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 15, 2014

TWiM #76: Genetic Biopixels and a Pathogenic Sweet Tooth

Hosts: Vincent RacanielloElio Schaechter, Michael Schmidt and Michele Swanson

Vincent, Elio, Michael, and Michele discuss the use of bacteria to build a genetic sensor for heavy metals, and how host sugars help enteric pathogens to expand after antibiotic treatment.

Right click to download TWiM #76 (48 MB .mp3, 67 minutes).

Subscribe to TWiM (free) on iTunesZune 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, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at and tag them with twim.

April 14, 2014

By Chance and Necessity: The Role of the Cytoskeleton in the Genesis of Eukaryotes

by Daniel P. Haeusser

How did Eukaryotes Evolve from Prokaryotes?

Figure1 Figure 1. The mysterious root of the eukaryotic origin. Evolution of prokaryotes into eukaryotes undoubtedly involved mitochondrial acquisition, but the full details of the story are far from certain. Source.

One of the most exciting and enduring obscurities of biology lies in the early stages of the evolution of “our” eukaryotic cells (Figure 1). The endosymbiotic theory accounts well for the present existence of the mitochondrial and chloroplast organelles of eukaryotes. Although there is evidence for present day inter-bacterial endosymbiosis (also see here and here), the details of the route leading to the establishment of organelles remain enigmatic.

Even murkier is the question regarding the origin of the nucleus (Figure 2). While prokaryotic cells with organelles arguably exist and scientists have identified Planctomycetes that enclose their DNA with internal membrane continuous with the cell membrane, a truly independent membrane-bound nucleus prevails as the defining hallmark of the eukaryotes. (A recent report even calls this textbook difference into question! However, another study calls these conclusions into question.)

Unlike the clear bacterial origin of the mitochondria and chloroplast, it turns out that no single existing model has received broad acceptance to explain the existence of the nucleus. Scientists have speculated that it could have arisen from an endosymbiotic event between an archaeon and a bacterium (though who engulfed whom is also uncertain). Some have proposed that an autonomous internal gathering of cell membrane as in Planctomycetes formed the eventual independent nuclear organelle, and yet others have even suggested infection by an enveloped virus as playing a role.

Figure2 Figure 2. Two of the prevailing models for the origin of the nucleus. Source.

Not only are details on the evolution of these eukaryotic innovations (nucleus and mitochondria or chloroplast) shrouded in mystery, but just as unclear is the temporal relation between their developments. Which came first, the nucleus or the mitochondrion?

A recent online article by Ed Yong for Nautilus Magazine gives a comprehensive summary of one of the prevailing hypotheses proposed to answer that question. The general crux is that the relatively sudden marriage of two prokaryotes into one stable individual cell occurred just once in the evolutionary history of life on Earth, and that allowed the emergence of an entire new branch on the tree of life. Here, the engulfment of a bacterium by an archaeon permitted the development of mitochondria. This union augmented and expanded the metabolic and energy generation capabilities of the new organism, thereby permitting genome size expansion and organelle proliferation (compartmentalization). All this gave sudden rise to the establishment of the hugely differentiated eukaryotic lineage.

Figure3 Figure 3. Labeled eukaryotic skeleton (Bovine pulmonary artery endothelial cells). Microtubules are shown in green and actin in red. DNA in the nucleus is shown in blue.

Some pieces of evidence detailed in the Nautilus article are consistent with a model where mitochondrial acquisition ‘licensed’ the genesis of eukaryotes. Yet, the jarring thing about this mitochondria-centric hypothesis is that it says nothing about the nucleus. The big problem with mitochondrial acquisition alone as the driving force of eukaryogenesis is that such a development is not a simple matter of metabolic and energy concerns. As recognized in Yong’s article, prokaryotes also largely lack eukaryotic ‘architecture’, leaving them “forever constrained in size and complexity,” an idea also discussed in an essay by Kevin Young. The mitochondrion alone is not a ready system for getting things around a cell as it increases in size and complexity. The cell would still lack the architecture and machinery to be released from the limits of simple diffusion, a significant barrier between the small prokaryotes and the (usually) larger eukaryotic cells.

In short, the mitochondria-centric hypothesis for eukaryotic genesis ignores the important uniqueness of the eukaryotic cytoskeleton (Figure 3). So, let’s take the cytoskeleton into consideration.

Why Are Prokaryotes Different from Eukaryotes?

A superb, recent essay by Julie Theriot addresses these issues with a focus on comparing eukaryotes to bacteria (not to archaea). Theriot’s essay probes deeply and meaningfully into the question of ‘why are prokaryotes and eukaryotes different’. With expertise in the cytoskeleton, her ruminations on this ‘why’ question rest on that dynamic architecture of eukaryotes that permits them to reach proportions of growth and organization rarely seen in prokaryotes.

To summarize her major points: While we now know that the cytoskeleton is present and broadly conserved across all domains of life (with diverse proteins in the actin, tubulin, and intermediate filament families), bacteria notably lack a special class of cytoskeleton-related proteins: the nucleated filament assembly factors and the motor proteins. Eukaryotes make ample use of these tools. By providing a mechanism for polarized assembly that permits motor protein directionality and inherently oriented filament growth, the eukaryotic cytoskeleton is the architectural machinery that achieves functions such as chromosome movement, vesicle and organelle transport, and endocytosis. These, in turn, help the cell attain sizes and complexities that otherwise would be unattainable.

