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

16 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

Keywords

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

ASJC Scopus subject areas

  • Biotechnology
  • Aquatic Science

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