Aquatic Viruses
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Iguana marina. Marine Iguana

Iguana marina. Marine Iguana | Aquatic Viruses | Scoop.it
Project Noah is a tool that nature lovers can use to explore and document local wildlife and a common technology platform that research groups can use to harness the power of citizen scientists everywhere.
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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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Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses.

African swine fever virus, a double-stranded DNA virus that infects pigs, is the only known member of the Asfarviridae family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting Acanthamoeba castellanii Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% G+C content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between African swine fever virus, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing African swine fever virus, faustovirus, pacmanvirus, and kaumoebavirus.
IMPORTANCE Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the Asfarviridae family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.
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Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses

Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses | Aquatic Viruses | Scoop.it
Global climate change-induced warming of the Artic seas is predicted to shift the phytoplankton community towards dominance of smaller-sized species due to global warming. Yet, little is known about their viral mortality agents despite the ecological importance of viruses regulating phytoplankton host dynamics and diversity. Here we report the isolation and basic characterization of four prasinoviruses infectious to the common Arctic picophytoplankter Micromonas. We furthermore assessed how temperature influenced viral infectivity and production. Phylogenetic analysis indicated that the putative double-stranded DNA (dsDNA) Micromonas polaris viruses (MpoVs) are prasinoviruses (Phycodnaviridae) of approximately 120 nm in particle size. One MpoV showed intrinsic differences to the other three viruses, i.e., larger genome size (205 ± 2 vs. 191 ± 3 Kb), broader host range, and longer latent period (39 vs. 18 h). Temperature increase shortened the latent periods (up to 50%), increased the burst size (up to 40%), and affected viral infectivity. However, the variability in response to temperature was high for the different viruses and host strains assessed, likely affecting the Arctic picoeukaryote community structure both in the short term (seasonal cycles) and long term (global warming).
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A Student’s Guide to Giant Viruses Infecting Small Eukaryotes: From Acanthamoeba to Zooxanthellae

The discovery of infectious particles that challenge conventional thoughts concerning “what is a virus” has led to the evolution a new field of study in the past decade. Here, we review knowledge and information concerning “giant viruses”, with a focus not only on some of the best studied systems, but also provide an effort to illuminate systems yet to be better resolved. We conclude by demonstrating that there is an abundance of new host–virus systems that fall into this “giant” category, demonstrating that this field of inquiry presents great opportunities for future research.
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Isolation and Characterization of a Double Stranded DNA Megavirus Infecting the Toxin-Producing Haptophyte Prymnesium parvum

Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms globally, leading to large-scale fish kills that have severe ecological and economic implications. For the model haptophyte, Emiliania huxleyi, it has been shown that large dsDNA viruses play an important role in regulating blooms and therefore biogeochemical cycling, but much less work has been done looking at viruses that infect P. parvum, or the role that these viruses may play in regulating harmful algal blooms. In this study, we report the isolation and characterization of a lytic nucleo-cytoplasmic large DNA virus (NCLDV) collected from the site of a harmful P. parvum bloom. In subsequent experiments, this virus was shown to infect cultures of Prymnesium sp. and showed phylogenetic similarity to the extended Megaviridae family of algal viruses.
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Special Issue "Marine Viruses 2016"

Special Issue "Marine Viruses 2016" | Aquatic Viruses | Scoop.it

The aim of this special issue is to highlight the progress in our understanding of the role of viruses in the marine environment by presenting novel research on the ecology, distribution and diversity of marine viruses and the influence of virus-host interactions on e.g. mortality, element cycling and evolution of marine microbial communities.

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Oceans: our allies against climate change

Oceans: our allies against climate change | Aquatic Viruses | Scoop.it
05 Oct 2017 It is well known that forests, especially rainforests, are key allies in our fight against climate change as they absorb greenhouse gas emissions. But did you know that oceans are the earth’s main buffer against climate change?
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What you didn't know about viruses in the ocean 

Marine viruses are the dark matter of the world's oceans. We know more about deep space than we do of the viruses we share Planet Earth with. Together
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Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea

Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea | Aquatic Viruses | Scoop.it
PLoS One. 2017 Jan 25;12(1):e0169841. doi: 10.1371/journal.pone.0169841. eCollection 2017.

