Small Things Considered

A Condominium Plant

A section of a stem of L. a. africana. The swollen
section to the left is a domatium showing the entry
slit created by the resident ants, Petalomyrmex phylax.
Arrows point to worker ants. Source.

by Merry

Early in childhood, we learned that the plants and animals around us are discrete entities with definite boundaries. A dog might have fleas, but fleas and dogs are separate and distinct individuals. With our increased familiarity with symbioses—especially those of the obligate sort—have come many instances where "separate" individuals can seemingly survive only as part of a functioning association. Here is yet another example.

For more than twenty-five years, Doyle Mckey, now a professor in ecology, University of Montpellier II, France, has been studying one species of tree, Leonardoxa africana africana (Fabaceae or Leguminosae)—known locally as the bush-boer bean. Likely you've never seen one of them as they are found only in a narrow strip of humid coastal rain forest in southern Cameroon. This particular tree is a myrmecophyte, i.e., an ant-plant. (For those who relish words as we do, myrmecophyte is from the ancient Greek myrmeco, "ant" and phyton, "plant." Myrmecophyte is not to be confused with myrmecophile, a general term for any organism that lives in association with ants, or with the Myrmecophila, a genus of myrmecophytic orchids.)

The Leopard and the Mouse: A Microbiologist's Take

by Fred Neidhardt

Photo credit: Casey Gutteridge/Solentnews.biz.

Nineteen-year-old photography student Casey Gutteridge captured this extraordinary scene at the Santago Rare Leopard Project in Hertfordshire, UK. Casey, who was photographing the leopard Sheena for a course project, said: I have no idea where the mouse came from—he just appeared in the enclosure after the keeper had dropped in the meat for the leopard. He didn't take any notice of the leopard, just went straight over to the meat and started feeding himself. But the leopard was pretty surprised—she bent down and sniffed the mouse and flinched a bit like she was scared. In the meantime the mouse just carried on eating like nothing had happened. But even a gentle shove does not deter the little creature from getting his fill...the mouse continued to eat the leopard's lunch and show the leopard who was boss! Sheena was brought in to the Santago Rare Leopard Project from a UK zoo when she was just four months old.

So, what was going on? How can one explain this unusual behavior of (likely) predator and (likely) prey?

Marine Archaea and the Nitrogen Cycle

by Douglas Bartlett

What is more stirring than to contemplate the cycles of matter in nature? We sense that we witness vital transactions of this planet’s metabolism, a fulfilling thought. Such matters speak particularly loudly to us microbiologists: not only do global fluxes concern the elements of life but are to a great extent driven by microbial activities. In this vein, here is some important news.

Analyses of the nitrogen budget in the oceans suggest that a whole lot more nitrogen is being fixed than was recognized. Who does this extra nitrogen fixation? A recent paper from the laboratory of Victoria Orphan at Cal Tech provides clues that may help balance the nitrogen budget. These researchers studied the syntrophic aggregate of archaea belonging to the ANME-2 group and bacteria belonging to the Desulfosarcina/Desulfococcus. These consortia are a big deal: they consume about 80% of the methane released from seeps in marine sediments. Intriguing here is that their metagenomic analysis revealed that they contain genes for nitrogenase, the key enzyme in nitrogen fixation. So, do these partnerships fix nitrogen? And, if so, does this contribute substantially to that arm of the nitrogen cycle? The answer seems to be yes to the first and, "well, to some extent,” to the second.

Genomic Secrets of P. infestans, the Master of Potato Blight

This is the third and final post for our week of the oomycetes. In our first post, Elio provided the foundation by answering five key questions about this often neglected and misunderstood group. This was followed by a reminder from Mercè Piqueras of the role one member, the potato blight pathogen, has played in our history. Here in this final offering, Merry explores what we now—more than 150 years after The Great Famine—know about this pathogen's tactics from its genome sequence.

by Merry

No fungicide has ever been found to which P. infestans could not ultimately adjust…Indeed, no potato has ever been developed with defenses that Phytophthora could not ultimately breach. (Glenn Garelik. Source)

More than 150 years after the historic Irish potato famine, the deadly pathogen responsible for potato blight, Phytophthora infestans, is now destroying more than $3 billion worth of potatoes each year. What is the secret of it's pathogenic success? Hoping to find some answers in its genome, a team of 96 researchers have sequenced virtually its entire 240 Mb genome. This is by far the largest and most complex genome sequenced among the chromalveolates, a diverse eukaryote supergroup that includes not only the stramenopiles (the oomycetes, diatoms, and some algae) but also the dinoflagellates and the apicomplexans.

Why so much DNA? That's more than double that of Caenorhabditis elegans.

A Mold That Changed the Course of History

In this, the second of our three posts focusing on the oomycetes, we are pleased to offer a post from the blog by Mercè Piqueras, La lectora corrent (The Common Reader), translated here from Catalan.

by Mercè Piqueras

Micrograph of an oospore of Phytophthora
infestans. Source.

Recently, Nature published an article about the genome sequence and analysis of Phytophthora infestans, the oomycete that caused the potato blight in the nineteenth century that changed the course of history. Phytophthora infestans is the reason that today about 11% of the population of the United States is of Irish origin and that the population of Ireland was lower at the end of the 20th century than it had been in the first half of the 19th century.

Symptoms of potato late blight on potato
leaves. Source.

