Metagenomic analysis of microorganisms in an ancient ice core

• Project/Area Number: 17H01854
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Environmental dynamic analysis
• Research Institution: University of Yamanashi
• Principal Investigator: SEGAWA Takahiro 山梨大学, 大学院総合研究部, 特任助教 (90425835)
• Co-Investigator(Kenkyū-buntansha): 竹内 望 千葉大学, 大学院理学研究院, 教授 (30353452) ; 森 宙史 国立遺伝学研究所, 情報研究系, 助教 (40610837) ; 米澤 隆弘 東京農業大学, 農学部, 准教授 (90508566)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000); Fiscal Year 2019: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000); Fiscal Year 2018: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2017: ¥10,920,000 (Direct Cost: ¥8,400,000、Indirect Cost: ¥2,520,000)
• Keywords: アイスコア / 古代DNA / メタゲノム / 微生物 / 環境変動 / ゲノム / 遺伝子

Outline of Final Research Achievements

Ice cores drilled from glaciers can provide a means of direct analysis of microbes that grew in the past. We directly estimated bacterial mutation rates based on ancient DNA analyses of ice core samples that dates back to 12, 500 cal years before present. The mutation rate of bacterial ITS region was estimated by comparing ancient and modern populations. Bayesian demographic analysis revealed that bacterial population sizes increased during the Holocene. In addition, to understand the mechanism by which snow microorganisms form geographically specific population structures and how they migrate across the global cryosphere, here we study samples from glaciers and ice core samples. Our results enhance understanding of the enigmatic time scale of microevolution, which has the potential to elucidate environmental responses of microorganisms to the drastic climatic change events of the Quaternary.

Academic Significance and Societal Importance of the Research Achievements

古い年代のＤＮＡを解析することは，過去の地球環境を推定するうえで非常に重要な情報を提供するため，寒冷環境から採取された古代試料からのＤＮＡ解析は近年非常に注目されている．そういった中でも本研究は，アイスコア試料に封じ込められた古代試料からの遺伝子情報を年代順に解析し，環境変動との関連性や分子進化を解析した独創的なものであり，こうした前例の乏しい研究を世界に先駆けて遂行し，成果を上げることは，日本の極域研究と環境ゲノム研究の発展のためにも重要である．

Research Products

• [Int'l Joint Research] Natural History Museum of Denmark(デンマーク)
• [Int'l Joint Research] Natural History Museum of Denmark(デンマーク)
• [Int'l Joint Research] Natural History Museum of Denmark(Denmark)
• [Journal Article] Evaluation of reported sediment samples from 20 Ma using a molecular phylogenetic approach: comment on Liu et al. (2017) (2020)
  • Author(s): Takahiro Segawa and Takahiro Yonezawa
  • Journal Title: Environmental Microbiology Volume: 22 Issue: 3 Pages: 813-818
  • DOI: 10.1111/1462-2920.14923
  • Peer Reviewed
• [Journal Article] Variations in Albedo and its Relationship with Surface Dust at Urumqi Glacier No. 1 in Tien Shan, China (2020)
  • Author(s): Yue, X., Li, Z., Zhao, J., Fan, J., Takeuchi, N., Wang, L.
  • Journal Title: Frontiers in Earth Science Volume: 8 Pages: 110-110
  • DOI: 10.3389/feart.2020.00110
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Subglacial water pressure and ice-speed variations at Johnsons Glacier, Livingston Island, Antarctic Peninsula (2019)
  • Author(s): SUGIYAMA SHIN、NAVARRO FRANCISCO J.、SAWAGAKI TAKANOBU、MINOWA MASAHIRO、SEGAWA TAKAHIRO、ONUMA YUKIHIKO、OTERO JAIME、VASILENKO EVGENY V.
