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Yuya Tsukamoto

Section

Graduate School of Science

Job title

Assistant Professor

Degree

researchmap

https://researchmap.jp/yuyatsukamoto

J-GLOBAL ID

202101015806870081

e-Rad No.

70890458

ORCID

https://orcid.org/0000-0002-1980-3423

Research History 3

2025/11 - Present

Tohoku University　Graduate School of Science Department of Earth Science　Assistant Professor
2023/04 - 2025/10

RIKEN
2020/04 - 2023/03

The University of Tokyo　Atmosphere and Ocean Research Institute　Project Resercher

Education 1

Tohoku University　Graduate School of Science　Department of Earth Science

2017/04 - 2020/03

Professional Memberships 2

日本地球惑星科学連合

2015/04 - Present
日本地球化学会

Research Interests 3

金属酸化菌
初期地球
極限環境微生物

Research Areas 3

Natural sciences / Solid earth science /
Natural sciences / Solid earth science /
Natural sciences / Biogeoscience /

Awards 1

Light-driven Proton Pumps as a Potential Regulator for Carbon Fixation in Marine Diatoms

2023/10

Papers 14

Draft genome sequence of Rosettibacter sp. KY25 isolated from a terrestrial hot spring, Japan Peer-reviewed

Shigeru Kawai, Yuya Tsukamoto, Yusuke Tsukatani, Yuu Hirose, Arisa Nishihara

Microbiology Resource Announcements　2026/03/17
Publisher: American Society for Microbiology
DOI： 10.1128/mra.01464-25 　

eISSN： 2576-098X

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ABSTRACT We report here the draft genome sequence of a thermophilic heterotrophic bacterium, Rosettibacter sp. strain KY25, isolated from hot spring-associated microbial mats in Japan. The genome of KY25 is 3,177,379 bp in length and contains 2,668 predicted coding sequences, which include genes required for aerobic respiration, nitrate reduction, and sugar utilization.
Caldiplasma sukawensis gen. nov., sp. nov., and Cuniculiplasma thermophilum sp. nov., mesophilic, acidophilic, cell–wall–less, archaea of the order Thermoplasmatales, isolated from extremely acidic hot spring Peer-reviewed

Yuya Tsukamoto, Hiroyuki D. Sakai, Yoshinori Takano, Toshiki Koga, Arisa Nishihara, Shigeru Kawai, Susumu Yoshizawa, Moriya Ohkuma

Systematic and Applied Microbiology　126686-126686　2025/12
Publisher: Elsevier BV
DOI： 10.1016/j.syapm.2025.126686 　

ISSN： 0723-2020
Seasonal variation in bacterial community composition in the brackish meromictic Lake Suigetsu Peer-reviewed

Takafumi Kataoka, Yuki Sato-Takabe., Yunosuke Nakamura, Takuhei Shiozaki, Yuya Tsukamoto, Satoshi Hanada

Antonie van Leeuwenhoek　119　(1)　2025/11/21
Publisher: Springer Science and Business Media LLC
DOI： 10.1007/s10482-025-02212-7 　

ISSN： 0003-6072

eISSN： 1572-9699
Phosphate behavior during submarine hydrothermal alteration of ca. 3.455 Ga basaltic seafloor rocks from Pilbara, Western Australia Peer-reviewed

Yuya Tsukamoto, Takeshi Kakegawa

Geochimica et Cosmochimica Acta　2025/10

DOI： 10.1016/j.gca.2025.06.013 　
Oceaniferula spumae sp. nov., a novel Verrucomicrobiota bacterium, isolated from sea foam at Noto Peninsula, Ishikawa, Japan Peer-reviewed

Can Huang, Chunqi Jiang, Yuki Sato-Takabe, Yoko Makabe-Kobayashi, Yuya Tsukamoto, Susumu Yoshizawa, Koji Hamasaki

International Journal of Systematic and Evolutionary Microbiology　75　(7)　2025/07/07
Publisher: Microbiology Society
DOI： 10.1099/ijsem.0.006828 　

