A simple and efficient method for concentration of ocean viruses by chemical flocculation

John, Seth G.; Mendez, Carolina B.; Deng, Li; Poulos, Bonnie T.; Kauffman, Kathryn M.; Kern, Suzanne E.; Brum, Jennifer R.; Polz, Martin F.; Boyle, Edward A.; Sullivan, Matthew B.

doi:10.1111/j.1758-2229.2010.00208.x

Cited by 270 publications

(222 citation statements)

References 52 publications

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“…Additionally, Station M114 was sampled at the OMZ region at 294 m depth. For each sample, 80 L of seawater were 0.22 µm-filtered and viruses were concentrated from the filtrate using iron chloride flocculation 47 followed by storage at 4°C. More details about the sampling and additional variables used in the Malaspina expedition can be found in 53 .…”

Section: Malaspina Expeditionmentioning

confidence: 99%

“…For TARA station 100, two different peaks of chlorophyll were observed, so two samples were taken at the shallow (100_DCM) and deep (100_dDCM) chlorophyll maximum. For each sample, 20 L of seawater were 0.22 µm-filtered and viruses were concentrated from the filtrate using iron chloride flocculation 47 followed by storage at 4ºC. After resuspension in ascorbic-EDTA buffer (0.1 M EDTA, 0.2 M Mg, 0.2 M ascorbic acid, pH 6.0), viral particles were concentrated using Amicon Ultra 100 kDa centrifugal devices (Millipore), treated with DNase I (100U/mL) followed by the addition of 0.1M EDTA and 0.1M EGTA to halt enzyme activity, and extracted as previously described 48 .…”

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confidence: 99%

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Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

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692

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Tara Oceans CoordinatorsInternational audienceOcean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups. This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks

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Section: Malaspina Expeditionmentioning

confidence: 99%

mentioning

confidence: 99%

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

Self Cite

692

885

View full text Add to dashboard Cite

show abstract

“…To determine the prevalence of these polymerases in our metagenomic libraries the VIROME databank was queried with the set of S15 DNA pol g sequences from the mitochondria, cyanophage and the Global Ocean Survey Yooseph et al, 2007) and BroadPhage (John et al, 2011) data sets (BLASTP E-score p10 À 10 ). This gene does not appear to be abundant in our metagenomic libraries, as only seven ORFs with homology to DNA pol g were found in the VIROME database.…”

Section: Discussionmentioning

confidence: 99%

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

et al. 2013

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Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an a-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton.

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“…In fact, one particular podovirus DNA polymerase sequence is present in several aquatic and terrestrial environments (Breitbart et al, 2004a). A much larger-scale Pacific Ocean viral metagenomic data set employing quantitative methodologies (John et al, 2011;Solonenko et al, in press) is now available to examine biogeography, but such studies have not yet been conducted. This is because the database representation for sequence comparisons are so poor that most ocean viruses are not yet identifiable (for example, Angly et al, 2006;.…”

Section: Introductionmentioning

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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A simple and efficient method for concentration of ocean viruses by chemical flocculation

Cited by 270 publications

References 52 publications

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

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

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