Figure4 Figure 4. Some of the techniques evolved by pathogenic bacteria to subvert the host cell cytoskeleton using bacteria-derived secreted eukaryotic cytoskeletal regulators. Source.

Theriot correctly points out that, in theory, bacteria are capable of making such cytoskeleton-related factors. Indeed, several pathogens contain genes for proteins that alter and control cytoskeleton assembly (e.g. here), including through nucleation (e.g. here). But bacteria export these proteins for use on the host(Figure 4), never (that we know of) for their own cytoskeleton. So why didn’t they learn to use their cytoskeletons in the same way to gain some of the benefits that the eukaryotes enjoy? Why not follow the eukaryotic route?

Possible answers to these questions receive due consideration in Theriot’s essay, but what I found most fascinating is her observation that bacteria have a trove of genes that encode different varieties of the major cytoskeleton protein families, particularly with actin homologs. It seems as though bacteria have evolved one distinct homolog for each cellular function. Eukaryotes, by contrast, mostly contain just one type of each family member, which is then specifically regulated to perform several distinct functions. Could this explain why bacteria don’t use their cytoskeleton like eukaryotes?

With Theriot’s essay and the Nautilus article in mind, I wondered whether the existing unique properties of the eukaryotic cytoskeleton could fit into models for those cryptic early steps in the evolution of eukaryotes from prokaryotes. So, let’s circle back to the question of eukaryogenesis, but now with the cytoskeleton in mind.

“Every Act of Creation is First an Act of Destruction” – Pablo Picasso

What if the first endosymbiotic merging that permitted the outburst of the eukaryotic lineage were not that of mitochondrial acquisition (a bacterium engulfed by an archaeon), but rather the reverse, something more akin to what has been considered a possible origin of the nucleus, the engulfment of an archaeon by a bacterium.

Theriot’s essay avoids discussion of archaea, perhaps because we know precious little about them. In visual appearance, archaea and bacteria are look-alikes, but archaea contain genetic and mechanistic facets that are both bacteria-like and eukaryote-like. The cytoskeletons of archaea are similarly mixed: while many encode bacterial components such as ftsZ, their overall cytoskeleton composition is closer to the eukaryotes’. Crenactin, for instance, is phylogenetically nearest to canonical actin rather than to the myriad actin homologs found in bacteria. We don’t know enough about archaeal cytoskeleton control yet to figure out if they have nucleated assembly factors, motor proteins, or any of the other unique properties of the eukaryotic cytoskeleton. But given the presence of other rudimentary eukaryotic systems in archaea, such as ubiquitination, it's reasonable to hypothesize that some archaea may employ and control their cytoskeletal architecture in ways closer to those of eukaryotes.

So then, imagine if a bacterium with its cytoskeleton composed of multiple, monofunctional actin/tubulins were to engulf an archaeon with a relatively simpler cytoskeleton consisting of a single member of the actin and tubulin families each. Were the engulfed archaeon capable of growth and further replication within its new host, some cells would die with time, leaking archaeal contents into the bacterial host cytoplasm. I propose that this could include ‘eukaryotic-like’ cytoskeletal proteins and regulatory system components like proto-motor proteins and nucleation factors.

The presence in the same bacterium of multiple actin and tubulin homologs carries the risk of cross talk between the regulator and those homologs. If so, this may preclude or at least discourage the evolution of task-specific regulators that affect assembly like nucleation proteins, or factors like motor proteins. Thus, if the cell needs to nucleate one actin homolog involved in plasmid segregation, it may not want to have to nucleate the other actin homolog, e.g. one involved in maintaining cell shape. Unique factors would then need to evolve for each cytoskeleton homolog, a demanding task. On the other hand, the ‘single member’ system of the archaea may allow for the innovation of these kinds of regulatory systems. They could comprise a small set of regulators whose activity can be modulated depending on where and when they’re needed. Inside their bacterial host, these archaeal regulatory factors are now free to act via crosstalk on the bacterial homologs.

This potential for disastrous cross-talk of a single regulator on different homologous cytoskeleton family members in a single cell would also explain why several bacterial species appear perfectly capable of evolving eukaryotic-like cytoskeleton control for export during pathogenesis (in trans), yet eschew adoption of such systems in cis. Their relatively broad repertoire of highly similar cytoskeletal components simply makes it too risky a proposition.

Figure5 Figure 5. (Left) Pablo Picasso’s Violon (Violin) 1911-12, Kröller-Müller Museum, Netherlands. Just as the audience’s image of a violin is destroyed through deconstruction within the oval frame to achieve Picasso’s art, so too may a bacterial cytoskeleton have been disrupted under the influence of archaeal-evolved factors following endosymbiosis. (Right) Chance and Necessity by Jacques Monod. Borrowing Monod’s title, the chance merging of two distinct systems for cytoskeletal regulation may, by necessity, have influenced eukaryogenesis.

