12 posts · 8,666 views
I am an actively retired microbiologist, currently living in San Diego, California. I spent most of my research career working on growth physiology and bacterial cell organization. In 1985-86, I served as president of the ASM. I have a deep love of teaching, and have been told that my natural habitat is the other side of the lectern. I have authored several textbooks and co-edited treatises. I continue to write. After retirement, I have tried to satisfy my curiosity in broader microbiological phenomena, especially those related to ecology and symbiotic relationships. My hobby is wild mushrooms. For a short account of my activities, visit my home page. http://www.bio.sdsu.edu/faculty/schaechter.htm I can be reached at mschaech at sunstroke dot sdsu dot edu.
Small Things Considered
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- November 30, 2009
- 08:30 AM
- 653 views
A Condominium Plant
by Merry Youle in Small Things Considered
Early in childhood, we learned that the plants and animals around us are discrete entities with definite boundaries. A dog might have fleas, but fleas and dogs are separate and distinct individuals. With our increased familiarity with symbioses—especially those of the obligate sort—have come many instances where "separate" individuals can seemingly survive only as part of a functioning association. Here is yet another example.
For more than twenty-five years, Doyle Mckey, now a professor in ecology, University of Montpellier II, France, has been studying one species of tree, Leonardoxa africana africana (Fabaceae or Leguminosae)—known locally as the bush-boer bean. Likely you've never seen one of them as they are found only in a narrow strip of humid coastal rain forest in southern Cameroon. This particular tree is a myrmecophyte, i.e., an ant-plant. ... Read more »
Defossez, E., Selosse, M., Dubois, M., Mondolot, L., Faccio, A., Djieto-Lordon, C., McKey, D., & Blatrix, R. (2009) Ant-plants and fungi: a new threeway symbiosis. New Phytologist, 182(4), 942-949. DOI: 10.1111/j.1469-8137.2009.02793.x
- November 20, 2009
- 09:54 AM
- 1,184 views
Genomic Secrets of P. infestans, the Master of Potato Blight
by Merry Youle in Small Things Considered
No fungicide has ever been found to which P. infestans could not ultimately adjust…Indeed, no potato has ever been developed with defenses that Phytophthora could not ultimately breach.
More than 150 years after the historic Irish potato famine LINK 2, the deadly pathogen responsible for potato blight, Phytophthora infestans, is now destroying more than $3 billion worth of potatoes each year. What is the secret of it's pathogenic success? Hoping to find some answers in its genome, a team of 96 researchers have sequenced LINK 3 virtually its entire 240 Mb genome. This is by far the largest and most complex genome sequenced among the chromalveolates, LINK 4 a diverse eukaryote supergroup that includes not only the stramenopiles (the oomycetes, diatoms, and some algae) but also the dinoflagellates and the apicomplexans.
Why so much DNA? That's more than double that of Caenorhabditis elegans. Tellingly, though, the number of genes in this oomycete is not twice as large. ... Read more »
Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T.... (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461(7262), 393-8. PMID: 19741609
- November 5, 2009
- 09:02 AM
- 493 views
It Was The Worst of Times, It Was the Best of Times
by Moselio Schaechter in Small Things Considered
by Elio
At the end of the Permian period, about 250 million years ago and not long before the dinosaurs appeared, life on Earth experienced its greatest catastrophe: a mass extinction that did away with the vast majority of life forms on land and sea. The question arises, who ate the carcasses of the deceased? Surely bacteria and protozoa digested the animal corpses, most likely reaching unusually high population sizes as the result. But who took care of the masses of dead plant material? Fungi are quite good at digesting plants, especially woody plants. So, did the fungi also become prevalent after the catastrophe?
There is evidence for this belief. ... Read more »
Sephton, M., Visscher, H., Looy, C., Verchovsky, A., & Watson, J. (2009) Chemical constitution of a Permian-Triassic disaster species. Geology, 37(10), 875-878. DOI: 10.1130/G30096A.1
- October 5, 2009
- 10:38 AM
- 555 views
All for One, and One for All!
by Moselio Schaechter in Small Things Considered
By Mark Martin
When I recently attended the Sixth International Symbiosis Society Congress in Madison, Wisconsin, I was awed by the fascinating forms that symbiotic relationships take among diverse organisms. One talk that particularly intrigued me was from the laboratory of Marilyn Roossinck LINK 1 of the Samuel Roberts Nobel Foundation in Oklahoma, which described the mutualistic relationship between a virus, an endophytic fungus, a monocot, and elevated temperatures in geothermal soils. It also made me consider how readily we seem to associate the word "virus" with pathogenic associations, when nature is often far more subtle when it comes to mutualistic partnerships.
The story began in 2002 when it was found that a type of grass growing in the geothermal zones of Yellowstone National Park—panic grass, Dichanthelium lanuginosum LINK 2—was able to survive intermittent high temperatures in geothermal soils (up to 65 °C.) due to its association with an endophytic fungus, Curvularia protuberata LINK 3. The fungus is essential to the plant's ability to tolerate temperatures that are lethal to the non-colonized plant. Panic grass, incidentally, has nothing to do with botanical phobias; instead, the name LINK 13 derives from the Latin panicum, referring to foxtail millet.
