Aquatic Viruses
Follow
Find
2.0K views | +0 today
Scooped by Ed Rybicki
onto Aquatic Viruses
Scoop.it!

Pig Flu Virus Strain Shown to Have Pandemic Potential

Pig Flu Virus Strain Shown to Have Pandemic Potential | Aquatic Viruses | Scoop.it
The emergence of the H1N1 influenza virus that leapt from pigs to humans in 2009, triggering a global pandemic, reminded us of the need to monitor animals such as pigs that can host the development of dangerous viral strains.

A study published today re-emphasizes that need. Young-Ki Choi at Chungbuk National University in Cheongju, South Korea, and his colleagues have isolated a new strain of H1N2 influenza from Korean pigs that kills infected ferrets — the model animal of choice for influenza work — and can spread through the air.

 

Be afraid - a little.

more...
No comment yet.
Aquatic Viruses
mol-biol, bioinformatics and biology
Your new post is loading...
Scooped by Chris Upton + helpers
Scoop.it!

Now curated by Ed Rybicki:

If you would like to help curate it, please:

 

 contact: cupton at uvic dot ca

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

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.

 
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

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.

 

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

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.

 
Ed Rybicki's insight:

Sewage is aquatic...B-)

more...
No comment yet.
Rescooped by Ed Rybicki from Virology News
Scoop.it!

Biodiversity: So much more than legs and leaves

Biodiversity: So much more than legs and leaves | Aquatic Viruses | Scoop.it

Microorganisms inhabit virtually every possible niche on Earth, including those at the outer envelope of survival. However, the focus of most conservation authorities and ecologists is the 'legs and leaves' side of biology -the 'macrobiology' that can be seen with the naked eye. There is little apparent concern for the preservation of microbial diversity, or of unique microbial habitats. Here we show examples of the astounding microbial diversity supported by South Africa's ecosystems and argue that because microbes constitute the vast majority of our planet's species they should be considered seriously in the future protection of our genetic resources.

 

Ed Rybicki's insight:

This is our stab at getting South African science funders to take microbial diversity seriously.  I helped write it, obviously.  And it's Open Access!

more...
Ed Rybicki's curator insight, January 28, 4:32 AM

In praise of small things B-)

Scooped by Ed Rybicki
Scoop.it!

Narcolepsy an autoimmune disease - and how it is associated with swine flu

Narcolepsy an autoimmune disease - and how it is associated with swine flu | Aquatic Viruses | Scoop.it

As the H1N1 swine flu pandemic swept the world in 2009, China saw a spike in cases of narcolepsy — a mysterious disorder that involves sudden, uncontrollable sleepiness. Meanwhile, in Europe, around 1 in 15,000 children who were given Pandemrix — a now-defunct flu vaccine that contained fragments of the pandemic virus — also developed narcolepsy, a chronic disease.

Immunologist Elizabeth Mellins and narcolepsy researcher Emmanuel Mignot at Stanford University School of Medicine in California and their collaborators have now partly solved the mystery behind these events, while also confirming a longstanding hypothesis that narcolepsy is an autoimmune disease, in which the immune system attacks healthy cells..

Ed Rybicki's insight:

It has been an interesting set of observations that have led up to this: I have chronicled some of them here in Virology News, as I picked up on how both the H1N1 2009pdm vaccine and the native virus seemed to be associated with narcolepsy.

And now the mystery is partly solved: some genetically-predisposed individuals produce CD4+ T-cells that recognise enogenous hypocretin, that are triggered by swine flu - and perhaps also by other flu virus.

That is, of course, not the whole story - but at least we are part fo the way to understanding how this puzzling and rather disturbing correlation of particular influenza viruses and narcolepsy occurs.

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

The REAL Hard Rock Café: microbial denizens of hardened rocks

The REAL Hard Rock Café: microbial denizens of hardened rocks | Aquatic Viruses | Scoop.it

Scientists are digging deep into the Earth's surface collecting census data on the microbial denizens of the hardened rocks.  What they're finding is that, even miles deep and halfway across the globe, many of these communities are somehow quite similar.

Ed Rybicki's insight:

Hey, it's a microbial planet!  And where there's bugs, there are viruses....

more...
No comment yet.
Rescooped by Ed Rybicki from Virology and Bioinformatics from Virology.ca
Scoop.it!

