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Microbial oceanography: Killers of the winners

More than 20 years ago, the discovery of billions of viruses in the oceans was big news, worthy of articles in Nature1 and on the front page of the Washington Post. A year later another Naturereport was published, this time about the most abundant bacterial group in the oceans, cryptically called SAR11. The two stories now come together in a paper published on Nature's website today. Zhao et al. describe DNA viruses that they call 'pelagiphages' and which infect laboratory-grown representatives of SAR11 bacteria. The authors use genomic-sequence data to argue that pelagiphages are among the most abundant viruses in the oceans and perhaps the entire biosphere. The report ends long-running speculation about SAR11, but prompts new questions about marine viruses and the control of microbes in the oceans.

Ed Rybicki's insight:

Seriously big finding - there's a sea of opportunity out there!

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Ed Rybicki's curator insight, February 14, 2013 2:35 AM

GREAT field to be in!!

Aquatic Viruses
mol-biol, bioinformatics and biology
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Now curated by Mya Breitbart and Ed Rybicki:

If you would like to help curate it, please:

 

 contact: cupton at uvic dot ca

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Exclusive cross-domain networks in the sea

Exclusive cross-domain networks in the sea | Aquatic Viruses | Scoop.it
The identification of an exchange of nutrients and signalling molecules between a planktonic alga and a bacterium demonstrates that targeted mutualistic interactions occur across domains of life in the oceans.
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All life is one B-)

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A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes | Aquatic Viruses | Scoop.it
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
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Diseases loom large for tropical corals

Diseases loom large for tropical corals | Aquatic Viruses | Scoop.it
As greater atmospheric carbon dioxide boosts sea temperatures, tropical corals face a bleak future. New climate model projections show that conditions are likely to increase the frequency and severity of coral disease outbreaks.
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Viruses Help Microbial Hosts Cope with Life at the Extremes

Viruses Help Microbial Hosts Cope with Life at the Extremes | Aquatic Viruses | Scoop.it
Microbes may benefit from viral infections mixing and matching DNA.

 

A new study reveals that viruses lend a surprisingly helpful hand to microbes eking out a living near deep-sea hydrothermal vents.

When they infect the vent’s resident bacteria and archaea, the viruses mix and match the single-celled creatures’ genes. As a result, the microbes can benefit from possessing a wide range of genes in a way that broadens their repertoire of responses to the quick-changing, harsh conditions of the vent environment.

The findings, published in PLOS ONE in October 2014, could offer insight into the development of life on Earth as well as on Solar System moons, such as Saturn’s Enceladus and Jupiter’s Europa, which both have suspected hydrothermal vent activity in their subsurface oceans.

“Viruses can affect the evolution of the hosts they infect, and in unexpected ways,” said study lead author Rika Anderson, a Postdoctoral Program Fellow with the NASA Astrobiology Institute, and at the time of the study a doctoral student at the University of Washington.

- See more at: http://www.astrobio.net/topic/origins/extreme-life/viruses-help-microbial-hosts-cope-with-life-at-the-extremes/#sthash.oUPOXzyP.z5pltXLB.dpuf

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Here Are All the [faeces]-Inducing Pathogens Carried by NYC's Rats

Here Are All the [faeces]-Inducing Pathogens Carried by NYC's Rats | Aquatic Viruses | Scoop.it
So much diarrhea. Just so much.
Ed Rybicki's insight:

Alarmist to a silly degree. Y. enterocolitica isn't a virus; I'll bet you the anelloviruses are rat-specific; so too the parvo; circovirus almost certainly isn't the dog one...and so on.  See what comes of eltting a non-virologist analyse results? 

 

Oh, and the word poop is for 5-yr-olds. So I censored it.

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Boiling water three times faster - with TMV!

Boiling water three times faster - with TMV! | Aquatic Viruses | Scoop.it
A combination of nanotechnology and a virus found on tobacco could save huge amounts of energy in industrial processes

 

Scientists have found a way to boil water faster, although they admit the discovery is unlikely to revolutionise tea-making.

The technology works by coating a heating element with a virus found on tobacco plants. The coating dramatically reduces the size and number of bubbles that form around the element as it gets warmer. Air pockets caused by bubbles temporarily insulate heating elements from the surrounding water, slowing down the transfer of heat.

A coating made from the tobacco virus tripled the efficiency of boiling water, scientists said, which could save vast quantities of energy in industrial power plants or large-scale electronic cooling systems.

Ed Rybicki's insight:

I don't see why it wouldn't revolutionise tea-making as well??