ISSN： 1466-5026

eISSN： 1466-5034

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A Gram-stain-negative, aerobic, rod-shaped bacterium, designated as NT6N^T, was isolated from sea foam collected at the Maura Coast of the Noto Peninsula, Ishikawa, Japan. Strain NT6N^T was able to grow optimally at pH 7.8, 25–30 °C with 3.5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NT6N^T belonged to the genus Oceaniferula of the family Verrucomicrobiaceae and was most closely related to Oceaniferula flava corrig. 5K15^T (98.3%) and Oceaniferula marina N1E253^T (95.7%). Furthermore, in silico average nt identity values between strain NT6N^T and its closest related species, O. flava 5K15^T and O. marina N1E253^T, were 76.2% and 70.5%, respectively. The digital DNA–DNA hybridization values for the two comparisons were 20.2% and 19.6%, respectively. The chemotaxonomic characteristics showed that strain NT6N^T had MK-9 and MK-8 as its main components of menaquinone and the main cellular fatty acids were iso-C_14 : 0, anteiso-C_15 : 0, iso-C_16 : 0 and iso-C_12 : 0. The major polar lipids of strain NT6N^T comprised phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The genome of strain NT6N^T had a length of 4.65 Mbp with 52.1 mol% G+C content, containing 3,914 protein-coding genes and 68 RNA genes. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain NT6N^T represents a novel species within the genus Oceaniferula, for which the name Oceaniferula spumae sp. nov. is proposed. The type strain is NT6N^T (=JCM 36658^T=DSM 117338^T=MCCC 1K09726^T).
Changes in microbial community structure related to biodegradation of eelgrass (Zostera marina) Peer-reviewed

Md Mehedi Iqbal, Masahiko Nishimura, Yuya Tsukamoto, Susumu Yoshizawa

Science of The Total Environment　172798-172798　2024/04
Publisher: Elsevier BV
DOI： 10.1016/j.scitotenv.2024.172798 　

ISSN： 0048-9697
Draft genome sequences of three rhodopsin possessing Croceitalea sp. strains, isolated from the sea surface microlayer in Japan. International-journal Peer-reviewed

Mako Takada, Chunqi Jiang, Youta Sugai, Masumi Hasegawa-Takano, Takayoshi Fujiwara, Yuya Tsukamoto, Yu Nakajima, Yosuke Nishimura, Susumu Yoshizawa

Microbiology resource announcements　e0003824　2024/02/16

DOI： 10.1128/mra.00038-24 　

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Here, we present the draft genome sequences of three Croceitalea sp. strains containing microbial rhodopsins, isolated from the Japanese coastal sea surface microlayer, which is exposed to intense sunlight. This study will contribute to the understanding of the genus Croceitalea and the diversity of microbial rhodopsins.
Phototrophy by antenna-containing rhodopsin pumps in aquatic environments Peer-reviewed

Ariel Chazan, Ishita Das, Takayoshi Fujiwara, Shunya Murakoshi, Andrey Rozenberg, Ana Molina-Márquez, Fumiya K. Sano, Tatsuki Tanaka, Patricia Gómez-Villegas, Shirley Larom, Alina Pushkarev, Partha Malakar, Masumi Hasegawa, Yuya Tsukamoto, Tomohiro Ishizuka, Masae Konno, Takashi Nagata, Yosuke Mizuno, Kota Katayama, Rei Abe-Yoshizumi, Sanford Ruhman, Keiichi Inoue, Hideki Kandori, Rosa León, Wataru Shihoya, Susumu Yoshizawa, Mordechai Sheves, Osamu Nureki, Oded Béjà

Nature　615　(7952)　535-540　2023/03/01
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41586-023-05774-6 　

ISSN： 0028-0836

eISSN： 1476-4687
Light-driven Proton Pumps as a Potential Regulator for Carbon Fixation in Marine Diatoms Peer-reviewed

