Skip to main content
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Accessibility Statement
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian
  • Log in
  • My Cart

Main menu

  • Home
  • Articles
    • Current
    • Special Feature Articles - Most Recent
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • List of Issues
  • Front Matter
  • News
    • For the Press
    • This Week In PNAS
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Editorial and Journal Policies
    • Submission Procedures
    • Fees and Licenses
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Accessibility Statement
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian

User menu

  • Log in
  • My Cart

Search

  • Advanced search
Home
Home

Advanced Search

  • Home
  • Articles
    • Current
    • Special Feature Articles - Most Recent
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • List of Issues
  • Front Matter
  • News
    • For the Press
    • This Week In PNAS
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Editorial and Journal Policies
    • Submission Procedures
    • Fees and Licenses

New Research In

Physical Sciences

Featured Portals

  • Physics
  • Chemistry
  • Sustainability Science

Articles by Topic

  • Applied Mathematics
  • Applied Physical Sciences
  • Astronomy
  • Computer Sciences
  • Earth, Atmospheric, and Planetary Sciences
  • Engineering
  • Environmental Sciences
  • Mathematics
  • Statistics

Social Sciences

Featured Portals

  • Anthropology
  • Sustainability Science

Articles by Topic

  • Economic Sciences
  • Environmental Sciences
  • Political Sciences
  • Psychological and Cognitive Sciences
  • Social Sciences

Biological Sciences

Featured Portals

  • Sustainability Science

Articles by Topic

  • Agricultural Sciences
  • Anthropology
  • Applied Biological Sciences
  • Biochemistry
  • Biophysics and Computational Biology
  • Cell Biology
  • Developmental Biology
  • Ecology
  • Environmental Sciences
  • Evolution
  • Genetics
  • Immunology and Inflammation
  • Medical Sciences
  • Microbiology
  • Neuroscience
  • Pharmacology
  • Physiology
  • Plant Biology
  • Population Biology
  • Psychological and Cognitive Sciences
  • Sustainability Science
  • Systems Biology
Research Article

Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system

Fumio Inagaki, Marcel M. M. Kuypers, Urumu Tsunogai, Jun-ichiro Ishibashi, Ko-ichi Nakamura, Tina Treude, Satoru Ohkubo, Miwako Nakaseama, Kaul Gena, Hitoshi Chiba, Hisako Hirayama, Takuro Nunoura, Ken Takai, Bo B. Jørgensen, Koki Horikoshi, and Antje Boetius
PNAS September 19, 2006 103 (38) 14164-14169; https://doi.org/10.1073/pnas.0606083103
Fumio Inagaki
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: inagaki@jamstec.go.jp
Marcel M. M. Kuypers
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Urumu Tsunogai
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jun-ichiro Ishibashi
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ko-ichi Nakamura
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tina Treude
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Satoru Ohkubo
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Miwako Nakaseama
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kaul Gena
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hitoshi Chiba
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hisako Hirayama
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Takuro Nunoura
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ken Takai
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Bo B. Jørgensen
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Koki Horikoshi
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Antje Boetius
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  1. Communicated by Norman H. Sleep, Stanford University, Stanford, CA, July 21, 2006 (received for review March 10, 2006)

Related Article

  • Lakes of liquid CO2 in the deep sea
    - Sep 13, 2006
  • Article
  • Figures & SI
  • Info & Metrics
  • PDF
Loading

Article Figures & SI

Figures

  • Fig. 1.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 1.

    Overview of the Yonaguni Knoll IV hydrothermal field at the southern Okinawa Trough. (A) Location map of the Yonaguni Knoll IV. (B) “Lion chimney,” one of the most active black smoker vents in this field. (C) “Crystal chimney,” one of the vapor-rich clear smoker vents adjacent to the Tiger black smoker. The emission of liquid CO2 droplets was observed in close proximity. (D) White patchy area, “CO2-hydrate zone,” ≈50 m southward from the Tiger chimney. (E) Continuous emission of liquid CO2 droplets from the “CO2 lake” overlying hydrates. White arrows in C and E indicate the emission of liquid CO2 droplets. The video of these hydrothermal events recorded by DSV Shinkai 6500 is available as Movie 1, which is published as supporting information on the PNAS web site.

