Small Things Considered

The European Academy of Microbiology

We translate and offer a post from the Spanish blog Esos Pequeños Bichitos (Those Small Bugs).

by Miguel Vicente

The Logo of the EAM. Microbiology began
in Europe with the observations of
Leeuwenhoek, and one of his drawings
has been used for their logo. (redrawn
by M. V.)

On June 29,2009, the European Academy of Microbiology (EAM) was established in the Swedish city of Gothenburg. The objective of the academy is to provide a voice for European microbiology and to foster its quality and dissemination within Europe. Its goals include the expansion of scientific knowledge regarding key issues of microbiological relevance, fostering meetings and congresses, and establishing advanced courses.

The EAM will include microbiologists with a notable record of publication, patents or inventions, significant achievements in clinical work or teaching, and contributions to the microbiological community.

An Iconoclastic Endosymbiont

The cicada Diceroprocta semicincta
(male). Size: 3/4 inch. Source.

by Merry

The endosymbionts of insects provide an unending parade of novelty. They seem to knock on our door, one after the other, each purveying some new twist of microbial evolution. They break the rules, remodel the genetic code, and blur the line between organism and organelle. Here is one more that seems to particularly delight in defying convention.

The average GC content of bacterial genomes varies widely, from 17% to 75%. Moreover, the variation is not random, i.e., the percent GC correlates roughly with genome size. The larger the genome, the higher the GC content. This shows up most dramatically at the low end of the scale, among the insect endosymbionts with greatly reduced genomes. They exhibit the lowest GC percentage. One can't help but wonder why. The argument put forward to explain this has gone like so. All DNA is subject to continual alteration. Two of the common chemical changes are the spontaneous deamination of cytosine and the oxidation of guanosine by reactive oxygen species. Both of these reactions, if not repaired, change a GC to an AT pair. Endosymbionts with reduced genomes have fewer DNA repair genes. Ergo, over time their DNA would accumulate unrepaired GC to AT shifts, thus lowering the average GC% of their genomes.

This made a tidy story.

Talmudic Question #51

Is it possible that prototypical bacterial endospores (e.g., those of Bacillus subtilis) carry out some metabolic activities, albeit at extremely slow rates?

All the News That’s Fit to Print

Olivia Judson. Source.

by Elio

The august New York Times proclaims that on its masthead, and well it should. On July 21, they published a column by the highly regarded author and evolutionary biologist Olivia Judson entitled Microbes 'R' Us. In it, Judson gives a brief but illuminating account of aspects of our intestinal microbiome. Not only is this written in her authoritative and highly readable style, but the article also includes references to the primary literature. How often do you see that done by your town's newspaper?

The Ten Minute Leeuwenhoek Microscope

by Patrick Keeling

Patrick melts a glass tube (while looking away!) to make
a Leeuwenhoek microscope at the UBC Advanced
Molecular Biology Labs High School Science Teacher
Conference (October, 2008). Source.

I was on leave from teaching for a couple of years. The summer before re-starting my third year Protistology course I began to think about some things I wanted to change. One thing I wanted to do was to add a section on the history of microbiology to put things into perspective and hopefully connect students with the material a bit. My colleague, Max Taylor, had a replica of a van Leeuwenhoek microscope that he once showed to me, and I thought it would be fun to make one as close to the original design as possible to show the class what it was like. I did some superficial snooping around about how it was built, including finding the original paper in the Proceedings of the Royal Society where he described the design. I realized it would be pretty straightforward, including making a lens that was pretty close to the ones he would have used.

Deep down I knew that this was mostly to find some excuse to buy an anvil because, seriously, what kind of guy does NOT want to have his own anvil? So, one anvil, a big hammer, and a bit of brass later, I had made all the components for two Leeuwenhoek microscopes. I later found a superbly detailed web page describing how to do it that would have saved a lot of trial and error (especially my mistake in threading both holes in the L-shaped piece that connects to the microscope plate to the stage), a source that I would recommend to anyone who wants to make one of these.

Mycobacteria Make Spores?

by Peter Setlow

The title page of Robert Koch’s original article,
The Etiology of Tuberculosis, published in the
Berliner Klinische Wochenschrift, April 10, 1882.

Rarely does news come along that threatens to overturn our cherished beliefs. Since early after the discovery of tubercle bacilli by Robert Koch in 1882, the mycobacteria have been considered not to be spore formers. Now this is being challenged by a new report.

