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

Mar Biotechnol (NY). 2011 Oct;13(5):900-8. doi: 10.1007/s10126-010-9351-6. Epub 2011 Jan 29.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Cell Membrane / chemistry
  • Cell Membrane / metabolism
  • DNA, Bacterial / genetics*
  • Genomics / methods*
  • Hydrothermal Vents*
  • Phylogeny
  • Water Microbiology*

Substances

  • Bacterial Proteins
  • DNA, Bacterial