  • Journal Title: Journal of Glaciology Volume: 65 Issue: 252 Pages: 689-699
  • DOI: 10.1017/jog.2019.45
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Annual layer counting using pollen grains of the Grigoriev ice core from the Tien Shan Mountains, central Asia (2019)
  • Author(s): Takeuchi Nozomu、Sera Shuntaro、Fujita Koji、Aizen Vladimir B.、Kubota Jumpei
  • Journal Title: Arctic, Antarctic, and Alpine Research Volume: 51 Issue: 1 Pages: 299-312
  • DOI: 10.1080/15230430.2019.1638202
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Bacterial community changes with granule size in cryoconite and their susceptibility to exogenous nutrients on NW Greenland glaciers (2019)
  • Author(s): Uetake Jun、Nagatsuka Naoko、Onuma Yukihiko、Takeuchi Nozomu、Motoyama Hideaki、Aoki Teruo
  • Journal Title: FEMS Microbiology Ecology Volume: 95 Issue: 7 Pages: 1-8
  • DOI: 10.1093/femsec/fiz075
  • Peer Reviewed / Open Access
• [Journal Article] Variations in phototroph communities on the ablating bare-ice surface of glaciers on Br_ggerhalv_ya, Svalbard (2019)
  • Author(s): Takeuchi, N., Tanaka, S., Konno, Y., Irvine-Fynn, T.D.L., Rassner, S.M.E. and Edwards, A.
  • Journal Title: Frontiers in Earth Science Volume: 7 Pages: 4-4
  • DOI: 10.3389/feart.2019.00004
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior (2019)
  • Author(s): Takahiro Segawa, Satoshi Fukuchi, Dylan Bodington, Sayaka Tsuchida, Pierre Philippe Mbehang Nguema, Hiroshi Mori and Kazunari Ushida
  • Journal Title: microorganisms Volume: 7(4) Issue: 4 Pages: 99-99
  • DOI: 10.3390/microorganisms7040099
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Draft genome sequence of Clostridium tagluense strain A121T, isolated from a permafrost core in the Canadian high Arctic. (2019)
  • Author(s): Murakami T, Mori H, Shcherbakova VA, Yoshimura Y, Segawa T.
  • Journal Title: Microbiol Resour Announc. Volume: 8 Issue: 5
  • DOI: 10.1128/mra.01630-18
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Taxonomic re-examination of “Chloromonas nivalis (Volvocales, Chlorophyceae) zygotes” from Japan and description of C. muramotoi sp. nov. (2019)
  • Author(s): Matsuzaki, R., Nozaki, H., Takeuchi, N., Hara, Y., Kawachi, M.
  • Journal Title: PROS ONE Volume: 14 Issue: 1 Pages: e0210986-e0210986
  • DOI: 10.1371/journal.pone.0210986
  • Peer Reviewed / Open Access
• [Journal Article] Latent environment allocation of microbial community data (2018)
  • Author(s): Higashi K, Suzuki S, Kurosawa S, Mori H, Kurokawa K.
  • Journal Title: PLoS Comput Biol. Volume: 14 Issue: 6 Pages: e1006143-e1006143
  • DOI: 10.1371/journal.pcbi.1006143
  • Peer Reviewed / Open Access
• [Journal Article] Bipolar dispersal of red-snow algae (2018)
  • Author(s): Segawa, T., Matsuzaki, R., Takeuchi, N., Akiyoshi, A., Navarro, F., Sugiyama, S., Yonezawa, T., Mori, H.
  • Journal Title: Nature communications Volume: 9 Issue: 1 Pages: 3094-3094
  • DOI: 10.1038/s41467-018-05521-w
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Observations and modelling of algal growth on a snowpack in north-western Greenland (2018)
  • Author(s): Onuma Yukihiko、Takeuchi Nozomu、Tanaka Sota、Nagatsuka Naoko、Niwano Masashi、Aoki Teruo
  • Journal Title: The Cryosphere Volume: 12 Issue: 6 Pages: 2147-2158
  • DOI: 10.5194/tc-12-2147-2018
  • Peer Reviewed / Open Access
• [Journal Article] Temporal variations of cryoconite holes and cryoconite coverage on the ablation ice surface of Qaanaaq Glacier in northwest Greenland (2018)
  • Author(s): Takeuchi Nozomu、Sakaki Ryutaro、Uetake Jun、Nagatsuka Naoko、Shimada Rigen、Niwano Masashi、Aoki Teruo
  • Journal Title: Annals of Glaciology Volume: 59 Issue: 77 Pages: 21-30
  • DOI: 10.1017/aog.2018.19
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] High Mitochondrial Diversity in a New Water Bear Species (Tardigrada: Eutardigrada) from Mountain Glaciers in Central Asia, with the Erection of a New Genus Cryoconicus (2018)
  • Author(s): Zawierucha, K., Stec, D., Lachowska-Cierlik, D., Takeuchi, N., Li, Z., Michalczyk.