Susumu Yoshizawa, Tomonori Azuma, Keiichi Kojima, Keisuke Inomura, Masumi Hasegawa, Yosuke Nishimura, Masuzu Kikuchi, Gabrielle Armin, Yuya Tsukamoto, Hideaki Miyashita, Kentaro Ifuku, Takashi Yamano, Adrian Marchetti, Hideya Fukuzawa, Yuki Sudo, Ryoma Kamikawa

Microbes and Environments　38　(2)　n/a-n/a　2023
Publisher: Japanese Society of Microbial Ecology
DOI： 10.1264/jsme2.me23015 　

ISSN： 1342-6311

eISSN： 1347-4405
Mineralogical and Genomic Constraints on the Origin of Microbial Mn Oxide Formation in Complexed Microbial Community at the Terrestrial Hot Spring Peer-reviewed

Yuya Tsukamoto, Takeshi Kakegawa

Life　12　(6)　816-816　2022/05/30
Publisher: {MDPI} {AG}
DOI： 10.3390/life12060816 　

ISSN： 2075-1729

eISSN： 2075-1729

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Manganese (Mn) oxides are widespread on the surface environments of the modern Earth. The role of microbial activities in the formation of Mn oxides has been discussed for several decades. However, the mechanisms of microbial Mn oxidation, and its role in complex microbial communities in natural environments, remain uncertain. Here, we report the geochemical, mineralogical, and metagenomic evidence for biogenic Mn oxides, found in Japanese hot spring sinters. The low crystallinity of Mn oxides, and their spatial associations with organic matter, support the biogenic origin of Mn oxides. Specific multicopper oxidases (MCOs), which are considered Mn-oxidizing enzymes, were identified using metagenomic analyses. Nanoscale nuggets of copper sulfides were, also, discovered in the organic matter in Mn-rich sinters. A part of these copper sulfides most likely represents traces of MCOs, and this is the first report of traces of Mn-oxidizing enzyme in geological samples. Metagenomic analyses, surprisingly, indicated a close association of Mn oxides, not only in aerobic but also in anaerobic microbial communities. These new findings offer the unique and unified positions of Mn oxides, with roles that have not been ignored, to sustain anaerobic microbial communities in hot spring environments.
Draft Genome Sequence of the Aerobic Anoxygenic Phototrophic Bacterium Roseobacter sp. Strain OBYS 0001, Isolated from Coastal Seawater in Otsuchi Bay, Japan Peer-reviewed

Yuki Sato-Takabe, Yu Nakajima, Yuya Tsukamoto, Koji Hamasaki, Takuhei Shiozaki

Microbiology Resource Announcements　10　(28)　2021/07/15
Publisher: American Society for Microbiology
DOI： 10.1128/mra.00488-21 　

eISSN： 2576-098X

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Here, we report the draft genome sequence of the aerobic anoxygenic phototrophic bacterium <italic>Roseobacter</italic> sp. strain OBYS 0001, isolated from coastal seawater in Ostuchi Bay, Japan. This genome sequence could be useful for our understanding of the variation in photosynthesis-related genes among aerobic anoxygenic phototrophs.
Biochemical properties of CumA multicopper oxidase from plant pathogen, Pseudomonas syringae Peer-reviewed

Konan Ishida, Yuya Tsukamoto, Masaki Horitani, Tomohisa Ogawa, Yoshikazu Tanaka

Bioscience, Biotechnology, and Biochemistry　85　(9)　1995-2002　2021/07/09
Publisher: Oxford University Press (OUP)
DOI： 10.1093/bbb/zbab123 　

