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Metagenomic Analysis of 0.2-μm-Passable Microorganisms in Deep-Sea Hydrothermal Fluid

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Abstract

We pyrosequenced the bulk DNA extracted from microorganisms that passed through 0.2-μm-pore-size filters and trapped by 0.1-μm-pore-size filters in the hydrothermal fluid of the Mariana Trough. Using the 454-FLX sequencer, we generated 202,648 sequences with an average length of 173.8 bases. Functional profiles were assigned by the SEED Annotation Engine. In the metagenome of the 0.2-μm-passable microorganisms, genes related to membrane function, including potassium homeostasis classified as membrane transport, and multidrug-resistance efflux pumps classified as virulence, were dominant. There was a higher proportion of genes pertinent to the subsystem of membrane transport in our metagenomic library than in other oceanic and hydrothermal vent metagenomes. Genes associated with a RND-type efflux transporter for exogenous substances were specifically identified in the present study. After a comparative analysis with the genome of the known ultramicrobacterium Sphingopyxis alaskensis RB2256, we discovered 1,542 cases of significant hits (E < 1 × 10−2) in our metagenome, and 1,172 of those were related to the DNA repair protein RadA. In this way, the microbial functional profile of 0.2-μm-passable fraction in the present study differs from oceanic metagenomes in the 0.2-μm-trapped fractions and hydrothermal vent metagenomes reported in previous research.

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Acknowledgment

The authors are obliged to Dr. Motoo Utusmi for cruise opportunities and to the crews and operation teams of RV Yokosuka and DSV Shinkai 6500, Japan Agency for Marine-Earth Science and Technology, for sample collection and onboard assistance. We are very much obliged to Dr. Ryo Kaneko, who filtered deep-sea hydrothermal fluid onboard the ship. This work was supported by the Special Coordination Fund “Archaean Park Project” from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan; the Fund “Construct the Genetic Resource Library of Unidentified Microbes Based on Genome Information” from the New Energy and Industrial Technology Development Organization, Japan; and Grants-in-Aid for Scientific Research (17657032) from the Japan Society for the Promotion of Science.

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  1. Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan

    Ryosuke Nakai & Takeshi Naganuma

  2. Nagahama Institute of Bio-Science and Technology, 1266, Tamura-cho, Nagahama, Shiga, 526-0829, Japan

    Takashi Abe

  3. Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku, Tokyo, 162-8480, Japan

    Haruko Takeyama

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  1. Ryosuke Nakai
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  2. Takashi Abe
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  4. Takeshi Naganuma
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Correspondence to Takeshi Naganuma.

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Nakai, R., Abe, T., Takeyama, H. et al. Metagenomic Analysis of 0.2-μm-Passable Microorganisms in Deep-Sea Hydrothermal Fluid. Mar Biotechnol 13, 900–908 (2011). https://doi.org/10.1007/s10126-010-9351-6

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