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On Small Things Considered we share our appreciation for the width and depth of microbial activities on this planet. We enjoy writing about unusual and unexpected phenomena in the microbial world. Fortunately, these come our way with great frequency. We rely on contributors with all levels of experience, from undergraduate and graduate students to distinguished microbiologists. Our "Teachers’ Corner" facilitates the use of the blog in the classroom. Some of our blog’s idiosyncratic features include our "Talmudic Questions" (queries that cannot be answered by simply looking them up with Google), "Of Terms in Biology," and our "Fine Reading" posts, each of which features an exceptional research paper. Small Things Considered is sponsored by the American Society for Microbiology.
Elio Schaechter
13 posts
Merry Youle
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by Micah Manary in Small Things Considered
The ancient genes versus environment argument (i.e., nature versus nurture) about the development of the infant human brain has taken a swerve in a direction few thought possible. A recent paper by investigators from Sweden and Singapore reports on studies using a mouse model to demonstrate that the presence of the gut microbiota significantly influences the developing brain, influencing developmental pathways that affect both motor control and anxiety-related behaviors. The implications for human development are certainly not yet realized, but could be profound. Our anxiety, motor control, and even cognitive pathways are implicated in this paper. Microbes may indeed be subtly changing our brain early on—and for what purposes we cannot yet say. The article would imply that this interaction is beneficial to us, and thus indirectly to our microbiota, but the mere fact that microorganisms can shape our minds brings up many more questions about how humans develop their identity.... Read more »
Heijtz RD, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, Hibberd ML, Forssberg H, & Pettersson S. (2011) Normal gut microbiota modulates brain development and behavior. Proceedings of the National Academy of Sciences of the United States of America, 108(7), 3047-52. PMID: 21282636
by Moselio Schaechter in Small Things Considered
The practice of agriculture is not limited to humans: ants, termites, and snails all grow fungi, and who knows who else do something similar. But not many have claimed that such activities are to be found among simpler organisms. Now we have a report that slime molds have also gone down the road to agriculture. Dictyostelium discoideum, the best studied of the cellular slime molds, is a social amoeba that thrives by grazing on bacteria. Given ample bacterial food, these organisms grow as single cells. When food becomes scarce, they aggregate into pretty, differentiated fruiting bodies (called sorus, plural sori) consisting of a round mass of spores held up by a stalk. The spores eventually become dispersed, to repeat the cycle at a new site. The entire epic can be viewed in a dramatic documentary available here. (This movie is narrated in German, giving you the opportunity to hone your skills in that language.)
What is new here is that about one third of 35 clones of this species collected in the wild do something extra, namely they carry bacteria with them as they differentiate. They even include them within their sori. Once released, the spores have the ready opportunity to enjoy the source of food providently supplied for them. But non-farmers eat up all the available food before differentiating, whereas the farmers leave about half of the bacteria uneaten. It’s a little bit like humans not eating a whole grain harvest, but carrying some along when migrating to provide seeds for future sowing.
... Read more »
Brock DA, Douglas TE, Queller DC, & Strassmann JE. (2011) Primitive agriculture in a social amoeba. Nature, 469(7330), 393-6. PMID: 21248849
by Dean Dawson in Small Things Considered
Who hasn't heard of Candida? It’s one of the most common fungal pathogens of humans. It is also a commensal organism, living mainly in people’s gastrointestinal tract. The diseases it causes range from a fairly mild vaginitis to deadly opportunistic systemic infections. In fact, Candida species are a major cause of nosocomial bloodstream infections. Candidas are close relatives of the baker’s yeast, Saccharomyces cerevisiae, but live by very different rules.