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The unforeseen impact of densoviruses

The unforeseen impact of densoviruses | Aquatic Viruses | Scoop.it
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I thank Flavia Flaviani for sending me this B-)

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An inexpensive, accurate and precise wet-mount method for enumerating aquatic viruses

Viruses affect biogeochemical cycling, microbial mortality, gene flow, and metabolic functions in diverse environments through infection and lysis of microorganisms. Fundamental to quantitatively investigating these roles is the determination of viral abundance in both field and laboratory samples. One current, widely-used method to accomplish this in aquatic samples is the ‘filter-mount’ method in which samples are filtered onto costly 0.02 μm-pore-size ceramic filters for enumeration of viruses with epifluorescence microscopy. Here we describe a cost-effective (ca. 500-fold lower materials cost) alternative virus enumeration method in which fluorescently-stained samples are wet-mounted directly onto slides, after optional chemical flocculation of viruses in samples with viral concentrations <5×107 mL-1. The concentration of viruses in the sample is then determined from the ratio of viruses to a known concentration of added microsphere beads via epifluorescence microscopy. Virus concentrations obtained using this wet-mount method, with and without chemical flocculation, were significantly correlated with, and had equivalent precision to, those from the filter-mount method across concentrations ranging from 2.17×106 to 1.37×108 viruses mL-1 when tested using cultivated viral isolates and natural samples from marine and freshwater environments. In summary, the wet-mount method is significantly less expensive than the filter-mount method, and is appropriate for rapid, precise and accurate enumeration of aquatic viruses over a wide range of viral concentrations (≥1×106 viruses mL-1) encountered in field and laboratory samples.

 

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Accelerated pace of discovery transforms marine virology

Accelerated pace of discovery transforms marine virology | Aquatic Viruses | Scoop.it

Marine viruses have important roles in microbial mortality, gene transfer, metabolic reprogramming and biogeochemical cycling. In this Review, we discuss recent technological advances in marine virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology. We also describe the reprogramming of microbially driven processes by viral metabolic genes, the identification of novel viruses using cultivation-dependent and cultivation-independent tools, and the potential for modelling studies to provide a framework for studying virus–host interactions. These transformative advances have set a rapid pace in exploring and predicting how marine viruses manipulate and respond to their environment.

  

Ed Rybicki's insight:

Excellent stuff!!  I have been fascinated by this field for years; I only hope we can stay in it a while.

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Rising to the challenge: accelerated pace of discovery transforms marine virology : Nature Reviews Microbiology : Nature Publishing Group

Mya Breitbart's insight:

Fantastic new review about recent advances in marine virology by Jenn Brum and Matt Sullivan@

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Looking at protists as a source of pathogenic viruses

Looking at protists as a source of pathogenic viruses | Aquatic Viruses | Scoop.it

In the environment, protozoa are predators of bacteria and feed on them. The possibility that some protozoa could be a source of human pathogens is consistent with the discovery that free-living amoebae were the reservoir of Legionella pneumophila, the agent of Legionnaires' disease. Later, while searching for Legionella in the environment using amoeba co-culture, the first giant virus, Acanthamoeba polyphaga mimivirus, was discovered. Since then, many other giant viruses have been isolated, includingMarseilleviridae, Pithovirus sibericum, Cafeteria roenbergensis virus and Pandoravirus spp. The methods used to isolate all of these viruses are herein reviewed. By analogy to Legionella, it was originally suspected that these viruses could be human pathogens. After showing by indirect evidence, such as sero-epidemiologic studies, that it was possible for these viruses to be human pathogens, the recent isolation of some of these viruses (belonging to the Mimiviridae and Marseilleviridae families) in humans in the context of pathologic conditions shows that they are opportunistic human pathogens in some instances.

 

Mimivirus picture courtesy of Russell Kightley Media

  

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Characterisation of three novel giant viruses reveals huge diversity among viruses infecting Prymnesiales (Haptophyta)

We have isolated three novel lytic dsDNA-viruses from Raunefjorden (Norway) that are putative members of the Mimiviridae family, namely Haptolina ericina virus RF02 (HeV RF02), Prymnesium kappa virus RF01 (PkV RF01), and Prymnesium kappa virus RF02 (PkV RF02). Each of the novel haptophyte viruses challenges the common conceptions of algal viruses with respect to host range, phylogenetic affiliation and size. PkV RF01 has a capsid of ~310 nm and is the largest algal virus particle ever reported while PkV RF01 and HeV RF02 were able to infect different species, even belonging to different genera. Moreover, PkV RF01 and HeV RF02 infected the same hosts, but phylogenetic analysis placed them in different groups. Our results reveal large variation among viruses infecting closely related microalgae, and challenge the common conception that algal viruses have narrow host range, and phylogeny reflecting their host affiliation.

  
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Thanks Mya!

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MERS-CoV in Korea and China

MERS-CoV in Korea and China | Aquatic Viruses | Scoop.it
The World Health Organization reports on newly confirmed cases of Middle East respiratory syndrome coronavirus infections in the two countries, as well as in Qatar and Saudi Arabia.
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SARS-CoV started this way....