The Picasso quote that titles this section could be equally apt for this proposed version of eukaryogenesis (Figure 5, left). To summarize and repeat: The chance mixing of two distinct modes of cytoskeleton regulation in merged organisms (one with many similar members with unique functions and the other with single members with broad functions) would potentially result in a war for control. Because of regulatory crosstalk, one system would need to eventually win out. Perhaps the products of the endobacterial archaeal genome interfered with, and ultimately destroyed, the bacterial cytoskeletal system, creating a novel one in its place.

An archaeal cytoskeleton with rudiments of nucleation and motor proteins, but now within a bacterium with its own unique genes for metabolism, creates a novel organism with the architectural system needed for further evolution. This could include the compartmentalization of a newly merged genome under the control of an archaeal-derived cytoskeleton. With the acquisition of energy-generating organelles and further compartmentalization, larger physical dimensions and a bigger genome size could be attained. More stable, these early eukaryotes would displace any amitochondrial species and, with a finer tuning of their cytoskeleton, develop more innovations.

According to this model I’m proposing, the key event in the eukaryogenesis is, to reference Monod (Figure 5, right), the chance merging of two systems by the necessity of regulatory cross-talk gaining dominant control over homologs of the other system. Above all, such a model predicts that we should be able to find existing archaea with genes that encode nucleation factors and/or motor proteins used to control the functions of its own cytoskeleton. To my knowledge they have not yet been found, but I don’t think that we’ve looked particularly hard either.

Are there problems with this line of thinking? Are there other considerations? Most importantly, what kind of experiments do you think would currently be possible to address these speculative models? The mystery of eukaryogenesis still has a lot of questions, and like with many things in science, I don’t think that our curiosity will soon be satisfied.


Daniel is a postdoctoral fellow in the Margolin Lab in the Department of Microbiology & Molecular Genetics at the University of Texas, Houston Medical School. He also teaches as an adjunct professor at the University of Houston-Downtown in the Department of Natural Sciences.

April 10, 2014

Talmudic Question #107

Suppose you are once again strolling on that deserted beach and again, on cue, the genie reappears. This time he is offering you some mice from a lineage that he has bred for hundreds or more generations under germ-free conditions.  Would you expect to find any genetic changes in these mice? If so, what might they be?

April 07, 2014

The Oldest Gem Tells its Tale

by Gemma Reguera

A rocky beginning

Figure 1. The dramatic beginnings of Earth as a molten planet bombarded by asteroids and meteors. Source.

Modern Earth is nothing like it was in its early days. Our planet was formed some 4.56 billion years ago when a giant stellar cloud collapsed on itself due its massive size and gravitational force. The explosion also generated the sun and many other planetary bodies, including those that would eventually become the planets of the Solar system. This early Earth was a planet of molten rock surrounded by a layer of hydrogen and helium gases. These gases were likely blown away by the intense solar wind, leaving the planet without a protective atmosphere and making it more vulnerable to bombardment by asteroids and meteorites. At this time, it had a moon called Theia, which some theories believed collided with the Earth with such force that it tilted the planet and made the moon. The impact is also believed to have stimulated the circulation of magma, intensifying volcanic activity in what was already a very inhospitable planet. Not surprisingly, this early era in Earth’s history is called the Hadean (Hell-like) eon. These were indeed hellish conditions that prevented the emergence of life. Yet the Earth began to cool down and, at some point, a thin, but stable continental crust was formed. These ‘milder’ conditions also promoted the condensation of water released through the outgassing of volcanoes. And so a primitive ocean was formed. The volcanic outgassing also released gases such as ammonia, carbon dioxide, and methane and created a primitive atmosphere that helped protect the planet from meteorite bombardment and radiation. It may have been a rocky beginning, but once the planet cooled down enough to form continents and oceans, it was ready to harbor life.

Figure2 Figure 2. Timeline showing the formation of Earth some 4.56 billion years ago and some major geological and biological events in the history of our planet. The Jack Hills zircon rock dates back to the time when the Earth was in its early stages of evolution, after the moon was formed. (Image credit: Andree Valley). Source.

Hadean or Archean life?

Dating the emergence of life on Earth is a daunting task. We can date when life was already thriving based on the age of microfossils, i.e., mineralized structures whose size, shape, and chemical composition matched those of modern microbes. But even these ‘proofs’ can be misleading. In the 1980s, for example, scientists discovered 3.5-billion-year-old mineralized filamentous structures in the Apex Chert formation in western Australia, which were strikingly similar to cyanobacteria. The ‘microfossils’ were later shown to be inorganic mineral formations. So far, the oldest microfossils may be the carbonaceous spheroidal microstructures of the Moodies Group in South Africa (3.2 billion years old) and microfossils from the Strelley Pool Formation in Western Australia, which are believed to represent 3.4-billion-year-old sulphur-metabolizing cells. Hence, the microfossil data supports the notion that life was already thriving in the mid-Archaean eon. But how far back in time does life go?

In the absence of microfossils, scientists are focusing on geological evidence to ascertain the time when the continents and oceans formed to mark the time when planetary conditions could have supported the most primitive forms of life. Isotopic evidence from the Isua Greenstone Belt in Greenland suggests that the planet had liquid water 3.8 billion years ago, early in the Archean eon. However, the geological record, in the form of an ancient rocky formation in the Canadian Artic called Acasta Gneiss, suggests that a continental crust already existed approximately 4 billion years ago. The formation of this continental crust depended on conditions that would have also favored the formation of oceans and the emergence of life. Hence, it is also possible that life originated in the Hadean eon.

