Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota

Philosof, Alon; Yutin, Natalya; Flores‐Uribe, José; Sharon, Itai; Koonin, Eugene V.; Béjà, Oded

doi:10.1016/j.cub.2017.03.052

Cited by 84 publications

(100 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To increase our knowledge regarding uncultured cyanophages, we examined metagenomic assemblies from the Red Sea (Philosof et al, 2017) and Tara Oceans expedition microbiomes and viromes (Brum et al, 2015;Sunagawa et al, 2015). Four contigs (Supporting Information File S1) of putative viral genomes related to BAC21E04 were identified.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus ‘relic’ prophage

Flores‐Uribe

Philosof

Sharon

et al. 2019

Environ Microbiol Rep

Self Cite

View full text Add to dashboard Cite

Summary Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Salmon results showed no detection of petB on any of the virome samples, indicating that cyanobacterial contamination in these samples is improbable. However, 24 of the 36 samples where the MAGs were detected correspond to the bacterial fraction (0.2-3.0 μm) probably indicating ongoing infections during sampling (Philosof et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus ‘relic’ prophage

Flores‐Uribe

Philosof

Sharon

et al. 2019

Environ Microbiol Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Our knowledge of the virosphere is scant. Although viruses are the most abundant source of nucleic acid on earth, with every species of cellular life likely harboring multiple viruses, until recently most studies of virus biodiversity and evolution were of limited scope, with a strong focus on aquatic environments and prokaryotic DNA viruses (Angly et al, 2006;Culley et al, 2006;Desnues et al, 2008;Paez-Espino et al, 2016;Philosof et al, 2017). Far less is known about the diversity of RNA viruses in terrestrial organisms.…”

Section: Introduction: Virology In the Age Of Metagenomicsmentioning

confidence: 99%

Meta-transcriptomics and the evolutionary biology of RNA viruses

2018

View full text Add to dashboard Cite

Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel invertebrate viruses. In particular, meta-transcriptomics shows that the RNA virus world is more fluid than previously realized, with relatively frequent changes in genome length and structure. As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. Given that most viruses in the future will likely be characterized using metagenomics approaches, and that we have evidently only sampled a tiny fraction of the total virosphere, we suggest that proposals for virus classification pay careful attention to the wonders unearthed in this new age of virus discovery.

show abstract

“…Despite this remarkable progress, knowledge of viral diversity and ecology in freshwater systems is nowhere near comprehensive, remaining far behind that of their marine counterparts, which have been analyzed in global-scale investigations (46-51), including the sampling of dsDNA viral genetic diversity in the surface ocean near saturation levels (33,49,52). Some major achievements in marine viromics include the identification of viruses infecting the dominant bacterioplankton lineages (53)(54)(55)(56), which have eluded cultivation-based efforts (57)(58)(59)(60). In freshwater systems, in addition to viruses that infect cyanobacteria (61)(62)(63)(64), which are relatively amenable to cultivation, several viruses that infect ubiquitous freshwater bacterioplankton lineages have been identified in the last few years, including isolated viruses that infect LD28 (Ca.…”

Section: Introductionmentioning

confidence: 99%

Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake

Okazaki

Nishimura

Yoshida

et al. 2019

Preprint

View full text Add to dashboard Cite

The use of metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and the ecological relationships between viruses and hosts remain poorly understood. In this study, we conducted a large-scale metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.22-5.0 μm) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome-assembled genomes. Spatiotemporal, intra-and extra-cellular dynamics of individual viruses assessed through metagenomic read coverage revealed a hypolimnion-specific viral community analogous to the vertically-stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly due to lysogenic induction, presumably reflecting low bacterial productivity in the hypolimnion. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfurlimited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., LD12 and Ca. Nitrosoarchaeum). Comparison with published metagenomes revealed phylogeographic connectivity of viral communities in geographically isolated habitats, probably following the phylogeographic connectivity of their hosts. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous, and abundant viral groups in freshwater systems, with high lytic replication rates in surface waters. This result suggested that freshwater Actinobacteria are under high viral lytic pressure, which likely facilitated their genomic micro-diversification to elude viral recognition. Significance StatementMetagenomics allows for the reconstruction of bacterial and viral genomes without cultivation, contributing substantially to elucidation of bacterial and viral diversity and their key ecological roles.In this study, we report the largest-scale metagenomic exploration of freshwater prokaryotic viruses to date. We investigated the hypolimnion of a deep freshwater lake and tracked viruses throughout their life cycles, including both intra-and extra-cellular phases. This method allowed us to reconstruct both viral and host genomes and characterize numerous novel virus-host interactions, including those involving ubiquitous freshwater bacterial lineages. When the data were compared with published metagenomic datasets, we uncovered genome-resolved phylogeographic connectivity among viruses from geographically isolated habitats and identified ecologically important viral groups that are ubiquitous in aquatic habitats.In total, 12 water samples were collected at a pelagic site on Lake Biwa, the largest freshwater lake in Japan. The epilimnion (5 m) was ...

show abstract

Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota

Cited by 84 publications

References 41 publications

A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus ‘relic’ prophage

A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus ‘relic’ prophage

Meta-transcriptomics and the evolutionary biology of RNA viruses

Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake

Contact Info

Product

Resources

About