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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 Ed Rybicki:

If you would like to help curate it, please:

 

 contact: cupton at uvic dot ca

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Marine ssDNA viruses are a more diverse group of pathogens than previously thought

Marine ssDNA viruses are a more diverse group of pathogens than previously thought | Aquatic Viruses | Scoop.it
Viruses are known as the most abundant and genetically diverse life forms on the planet, but there is still a lack of information on many of the various types that make up this group, including the phylogenetic relationships between them. Single-stranded DNA (ssDNA) viruses have previously been divided up into seven known families and are known to infect many plants and animals, and have small genomes (between 1.4 and 8.5 kb). Of these seven families, there are currently two groups of bacteriophages (Inoviridae andMicroviridae) and five that infect eukaryotes (Nanoviridae and Geminiviridae which infect plants; and Circoviridae, Parvoviridae and Anelloviridae which infect animals). The genomes of these ssDNA viruses are able to encode as few as two genes; a capsid and a replication initiator. 
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Salt on Mars turns ice into water

Salt on Mars turns ice into water | Aquatic Viruses | Scoop.it
Despite below-freezing conditions, a type of salt on Mars may melt ice to form water, just like salts do on Earth's slippery winter walkways and roads.
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And where there's water - even saturated with salts - there's bacteria.  And viruses, obviously.

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High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments | Aquatic Viruses | Scoop.it

Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (~14 Ma old) and the most oligotrophic subsurface sediments of the world’s oceans (South Pacific Gyre (SPG)). The numbers of viruses (104–109 cm−3, counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.

 
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A Framework for a Marine Biodiversity Observing Network Within Changing Continental Shelf Seascapes

A Framework for a Marine Biodiversity Observing Network Within Changing Continental Shelf Seascapes | Aquatic Viruses | Scoop.it

Continental shelves and the waters overlying them support numerous industries as diverse as tourism and recreation, energy extraction, fisheries, transportation, and applications of marine bio-molecules (e.g., agribusiness, food processing, pharmaceuticals). Although these shelf ecosystems exhibit impacts of climate change and increased human use of resources (Halpern et al., 2012; IPCC, 2013, 2014; Melillo et al., 2014), there are currently no standardized metrics for assessing changes in ecological function in the coastal ocean. Here, we argue that it is possible to monitor vital signs of ecosystem function by focusing on the lowest levels of the ocean food web. Establishment of biodiversity, biomass, and primary productivity baselines and continuous evaluation of changes in biological resources in these economically and ecologically valuable regions requires an internationally coordinated monitoring effort that fully integrates natural, social, and economic sciences to jointly identify problems and design solutions. Such an ocean observing network is needed to protect the livelihoods of coastal communities in the context of the goals of the Future Earth program (Mooney et al., 2013) and of the Intergovernmental Platform on Biodiversity and Ecosystem Services (http://www.ipbes.net). The tools needed to initiate these assessments are available today.

 
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The elemental composition of marine virus particles

In marine environments, virus-mediated lysis of host cells leads to the release of cellular carbon and nutrients and is hypothesized to be a major driver of carbon recycling on a global scale. However, efforts to characterize the effects of viruses on nutrient cycles have overlooked the geochemical potential of the virus particles themselves, particularly with respect to their phosphorus content. In this Analysis article, we use a biophysical scaling model of intact virus particles that has been validated using sequence and structural information to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. By extrapolating particle-scale estimates to the ecosystem scale, we propose that, under certain circumstances, marine virus populations could make an important contribution to the reservoir and cycling of oceanic phosphorus.

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Expression and characterization of major capsid protein of C roenbergensis virus

The genome of CroV has a size of 744kb and encodes for 544 predicted genes. CroV derived its name from its host, a unicellular marine zooplankton Cafeteria roenbergensis (Cro) that is the major microbial grazer in the ocean. By controlling Cro's population, CroV has a great impact on the marine ecological system. CroV is covered by a protein shell (capsid) comprised of major capsid proteins (MCP) and minor capsid proteins (mCP). The capsid not only protects the genetic material of the virus, but also helps in host-virus recognition, which is the critical initial step for viral infection. This research focuses on obtaining large amount homogenous CroV MCP for future structural studies that will facilitate the understanding of the roles of MCP in the viral life cycle. 