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Ocean's hidden world of plankton revealed in 'enormous database'

Ocean's hidden world of plankton revealed in 'enormous database' | Aquatic Viruses | Scoop.it
Thousands of species of the ocean's tiniest organisms are revealed in a series of studies.

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Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton

Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton | Aquatic Viruses | Scoop.it
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
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Haloviruses of archaea, bacteria, and eukaryotes

Hypersaline environments up to near saturation are rich reservoirs of extremophilic viruses. One milliliter of salt water may contain up to 109 viruses which can also be trapped inside salt crystals. To date, most of the ∼100 known halovirus isolates infect extremely halophilic archaea, although a few bacterial and eukaryotic viruses have also been described. These isolates comprise tailed and tailless icosahedral, pleomorphic, and lemon-shaped viruses which have been classified according to features such as host range, genome type, and replication. Recent studies have revealed that viruses can be grouped into a few structure-based viral lineages derived from a common ancestor based on conserved virion architectural principles and the major capsid protein fold.

Ed Rybicki's insight:

...and we're looking for them...B-)  Hey, Flavia and Maya?!

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New 'Intraterrestrial' Virus Found in Ocean Depths

New 'Intraterrestrial' Virus Found in Ocean Depths | Aquatic Viruses | Scoop.it

There are some pretty strange creatures found in the extreme temperature and pressure environment of the ocean bottom. But some of the weirdest are archaea, a primitive single-celled microorganism that scientists believe resemble the earliest life forms in the planet’s seas 3.5 billion years ago. Some archaea, which resemble bacteria but have a different genetic makeup, have developed the ability to eat methane and breathe sulfur or metal instead of oxygen — qualities that enable it to survive in deep ocean methane seeps on the sea floor, which would be inhospitable to most life forms.

 

But now, scientists from the University of California-Santa Barbara, supported by a National Science Foundation grant, have found something that’s even weirder. They’ve discovered a new virus that infects archaea, and in the process actually targets one of its own genes for mutation. Interestingly, the archaea itself has a similar ability to modify its genes.

  

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Influence of environmental variables in the efficiency of phage therapy in aquaculture

Influence of environmental variables in the efficiency of phage therapy in aquaculture | Aquatic Viruses | Scoop.it
Aquaculture facilities worldwide continue to experience significant economic losses because of disease caused by pathogenic bacteria, including multidrug-resistant strains. This scenario drives the search for alternative methods to inactivate pathogenic ...
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Metagenomic characterization of viral communities in corals

Metagenomic characterization of viral communities in corals | Aquatic Viruses | Scoop.it

Reef-building corals form close associations with organisms from all three domains of life and therefore have many potential viral hosts. Yet knowledge of viral communities associated with corals is barely explored. This complexity presents a number of challenges in terms of the metagenomic assessments of coral viral communities and requires specialized methods for purification and amplification of viral nucleic acids, as well as virome annotation. In this minireview, we conduct a meta-analysis of the limited number of existing coral virome studies, as well as available coral transcriptome and metagenome data, to identify trends and potential complications inherent in different methods. The analysis shows that the method used for viral nucleic acid isolation drastically affects the observed viral assemblage and interpretation of the results. Further, the small number of viral reference genomes available, coupled with short sequence read lengths might cause errors in virus identification. Despite these limitations and potential biases, the data show that viral communities associated with corals are diverse, with double- and single-stranded DNA and RNA viruses. The identified viruses are dominated by double-stranded DNA-tailed bacteriophages, but there are also viruses that infect eukaryote hosts, likely the endosymbiotic dinoflagellates, Symbiodinium spp., host coral and other eukaryotes in close association.

 
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Life in a phage world

Life in a phage world | Aquatic Viruses | Scoop.it

To celebrate a century of phage exploration, we invite you to get intimate with 30 diverse phages in this premier phage field guide. In these 404 pages you'll learn who these phages are, where on Earth they've been found, who their close relatives are, how their genomes are structured, and how they trick their hosts into submission. Researchers who have devoted their lives to phage also recount their experiences in pursuit of their quarry.

 
Ed Rybicki's insight:

WHAT a good idea - in our continuing celebration of The Centenary of the Phage.  Thanks Zwirko!

