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 22, 2014

The Tale of a Tubeworm and a Biofilm

by Jordan Kesner, Bryan Hancock, and Nicole Nalbandian

Figure1 Figure 1. Tubeworm Life Stages. Left, larva of H. elegans. Right, Adult H. elegans with tube. Courtesy of Brian Nedved.

The oceans of our world harbor an incredible diversity of life, the vast majority of which has yet to be observed or characterized. This is part of what makes the study of marine biology so exciting; there is, in essence, an endless sea of new and exciting underwater discoveries to be made. When a biologist thinks of the creatures that inhabit our oceans, one of the prominent examples that often comes to mind is the tubeworm, a metazoan with a characteristic tube-like outer shell. The most likely image one thinks of is of the giant chemosynthetic tubeworms inhabiting the darkest recesses of the oceans near hydrothermal vents. In fact, many different species of tubeworms exist in the various regions of the ocean, and they are often involved in complex symbiotic relationships with other forms of marine life. The elongated, calcified, tube-like ‘shell’ in which adult worms live actually only represents half of their life cycle. They also exist in the juvenile state as free-swimming larvae, which actively seek out new surfaces to colonize. When a tubeworm larva decides it has found a good spot to settle, it initiates metamorphosis that results in anchoring itself to a solid substrate and begin growing into an adult worm.  After the adult worms release gametes into the water, they join to form new larvae, thus completing the life cycle.

Figure2 Figure 2. Colonies of P. luteo on agar. Courtesy of Nicholas Shikuma.

Bacterial Prodding

Recently, biologists have discovered that bacterial biofilms  are important participants in the life cycle of many marine invertebrates. For invertebrates such as the tubeworm, Hydroides elegans (well known by seafaring types for its role in biofouling), bacterial biofilms are known to produce a signal required by the larval stage of the worm to become able to settle and develop into a mature, stationary adult. When they receive this signal, the larvae of H. elegans embed themselves into the bacterial biofilm. H. elegans typicallylives in shallow waters in the so-called ‘benthic zone’, or lowest depth, where it shares an interesting relationship with a bacterium, Pseudoalteromonas luteoviolacea (P. luteo). Thisis a biofilm-forming bacterium that is responsible for inducing metamorphosis in H. elegans. Until recently, what this signal was and how it functioned remained enigmatic.

Figure3 Figure 3. Structural components of assembled MACs. Courtesy of Nicholas Shikuma.

Here we examine a recently published paper by Shikuma et al. that sheds light on this fascinating bacterium-tubeworm relationship. The authors took a close look at a cluster of genes found in P. luteo that had previously been identified as essential to their ability to induce metamorphosis in the tubeworm.  They found that some of the sequences resembled a family of bacterial genes encoding the bioactive agents called bacteriocins. Surprisingly, some bacteriocins share morphological and sequence similarity with the tail structures of phages. Many phage use contractile tails to breach the cellular envelopes of their bacterial hosts and gain access to the cytoplasm. The phage tail-like bacteriocins have all the tail components of a functional phage but without the DNA filled head of the virus, a most striking example of evolution leading to multiple uses of a biological structure.  And these structures are also used for a kind of bacterial protein secretion called Type VI or in the virulence of the bacterium Photorhabdus against moths. But, remarkably, phage tail-like structures have yet other uses. This paper shows convincingly that it is these structures that provide the signal for a beneficial activity, the initiation of metamorphosis in H. elegans. The authors appropriately name these proteins MACs, for Metamorphosis-Associated Contractile Structures.

Figure4 Figure 4. Mutant MACs do not induce metamorphosis. Source.

Surprises From Phage-like Tails

One of the most interesting aspects of this study was the elucidation of the physical structure of the MAC proteins. The MACs of P. luteo are made of four major proteins: the baseplate, the sheath, and two tube proteins, each encoded by a separate ORF.  In vitro, MACs are released extracellularly when a small percentage (approximately 2.4%) of the P. luteo in a biofilm population lyse. To investigate which components of the MAC complex are required for induction of metamorphosis, these researchers made mutants deficient in the MAC structural genes. Each construct contained a baseplate-GFP fusion protein to allow visualization of the released MACs. Next, they purified the MACs and added them to H. elegans. None of the mutant proteins were able to induce metamorphosis.This suggests that the full and intact MAC complex is required in the H. elegans lifecycle.

Figure5 Figure 5. Cryo-EM images of MAC Superstructure. Source.