  • Journal Title: Annales Zoologici Volume: 68 Issue: 1 Pages: 179-201
  • DOI: 10.3161/00034541anz2018.68.1.007
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] High-Throughput flaA Short Variable Region Sequencing to Assess Campylobacter Diversity from Fecal Samples from Birds (2018)
  • Author(s): Qian Zhang, Gabriel Asad Al-Ghalith, Mayumi Kobayashi, Takahiro Segawa, Mitsuto Maeda, Satoshi Okabe, Dan Knights, Satoshi Ishii
  • Journal Title: Frontiers in Microbiology Volume: 9 Pages: 2201-2201
  • DOI: 10.3389/fmicb.2018.02201
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community (2018)
  • Author(s): Murakami, T., Segawam T., Takeuchi, N., Barcaza, G., Lavarcam P., Kohshima, S., Hongoh, Y.
  • Journal Title: Environmental Microbiology Volume: 20 Issue: 11 Pages: 4170-4183
  • DOI: 10.1111/1462-2920.14420
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core (2018)
  • Author(s): Segawa Takahiro、Takeuchi Nozomu、Fujita Koji、Aizen Vladimir B.、Willerslev Eske、Yonezawa Takahiro
  • Journal Title: Heredity Volume: - Issue: 6 Pages: 1-1
  • DOI: 10.1038/s41437-017-0040-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Nitrogen Cycle Evaluation (NiCE) Chip for the Simultaneous Analysis of Multiple N-Cycle Associated Genes. (2018)
  • Author(s): Mamoru Oshiki, Takahiro Segawa, and Satoshi Ishii
  • Journal Title: Applied and Environmental Microbiology Volume: - Issue: 8
  • DOI: 10.1128/aem.02615-17
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] VITCOMIC2: Visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing. (2018)
  • Author(s): Mori H, Maruyama T, Yano M, Yamada T, Kurokawa K
  • Journal Title: BMC Syst. Biol. Volume: 12 Issue: S2 Pages: 30-30
  • DOI: 10.1186/s12918-018-0545-2
  • Peer Reviewed / Open Access
• [Journal Article] Biogeography of cryoconite forming cyanobacteria on polar and Asian glaciers (2017)
  • Author(s): Segawa, T., Yonezawa, T., Edwards, A., Akiyoshi, A., Tanaka, S., Uetake, J., Irvine‐Fynn, T., Fukui, K., Li, Z., Takeuchi, N.
  • Journal Title: Journal of Biogeography Volume: 44 Issue: 12 Pages: 2849-2861
  • DOI: 10.1111/jbi.13089
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Target virus log10 reduction values determined for two reclaimed wastewater irrigation scenarios in Japan based on tolerable annual disease burden (2017)
  • Author(s): Toshihiro Ito, Masaaki Kitajima, Tsuyoshi Kato, Satoshi Ishii, Takahiro Segawa, Satoshi Okabe, Daisuke Sano
  • Journal Title: Water Research Volume: 125 Pages: 438-448
  • DOI: 10.1016/j.watres.2017.08.057
  • Peer Reviewed / Open Access
• [Presentation] Global distribution and dispersal pattern of snow algae (2019)
  • Author(s): Takahiro Segawa, Ryo Matsuzaki, Ayumi Akiyoshi, Takahiro Yonezawa, Francisco Navarro, Hiroshi Mori, Nozomu Takeuchi.
