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

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 contact: cupton at uvic dot ca

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Factors affecting virus dynamics and microbial host–virus interactions in marine environments

Factors affecting virus dynamics and microbial host–virus interactions in marine environments | Aquatic Viruses | Scoop.it

Marine microorganisms constitute the largest percentage of living biomass and serve as the major driving force behind nutrient and energy cycles. While viruses only comprise a small percentage of this biomass (i.e., 5%), they dominate in numerical abundance and genetic diversity. Through host infection and mortality, viruses affect microbial population dynamics, community composition, genetic evolution, and biogeochemical cycling. However, the field of marine viral ecology is currently limited by a lack of data regarding how different environmental factors regulate virus dynamics and host–virus interactions. The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production. Considering the ecological importance of viruses in the marine ecosystem and the increasing pressure from anthropogenic activity and global climate change on marine systems, a synthesis of existing information provides a timely framework for future research initiatives in viral ecology.

 
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Marine mutants wash up on shore: two-headed dolphin a sign of chemical poisoning tipping point

Marine mutants wash up on shore: two-headed dolphin a sign of chemical poisoning tipping point | Aquatic Viruses | Scoop.it
Marine mutants wash up on shore: two-headed dolphin a sign of chemical poisoning tipping point (Marine mutants wash up on shore: two-headed dolphin a sign of chemical poisoning tipping point http://t.co/4c0zQooEOH)...
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TWiV 301: Marine viruses and insect defense

TWiV 301: Marine viruses and insect defense | Aquatic Viruses | Scoop.it
Vincent speaks with Carla and Curtis about RNA interference and antiviral defense in fruit flies, and viruses in the sea, the greatest biodiversity on Earth.
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A case study of enteric virus removal and insights into the associated risk of water reuse for two wastewater treatment pond systems in Bolivia

A case study of enteric virus removal and insights into the associated risk of water reuse for two wastewater treatment pond systems in Bolivia | Aquatic Viruses | Scoop.it
Mya Breitbart's insight:

Open Access til October - check it out!

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Viruses might tame some algal blooms

Viruses might tame some algal blooms | Aquatic Viruses | Scoop.it
The rapid demise of a giant, carbon-spewing algal bloom points to the influence of viral wranglers.
Ed Rybicki's insight:

We hope so - after all. we've got samples going temporally right through a coupe of blooms!  But not Emiliana huxleyii.

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A microbial ecosystem beneath the West Antarctic ice sheet : Nature : Nature Publishing Group

A microbial ecosystem beneath the West Antarctic ice sheet : Nature : Nature Publishing Group | Aquatic Viruses | Scoop.it
Liquid water has been known to occur beneath the Antarctic ice sheet for more than 40 years, but only recently have these subglacial aqueous environments been recognized as microbial ecosystems that may influence biogeochemical transformations on a global scale. Here we present the first geomicrobiological description of water and surficial sediments obtained from direct sampling of a subglacial Antarctic lake. Subglacial Lake Whillans (SLW) lies beneath approximately 800 m of ice on the lower portion of the Whillans Ice Stream (WIS) in West Antarctica and is part of an extensive and evolving subglacial drainage network. The water column of SLW contained metabolically active microorganisms and was derived primarily from glacial ice melt with solute sources from lithogenic weathering and a minor seawater component. Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. Our results confirm that aquatic environments beneath the Antarctic ice sheet support viable microbial ecosystems, corroborating previous reports suggesting that they contain globally relevant pools of carbon and microbes that can mobilize elements from the lithosphere and influence Southern Ocean geochemical and biological systems.
Ed Rybicki's insight:

But no mention of viruses.  Whyever not??

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The ISME Journal - Depth-stratified functional and taxonomic niche specialization in the "core" and "flexible" Pacific Ocean Virome

The ISME Journal - Depth-stratified functional and taxonomic niche specialization in the "core" and "flexible" Pacific Ocean Virome | Aquatic Viruses | Scoop.it

Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established ‘core’ (180 PCs; one-third new to science) and ‘flexible’ (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron–sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.