Candida has been the focus of intense research at the molecular level for only the past fifteen years or so, and it has not been an easy road. These organisms, it turns out, have a slightly different genetic code than most others, rendering the standard molecular tools less useful. Additionally, Candida does not exhibit the mating and spore formation behaviors of its cousins Saccharomyces cerevisiae and Aspergillus, which made them popular organisms for fast-moving molecular genetic studies. But the development of new tools and a growing community of researchers have revealed in the past few years that Candida has evolved its own unorthodox mechanisms and lifestyles that probably greatly enhance its ability to adapt to changes in its host environments.... Read more »
Poláková S, Blume C, Zárate JA, Mentel M, Jørck-Ramberg D, Stenderup J, & Piskur J. (2009) Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata. Proceedings of the National Academy of Sciences of the United States of America, 106(8), 2688-93. PMID: 19204294
Bennett, R. (2010) Coming of Age—Sexual Reproduction in Candida Species. PLoS Pathogens, 6(12). DOI: 10.1371/journal.ppat.1001155
by Merry Youle in Small Things Considered
When you read the title—The Great Epidemic—what came to mind? The Black Death (Yersinia pestis) that in two years killed 20 million people in Europe—approximately 30-60% of the population? The 1918 flu pandemic with its tally of 50 million dead in three years? AIDS, with a death toll projected to reach 200 million by 2025? Or perhaps that 20th century epidemic that struck down over three and a half billion in North America in the space of a few decades—the American chestnut blight? These chestnut trees, Castanea dentata to be precise, were stately giants often 100 feet or more in height with crowns that spanned 100 feet. Their straight trunks provided billions of dollars worth of beautiful, rot-resistant wood, and the bountiful nuts provided far more than the traditional stuffing for Thanksgiving turkeys. Combined they had made up a quarter of the forest canopy from Maine to Mississippi.... Read more »
Dawe AL, & Nuss DL. (2001) Hypoviruses and chestnut blight: exploiting viruses to understand and modulate fungal pathogenesis. Annual review of genetics, 1-29. PMID: 11700275
by Merry Youle in Small Things Considered
Bacteria that are born genetically equal aren't necessarily the same. The same genome, residing in cells side-by-side in the same medium in the same flask, does not guarantee the same phenotype. One example that comes to mind is the persisters in E. coli populations—the small number of cells that spontaneously stop growing. If the population is hit by a β-lactam antibiotic, those cells escape death. Similarly, under lab conditions that trigger genetic competence in B. subtilis, only a small fraction of the cells make the switch to competence.
B. subtilis cells growing in a rich growth medium offer yet another example. Here genetically identical cells comprise two distinct types. Most are flagellated and actively swimming about as individuals, while a minority have no flagella and form long chains. The game is different in cells in the stationary phase where virtually all of the cells are found in long chains, bound together by an abundant matrix. Losick, Kolter, and colleagues have been working with this system for some years (for earlier papers, click here and here) seeking to determine how such bimodal cell populations are established and maintained in growing cultures.... Read more »
Chai Y, Norman T, Kolter R, & Losick R. (2010) An epigenetic switch governing daughter cell separation in Bacillus subtilis. Genes , 24(8), 754-65. PMID: 20351052
by Moselio Schaechter in Small Things Considered
by S. Marvin Friedman
How can thermophilic bacteria not only survive, but actually proliferate, at elevated temperatures that would be lethal to all other forms of life? After extensive research during the past five decades, this question has been answered in a general way, but the molecular basis for this unusual capability has not been clearly resolved. Thermophiles [I use this term to include both thermophiles (optimal growth temperatures of 50-70 °C) and hyperthermophiles (optimal growth temperatures 80 °C)] synthesize intrinsically thermostable cellular components and/or extrinsic stabilizing factors (chaperonins and polyamines, for example).
