski, Suzanne, and Chohnan, Shigeru

Subjects
Pantothenic acid -- Research, Bacteria, Thermophilic -- Genetic aspects, Bacteria, Thermophilic -- Research, Coenzymes -- Research, Biological sciences
Abstract

Pantothenate kinase (CoaA) catalyzes the first step of the eoenzyme A (CoA) biosynthetic pathway and controls the intracellular concentrations of CoA through feedback inhibition in bacteria. An alternative enzyme found in archaea, pantoate kinase, is missing in the order Thermoplasmatales. The PTO0232 gene from Picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type I CoaA. The cloned gene clearly complements the poor growth of the temperature-sensitive Escherichia coli CoaA mutant strain ts9, and the recombinant protein expressed in E. coli cells transfers phosphate to pantothenate at pH 5 and 55 [degrees]C. In contrast to E. coli CoaA, the P. torridus enzyme is refractory to feedback regulation by CoA, indicating that in P. torridus cells the CoA levels are not regulated by the CoaA step. These data suggest the existence of two subtypes within the class of prokaryotic type I CoaAs. doi: 10.1128/JB.01021-09

Published
2010

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