Moselio Schaechter

  • The purpose of this blog is to share my appreciation for the width and depth of the microbial activities on this planet. I will emphasize the unusual and the unexpected phenomena for which I have a special fascination... (more)

    For the memoirs of my first 21 years of life, click here.

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April 17, 2014

Terms of Biology – Syntrophy

by Elio

Figure1 Figure 1. An example of syntrophy. Here, benzoate degradation is carried out by a model syntrophic consortium. Dashed blues lines indicate additional sources of cell carbon for the methanogens. Source.

Syntrophy or “eating together” is a kind of symbiosis widespread in biology and of great importance for key biochemical transactions on this planet. Indeed, the cycling of carbon in many of its aspects depends on microbial syntrophy. Thus, the breakdown of waste material critically depends on chemical modifications brought about by microbial syntrophic associations. The phenomenon basically, requires reverse electron transfer, i. e., the input of energy to drive critical redox reactions.

The term syntrophy was first used in microbiology to describe the association between chemotrophic sulfate reducing and phototrophic sulfur oxidizing bacteria. Syntrophy exists between two species of bacteria, two of archaea, or one of each. Lucky for us, a fine essay on this subject was written a few years ago by McInerney, Sieber, and Gunsalus. A later, more detailed review by the same authors is found here, and by others here as well. You will encounter a large variety of fascinating syntrophic associations as well as learning of the ingenious ways that microbes have evolved to squeeze out the last drop of energy from thermodynamically unfavorable reactions. A classic example of symbiotic syntrophy involves an archaeon that can convert methane into CO2 and hydrogen by virtue of a sulfate-reducing bacterium siphoning off the hydrogen byoxidizing into into H2S. And more complex systems abound. For instance, in a tripartite relationship, bacteria in anaerobic environments degrade polymers into acetate, long chain fatty acids, and other compounds, other microbes convert these into hydrogen, formate, and acetate, and a third group use these to make methane and CO2.

The authors pose the question of how do syntrophic cell partners communicate? The answers are not obvious and require further investigation. But a great deal is known already. In the authors’ words: Genomic analysis has revealed the genetic blueprints of model syntrophic substrate-utilizing microorganisms, which in turn has provided insights into the metabolic pathways operative for carbon and electron flow to the end products acetate, hydrogen, and formate. The emerging bio- chemical paradigm includes the need for reverse electron transfer via membrane-bound as well as cytoplasmic confurcation-type enzymes that dispose of electrons as hydrogen and/or formate. Syntrophic strategies truly exist at the thermodynamic limits of life."

March 24, 2014

Six to Tango

by Elio

Something There Is That Likes Symbioses

Figure1 Figure 1.

One genome at a time can be exciting, but two even more so. I’m not entirely sure why this is, although it may explain our fascination with sex. And what if more than two entities were involved? What if the intimacy were not just between two individual organisms, but between a greater number of different ones? Not merely a happy couple, not even limited to a ménage à trois, but an exuberant symbiotic orgy? What could be lovelier?

High on the list of symbiotic wonders are the sap-sucking insects (aphids, mealybugs, psyllids) and their bacterial endosymbionts. The partners appear to have evolved together and to have established a harmonious coexistence eons ago (see Fig. 1). This follows from the fact that plant sap is essentially a sugar solution, so if that’s all an insect eats, how does it get the amino acids, vitamins, and other essential nutrients it cannot make itself? The answer is from the endosymbiotic bacteria it carries within specialized cells in its abdomen called bacteriocytes. These welcome guests provide their host with many—but not always all—the missing nutrients. This theme of “feeding through symbiosis” is repeated up the evolutionary scale, culminating in our phylogenetic neighborhood with the ruminants.

Continue reading "Six to Tango" »

January 13, 2014

How do they make it work? Genomic Revelations on a Bacterial Consortium

by Johnna L. Roose

Figure1 Fig. 1. A Happy Couple. Source.

Do you ever look at a couple and wonder… ‘Why are they together? What does X see in Y. I just don’t get it.  Is X in it only for the money’?  Who doesn’t at times ponder about such matters? There’s practically an entire economy based on it. However, you didn’t find this article while waiting to check out in the grocery line. This post isn’t about celebrities; it’s about microbes.  No matter—some microbe relationships have us scratching our heads and, to the same degree, casting premature judgment.