There is also geological evidence that ‘soon’ (100 million years!) after the formation of the Acasta Gneiss rocks the Earth was heavily bombarded with asteroids (the so-called ‘late bombardment’ or ‘late heavy bombardment’). This was a major cataclysm that many believed melted the Earth again and sterilized it. Hence, many argue that, if life had emerged in the Hadean period, it would have been wiped off from the planet. Modern life, then, would have evolved from Archean ancestors. Yet a planet-wide sterilization would have required the Earth to melt completely. If so, ancient rock formations such as the Acasta Gneiss, which predates the cataclysm, would have melted as well. A more likely scenario is that only parts of the planet were impacted by the bombardment and that melting was local, rather than global. This would have allowed for the preservation of at least part of the Hadean continental crust and biosphere. These survivors would have withstood the high temperatures and acidity of the Hadean ocean. Volcanic activity may have also been very intense at the bottom of the oceans during this time, releasing iron into the hot ocean sediments. But iron, hot temperatures, and acidic waters are conditions that we know sustain the growth of some heat-loving (hyperthermophilic) microbes around modern hydrothermal vents at the bottom of the oceans. Thus, microbial life under such extreme conditions is possible. In fact, these primitive microbial activities based on iron respiration at hot temperatures may have also contributed to the formation of ancient rocks known as banded-iron formations some 3.8 billion years ago. So it is indeed very possible that microbial life is much older than we are taught in school and may in fact date back to the Hadean eon.

The gem of all rocks

Figure 3. The decay chain of uranium and thorium inside the Jack Hills zircons allowed scientists to date the crystal’s formation to 4.2 billion years ago. Source.

A Hadean origin of life relies heavily on geological evidence dating the time in Earth’s history when continents and oceans formed. To investigate this, geologists focused their studies on the ancient Jack Hills rock formation in Western Australia, which is believed to harbor some of the oldest rocks on Earth. This site contains zircons, a type of zirconium silicate crystals that are durable and resilient to the passage of times. Zircons contain uranium (U) and thorium (Th), which decay radioactively within the crystal. This generates internal radiation and changes the crystal’s structure, color, and density over time. Most importantly, the progressive radioactive decay of these elements generates new elements in defined, sequential steps, each taking a precise amount of time. For example 238U, the most abundant U isotope, has a half-life of 4.5 billion years, i.e., it would take all this time for half of the U in the zircons to decay to the next element in the decay chain, 234Th. Once  thorium is formed, it takes only 24.5 days for half of it to decay to 234Pa and just a little over 1 minute to generate 234U. The chain reaction continues through various elements until the formation of a non-radioactive, stable element (206Pb), which ends the decay chain. Similarly, the more rare 235U isotope decays through a chain of elements to form 207Pb. Hence, by measuring the amount of U and Th and their decay products of U and Th, in particular the radiogenic lead isotopes (207Pb and 206Pb), geologists can precisely date the age of zircon.

Figure 4. Nanoscale analyses of the 207Pb/206Pb ratios by atom-probe tomography identified Pb clusters in specific atomic arrangements expected from the natural radioactive decay of U and Th within the crystal. This helped rule out any bias of the measurement of 207Pb/206Pb ratios due to lead mobility and provided solid evidence that the crystal was 4.4 billion year old! (credit: John Valley, University of Wisconsin). Source.

In 2001, an international team of scientists performed radiometric studies on several spots on a new zircon crystal from the Jack Hills site. The results varied with the spot analyzed but all established that the crystal was between 4.2 and 4.35 billion years old! Furthermore, the oxygen isotopic analyses in the zircon were within the ranges expected for a rock that was formed when magma was suddenly cooled upon interacting with water. Hence, these results suggested that a stable continental crust and oceans might have already existed early on in the Hadean eon. Perhaps not unexpectedly, these provocative studies, which were published in Nature, generated a lot of controversy. Many questioned the reliability of the radiometric assays, based on the fact that little is known about how the internal radiation generated inside the zircon affects its structure and the mobility of the radiogenic lead isotopes. Fractures in the crystal could, for example, concentrate the lead isotopes in defined spots and give artifactually high estimates of abundance. After more than a decade, some of the same authors published a new study, this time in Nature Geoscience, which put the controversy to rest. This time the team used a powerful technique called atom-probe tomography to simultaneously identify, quantity, and map the atomic position of the radioactive elements and decay products and any other elements that could have migrated inside the crystal and ‘contaminate’ the sample. The specific arrangement of the radiogenic Pb atoms allowed the scientists to differentiate spots where they had concentrated due to migration from those directly produced from the decay of the internal, native U and Th elements. The Pb nanoclusters formed by internal radioactive decay had 207Pb/206Pb ratios corresponding to ages up to 4.4 billion years old! That’s ‘just’ 160 million years after the Earth was formed and soon after the formation of the moon.

Figure 5. A planet of microbes. Source.

