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Deep-ocean carbon sinks: Basic research on dark ocean microorganisms

Deep-ocean carbon sinks: Basic research on dark ocean microorganisms | Aquatic Viruses | Scoop.it

Although microbes that live in the so-called "dark ocean"-- below a depth of some 600 feet where light doesn't penetrate -- may not absorb enough carbon to curtail global warming, they do absorb considerable amounts of carbon and merit further 

study.

That is one of the findings of a paper published in the International Society of Microbial Ecology (ISME) Journal by Tim Mattes, associate professor of civil and environmental engineering in the University of Iowa College of Engineering, and his colleagues.

Mattes says that while many people are familiar with the concept of trees and grass absorbing carbon from the air, bacteria, and ancient single-celled organisms called "archaea" in the dark ocean hold between 300 million and 1.3 billion tons of carbon.

"A significant amount of carbon fixation occurs in the dark ocean," says Mattes. "What might make this surprising is that carbon fixation is typically linked to organisms using sunlight as the energy source."

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Aquatic Viruses
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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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Vaccine for Mers coronavirus 'looks promising'

Vaccine for Mers coronavirus 'looks promising' | Aquatic Viruses | Scoop.it
A prototype vaccine against the lung infection MERS coronavirus shows promising results, scientists say.
Ed Rybicki's insight:

Be nice IF THEY SAID WHAT IT WAS!!

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'Fishing expedition' nets nearly tenfold increase in number of sequenced virus genomes

'Fishing expedition' nets nearly tenfold increase in number of sequenced virus genomes | Aquatic Viruses | Scoop.it
Using a specially designed computational tool as a lure, scientists have netted the genomic sequences of almost 12,500 previously uncharacterized viruses from public databases.
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Biodiversity and distribution of polar freshwater DNA viruses

Biodiversity and distribution of polar freshwater DNA viruses | Aquatic Viruses | Scoop.it

Viruses constitute the most abundant biological entities and a large reservoir of genetic diversity on Earth. Despite the recent surge in their study, our knowledge on their actual biodiversity and distribution remains sparse. We report the first metagenomic analysis of Arctic freshwater viral DNA communities and a comparative analysis with other freshwater environments. Arctic viromes are dominated by unknown and single-stranded DNA viruses with no close relatives in the database. These unique viral DNA communities mostly relate to each other and present some minor genetic overlap with other environments studied, including an Arctic Ocean virome. Despite common environmental conditions in polar ecosystems, the Arctic and Antarctic DNA viromes differ at the fine-grain genetic level while sharing a similar taxonomic composition. The study uncovers some viral lineages with a bipolar distribution, suggesting a global dispersal capacity for viruses, and seemingly indicates that viruses do not follow the latitudinal diversity gradient known for macroorganisms. Our study sheds light into the global biogeography and connectivity of viral communities.

 
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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.
Ed Rybicki's insight:

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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A Vomiting Machine Shows How Viruses Spread in Puke

A Vomiting Machine Shows How Viruses Spread in Puke | Aquatic Viruses | Scoop.it
SOMEWHERE ON THE North Carolina State campus, a machine has been puking vanilla pudding. Aerosolized vomit-pudding sprays out of its mouth, which stretches open in permanent retching position. Unpleasant? Not as unpleasant as the real-life scenario the vomiting machine is testing: whether norovirus spreads through aerosolized human puke.

Bad news, the answer is probably yes, according to the vomiting machine researchers who published their results in PLoS ONE today. Norovirus causes 20 million cases of food poisoning in the US every year—usually on cruises and other confined spaces with cafeterias. The virus is highly contagious. Epidemiologists have long suspected that barfing sends the virus airborne, allowing it to land on new surfaces or, for the especially unlucky bystander, right in his or her mouth. Gross, but very convenient for a virus that causes puking.
Ed Rybicki's insight:

Sweet! B-)

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Team discovers the ancient origins of deadly Lassa virus

Team discovers the ancient origins of deadly Lassa virus | Aquatic Viruses | Scoop.it
Working as part of an international team in the United States and West Africa, a researcher at The Scripps Research Institute (TSRI) has published new findings showing the ancient roots of the deadly Lassa virus, a relative of Ebola virus, and how Lassa virus has changed over time.
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Viral dark matter and virus-host interactions resolved from publicly available microbial genomes

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes | Aquatic Viruses | Scoop.it
The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. Here we mined publicly available bacterial and archaeal genomic datasets to identify 12,498 high‑confidence viral genomes linked to their microbial hosts. These data augment public datasets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that ( i ) 264 new viral genera were identified (doubling known genera) and ( ii ) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and co‑infection prevalences, as well as evaluation of in silico virus-host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.
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Life under the ice: Antarctica

Antarctica’s apparent barrenness hides an abundance of living organisms.

Look in a different direction, however, and the illusion fades. Scott knew this. “As one looks across the barren stretches of the pack, it is sometimes difficult to realise what teeming life exists immediately beneath its surface,” he wrote. “Beneath the placid ice floes and under the calm water pools the old universal warfare is raging incessantly in the struggle for existence.” There is life in Antarctica; you just need to know where to look.

Ed Rybicki's insight:

And Flavia Flaviani's results will add considerably to this richness...B-)

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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.
Ed Rybicki's insight:

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
Ed Rybicki's insight:

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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