These phylogenomic results reported here suggest a substantial expansion of the family Mimiviridae. The proposed expanded family encompasses a greater diversity of viruses including a group of viruses with much smaller genomes than those of the original members of the Mimiviridae. If the OLPG group is included in an expanded family Mimiviridae, it becomes the only family of giant viruses currently shown to host virophages. The mimiCOGs are expected to become a key resource for phylogenomics of giant viruses.
Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a 'fourth supergroup' along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity.
Ed Rybicki's insight:
I like this quote:
"Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet's biosphere."
Absolutely...!! Thanks to my old friend Paul Janssen for pointing this out.
Deep sea trenches act as hot spots for microbial activity, according to new research.
Ed Rybicki's insight:
"even though deep sea trenches like the Mariana Trench only amount to about two percent of the World Ocean area, they have a relatively larger impact on marine carbon balance -- and thus on the global carbon cycle"
When I talk about viruses, I have to struggle with big numbers.
If you get sick with the flu, for example, every infected cell in your airway produces about 10,000 new viruses. The total number of flu viruses in your body can rise to 100 trillion within a few days. That’s over 10,000 times more viruses than people on Earth.
If there can be so many viruses in a single person, how many viruses are there in total on our planet? I’ve hunted around for a number, and the one I’ve seen most often is 1031. As in, 10000000000000000000000000000000. As in over 10 million times more viruses than there are stars in the universe. As in, if you were to stack one virus on top of another, you’d create a tower that would stretch beyond the moon, beyond the sun, beyond Alpha Centauri, out past the edge of the Milky Way, past neighboring galaxies, to reach a height of 200 million light years.
Project Noah is a tool that nature lovers can use to explore and document local wildlife and a common technology platform that research groups can use to harness the power of citizen scientists everywhere.
Oil-burning ships are fertilising the north Pacific with iron – inadvertently putting a proposed geoengineering idea into practice (Sooty #ships may be geo-engineering by accident - #Environment | New Scientist | @scoopit
Deadly virus threatens Phl shrimp industry Philippine Star MANILA, Philippines - The Bureau of Fisheries and Aquatic Resources (BFAR) on Friday warned against the existence of a deadly virus that may kill the country's shrimp industry.
As dominant members of marine mesozooplankton communities, copepods play critical roles in oceanic food webs and biogeochemical cycling. Despite the ecological significance of copepods, little is known regarding the causes of copepod mortality, and up to 35% of total copepod mortality cannot be accounted for by predation alone. Viruses have been established as ecologically important infectious agents in the oceans; however, viral infection has not been investigated in mesozooplankton communities. Here we used molecular and microscopic techniques to document viral infection in natural populations of the calanoid copepods Acartia tonsa (Dana) and Labidocera aestiva(Wheeler) in Tampa Bay, FL. Viral metagenomics revealed previously undocumented viruses in each species, named Acartia tonsa copepod circo-like virus (AtCopCV) andLabidocera aestiva copepod circo-like virus (LaCopCV). LaCopCV was found to be extremely prevalent and abundant in L. aestiva populations, with up to 100% prevalence in some samples and average viral loads of 1.13 × 105 copies per individual.
During establishment of primary cell culture from the kidney of a dead Pacific white-sided dolphin (Lagenorhynchus obliquidens), a cytopathic effect was observed. Polymerase chain reaction with a set of herpesvirus consensus primers yielded a fragment of the expected size. Nucleotide sequencing of the product indicated that the isolated virus was closely related to an alphaherpesvirus detected in a bottlenose dolphin in the United States, but the sequence identity at the protein level was low (86.6 %). Phylogenetic analysis of the encoded sequence confirmed that the new isolate belonged to the subfamily Alphaherpesvirinae and clustered together with other cetacean alphaherpesviruses. The complete gene encoding glycoprotein B (2,757 bp) was amplified from the novel isolate; the encoded protein was compared with the corresponding protein of other herpesviruses, revealing that this virus belongs to the genus Varicellovirus. Taken together, these results suggest that this virus corresponds to a novel herpesvirus capable of infecting Pacific white-sided dolphins.
A meeting of government officials reveals that medical equipment is becoming riddled with malware.
In a typical example, at Beth Israel Deaconess Medical Center in Boston, 664 pieces of medical equipment are running on older Windows operating systems that manufactures will not modify or allow the hospital to change—even to add antivirus software—because of disagreements over whether modifications could run afoul of U.S. Food and Drug Administration regulatory reviews, Fu says.
As a result, these computers are frequently infected with malware, and one or two have to be taken offline each week for cleaning, says Mark Olson, chief information security officer at Beth Israel.
"I find this mind-boggling," Fu says. "Conventional malware is rampant in hospitals because of medical devices using unpatched operating systems. There's little recourse for hospitals when a manufacturer refuses to allow OS updates or security patches."
The worries over possible consequences for patients were described last Thursday at a meeting of a medical-device panel at the National Institute of Standards and Technology Information Security & Privacy Advisory Board, of which Fu is a member, in Washington, D.C. At the meeting, Olson described how malware at one point slowed down fetal monitors used on women with high-risk pregnancies being treated in intensive-care wards.
"Viruses with genomes greater than 300 kb and up to 1200 kb are being discovered with increasing frequency. These large viruses (often called giruses) can encode up to 900 proteins and also many tRNAs. Consequently, these viruses have more protein-encoding genes than many bacteria, and the concept of small particle/small genome that once defined viruses is no longer valid. Giruses infect bacteria and animals although most of the recently discovered ones infect protists. Thus, genome gigantism is not restricted to a specific host or phylogenetic clade. To date, most of the giruses are associated with aqueous environments. Many of these large viruses (phycodnaviruses and Mimiviruses) probably have a common evolutionary ancestor with the poxviruses, iridoviruses, asfarviruses, ascoviruses, and a recently discovered Marseillevirus. One issue that is perhaps not appreciated by the microbiology community is that large viruses, even ones classified in the same family, can differ significantly in morphology, lifestyle, and genome structure. This review focuses on some of these differences rather than provides extensive details about individual viruses."