Using cryoelectron microscopy, the group obtained stunning images of MACs in what is assumed to be a close representation of their native state. MACs do not function individually. Rather, they make highly ordered arrays that are held in place in supramolecular hexagonal lattices. This is the first time such a complex structure consisting of phage-like tails has ever been observed, and it may give insight into the native structures of related bacteriocins. The MAC tube protein appears to exist in one of two conformations thought to represent two different functional states: one in which the tube protein is still present in the MAC complex, and one in which it is missing. Based on this and knowledge of how phages inject their DNA into host cells, one could speculate that the MACs function as a molecular gun, irreversibly firing the tube protein into the cell membrane of the larva of H. elegans.  The nature of the stimulus that causes the MAC tube protein to be fired from the complex is not yet known. The novelty of the data produced by Shikuma et al. opens the door to many other exciting questions that the authors hope to answer in future studies. Some of these already come to mind: how exactly do MACs interact with the larvae, how is the tube fired from the complex, how many MACs are required to induce metamorphosis, what is the nature of the symbiosis between bacteria and tubeworm, how is the synthesis of the MACs regulated in the bacteria, and so forth.

Figure6 Figure 6. The two states of the molecular gun, MAC Complex. Source.

Novel Structures, Novel Signals

Preliminary data suggest that the hexagonal lattice protein that holds the MAC superstructure in place (termed MAC-L) is required for larval metamorphosis. This would seem to indicate that the large, multi-MAC complexes provide the signal, and that individual MAC complexes are not sufficient. The next step in this research will be to annotate the bacterial genome by knocking out specific segments of the genes associated with the MAC proteins. Doing so will allow identification of the key structural components required for the function of MACs. In his own words, Dr. Shikuma “would like to explore the direct interactions of P. luteo with H. elegans to determine precisely how the MAC complex interacts with the larvae.” He is also interested in exploring the phylogenetic diversity of various bacterial species that synthesize MACs.

The pioneering work done here paves the way for more intensive study into MACs and specifically of their relationship to animal life cycles. Who knows, such a structural bacterial element might carry out a beneficial function in humans. Wouldn't that be a novel and exciting concept? It does not seem too farfetched to think that MACs and phage tail-like structures may be useful to humans in the future. Maybe in agriculture, where MACs, in aiding certain organisms to complete their life cycle, may lead to propagation of new animal species in captivity and to other beneficial uses. Could MACs created in gut microbes mediate an immune response in the body? The future seems bright in MACland.

 

Authors


The authors of this paper are participants in the 2014 Winter quarter UCSD/SDSU Integrative Microbiology graduate course. The authors contributed equally to this work.

Note from the authors: This project would not have been possible without the collaborative effort of many people with a wide range of expertise; Special thanks to Michael Hadfield for his expertise in tubeworm biology and Martin Pilhofer for his electron microscopy work.

We sincerely thank Dr. Shikuma for meeting with us personally to answer all questions regarding the study.

ResearchBlogging.org



Tran, C., & Hadfield, M. (2011). Larvae of Pocillopora damicornis (Anthozoa) settle and metamorphose in response to surface-biofilm bacteria Marine Ecology Progress Series, 433, 85-96 DOI: 10.3354/meps09192

Shikuma NJ, Pilhofer M, Weiss GL, Hadfield MG, Jensen GJ, & Newman DK (2014). Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science (New York, N.Y.), 343 (6170), 529-33 PMID: 24407482

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 10, 2014

The Cold Side Of Microbial Life

by Gemma Reguera

The Cold Side Of The Earth

Figure1 Figure 1. The Arctic and boreal regions of the Earth (or Northern lands) are shown in color, each color corresponding to a different type of above-ground vegetation. Source.

In the midst of one of the worst Michigan winters on record, I felt inspired to learn more about how microbes cope with the cold (it is true: misery does indeed like company). So it happens that the polar vortex that has visited our northern states a few times this season has given us a glimpse at the subzero temperatures that prevail in the northern lands of our planet, sometimes all year round. The most northern areas are what we generally know as the Arctic, a treeless region that is either barren of vegetation or limited to tundra (shrubs, grass, lichens, etc.). As you continue going south, you enter the boreal region, characterized by its thick coniferous forests. The soils in these northern lands are called permafrost because they remain frozen for long periods of time. The almost permanent frozen state of these soils limits microbial activity and the turnover of organic matter. Not surprisingly, permafrost soils store approximately 25% of all of the planet’s soil organic matter.

For all their frigid circumstances, do not assume that permafrost microbes are in a perpetual state of hibernation. These frozen soils harbor a broad diversity of microbes. Furthermore, bulk measurements indicate that there is microbial metabolic activity despite the subzero temperature regimes. Just how much, we don’t know. Scientists fear that global warming will continue to thaw large areas of permafrost, promoting microbial activities and the turnover of the large quantities of organic matter trapped in the soils. This could lead to the release of substantial amounts of carbon into the atmosphere in the form of carbon dioxide and the greenhouse gas methane. However, with the limited information we have, it is difficult to predict how the permafrost microbial communities will respond to global warming.

