130 posts · 117,000 views
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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- October 11, 2010
- 01:00 PM
- 995 views
Cheap Exports
by Daniel Smith in Small Things Considered
by Daniel Smith
Evolution is often thought of in functional terms. Mutations that improve or diversify a protein’s function are selected for, whereas disruptive mutations are selected against. However, economy can also play a role in protein evolution.
Amino acids used in proteins vary in size, complexity and chemical characteristics, which makes some cheaper to synthesize than others. Consequently, some proteins are more economical to produce than others. by Daniel Smith
Evolution is often thought of in functional terms. Mutations that improve or diversify a protein’s function are selected for, whereas disruptive mutations are selected against. However, economy can also play a role in protein evolution.
Amino acids used in proteins vary in size, complexity and chemical characteristics, which makes some cheaper to synthesize than others. Consequently, some proteins are more economical to produce than others. Previous studies have shown that abundant proteins are often less expensive to make, thus reducing their cellular cost. However, the connection between a protein's location and its expense has not been appreciated. ... Read more »
Smith DR, & Chapman MR. (2010) Economical evolution: microbes reduce the synthetic cost of extracellular proteins. mBio, 1(3). PMID: 20824102
- October 4, 2010
- 01:00 PM
- 392 views
The Ins & Outs of Those Mysterious Microcompartments
by Alan Derman in Small Things Considered
by Alan Derman
The planet's most abundant enzyme is also one of its lousiest. It's RuBisCO, the photosynthetic enzyme that mediates the fixation of CO2 by catalyzing its incorporation into the five carbon ribulose-1,5-bisphosphate (RuBP). Routinely it goofs and incorporates O2 instead, producing the useless and potentially harmful phosphoglycolate, which cells must then expend energy to dispose of. And even if O2 is not around to confuse the enzyme, the Km of cyanobacterial RuBisCO for CO2 is still greater than 150 μM. The CO2 concentration in the aquatic environments where cyanobacteria live is typically less than 15 μM. Cyanobacteria and other RuBisCO-containing bacteria deal with ill-behaved RuBisCO by confining it in microcompartments called carboxysomes. Confinement of RuBisCO turns out to be for its own good, and for the good of the cell as well.
The carboxysome is not your typical membrane-bound organelle.... Read more »
Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS, Jefferson RE, Yeates TO, & Bobik TA. (2010) Short N-terminal sequences package proteins into bacterial microcompartments. Proceedings of the National Academy of Sciences of the United States of America, 107(16), 7509-14. PMID: 20308536
- September 27, 2010
- 01:00 PM
- 440 views
Commuting to Work
by Moselio Schaechter in Small Things Considered
by Elio
An underwater microbial mat has been found in fairly shallow waters off the coast of Chile and, according to headlines (click here and here), it’s the size of Greece, or about 132,000 km2 (or for us norte-americanos, about the size of Alabama). These communities of sulfide-oxidizing bacteria have been known for some time, but their attention has been highlighted by the recent version of the Census of Marine Life. In fact, they were discovered in 1963 by the oceanographer and microbiologist Victor Gallardo of Chile’s University of Concepción. Scientists may not have known much about these huge mats much earlier on, but the local fishermen sure did and called them estopa, Spanish for burlap or unwashed wool or flax.