eISSN： 1347-6947

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<title>Abstract</title> Multicopper oxidases have a wide range of substrate specificity to be involved in various physiological reactions. Pseudomonas syringae, a plant pathogenic bacterium, has a multicopper oxidase, CumA. Multicopper oxidases have ability to degrade plant cell wall component, lignin. Once P. syringae enter apoplast and colonize, they start to disrupt plant immunity. Therefore, deeper understanding of multicopper oxidases from plant pathogens, help to invent measures to prevent invasion into plant cell, which bring agricultural benefits. Several biochemical studies have reported lower activity of CumA compared with other multicopper oxidase called CotA. However, the mechanisms underlying the difference in activity have not yet been revealed. In order to acquire insight into them, we conducted a biophysical characterization of PsCumA. Our results show that PsCumA has weak type I copper EPR signal, which is essential for oxidation activity. We propose that difference in the coordination of copper ions may decrease reaction frequency.
Discovery of a 3.46 billion-year-old impact crater in Western Australia

Hiroshi Ohmoto, Uschi Graham, Zi-Kui Liu, Yuya Tsukamoto, Yumiko Watanabe, Hiroshi Hamasaki, Andrew Chorney

2021/01/16
Publisher: Wiley
DOI： 10.1002/essoar.10505838.1 　
Geochemical and mineralogical studies of ca.12 Ma hydrothermal manganese-rich rocks in the Hokuroku district in Japan Peer-reviewed

Yuya Tsukamoto, Kenta Nonaka, Akizumi Ishida, Takeshi Kakegawa

Ore Geology Reviews　121　103539-103539　2020/06

DOI： 10.1016/j.oregeorev.2020.103539 　

ISSN： 0169-1368

eISSN： 1872-7360

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Presentations 15

嫌気性マンガン酸化菌群の培養化と生理代謝機能予測

塚本雄也, 福士圭介, 清水美智留, 大熊盛也, 吉澤晋

第72回日本地球化学会　2025/09/17
Behavior of phosphate during the submarine hydrothermal alteration of ca. 3.455 Ga Apex Basalt, Australia

Yuya Tsukamoto, Takeshi Kakegawa

2025/07/10
比較メタゲノム解析により明らかにする鉄温泉の微生物系統・機能遺伝子の特徴

塚本雄也, 大熊盛也, 吉澤晋

第71回日本地球化学会　2024/09/20
太古代海底熱水活動による玄武岩質海洋地殻内でのリンの挙動とリン供給源としての重要性

塚本雄也, 掛川武

第71回日本地球化学会　2024/09/18
マンガン酸化に着目した地球微生物学的研究の重要性 Invited

塚本雄也

第70回日本地球化学会　2023/09/23
リン供給源としての初期地球・海底熱水活動の重要性と微生物生態系への作用 Invited

塚本雄也

第2回リンと生命の起源研究会　2023/09/12
Phosphate leaching from Archean basaltic oceanic crust by unique submarine hydrothermal processes Invited

塚本雄也, 掛川武

日本地球惑星科学連合大会　2023/05/25
Phylogenic and functional diversity of microbial ecosystems based on iron-oxidizing chemolithoautotroph

塚本雄也, 吉澤晋

日本地球惑星科学連合大会　2023/05/23
再構築ゲノム情報に基づく貧酸素環境下で独立栄養なマンガン酸化菌群の培養化

塚本雄也, 高見英人, 吉澤晋

第17回日本ゲノム微生物学会　2023/03/08
鉱物学・分子生物学的研究に基づく陸上温泉に産するマンガン酸化物の起源の制約

塚本雄也, 掛川武

日本地球化学会　2022/09/07
Mechanisms of Mn oxidation by Mn-oxidizing bacteria in Fe- and CO2-rich hot spring in Japa

塚本雄也, 掛川武

日本地球化学会年会　2020/11
Phosphate Flux from Oceanic Crust to the Archean Oceans: Evidence from the 3.46 Ga Apex Basalt

Tsukamoto, Y, Kakegawa, T, Graham, U, Liu, Z, Ito, A, Ohmoto, H

Goldschmidt Conference　2019/08
Significances of 12 Ma manganese ores in the Hokuroku district, Akita: unique Mn accumulation and interaction with organic matter during submarine hydrothermal activities