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Irido-, polyoma- and a new fish papillomavirus in lymphocystis disease affected gilthead seabream

Lymphocystis disease is a geographically widespread disease affecting more than 150 different species of marine and freshwater fish. The disease, provoked by the iridovirus lymphocystis disease virus (LCDV), is characterized by the appearance of papilloma-like lesions on the skin of affected animals that usually self-resolve over time. Development of the disease is usually associated with several environmental factors and, more frequently, with stress conditions provoked by the intensive culture conditions present in fish farms. In gilthead seabream (Sparus aurata), an economically important cultured fish species in the Mediterranean area, a distinct LCDV has been identified but not completely characterized yet. We have used direct sequencing of the virome of lymphocystis lesions from affected S. aurata to obtain the complete genome of a new LCDV-Sa species that is the largest vertebrate iridovirus sequenced to date. Importantly, this approach allowed us to assemble the full-length circular genome sequence of two previously unknown viruses belonging to the papilloma- and polyomaviruses termed Sparus aurata papillomavirus 1 (SaPV1) and Sparus aurata polyomavirus 1 (SaPyV1), respectively. Epidemiological surveys showed that lymphocystis disease was frequently associated with the concurrent appearance of one or both of the new viruses. SaPV1 has unique characteristics such as an intron within the L1 gene and, as the first member of the Papillomaviridae family described in fish, provides evidence for a more ancient origin of this family than previously thought.
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A Viral Immunity Chromosome in a Marine Picoeukaryote

A Viral Immunity Chromosome in a Marine Picoeukaryote | Aquatic Viruses | Scoop.it
Author Summary We propose that chromosome 19 of O .
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Ocean worlds: The search for life in the solar system’s other seas

Ocean worlds: The search for life in the solar system’s other seas | Aquatic Viruses | Scoop.it
Our best chance to find alien life lies in the vast oceans inside the icy moons of Saturn and Jupiter – and we don’t have to leave Earth to start looking
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And where there's life...yes, yes; viruses!
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Comparison of concentration methods for detection of hepatitis A virus in water samples

Abstract: Hepatitis A virus is a pathogen associated with water pollution. Contaminated drinking water can cause hepatitis A outbreaks, lead to economic losses, and even threaten human lives. It is difficult to detect low levels of hepatitis A virus in water, so the virus must be concentrated in order to quantify it accurately. Here, we present a simple, rapid, efficient technique for the concentration and detection of hepatitis A virus in water. Our data showed that adding phosphate-buffered saline to the water, pre-filtering the water, and adding Trizol reagent directly to the filtration membrane can significantly improve concentration efficiency. Of three types of filtration membranes studied (mixed cellulose ester membrane, polyvinylidene fluoride membrane, and nylon membrane), the concentration efficiency using mixed cellulose ester membrane with a 0.1-μm pore size was the highest, reaching 92.62 ± 5.17%. This method was used to concentrate hepatitis A virus in water samples from Donghu Lake. Using SYBR Green real-time reverse transcription polymerase chain reaction analysis, the detection sensitivity of this method reached 101 copies/μL and its concentration efficiency reached 79.45 ± 9.88%.

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The enigmatic archaeal virosphere

The enigmatic archaeal virosphere | Aquatic Viruses | Scoop.it

One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus–host interactions, including interactions with archaeal CRISPR–Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.