Not so hellish after all

The Jack Hills zircon tells an amazing tale about the evolution of early Earth. It tells us that the planet had cooled enough to form a continental crust not that long (160 millions) after its formation. In this short period of time, the planet transitioned from being a ball of magma (as depicted in Fig. 1) to a planet with continental crust and a hydrosphere. It also had the moon,was already tilted, and had both a magnetic field and an atmosphere. It was still hot, the ocean was acidic, and the atmosphere saturated with toxic gases, that’s for sure. But these conditions, as hellish as they may sound, could have supported the emergence of life. As a microbiologist, I am mesmerized by the fact that life may in fact be almost as old as the Earth itself (a ‘few’ -one or two hundred- million years, give and take ;o). Perhaps most important is the fact that the Earth and microbes have been companions for such a long time. This partnership has been a major catalyst in our planet’s transformation from a ball of magma to the green and blue planet of today. Without them, we, humans, would not have existed. Without them, we will not be here tomorrow. And that’s what’s most beautiful about the gem’s tale.


Gemma is associate professor in the Department of Microbiology and Molecular Genetics, Michigan State University and an Associate Blogger at STC.

Wilde SA, Valley JW, Peck WH, & Graham CM (2001). Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago. Nature, 409 (6817), 175-8 PMID: 11196637

Valley, J., Cavosie, A., Ushikubo, T., Reinhard, D., Lawrence, D., Larson, D., Clifton, P., Kelly, T., Wilde, S., Moser, D., & Spicuzza, M. (2014). Hadean age for a post-magma-ocean zircon confirmed by atom-probe tomography Nature Geoscience, 7 (3), 219-223 DOI: 10.1038/ngeo2075

April 03, 2014

The “Microbe Hunters” by Paul DeKruif - A Major Force in Microbiological History

by Elio

The chances are good that when you ask a senior microbiologist how he or she got into this science, they will tell you that they were influenced as teenagers by reading  “Microbe Hunters.” I was about 14 years old when I did, and I became transfixed by the glorious and intrepid achievements of our forefathers, told in a jaunty and florid style. There was nothing else I wanted to do with myself than to become a Microbe Hunter.

Figure1 Figure 1. Microbe Hunters (1950 edition)

This book was written in 1926, two years before my birth, by the microbiologist Paul DeKruif, whose career was as checkered as it was unusual. He graduated in 1916 from University of Michigan with a PhD in microbiology and, after World War I, got the job at the Rockefeller Institute. This, however, did not last long because his lifestyle included writing for the general public, which at the time was frowned upon by the establishment. He also hung out with such suspect characters as Carl Sandburg, H.L.  Mencken, and Sinclair Lewis, of whom he became a welcome drinking companion. DeKruif became the source of microbiological information for Lewis’ best-selling book, Arrowsmith. In this book, a somewhat persecuted microbiologist works on developing phage therapy in a lab he had built in his own home.

Figure2 Figure 2. Paul DeKruif. Source.

”Microbe Hunters” rapidly became a huge success. It was translated into all major languages and inspired two Hollywood movies. It still sells well. But for all its appeal, it received serious criticism. DeKruif wrote in a “jazz style,” where bravura at times seems to be more important that the facts. To make the narrative conform to his “voice,” DeKruif not only made up dialog from whole cloth but also took liberties with the facts.  So much so that one of the people depicted in the book, the British microbiologist Ronald Ross, threated a lawsuit. The matter was resolved by omitting the chapter on Ross from the British edition! But such thorny facts do not detract from the impact of the book. As I can attest, if you read it at a susceptible time of life, you will be carried away by the pungency of the tales, the spirited portrayal of the protagonists and the glory of the achievements.

For more on the book and its author, click here for an article by Robin Marantz Henig and here for a video clip of a lecture by John M. Lehman.

April 01, 2014

TWiM #75: Pellicles on Pickle Jars

Hosts: Vincent RacanielloElio Schaechter, Michael Schmidt and Michele Swanson

Vincent, Elio, Michael, and Michele discuss a symbiosis between two bacteria that increases the virulence of oral biofilms, and the assembly of amyloid fibers, which are needed for biofilm formation.

Right click to download TWiM #75 (59 MB .mp3, 81 minutes).

Subscribe to TWiM (free) on iTunesZune 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, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at and tag them with twim.

March 31, 2014

From Geology to Biology: A Serpentine Story of Early Life

by Samantha Trumbo

Figure1 Figure 1. The carbonate white smoker chimneys of The Lost City Hydrothermal Field. Source.

Over 4.5 billion years ago, the Earth was a superheated sphere of molten rock, radiating heat to space at over 2000 K. A billion years later, it had global oceans, teeming with microorganisms. In that time, the Earth underwent massive geological changes, somehow serendipitously creating conditions right enough to lead to the spontaneous emergence of cellular life. It has been suggested that these primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean, and that similar environments could host extraterrestrial life elsewhere in the solar system. Until recently, our typical picture of such hydrothermal vent systems was that of the gargantuan black smoker chimneys driven by mid-ocean ridge volcanism. Here, hyperthermophilic chemolithotrophic archaea brave the extremely hot, acidic, sulfurous waters in order to oxidize inorganic compounds released in the vent fluids. However, with the year 2000 discovery of the Lost City Hydrothermal Field and its cooler, alkaline “white smokers” (Figure 1), our view of sea-floor hydrothermal environments has begun to change. Many scientists are now turning their attention to these off-axis (some kilometers from the volcanic mid-ocean ridge) hydrothermal environments, and to their geological driving force, a process called serpentinization. Might this be the energy source for the first life on Earth and, who knows, for life elsewhere?