The genus Mycobacterium encompasses a number of major human pathogens including M. tuberculosis, among the most common pathogens carried by humans. A hallmark of M. tuberculosis infections is the ability of the organism to persist asymptomatically for long periods in the host, and then reappear and cause disease. The new paper by Ghosh et al. from Uppsala University in Sweden claims that members of some Mycobacterium species form spores that resemble those produced by well-studied Bacillus species. The authors worked primarily with M. marinum, a relatively fast-growing mycobacterium with a doubling time of 4-6 hours. In old cultures they observed forms that resembled spores not only in their morphology and their resistance, but also in their accumulation of dipicolinic acid, a signature molecule associated with spores of Bacillus species. Putative spores were also observed in old M. bovis cultures. In addition, they found that Mycobacterium genomes, including that of M. tuberculosis, contain homologs of genes important for sporulation of the model spore former, Bacillus subtilis. At least some of these genes were transcribed only in old M. marinum cultures.

Life in a Big Mac

by Merry

IFs make it to the Mac. Image of P. caudatum
fed a mixture of prey bacteria (green) and IFs
of H. obtusa (yellow). The IFs (arrow) are in
the Mac, the prey bacteria in food vacuoles.
Bar: 25 μm. Source.

From the bacterial point of view, a paramecium is a microcosm offering several tempting niches for colonization. When you collect a paramecium from nature, it's likely to have hundreds—even thousands—of bacterial endosymbionts on board, in different locations. Some will likely be in the cytoplasm, others in other cellular compartments, including the nuclei. To remind you, the ciliates evolved their own particular approach to nuclear compartments. They have two kinds of nuclei, macronuclei (we'll call them Macs) and micronuclei (Mics), typically two or more of each. The Macs carry out all the RNA transcription during normal vegetative growth; the Mics transmit the germline genome to subsequent generations. Both the Mics and the Macs are hosts to specific symbionts. While locations in mitochondria and nuclei have been observed for bacterial pathogens of animal cells, they are relatively uncommon.

So far, nine endosymbionts are known to live within the nuclei of paramecia, about half in the Mics, half in the Macs. These nine species, α-proteobacteria all, have been lumped together into the genus Holospora because of their similar cytology and lifestyle. Their closest known relatives are Rickettsia and Ehrlichia. They all appear to be obligate endosymbionts, i.e., are not known to live outside their hosts. All are host-specific and nuclei-specific.

Fine Reading: In the Company of Ciliates

by Merry

Organisms such as ciliates that dine daily on bacteria run the risk of getting an infection. Indeed, ciliates—large, complex cells—are host in nature to gazillion different bacteria that they acquire primarily through phagocytosis at their "mouth." Resident bacteria are generally termed symbionts even though only a few of them have been studied enough to reveal the nature of their intimate relationship. The stories of those chosen few are recounted in an engrossing review by Hans-Dieter Görtz.

Some ciliated protozoa found in lakes and rivers. Those placed towards the top left are
typically found in the open water of lakes; those close to the centre at the base are all
anaerobic. The remainder are generally found in sediments and detritus, and attached to
submerged surfaces (e.g. aquatic animals and plants). All are drawn to scale (bar at the
right-hand side = 1 mm). Source.

The Viral Selenoprotein Theory

Indian paintbrush in bloom. These
plants absorb selenium from the soil
and concentrate it in their tissues.
The edible, sweet flowers were con-
sumed in moderation by various Amer-
indian tribes as a condiment. The high
selenium content, especially in roots
and green parts, makes it potentially
toxic in large quantities. Source.

by Chitra Rajakuberan*

Just when you thought that HIV has bared all its secrets, new ones come along. The HIV genome encodes 3 main polyproteins and six regulatory proteins. Like all other viruses, HIV relies extensively on the host for replication; of course, what sets it apart from most other viruses is its remarkable ability to integrate into the host genome and lie dormant for long periods of time.

Almost all the identified ORFs of HIV have been implicated in its pathogenesis. However, recent bioinformatics reports suggest that HIV may in fact encode for additional frame-shifted proteins. This is a fascinating story that didn't start with HIV. The frame-shift is brought about by RNA structures called pseudoknots. A pseudoknot is defined as an RNA secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot structure was first recognized in the turnip yellow mosaic virus in 1982.