Are we missing half of the viruses in the ocean?

Steward, Grieg F.; Culley, Alexander I.; Mueller, Jaclyn A.; Wood‐Charlson, Elisha M.; Belcaid, Mahdi; Poisson, Guylaine

doi:10.1038/ismej.2012.121

Cited by 165 publications

(164 citation statements)

References 49 publications

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“…Yet, currently available methods have potential limitations. For example, ssDNA and RNA viruses [11,42] and giant viruses [38] are under-counted when estimates are made via epiflourescence microscopy with standard DNA based stains. Likewise, virus-like particles may not always necessarily represent viruses, and total abundance estimates could include contributions from gene-transfer agents .…”

Section: G Outlier Identificationmentioning

confidence: 99%

Re-examination of the relationship between marine virus and microbial cell abundances

et al. 2016

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Marine viruses are critical drivers of ocean biogeochemistry and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 10 8 per ml. Over many years, a consensus has emerged that virus abundances are typically 10-fold higher than prokaryote abundances. The use of a fixed-ratio suggests that the relationship between virus and prokaryote abundances is both predictable and linear. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5671 prokaryote and virus abundance estimates from 25 distinct marine surveys to characterize the relationship between virus and prokaryote abundances. We find that the median virus-to-prokaryote ratio (VPR) is 10:1 and 16:1 in the near-and sub-surface oceans, respectively. Nonetheless, we observe substantial variation in the VPR and find either no or limited explanatory power using fixed-ratio models. Instead, virus abundances are better described as nonlinear, power-law functions of prokaryote abundances -particularly when considering relationships within distinct marine surveys. Estimated power-laws have scaling exponents that are typically less than 1, signifying that the VPR decreases with prokaryote density, rather than remaining fixed. The emergence of power-law scaling presents a challenge for mechanistic models seeking to understand the ecological causes and consequences of marine virusmicrobe interactions. Such power-law scaling also implies that efforts to average viral effects on microbial mortality and biogeochemical cycles using "representative" abundances or abundanceratios need to be refined if they are to be utilized to make quantitative predictions at regional or global ocean scales.

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Section: G Outlier Identificationmentioning

confidence: 99%

Re-examination of the relationship between marine virus and microbial cell abundances

et al. 2016

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“…Finally, 65-93% (reviewed by and 41-81% (Culley et al, 2006;Steward et al, 2013) of sequences in marine DNA and RNA viral metagenomes, respectively, are not represented in existing genomic databases. Given that observed non-tailed virus capsid diameters were largely inconsistent with those from cultivated marine non-tailed viruses, we posit that non-tailed viruses may comprise the majority of this vast 'unknown' marine viral metagenomic sequence space.…”

Section: Discussionmentioning

confidence: 99%

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

2013

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Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world’s oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world’s oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51–92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.

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“…Aquatic environments contain particularly diverse forms of viruses, including single-stranded (ss) and double-stranded (ds) DNA and RNA viruses with genomes that range in size from less than 2,000 bases to more than 2 million bases 4 . Although dsDNA viruses that infect bacteria (bacteriophages) are the best studied to date, recent work suggests that around 50% of marine viruses have ssDNA or RNA genomes 8 . Metagenomic data are changing our views on virus diversity and are therefore challenging the way in which we recognize and classify viruses 9 .…”

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confidence: 99%

Virus taxonomy in the age of metagenomics

et al. 2017

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| The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV. NATURE REVIEWS | MICROBIOLOGY VOLUME 15 | MARCH 2017 | 161 CONSENSUS STATEMENT © 2 0 1 7 M a c m i l l a n P u b l i s h e r s L i m i t e d , p a r t o f S p r i n g e r N a t u r e . A l l r i g h t s r e s e r v e d .

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Are we missing half of the viruses in the ocean?

Cited by 165 publications

References 49 publications

Re-examination of the relationship between marine virus and microbial cell abundances

Re-examination of the relationship between marine virus and microbial cell abundances

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

Virus taxonomy in the age of metagenomics

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