Serpentinization is a geological process involving reactions between water and the rocks of the lower ocean crust and upper mantle. These rocks contain minerals (olivine and pyroxene) that are thermodynamically stable at the high temperatures and pressures that prevail deep within the Earth. However, when exposed to near-surface environments, they react with water to form what is generally known as serpentinite rocks (Figure 2). The main reactions driving serpentinization are:

Fe2SiO4  + 5Mg2SiO4  + 9H2O → 3Mg3Si2O5(OH)4  + Mg(OH)2  + 2Fe(OH)2

fayalite olivine + forsterite olivine + water serpentine + brucite  + iron hydroxide

Mg2SiO4  + MgSiO3  + 2H2O → Mg3Si2O5(OH)4

forsterite + pyroxene + water serpentine

3Fe(OH)2 → Fe3O4  + 2H2O + H2

iron hydroxide → magnetite + water + hydrogen

Figure2 Figure 2. A photomicrograph of a serpentinite rock obtained with a polarizing petrographic microscope. The grey snake-like veins are serpentinite minerals and the light colored grains are residual, unaltered olivine minerals. The field of view is 2.5 mm. Source.

The molecular hydrogen released during serpentinization reduces sulfates and carbonates and generates hydrogen sulfide and methane. Further reactions can result in short-chain hydrocarbons, as well as formate and acetate. At temperatures below 150°C, the reactions increase the pH of the fluids (commonly to ~10) and promote the co-precipitation of Ca2+ and carbonate as calcium carbonate. The reactions are also highly exergonic, releasing heat and contributing to the circulation of the vent fluids through cracks in the rocks. The chemical alteration of rocks during serpentinization also reduces their density, increasing their volume and promoting their uplift from the parent rock materials. This is the reason why serpentinites are common in ophiolites, portions of the ocean crust uplifted onto land. Serpentinization also occurs in oceanic ridge and trench environments, where ocean crust is brought into contact with water via the tectonic processes of plate spreading and subduction. However, as demonstrated by Lost City, it can also occur several kilometers off the ridge axis. Here, heat flow is much less extreme than that in volcanic ridge environments, and conditions seem more hospitable for the emergence of cellular life.

Serpentinization has even been suggested as a possible past or ongoing process on Mars, as well as Jupiter’s moons Europa, Ganymede, and perhaps Callisto, and Saturn’s moons Titan and Enceladus, all of which show evidence for subsurface liquid water oceans. Therefore, the significance of the process to the origin of life on Earth and to life on Earth today has implications for the search for habitable (or, who knows, inhabited) extraterrestrial environments.

Serpentinization and the Origin of Life

The unifying energy strategy of all known forms of life is chemiosmosis, or the use of a proton gradient across biological membranes for energy generation. In 2010, Russell et al. published their serpentinization theory of the origin of life, which revolves around the idea of the process providing the first life with an analogous natural pH gradient across a preformed abiotic membrane. The idea is that, this way, life only had to capitalize on a preexisting arrangement rather than invent chemiosmosis on its own.

During the process of sea-floor serpentinization, the volume of the altered rocks increases, further fracturing the parent rock and releasing heat, thus promoting more water percolation. The process becomes self-sustaining, with hydrogen and vent fluids circulating continuously through the fractures for long periods of time. When they react with the cold seawater, the alkaline vent fluids precipitate as porous mineral mounds or chimneys. The pores are surrounded by semipermeable mineral membranes, which help concentrate organic secondary products of serpentinization in microcompartments, as the vent fluid moves through the honeycombed structure.

Key to the theory is that the ancient ocean was much different from our ocean today. First, it was mildly acidic (~ pH 6), and would have formed a natural pH gradient with the alkaline vent fluid (pH ~10-11) across the mineral membranes of the compartments. The gradient’s direction would have been alkaline on the inside and acidic on the outside, as in modern cells. Second, intense volcanism contributed to an abundance of dissolved metals in the acidic ocean, which would have precipitated on the chimneys, perhaps helping mediate hydrogenation and redox reactions. Russell and colleagues argue that the natural compartmentalization, pH gradient, and catalytic properties provided by the chimney pores, along with the moderate, but warm temperatures and sufficient supplies of CO2 and H2, provided the perfect environment for the emergence of primitive cellular life. Such life, they posit, may have been equivalent to biological catalysts of the abiotic methanogenesis and acetogenesis resulting from serpentinization. The primitive microbes would have harnessed the energy of the natural proton gradient to boost the exergonic reduction of CO2, making methanogenesis and/or acetogenesis the most ancient of biological metabolisms. Biology, here, becomes a mere modification of a preexisting, thermodynamically favorable abiotic process.

What Can We Say of Serpentinization-hosted Life Today?

