Aquatic Viruses
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Pan genome of the phytoplankton Emiliania underpins its global distribution.

Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

 
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Great achievement - with a LOT of authors.  Including our very own Declan Schroeder: ex-student and collaborator!

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

If you would like to help curate it, please:

 

 contact: cupton at uvic dot ca

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Ocean worlds: The search for life in the solar system’s other seas

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

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

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Uncovering Earth’s virome

Uncovering Earth’s virome | Aquatic Viruses | Scoop.it
Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold. Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses. Using CRISPR spacers and transfer RNA matches to link viral groups to microbial host(s), we doubled the number of microbial phyla known to be infected by viruses, and identified viruses that can infect organisms from different phyla. Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups. Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host–virus interactions.

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What a planet needs to sustain life

What a planet needs to sustain life | Aquatic Viruses | Scoop.it
"Venus is too hot, Mars is too cold, and Earth is just right," says planetary scientist Dave Brain. But why? In this pleasantly humorous talk, Brain explores the fascinating science behind what it takes for a planet to host life -- and why humanity may just be in the right place at the right time when it comes to the timeline of life-sustaining planets.
Ed Rybicki's insight:
Oceans: it needs water oceans. And if Earth, Enceladus, Europa, Ganymede, and possibly Triton and Pluto all have them, AND Titan has hydrocarbon oceans...then maybe they all have life too. Which would mean the solar system is CRAWLING with it. And viruses, obviously B-)
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Cancer: Transmissible tumours under the sea

In some species, cancer cells can be directly transmitted between individuals. An analysis in shellfish now shows that some transmissible cancers can even cross the species barrier.
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The Ferrojan Horse Hypothesis: Iron-Virus Interactions in the Ocean

The Ferrojan Horse Hypothesis: Iron-Virus Interactions in the Ocean | Aquatic Viruses | Scoop.it
Iron is an essential nutrient and the sub-nanomolar concentrations of iron in open ocean surface waters are often insufficient to support optimal biological activity. More than 99.9% of dissolved iron in these waters is bound to organic ligands, yet determining the identity of these ligands in seawater remains a major challenge. Among the potential dissolved organic ligands in the colloidal fraction captured between a 0.02 µm and a 0.2 µm filter persists an extremely abundant biological candidate: viruses, most of which are phages (viruses that infect bacteria). Recent work in non-marine model systems has revealed the presence of iron ions within the tails of diverse phages infecting Escherichia coli. Based on these findings and the presence of conserved protein motifs in marine phages, here we present several lines of evidence to support the hypothesis that phages are organic iron-binding ligands in the oceans. With average concentrations of 10^7 phages per milliliter surface seawater, we predict that phages could contain up to 0.7 pM iron, a value equivalent to as much as 70% of the colloidal fraction of organically complexed dissolved iron in the surface ocean. Additionally, the production and uptake of siderophores, a strategy that bacteria have developed for assimilating iron, renders cells vulnerable to phage infection due to the dual-function of these cell surface receptors. Iron ions present in phage tails enable phages to exploit their bacterial host’s iron-uptake mechanism via the “Ferrojan Horse Hypothesis” proposed herein, where the apparent gift of iron leads to cell lysis. Finally, if host iron stores are recycled during the assembly of progeny phages, as much as 14% of the cellular iron released into the water column upon lysis would already be incorporated into new phage tails. The potential role of phages as iron-binding ligands has significant implications for both oceanic trace metal biogeochemistry and marine phage-host interactions.
Ed Rybicki's insight:
Viruses as agents of biogeochemical engineering of our planet!
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Prof Helen Rees receives S African national order

Prof Helen Rees receives S African national order | Aquatic Viruses | Scoop.it
Prof Helen Rees (internationally renowned expert in HIV prevention, reproductive health and vaccines) was recently honoured with a national order.

“Wits congratulates all those honoured, and especially those Witsies who have made a mark in our society. We commend the countless contributions made by Prof Helen Rees to address today’s biggest global health challenges through her outstanding research and intellectual achievement at the highest level,” says Prof Adam Habib, Wits Vice-Chancellor and Principal.