 

Mya Breitbart's insight:

Very nice comparison of auxiliary metabolic genes throughout the water column - and interesting that they found photosynthetic AMGs in the deep ocean showing vertical flux of viral particles!

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A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes : Nature Communications : Nature Publishing Group

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes : Nature Communications : Nature Publishing Group | Aquatic Viruses | Scoop.it

Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ~97 kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome.

Mya Breitbart's insight:

Not quite about Aquatic Viruses, but too cool not to share.  PS - love the name!

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Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space | Aquatic Viruses | Scoop.it
Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 107 Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations. These population-based, host-linked viral ecological data suggest that, for this single host and seawater sample alone, there are at least 26 double-stranded DNA viral populations with estimated relative abundances ranging from 0.06 to 18.2%. These populations include previously cultivated cyanophage and new viral types missed by decades of isolate-based studies. Nucleotide identities of homologous genes mostly varied by less than 1% within populations, even in hypervariable genome regions, and by 42-71% between populations, which provides benchmarks for viral metagenomics and genome-based viral species definitions. Together these findings showcase a new approach to viral ecology that quantitatively links objectively defined environmental viral populations, and their genomes, to their hosts.
Mya Breitbart's insight:

Very cool method for linking marine phage with their hosts...

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Ed Rybicki's comment, July 17, 2:17 PM
And one we will note immediately - hey, Marla and Lonnie?!
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Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the bacterial and eukaryotic kingdoms, largely due to the absence of any universal phylogenetic marker. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as portal protein, major capsid protein, and tail sheath protein, auxiliary metabolism genes, such as psbA, psbB, and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats.

 
Mya Breitbart's insight:

Since there is no universal gene found in all viruses - these "signature genes" provide a good method for surveying subsets of viral diversity

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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.
Ed Rybicki's insight:

And where there's water - even saturated with salts - there's bacteria.  And viruses, obviously.

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Ocean's living carbon pumps: When viruses attack giant algal blooms, global carbon cycles are affected

Ocean's living carbon pumps: When viruses attack giant algal blooms, global carbon cycles are affected | Aquatic Viruses | Scoop.it
By some estimates, almost half of the world's organic carbon is fixed by marine organisms called phytoplankton -- single-celled photosynthetic organisms that account for less than one percent of the total photosynthetic biomass on Earth. When giant algal blooms get viral infections, global carbon cycles are affected, scientists have now discovered.
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Seals Can Spread Avian Flu to People??

Seals Can Spread Avian Flu to People?? | Aquatic Viruses | Scoop.it
Seals Can Spread Avian Flu to People Environment News Service WASHINGTON, DC, September 3, 2014 (ENS) – The avian flu virus that caused widespread harbor seal deaths in 2011 can spread to and infect other mammals and potentially humans, new...
Ed Rybicki's insight:

Right up there with "Ebola is airborne!" if you ask me, but still....

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Ecology and evolution of viruses infecting uncultivated SUP05 bacteria

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria | Aquatic Viruses | Scoop.it

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks specific virus-host interaction dynamics remain cryptic. Here we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNACaudoviralesand ssDNAMicroviridae. Infection frequencies suggest that ~1/3 of SUP05 bacteria are viral-infected, with higher infection frequency where oxygen-deficiency was most severe. ObservedMicroviridaeclonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together these results demonstrate closely coupled SUP05 virus-host co-evolutionary dynamics with potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.

 
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PhD position Sea Turtle Ecology and Evolution (1.0 fte) (214219) University of Groningen

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Found via twitter

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Global marine bacterial diversity peaks at high latitudes in winter

The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
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The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing | Aquatic Viruses | Scoop.it