Fig. 2. Scanning electron micrographs of “Chlorochromatium aggregatum”. (A,B) Epibionts are shown in false color green, central bacteria in false color purple. (B) The central rod is dividing, and most of the epibiont cells have dissociated from the consortium. Scale bar in (B) equals 1 μm. Source.

Two Heads Beat One

One great example of such a conundrum is represented by the phototrophic consortium Chlorochromatium aggregatum, (this invalid name derives from an ancient era, when it was thought to be a single organism). In fact this is an unusually sophisticated prokaryotic symbiosis between a central motile heterotroph (Candidatus Symbiobacter mobilis) surrounded by multiple epibiont cells of a photoautotrophic green sulfur bacterium (Chlorobium chlorochromatii) (Figure 1). At first glance, this seems like a reasonable pairing, to combine mobility with photosynthetic autotrophy for the benefit of both organisms. Taking a deeper look at this relationship raises more questions. According to Don Bryant, "The relationship of these organisms is that of a highly dysfunctional marriage between a workaholic/nitrogen fixer/primary producer that is strictly anaerobic, and an oxygen-requiring, stressed-out, addicted soccer person that provides the bus, the driver and the GPS system.” Thus, in the microbial world as elsewhere, relationships are more complicated than they seem to be.

To gain insights as to how these organisms make this tryst work, researchers have, not surprisingly, turned to genomics for answers. In Genome Biology, Liu and co-authors report the complete genome sequences of both Chl. chlorochromatii and Ca. S. mobilis (Figure 2).  They uncovered plenty of interesting details on the intimate relationship between these two organisms.

Continue reading "How do they make it work? Genomic Revelations on a Bacterial Consortium" »

September 26, 2013

Who Would Have Thought? Biggest Flower, Biggest Gene Thief

by Elio

Rafflesias in the tropical rain forests of Southeast Asia produce some of the biggest flowers in the world—up to one meter in diameter. Adding to their notoriety is their carrion-like smell to attract insects for pollination service. They’re not microbes by anyone's definition of the term. The reason they make an appearance in these pages is that they have stolen a larger proportion of their genome via horizontal gene transfer (HGT) than any other organism we know of. Between 24% and 41% of their mitochondrial DNA is of foreign origin, and even in their nucleus a whopping 2.1% of the genes were imported.


Fully opened flower of Rafflesia arnoldii from the Palupu
Reserve near Bukittinggi, Indonesia. Photo by Troy Davis.

Plant genomes seem to be especially rife in genes acquired by HGT, and this is particularly true for the parasitic kinds, of which the Rafflesias are impressive examples. These freeloaders have no leaves or stems, no plastids anywhere—thus no photosynthesis. They live off host vines whose nutrients they harvest via haustoria, absorptive organs that penetrate into the host’s tissues. These un-plantlike plants exist concealed within their host vines, only occasionally offering a showy reproductive structure to the outer world—reminiscent of the mushrooms formed by underground fungal mycelia. Now we have learned that they are not only trophic parasites, but also genomic thieves.

Continue reading "Who Would Have Thought? Biggest Flower, Biggest Gene Thief" »

August 26, 2013

Mycorrhizal Fungi: The World’s Biggest Drinking Straws And Largest Unseen Communication System

by Elio

Figure 1. Mycorrhizal fungal filaments around a plant root. Source.

Quick, which is the biggest symbiotic association on Earth? Did you guess the mycorrhizae? They are the huge symbioses between fungi and the roots of most terrestrial plants. Their total size is not easy to measure because not all the fungal filaments in soils are mycorrhizal nor are the mycorrhizal ones always mycorrhizing (a new verb?). Even so, one can make the case that the combined mass of the participating fungi and plant roots is colossal. A friend, the soil microbiologist David Lipson, tells me that the mass of mycorrhizal fungi on the planet is estimated to be somewhere around 1-3 x 1010 tons (that’s between 1.4 and 4 tons per person). We are obviously talking about a topic that deserves much more of our attention than it has received to date.

Plants depend on mycorrhizal fungal filaments to supply them with a stunning proportion of their needed water and minerals. In some forests, these fungi provide the plants with up to 80% of their nitrogen and 90% of their phosphorus. The fungi, in turn, depend on plants to provide them with organic compounds needed for their own growth. Although it had been stated that this traffic in carbon is unidirectional—plants-to-fungi—some 400 species of non-photosynthetic plants (e.g., Indian pipes) that lack chlorophyll are proof to the contrary. For these mycoheterotrophs, mycorrhizae are the primary suppliers of essential carbon compounds.