ORDER OF THE BAOBAB

Recognising South Africans who have contributed to community service, business and economy, science, medicine and technological innovation, was awarded to:

Professor Helen Rees (OBE) – Order of the Baobab (Silver)

Executive Director of the Wits Reproductive Health and HIV Institute, Rees has a long and distinguished career as an internationally renowned expert in HIV prevention, reproductive health, vaccines and drug regulation. She serves in leadership roles in both national and international structures and chaired, and continues to chair, various councils and research bodies of the World Health Organization related to Ebola vaccines, polio and immunisation. She is currently chair of the Medicines Control Council and was appointed to this position by the Minister of Health.

In 2001 Professor Rees was made an Officer of the Most Excellent Order of the British Empire (OBE).

The Order of the Baobab (Silver) is awarded to Rees for her excellent contribution in the field of medical science and research. Her work gives hope to communities who have been affected by the scourge of HIV and AIDS.
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HoloVir: A workflow for investigating the diversity and function of viruses in invertebrate holobionts

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterise holobiont viral communities across species, environments, or experiments.
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Biogeography of bacteriophages at four hydrothermal vent sites in the Antarctic

In this study, which was carried out within the ChEsSO consortium project (Chemosynthetically driven ecosystems south of the Polar Front), we sampled two hydrothermal vent sites on the East Scotia Ridge, Scotia Sea, one in the Kemp Caldera, South Sandwich Arc and one in the Bransfield Strait, north-west of the Antarctic Peninsula, which exhibit strong differences in their chemical characteristics. We compared a subset of their bacteriophage population by Sanger- and 454-sequencing of g23, which codes for the major capsid protein of T4likeviruses. We found that the sites differ vastly in their bacteriophage diversity, which reflects the differences in the chemical conditions and therefore putatively the differences in microbial hosts living at these sites. Comparing phage diversity in the vent samples to other aquatic samples, the vent samples formed a distinct separate cluster, which also included the non-vent control samples that were taken several hundred meters above the vent chimneys. This indicates that the influence of the vents on the microbial population and therefore also the bacteriophage population extends much further than anticipated.
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Giant viruses of the Kutch Desert

The Kutch Desert (Great Rann of Kutch, Gujarat, India) is a unique ecosystem: in the larger part of the year it is a hot, salty desert that is flooded regularly in the Indian monsoon season. In the dry season, the crystallized salt deposits form the “white desert” in large regions. The first metagenomic analysis of the soil samples of Kutch was published in 2013, and the data were deposited in the NCBI Sequence Read Archive. At the same time, the sequences were analyzed phylogenetically for prokaryotes, especially for bacteria. In the present work, we identified DNA sequences of recently discovered giant viruses in the soil samples from the Kutch Desert. Since most giant viruses have been discovered in biofilms in industrial cooling towers, ocean water, and freshwater ponds, we were surprised to find their DNA sequences in soil samples from a seasonally very hot and arid, salty environment.
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Cyanophage and Algal Virus - Special Issue of Virologica Sinica

Cyanophage and Algal Virus - Special Issue of Virologica Sinica | Aquatic Viruses | Scoop.it
Electron microscopy images of three types of cyanophages: 1) upper left: AsGV-L cyanophage particles, showing geminivirus-like morphology with two incomplete icosahedra joined together; 2) lower left: MaCV-L cyanophage particles,showing corticovirus-like and round shape with icosahedral symmetry and a non-enveloped capsid; 3) right: cyanophage PP virions , with short and stubby tail structures. Images painted with pseudo-colors. (Cover designed by Meng Wang, Wuhan
IOV.)
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Another useful resource - also a couple of years old
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Linking Virus Genomes with Host Taxonomy

Linking Virus Genomes with Host Taxonomy | Aquatic Viruses | Scoop.it
Environmental genomics can describe all forms of organisms—cellular and viral—present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts.