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Diverse small circular DNA viruses circulating amongst estuarine molluscs

Diverse small circular DNA viruses circulating amongst estuarine molluscs | Aquatic Viruses | Scoop.it

Our understanding of the diversity and abundance of circular replication associated protein (Rep) – encoding single stranded (CRESS) DNA viruses has increased considerably over the last few years due to a combination of modern sequencing technologies and new molecular tools. Studies have used these to identify and recover CRESS DNA viruses from a range of different marine organisms, including copepods, shrimp and molluscs. In our study we identify 79 novel CRESS DNA viruses from three mollusc species (Austrovenus stutchburyi, Paphies subtriangulata and Amphibola crenata) and benthic sediments from the Avon-Heathcote estuary in Christchurch, New Zealand. The genomes recovered have varying genome architectures, with all encoding at least two major ORFs that have either unidirectional or bidirectional organisation. Analysis of the Reps of the viral genomes showed they are all highly diverse, with only one Rep sequence sharing 65% amino acid identity with the Rep of gastropod-associated circular DNA virus (GaCSV). Our study adds significantly to the wealth of CRESS DNA viruses recovered from freshwater and marine environments and extends our knowledge of the distribution of these viruses.

 

Ed Rybicki's insight:

Geminivirologists: they get everywhere.  Like ssDNA viruses B-)

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Oysters as hot spots for mimivirus isolation

Oysters as hot spots for mimivirus isolation | Aquatic Viruses | Scoop.it

Viruses are ubiquitous organisms, but their role in the ecosystem and their prevalence are still poorly understood. Mimiviruses are extremely complex and large DNA viruses. Although metagenomic studies have suggested that members of the family Mimiviridae are abundant in oceans, there is a lack of information about the association of mimiviruses with marine organisms. In this work, we demonstrate by molecular and virological methods that oysters are excellent sources for mimiviruses isolation. Our data not only provide new information about the biology of these viruses but also raise questions regarding the role of oyster consumption as a putative source of mimivirus infection in humans.

 

Mimivirus graphic courtesy of Russell Kightley Media

 

Ed Rybicki's insight:

Damn things are everywhere!

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The expanding family Marseilleviridae

The family Marseilleviridae encompasses giant viruses that replicate in free-living Acanthamoebaamoebae. Since the discovery of the founding member Marseillevirus in 2007, 7 new marseilleviruses have been observed, including 3 from environmental freshwater, one from a dipteran, and two from symptom-free humans. Marseilleviruses have ≈250-nm-large icosahedral capsids and 346–386-kb-long mosaic genomes that encode 444–497 predicted proteins. They share a small set of core genes with Mimivirus and other large and giant DNA viruses that compose a monophyletic group, first described in 2001. Comparative genomics analyses indicate that the family Marseilleviridae currently includes three lineages and a pan-genome composed of ≈600 genes. Antibodies against marseilleviruses and viral DNA have been observed in a significant proportion of asymptomatic individuals and in the blood and lymph nodes of a child with adenitis; these observations suggest that these giant viruses may be blood borne and question if they may be pathogenic in humans.

  
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Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

Virophages are a unique group of circular double-stranded DNA viruses that are considered parasites of giant DNA viruses, which in turn are known to infect eukaryotic hosts. In this study, the genomes of three novel Yellowstone Lake virophages (YSLVs)—YSLV5, YSLV6, and YSLV7—were identified from Yellowstone Lake through metagenomic analyses. The relative abundance of these three novel virophages and previously identified Yellowstone Lake virophages YSLV1 to -4 were determined in different locations of the lake, revealing that most of the sampled locations in the lake, including both mesophilic and thermophilic habitats, had multiple virophage genotypes. This likely reflects the diverse habitats or diversity of the eukaryotic hosts and their associated giant viruses that serve as putative hosts for these virophages. YSLV5 has a 29,767-bp genome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a close evolutionary relationship with YSLV1 to -4, whereas YSLV5 and YSLV7 are distantly related to the others, and YSLV7 represents the fourth novel virophage lineage. In addition, the genome of YSLV5 has a G+C content of 51.1% that is much higher than all other known virophages, indicating a unique host range for YSLV5. These results suggest that virophages are abundant and have diverse genotypes that likely mirror diverse giant viral and eukaryotic hosts within the Yellowstone Lake ecosystem.

 
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Thanks Chris!

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Diversity of viral photosystem-I psaA genes

Diversity of viral photosystem-I psaA genes | Aquatic Viruses | Scoop.it

Marine photosynthesis is one of the major contributors to the global carbon cycle and the world’s oxygen supply. This process is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding photosystem-II (PSII) reaction center proteins are found in many cyanophage genomes, and are expressed during the infection of their hosts. On the basis of metagenomics, cyanophage photosystem-I (PSI) gene cassettes were recently discovered with two gene arrangements psaJFCABKED and psaDCAB. It was suggested that the horizontal transfer of PSII and PSI genes is increasing phage fitness. To better understand their diversity, we designed degenerate primers to cover a wide diversity of organisms, and using PCR we targeted the psaCA arrangement, which is unique to cyanophages cassettes. We examined viral concentrates from four islands in the Pacific Ocean and found samples containing the psaCA arrangement. Analyses of the amplified viral psaA gene revealed six subgroups varying in their level of similarity and %G+C content, suggesting that the diversity of cyanophage PSI genes is greater than originally thought.

 
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