Aficionados of the giant sulfur-oxidizing bacterium Thiomargarita namibiensis and other bacterial gargantuas likely include Thioploca, the occupants of these mats, in their catalog of microbial marvels. This is a genus of gliding, filamentous bacteria that live in aquatic sediments where they face the same problem as Thiomargarita, namely how to hook up their fuel (sulfides) with their final electron acceptors (nitrates). (For details of their metabolism, see a recent paper.)... Read more »
Teske A, Jørgensen BB, & Gallardo VA. (2009) Filamentous bacteria inhabiting the sheaths of marine Thioploca spp. on the Chilean continental shelf. FEMS microbiology ecology, 68(2), 164-72. PMID: 19573198
Høgslund S, Revsbech NP, Kuenen JG, Jørgensen BB, Gallardo VA, van de Vossenberg J, Nielsen JL, Holmkvist L, Arning ET, & Nielsen LP. (2009) Physiology and behaviour of marine Thioploca. The ISME journal, 3(6), 647-57. PMID: 19262616
- September 13, 2010
- 01:00 PM
- 1,328 views
Bacterial Physiology and Virulence: The Cultures Converge
by Fred Neidhardt in Small Things Considered
by Fred Neidhardt
Growth dominates the attention of many bacteriologists. It has done so for over a century, inspiring explorations into the complex biochemistry and physiology that produce new cells able to grow, survive harsh environments, and live to grow another day.
Likewise, since the earliest days of microbiology, virulence has been a central focus. In fact, studies of how bacteria cause disease have in sheer number dominated the field for the simple reason that more than intellectual curiosity has been involved: human health has demanded that one learn to cure infectious diseases and protect against them.
Until recently, researchers in these two arenas of microbial exploration shared precious little beyond basic technology and a knowledge of bacterial cell structure and function. ... Read more »
Dalebroux ZD, Svensson SL, Gaynor EC, & Swanson MS. (2010) ppGpp conjures bacterial virulence. Microbiology and molecular biology reviews : MMBR, 74(2), 171-99. PMID: 20508246
- September 6, 2010
- 01:00 PM
- 680 views
Listeria's Visiting Card
by Moselio Schaechter in Small Things Considered
by Elio
During infection, host and parasite carry out repeated and intense conversations that often rise to the level of shouting matches. The language they use is chemical, the words and sentences eloquent and forceful. Eavesdropping on the conversation between Listeria monocytogenes LINK 5 and immune cells of its host, Portnoy and colleagues LINK 1 discovered an intriguing linguistic use for a novel “second messenger,” cyclic-di-AMP (c-di-AMP).
It has been known that Listeria, like many intracellular pathogens, promotes the making of an interferon (IFN-), LINK 2 which in turn signals cells of the immune system, thus activates them. But what sets this in motion? What are the signals emitted by Listeria and how are they “heard” by the host cells? The answer is that the bacteria excrete c-di-AMP, which activates the so-called cytosolic surveillance pathway. ... Read more »
Woodward JJ, Iavarone AT, & Portnoy DA. (2010) c-di-AMP secreted by intracellular Listeria monocytogenes activates a host type I interferon response. Science (New York, N.Y.), 328(5986), 1703-5. PMID: 20508090
- August 30, 2010
- 01:00 PM
- 1,649 views
Plasmalogens Have Evolved Twice
by Moselio Schaechter in Small Things Considered
by Howard Goldfine.