Viral quasispecies inference from 454 pyrosequencing - BMC Bioinformatics. 2013

AbstractBACKGROUND:

Many potentially life-threatening infectious viruses are highly mutable in nature. Characterizing the fittest variants within a quasispecies from infected patients is expected to allow unprecedented opportunities to investigate the relationship between quasispecies diversity and disease epidemiology. The advent of next-generation sequencing technologies has allowed the study of virus diversity with high-throughput sequencing, although these methods come with higher rates of errors which can artificially increase diversity.

RESULTS:

Here we introduce a novel computational approach that incorporates base quality scores from next-generation sequencers for reconstructing viral genome sequences that simultaneously infers the number of variants within a quasispecies that are present. Comparisons on simulated and clinical data on dengue virus suggest that the novel approach provides a more accurate inference of the underlying number of variants within the quasispecies, which is vital for clinical efforts in mapping the within-host viral diversity. Sequence alignments generated by our approach are also found to exhibit lower rates of error.

CONCLUSIONS:

The ability to infer the viral quasispecies colony that is present within a human host provides the potential for a more accurate classification of the viral phenotype. Understanding the genomics of viruses will be relevant not just to studying how to control or even eradicate these viral infectious diseases, but also in learning about the innate protection in the human host against the viruses.


Via burkesquires
more...
No comment yet.
Rescooped by Ed Rybicki from Virology and Bioinformatics from Virology.ca
Scoop.it!

Agalma: an automated phylogenomics workflow

BACKGROUND:

In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a few genes to hundreds or thousands of genes. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and genomes. Implementing such a phylogenomic study, however, is computationally intensive, requires the coordinated use of many complex software tools, and includes multiple steps for which no published tools exist. Phylogenomic studies have therefore been manual or semiautomated. In addition to taking considerable user time, this makes phylogenomic analyses difficult to reproduce, compare, and extend. In addition, methodological improvements made in the context of one study often cannot be easily applied and evaluated in the context of other studies.

RESULTS:

We present Agalma, an automated tool that constructs matrices for phylogenomic analyses. The user provides raw Illumina transcriptome data, and Agalma produces annotated assemblies, aligned gene sequence matrices, a preliminary phylogeny, and detailed diagnostics that allow the investigator to make extensive assessments of intermediate analysis steps and the final results. Sequences from other sources, such as externally assembled genomes and transcriptomes, can also be incorporated in the analyses. Agalma is built on the BioLite bioinformatics framework, which tracks provenance, profiles processor and memory use, records diagnostics, manages metadata, installs dependencies, logs version numbers and calls to external programs, and enables rich HTML reports for all stages of the analysis. Agalma includes a small test data set and a built-in test analysis of these data. In addition to describing Agalma, we here present a sample analysis of a larger seven-taxon data set. Agalma is available for download at https://bitbucket.org/caseywdunn/agalma.

CONCLUSIONS:

Agalma allows complex phylogenomic analyses to be implemented and described unambiguously as a series of high-level commands. This will enable phylogenomic studies to be readily reproduced, modified, and extended. Agalma also facilitates methods development by providing a complete modular workflow, bundled with test data, that will allow further optimization of each step in the context of a full phylogenomic analysis.


Via burkesquires
Ed Rybicki's insight:

Looks to be good for Marine Viromics?

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Previously unknown and highly divergent ssDNA viruses populate the oceans

Previously unknown and highly divergent ssDNA viruses populate the oceans | Aquatic Viruses | Scoop.it

Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.

 
Ed Rybicki's insight:

Bugger!  We wanted to do this...B-)  I suppose we still can - southern ocean samples!!

more...
No comment yet.
Rescooped by Ed Rybicki from Virology and Bioinformatics from Virology.ca
Scoop.it!

The MaSuRCA genome assembler

The MaSuRCA genome assembler | Aquatic Viruses | Scoop.it

Motivation: Second-generation sequencing technologies produce high coverage of the genome by short reads at a low cost, which has prompted development of new assembly methods. In particular, multiple algorithms based on de Bruijn graphs have been shown to be effective for the assembly problem. In this article, we describe a new hybrid approach that has the computational efficiency of de Bruijn graph methods and the flexibility of overlap-based assembly strategies, and which allows variable read lengths while tolerating a significant level of sequencing error. Our method transforms large numbers of paired-end reads into a much smaller number of longer ‘super-reads’. The use of super-reads allows us to assemble combinations of Illumina reads of differing lengths together with longer reads from 454 and Sanger sequencing technologies, making it one of the few assemblers capable of handling such mixtures. We call our system the Maryland Super-Read Celera Assembler (abbreviated MaSuRCA and pronounced ‘mazurka’).