Innovative and alluring as this theory is, it is also important to look to modern serpentinization-hosted ecosystems in our attempt to understand its importance to life. The Lost City Hydrothermal Field represents our best modern example of this type of activity, as we discussed in this blog before. Located about 20 km west of the Mid-Atlantic Ridge on the Atlantis Massif, Lost City consists of towering (up to 60 m) carbonate hydrothermal chimneys (Figure 1), through which serpentinization-derived vent fluids rise to meet the ocean. In accord with the origin of life theory, the vent fluids are alkaline (pH 9-11) and the chimneys are porous. However, modern oceans are no longer acidic, but slightly basic. Furthermore, the modern vent chimneys of Lost City are formed of carbonate and are less metal-rich than their ancient forbearers. Nevertheless, Lost City hosts abundant microbial life, which could hold valuable clues to understanding the early days of the evolution of life on Earth.

Figure3 Figure 3. Transmission electron micrographs of thin sections of the LCMS biofilms growing on the carbonate chimney show sarcinal cell morphologies, some (D) with intracellular membrane stacks. Source.

The Lost City microbes live as biofilms on the inner walls of the chimneys and are dominated by a single 16S rRNA phylotype of archaea, the so-called Lost City Methanosarcinales (LCMS). The Methanosarcinales are methanogens with a characteristic irregular coccoid or ‘sarcinal’ morphology, which is easily appreciated in transmission electron micrographs of the Lost City biofilms (Figure 3). The low phylogenetic diversity of the Lost City biofilms is surprising when you consider that it is a relatively stable ecosystem and that the chimneys are 100 years old! In 2011, Brazelton et al. confirmed the validity of the 16s rRNA data using LCMS-specific fluorescent probes (FISH technique): the LCMS cells accounted for >80% of all the biofilm cells detectable by FISH. They were indeed the dominant group! They also used stable isotope techniques to assess the ability of the biofilms to cycle methane, detecting high rates for both methane production and oxidation. Both processes were stimulated by H2, suggesting that they were not in competition but performed cooperatively. In case you were wondering, the researchers also detected a few bacteria, but the most abundant sequences were from groups involved in sulfur—rather than methane-cycling. Hence, the LCMS archaea appeared to be the major drivers of the biofilm activities.

Figure4 Figure 4. Hypothetical syntrophic interactions of the two hypothesized LCMS cell types. Source.

Looking closely, the micrographs of the Lost City biofilms do indeed show two cell types (Figure 3). One group of cells had the characteristic sarcinal morphology and contained stacks of intracellular membranes similar to those found in methane-consuming microbes. By contrast, the other cell type lacked the membrane structures. The parallel between the biofilm’s metabolic and morphological diversification suggests that methane cycling may involve two types of LCMS microbes, which perhaps interact syntrophically to utilize the H2 and CH4 from the vent fluids, the latter process using sulfate as the terminal electron acceptor (Figure 4). Such physiological diversification in an otherwise homogenous phylotype could be generated through lateral gene transfer. This is known to happen in other members of the Methanosarcinales, and metagenomic analyses of the LCMS biofilms did in fact reveal a high abundance and diversity of transposase sequences. The metagenomic studies also suggested that at least some of the microbes in the LCMS biofilms may use acetate as a carbon substrate in place of CO2. CO2 is relatively scarce in the Lost City fluids compared to acetate, so the ability of the biofilm cells to metabolize acetate may help alleviate the carbon-limitation that is likely to prevail in this environment. A partial nitrogenase operon and a high diversity of nifH sequences were also identified in the metagenomes, which would allow some microbes to fix N2 (likely the most abundant form of nitrogen in Lost City fluids).

Brazelton and collaborators note that the talents of the LCMS biofilms may provide insights into the early evolution of life on Earth. Unity of biochemistry strongly suggests that all life on Earth has a common ancestor, from which life diversified to fill many ecological niches. The researchers point out that such an ancestor could have inhabited a biofilm in which genes and metabolites exchanged freely, as seen at Lost City. Differentiation similar to that in the LCMS biofilms could have led to diversification from this common ancestral gene pool, thus facilitating the early evolution of life. If so, the Lost City biofilms could provide a modern analog for the study of the ancient evolutionary processes that led to the great diversity of modern life.

Not surprisingly, Lost City and other emerging serpentinization-hosted ecosystems are now the focus of numerous studies. In the future, we can expect more exciting developments and intriguing insights into the role serpentinization plays in accommodating life on a global (or perhaps even larger) scale.


Samantha is a first-year graduate student working under Dr. Douglas Bartlett at the Scripps Institution of Oceanography of the University of California at San Diego.

Brazelton WJ, Mehta MP, Kelley DS, & Baross JA (2011). Physiological differentiation within a single-species biofilm fueled by serpentinization. mBio, 2 (4) PMID: 21791580

Russell MJ, Hall AJ, & Martin W (2010). Serpentinization as a source of energy at the origin of life. Geobiology, 8 (5), 355-71 PMID: 20572872

March 27, 2014

Pictures Considered #15. The Dynamo at Work

by Christoph Weigel

ATPase_Fig1_half_300 Figure 1. Movie appr. in real time (i.e. depends also on your browser); actual rate without actin load ~100 rev/sec. Source.