The MMETSP is a significant step in recognizing that purpose-built reference databases from ecologically key biomes are essential for all domains of life. Nevertheless, it is only the beginning, and important biases remain that should be addressed. The MMETSP relies primarily on cultured organisms, and this introduces a different set of biases, most obviously, favoring organisms that are photosynthetic. Eukaryotic heterotrophs have critical ecological roles but are under-represented. Indeed, the natural diversity of eukaryotic heterotrophs is huge in general (Figure 1A), and the four most commonly recovered sequences retrieved in environmental surveys of marine samples worldwide correspond to lineages for which most members are uncultivated (e.g.,Marine Stramenopiles (MAST) and Marine Alveolates (MALV) [22]–[24]). These are probably heterotrophs, but we lack a solid biological definition for most of these cells and have become adroit at ignoring heterotrophs in general. Similarly, organisms from the open ocean are underrepresented. Culture-independent methods for generating transcriptomes and genomes and, in some cases, transcriptomes and genomes from single cells will be essential to moving beyond this problem. Methodologies for population [25]–[27] and single-cell genomics and transcriptomics are advancing rapidly [4],[28]–[30], transitioning from technological feats to something we should expect to work routinely. This transition holds great promise for filling the rather substantial gap in our knowledge imposed by uncultivated protists, as well as allowing us to carry out condition-specific analyses of expressed genes in difficult-to-work-with systems. The MMETSP program foreshadows this development by sequencing a small set of culture-independent samples.

 

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Viruses Throughout Life & Time: Friends, Foes, Change Agents

Viruses Throughout Life & Time: Friends, Foes, Change Agents | Aquatic Viruses | Scoop.it
"Viruses Throughout Life & Time: Friends, Foes, Change Agents" aims to increase awareness of the viral world by examining the role of viruses in biological systems and as major drivers of evolution.
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Host-Dependent Differences in Abundance, Composition and Host-Range of Cyanophages from the Red Sea

Host-Dependent Differences in Abundance, Composition and Host-Range of Cyanophages from the Red Sea | Aquatic Viruses | Scoop.it

Cyanobacteria coexist in the oceans with a wealth of phages that infect them. While numerous studies have investigated Synechococcus phages, much less data is available for Prochlorococcus phages. Furthermore, little is known about cyanophage composition. Here we examined the abundance and relative composition of cyanophages on six cyanobacterial hosts in samples collected during spring and summer from the Red Sea. Maximal abundances found on Synechococcus of 35,000 phages/ml are within ranges found previously whereas the 24,000 phages/ml found on Prochlorococcus are approximately 10-fold higher than previous findings. T7-like, T4-like and “unknown” phages were isolated on all hosts, including many T4-like phages on HL Prochlorococcus strains, whereas TIM5-like phages were found only on Synechococcus. Large differences in cyanophage abundance and composition were found for different hosts on the same sampling date as well as for the same host on different dates with few predictable patterns discerned. Host-range analyses showed that T7-like and TIM5-like phages were quite host-specific, whereas the breadth of hosts for T4-like phages was related to host type: those isolated on HL Prochlorococcus were considerably more host-specific than those on LL Prochlorococcus or Synechococcus. These host-related differences likely contribute to the complexity of host-phage interactions in the oceans.

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Phage-bacteria network analysis and its implication for the understanding of coral disease

Phage-bacteria network analysis and its implication for the understanding of coral disease | Aquatic Viruses | Scoop.it

Multiple studies have explored microbial shifts in diseased or stressed corals, however little is known about bacteriophage interactions with microbes in this context. This study characterized microbial 16S rRNA amplicons and phage metagenomes associated with Montastraea annularis corals during a concurrent white plague disease outbreak and bleaching event. Phage consortia differed between bleached and diseased tissues. Phages in the family Inoviridae were elevated in diseased or healthy tissues compared to bleached portions of diseased tissues. Microbial communities also differed between diseased and bleached corals. Bacteria in the orders Rhodobacterales and Campylobacterales were increased while Kiloniellales was decreased in diseased compared to other tissues. A network of phage-bacteria interactions was constructed of all phage strains and 11 bacterial genera that differed across health states. Phage-bacteria interactions varied in specificity: phages interacted with 1-8 bacterial hosts while bacteria interacted with up to 59 phages. Six phages were identified that interacted exclusively with Rhodobacterales and Camplyobacterales. These results suggest that phages have a role in controlling stress-associated bacteria, and that networks can be utilized to select potential phages for mitigating detrimental bacterial growth in phage therapy applications.

Mya Breitbart's insight:

Very interesting --- links between coral health, bacterial communities, and phages!  Also one of the first studies to find Inoviruses in the oceans that I'm aware of.

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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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