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The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics

The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics | Aquatic Viruses | Scoop.it

Viruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the RNA virioplankton is dominated by viruses with positive-sense, single-stranded (+ss) genomes that have features in common with those of eukaryote-infecting viruses in the order Picornavirales (picornavirads). In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics. Amplification of RNA-dependent RNA polymerase (RdRp) genes from fractions of a buoyant density gradient suggested that the distribution of two major subclades of the marine picornavirads was largely congruent with the distribution of total virus-like RNA, a finding consistent with their proposed dominance. Analyses of the RdRp sequences in the library revealed the presence of many diverse phylotypes, most of which were related only distantly to those of cultivated viruses. Phylogenetic analysis suggests that there were hundreds of unique picornavirad-like phylotypes in one 35-liter sample that differed from one another by at least as much as the differences among currently recognized species. Assembly of the sequences in the metagenome resulted in the reconstruction of six essentially complete viral genomes that had features similar to viruses in the families Bacillarna-, Dicistro-, and Marnaviridae. Comparison of the tropical seawater metagenomes with those from other habitats suggests that +ssRNA viruses are generally the most common types of RNA viruses in aquatic environments, but biases in library preparation remain a possible explanation for this observation.

 
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Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing | Aquatic Viruses | Scoop.it

Thanks to high-throughput sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research; thus, we are experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data. However, there are currently no common standards used to convey the quality, and therefore utility, of these various genome sequences. Here, we propose five “standard” categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing.


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Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

Viruses are the most abundant biological entities in the oceans and a pervasive cause of mortality of microorganisms that drive biogeochemical cycles. Although the ecological and evolutionary effects of viruses on marine phototrophs are well recognized, little is known about their impact on ubiquitous marine lithotrophs. Here, we report 18 genome sequences of double-stranded DNA viruses that putatively infect widespread sulfur-oxidizing bacteria. Fifteen of these viral genomes contain auxiliary metabolic genes for the α and γ subunits of reverse dissimilatory sulfite reductase (rdsr). This enzyme oxidizes elemental sulfur, which is abundant in the hydrothermal plumes studied here. Our findings implicate viruses as a key agent in the sulfur cycle and as a reservoir of genetic diversity for bacterial enzymes that underpin chemosynthesis in the deep oceans.

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Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein

Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein | Aquatic Viruses | Scoop.it

The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae [microvirus-like] were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles.

 

Ed Rybicki's insight:

GREAT paper!  As someone with a keen interest in ssDNA viruses - of eukaryotes, though - it is interesting that these should have missed so badly in traditional metagenome screens. Meaning those ones which don't target circular ssDNA.

 

We shall be doing this stuff on desert water, just see if we don't.

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Life By The Numbers: Viruses!

Life By The Numbers: Viruses! | Aquatic Viruses | Scoop.it
Episode Extra: Life By The Numbers


How do we know how many viruses there are in the ocean?


(This post helps explain some of the science in the latest episode of my show. It’s impossible to get all the details into a few minutes. Watch the episode here if you haven’t already. Seriously. Watch it, already!)


A lot of people seem pretty blown away by one of the numbers I presented in the video, that all the viruses in the ocean, laid end-to-end, would stretch 100 times the diameter of the Milky Way. Here’s where that number comes from:


Curtis Suttle is a biologist at the University of British Columbia who studies marine viruses. In a 2005 Nature paper, he explained how quickly our knowledge of viruses in the seas is growing and how much impact they have on the marine biosphere. First, the math:


After spending years counting (yes, counting) viruses in different parts of the ocean, Suttle determined that any liter of seawater contains about 3 billion viruses (3x109). There’s more near the surface, and fewer deep down (even viruses 100 meters below the seabed!), but that’s an average. These include viruses from many different families, although distant oceans can house viruses with nearly identical genes. This means that the ocean’s viruses are constantly swapping and trading genetic material. Think about what that means for how they drive evolution in marine environments! 


Marine biologists have estimated (ESTIMATED) that the oceans hold about  1.3x1021 liters of seawater. Good luck reconciling that number in your head. It’s kind of impossible. Do the math and you get 4x1030 viruses, also a rather ridiculous number. Viruses vary in size quite a bit, but using an average of 100 nanometers, that means they would span 10 million light years. One light year is almost 6 trillion miles, so you can see where this is going … express train to silly-ville. The Milky Way is about 100,000 light years across, so that’s where the number comes from.


Even more interesting is the weight of viruses in the ocean. Ecologists often measure biomass in carbon, because it’s important how much of these building blocks of organic life a particular piece of life (or dead stuff) contains. When something containing a lot of carbon dies, that carbon has to be recycled somewhere. Things that are made of a lot of carbon have to eat a lot of carbon. See what I mean?


The average virus contains about 0.2 femtograms of carbon, which isn’t much by itself. But all of them together contain 200 megatons of carbon, which is the same amount of carbon in 75 million blue whales.