  • Fig. 2.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 2.

    Scheme of the examined sediment sample from the “CO2-hydrate zone” and related geochemical depth profiles. (A) Location of liquid CO2/CO2-hydrate interface, sediment cover, and pavement in core 819NK, and in situ temperatures. (B) Profiles of pH (open diamonds) and alkalinity (as CaCO3, filled diamonds) in pore waters. (C) Concentrations of SO4 2− (filled squares) and Cl− (open squares) in pore water. (D) Concentration of methane and CO2 in headspace. (E) Carbon isotopic compositions of methane (red circles, t = 0; white circles, t = 14 h) and CO2 (light blue circles) in headspace. The data from top layer (single points) and sediment column (connected by lines) correspond to 819 pavement and 819NK sediment core, respectively, both obtained from the CO2-hydrate zone.

  • Fig. 3.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 3.

    Phylogenetic trees of archaeal (A) and bacterial (B) 16S rRNA gene sequences from the liquid CO2-hydrate hydrothermal system as marked in red and blue, respectively. The trees were inferred by neighbor-joining analysis by using manually aligned homologous positions of 16S rRNA sequences. The number of related clones with a 97% similarity sequence cutoff are indicated in parentheses. The results of 100 bootstrap trials are shown at each phylogenetic branch. (Scale bars: 0.05-nt substitution per sequence position.)

  • Fig. 4.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 4.

    Carbon isotopic compositions of archaeal and bacterial lipids extracted from 819p pavements (red) and 819NK core sediments (blue) in the CO2-hydrate zone and 818 core sediments (black) obtained from outside of the CO2-hydrate zone (>50 m). Carbon isotopic compositions of CO2 and methane were obtained from liquid CO2 droplets collected in situ by the gas-tight sampler. The δ13C value of algal organic carbon (OC) was calculated from the δ13C value of phytol from core 818, assuming an isotopic offset between phytoplanktonic biomass and phytol of +4‰ (33). Bars indicate SDs (n = 2–6).

Data supplements

  • Inagaki et al. 10.1073/pnas.0606083103.

    Supporting Information

    Files in this Data Supplement:

    Supporting Figure 5
    Supporting Figure 6
    Supporting Figure 7
    Supporting Figure 8
    Supporting Movie 1




    Fig. 5. Vertical profiles of temperature measured in situ (A), total sulfur content (B), total cell abundance (C), relative abundance of Archaea (D), clonal frequency of ANME-related archaeal clone sequences (E), and clonal frequency of Deltaproteobacteria sequences. The plotted depths in B–D correspond to sampling depths of core 819NK sediments on board, which has expanded slightly by the effect of phase transition of CO2 during the recovery.





    Fig. 6. Phylogenetic tree of methyl coenzyme M reductase a-subunit genes (mcrA) from liquid CO2/CO2-hydrate-bearing sediments at the Yonaguni Knoll IV hydrothermal field. The sequences obtained from the sediments are indicated by red characters. The phylogenetic distance was determined by the neighbor-joining method by using manually aligned nucleic acid sequences. Bootstrap numbers indicate the score of 100 replicates.





    Fig. 7. Phylogenetic tree of ribulose 1,5-bisphosphate carboxylase (Rubisco: cbbL) genes from liquid CO2/CO2-hydrate-bearing sediments at the Yonaguni Knoll IV hydrothermal field. The sequences obtained from the sediments are indicated by red characters. The phylogenetic distance was determined by the neighbor-joining method by using manually aligned nucleic acid sequences. Bootstrap numbers indicate the score of 100 replicates.





    Fig. 8. Concentrations of major lipid components extracted from 819 pavement and core 819NK samples of the CO2-hydrate zone.