Continue reading "The Cold Side Of Microbial Life" »

February 17, 2014

The Fungus That Killed Darwin’s Frog

by Gemma Reguera

A Mouthful of Kids

Figure1 Figure 1. A ‘pregnant’ male Darwin frog carries its babies in the vocal pouch (left) until they are big enough to be spat out (right). Sources here and here.

In his second expedition to South America, Darwin discovered many new species of animals and plants. The field observations obtained throughout this 5-year expedition provided the intellectual framework for the maturation of his ideas on evolution. It also introduced the world to a tiny (2-3 cm in length) frog known as Darwin’s frog. The group includes the northern (Rhinoderma rufum) and the southern (Rhinoderma darwinii) species, which inhabit the central and southern forests of Chile (and adjacent areas of Argentina), respectively. As in many other amphibians, fecundation is external. However, Darwin’s frogs do not leave the fecundated eggs on the ground and exposed to environmental insults and predators. The males scoop them with their mouths and incubate them in their vocal sac. The dedicated dads feed their offspring after the eggs hatch, producing secretions analogous to milk that allow the tadpoles to grow in a protected environment, sometimes until they have fully developed into froglets. When the young are mature enough to fend for themselves, the male frog literally spits them out. You can see a short video describing this amazing reproductive strategy following this link. This behavior, generally known as neomelia, allows the male ‘surrogates’ to care for the eggs and then the young, maximizing survival throughout the critical tadpole stage. Unfortunately, deforestation in the regions inhabited by these frogs has resulted in vast habitat losses, leaving Darwin’s frogs in precarious conditions. The last sight of a northern Darwin frog was reported in 1980, leading researchers to suspect that this particular species went extinct years ago. The species has been tagged as ‘possibly extinct’. The southern species, R. darwinii, which has traditionally occupied a much larger region, has been able to survive, but population numbers have declined dramatically.

Continue reading "The Fungus That Killed Darwin’s Frog" »

November 18, 2013

Antarctica's Deep Lake: A Frigid Home for Steadfast Archaea

by Elio

Some time ago, we asked this Talmudic Question: Can you think of a place on Earth where there is free water but no microbes? (A sterile flask of nutrient broth in a lab, the insides of the body, or an IV bag in a hospital don't count.) Someone answered that perhaps deep in Antarctica there would be a buried lake that was sterile. Not so. The early returns from the deep drilling of the buried Vostok Lake indicated the presence of microbes even there. But other sites in that continent come close to being just such an environment because their microbial population is unusually thin. So, let’s rephrase the question: “Can you think of natural places where there is free water but, comparatively speaking, few microbes?” (Pick your own limit, but <105 cells/ml seems thin to me.)

Figure1 Fig. 1. Deep Lake. Credit: University of New South Wales. Source.

In answer, I point to Deep Lake, a most unusual environment in East Antarctica. Despite its low temperature, it never freezes. The reason? Its waters contain 27% salt (w/v, almost 5M of NaCl), just a tad below the salinity of the Dead Sea (33.7% w/v) and about ten times that of the oceans. That salinity keeps the lake liquid despite temperatures being as low as -40° C for the ambient air and -20° C throughout its depths. What stalwart microbes do you find here? Mainly, some unusual salt-loving Archaea, aka haloarchaea. They have been studied in some detail, with some unexpected findings. Four species make up about three quarters of the total population. They belong to a different genus each, all within the family Halobacteriaceae (the ‘-bacteriaceae’ being a holdover from older, “pre-archaeal” taxonomy). Like other haloarchaea, some of these isolates harbor two or three chromosomes, or replicons, totaling nine replicons among them. Each species has its own predilection for particular depths. They can be cultivated, as long as you have a lot of patience. One of them grows at temperatures from -1° C to 40° C, fastest at 33° C. When cultured in the laboratory at -1°C, the temperature of the top of the lake, the cells double six times per year. At that rate, the authors calculate that it would take 10 years for a single cell to fully populate the lake.

Continue reading "Antarctica's Deep Lake: A Frigid Home for Steadfast Archaea" »

November 08, 2013

A Whiff of Gastronomy

by Elio

Figure1 Fig. 1. The black truffle Tuber melanosporum. Source.