Why is that important? I mean, you can’t picture what 75 million blue whales look like, right? But maybe you can imagine the impact 75 million blue whales could have on the ocean ecosystem. It would be significant to say the least. That’s why it’s important to understand how even the smallest units of the biosphere can really throw their weight around when viewed as a whole.


Does this mean viruses are a successful species? What do you think?
Ed Rybicki's insight:

Naturlich...!!

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Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing | Aquatic Viruses | Scoop.it

Recent advances in molecular approaches and DNA sequencing have greatly progressed the field of ecology and allowed for the study of complex communities in unprecedented detail. Next generation sequencing (NGS) can reveal powerful insights into the diversity, composition, and dynamics of cryptic organisms, but results may be sensitive to a number of technical factors, including molecular practices used to generate amplicons, sequencing technology, and data processing. Despite the popularity of some techniques over others, explicit tests of the relative benefits they convey in molecular ecology studies remain scarce. Here we tested the effects of PCR replication, sequencing depth, and sequencing platform on ecological inference drawn from environmental samples of soil fungi. We sequenced replicates of three soil samples taken from pine biomes in North America represented by pools of either one, two, four, eight, or sixteen PCR replicates with both 454 pyrosequencing and Illumina MiSeq. Increasing the number of pooled PCR replicates had no detectable effect on measures of α- and β-diversity. Pseudo-β-diversity – which we define as dissimilarity between re-sequenced replicates of the same sample – decreased markedly with increasing sampling depth. The total richness recovered with Illumina was significantly higher than with 454, but measures of α- and β-diversity between a larger set of fungal samples sequenced on both platforms were highly correlated. Our results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs. This study also demonstrates the potential for continuous integration of older datasets with newer technology.

 
Via Mel Melendrez-Vallard, burkesquires
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Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries

In 2003, Acanthamoeba polyphaga mimivirus (APMV) was first described and began to impact researchers around the world, due to its structural and genetic complexity. This virus founded the family Mimiviridae. In recent years, several new giant viruses have been isolated from different environments and specimens. Giant virus research is in its initial phase and information that may arise in the coming years may change current conceptions of life, diversity and evolution. Thus, this review aims to condense the studies conducted so far about the features and peculiarities of APMV, from its discovery to its clinical relevance.

Via Ken Yaw Agyeman-Badu
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Get the ocean's 'fingerprint' in a water sample

Get the ocean's 'fingerprint' in a water sample | Aquatic Viruses | Scoop.it
Scientists say eDNA sampling techniques could make assessing the biodiversity of marine ecosystems as easy as taking a water sample.
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Ostreid herpesvirus 1 infection among Pacific oysters, Crassostrea giga, spat: virus replication and circulation related to water temperature prior the onset of mortality

A number of bivalve species worldwide, including the Pacific oyster,Crassostrea gigas, have been affected by mass mortality events associated with herpesviruses and resulting in significant losses. A particular herpesvirus was purified from naturally infected larval Pacific oysters and its genome was entirely sequenced. This virus has been classified asOstreid herpesvirus 1 (OsHV-1) within the Malacoherpesviridae family. Since 2008, mass mortality outbreaks among C. gigas in Europe have been related to the detection of a variant of OsHV-1 called μVar.

Additional data is necessary to better describe mortality events in relation with environmental parameter fluctuations and OsHV-1 detection. For this purpose, a single batch of Pacific oyster spat was deployed in 4 different locations in the Marennes-Oleron area (France) including a pond (“claire”), a shellfish nursery and two locations in the field. Mortality rates were recorded based on regular observation and samples were collected to search and quantify OsHV-1 DNA by real time PCR. Although similar massive mortality rates were reported at 4 sites, mortality was detected earlier in the pond and in the nursery than at both field sites. This difference may be related to earlier increases of water temperature. Mass mortality was observed among oysters a few days after increases of the number of PCR positive oysters and viral DNA amounts were recorded. A initial increment in the number of PCR positive oysters was reported at both field sites during the survey in absence of significant mortality. During this period the water temperature was below 16°C.

Ed Rybicki's insight:

Clever idea: trawling for viruses with bait organisms in an aquaculture setting.

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Viruses: unlocking the greatest biodiversity on Earth

Viruses: unlocking the greatest biodiversity on Earth | Aquatic Viruses | Scoop.it
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I would have loved to have been there.

