Small Things Considered

The Colors of the Microbial Rainbow

by Gemma Reguera

The only part of the electromagnetic spectrum that is visible to the human eye is in the narrow region between 390 and 750 nm, which contains all the colors of the rainbow and is referred to as the visible or vis light spectrum (vertical arrow at the bottom). Source.

Our appreciation of the colors of nature is limited by the narrow wavelengths of the electromagnetic spectrum that our eyes can detect. This portion of the electromagnetic spectrum between 390 and 750 nm is what we refer to as the visible (vis) light or, simply, light.  We cannot see below (ultraviolet light) or above (infrared light) these wavelengths. Yet this narrow margin of detection allows us to see all the colors of the rainbow, spreading across the visible spectrum from violet (shortest wavelength) to red (longest wavelength). You can see the color palette of visible light in the rainbow up in the sky on a rainy day, as light is dispersed by water droplets. You can also reveal the full color of the visible spectrum using a glass prism: the change of speed of the light as it crosses the glass medium changes the direction of the light waves and enables their dispersion.

Iridescence from soap bubbles (left), shells (middle) and the exoskeleton of a golden stag beetle (right). Source.

Some natural surfaces can produce even more complex optical effects than rain droplets or a glass prism by selectively reflecting light of specific wavelengths and, therefore, specific colors. One optical effect, in particular, the one called iridescence, produces some of the most intense colorations in nature such as the rainbow-like coloration of soap bubbles, the inside of some shells, and the bright colors of the exoskeleton of some insects. The word iridescence originates from the Greek iris, which means ‘rainbow’, and refers to the optical property of some surfaces to change color and its intensity with the illumination or the viewing angle. Iridescent surfaces are uniquely structured in a way that causes the reflected light waves to interact physically with each other. The crests and troughs of the reflected light waves sometimes align (they are ‘in phase’) and reinforce each other, thus increasing the intensity of the reflected color. By contrast, if the reflected light waves are out of phase, they can cancel each other out and those particular colors never manifest. The final effect of this optical interference is the production of one or more predominant colors, the type and intensity changing with the angle of illumination and/or observation. Thus, iridescent colors are ‘structural’: they do not result from pigmentation but from physical interactions between light and surfaces.

Fungal Meningitis Bulletin

by Elio

Exserohilum rostratum conidia. Source: AP Photo/CDC

We seldom post items of immediacy, but here we interrupt our leisurely ways to write about the current disastrous meningitis outbreak caused by the injection of fungus-contaminated steroids and other drugs. As microbiologists, the question comes to mind at once: Who is the pathogen? The fungus implicated is Exserohilum rostratum (although a couple of cases were due to the more familiar Aspergillus fumigatus and to a Cladosporium). Like many good fungi, E. rostratum has a couple of synonyms: Setosphaeria rostrata and Helminthosporium rostratum. If you never heard of them, you’re in good company. Neither had an expert on fungal infections who I asked, nor had I despite occasional dealings with fungi. The reason is that there are lots of species of such molds, many of which cause exceedingly rare human diseases.

E. rostratum is one of the dematiaceous or darkly pigmented molds that is found in soil, on plants and in stagnant water. Like many molds, it can be identified under the microscope by the morphology of its conidia (asexual spores), which are quite distinctive. The rare human infections it causes are typically of external body sites, e.g., the skin, cornea. Being common in the environment, it is likely that it contaminated the injectable medications before they were packaged.

The Tyranny of Phylogeny: An Exhortation

by Elio

There are days when I wish that the Woesian Three Domain scheme were wrong. Not that I would be happier if there were four or five or whatever number of domains. What would please me would be an escape from what I feel is an unnecessarily oppressive way of thinking, the seating of phylogeny (and its acolyte, genomics) alone at the head of the table. Why do I say this? Because as essential as phylogeny is to our understanding of the evolution of living organisms, equally vital is ecology to comprehend present day life. While it’s good to know where you come from, it’s equally important to know where you are and what you’re doing there. The Spanish philosopher Ortega y Gasset said it well: Yo soy yo y mi circunstancia (I am I and my circumstance).

A sole focus on phylogeny forces the past ahead of the present. Compare the two figures; they represent two different worldviews. One highlights the deep clefts between the three domains, the other is integrative and does away with such barriers. Maybe it is not phylogeny’s job to emphasize ecology, but neither should we be fixated on evolution alone. Obviously no one is, so I apologize for erecting a straw man. Yet let me voice a wish: I would like to see a wider ranging acknowledgement of each organism’s give-and-take with its environment. Famed evolutionary biologist and geneticist Dobzhansky once said: Nothing in Biology makes sense except in the light of evolution. Do I dare modify this well-known dictum to read: Nothing in Biology makes sense except in the light of evolution and ecology.