Ah, truffles! They are the gourmet’s celebration, the cook’s inspiration, the common man’s anticipation. And they demand quite a price, which at last count hovered around $2,000 a pound for Italian white truffles, the French black truffles being cheaper, but still not within the reach of most people. And their production is decreasing. So it befalls few mortals to dine on these delicacies. But there is hope. As many of you know, truffle oil is used quite widely in restaurants. So, where does truffle oil come from? Did it ever see a truffle? Before going there, let’s agree that the price is right. You can find all sorts of truffle oil on the Internet for as little as $5 per ounce. It even comes in a kosher variety.

 

Figure2
Fig. 2. 2,4 Dithiapentane.

Alas, truffle oil has not been within smelling distance of a real truffle but is simply some sort of regular vegetable oil, often olive oil, that has been doctored by the addition of the ether, 2,4 dithiapentane. This is one of the main odor-producing compounds in truffles and, to a debatable approximation, it emulates the real aroma. Many expert food connoisseurs disagree and maintain that it doesn’t resemble the real thing. Also, some are bothered by the artificial nature of this concoction. In defense of truffle oil, the flavor it imparts to food is quite impressive. It does remind me of the taste of the few truffles I have been lucky enough to eat—metallic, pungent, earthy, and very distinctive. It may not be the real thing but it does contribute a nice bite to otherwise uninspired dishes. I, for one, am on the side of the folks who enjoy it. The only allowance needed is to agree that even an imitation may taste good.

Continue reading "A Whiff of Gastronomy" »

October 21, 2013

A Bacterial Body Clock: Cryptic Periodic Reversals In Paenibacillus dendritiformis

by Monika Buczek

Figure1

As humans we live our lives in 24-hour increments—waking, eating, and sleeping at specific times dictated to us not solely by our discerning willpower, but also by the greater underlying persuasion of our circadian rhythm. Based on the earth’s rotation from day into night, we have internalized a deeply rooted clock that drives how we behave in response to our genetic expression patterns. It’s not hard to imagine that several other organisms respond to an internal sense of time. Sure enough, the 24-hour circadian rhythm is a highly conserved behavior—from complex mammals down to plants, fungi, and cyanobacteria. Interestingly, there are also examples of different temporal rhythm patterns—ranging from years and seasons to minutes and seconds. A curious example is that of the bacterium Paenibacillus dendritiformis, which seems to have its own internal clock of a mere 20 seconds.

Continue reading "A Bacterial Body Clock: Cryptic Periodic Reversals In Paenibacillus dendritiformis" »

September 30, 2013

E. coli Keeps Its Powder Dry

by S. Marvin Friedman

Figure1
Figure 1. Left: Dictyostelium discoideum aggregating into a fruiting body. Source. Right: Adult Caenorhabditis elegans male. Source.

Whether inhabiting soil, fresh water, or marine ecosystems, bacteria are constantly facing the threat of numerous and effective predators such as protists, nematodes, or phages. To defend against such predation, bacteria have evolved a number of strategies, including getting larger in size, moving faster, producing defensive secondary metabolites, and forming biofilms. Because of its anthropocentric appeal, one strategy stands out—keeping a locked armory of genetic weapons. The strategy involves breaking open the armory when confronted by perils—activating the genes that were locked mostly to save the cost of expressing them when not needed.

Continue reading "E. coli Keeps Its Powder Dry" »

September 23, 2013

The Microscopic Flash Mob

by Melissa Wilks

Every day we see animals migrating through the air, across plains, and in the oceans, in beautifully coordinated patterns; starlings flock together in the thousands while sardines swim together in enormous shoals. These social behaviors are important in allowing animals to socialize, avoid predators, and find refuge and food. But what about smaller organisms? Although more difficult to visualize, microorganisms can perform these coordinated behaviors as well. As is true for birds and fish, figuring out how and why bacterial cells communicate to organize their movements will help understand the behavior of bacteria in the environment.

Figure0
Figure 0. Ripples on the Camas Prairie of northern Montana. Source.

Myxococcus xanthus is a soil dwelling microbe that has attracted the attention of microbiologists in part due to its predatory activity. To survive in environments where nutrients are scarce, it kills and breaks open other bacteria and feeds on the released nutrients. During times of starvation, M. xanthus cells self-organizes into fruiting bodies, macroscopic dome-shaped mounds that contain over 100,000 cells each. In these structures, the cells differentiate into metabolically inactive spores that remain dormant and allow survival until times get better. Since the 1960s, M. xanthus cells have also been known for organizing their movements across a solid surface to produce waves; this phenomenon, called rippling, resembles the waves produced when you throw a rock into a pond, and can be seen in nature on a scale ranging from the microscopic to the geologic.

Continue reading "The Microscopic Flash Mob" »

August 26, 2013

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

by Elio

Figure1
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" »

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