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Plant genomes enclose footprints of past infections by giant virus relatives

Plant genomes enclose footprints of past infections by giant virus relatives | Aquatic Viruses | Scoop.it

Nucleocytoplasmic large DNA viruses (NCLDVs) are eukaryotic viruses with large genomes (100 kb–2.5 Mb), which include giant Mimivirus, Megavirus and Pandoravirus. NCLDVs are known to infect animals, protists and phytoplankton but were never described as pathogens of land plants. Here, we show that the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii have open reading frames (ORFs) with high phylogenetic affinities to NCLDV homologues. The P. patens genes are clustered in DNA stretches (up to 13 kb) containing up to 16 NCLDV-like ORFs. Molecular evolution analysis suggests that the NCLDV-like regions were acquired by horizontal gene transfer from distinct but closely related viruses that possibly define a new family of NCLDVs. Transcriptomics and DNA methylation data indicate that the NCLDV-like regions are transcriptionally inactive and are highly cytosine methylated through a mechanism not relying on small RNAs. Altogether, our data show that members of NCLDV have infected land plants.

  
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Ed Rybicki's curator insight, June 30, 7:29 AM

They're everywhere....including in moss and other genomes, apparently.

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The virion of Cafeteria roenbergensis virus contains a complex suite of proteins for transcription and DNA repair

Cafeteria roenbergensis virus (CroV) is a giant virus of the Mimiviridae family that infects the marine phagotrophic flagellate C. roenbergensis. CroV possesses a DNA genome of ~730 kilobase pairs that is predicted to encode 544 proteins. We analyzed the protein composition of purified CroV particles by liquid chromatography–tandem mass spectrometry (LC–MS/MS) and identified 141 virion-associated CroV proteins and 60 host proteins. Data are available via ProteomeXchange with identifier PXD000993. Predicted functions could be assigned to 36% of the virion proteins, which include structural proteins as well as enzymes for transcription, DNA repair, redox reactions and protein modification. Homologs of 36 CroV virion proteins have previously been found in the virion of Acanthamoeba polyphaga mimivirus. The overlapping virion proteome of CroV and Mimivirus reveals a set of conserved virion protein functions that were presumably present in the last common ancestor of the Mimiviridae.

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I love this stuff: I am going to work VERY hard at getting money to carry on with our modest project.

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PRIDE Archive: Virion proteome of Cafeteria roenbergensis virus strain BV-PW1

PRIDE Archive: Virion proteome of Cafeteria roenbergensis virus strain BV-PW1 | Aquatic Viruses | Scoop.it
EMBL-EBI

This project describes the protein composition of the Cafeteria roenbergensis virus (CroV, strain BV-PW1: TaxID 693272) particle, a giant marine DNA virus that infects the heterotrophic nanoflagellate microeukaryote C. roenbergensis. CroV is a member of the Nucleo-Cytoplasmic Large DNA Virus clade and related to Acanthamoeba polyphaga mimivirus. CroV possesses a DNA genome of ~730 kilobase pairs that encodes 544 predicted proteins. We analyzed the protein composition of purified CroV particles by liquid chromatography - tandem mass spectrometry (LC-MS/MS) and identified 141 virion-associated CroV proteins. Predicted functions could be assigned to 37% of these proteins, which include structural proteins as well as enzymes for transcription, DNA repair, redox reactions and protein modification. Homologs of 36 CroV virion proteins have previously been found in the virion of Acanthamoeba polyphaga mimivirus. This study shows that giant DNA virus particles contain more than one hundred viral proteins that include specific enzymatic functions.

 
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Metagenomic analysis of the viral community in Namib Desert hypoliths

Metagenomic analysis of the viral community in Namib Desert hypoliths | Aquatic Viruses | Scoop.it

Hypolithic microbial communities are specialized desert communities inhabiting the underside of translucent rocks. Here, we present the first study of the viral fraction of these communities isolated from the hyperarid Namib Desert. The taxonomic composition of the hypolithic viral communities was investigated and a functional assessment of the sequences determined. Phylotypic analysis showed that bacteriophages belonging to the order Caudovirales, in particular the family Siphoviridae, were most prevalent. Functional analysis and comparison with other metaviromes revealed a relatively high frequency of cell wall-degrading enzymes, ribonucleotide reductases (RNRs) and phage-associated genes. Phylogenetic analyses of terL and phoH marker genes indicated that many of the sequences were novel and distinct from known isolates, and the class distribution of the RNRs suggests this is a novel environment. The composition of the viral hypolith fraction containing many Bacillus-infecting phages was not completely consistent with Namib hypolith phylotypic surveys of the bacterial hosts, in which the cyanobacterial genus Chroococcidiopsis was found to be dominant. This could be attributed to the lacking of sequence information about hypolith viruses/bacteria in public databases or the possibility that hypolithic communities incorporate viruses from the surrounding soil.

 

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Not quite aquatic, but metagenomic nonetheless.  A good practice ground!!

