Giant viruses join as another ancestral superkingdom

Mimivirus in amoeba. Credit: Professor Didier Raoult, Rickettsia Laboratory, La Timone, Marseille, France

A study of the proteins of giant viruses adds them to the list of primitive life forms that have existed since the dawn of life.  They seem to constitute a fourth superkingdom. Professor Gustavo Caetano-Anollés led the analysis.

Scientists found ancient structural patterns in the folds of the virus proteins, which are virtually molecular fossils. Folds that are common to all organisms studied are the oldest. Less common folds are, literally, new wrinkles.

The researchers looked at archaea, bacteria, eukaryotes, and both kinds of viruses. The giant viruses have  biochemistry for making proteins, which small viruses have lost.

Modern viruses have lost much of their biochemical machinery and become obligate parasites of an extreme kind.

Giant Viruses Coexisted With the Cellular Ancestors and Represent a Distinct Supergroup Along With Superkingdoms Archaea, Bacteria and Eukarya

Taxon of the week: Aeromonas

Aeromonas colonies on blood agar (image from Janda & Abbott)

I’ve found a new website: Catalogue of Organisms. Their post, “Taxon of the week: Aeromonas” describes a genus of aquatic bacteria that are responsible for some ugly infections in fish, humans, and other animals: The Genus Aeromonas: Taxonomy, Pathogenicity, and Infection by J. Michael Janda and Sharon L. Abbott.

The bacterial colonies to the left are illuminated by transmitted light.

Nomenclature Rule

In Life: An Unauthorized Biography, Richard Fortey documented a biologists’ rule:

The most primitive of  bacteria are known by the most wondrous jargon, mastery of which is guaranteed to cause jaws to drop at social functions, for the correct designation of many of them is ‘chemolithoautotrophic hyperthermophiles.’ Since these bacteria are only a thousandth of a millimetre long — minute rods, discs, or cocci (spheres), this affords an example of a rule well known to biologists: that the length of the description is inversely proportional to the size of the organism.

No doubt Fortey is an accomplished raconteur, but I find his written work almost unbearably wordy and have to take it in small doses.

Dangerous flu virus!

Flu virus (CDC image)

A virologist, has created an avian flu virus that’s easily transmissible between ferrets–which means it’s probably easily transmissible between people–unlike other strains of the H5N1 virus. His method was relatively low-tech, which means it might be available to another researcher who could hold the world hostage.  Now he wants to publish. Mother Jones has the story.

Fouchier hopes to publish the results of experiments that many scientists believe should never have been done in the first place. He and Yoshihiro Kawaoka, a virologist at the University of Wisconsin who is reportedly seeking to publish a similar study, have long pursued this line of research, hoping to determine whether H5N1 has the potential to become infectious in people, a jump that could trigger a worldwide pandemic. Knowing the specific genetic mutations that make the virus transmissible, Fouchier told Science, will help researchers respond quickly if this sort of killer virus were to emerge in nature.

Fouchier admits that his creation “is probably one of the most dangerous viruses you can make.”

This type of research is euphemistically known as “dual-use,” which means it could be used for good or evil.

… Some scientists think any work this dangerous should be vetted by an international panel; others reject the notion.

But such decisions, then and now, have been left largely in the hands of the researchers. The U.S. National Science Advisory Board for Biosecurity, an NIH advisory panel, is currently reviewing the Fouchier and Kawaoka papers, according to Science. But in 2007, the board recommended against mandating prior reviews of dual-use research. Instead, it suggested that scientists alert their institutional review boards to any experiments of concern—something they were supposed to be doing already. Keim, who sits on the NSABB, told Science that any potential risks should be flagged at “the very first glimmer of an experiment…You shouldn’t wait until you have submitted a paper before you decide it’s dangerous.”

Even older fossils at 3.4 billion years

fossil bacteria

Fossil bacteria from 3.4 billion years ago are the world’s oldest fossils.

The microfossils were found in a remote part of Western Australia called Strelley Pool. They are very well preserved between the quartz sand grains of the oldest beach or shoreline known on Earth, in some of the oldest sedimentary rocks that can be found anywhere.

They are from a billion years before plants generated our oxygen atmosphere.

The fossils are very clearly preserved showing precise cell-like structures all of a similar size. They look like well known but much newer microfossils from 2 billion years ago, and are not odd or strained in shape.

The fossils suggest biological-like behaviour. The cells are clustered in groups, are only present in appropriate habitats and are found attached to sand grains.

And crucially, they show biological metabolisms. The chemical make-up of the tiny fossilised structures is right, and crystals of pyrite (fool’s gold) associated with the microfossils are very likely to be by-products of the sulphur metabolism of these ancient cells and bacteria.

UPDATE:  Jerry Coyne has more details, and more photos, about these fossils. (They may be primitive single-celled organisms rather than bacteria.)  Newly found: the world’s oldest fossils . Larry Moran explains the biochemistry that tells us these bacteria digested sulphur in The Oldest Cells.

Sulfuric-acid speleogenetic extremophiles

Rock-eating microbes live in caves:

Abstract: A handful of investigative teams in several parts of the world are studying abundant biological communities in caves formed by sulfuric-acid speleogenesis. These caves are atypical in terms of origin, chemistry, and ecosystem properties. They prominently display sulfur minerals, characteristic cavity topologies, and notable biological diversity and biological productivity resulting directly from the conditions that produce the caves. Even long-inactive systems still harbor some of these indicators. The microbial and macroscopic ecosystems within sulfuric-acid speleogenetic caves are geologically mediated and maintained. This geological mediation is a theme connecting them with other sulfur-driven ecosystems on Earth, including deep-sea hydrothermal vents, sulfurous near-surface hydrothermal systems, and solfataras. Evidence exists for potentially significant microbial participation in the process of speleogenesis itself. Recent results confirming the high relative abundance of sulfur on Mars, an apparent sedimentary basin with high sulfate concentration, near-surface indicators of ice and water, and trace detection of reduced gases (especially methane) in the Martian atmosphere, possibly deriving from subsurface microbial sources, set the stage for suggesting that sulfuric-acid speleogenetic systems may be useful as astrobiological analogs for hypothetical Mars ecosystems. Unique speleogenetic mechanisms may occur on Mars and could provide subsurface void space suitable for habitation by such hypothetical microbial systems.

They are found in Lechuguilla Cave, which is part of the Carlsbad Cavern system in New Mexico.

The massive gypsum deposits lining Lechuguilla’s limestone walls had suggested to some geologists that its tunnels were carved not by runoff flowing from the surface—as was long considered the case with all limestone caves—but by strong chemical reactions between ancient groundwater and hydrogen sulfide rising from a deep subterranean source. Hydrogen sulfide associated with petroleum deposits in the rich Delaware Basin field was believed to have been chemically converted to sulfuric acid, which could eat into limestone like gasoline poured into a styrofoam cup. In the early 1980s, few in the geological establishment had accepted this theory, originally applied to Carlsbad Cavern. But then the discovery and early exploration of Lechuguilla had confirmed it (virtual tour).

Microbiology and immunology research at Western

The University of Western Ontario has more than thirty researchers working on the molecular and cellular biology of microorganisms or the immune system. Here’s an index to them and their research projects. Several of the researchers are accepting graduate students. Have a look and see if anything strikes your fancy.

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