Metagenomic Approach to the Study of Halophages: The Environmental Halophage 1

Environ Microbiol. 2007 Jul;9(7):1711-23. doi: 10.1111/j.1462-2920.2007.01289.x.

Abstract

Hypersaline environments, such as crystallizer ponds of solar salterns, show one of the highest concentration of viruses reported for aquatic systems. All the halophages characterized so far are isolates obtained by cultivation from described haloarchaeal species that have only low abundance in the environment. We employed a culture-independent metagenomic approach to analyse for the first time complete genomes in the halophage community and explored the in situ diversity by transmission electron microscopy and pulsed-field gel electrophoresis. We report the genomic sequence of a not yet isolated halophage (named as environmental halophage 1 'EHP-1') whose DNA was obtained from crystallizer samples with a salinity of 31%. The sequenced genome has a size of 35 kb and a G + C content around 51%. The G + C content is lower than that of previously characterized halophages. However, G + C content and codon usage in EHP-1 are similar to the recently cultivated and sequenced Haloquadratum walsbyi, the major prokaryotic component in solar salterns around the world. Forty open reading frames have been predicted, including genes that putatively code for proteins involved in DNA replication (ribonucleotide reductases, thymidylate kinase) normally found in lytic viruses.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteriophages / genetics*
  • Bacteriophages / ultrastructure
  • Base Composition
  • Base Sequence
  • Biodiversity*
  • Blotting, Southern
  • Cluster Analysis
  • Codon / genetics
  • DNA Primers / genetics
  • Genome Components
  • Genome, Viral / genetics*
  • Halobacteriaceae / virology*
  • Microscopy, Electron, Transmission
  • Molecular Sequence Data
  • Phylogeny*
  • Restriction Mapping
  • Seawater / microbiology*
  • Seawater / virology
  • Sequence Analysis, DNA
  • Spain
  • Water Microbiology*

Substances

  • Codon
  • DNA Primers

Associated data

  • GENBANK/DQ238866
  • GENBANK/EF503711
  • GENBANK/EF503712
  • GENBANK/EF503713
  • GENBANK/EF503714