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Marine Viruses: Key Players in Marine Ecosystems

Viruses were recognized as the causative agents of fish diseases, such as infectious pancreatic necrosis and Oregon sockeye disease, in the early 1960s [1], and have since been shown to be responsible for diseases in all marine life from bacteria to protists, mollusks, crustaceans, fish and mammals [2].[...]
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Marine Prasinoviruses and Their Tiny Plankton Hosts: A Review

Marine Prasinoviruses and Their Tiny Plankton Hosts: A Review | Aquatic Viruses | Scoop.it
Viruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism–virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host–virus system for examination of cellular and molecular processes in the marine environment.
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Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment

Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment | Aquatic Viruses | Scoop.it
Effects of elevated pCO2 on Emiliania huxleyi genetic diversity and the viruses that infect E. huxleyi (EhVs) have been investigated in large volume enclosures in a Norwegian fjord. Triplicate enclosures were bubbled with air enriched with CO2 to 760 ppmv whilst the other three enclosures were bubbled with air at ambient pCO2; phytoplankton growth was initiated by the addition of nitrate and phosphate. E. huxleyi was the dominant coccolithophore in all enclosures, but no difference in genetic diversity, based on DGGE analysis using primers specific to the calcium binding protein gene (gpa) were detected in any of the treatments. Chlorophyll concentrations and primary production were lower in the three elevated pCO2 treatments than in the ambient treatments. However, although coccolithophores numbers were reduced in two of the high-pCO2 treatments; in the third, there was no suppression of coccolithophores numbers, which were very similar to the three ambient treatments. In contrast, there was considerable variation in genetic diversity in the EhVs, as determined by analysis of the major capsid protein (mcp) gene. EhV diversity was much lower in the high-pCO2 treatment enclosure that did not show inhibition of E. huxleyi growth. Since virus infection is generally implicated as a major factor in terminating phytoplankton blooms, it is suggested that no study of the effect of ocean acidification in phytoplankton can be complete if it does not include an assessment of viruses.
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Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery

Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery | Aquatic Viruses | Scoop.it
Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses—EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis. The viruses clustered into distinct clades, based on their DNA polymerase gene as well as full genome comparisons. We discuss the use of such clustering and suggest that a gene-by-gene investigation approach may be more useful when the goal is to reveal differences related to functionally important genes. A multi domain “Best BLAST hit” analysis revealed that 84% of the EhV genes have closer similarities to the domain Eukarya. However, 16% of the EhV CDSs were very similar to bacterial genes, contributing to the idea that a significant portion of the gene flow in the planktonic world inter-crosses the domains of life.
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NZ needs a Ministry for the Oceans to protect our huge marine resource

NZ needs a Ministry for the Oceans to protect our huge marine resource | Aquatic Viruses | Scoop.it
OPINION: NZ's seen as a lucky country, but we have to be ambitious to protect one of our jewels.
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Little diatoms have big influence on ocean nutrients - Futurity

Little diatoms have big influence on ocean nutrients - Futurity | Aquatic Viruses | Scoop.it
Diatoms are each just single cells, but they have a significant impact on the dispersal of nutrients and trace elements in global marine waters.
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Did oceans gain, lose, gain ability to support life?

Did oceans gain, lose, gain ability to support life? | Aquatic Viruses | Scoop.it
Early Earth may have had enough oxygen for cells to evolve a billion years before life took hold. "That doesn't mean that they did—but they could have."
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Vast and Pristine, Russia’s Lake Baikal Is Invaded by Toxic Algae

Vast and Pristine, Russia’s Lake Baikal Is Invaded by Toxic Algae | Aquatic Viruses | Scoop.it
Untreated sewage fuels algal blooms in the world’s largest freshwater lake, home to scores of unique plant and animal species.
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Need to get some viruses in there...?
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Transmission of new virus believed to occur between farmed and wild fish

Transmission of new virus believed to occur between farmed and wild fish | Aquatic Viruses | Scoop.it
In 2010, researchers found a new fish virus that was named piscine reovirus (PRV).
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A catalogue of 136 microbial draft genomes from Red Sea metagenomes

A catalogue of 136 microbial draft genomes from Red Sea metagenomes | Aquatic Viruses | Scoop.it
Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance.
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New Planet Found Orbiting Proxima Centauri

New Planet Found Orbiting Proxima Centauri | Aquatic Viruses | Scoop.it
The alien world is warmed by the light of Proxima Centauri, a red dwarf star that sits just 4.24 light-years away.
Ed Rybicki's insight:
And of course, if it has water, it'll have life, and where's there's life, there's viruses B-)
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