Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

Coutinho, Felipe H.; Silveira, Cynthia B.; Gregoracci, Gustavo Bueno; Thompson, Cristiane C.; Edwards, Robert A.; Brussaard, Corina P. D.; Dutilh, Bas E.; Thompson, Fabiano L.

doi:10.1038/ncomms15955

Cited by 244 publications

(239 citation statements)

References 80 publications

Supporting

Mentioning

225

Contrasting

Unclassified

Order By: Relevance

“…SSR virome assemblies were performed via a random subsampling approach as previously described (72), designed to obtain as long as possible contigs by reducing the microdiversity within the samples (73,74). Briefly, the assembling strategy was based on random selection of a subset of the reads: 1% (75×), 5% (50×), 10% (50×), 25% (25×), 75% (25×), 100% (1×) from each sample and then assembling these subsets individually with IDBA_UD (v 1.1.2)(75) using the default parameters.…”

Section: Metagenomic Assembly and Function Analysismentioning

confidence: 99%

Metagenomic characterization of the viral community of the South Scotia Ridge

Yang¹,

Gao²,

Jiang

et al. 2018

Preprint

View full text Add to dashboard Cite

Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous genetic diversity. While their great influence on the marine ecosystems is widely acknowledged, current information about their diversity remains scarce. A viral metagenomic analysis of two surfaces and one bottom water sample was conducted from sites on the South Scotia Ridge (SSR) near the Antarctic Peninsula, during the austral summer 2016. The taxonomic composition and diversity of the viral communities were investigated and a functional assessment of the sequences was determined. Phylotypic analysis showed that most viruses belonging to the order Caudovirales, in particular, the family Podoviridae (41.92-48.7%), which is similar to the viral communities from the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many of the sequences associated with Caudovirales and NCLDV were novel and distinct from known complete phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found in SSR area and complete and partial Pgvv-like were obtained which may have an influence on host-virus interactions in the area during summer. Our study expands the existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.Importance In this study, we used high-throughput sequencing and bioinformatics analysis to analyze the viral community structure and biodiversity of SSR in the open sea near the Antarctic Peninsula. The results showed that the SSR viromes are novel, oceanic-related viromes and a high proportion of sequence reads was classified as unknown. Among known virus counterparts, members of the order Caudovirales were most abundant which is consistent with viromes from the Pacific Ocean. In addition, phylogenetic analyses based on the viral marker genes (TerL and MCP) illustrate the high diversity among Caudovirales and NCLDV. Combining deep sequencing and a random subsampling assembly approach, a new Pgvv-like group was also found in this region, which may a signification factor regulating virus-host interactions.

show abstract

Section: Metagenomic Assembly and Function Analysismentioning

confidence: 99%

Metagenomic characterization of the viral community of the South Scotia Ridge

Yang¹,

Gao²,

Jiang

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…In summary, this work shows the benefits of single‐cell genomics to increase our understanding of virus‐host associations in natural protist communities. Although our knowledge of the marine viral diversity is constantly expanding since the development of metagenomics (Coutinho et al, ; Mizuno et al, ; Paez‐Espino et al, ), it has been estimated that the majority (63%–93%) of viral sequences in marine metagenomes are not represented in public databases (Hurwitz & Sullivan, ), emphasizing the need for further isolation, characterization and sequencing of specific marine viruses (Middelboe & Brussaard, ). A minute fraction of protist viruses is annotated to date (~100 sequenced genomes, ~0.6% of all viral genomes) in NCBI Genome database (July 2018), explaining the majority of unassigned viral sequences in our study.…”

Section: Discussionmentioning

confidence: 99%

“…Our knowledge of marine viral diversity and biogeography has been constantly expanding during this last decade with the advent of viral metagenomics (e.g., Coutinho et al, ; Mizuno, Rodriguez‐Valera, Kimes, & Ghai, ; Paez‐Espino et al, ). Multiple studies unveiled a large novel diversity of uncultured viruses, indicating their key roles in nutrient cycling and trophic networks (Brum et al, ; Roux et al, ).…”

Section: Introductionmentioning

confidence: 99%

Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics

et al. 2019

View full text Add to dashboard Cite

Viruses are the most abundant biological entities on Earth and have fundamental ecological roles in controlling microbial communities. Yet, although their diversity is being increasingly explored, little is known about the extent of viral interactions with their protist hosts as most studies are limited to a few cultivated species. Here, we exploit the potential of single‐cell genomics to unveil viral associations in 65 individual cells of 11 essentially uncultured stramenopiles lineages sampled during the Tara Oceans expedition. We identified viral signals in 57% of the cells, covering nearly every lineage and with narrow host specificity signal. Only seven out of the 64 detected viruses displayed homologies to known viral sequences. A search for our viral sequences in global ocean metagenomes showed that they were preferentially found at the DCM and within the 0.2–3 µm size fraction. Some of the viral signals were widely distributed, while others geographically constrained. Among the viral signals we detected an endogenous mavirus virophage potentially integrated within the nuclear genome of two distant uncultured stramenopiles. Virophages have been previously reported as a cell's defence mechanism against other viruses, and may therefore play an important ecological role in regulating protist populations. Our results point to single‐cell genomics as a powerful tool to investigate viral associations in uncultured protists, suggesting a wide distribution of these relationships, and providing new insights into the global viral diversity.

show abstract

“…Notable exceptions are the giant viruses isolated 569 from marine flagellates Cafeteria roenbergensis (12) and Bodo saltans (35). The principal approach for 570 inferring the virus host range from metagenomics data is the analysis of co-occurrence of virus sequences with 571 those of potential hosts (124,125). However, virtually no 18S rRNA gene sequences of eukaryotic origin were 572 detected in the Loki's Castle sediment samples, in a sharp contrast to the rich prokaryotic microbiota (61, 62).…”

mentioning

confidence: 99%