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Domain-level identification and quantification of relative prokaryotic cell abundance in microbial communities by Micro-FTIR spectroscopy

Authors

  • Motoko Igisu,

    Corresponding author
    1. Department of Earth Science and Astronomy, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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  • Ken Takai,

    1. Subsurface Geobiology Advanced Research (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
    2. Precambrian Ecosystem Laboratory, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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  • Yuichiro Ueno,

    1. Precambrian Ecosystem Laboratory, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
    2. Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan.
    3. Research Center for the Evolving Earth and Planets, Tokyo Institute of Technology, Tokyo, Japan.
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  • Manabu Nishizawa,

    1. Precambrian Ecosystem Laboratory, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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  • Takuro Nunoura,

    1. Subsurface Geobiology Advanced Research (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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  • Miho Hirai,

    1. Subsurface Geobiology Advanced Research (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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  • Masanori Kaneko,

    1. Department of Earth and Planetary Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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  • Hiroshi Naraoka,

    1. Department of Earth and Planetary Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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  • Mie Shimojima,

    1. Research Center for the Evolving Earth and Planets, Tokyo Institute of Technology, Tokyo, Japan.
    2. Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.
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  • Koichi Hori,

    1. Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.
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  • Satoru Nakashima,

    1. Department of Earth and Space Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan.
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  • Hiroyuki Ohta,

    1. Research Center for the Evolving Earth and Planets, Tokyo Institute of Technology, Tokyo, Japan.
    2. Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.
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  • Shigenori Maruyama,

    1. Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan.
    2. Research Center for the Evolving Earth and Planets, Tokyo Institute of Technology, Tokyo, Japan.
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  • Yukio Isozaki

    1. Department of Earth Science and Astronomy, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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E-mail igisu@ea.c.u-tokyo.ac.jp; Tel. (+81) 3 5454 6622; Fax (+81) 3 5465 8244.

Summary

Domain-level identification of microbial cells or cell-like structures is crucial for investigating natural microbial communities and their ecological significance. By using micro-Fourier transform infrared (micro-FTIR) spectroscopy, we established a technical basis for the domain-level diagnosis and quantification of prokaryotic cell abundance in natural microbial communities. Various prokaryotic cultures (12 species of bacteria and 10 of archaea) were examined using micro-FTIR spectroscopic analysis. The aliphatic CH3/CH2 absorbance ratios (R3/2) showed domain-specific signatures, possibly reflecting distinctive cellular lipid compositions. The signatures were preserved even after chemical cell fixation (formaldehyde) and nucleic acid staining (DAPI) processes – techniques that are essential in studying microbial ecology. The micro-FTIR technique was successfully applied for quantification of the bacteria/archaea abundance ratio in an active microbial mat community in a subsurface hot aquifer stream. We conclude that the micro-FTIR R3/2 measurement is both fast and effective for domain-level diagnosis and quantification of first-order prokaryotic community structures.

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