Some biologists go blissfully through life without paying much attention to lipids. They do this at their own risk, because there are innumerable things to be learned from their study, including, as we will see here, many relevant to the understanding of evolution. Lipids come in unexpected and exciting varieties, a point that has been acknowledged in this blog (for examples, see here and here)
The lipids that make up the membranes of prokaryotes are polar, that is, they have a moiety such as phosphate, linked to one of the carbons of their glycerol backbone (non-polar triglycerides are generally not known to be made by prokaryotes). The lipids of aerobic and facultative bacteria are mainly of the phospholipid or glycolipid type, in which the first two carbons of the glycerol backbone are linked to long-chain fatty acid esters (Figure). The situation, however, is different in many anaerobes, including both Gram-positive and Gram-negative species, in which the membranes contain both diacyl lipids and compounds known as plasmalogens, in which the chain linked to the first carbon of the glycerol is attached through an O-alk-1’-enyl ether bond (Figure) rather than an ester bond.... Read more »
Goldfine, H. (2010) The appearance, disappearance and reappearance of plasmalogens in evolution. Progress in Lipid Research. DOI: 10.1016/j.plipres.2010.07.003
- August 12, 2010
- 01:00 PM
- 618 views
Biofilms Over Troubled Waters
by Moselio Schaechter in Small Things Considered
by Mark O. Martin
The old saying “pouring oil on troubled waters” is a metaphor for bringing peace to a turbulent situation. Recent events in the Gulf of Mexico have proved the contrary, that oil poured (or spilled) upon seawater can produce the very antithesis of calm. After many weeks of concern, and with the long term threat of possible subsurface oil still strong, recent reports note that the oil slicks at the surface have become more difficult to find. What is happening? To be sure, dispersal over time is inevitable, but there may be more to the “vanishing” oil slicks.... Read more »
Cunliffe M, & Murrell JC. (2009) The sea-surface microlayer is a gelatinous biofilm. The ISME journal, 3(9), 1001-3. PMID: 19554040
- August 9, 2010
- 01:00 PM
- 707 views
When the End Is the Story
by Welkin Johnson in Small Things Considered
by Welkin Johnson It looks like a herpesvirus, but does it replicate like one? Electronmicrographs showing mature HHV-6 particles emerging from an infected cell. Source. Sometimes, discovery in biology is about discerning rules and sometimes it is about pursuing exceptions. In this spirit, Human Herpesvirus six (HHV-6), the etiologic agent of the common childhood illness roseola infantum, is shaping up...... Read more »
Arbuckle JH, Medveczky MM, Luka J, Hadley SH, Luegmayr A, Ablashi D, Lund TC, Tolar J, De Meirleir K, Montoya JG.... (2010) The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro. Proceedings of the National Academy of Sciences of the United States of America, 107(12), 5563-8. PMID: 20212114
- August 5, 2010
- 01:00 PM
- 1,155 views
Fine Reading: The Sex Habits of Fungi
by Moselio Schaechter in Small Things Considered
by Elio
As luck would have it, two pieces of writing on the sex habits of fungi appeared within days of each other. One is light reading, a post in the admirable Cornell Mushroom Blog entitled A Fungus Walks Into a Singles Bar. This is a précis into the complex story of fungal sexuality. It takes you...... Read more »
Raudaskoski, M., & Kothe, E. (2010) Basidiomycete Mating Type Genes and Pheromone Signaling. Eukaryotic Cell, 9(6), 847-859. DOI: 10.1128/EC.00319-09
- August 2, 2010
- 01:00 PM
- 692 views
An Inactive Mine Provides Active Opportunities
by Moselio Schaechter in Small Things Considered
by Elio
Metagenomics is a fine tool indeed for surveying a microbial community in concert, treating both the cultured and uncultured equally. When the sample studied is rich in microbial variety, as often is the case, the pieces of genomes can be reluctant to reveal the genetic heritage of whole microbes. But there are a few particular environments that are dominated by a handful of species at most, and here this approach allows the reconstruction of complete genomes. That is the case with the acid mine drainage from mineral or coal mines. When mining ceases, all hell can break loose (anthropocentrically speaking). Microbes oxidize sulfides such as pyrite (iron sulfide) into sulfuric acid, which in turn solubilizes iron, copper, arsenic, silver, gold, and other heavy metals. Water no longer being pumped from the mine, this gemish of minerals emerges from seeps and other openings to become a highly toxic, low pH stream that eventually pollutes larger bodies of water. But for some bacteria and archaea, this is a juicy place to live and thrive. ... Read more »
Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, & Banfield JF. (2010) Enigmatic, ultrasmall, uncultivated Archaea. Proceedings of the National Academy of Sciences of the United States of America, 107(19), 8806-11. PMID: 20421484
- July 26, 2010
- 01:00 PM
- 1,051 views
A Giant Among Giants
by Merry Youle in Small Things Considered
Without a doubt, Mimivirus is remarkable. For a virus, it is extraordinarily large and complex. But it is hardly one of a kind. The more that researchers look for large viruses, the more they find.
