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

Ryosuke Nakai, Takashi Abe, Haruko Takeyama, Takeshi Naganuma

    Research output: Contribution to journalArticle

    12 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)900-908
    Number of pages9
    JournalMarine Biotechnology
    Volume13
    Issue number5
    DOIs
    Publication statusPublished - 2011 Oct

    Fingerprint

    Metagenome
    Metagenomics
    hydrothermal fluid
    Oceans and Seas
    deep sea
    microorganism
    hydrothermal vent
    membrane
    microorganisms
    Hydrothermal Vents
    gene
    filter
    DNA
    filters
    homeostasis
    Membranes
    virulence
    repair
    transporters
    engine

    Keywords

    • Comparative genomics
    • Deep sea
    • Environmental DNA
    • Metagenomics
    • Ultra-micro-sized organisms

    ASJC Scopus subject areas

    • Aquatic Science
    • Biotechnology

    Cite this

    Metagenomic Analysis of 0.2-μm-Passable Microorganisms in Deep-Sea Hydrothermal Fluid. / Nakai, Ryosuke; Abe, Takashi; Takeyama, Haruko; Naganuma, Takeshi.

    In: Marine Biotechnology, Vol. 13, No. 5, 10.2011, p. 900-908.

    Research output: Contribution to journalArticle

    Nakai, Ryosuke ; Abe, Takashi ; Takeyama, Haruko ; Naganuma, Takeshi. / Metagenomic Analysis of 0.2-μm-Passable Microorganisms in Deep-Sea Hydrothermal Fluid. In: Marine Biotechnology. 2011 ; Vol. 13, No. 5. pp. 900-908.
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