Via Cindy
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Transmission of new virus believed to occur between farmed and wild fish

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

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

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

Chloroviruses are large, icosahedral, dsDNA-containing viruses that replicate in certain unicellular, chlorella-like green algae [1,2]. They exist in freshwater throughout the world with titers as high as thousands of plaque-forming units (PFU) per ml of indigenous water although titers are typically 1–100 PFU/ml. Titers fluctuate during the year with the highest titers typically occurring in the spring and late fall. Known chlorovirus hosts, which are normally symbionts and are often referred to as zoochlorellae, are associated with either the protozoan Paramecium bursaria (Fig 1A), the coelenterate Hydra viridis, or the heliozoan Acanthocystis turfacea. Zoochlorellae are resistant to viruses in their symbiotic state. Fortunately, some zoochlorellae grow independently of their partners in the laboratory, permitting plaque assay of the viruses (Fig 1B) and synchronous infection of their hosts, which allows one to study the virus life cycle in detail.

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What a 4-Billion-Year-Old Organism Says About Life in Space

What a 4-Billion-Year-Old Organism Says About Life in Space | Aquatic Viruses | Scoop.it
A new study may have big implications for life in space too
Ed Rybicki's insight:
...and of course, if they find life on Europa, Ganymede or Pluto, it'll have viruses...B-)
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Ocean viruses may have impact on Earth’s climate

Ocean viruses may have impact on Earth’s climate | Aquatic Viruses | Scoop.it
Infection of sea microbes is preventing them from sucking up carbon dioxide
Ed Rybicki's insight:
Interesting...because OTHER cyanophages actually INCREASE photosynthetic efficiency by providing better photosystem genes...so who to believe??
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Does the DHET research output subsidy model penalise S African high-citation publication?

South African universities are awarded annual subsidy from the Department of Higher Education and Training (DHET) based on their research publication output. Journal article subsidy is based on the number of research publications in DHET-approved journals as well as the proportional contribution of authors from the university. Co-authorship with other institutions reduces the subsidy received by a university, which may be a disincentive to collaboration. Inter-institutional collaboration may affect the scientific impact of resulting publications, as indicated by the number of citations received. We analysed 812 journal articles published in 2011 by authors from the University of Cape Town’s Faculty of Health Sciences to determine if there was a significant relationship between subsidy units received and (1) citation count and (2) field-weighted citation impact. We found that subsidy units had a significant inverse relationship with both citation count (r= -0.247; CI = -0.311 – -0.182; p<0.0001) and field-weighted citation impact (r= -0.192; CI= -0.258 – -0.125; p<0.0001). These findings suggest that the annual subsidy awarded to universities for research output may inadvertently penalise high-citation publication. Revision of the funding model to address this possibility would better align DHET funding allocation with the strategic plans of the South African Department of Science and Technology, the National Research Foundation and the South African Medical Research Council, and may better support publication of greater impact research.
Ed Rybicki's insight:
Well,of course: any scheme that awards more money to papers having more authors from your own institution will do that!
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Estimating species richness using environmental DNA

Estimating species richness using environmental DNA | Aquatic Viruses | Scoop.it
The foundation for any ecological study and the for effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.
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Computational prospecting the great viral unknown

Bacteriophage play an important role in host-driven biological processes by controlling bacterial population size, horizontally transferring genes between hosts, and expressing host-derived genes to alter host metabolism. Metagenomics provides the genetic basis for understanding the interplay between uncultured bacteria, their phage, and the environment. In particular, viral metagenomes (viromes) are providing new insight into phage-encoded host genes (i.e., auxiliary metabolic genes; AMGs) that reprogram host metabolism during infection. Yet, despite deep sequencing efforts of viral communities, the majority of sequences have no match to known proteins. Reference-independent computational techniques, such as protein clustering, contig spectra, and ecological profiling are overcoming these barriers to examine both the known and unknown components of viromes. As the field of viral metagenomics progresses, a critical assessment of tools is required as the majority of algorithms have been developed for analyzing bacteria. The aim of this paper is to offer an overview of current computational methodologies for virome analysis and to provide an example of reference-independent approaches using human skin viromes. Additionally, we present methods to carefully validate AMGs from host contamination. Despite computational challenges, these new methods offer novel insights into the diversity and functional roles of phage in diverse environments.
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Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom | Aquatic Viruses | Scoop.it
Rapid variation in the phytoplankton and bacterioplankton communities of a spring bloom provides new insights into the biological and physical parameters affecting plankton succession.
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And viruses??
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Oncogenic Viruses and Cancer -- Virologica Sinica