Why on earth would one stare—even for a few seconds—at this blurry, low-res, pixelated movie (to the right), watching a jittery rod tumbling counterclockwise around its pivot? Because it's ATP synthase, a key enzyme of the energy metabolism in every living cell, that's rotating there. And when a molecule does its job by a rotational movement, well, then it takes a movie to demonstrate this. We turn thus to 'very small things considered': an enzymatically active ~530 kDa multi-subunit protein complex with a diameter of  ~9 nm and a length of ~20 nm. Biophysicists finally showed in 1997 what biochemists and crystallographers had suspected for quite a while but could not prove by their own experimental methodologies: ATP synthase—also known as FoF1-ATPase, or complex V of the respiratory chain—is a molecular dynamo. First a closer look into the screenplay for the movie before peeking briefly at the bigger picture...

Molecular tinkering, the professional way

Noji and colleagues assembled their object of interest in three separate steps, all standard lab procedures, by 'affinity coupling' of the individual components. First, they prepared F1 particles (with the subunit composition: α3β3γ) of ATP synthase with His-tags at the N-termini of the β subunits to affix them to Ni-NTA covered microscope slides and a biotin-tag at the γ subunit. Second, to construct an actin probe conjugated to a red-orange fluorescent dye they coupled ~1 µm-rods of polymerized and biotinylated actin to rhodamine phalloidine. Lastly they coupled the biotinylated actin rods to the biotinylated γ subunits of ATP synthase via streptavidin. The whole assembly is shown schematically in Figure 2. When infused with ATP in buffer solution, a small percentage of the molecular assemblies started rotating―in all cases counterclockwise―as seen under the epifluorescence microscope and filmed for Figure 1.

Continue reading "Pictures Considered #15. The Dynamo at Work" »

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" »

March 20, 2014

Why Do Viruses Cause Disease?

by Vincent Racaniello

This article was first published on 7 FEBRUARY 2014 in the Virology Blog and is reprinted here by gracious permission of the author.


Virulence, the capacity to cause disease, varies markedly among viruses. Some viruses cause lethal disease while others do not. For example, nearly all humans infected with rabies virus develop a disease of the central nervous system which ultimately leads to death. In contrast, most humans are infected with circoviruses with no apparent consequence. Is there a benefit for a virus to be virulent?

One explanation for viral virulence is that it facilitates transmission. However, a comparison of infections caused by two enteric viruses, poliovirus and norovirus, does not support this general view. Both viruses infect the gastrointestinal tract and are spread efficiently among humans by fecal contamination. However, norovirus infection causes vomiting and diarrhea, while poliovirus infection of the intestine is without symptoms (the rare invasion of the nervous system, and subsequent paralysis, is an accidental dead end). Both viruses have successfully colonized humans for many years, so why does only one of them cause gastrointestinal tract disease?

Continue reading "Why Do Viruses Cause Disease?" »

March 18, 2014

TWiM #74: It Came from the Siberian Permafrost

Hosts: Vincent RacanielloElio Schaechter, and Michael Schmidt

Vincent, Elio, and Michael discuss a huge 30,000 year old virus recovered from Siberia, and nested symbiosis facilitated by horizontal gene transfer from bacteria to insect.

Right click to download TWiM #74 (51 MB .mp3, 70 minutes).

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

March 17, 2014

The Bacterial Chromosome: A Physical Biologist's Apology. A Perspective.

by Suckjoon Jun

I entered the bacterial chromosome field in 2004 as a fresh Ph.D. trained in theoretical physics. Ten years is not long enough for one to gain the depth and breadth of a scientific discipline of long history, certainly not for an early career scientist to write an essay of the status of A Mathematician’s Apology (Hardy 1940). Nevertheless, I agreed to write this Perspective as a physicist who entered biology, because my colleagues are often curious to know what drives physicists to become (physical) biologists, and make them stay in biology despite many challenges. I also wanted to share several lessons I have learned because, while some of them are personal and specific to my field, I have a good reason to believe that they might resonate with many future travelers. This Perspective is for them.

I would like to start with the story of one of the most familiar and yet mysterious forces in nature—gravity. Galileo is said to have dropped two balls of different masses from leaning Tower of Pisa in Italy some five hundred years ago. His experiment was to demonstrate that, on the contrary to Aristotle’s theory, the falling rate of the balls was independent of their mass. A modern version of this experiment was performed on the Moon by the Commander of Apollo 15 with a hammer and a feather. For a movie of this experience, click here. When released from the same height at the same time, the two falling bodies hit the surface of the Moon simultaneously! On the Earth, however, the feather would have fluttered, as if alive, because of the air.

Initially attracted to the beauty of Amsterdam, I started my post-doctoral research at AMOLF, an interdisciplinary research institute known for exciting interactions at the interface between physical and biological sciences. The forces I was interested in were much less tangible than gravity. In particular, I was supposed to explain the driving force underlying segregation of a replicating chromosome in Escherichia coli. It sounded simple to me, except that I barely knew anything about bacteria, certainly without realizing that it was one of the long-standing problems in biology. I knew the DNA biophysics literature fairly well, but when I saw the beautiful 1992 illustration of E. coli in Goodsell, it was obvious that something like the wormlike chain model was not going to be very useful to understand segregation of the whole chromosome. What worried me was the directionality—if I were a small protein sitting on a replicating chromosome, could I tell which DNA segment belongs to which sister DNA? Physicists like questions like that, whether they are rooted in physics or biology.

Continue reading "The Bacterial Chromosome: A Physical Biologist's Apology. A Perspective." »

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