塚本雄也, 掛川武

日本地球惑星連合大会　2019/05
Discovery of Ni-Fe phosphides in the 3.46 Ga-old Apex Basalt: Implications on the phosphate budget of the Archean oceans

Tsukamoto, Y, Kakegawa, T, Graham, U, Liu, Z, Ito, A, Ohmoto, H

Goldschmidt Conference　2018/07
Origin and Significance of Neogene Manganese Ores in the Hokuroku District, Japan

Goldschmidt Conference　2017/05

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Research Projects 8

独自培養株で解く鉱物が創る元素濃集場の役割

塚本雄也

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 若手研究

2026/04 - 2029/03
難培養性アーキアの培養で紐解くアーキア進化史

Offer Organization: 公益財団法人クリタ水・環境科学振興財団

2025/10 - 2026/09
新規な始原的嫌気性鉄酸化菌の培養化による初期地球-鉄代謝生命圏の再検証

塚本雄也

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 特別研究員奨励費

Institution: 国立研究開発法人理化学研究所

2023/04 - 2026/03
鉄温泉から培養化した化学合成独立栄養細菌から初期生命像を探る

塚本雄也

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 若手研究

Institution: 東京大学

2023/04 - 2026/03
独自の培養化戦略により解き明かす原始的鉄酸化菌の生き様

Offer Organization: 公益財団法人クリタ水・環境科学振興財団

2022/10 - 2023/09
初期地球模擬環境におけるマンガン酸化の多様性-酸素発⽣型光合成の出現時期の解明に向けて-

Offer Organization: 公益財団法人日本科学協会

System: 笹川科学研究助成

2021/04 - 2022/03
太古代生命圏の再検証：生体必須元素に着目して

塚本雄也

Offer Organization: 日本学術振興会

System: 科学研究費助成事業特別研究員奨励費

Category: 特別研究員奨励費

Institution: 東北大学

2019/04 - 2021/03

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地球生命の進化を考える上で、地球表層環境における生体必須元素の挙動を理解することは必須である。この中にはリンとマンガンのように海洋や大気ではなく岩石に多く保存されているものがあり、これらの元素の岩石から海洋、そして生命圏までの挙動はほとんど理解されていない。そこで本研究は現世と太古代における海底熱水活動に伴うマンガンとリンの挙動について理解することを目的とした。まず、秋田県北鹿地域に産する1200万年前に形成したマンガン酸化物の成因と微生物の形成に対する関与を理解するために、地質調査と採取した岩石サンプルからマンガン鉱物の種類や化学組成などを走査型電子顕微鏡やラマン分光分析を用いて明らかにした。またマンガン酸化物と炭素からなるコロフォーム構造を発見した。これは過去に報告例がなく、透過型電子顕微鏡によるナノスケールの観察結果などから、マンガンをエネルギー源とする微生物マットの痕跡であると結論づけた。これらの成果はOre Geology Reviews誌にて報告した。次に西オーストラリア・ピルバラで見られる34.6億年前ごろに形成したApex Basaltを調査した。Apex Basaltは当時の海洋底を構成していた玄武岩であるとともに、同時期に起こった海底熱水活動の影響を受けている。今回は形成後の変質や風化の影響の少ないドリルコア(ABDP#1)を用いて、リンとマンガンの元素濃度プロファイルや鉱物観察を踏まえて海底熱水活動に伴う両元素の挙動を研究した。その結果、リンとマンガン濃度の減少と熱水変質の度合いは相関していることがわかった。また鉱物種の変化もこの結果を支持した。本研究で初めて、当時の海底熱水活動がマンガン・リンの供給源となりうることを明らかにした。本研究によって、海底熱水活動に伴うマンガンとリンの岩石から海洋、そして生命圏への挙動を明らかにした。
化石DNA解析による1200万年前海底熱水系微生物のMn酸化酵素の復元:未知酵素の発見に向けて

Offer Organization: 公益財団法人日本科学協会

System: 笹川科学研究助成

2018/04 - 2019/03

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