Small Things Considered

De Profundis…

by Elio

We are fond of posting “Talmudic Questions,” questions we consider to be more interesting than their answers. The very first of them, dated December 1, 2006, reads as follows:

Where on Earth would one expect to find a single species of microbes (a pure culture) for sustained periods of time? Symbioses (mutualistic or parasitic) do not count, neither do Petri dishes.”

Scanning electron micrograph of a sample from a
different mine, a mere 648 meters down, where D.
audaxviator is also the predominant organism. The
tiny globular objects are presumably silicates, which
have been found to precipitate upon cooling after
sample collection. Source

It turns out there is now a candidate (actually, a Candidatus) nominated for this lonesome role. It is a bacterium, named Candidatus Desulforudis audaxviator, found in the ground water of a South African gold mine, 2.8 km below the surface. Here, in this challenging locale, D. audaxviator accounts for at least 99.9% of all living things (with the remaining fraction thought to be trace contaminants from the mine or lab). A fair amount is known about it, even though it has yet to be cultured. It is a Gram-positive obligate anaerobe, a member of the Firmicutes and somewhat related to the Clostridia. Home is warm and alkaline—around 60 °C and pH 9.3. Its fully sequenced genome tells us that it is probably motile and a sporeformer, and that it makes its living from oxidizing hydrogen using sulfate as the electron acceptor. Both of those substances are relatively abundant in its habitat. Its hydrogen "fuel" is probably formed as a by-product of the radioactive decay of uranium within the earth. Thus D. audaxviator carries the banner for Life Without Sunlight to new depths.

However, this is not life at it’s fullest.

How Many Genomes Does It Take to Change a Light Bulb?

by Elio

The cedar aphid and a TEM of a cell containing two endo-
symbiotic bacteria. Courtesy of A. Latorre and J. M. Gosalbes.

Let me rephrase that. How many genomes does it take for an aphid to make tryptophan? If you thought it was one, you'd be wrong: the answer is two, neither being the aphid’s. Remember that aphids live off plant sap that is poor in some amino acids? And that they get some of the missing amino acids from the metabolism of an endosymbiont, Buchnera aphidicola? That’s true enough, but it turns out that in the cedar aphid, Cinara cedri, the resident Buchnera has lost its ability to supply the host with tryptophan. According to investigators from the University of Valencia, Spain, this Buchnera carries the trpEG genes on a plasmid, but lacks trpDCBA, the remaining genes of the pathway.

Recent Blog Items We've Enjoyed—Fall Harvest

Phage-hunter Tim Sampson of Blogging for Bacteriophages has a mind-boggling calculation about how far the phages of this planet would stretch if laid end to end. Plus a phage ballad.

Seen through the eyes of J. A. Ginsburg armed with 10x lens, lichens get their time of day at Germtales.

Slime molds also get their attention in an erudite essay in Christopher Taylor’s Catalogue of Organisms.

Kathie Hodge reports in the Cornell Mushroom Blog that she and others were on NPR Science Friday on September 12, 2008, in a program entitled Fungi: The Good, The Bad, And The Edible.

A. J. Cann’s MicrobiologyBytes is always there to provide incisive analyses of late-breaking microbiological news.

And microbiological news with a personal touch abounds in Tara Smith’s Aetiology.

Intraterrestrials

by Manuel Sanchez

Among Jules Verne's famous works is Journey to the Center of the Earth. Have you read the book or seen one of the movie versions? If so, you will remember that when the fearless explorers descended into the depths of a volcano, they encountered prehistoric life forms such as plesiosaurs. It turns out that Verne wasn't far off. When we descend into the Earth's depths, we may not find gigantic living forms, but we do encounter microbes aplenty. In addition, volcanoes have a lot to do with this story.

Fine Reading: Metagenomics

Nothing like being lazy on a nice Autumn weekend. If you are so inclined, and yet you are wondering about metagenomics and specifically about what it has done for our understanding of the microbial world, here’s a satisfying piece by Hugenholtz and Tyson. For those who can't wait to read it, here are some of the main conclusions.

Source

Among other things, microbial metagenomics:

• reveals natural communities in their richness and complexity. Metagenomics can not only identify the principal partners of a microbial consortium but also many of their metabolic capabilities.
• has great potential for stumbling across novel findings, some of which have significantly altered our view of global processes. One example is proteorhodopsin, the light-driven proton pump, discovered to be abundant in microbes in marine habitats where there is light.

Where Art Thou, O Nucleoid?

by Conrad Woldringh

In a post on May 12, Elio asked where ribosomes are located in bacterial cells. According to a 2006 paper by Ortiz et al., "the ribosomes are evenly distributed throughout the cytosol" and "no distinct nucleoid territory was observed." This prompts one to also ask: Where art thou, o nucleoid? Do their observations indeed indicate that, in the small cells of Spiroplasma melliferum (Figure E; volume ~0.02 µm³), the ribosomes (number ~1000) and DNA (genome size 1.46 Mbp) co-mingle and that a phase separation between cytoplasm and nucleoid is absent?

Talmudic Question #39

Except for viroids, can you think of any place where there are “naked,” (capsidless) viruses outside of hosts?

Fine Reading: A Quick Guide to the Bacterial Flagellar Motor

by Elio

Schematic diagram of the flagellar motor.
The flagellar motor is a macromolecular
assembly made of approximately 20
different proteins. It extends from the
cell interior (bottom) to the exterior
(top), spanning across three membranes:
first the cytoplasmic membrane, then
the peptidoglycan layer, and lastly the
outer membrane. Its components are
termed the rotor, stators, drive shaft,
bushing, rotation-switch regulator, and
so on. Source.

The bacterial flagellar motor deserves great write-ups. Hardly anything in biology is more fascinating than this marvel of miniaturization. Not surprisingly, this smallest and most perfect of electric motors has a worthy advocate. Howard C. Berg of Harvard, who has himself contributed a great deal to our understanding of how the flagellar motor works, has written a short but powerful précis in Current Biology. It will take you but ten minutes to read it, unless you pause and think about the many gems therein.

News from the Department of Mimivirology: Part II

New and tantalizing facts continue to emerge from those on the frontlines studying the giant viruses. A recent paper by La Scola et al. reports the discovery of a novel virus found in amoebas that requires mimivirus for replication. This defective virus has been called Sputnik (for fellow traveler). This exciting finding expands even further the frontiers of virology.

Such news elicits spirited debate and thoughtful commentary in the blogosphere, such as here and here. We asked two virologists for comment, one from the perspective of the adeno-associated viruses, the other from the world of phages.