Oncogenic Viruses and Cancer -- Virologica Sinica | Aquatic Viruses | Scoop.it
Viruses are leading causes of different types of human cancers, accounting for
about 20% of total cases. Seven viruses are currently considered oncogenic
viruses, including hepatitis B virus (HBV), hepatitis C virus (HCV), human
papillomavirus (HPV), Epstein Barr virus (EBV), human herpes virus 8 (HHP8),
Merkel cell polyomavirus (MCPyV), and human T-lymphotropic virus type 1
(HTLV-1). The molecular mechanisms of viral oncogenesis are complex and
may involve the induction of chronic inflammation, disruption of host genetic
and epigenetic integrity and homeostasis, interference with cellular DNA
repair mechanisms resulting in genome instability and cell cycle dysregulation.
Genetic and epigenetic alterations induced by infection and replication of
oncogenic viruses may lead to the appearance and proliferation of cancer
stem cells, which are important for the initiation, progression, metastasis,
relapse, and chemotherapy resistance of cancers. The cover illustrates the
seven oncoviruses that could lead to human cancer.
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Decoupling Physical from Biological Processes to Assess the Impact of Viruses on a Mesoscale Algal Bloom

Decoupling Physical from Biological Processes to Assess the Impact of Viruses on a Mesoscale Algal Bloom | Aquatic Viruses | Scoop.it
Here, we address this challenge and quantify algal blooms’ turnover using a combination of satellite and in situ data, which allows identification of a relatively stable oceanic patch that is subject to little mixing with its surroundings. Using a newly developed multisatellite Lagrangian diagnostic, we decouple the contributions of physical and biological processes, allowing quantification of a complete life cycle of a mesoscale (∼10–100 km) bloom of coccolithophores in the North Atlantic, from exponential growth to its rapid demise. We estimate the amount of organic carbon produced during the bloom to be in the order of 24,000 tons, of which two-thirds were turned over within 1 week. Complimentary in situ measurements of the same patch area revealed high levels of specific viruses infecting coccolithophore cells, therefore pointing at the importance of viral infection as a possible mortality agent. Application of the newly developed satellite-based approaches opens the way for large-scale quantification of the impact of diverse environmental stresses on the fate of phytoplankton blooms and derived carbon in the ocean.
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Viruses associated with coral reefs

Research into viruses associated with coral reefs is a newly emerging field. Corals form an important symbiotic relationship with the dinoflagellate species Symbiodinium, which the coral relies heavily upon for nutrients and calcification. Coral bleaching is the result of disruption of this symbiosis when the algae and/or its photosynthetic pigments are lost from the coral tissues. Environmental stressors, including elevated sea surface temperatures and increased UV light exposure, have been implicated in coral bleaching. We set out to test the hypothesis thatSymbiodinium in culture plays host to a latent virus that switches to a lytic infection under stress, such as UV exposure or elevated temperature. Analysis of Symbiodinium cultures (isolated from corals on the Great Barrier Reef) using flow cytometry and transmission electron microscopy (TEM), revealed an active viral infection was ongoing, regardless of experimental conditions. Morphological analysis using TEM revealed filamentous and icosahedral virus-like particles associated with Symbiodiniumcultures. We present genomic data of the virus assemblages isolated from cultured Symbiodinium cells that indicate this dinoflagellate is targeted by both a dsDNA virus, related to members of the Nucleo-Cytoplasmic Large dsDNA Virus family (NCLDV), and a novel ssRNA virus related to the Orthoretrovirinae. Further investigations are underway to detect viruses in freshly isolated Symbiodinium from reef corals and to compare these with viruses observed in laboratory cultures of this symbiotic alga. We aim to develop molecular diagnostic probes to detect viruses in field samples to help monitor and assess the impact of viruses in coral bleaching and other climate change-related events, which have huge implications for the health of coral reefs to future global climate scenarios.

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