Mimivirus image courtesy Russell Kightley Media. Thanks Ken Y A-B!
Virophages, e.g., Sputnik, Mavirus, and Organic Lake virophage (OLV), are unusual parasites of giant double-stranded DNA (dsDNA) viruses, yet little is known about their diversity. Here, we describe the global distribution, abundance, and genetic diversity of virophages based on analyzing and mapping comprehensive metagenomic databases. The results reveal a distinct abundance and worldwide distribution of virophages, involving almost all geographical zones and a variety of unique environments. These environments ranged from deep ocean to inland, iced to hydrothermal lakes, and human gut- to animal-associated habitats.
Giant viruses in the genus Chlorovirus (family Phycodnaviridae ) infect eukaryotic green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was sequenced more than 15 years ago, and to date there are only 6 fully sequenced chloroviruses in public databases. Presented here are the draft genome sequences of 35 additional chloroviruses collected across the globe; they infect one of three different green algal species. These new data allowed us to analyze the genomic landscape of 41 chloroviruses, which revealed some remarkable features about these viruses.
I remember visiting James van Etten in Lincoln, Nebraska, just after his group had characterised PBCV-1: that was in 1982, and that virus was BIIIG news, in an environment where very few viruses had been sequenced at all, and definitely nothing as large as a chlorovirus. Strange that so few have been sequenced - but that will definitely change now.
A melt of Greenland's ice is washing large amounts of the nutrient iron into the Atlantic Ocean where it might aid marine life in a rare positive side-effect of climate change, a study showed on Sunday.
Ed Rybicki's insight:
...and viruses: we should see what it does to viruses.
Phenomena: National Geographic If you don't have an immune system, you don't last long in this parasite-riddled world. Your body receives a steady stream of invaders–viruses, bacteria, and other pathogens–which it has to recognize and fight.
Coral viruses. Viruses infecting marine molluscs. The viral ecology of aquatic crustaceans. Viruses of fish. Ecology of viruses infecting ectothermic vertebrates-the impact of ranavirus infections on amphibians.
More than 20 years ago, the discovery of billions of viruses in the oceans was big news, worthy of articles in Nature1 and on the front page of the Washington Post. A year later another Naturereport was published, this time about the most abundant bacterial group in the oceans, cryptically called SAR11. The two stories now come together in a paper published on Nature's website today. Zhao et al. describe DNA viruses that they call 'pelagiphages' and which infect laboratory-grown representatives of SAR11 bacteria. The authors use genomic-sequence data to argue that pelagiphages are among the most abundant viruses in the oceans and perhaps the entire biosphere. The report ends long-running speculation about SAR11, but prompts new questions about marine viruses and the control of microbes in the oceans.
Ed Rybicki's insight:
Seriously big finding - there's a sea of opportunity out there!
"Culturable bacterial abundance at 11 different depths of a 50.26 m ice core from the Tallaksenvarden Nunatak, Antarctica, varied from 0.02 to 5.8 × 103 CFU ml−1 of the melt water. A total of 138 bacterial strains were recovered from the 11 different depths of the ice core. Based on 16S rRNA gene sequence analyses, the 138 isolates could be categorized into 25 phylotypes belonging to phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. All isolates had 16S rRNA sequences similar to previously determined sequences (97.2–100%). No correlation was observed in the distribution of the isolates at the various depths either at the phylum, genus or species level. The 25 phylotypes varied in growth temperature range, tolerance to NaCl, growth pH range and ability to produce eight different extracellular enzymes at either 4 or 18 °C. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a significant proportion of the total fatty acid composition."
The very first building in the world with a shading system consisting of live micro-algae is being built in the suburb of Wilhemsburg in Hamburg. The “algae house” will be complete in 2013 and will comprise approximately 200 square meters of such elements.
Designed for the International Building Exhibition in Hamburg, the zero-energy house will be the first real-life test for the new façade system. Algae in the bio-reactor façades grow faster in bright sunlight to provide more shade. The bio-reactors power the building by capturing solar thermal heat and producing biomass that can be harvested.
19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region
Earlier this year, a 17-year-old French woman arrived at her ophthalmologist with pain and redness in her left eye. She woman had been using tap water to dilute the cleaning solution for her contact lenses, and even though they were meant to be replaced every month, she would wear them for three. As a result, the fluid in her contact lens case had become contaminated with three species of bacteria, an amoeba called Acanthamoeba polyphaga that can caused inflamed eyes.
The mystery of the woman’s inflamed eyes was solved, but Bernard La Scola and Christelle Desnueslooked inside the amoeba, they found more surprises.
It was carrying two species of bacteria, and a giant virus that no one had seen before—they called it Lentille virus. Inside that, they found a virophage—an virus that infects other viruses—which they called Sputnik 2. And in both Lentille virus and Sputnik 2, they found even smaller genetic parasites – tiny chunks of DNA that can hop around the genomes of the virus, and stow away inside the virophage. They called these transpovirons.
So, the poor red eyes of the French patient were carrying an entire world of parasites, nested within one another like Russian Matryoshka nesting dolls. The transpovirons were hidden in the virophage, which infected the giant virus, which infected the amoeba, which infected the woman’s eyes.