Although phages generally tend to have small genomes, some managing with but a handful of genes, a glance at the current NCBI list reveals that there are now eight with sequenced genomes that amount to more than 200 kb. A Pseudomonas phage tops the list with 317 kb, but the not-yet-sequenced genome of Bacteriophage G of Bacillus megaterium is reported to be ~670 kb.... Read more »
Van Etten JL. (2003) Unusual life style of giant chlorella viruses. Annual review of genetics, 153-95. PMID: 14616059
Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, & Fournier PE. (2006) Mimivirus and the emerging concept of "giant" virus. Virus research, 117(1), 133-44. PMID: 16469402
- July 12, 2010
- 01:00 PM
- 935 views
The Uncultured Bacteria
by Kim Lewis in Small Things Considered
The majority of bacteria will not grow on nutrient medium in the lab. The basic experiment is simple: take a sample from the environment, such as marine sediment or soil, mix with water, vortex, allow it to settle, dilute supernatant and take two droplets. Plate one on a Petri dish...... Read more »
D'Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, Epstein S, Clardy J, & Lewis K. (2010) Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chemistry , 17(3), 254-64. PMID: 20338517
- July 5, 2010
- 01:00 PM
- 799 views
The Sea Slug's Guide to Plastid Adoption
by Merry Youle in Small Things Considered
Having an intimate relationship with photosynthetic microbes is a widespread strategy adopted by numerous unicellular and multicellular organisms. Some eschew a committed relationship, and simply nab the plastids, sequestering them...... Read more »
Pierce, S., Curtis, N., & Schwartz, J. (2010) Chlorophyll a synthesis by an animal using transferred algal nuclear genes. Symbiosis, 49(3), 121-131. DOI: 10.1007/s13199-009-0044-8
Rumpho ME, Worful JM, Lee J, Kannan K, Tyler MS, Bhattacharya D, Moustafa A, & Manhart JR. (2008) Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proceedings of the National Academy of Sciences of the United States of America, 105(46), 17867-71. PMID: 19004808
- July 5, 2010
- 01:00 PM
- 461 views
The Sea Slug's Guide to Plastid Adoption
by Moselio Schaechter in Small Things Considered
by Merry A handsome E. chlorotica. Its rich green pigmentation is courtesy of plastids captured from its food source, the siphonaceous marine alga Vaucheria litorea (seen in the background). Source. Having an intimate relationship with photosynthetic microbes is a widespread strategy adopted by numerous unicellular and multicellular organisms. Some eschew a committed relationship, and simply nab the plastids, sequestering them...... Read more »
Pierce, S., Curtis, N., & Schwartz, J. (2010) Chlorophyll a synthesis by an animal using transferred algal nuclear genes. Symbiosis, 49(3), 121-131. DOI: 10.1007/s13199-009-0044-8
Rumpho ME, Worful JM, Lee J, Kannan K, Tyler MS, Bhattacharya D, Moustafa A, & Manhart JR. (2008) Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proceedings of the National Academy of Sciences of the United States of America, 105(46), 17867-71. PMID: 19004808
- June 28, 2010
- 01:00 PM
- 922 views
A Fastidious Bacteriophage
by Michael Yarmolinsky in Small Things Considered
by Michael Yarmolinsky
Patrons of upscale seafood restaurants are given the opportunity to see that the unfortunate creatures destined for the lobster pot are waving their antennae about. Savvy customers at downscale seafood markets evaluate questionable claims of freshness by smell. A fastidious bacteriophage would welcome the opportunity to gauge the quality of a potential meal, if only it could make that assessment. I was recently reminded, in the course of disposing of old reprints, that a bacteriophage named Chi can do so. It attacks only motile strains of bacteria, and then only if the flagella are active. How is this circumspect appraisal accomplished? ... Read more »
