Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

PLoS Genet. 2017 Sep 25;13(9):e1007018. doi: 10.1371/journal.pgen.1007018. eCollection 2017 Sep.

Abstract

Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (>0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assembly.

MeSH terms

  • Aquatic Organisms / genetics*
  • Aquatic Organisms / virology
  • Bacteriophages / genetics*
  • Genetic Variation*
  • Genome, Viral
  • High-Throughput Nucleotide Sequencing
  • Mediterranean Sea
  • Metagenome / genetics*
  • Molecular Sequence Annotation

Grant support

This work was supported by projects MEDIMAX BFPU2013-48007-P, VIREVO CGL2016-76273-P [AEI/FEDER, EU], (cofunded with FEDER funds) and Acciones de dinaminación REDES DE EXCELENCIA CONSOLIDER CGL2015-71523-REDC, from the Spanish Ministerio de Economía y Competitividad; and project AQUAMET PROMETEOII/2014/012 from Generalitat Valenciana. JMHM was supported with a PhD fellowship from the Spanish Ministerio de Economía y Competitividad (BES-2014-067828). MLP was supported with a Postdoctoral fellowship from the Valencian Consellería de Educació, Investigació, Cultura i Esport (APOSTD/2016/051). RGS was supported with a Predoctoral fellowship from the Valencian Consellería de Educació, Investigació, Cultura i Esport (ACIF/2016/050). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.