People who migrated to the United States in the 19th century did so for the same reason that pushes many people to migrate today to Europe from Latin American or African countries: to improve their living conditions, sometimes simply to survive. Hunger to the point of starvation was the main cause that pushed many Irish to go to the United States. That hunger even has a name of its own: The Great Famine in English and Am Gorta Mór in gaèlic The cause was potato blight, a pest that is still difficult to control today, although there are several ways to try to prevent it. Potatoes, originally from the Andean regions of South America, were introduced in England in the mid-16th century by Sir Walter Raleigh, who planted them in the fields of his estate in Ireland. In the 17th century the crop spread throughout the island, supplementing the Irish diet that had consisted mainly of cereals and dairy products. By the early 18th century, potatoes had become the staple food of the poor during the winter, and its culture became more and more widespread.

Five Questions About Oomycetes

by Elio

We recently reprinted an article by Patrick Keeling entitled Five Questions About Microsporidia. His fine discussion prompted us to attempt a similar examination of another highly important—but oft-neglected—group of microbes, the oomycetes or water molds. We will post three articles, the first one (herewith) describing oomycete biology, the other two focus on a particular oomycete: the late potato blight pathogen. There we will recount a bit of Irish history and then discuss aspects of the pathogen's genome.

What Makes Oomycetes Important to People?

Saprolegnia infection on the body of a koi fish.
Source.

As you know, the potato blight caused widespread famine in potato-dependent, mid-19th century Ireland. You may also be aware of a current malady, sudden oak death, that affects large numbers of trees in the Pacific coastal states of the USA. And if you are involved in agriculture in any way, you have likely heard of the downy mildews of lettuce, onions, spinach, strawberries, and other crops. Likewise, those concerned with aquaculture are alert to a variety of "fungal" diseases, including one called saprolegniasis that causes about a 10% mortality in pond-grown salmon.

What do these diseases have in common? They are all caused by oomycetes, a large group of organisms that resemble fungi morphologically but are distant from them phylogenetically. Pathogenic oomycetes cause massive destruction and huge losses in agriculture and aquaculture. They infect many animals, among them fish, crayfish, and mammals—including humans. Oomycetes, along with chytrid fungi, are thought to be involved in the current global decline of the frog populations. Since some oomycetes prey on pathogenic fungi, they are considered candidates for biological control of fungal infections of plants.

Because of their impact, much effort has been devoted to elucidating the genetics and biochemistry of particular oomycetes. Likely the best studied one is the agent of the potato blight, Phytophthora infestans. The literature about this organism is indeed impressive, commensurate with this organism's accomplishments as a pathogen.

Merry adds - Oomycete Mating Types and the Potato Blight

One of the points that Elio mentioned above has taken on major real world significance of late. That concerns the ability of the sexual oospores to survive in the environment for periods of a year or more, whereas the wall-less asexual zoospores can survive only within host tissues. The sexual life cycle requires, as you would imagine, a minimum of two mating types. This has major ramifications for the success of the oomycete pathogen responsible for potato blight, Phytophthora infestans.

Until 1976, only a single mating type, A-1, was found in almost all of its infections outside of Mexico (its region of origin). The ability of this blight to transform a whole field of potatoes from slightly diseased to almost completely destroyed in a few days is the result of its production of enormous numbers of zoospores. During the winter of 1976-77, mating type A-2 escaped from Mexico in a 25,000 metric ton shipment of potatoes exported to Europe, and has since become established worldwide. This poses several serious challenges to those who would cultivate or consume potatoes.

Talmudic Question #55

The Central Dogma of Molecular Biology has never been seriously challenged. Here is your chance: can you conceive of a mechanism whereby genetic information can flow directly from proteins to nucleic acids?

The Limitations of LB Medium

by Hiroshi Nikaido

LB medium, also known incorrectly as Luria-Bertani medium, is widely used to grow bacterial cultures, mainly because it is easy to prepare and provides a broad base of nutrients. LB broth contains, per ml, 10 mg tryptone (a mixture of peptides formed by the digestion of casein with the pancreatic enzyme, trypsin), 5 mg yeast extract (an autolysate of yeast cells), and 5 or 10 mg NaCl. It was formulated by Giuseppe Bertani in 1951 for studying lysogeny in Escherichia coli. He called it “Lysogeny Broth,” or LB. Notably, the original formulation included 1 mg/ml glucose, which has been dropped in more recent times. This medium was designed for work at low bacterial densities, a key point of this article.

While this may appear a tasty dish for many bacteria of research interest, it is an inappropriate choice for physiological studies wherein reproducibility is required. Since only bacterial cultures in balanced growth (achieved by sufficient time in exponential growth) have a reproducible average cell size and chemical composition, none of the components of liquid media should become exhausted during growth of the culture. Is this the case with LB broth? To answer this question, we must know what limits bacterial growth in LB broth.

It Was The Worst of Times, It Was the Best of Times

by Elio

At the end of the Permian period, about 250 million years ago and not long before the dinosaurs appeared, life on Earth experienced its greatest catastrophe: a mass extinction that did away with the vast majority of life forms on land and sea. The question arises, who ate the carcasses of the deceased? Surely bacteria and protozoa digested the animal corpses, most likely reaching unusually high population sizes as the result. But who took care of the masses of dead plant material? Fungi are quite good at digesting plants, especially woody plants. So, did the fungi also become prevalent after the catastrophe?