Samuel AD, Pitta TP, Ryu WS, Danese PN, Leung EC, & Berg HC. (1999) Flagellar determinants of bacterial sensitivity to chi-phage. Proceedings of the National Academy of Sciences of the United States of America, 96(17), 9863-6. PMID: 10449785
- June 21, 2010
- 01:00 PM
- 1,550 views
Our Counterintelligence Staph
by Moselio Schaechter in Small Things Considered
by Karen Schwarzberg, Mike Gurney, and Nikos Gurfield S. aureus biofilm formed overnight on silicon elastomer, a material used in catheters. Bar = 10 µm. Source. Typically, when one thinks about the commensal bacteria living with us, what comes to mind are the benefits they provide by aiding in food metabolism, producing vitamins, and preventing colonization by invading pathogenic bacteria....... Read more »
Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, Agata T, & Mizunoe Y. (2010) Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature, 465(7296), 346-9. PMID: 20485435
- June 14, 2010
- 01:00 PM
- 1,026 views
Uncovering Beauty in Proteins to Fight the Pneumococcal Fratricides
by César Sánchez in Small Things Considered
by César Sánchez From time to time, we dip into the microbiology blog by César Sánchez, Twisted Bacteria, and, with his permission, "borrow" a post such as this one. Streptococcus pneumoniae in spinal fluid. Source. This post is about pneumonia and pneumococci, fratricide at the cellular level, and a pretty protein. And there's a video too! First things first. Pneumonia...... Read more »
Pérez-Dorado I, González A, Morales M, Sanles R, Striker W, Vollmer W, Mobashery S, García JL, Martínez-Ripoll M, García P.... (2010) Insights into pneumococcal fratricide from the crystal structures of the modular killing factor LytC. Nature structural , 17(5), 576-81. PMID: 20400948
- May 31, 2010
- 01:00 PM
- 710 views
Promiscuous Bacteria and Viral Playboys
by Merry Youle in Small Things Considered
Bacteria have been sexually promiscuous, swapping genes with gusto, for a very long time. More than 15% of E. coli's genome has arrived via horizontal gene transfer (HGT), with some 200 installments having turned up since it diverged from Salmonella 100 million years ago. And, as you are probably thinking, those 200 are...... Read more »
Kenzaka T, Tani K, & Nasu M. (2010) High-frequency phage-mediated gene transfer in freshwater environments determined at single-cell level. The ISME journal, 4(5), 648-59. PMID: 20090786
- May 20, 2010
- 01:00 PM
- 831 views
Everyone Rowing in the Same Direction
by Merry Youle in Small Things Considered
Is there such a thing as an obligatorily multicellular prokaryote? We presented a case for their existence before, one that fueled our evolutionary imaginations. Unlike the myxobacteria, for example, which have both unicellular and multicellular stages, some magnetotactic bacteria appeared to be multicellular throughout their lives. Their multicellular coordination is apparent from their complex swimming behavior, their...... Read more »
Lefevre, C., Abreu, F., Lins, U., & Bazylinski, D. (2010) Nonmagnetotactic Multicellular Prokaryotes from Low-Saline, Nonmarine Aquatic Environments and Their Unusual Negative Phototactic Behavior. Applied and Environmental Microbiology, 76(10), 3220-3227. DOI: 10.1128/AEM.00408-10
- May 17, 2010
- 01:00 PM
- 531 views
You Are What You Eat
by Moselio Schaechter in Small Things Considered
by Karen Schwarzberg and Mike Gurney
Despite the rise of a global culture, deliciously distinct differences in diet still persist among various nationalities. Makes one wonder if, along with each cuisine, comes a distinctive microbiome. We now have the research tools needed to begin to explore such possibilities. A paper recently published in Nature by Hehemann et al. reports that, in at least one particular instance, we do harbor bacteria adapted to the traditional diet of our culture...... Read more »
Hehemann, J., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010) Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature, 464(7290), 908-912. DOI: 10.1038/nature08937
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