    Supporting Movie 1

    Movie 1. This movie shows the overview of the Yonaguni Knoll IV hydrothermal field at the southern Okinawa Trough, which was recorded by DSV Shinkai 6500 during the JAMSTEC expeditions YK03-05 and YK04-05. During the course of the movie, one can see the Lion and Tiger black smoker chimneys, the adjacent vapor-rich clear vent fluids from the Crystal chimney with emissions of liquid CO2 droplets in close proximity, macrofauna assemblages at the foot of the Tiger chimney mound, the white patchy area "CO2-hydrate zone," and the continuous emission of liquid CO2 from the sediment-hosted CO2 lake through the cored borehole (QuickTime).

PreviousNext
Back to top
Article Alerts
Email Article

Thank you for your interest in spreading the word on PNAS.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system
(Your Name) has sent you a message from PNAS
(Your Name) thought you would like to see the PNAS web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system
Fumio Inagaki, Marcel M. M. Kuypers, Urumu Tsunogai, Jun-ichiro Ishibashi, Ko-ichi Nakamura, Tina Treude, Satoru Ohkubo, Miwako Nakaseama, Kaul Gena, Hitoshi Chiba, Hisako Hirayama, Takuro Nunoura, Ken Takai, Bo B. Jørgensen, Koki Horikoshi, Antje Boetius
Proceedings of the National Academy of Sciences Sep 2006, 103 (38) 14164-14169; DOI: 10.1073/pnas.0606083103

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system
Fumio Inagaki, Marcel M. M. Kuypers, Urumu Tsunogai, Jun-ichiro Ishibashi, Ko-ichi Nakamura, Tina Treude, Satoru Ohkubo, Miwako Nakaseama, Kaul Gena, Hitoshi Chiba, Hisako Hirayama, Takuro Nunoura, Ken Takai, Bo B. Jørgensen, Koki Horikoshi, Antje Boetius
Proceedings of the National Academy of Sciences Sep 2006, 103 (38) 14164-14169; DOI: 10.1073/pnas.0606083103
Digg logo Reddit logo Twitter logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Mendeley logo Mendeley
Proceedings of the National Academy of Sciences: 103 (38)
Table of Contents

Submit

Sign up for Article Alerts

Jump to section

  • Article
    • Abstract
    • Results and Discussion
    • Conclusion and Prospects
    • Materials and Methods
    • Acknowledgments
    • Footnotes
    • References
  • Figures & SI
  • Info & Metrics
  • PDF

You May Also be Interested in

Abstract depiction of a guitar and musical note
Science & Culture: At the nexus of music and medicine, some see disease treatments
Although the evidence is still limited, a growing body of research suggests music may have beneficial effects for diseases such as Parkinson’s.
Image credit: Shutterstock/agsandrew.
Scientist looking at an electronic tablet
Opinion: Standardizing gene product nomenclature—a call to action
Biomedical communities and journals need to standardize nomenclature of gene products to enhance accuracy in scientific and public communication.
Image credit: Shutterstock/greenbutterfly.
One red and one yellow modeled protein structures
Journal Club: Study reveals evolutionary origins of fold-switching protein
Shapeshifting designs could have wide-ranging pharmaceutical and biomedical applications in coming years.
Image credit: Acacia Dishman/Medical College of Wisconsin.
White and blue bird
Hazards of ozone pollution to birds
Amanda Rodewald, Ivan Rudik, and Catherine Kling talk about the hazards of ozone pollution to birds.
Listen
Past PodcastsSubscribe
Goats standing in a pin
Transplantation of sperm-producing stem cells
CRISPR-Cas9 gene editing can improve the effectiveness of spermatogonial stem cell transplantation in mice and livestock, a study finds.
Image credit: Jon M. Oatley.

Similar Articles

Site Logo
Powered by HighWire
  • Submit Manuscript
  • Twitter
  • Facebook
  • RSS Feeds
  • Email Alerts

Articles

  • Current Issue
  • Latest Articles
  • Archive

PNAS Portals

  • Anthropology
  • Chemistry
  • Classics
  • Front Matter
  • Physics
  • Sustainability Science
  • Teaching Resources

Information

  • Authors
  • Editorial Board
  • Reviewers
  • Librarians
  • Press
  • Site Map
  • PNAS Updates

Feedback    Privacy/Legal

Copyright © 2021 National Academy of Sciences. Online ISSN 1091-6490