TWiM #44: Phage interruptus

Hosts: Vincent Racaniello, Michael Schmidt, and Elio Schaechter.

Vincent, Michael, Elio discuss the role of prophage excision in exit of Listeria from the phagosome, and analysis of bacterial communities in saliva.

Right click to download the audio file. (48 MB .mp3, 66 minutes)

Subscribe to TWiM (free) on iTunes, Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app.

Send your microbiology questions and comments (email or mp3 file) to twim@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.

A Kick in the Midgut

by S. Marvin Friedman

Malaria is one of the most devastating infectious diseases in the world today. About 400 million people are infected each year and of those 1.2 million die. Efforts to control malaria have been held back by the lack of an effective vaccine, the alarming rapidity with which Plasmodium, the protozoan parasite, develops drug resistance, plus the failure to eradicate the Anopheles mosquito vector. Fresh approaches to fight malaria are urgently needed, to be used singly or perhaps in combination. One novel approach to a vaccine was recently discussed in this blog.

Formation of Plasmodium berghei (a rodent parasite) oocysts in culture. A. Ookinetes. B. Transforming ookinete and C. young oocysts. F. Transformation begins with a small hump on the outer edge of the ookinete. Transforming ookinetes (“tooks”) then take on a snail-like appearance (v). The entire population of ookinetes transform in 12–36 h, depending on nutrient availability. Source.

Plasmodium undergoes an unusually large number of lifestyle changes in its trip from the female mosquito to a human and back. This is one of the most complex life cycles extant, with so many details that it taxes one’s memory. Each one of the dozen or so stages is labeled with a fancy name and ought be a target for intervention but, for a host of reasons, that has proven elusive. However, the parasite is especially vulnerable in one stage, the transition from a cell called the ookinete to one named the oocyst, which occurs in the mosquito’s midgut. Eventually, the oocysts cross the midgut epithelium into the insect’s circulatory space, the hemocoel. But before going across, the ookinetes are detected by recognition components of the mosquito’s immune system. Killing factors from both the midgut and nearby tissues are recruited and the ookinetes targeted for destruction. In some model systems, fewer that 5% of the ookinetes survive. This, then, is a bottleneck in the Plasmodium life cycle and an attractive place to try to intervene for extermination of the parasite.

Fine Reading: Predation

by Elio

Big Fish Eat Little Fish, by Pieter Brueghel the Elder, 1557. Source.

Big fish eat little fish, and so on, the ultimate “so on” being the microbes, which are typically placed at the bottom of the food web. In the oceans, bacteria are commonly set upon by protists, in soils also by nematodes and other small animals. And everywhere, there lurk virulent phages and even bacteriovorus bacteria. Add to the list a form of bacterial predation aptly called cannibalism, where a species attacks and destroys a close relative. With all these threats, microbes in nature continually face a perilous future. Predation is a broad term encompassing many kinds of interactions that take parasitism to the extreme—one party eating and the other being eaten. Our sympathy is often with the prey (the sheep being eaten by the wolf). On the other hand, we use a gentler term for the gobbling-up of prey, “grazing,” which brings to mind sheep pastorally nibbling on grass in a meadow and makes it easier for us to look kindly upon the predator.

Heterotrophic nanoflagellates such as these are major consumers of bacteria in the polar regions and contribute significantly to the carbon flux from dissolved organic carbon (DOC) via bacteria to larger organisms such as ciliates and metazoans. Source.

Ubiquitous as it is, predation influences the population structure of both prey and predator in multiple ways and on a large scale. More often than not, the predator becomes the prey and vice versa. These complex goings-on are central to the cycling of matter and energy on Earth. Predation, being everywhere, is hard to overlook. But despite it having such a key role, in microbial conversation predation often plays second fiddle to such glitzy subjects as intermicrobial communication or symbiosis (sensu mutualism). Mind you, it’s all part of one puzzle, but what you call the parts of the puzzle matters. I was prompted to voice these concerns by a recent review by Alexandre Jousset, which I found illuminating. It deals mainly with the ways microbes avoid being prey. (I should note that a current review about the other half, the ways the predators carry out their job, seems also called for.)

Who Would Have Thought It?Bacterial Cannonballs!

by Elio

Surprises are the stuff of science, but some discoveries are more surprising than others. This column is where I’ll share some findings that strike me as most unexpected.

Biomineralization has long been recognized as an important albeit not always appreciated process in microbiology. Too bad, because microbes have literally made mountains. They have formed huge rock deposits, such as the celebrated White Cliffs of Dover, these being the accumulation of calcium carbonate shells of the alga, Emiliania huxleyi. As with these carbonate shells, microorganisms most often deposit such minerals extracellularly. For other examples discussed in this blog, click here and here.