Continue reading "Mycorrhizal Fungi: The World’s Biggest Drinking Straws And Largest Unseen Communication System" »

July 29, 2013

Fine Reading: The Second Skin – Ecological Role Of Epibiotic Biofilms On Marine Organisms

by Elio

In contrast to air, the ocean represents a benign environment for most living organisms: With the exception of some harsh marine environments, the means of physicochemical properties are generally not far off the optimum of most species and their fluctuations are moderate, rarely exceeding biological tolerance limits. So begins a review by Wahl and colleagues on the virtues of marine waters as a habitat. I can’t say that I had given this much thought. Anticipating interesting insights, I read on: As a consequence, insulating coatings of the epidermis such as hair, feathers, wax are not required in the marine realm. No big surprises there, but the implications of it, as explored by these authors, are vast and far-reaching.

Figure 1. Biofouling coating test. 12 x 12 inch test panels exposed at the intake of a power plant for 1 year. Some of these panels were uncoated controls, others were coated with various nontoxic compounds intended to inhibit biological fouling. Minor benefits, if any, can be attributed to the coatings. Score: 1 for nature, 0 for coatings! Source.

Lacking such protective barriers, the body surfaces of marine organisms more intimately engage with the environment and participate in actively acquiring essential nutrients, gases, light, and information. Bathed continually in seawater, these surfaces invite colonization by microbial biofilms, a “second skin.” Such living coverings tend to be thicker and more permanent among aquatic organisms than terrestrial ones (especially if you take a shower every day). While such biofilms can be essential partners, the wrong participants or excessive growth can be detrimental, leading, for instance, to fouling. We associate 'fouling' with biofilms that interfere with our activities, such as the communities that form on the hulls of ships, on membranes in desalination plants, or on catheters. But fish, algae, and other ocean dwellers also are beset by fouling that can reduce exchanges with their environment, alter buoyancy, impede motility, influence feeding, or even interfere with mating. Numerous factors come into play to influence the density of the epibionts colonizing animals and algae.

Continue reading "Fine Reading: The Second Skin – Ecological Role Of Epibiotic Biofilms On Marine Organisms" »

July 08, 2013

Let There Be Light!

by S. Marvin Friedman

As discussed in a recent epic Perspective on the animal-microbe symbioses (and commented in this blog), we are beginning to understand the many contributions made by each partner. One of the most widely studied symbioses is that of the luminous bacterium Vibrio fischeri and the Hawaiian Bobtail squid, Euprymna scolopes. In a recent publication, Heath-Heckman and coworkers determined that bacterial bioluminescence regulates the expression of a squid circadian rhythm (cryptochrome) gene (cryptochromes are a family of blue light receptor proteins involved in circadian rhythms of animals and plants).

Fig. 1: The Hawaiian Bobtail Squid. Credit: Source.

Over the past few years, bacterial partners have been implicated in their host’s circadian rhythms. For example, in humans, immune competence requires that such rhythms be intact. Normal functions of the gut, such as peristaltic activity, undergo circadian rhythms that are likely to be impacted by the gut microbiota. Likewise, several conditions, such as obesity, diabetes, depression, and sleep disorders are associated with aberrant circadian rhythms and imbalances in the gut microbiota. Tantalizing though this is, in none of these systems has a direct interaction between symbiont and host been demonstrated. The first instance involves the squid and its vibrio.

Continue reading "Let There Be Light!" »

June 13, 2013

Fine Reading: The gut microbiota of insects – diversity in structure and function

by Elio

Now that the mammalian intestinal microbiome has been promoted to organ status, might not such stately respectability be granted to the gut microbiota of other metazoans? If looking for a worthy candidate for such recognition, one could not do better than to consider the varied communities dwelling in the guts of insects. A recent review by Engel and Moran points out that beneficial intestinal microbes here: upgrade nutrient-poor diets, aid digestion of recalcitrant food components, protect from predators, parasites and pathogens, contribute to inter- and intraspecific communication, affect efficiency as disease vectors, and govern mating and reproductive systems. Microbes, it is clear, have contributed mightily to insect success.

