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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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Looking at protists as a source of pathogenic viruses

Looking at protists as a source of pathogenic viruses | Aquatic Viruses | Scoop.it

In the environment, protozoa are predators of bacteria and feed on them. The possibility that some protozoa could be a source of human pathogens is consistent with the discovery that free-living amoebae were the reservoir of Legionella pneumophila, the agent of Legionnaires' disease. Later, while searching for Legionella in the environment using amoeba co-culture, the first giant virus, Acanthamoeba polyphaga mimivirus, was discovered. Since then, many other giant viruses have been isolated, includingMarseilleviridae, Pithovirus sibericum, Cafeteria roenbergensis virus and Pandoravirus spp. The methods used to isolate all of these viruses are herein reviewed. By analogy to Legionella, it was originally suspected that these viruses could be human pathogens. After showing by indirect evidence, such as sero-epidemiologic studies, that it was possible for these viruses to be human pathogens, the recent isolation of some of these viruses (belonging to the Mimiviridae and Marseilleviridae families) in humans in the context of pathologic conditions shows that they are opportunistic human pathogens in some instances.

 

Mimivirus picture courtesy of Russell Kightley Media

  

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Characterisation of three novel giant viruses reveals huge diversity among viruses infecting Prymnesiales (Haptophyta)

We have isolated three novel lytic dsDNA-viruses from Raunefjorden (Norway) that are putative members of the Mimiviridae family, namely Haptolina ericina virus RF02 (HeV RF02), Prymnesium kappa virus RF01 (PkV RF01), and Prymnesium kappa virus RF02 (PkV RF02). Each of the novel haptophyte viruses challenges the common conceptions of algal viruses with respect to host range, phylogenetic affiliation and size. PkV RF01 has a capsid of ~310 nm and is the largest algal virus particle ever reported while PkV RF01 and HeV RF02 were able to infect different species, even belonging to different genera. Moreover, PkV RF01 and HeV RF02 infected the same hosts, but phylogenetic analysis placed them in different groups. Our results reveal large variation among viruses infecting closely related microalgae, and challenge the common conception that algal viruses have narrow host range, and phylogeny reflecting their host affiliation.

  
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Underwater Sinkholes in Lake Huron are Habitats for Ancient Microbial Life

Underwater Sinkholes in Lake Huron are Habitats for Ancient Microbial Life | Aquatic Viruses | Scoop.it
Time, water, and geologic forces have converged to create underwater sinkholes where oxygen-poor and sulfur-rich groundwater support prolific microbial mats resembling life on early Earth.
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Viruses: where are the viruses??

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Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice

Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice | Aquatic Viruses | Scoop.it
Mya Breitbart's insight:

Human mucosal surfaces contain a wide range of microorganisms. The biological effects of these organisms are largely unknown. Large-scale metagenomic sequencing is emerging as a method to identify novel microbes. Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. The presence of ATCV-1 was associated with a modest but measurable decrease in cognitive functioning. A relationship between ATCV-1 and cognitive functioning was confirmed in a mouse model, which also indicated that exposure to ATCV-1 resulted in changes in gene expression within the brain. Our study indicates that viruses in the environment not thought to infect humans can have biological effects.

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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
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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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The expanding family Marseilleviridae

The family Marseilleviridae encompasses giant viruses that replicate in free-living Acanthamoebaamoebae. Since the discovery of the founding member Marseillevirus in 2007, 7 new marseilleviruses have been observed, including 3 from environmental freshwater, one from a dipteran, and two from symptom-free humans. Marseilleviruses have ≈250-nm-large icosahedral capsids and 346–386-kb-long mosaic genomes that encode 444–497 predicted proteins. They share a small set of core genes with Mimivirus and other large and giant DNA viruses that compose a monophyletic group, first described in 2001. Comparative genomics analyses indicate that the family Marseilleviridae currently includes three lineages and a pan-genome composed of ≈600 genes. Antibodies against marseilleviruses and viral DNA have been observed in a significant proportion of asymptomatic individuals and in the blood and lymph nodes of a child with adenitis; these observations suggest that these giant viruses may be blood borne and question if they may be pathogenic in humans.

  
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Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

Virophages are a unique group of circular double-stranded DNA viruses that are considered parasites of giant DNA viruses, which in turn are known to infect eukaryotic hosts. In this study, the genomes of three novel Yellowstone Lake virophages (YSLVs)—YSLV5, YSLV6, and YSLV7—were identified from Yellowstone Lake through metagenomic analyses. The relative abundance of these three novel virophages and previously identified Yellowstone Lake virophages YSLV1 to -4 were determined in different locations of the lake, revealing that most of the sampled locations in the lake, including both mesophilic and thermophilic habitats, had multiple virophage genotypes. This likely reflects the diverse habitats or diversity of the eukaryotic hosts and their associated giant viruses that serve as putative hosts for these virophages. YSLV5 has a 29,767-bp genome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a close evolutionary relationship with YSLV1 to -4, whereas YSLV5 and YSLV7 are distantly related to the others, and YSLV7 represents the fourth novel virophage lineage. In addition, the genome of YSLV5 has a G+C content of 51.1% that is much higher than all other known virophages, indicating a unique host range for YSLV5. These results suggest that virophages are abundant and have diverse genotypes that likely mirror diverse giant viral and eukaryotic hosts within the Yellowstone Lake ecosystem.

 
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Diversity of viral photosystem-I psaA genes

Diversity of viral photosystem-I psaA genes | Aquatic Viruses | Scoop.it

Marine photosynthesis is one of the major contributors to the global carbon cycle and the world’s oxygen supply. This process is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding photosystem-II (PSII) reaction center proteins are found in many cyanophage genomes, and are expressed during the infection of their hosts. On the basis of metagenomics, cyanophage photosystem-I (PSI) gene cassettes were recently discovered with two gene arrangements psaJFCABKED and psaDCAB. It was suggested that the horizontal transfer of PSII and PSI genes is increasing phage fitness. To better understand their diversity, we designed degenerate primers to cover a wide diversity of organisms, and using PCR we targeted the psaCA arrangement, which is unique to cyanophages cassettes. We examined viral concentrates from four islands in the Pacific Ocean and found samples containing the psaCA arrangement. Analyses of the amplified viral psaA gene revealed six subgroups varying in their level of similarity and %G+C content, suggesting that the diversity of cyanophage PSI genes is greater than originally thought.

 
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Software carpentry bootcamp

Software carpentry bootcamp | Aquatic Viruses | Scoop.it
And a software bootcamp landed in South Africa… I have to admit I had the best time during this two day course. But let’s start from the top: everyone knows what bootcamps are, well, almost everyon...
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A new(ish) blog from Flavia Flaviani, who is doing a PhD on Marine Viromics at the University of Cape Town

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Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch

Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch | Aquatic Viruses | Scoop.it
Mya Breitbart's insight:

Knowledge of ancient viruses is limited due to their low concentration and poor preservation in ancient specimens. Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. Using reverse genetics, we reconstituted the DNA virus, which replicated and systemically spread in a model plant species. Under constant freezing conditions, encapsidated viral nucleic acids may therefore be preserved for centuries. Our finding indicates that cryogenically preserved materials can be repositories of ancient viral nucleic acids, which in turn allow molecular genetics to regenerate viruses to study their biology

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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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