  • Organizer: The Tenth Symposium on Polar Science
  • Int'l Joint Research
• [Presentation] 世界の氷河に分布する雪氷藻類とシアノバクテリアの比較と地理的分布 (2019)
  • Author(s): 瀬川高弘, 米澤隆弘, 松崎令, 秋好歩美, 森宙史, 竹内望
  • Organizer: 日本微生物生態学会
• [Presentation] 古代DNA情報を用いた雪氷圏微生物叢の全球的集団構造とその変遷の解明 (2019)
  • Author(s): 米澤隆弘, 瀬川高弘
  • Organizer: 日本微生物生態学会
  • Invited
• [Presentation] アルタイ山脈ベルーハ氷河コアから復元する過去100年の硝酸同位体組成変動 (2019)
  • Author(s): 服部祥平，Lin Mang，竹内望，藤田耕史，Nicolas Caillon，Pete Akers，Vladimir Aizen，Stanislav Nikitin，Joel Savarino
  • Organizer: 雪氷研究大会
• [Presentation] 中央アジア・パミールアライ山域で掘削したアイスコアの花粉分析 (2019)
  • Author(s): 鋸屋遥香，竹内望，藤田耕史，川村賢二，對馬あかね，宮内謙史郎，堀燿一朗，Vladimir Aizen，Azamat Osmonov
  • Organizer: 雪氷研究大会
• [Presentation] 氷河上の雪氷微生物がアジア山岳域の高山生態系に与える影響：氷河から流出するクリオコナイトによる氷河後退域の土壌形成 (2019)
  • Author(s): 竹内 望，塩向 雅斗
  • Organizer: 日本地球惑星科学連合大会
  • Invited
• [Presentation] Spatial and temporal variations in stable isotopes and soluble ions on high mountain snow surface of Mt. Tateyama, Toyama Prefecture, Japan (2019)
  • Author(s): 竹内 望，杉山 涼
  • Organizer: 日本地球惑星科学連合大会
  • Int'l Joint Research
• [Presentation] 中央アジアパミール山域で掘削された浅層アイスコアのダストの鉱物構成の分析 (2019)
  • Author(s): 竹内 俊介，竹内 望，藤田 耕史，川村 賢二，對馬 あかね，Vladimir Aizen
  • Organizer: 日本地球惑星科学連合大会
• [Presentation] アジア・パミールアライ山域で掘削されたアイスコアの花粉分析 (2019)
  • Author(s): 鋸屋 遥香，竹内 望，藤田 耕史，川村 賢二，對馬 あかね，Vladimir Aizen，Azamat Osmonov
  • Organizer: 日本地球惑星科学連合大会
• [Presentation] 北極と南極の雪を赤く染める藻類の地理的分布 (2019)
  • Author(s): 瀬川 高弘
  • Organizer: 第13回日本ゲノム微生物学会年会
  • Invited
• [Presentation] Ancient DNA analysis of ice core samples (2018)
  • Author(s): Takahiro Segawa
  • Organizer: Future Perspective on Ancient Genomics in East Asia
  • Int'l Joint Research / Invited
• [Presentation] Bipolar dispersal of red-snow algae phylotypes (2018)
  • Author(s): Takahiro Segawa, Ryo Matsuzaki, Hiroshi Mori & Nozomu Takeuchi
  • Organizer: 2nd Snow algae meeting
  • Int'l Joint Research
• [Presentation] VITCOMIC2: Visualization and analysis tool for the phylogenetic composition of microbial communities based on 16S rRNA gene sequences (2018)
  • Author(s): Mori H. Kurokawa K.
  • Organizer: ASM Microbe 2018
  • Int'l Joint Research
• [Presentation] VITCOMIC2 and MicrobeDB.jp: Analyzing taxonomic composition of microbial communities based on 16S rRNA gene sequences without sequence clustering (2018)
  • Author(s): Mori H. Kurokawa K.
  • Organizer: ISME17
  • Int'l Joint Research
• [Presentation] Metagenome informatics to understand microbial communities (2018)
  • Author(s): Mori H.