Most proteins isolated from thermophiles are thermostable and the mechanisms underlying this property have been extensively studied. These investigations have their roots in the pioneering work on the heat stability of hemoglobin and ferredoxin carried out by Perutz in 1975. Some of the strategies reported to bring about protein thermostability include higher levels of charged amino acids on the protein surface that promote ionic interactions, amino acid preferences, hydrophobic cores, aliphatic side chains, disulfide bridges, and solute accumulation. It is obvious from these studies that a universal mechanism to achieve protein thermostability does not exist. The complexity of this problem is highlighted by differences that appear to be in play for multimeric proteins versus single polypeptide chains, for soluble proteins versus membrane proteins, and for proteins from thermophiles versus proteins from hyperthermophiles.... Read more »
Botting CH, Talbot P, Paytubi S, & White MF. (2010) Extensive lysine methylation in hyperthermophilic crenarchaea: potential implications for protein stability and recombinant enzymes. Archaea (Vancouver, B.C.). PMID: 20811616
by Moselio Schaechter in Small Things Considered
by Welkin E. Johnson
Perhaps more than any other biological discipline, the study of animal viruses is confined to the present. Virions are simply not the stuff of which robust fossils are made. Phylogenetic analysis can help by revealing deep relationships between extant viral lineages, yet such reconstructions lack detail (telling us nothing about transitional or extinct viral forms, the movement of viruses between species, or the timing of major events in viral evolution), and molecular clock estimates are notoriously imprecise when applied to viruses [1]. Until recently, ancient endogenous retroviruses (ERVs) were the closest thing to a fossil record available to scientists with a proclivity for combining virology and natural history. Happily, a trio of recent studies appearing in PLoS Genetics [2], PLoS Biology [3], and PLoS Pathogens [4] reveal an unexpected wealth of non-retroviral virus sequences embedded in the genome sequence databases, a virtual equivalent of the Burgess Shale, ripe for excavation by eager paleovirologists.... Read more »
Katzourakis A, & Gifford RJ. (2010) Endogenous viral elements in animal genomes. PLoS genetics, 6(11). PMID: 21124940
Gilbert C, & Feschotte C. (2010) Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS biology, 8(9). PMID: 20927357
Belyi VA, Levine AJ, & Skalka AM. (2010) Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLoS pathogens, 6(7). PMID: 20686665
by Moselio Schaechter in Small Things Considered
Now that news of the arsenic-eating bacteria has saturated cyberspace, the airwaves, and even old-fashioned newsprint, we step back to raise a larger question: Why have so few elements from the periodic table made it into living things? You seldom hear about anything past the first few rows in the table. Turns out this is a gross oversight. Many more elements, previously unsuspected, are to be found in a large number of metalloproteins. So, move over, arsenic and make room for other elements.
Until recently, the topic of metal ion cofactors and metalloproteins has been something of a biochemical stepchild. For sure, some researchers have avidly pursed it. However, in most cases, the presence of metal was revealed serendipitously after the protein was purified. But what if one set out to cast a wide net for metalloproteins? The authors of a recent paper did just that by examining the proteins of the archaeon Pyrococcus furiosus (a super-hyperthermophile that the authors call “a prototypical microbe,” an interesting point of view that we salute). They found several hundred such proteins containing an unexpected assortment of metals. ... Read more »
Cvetkovic A, Menon AL, Thorgersen MP, Scott JW, Poole FL 2nd, Jenney FE Jr, Lancaster WA, Praissman JL, Shanmukh S, Vaccaro BJ.... (2010) Microbial metalloproteomes are largely uncharacterized. Nature, 466(7307), 779-82. PMID: 20639861
by Moselio Schaechter in Small Things Considered
Who hasn’t walked along a previously flooded area and seen flakes of dried mud cakes magically curled up in geometrical shapes? At times, the curls are so pronounced that they make complete scrolls. The area looks like a field of shards. No big deal, just dried mud you might say (as you reach down, tempted to pick up some pieces to play with). Au contraire, such curlicue structures, known as roll-ups, are of considerable interest to geologists. Roll-ups are sedimentary structures capped with a surface layer of clay and organic material that form when the surface dries out. Once formed, they are quite resistant to wetting and weathering, the open curls much less so.