A. Generalized gut structure of insects. The foregut and hindgut are lined by a cuticle layer (black line), the midgut secretes a peritrophic matrix (dashed line). B-M: Gut structures of insects from different orders. If not specifically indicated, the gut of an adult insect is shown. Stipples depict the predominant localization of the gut bacteria. For plataspid stinkbug, the magnification shows bacteria localized in the midgut crypts. Source.

The microbial landscape of the insect gut microbiome is much different from that of mammals. The great diversity of insects is reflected in their digestive tracts that also differ greatly in anatomy and physiology, and thus accommodate microbiotas that vary in composition and number. The total number of bacteria present range from 109 per honey bee, to 105 in a fruit fly, to negligible numbers in the sap-feeders, the latter often carrying instead an abundance of bacterial endosymbionts. Pick any individual insect and likely it will have fewer species in its gut than you do, although there are exceptions. Perhaps the most diverse communities among the insects are those in the termites, which are teeming with bacteria and protists. The 19th century American paleontologist and biologist Joseph Leidy observed that when one ruptures the intestine of a termite, myriads of the living occupants escape, reminding one of the turning out of a multitude of persons from the door of a crowded meeting-house.

Continue reading "Fine Reading: The gut microbiota of insects – diversity in structure and function" »

May 27, 2013

Stuck in Phage Heaven

by Merry Youle

Fig 1 stuck in heaven
Figure 1. This image, intended to highlight the mechanism of the DNA packaging motor of phage T4, also provides a vivid representation of the 155 Hoc proteins (yellow) assembled into the capsid with their Ig-like domains extending outward. Green = major capsid protein; purple = vertex protein; blue = outer capsid proteins Soc; yellow = outer capsid protein Hoc. Source.

Ceteris paribus, the more prey, the better the hunting. The successful fisherman fishes where the fish are, the skillful pride of lions hunts where the wildebeest gather, and savvy phage predators hang out where the bacteria are. Such bacteria-rich locations include the protective mucus layer formed by animals to protect their vulnerable exposed surfaces. Bacteria—symbionts and pathogens alike—find mucus hospitable; it offers them food and a structured environment. The congregation of bacteria makes mucus a good place for phages to hunt their prey, and some have evolved to exploit this resource. Thus, while looking after their own interests, phages here also serve as an antimicrobial defense for their metazoan host.

The rule of thumb is that phage virions outnumber bacteria in most environments by roughly ten-to-one. Barr et al. recently reported that this ratio is increased more than four-fold in mucus sampled from a wide range of metazoans, from corals to humans. Unlike chemotactic bacteria, phages can’t actively move towards mucus. That there are more phages in mucus than in the adjacent milieu implies that when good fortune and diffusion brings them to the mucus layer, they adhere and stick around. The obvious question is how.

Continue reading "Stuck in Phage Heaven" »

May 02, 2013

Little Known Glomalin, a Key Protein in Soils

by Elio

A visible portion of the rhizosphere. Source.

If you had heard of glomalin, you are a better person than I am. Until a couple of months ago I wasn’t aware of its existence, which is close to sinful: it happens to be a very abundant protein in the soil rhizosphere, playing a key role in the soil’s mechanical properties and as repository of soil carbon. Glomalin is a glycoprotein (although the “glyco-“ may be overused here, as biochemical analyses suggest that it contains little in the way of sugars) that binds together silt, sand, or clay soil particles. By ‘supergluing’ the small, loose particles, this gooey protein makes larger granules or aggregates and protect the soils from the eroding forces of winds and water. So, where does glomalin come from? It is thought to be made by fungi, more specifically by members of the arbuscular mycorrhizal fungi, the Glomales (hence the name ‘glomalin’). The hyphae of these fungi synthesize glomalin as part of their stress response. They coat their outer surface with the protein to make a protective waxy coat that keeps the water and nutrients inside the cells. The glomalin coating also makes the fungal strings sticky so they bind soil particles, thus creating an protective ‘armor’ against environmental insults and microbial predators. Most importantly, the fungal “string bags” make soil aggregates. This improves water infiltration and retention in the soils and gas exchange, which makes them more fertile. For more information on glomalin click here.

Continue reading "Little Known Glomalin, a Key Protein in Soils" »

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