Via Chris Upton + helpers
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

PLOS Computational Biology: Ten Simple Rules for Cultivating Open Science and Collaborative R&D

PLOS Computational Biology: Ten Simple Rules for Cultivating Open Science and Collaborative R&D | Aquatic Viruses | Scoop.it

How can we address the complexity and cost of applying science to societal challenges?

Open science and collaborative R&D may help [1]–[3]. Open science has been described as “a research accelerator” [4]. Open science implies open access [5] but goes beyond it: “Imagine a connected online web of scientific knowledge that integrates and connects data, computer code, chains of scientific reasoning, descriptions of open problems, and beyond …. tightly integrated with a scientific social web that directs scientists' attention where it is most valuable, releasing enormous collaborative potential.” [1].

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

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."

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

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.

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

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...!!

more...
No comment yet.
Rescooped by Ed Rybicki from Virology and Bioinformatics from Virology.ca
Scoop.it!

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
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Expression patterns reveal niche diversification in a marine microbial assemblage

Expression patterns reveal niche diversification in a marine microbial assemblage | Aquatic Viruses | Scoop.it

Resolving the ecological niches of coexisting marine microbial taxa is challenging due to the high species richness of microbial communities and the apparent functional redundancy in bacterial genomes and metagenomes. Here, we generated over 11 million Illumina reads of protein-encoding transcripts collected from well-mixed southeastern US coastal waters to characterize gene expression patterns distinguishing the ecological roles of hundreds of microbial taxa sharing the same environment. The taxa with highest in situ growth rates (based on relative abundance of ribosomal protein transcripts) were typically not the greatest contributors to community transcription, suggesting strong top-down ecological control, and their diverse transcriptomes indicated roles as metabolic generalists. The taxa with low in situ growth rates typically had low diversity transcriptomes dominated by specialized metabolisms. By identifying protein-encoding genes with atypically high expression for their level of conservation, unique functional roles of community members emerged related to substrate use (such as complex carbohydrates, fatty acids, methanesulfonate, taurine, tartrate, ectoine), alternative energy-conservation strategies (proteorhodopsin, AAnP, V-type pyrophosphatases, sulfur oxidation, hydrogen oxidation) and mechanisms for negotiating a heterogeneous environment (flagellar motility, gliding motility, adhesion strategies). On average, the heterotrophic bacterioplankton dedicated 7% of their transcriptomes to obtaining energy by non-heterotrophic means. This deep sequencing of a coastal bacterioplankton transcriptome provides the most highly resolved view of bacterioplankton niche dimensions yet available, uncovering a spectrum of unrecognized ecological strategies.

 

more...
No comment yet.
Rescooped by Ed Rybicki from Virology News
Scoop.it!

Viruses affect an African flamingo population by killing their bacterial food source

Viruses affect an African flamingo population by killing their bacterial food source | Aquatic Viruses | Scoop.it

Trophic cascade effects occur when a food web is disrupted by loss or significant reduction of one or more of its members. In East African Rift Valley lakes, the Lesser Flamingo is on top of a short food chain. At irregular intervals, the dominance of their most important food source, the cyanobacterium Arthrospira fusiformis, is interrupted. Bacteriophages are known as potentially controlling photoautotrophic bacterioplankton. In Lake Nakuru (Kenya), we found the highest abundance of suspended viruses ever recorded in a natural aquatic system. We document that cyanophage infection and the related breakdown of A. fusiformis biomass led to a dramatic reduction in flamingo abundance. This documents that virus infection at the very base of a food chain can affect, in a bottom-up cascade, the distribution of end consumers. We anticipate this as an important example for virus-mediated cascading effects, potentially occurring also in various other aquatic food webs.


Via Chris Upton + helpers, Ed Rybicki
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Oil- and metal-munching microbes dominate deep sandstone formations

Oil- and metal-munching microbes dominate deep sandstone formations | Aquatic Viruses | Scoop.it
Halomonas are a hardy breed of bacteria. They can withstand heat, high salinity, low oxygen, utter darkness and pressures that would kill most other organisms.

And they "are at least as diverse as their surface-dwelling counterparts" and "Astonishingly little is known of this vast subsurface reservoir of biodiversity, despite our civilization's regular access to and exploitation of subterranean environments"

Ed Rybicki's insight:

...and they eat hydrocarbons...and fracking probably messes with them...basically, we're destroying what amounts to an enire biome without ever finding out anything about it.  Go, us!