... Read more »
Marquez, L., Redman, R., Rodriguez, R., & Roossinck, M. (2007) A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance. Science, 315(5811), 513-515. DOI: 10.1126/science.1136237
- September 21, 2009
- 09:57 AM
- 747 views
Good Guys, Bad Guys
by Merry Youle in Small Things Considered
Because it prefers to dine on some of our valued crop plants, the pea aphid (Acyrthosiphon pisum) LINK 1 is considered a major pest—thus a Bad Guy from our perspective. Pea aphids are not without their enemies. Enemy number one is a parasitoid wasp LINK 2, Aphidius ervi. As parasitoid wasps are wont to do, females provide for their offspring by depositing their eggs in the haemocoel of another insect, in this case a pea aphid. The wasp larva feeds and develops there for about a week, eventually killing the host. When the host viscera have been consumed, the larva causes the aphid’s cuticle to harden and dry. Soon, an adult A. ervi emerges from the aphid "mummy." Agriculturally speaking, parasitoid wasps are Good Guys, important partners in our integrated pest management LINK 3 strategies. You can buy wasp eggs for your fields by the hundreds or thousands online.
Early on it was noticed that aphid (A. pisum) clones vary greatly in their resistance to the wasps. In some, the development of the wasp larva is arrested and the host survives. Because the pea aphid was known to harbor Buchnera aphidicola LINK 4 as a primary endosymbiont and also as many as five other bacteria as secondary endosymbionts, it was suspected that this variation in resistance might be due to which endosymbionts are on board. ... Read more »
Oliver KM, Degnan PH, Hunter MS, & Moran NA. (2009) Bacteriophages encode factors required for protection in a symbiotic mutualism. Science (New York, N.Y.), 325(5943), 992-4. PMID: 19696350
Moran NA, Degnan PH, Santos SR, Dunbar HE, & Ochman H. (2005) The players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes. Proceedings of the National Academy of Sciences of the United States of America, 102(47), 16919-26. PMID: 16195380
- September 17, 2009
- 09:56 AM
- 940 views
Fine Reading: The Good-Enough Clockus of Prochlorococcus
by Moselio Schaechter in Small Things Considered
by Elio
The very first post on this blog (It Don't Mean a Thing If It Ain't Got That Swing) LINK 1 was about the circadian rhythm of cyanobacteria. They turn their photosynthetic apparatus on and off to match the daily course of light and dark. This is a true clock-driven circadian rhythm because it manifests whether or not the light is on or off, thus is not just a response to a stimulus.
What fascinated us then and continues to bedazzle us now is that this rhythm has an understandable biochemical basis. LINK 2 Three "oscillatory" proteins are involved: KaiA, KaiB, and KaiC. Together, they lead to a cycle of phosphorylation and dephosphorylation than not only sets the cellular clock of these organisms, but that can be simulated in vitro with purified proteins! And, to challenge our notion of what enzymes do, these proteins do their enzymatic thing at such a slow pace that the mind boggles! One of them, KaiC, hydrolyzes ATP at the lightning speed of 15 molecules per day! ... Read more »
Axmann, I., Duhring, U., Seeliger, L., Arnold, A., Vanselow, J., Kramer, A., & Wilde, A. (2009) Biochemical Evidence for a Timing Mechanism in Prochlorococcus. Journal of Bacteriology, 191(17), 5342-5347. DOI: 10.1128/JB.00419-09
- August 31, 2009
- 10:39 AM
- 477 views
Smallest Things Considered
by Merry Youle in Small Things Considered
What do stunted coconut palms, misshapen potato tubers, and peach trees with necrotic branches have in common? They are three of the numerous crops stricken with diseases caused by viroids, an astonishing group of minimalist plant pathogens. There isn't much to a viroid, just one single-stranded, circular RNA molecule. The largest viroid genome so far is 399 nucleotides, the smallest a mere 246—about one tenth the size of the smallest viruses (hepadnavirus LINK 2) and one hundredth the size of more typical viruses. Being labeled as "subviral," they are even less likely than the viruses to be granted a place on the tree of life LINK 1. They get by without capsid or membrane shell. They encode no proteins. They don't reverse-transcribe into DNA when they replicate. They never insert into the host genome. Some of them cause disease symptoms, some don't. They simply replicate inside plant cells and then their progeny move on to the next location to repeat the process. Their very existence raises questions, many without answers.