To explain why we're playing with mud cakes on this blog, it turns out that the roll-ups are largely biogenic... ... Read more »
Beraldi-Campesi H, & Garcia-Pichel F. (2010) The biogenicity of modern terrestrial roll-up structures and its significance for ancient life on land. Geobiology. PMID: 21040397
by S. Marvin Friedman in Small Things Considered
Three-dimensional configuration of a prion protein. Left = normal folding. Right = protein with the disease-associated amyloid folding. Source. What if there were a connection between the diseases caused by prions and Alzheimer’s? If that were the case, we'd expect a substantial increase in our understanding of both. Indeed, as we will see below, there is...... Read more »
Meyer-Luehmann M, Coomaraswamy J, Bolmont T, Kaeser S, Schaefer C, Kilger E, Neuenschwander A, Abramowski D, Frey P, Jaton AL.... (2006) Exogenous induction of cerebral beta-amyloidogenesis is governed by agent and host. Science (New York, N.Y.), 313(5794), 1781-4. PMID: 16990547
by Merry Youle in Small Things Considered
Like it or not, we can't shop around for a genetic code, nor do we have a choice of brand or model. We're pretty much stuck with the one we have at this point (although some researchers are modifying the code to synthesize proteins containing "designer amino acids"). The universal genetic code is just that, virtually universal. Oh, there are about 20 other "genetic codes" known but almost all of them are used only by mitochondria or else the differences are limited to start and stop codons. So how good is the one we have?... Read more »
Freeland, S., & Hurst, L. (1998) The Genetic Code Is One in a Million. Journal of Molecular Evolution, 47(3), 238-248. DOI: 10.1007/PL00006381
by Merry Youle in Small Things Considered
Back in 1983, researchers at Yale borrowed a microbiological tactic to study evolution at a "single gene locus" in a multicellular animal—the use of altered growth media to select for nutritional mutants. They confronted populations of Drosophila pseudoobscura with a growth medium containing either maltose or starch as the sole carbohydrate source and observed inherited changes to the α-amylase allozyme frequencies and the enzyme's location within the gut in the "starch flies." Interesting, useful, but not revolutionary.
A few years later a Yale Ph.D. student working with the same flies reported something unexpected. Looking at populations that had been reared on the maltose or starch medium for a year, she found that starch flies preferred to mate with starch flies rather than maltose flies, and likewise the maltose flies preferred maltose mates. In her paper she concluded that the new behavior was a pleiotropic by-product of the adaption to the different media.
And so the matter rested for about two decades until revisited by a group of five researchers from Israel and one from Maine, with some most intriguing—and microbial—insights. ... Read more »
Sharon G, Segal D, Ringo JM, Hefetz A, Zilber-Rosenberg I, & Rosenberg E. (2010) Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. PMID: 21041648
by Manuel Sánchez in Small Things Considered
Physical Virology. Such is the title of the article that appeared in Nature Physics. This is the name for a new discipline that is under development. Its focus is the study of viruses from a physical perspective. Seen this way, viruses are natural nanoparticles with distinct mechanical and thermodynamic properties
Professors W. Ross and G.J.L Wuite of the Foundation For Fundamental Research On Matter of the University of Amsterdam and R. Bruinsma of the Physics Department at UCLA summarize in that article the possible implications of this new discipline, especially for medicine.... Read more »
Roos, W., Bruinsma, R., & Wuite, G. (2010) Physical virology. Nature Physics, 6(10), 733-743. DOI: 10.1038/nphys1797
by S. Marvin Friedman in Small Things Considered
Bacteria capable of sporulation go out of their way to grow rather than sporulate. They will therefore try to obtain needed nutrients, even at the cost of killing their neighbors. When starved for nutrients, cells of Bacillus subtilis engage in cannibalism, that is they lyse their siblings and use the nutrients thus obtained to postpone their own sporulation. A similar phenomenon, termed fratricide, has been reported in Streptococcus pneumoniae where the killing of siblings is linked to the induction of competence and the release of DNA from lysed cells. The antimicrobial agents secreted within the same colony by either cannibalism or fratricide belong to the family of bacteriocins. Be’er and his colleagues now report a third unique situation where bacterial stress leads to sibling death.... Read more »
Be'er A, Ariel G, Kalisman O, Helman Y, Sirota-Madi A, Zhang HP, Florin EL, Payne SM, Ben-Jacob E, & Swinney HL. (2010) Lethal protein produced in response to competition between sibling bacterial colonies. Proceedings of the National Academy of Sciences of the United States of America, 107(14), 6258-63. PMID: 20308591
by Paula Welander in Small Things Considered
by Paula Welander
First Evolved! Last Extinct! This prokaryotic pride motto was coined by my undergraduate advisor (and good friend) Prof. Mark Martin. As a microbiologist, I love this motto for many reasons, but especially because it alludes to one of the underlying principles of my current research. Microbes were indeed the first to evolve and the metabolic inventions of ancient microbes greatly influenced the ancient Earth’s environment and the evolution of life. The interaction between the Earth and microbes has been recorded in sedimentary rocks that are billions of years old.
