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

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 ?m 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.

SUBMITTER: Lopez-Perez M

PROVIDER: S-EPMC5628999 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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

López-Pérez Mario M Haro-Moreno Jose M JM Gonzalez-Serrano Rafael R Parras-Moltó Marcos M Rodriguez-Valera Francisco F

PLoS genetics 20170925 9

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 dep ...[more]

PMID: 28945750

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Project description:Mediterranean coastal lagoons are affected by multiple threats (demographic pressures, eutrophication, climate change) expected to increase in the future and impact the ecosystem services provided. Conservation norms and scientific studies usually focus on large lagoons (> 0.5 km2) due to their economic importance, while they ignore smaller lagoons. These are poorly understood and often unprotected, despite their prevalence within the Mediterranean region and their importance. Qualitative and quantitative characterisation of small lagoons, in terms of functioning and sensitivity to global and local changes, are needed to develop appropriate management strategies. For this purpose, this work provides the first inventory of all Corsican lagoons and has investigated three of them of small size (Arasu, Santa Giulia, Balistra), characterised by contrasting anthropogenic contexts (highly modified/disturbed, medium disturbance, quasi-pristine). At the regional level, 91 of the 95 lagoons identified are < 0.5 km2, making Corsica a good example for the study of small Mediterranean lagoons. The three case studies showed differences in their seasonal biogeochemical cycles and phytoplankton communities (biomass, diversity, photosynthetic efficiency). Arasu and Santa Giulia lagoons showed an increase in watershed urbanisation (+ 12% and + 6% in 30 years), high phytoplankton biomass, low diversity and blooms of potentially harmful dinoflagellates. Conversely, Balistra lagoon showed a good status overall, but some anthropogenic pollution sources within its watershed. This study demonstrates the importance of small lagoons at regional and Mediterranean scale, and provides knowledge on studied local sites but also potential applications elsewhere. The importance of an integrated approach considering lagoons within their adjacent connected systems (watershed and sea) and anthropogenic contexts is highlighted.Supplementary informationThe online version contains supplementary material available at 10.1007/s12237-023-01182-1.

Dataset Information

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

Publications

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

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