  • Organizer: イルミナマイクロバイオロジーワークショップ 2018
  • Invited
• [Presentation] ヒマラヤ山脈エベレスト・クンブ氷河ウエスターンクームで掘削された浅層アイスコア中のデブリの起源および消耗域のデブリとの比較 (2018)
  • Author(s): 竹内 望，堀 燿一朗，吉田 稔，藤井 理行
  • Organizer: 日本地球惑星連合大会
• [Presentation] グリーンランド南東部ラッセル氷河のクリオコナイトおよびホールの空間分布 (2018)
  • Author(s): 石渡晃起，竹内望，渡辺茜
  • Organizer: 雪氷研究大会
• [Presentation] 世界の氷河に分布する雪氷藻類の比較と分散過程 －氷河上の雪氷藻類はどこからきたのか－ (2018)
  • Author(s): 竹内望，瀬川高弘，米澤隆弘，松崎令
  • Organizer: 雪氷研究大会
• [Presentation] 中央アジアパミール及び天山山脈の氷河雪氷中に含まれる鉱物ダストの比較研究 (2018)
  • Author(s): 竹内俊介，竹内望，堀燿一朗
  • Organizer: 雪氷研究大会
• [Presentation] グレゴリアアイスコアの酸素同位体比とキルギスで採取された年輪酸素同位体比の比較 (2018)
  • Author(s): 對馬あかね，佐野雅規，藤田耕史，竹内望
  • Organizer: 雪氷研究大会
• [Presentation] 2016 年中央アジア・パミールアライ山域で掘削したアイスコアの花粉分析 (2018)
  • Author(s): 鋸屋遥香，竹内望，藤田耕史，川村賢二，對馬あかね，宮内謙史郎（千葉大学），堀燿一朗，Vladimir Aizen，Azamat Osmonov
  • Organizer: 雪氷研究大会
• [Presentation] Biogeography and demographic analysis of cryoconite forming cyanobacteria on glaciers (2018)
  • Author(s): Takahiro Segawa, Takahiro Yonezawa, Arwyn Edwards, Koji Fujita, Vladimir Eisen, Nozomu Takeuchi
  • Organizer: 17th International Symposium on Microbial Ecology
  • Int'l Joint Research
• [Presentation] Bipolar distribution and dispersal pattern of snow algae (2018)
  • Author(s): Takahiro Segawa, Ryo Matsuzaki, Nozomu Takeuchi, Ayumi Akiyoshi , Francisco Navarro and Hiroshi Mori
  • Organizer: The Ninth Symposium on Polar Science
  • Int'l Joint Research
• [Presentation] Biogeography and demographic analysis of cryoconite-forming cyanobacteria on glaciers. (2018)
  • Author(s): Takahiro Segawa, Takahiro Yonezawa, Arwyn Edwards, Koji Fujita, Vladimir Eisen, Francisco Navarro, Zhongqin Li, Nozomu Takeuchi
  • Organizer: International Symposium on Cryosphere and Biosphere
  • Int'l Joint Research / Invited
• [Presentation] Ancient DNA analysis of extinct animal and ice core samples. (2018)
  • Author(s): Takahiro Segawa, Hiroshi Mori, Ayumi Akiyoshi, Nozomu Takeichi, Takahiro Yonezawa, Masami Hasegawa
  • Organizer: The Eighth Symposium on Polar Science
  • Int'l Joint Research / Invited
• [Presentation] 博物館資料のメタゲノム解析 (2018)
  • Author(s): 森宙史
  • Organizer: 第8回Museomics研究会
  • Invited
• [Presentation] パタゴニアに生息する氷河カワゲラの網羅的腸内細菌叢解析 (2017)
  • Author(s): 村上 匠, 瀬川 高弘, 竹内 望, Pedro Labarca, Gonzalo Barcaza Sepulveda, 幸島 司郎, 本郷 裕一
  • Organizer: 環境微生物系学会合同大会2017
• [Presentation] VITCOMIC2: visualization of the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing (2017)
  • Author(s): Mori H, Maruyama T, Yano M, Yamada T, Kurokawa K.
  • Organizer: ProkaGENOMICS 2017
  • Int'l Joint Research
• [Presentation] 微生物群集の系統組成推定・描画ツールVITCOMIC2の開発と応用 (2017)
  • Author(s): 森宙史
  • Organizer: NGS現場の会第五回研究会