Accessing this microbial record continues to be one of the challenges of geomicrobiology. One powerful strategy for understanding the microbial signatures in the rock record is the use of “molecular fossils” or biomarkers, organic compounds that are produced by select groups of microorganisms and, amazingly, are preserved in both modern and ancient sediments. Geochemists are able to extract these molecules from very old rocks and, based on their distribution in modern organisms, link specific groups of bacteria to ancient environments.... Read more »
Welander PV, Coleman ML, Sessions AL, Summons RE, & Newman DK. (2010) Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes. Proceedings of the National Academy of Sciences of the United States of America, 107(19), 8537-42. PMID: 20421508
by Moselio Schaechter in Small Things Considered
by Elio
Now here’s a question you’ve been asking all along about the interaction between the leaf cutting (Attine) ants, the fungi they cultivate, and the bacteria that make antifungals against unwanted fungal species. Have these bacteria evolved along with the ants to protect their gardens from unwanted "weeds," or do the ants pick up such bacteria from their environment? New data suggest both things happen.
To remind you, leaf-cutting ants practice fungiculture, and have been doing this for about 50 million years. The bits of leaves and flowers that they bring to the nest get chewed up, fertilized, placed in suitable “gardens” within the nest, and seeded with fungal material from previous gardens. Obviously, fungal gardens can be overrun by unwanted species, with disastrous results for the colony. To keep this from happening, the ants depend on selective antifungals made by actinomycetes. We have visited this topic in the past (click here and here).... Read more »
Barke J, Seipke RF, Grüschow S, Heavens D, Drou N, Bibb MJ, Goss RJ, Yu DW, & Hutchings MI. (2010) A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus. BMC biology, 109. PMID: 20796277
Poulsen M, & Currie CR. (2010) Symbiont interactions in a tripartite mutualism: exploring the presence and impact of antagonism between two fungus-growing ant mutualists. PloS one, 5(1). PMID: 20090958
by Merry Youle in Small Things Considered
by Merry
Bacteriophages are expert killers, having been delivering death to bacteria for several billion years. We are not the first organisms to recognize their skill. Bacteria themselves have borrowed the tail of a phage and fashioned from it a targeted bacterial killer for their own use.
We first became aware of this in 1925 when André Gratia observed that E. coli produced a proteinaceous agent that efficiently killed other E. coli, but not unrelated bacteria. Being proteinaceous and selective is what distinguishes these agents, the bacteriocins, from other antibiotics. Many are now known, made by both Gram-negatives and Gram-positives. Initially they were classified and named for who produced them. Thus colicin for that first one, monocin made by Gram-positive Listeria monocytogenes and pyocin for those made by Pseudomonas aeruginosa (formerly pyocynia).