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Infographic: What You Need To Know About MERS

Infographic: What You Need To Know About MERS | Aquatic Viruses | Scoop.it

With a second MERS case reported in the US, and growing concern globally over the threat we face from middle east respiratory syndrome, this infographic takes you through the current state of play.

 

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Open membranes are the precursors for assembly of large DNA viruses.

Nucleo cytoplasmic large DNA viruses (NCLDVs) are a group of double-stranded DNA viruses that replicate their DNA partly or entirely in the cytoplasm in association with viral factories (VFs). They share about 50 genes suggesting that they are derived from a common ancestor. Using transmission electron microscopy (TEM) and electron tomography (ET) we showed that the NCLDV vaccinia virus (VACV) acquires its membrane from open membrane intermediates, derived from the ER. These open membranes contribute to the formation of a single open membrane of the immature virion, shaped into a sphere by the assembly of the viral scaffold protein on its convex side. We now compare VACV with the NCLDV Mimivirus by TEM and ET and show that the latter also acquires its membrane from open membrane intermediates that accumulate at the periphery of the cytoplasmic VF. In analogy to VACV this membrane is shaped by the assembly of a layer on the convexside of its membrane, likely representing the Mimivirus capsid protein. By quantitative ET we show for both viruses that the open membrane intermediates of assembly adopt an 'open-eight' conformation with a characteristic diameter of 90 nm for Mimi- and 50 nm for VACV. We discuss these results with respect to the common ancestry of NCLDVs and propose a hypothesis on the possible origin of this unusual membrane biogenesis.


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Sequence Depth, Not PCR Replication, Improves Ecological Inference from NGS

Sequence Depth, Not PCR Replication, Improves Ecological Inference from NGS | Aquatic Viruses | Scoop.it

Recent advances in molecular approaches and DNA sequencing have greatly progressed the field of ecology and allowed for the study of complex communities in unprecedented detail. Next generation sequencing (NGS) can reveal powerful insights into the diversity, composition, and dynamics of cryptic organisms, but results may be sensitive to a number of technical factors, including molecular practices used to generate amplicons, sequencing technology, and data processing. Despite the popularity of some techniques over others, explicit tests of the relative benefits they convey in molecular ecology studies remain scarce. Here we tested the effects of PCR replication, sequencing depth, and sequencing platform on ecological inference drawn from environmental samples of soil fungi. We sequenced replicates of three soil samples taken from pine biomes in North America represented by pools of either one, two, four, eight, or sixteen PCR replicates with both 454 pyrosequencing and Illumina MiSeq. Increasing the number of pooled PCR replicates had no detectable effect on measures of α- and β-diversity. Pseudo-β-diversity – which we define as dissimilarity between re-sequenced replicates of the same sample – decreased markedly with increasing sampling depth. The total richness recovered with Illumina was significantly higher than with 454, but measures of α- and β-diversity between a larger set of fungal samples sequenced on both platforms were highly correlated. Our results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs. This study also demonstrates the potential for continuous integration of older datasets with newer technology.

 
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Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities

Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities | Aquatic Viruses | Scoop.it

Bacteria–phage coevolution, the reciprocal evolution between bacterial hosts and the phages that infect them, is an important driver of ecological and evolutionary processes in microbial communities. There is growing evidence from both laboratory and natural populations that coevolution can maintain phenotypic and genetic diversity, increase the rate of bacterial and phage evolution and divergence, affect community structure, and shape the evolution of ecologically relevant bacterial traits. Although the study of bacteria–phage coevolution is still in its infancy, with open questions regarding the specificity of the interaction, the gene networks of coevolving partners, and the relative importance of the coevolving interaction in complex communities and environments, there have recently been major advancements in the field. In this review, we sum up our current understanding of bacteria–phage coevolution both in the laboratory and in nature, discuss recent findings on both the coevolutionary process itself and the impact of coevolution on bacterial phenotype, diversity and interactions with other species (particularly their eukaryotic hosts), and outline future directions for the field.

 

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A giant Pseudomonas phage from Poland

A giant Pseudomonas phage from Poland | Aquatic Viruses | Scoop.it

A novel giant phage of the family Myoviridae is described. Pseudomonas phage PA5oct was isolated from a sewage sample from an irrigated field near Wroclaw, Poland. The virion morphology indicates that PA5oct differs from known giant phages. The phage has a head of about 131 nm in diameter and a tail of 136 × 19 nm. Phage PA5oct contains a genome of approximately 375 kbp and differs in size from any tailed phages known. PA5oct was further characterized by determination of its latent period and burst size and its sensitivity to heating, chloroform, and pH.

 
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Sewage is aquatic...B-)

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