What does a viroid look like? Well, that depends on the viroid. The thirty-plus species known so far fall into two groups. Most belong to the Pospiviroidae (PSTVd), named after the Potato Spindle Tuber ViroiD. Four species, including the Avocado SunBlotch ViroiD, make up their own group, the Avsunviroidae (ASBVd). Although all of them lack protective capsids, they are nevertheless highly structured. Most of their RNA genome base-pairs with complementary sequences in other parts of the same RNA molecule to form sections of double-helix. The PSTVds form rod-shaped structures, the ASBVds have more elaborate forms. (See figure.) For both groups, the bulges and loops are important for survival, replication, and trafficking. ... Read more »
Ding B. (2009) The biology of viroid-host interactions. Annual review of phytopathology, 105-31. PMID: 19400635
- August 10, 2009
- 10:22 AM
- 535 views
The Genes, The Whole Genes, & Nothing But The Genes
by Merry Youle in Small Things Considered
We have come to expect the unexpected of ciliates, and Oxytricha trifallax, with its genomic capers, does not disappoint. Like many of its more famous ciliate relatives (e.g., paramecium, tetrahymena, stentor), Oxytricha is a complex unicellular organism with many specialized cellular structures. Of course, they have the requisite cilia for locomotion, feeding, and sensing their environment. But they also have a "mouth," food vacuoles where digestion takes place, kidney-like contractile vacuoles for osmoregulation, and a pseudo-anus—the cytoproct. Not surprisingly, ciliates tend to be large cells, some measured in millimeters. Combined with a fast rate of growth, this may require more gene transcription than a diploid genome can support. To cope with this demand, ciliates employ a convoluted strategy, one unique so far to this group.... Read more »
Nowacki, M., Vijayan, V., Zhou, Y., Schotanus, K., Doak, T., & Landweber, L. (2007) RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature, 451(7175), 153-158. DOI: 10.1038/nature06452
Nowacki, M., Higgins, B., Maquilan, G., Swart, E., Doak, T., & Landweber, L. (2009) A Functional Role for Transposases in a Large Eukaryotic Genome. Science, 324(5929), 935-938. DOI: 10.1126/science.1170023
- August 3, 2009
- 09:56 AM
- 539 views
Playing the Light Organ Two Ways
by Moselio Schaechter in Small Things Considered
... Read more »
Tong, D., Rozas, N., Oakley, T., Mitchell, J., Colley, N., & McFall-Ngai, M. (2009) From the Cover: Evidence for light perception in a bioluminescent organ. Proceedings of the National Academy of Sciences, 106(24), 9836-9841. DOI: 10.1073/pnas.0904571106
- July 27, 2009
- 10:13 AM
- 546 views
An Iconoclastic Endosymbiont
by Moselio Schaechter in Small Things Considered
... Read more »
McCutcheon JP, McDonald BR, & Moran NA. (2009) Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS genetics, 5(7). PMID: 19609354
- June 4, 2009
- 10:13 AM
- 899 views
A Nuclear Family
by Merry Youle in Small Things Considered
Certain mussels called “bathymodiolins” are part of the spellbinding fauna of the dark world of oceanic hydrothermal vents and cold seeps. Similar to other metazoans in that realm, they rely on chemosynthetic bacteria for their nutrition. These mussels possess symbionts from two clades of γ-proteobacteria: chemoautotrophic sulfur oxidizers that fix CO2 using sulfide or thiosulfate as their energy source, and methane oxidizers that use methane for both carbon and energy. The symbionts are well-housed in specialized cells (bacteriocytes) in the gills of the mussels where the constant flow of water brings the needed substrates to them. A pleasant mutualistic arrangement.
... Read more »
Zielinski, F., Pernthaler, A., Duperron, S., Raggi, L., Giere, O., Borowski, C., & Dubilier, N. (2009) Widespread occurrence of an intranuclear bacterial parasite in vent and seep bathymodiolin mussels. Environmental Microbiology, 11(5), 1150-1167. DOI: 10.1111/j.1462-2920.2008.01847.x
- June 1, 2009
- 10:14 AM
- 1,098 views
Say, Brother, Can You Spare a DNA?
by Merry Youle in Small Things Considered
Mention horizontal gene transfer (HGT) in bacteria, and what comes to mind is the acquisition of new traits and capabilities across large evolutionary distances. Not so for the neisseriae. For them, HGT is a means to swap genes with other members of the species and to maintain the status quo in the face of assault on their genome by host defenses.
Infection by the human pathogen N. gonorrhoeae is met by the rapid recruitment of polymorphonuclear leukocytes (PMNs) to the site. PMNs are professional phagocytes that use a combination of antimicrobial proteins and reactive oxygen species (ROSs) to kill the engulfed invaders. Their ROS attack is effective against the gonococci and quickly kills the majority of them. However, a subpopulation not only survives within the phagosomes, it also replicates. A number of factors enable the gonococci to do this. An important one is having a means to repair the DNA damaged by the ROSs. This is where the HGT comes in.
... Read more »
Davidsen, T. (2004) Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Research, 32(3), 1050-1058. DOI: 10.1093/nar/gkh255
Hamilton, H., Dominguez, N., Schwartz, K., Hackett, K., & Dillard, J. (2005) Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system. Molecular Microbiology, 55(6), 1704-1721. DOI: 10.1111/j.1365-2958.2005.04521.x
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