As the list grew, it became evident that the bacteriocins are a heterogeneous bunch. Some of them, including colicin, are trypsin-sensitive proteins, typically encoded on plasmids. (For more information about this group, click here.) Others are trypsin-resistant particles that can be purified by the same techniques that are used to purify viruses. Under the electron microscope, they look exactly like phage tails. Some resemble the contractile tails of the Myoviridae complete with sheath, core, base plate, and tail fibers, others the flexible but non-contractile tails of the Siphoviridae. These headless phage particles contain no DNA. ... Read more »
Nakayama, K., Takashima, K., Ishihara, H., Shinomiya, T., Kageyama, M., Kanaya, S., Ohnishi, M., Murata, T., Mori, H., & Hayashi, T. (2000) The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Molecular Microbiology, 38(2), 213-231. DOI: 10.1046/j.1365-2958.2000.02135.x
by Kevin D. Young in Small Things Considered
by Kevin D. Young
My grandmother took a lot of pills. Each week she arranged them in little piles that she dropped into the compartments of a multi-well device, a way to be sure she took each group on the right day and at the right time. The neat thing (to a kid) was their range of colors and shapes–round ones, ovals, squares, triangles and even hot dog shapes, of every primary color and several pastels. Simply magical. But, of course, appearances were irrelevant. Pill size, shape, and color were dictated by medical tradition and marketing; none of these overt characteristics had any impact on their medicinal value. Efficacy was dictated solely by the nature of the compounds embedded in each lozenge.
A similar situation exists for bacteria. They, too, come in a range of sizes and shapes (though not colors, more’s the pity), and for decades these overt characteristics have been used to differentiate these organisms. However, with only slight hints to the contrary, morphology has not been thought to be medically important. Instead, as with my grandmother’s pills, a bacterium’s pathogenicity has been attributed solely to specific virulence factors embedded in these odd packages. This view is beginning to change.... Read more »
Sycuro LK, Pincus Z, Gutierrez KD, Biboy J, Stern CA, Vollmer W, & Salama NR. (2010) Peptidoglycan crosslinking relaxation promotes Helicobacter pylori's helical shape and stomach colonization. Cell, 141(5), 822-33. PMID: 20510929
by Moselio Schaechter in Small Things Considered
Is it OK with you if on Fungus Week we post an item that deals with fungal genes instead of whole fungi? We want to do this because of a startling finding, that some aphids are colored because they possess fungus-derived genes for making carotenoids. This is news because until now it was thought that animals cannot synthesize such pigments—only prokaryotes, fungi and plants can (which is why vitamin A—a carotenoid—is a vitamin). But there you have it, some aphids are green and others are reddish depending on which carotenoids they make. It had been thought that these animals get their carotenoids either from their diet or from bacterial endosymbionts. However the sap they live on has no such things, and their symbionts lack the genes for carotenoid biosynthesis. In addition, curing the insects of the symbionts does not affect the color. Lastly, the symbionts are inherited maternally, whereas color follows Mendelian inheritance.... Read more »
Moran NA, & Jarvik T. (2010) Lateral transfer of genes from fungi underlies carotenoid production in aphids. Science (New York, N.Y.), 328(5978), 624-7. PMID: 20431015
by Moselio Schaechter in Small Things Considered
Sooner or later, but usually sooner, anyone dealing with fungi will have to deal with the issue of spore dispersal. Many fungi, mushrooms included, are a spore’s way of spreading spores through the environment. They do this in varied and universally ingenious ways. Spores, like mammalian sperm, are made in excess, which enhances the chances of some “making it.” Anybody who has made the spore print from a mushroom can attest to the large number of spores produced. This is true not only for the Basidiomycetes, to which most mushrooms belong, but also for the larger Ascomycetes, (the group that includes not only yeast but also most molds, as well as larger organisms such as the cup fungi).
For dispersal to be efficient, the spores must travel a certain distance from their place of origin. They are ejected with great force, sometimes challenging our belief.... Read more »
Roper M, Seminara A, Bandi MM, Cobb A, Dillard HR, & Pringle A. (2010) Dispersal of fungal spores on a cooperatively generated wind. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20880834
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