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

A context for Chlorella Viruses: Size

A context for Chlorella Viruses: Size | Aquatic Viruses | Scoop.it
Chlorella viruses are big.  Consider the titles of the following review papers dealing with them: The Phycodnaviridae: The Story of How Tiny Giants Rule the World DNA Viruses: The Really Big Ones (...
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Decoding viral puzzles

Decoding viral puzzles | Aquatic Viruses | Scoop.it
The genome of viruses is usually enclosed inside a shell called capsid. Capsids have unique mechanic properties: they have to be resistant and at the same time capable of dissolving in order to release the genome into the infected cell.
Ed Rybicki's insight:

Love that structural stuf....

more...
ComplexInsight's curator insight, December 11, 2013 6:23 AM

interesting paper looking at capsid mechanisms. 

Scooped by Ed Rybicki
Scoop.it!

Metabolic reprogramming by viruses in the sunlit and dark ocean

Metabolic reprogramming by viruses in the sunlit and dark ocean | Aquatic Viruses | Scoop.it
Background

Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.

Results

Here we explore the nature and extent of viral metabolic reprogramming throughout the Pacific Ocean depth continuum. We describe 35 marine viral gene families with potential to reprogram metabolic flux through central metabolic pathways recovered from Pacific Ocean waters. Four of these families have been previously reported but 31 are novel. These known and new carbon pathway auxiliary metabolic genes were recovered from a total of 22 viral metagenomes in which viral auxiliary metabolic genes were differentiated from low-level cellular DNA inputs based on small subunit ribosomal RNA gene content, taxonomy, fragment recruitment and genomic context information. Auxiliary metabolic gene distribution patterns reveal that marine viruses target overlapping, but relatively distinct pathways in sunlit and dark ocean waters to redirect host carbon flux towards energy production and viral genome replication under low nutrient, niche-differentiated conditions throughout the depth continuum.

Conclusions

Given half of ocean microbes are infected by viruses at any given time, these findings of broad viral metabolic reprogramming suggest the need for renewed consideration of viruses in global ocean carbon models.

Ed Rybicki's insight:

Amen!

more...
No comment yet.
Rescooped by Ed Rybicki from Virology and Bioinformatics from Virology.ca
Scoop.it!

Fossil genes and microbes in the oldest ice on Earth

Although the vast majority of ice that formed on the Antarctic continent over the past 34 million years has been lost to the oceans, pockets of ancient ice persist in the Dry Valleys of the Transantarctic Mountains. Here we report on the potential metabolic activity of microbes and the state of community DNA in ice derived from Mullins and upper Beacon Valleys. The minimum age of the former is 100 ka, whereas that of the latter is ≈8 Ma, making it the oldest known ice on Earth. In both samples, radiolabeled substrates were incorporated into macromolecules, and microbes grew in nutrient-enriched meltwaters, but metabolic activity and cell viability were critically compromised with age. Although a 16S rDNA-based community reconstruction suggested relatively low bacterial sequence diversity in both ice samples, metagenomic analyses of community DNA revealed many diverse orthologs to extant metabolic genes. Analyses of five ice samples, spanning the last 8 million years in this region, demonstrated an exponential decline in the average community DNA size with a half-life of ≈1.1 million years, thereby constraining the geological preservation of microbes in icy environments and the possible exchange of genetic material to the oceans.

 


Via Chris Upton + helpers
more...
No comment yet.
Rescooped by Ed Rybicki from Virology and Bioinformatics from Virology.ca
Scoop.it!

Visualizing virus assembly intermediates inside marine cyanobacteria

Abstract - "Cyanobacteria are photosynthetic organisms responsible for ~25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET)1, 2. This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms."
Via C_Fleis
Ed Rybicki's insight:
Cool stuff! We gotta try that - Trevor??
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Viruses associated with coral epidemic of 'white plague'

Viruses associated with coral epidemic of 'white plague' | Aquatic Viruses | Scoop.it

They call it the "white plague," and like its black counterpart from the Middle Ages, it conjures up visions of catastrophic death, with a cause that was at first uncertain even as it led to widespread destruction -- on marine corals in the Caribbean Sea.

Ed Rybicki's insight:

Hah!  ssDNA viruses!!  I must get me to a coral reef with white spots....

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Deep microbes live long and slow

Deep microbes live long and slow | Aquatic Viruses | Scoop.it
A diverse range of life forms exists deep below Earth's surface, but they survive at an incredibly slow pace.  

Long-lived bacteria, reproducing only once every 10,000 years, have been found in rocks 2.5km (1.5 miles) below the ocean floor that are as much as 100 million years old.

Viruses and fungi have also been found.

The discoveries raise questions about how life persists in such extreme conditions.

more...
No comment yet.