Only in rare cases are minerals accumulated within microbes. The iron-containing magnetic inclusions called magnetosomes made by magnetotactic bacteria are one example of such intracellular biomineralization. Forming these ‘biomagnets’ within the cell makes sense, as it enables the cell to orient itself in a magnetic field. The sulfur bacteria also deposit their sulfur-storage granules intracellularly. That has been pretty much it for mineral inclusions within bacteria, until the recent discovery of calcified microcannonball-like bodies inside a new species of cyanobacteria. It’s nothing like anything you’ve seen before.

The shores of Lago de Alchichica showing copious microbialites. Source.

The waters of a Mexican volcanic lake, Lago de Alchichica, harbor microbialites (aka stromatolites or sedimentary deposits whose formation is influenced by microbial mat communities). Here lives Candidatus Gloeomargarita lithophora, a newly identified cyanobacterial species descended from an early cyanobacterial branch. The cells are stuffed full of spherical bodies of a rare calcium carbonate mineral called benstonite. Surprisingly, these benstonite spheres contain as much magnesium, strontium and barium as they do calcium. These metals are not found at these concentrations in the lake water, suggesting that the cells are acquiring them through an active transport system. Each cell contains on average 20 inclusions. Conveniently, these cyanobacteria can be grown in aquaria containing microbialites from the lake, where they form phototrophic biofilms on the glass walls.

TWiM #43: Bacterial Caveolae and Zapping Acne with Phages

Hosts: Vincent Racaniello, Michael Schmidt, and Elio Schaechter.

Vincent, Michael, Elio review formation of caveolae in a bacterium, and the limited genetic diversity and broad killing activity of P. acnes bacteriophages.

Right click to download the audio file. (55 MB .mp3, 79 minutes)

Subscribe to TWiM (free) on iTunes, Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app.

Links for this episode:

• Formation of caveolae in E. coli (cell)
• Phages of P. acnes (mBio)
• Movie of bacteriophage infection (Vimeo)
• Letters read on TWiM 043

Send your microbiology questions and comments (email or mp3 file) to twim@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.

Talmudic Question #91

Why don't eukaryotes (with few exceptions) have operons in their genomes?

Faster than a Speeding Bolt: Mycoplasma Walk This Way

(With a nod to Aerosmith)

by Daniel P. Haeusser

Many prokaryotes move actively in liquid (swim) or on moist solid surfaces (swarm and glide) toward or away from a stimulus, such as a nutrient, light, or oxygen. Not surprisingly, prokaryotes have evolved numerous means of locomotion built around distinct molecular mechanisms.

The motility of all animals, such as a human like Usain Bolt (A) or a goldfish (B) is based on the actin and myosin protein machinery. Many bacteria utilize completely different systems to achieve motility, such as the flagella in E. coli (C) or the unique ‘walking’ of M. mobile (D). These different motility systems are akin to various ways to make similar-looking boats move through the water, such as by the sails in Winslow Homer’s Breezing Up (A Fair Wind) (E) or the internal-combustion engine of the Batboat (F).

How distinct? A human running, a dog walking, an eagle flying, a fish swimming, a frog hopping, and a starfish crawling are each unique, but all share a root mechanism in the molecular properties of actin and myosin in muscle cells. For prokaryotes however, their movements don’t just look different; they often evolved from disparate molecular systems or organelles unique to a particular genus or even species . Some of the more-studied mechanisms of prokaryotic motility are flagellar-based swimming and swarming, type-IV pilus twitching motility, and the ‘adventurous’ motility of Myxococcus xanthus. This adventurous motility relies on both secreted polysaccharide and a helical motor that produces tread-like protrusions along the cell surface.

Among the handful of other known prokaryotic motility mechanisms are those employed by the Mycoplasma, a genus in the class Mollicutes of the low G+C Gram-positive bacteria (Firmicutes). (Video of Mycoplasma motility) The Mollicutes share several defining characteristics, most obviously the lack of cell wall that gives them their name (mollis is Latin for ‘soft’ or ‘pliable’). Therefore, although they phylogenetically fall in the Firmicutes, the Mollicutes have no cell wall for the Gram stain and are not susceptible to the antibiotics that target bacterial cell wall synthesis. In addition, the Mollicutes are some of the smallest cells known at 0.2 – 0.3 μm in length. Although they can be grown independently, these bacteria are often closely associated with host organisms, allowing the bacteria to attain drastically reduced genome sizes (The ~500,000 kilobases of M. genitalium is the lower limit for forming colonies on agar).