Microbial pigments: an untapped resource for teachers, artists and researchers

The journal PLoS Biology has launched a new series of articles on education "to present innovative approaches to teaching critical concepts, developments, and methods in biology." The title of the first article in the series is In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond.

From the article:

"Soil bacteria from the Streptomyces genus represent a source of interesting natural products that have been largely overlooked by artists, researchers, and teachers. This article is intended to encourage amateurs and professionals alike to explore this overflowing source of biopigments. Not only does this endeavor have the potential to lead us toward a fertile nexus between art and science, it may also lead to a more sustainable and environmentally friendly way to color the world around us in the future. The relevance of biopigments to many facets of science, technology, and society, makes this material an outstanding tool to engage students of varying academic interests across multiple age groups. Therefore, we encourage teachers of all levels to consider using biopigments as a vehicle to introduce the scientific method to their students. To facilitate the implementation of biopigments into science and art curricula, we have provided a list of useful online resources and information about procuring materials [...] as well as recommend ways to evaluate the effectiveness of the lesson [...]."

Original article (and image source):
Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A (2010) In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8(10): e1000510. doi:10.1371/journal.pbio.1000510
Image: “Elvis Lives!” painted on agar media plates using the bacterium Streptomyces coelicolor.



Related links:
- Microbial Art, a collection of unique artworks created using living bacteria, fungi, and protists.
- Painting With Penicillin: Alexander Fleming's Germ Art. The scientist created works of art using microbes, but did his artwork help lead him to his greatest discovery? By Rob Dunn. Smithsonian.com, July 12, 2010.
- Streptomyces: they're twisted! Twisted Bacteria, Aug 10, 2007.

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Gene transfer in bacterial arm races

The following videos are two short documentaries made by students in the MIT Graduate Program in Science Writing. Both films refer to a recent discovery of new antibiotics by scientists at the Massachusetts Institute of Technology and the University of Florida. But, please, don't say: "bah, another antibiotic discovering, so boring". What makes this an interesting story is not the particular antibiotics themselves (we'll see if they ever become useful), but the way they were discovered. Or should we say "created"?

It's been known for some time that the genomes of many microbes contain genes putatively coding for the production of many small molecules. Some of these molecules may have antibiotic, anticancer or other potentially useful activities. By looking at the genomic DNA sequence, scientists can often predict that such a microbe has the potential to produce specific metabolites, belonging to defined structural classes (polyketides, non-ribosomal peptides, glycosides, etc.). However, very often, the predicted metabolites are not detected when the microbe is cultured under standard laboratory conditions. Why is this? The usual explanation is that these molecules are only produced under specific circumstances that the microorganism faces in its natural environment.

With this idea in mind, the above mentioned researchers tried to find antibiotics in the cultures of a bacterium called Rhodococcus fascians (let's call it "Rhodo"). Rhodo belongs to a group of bacteria known as actinomycetes, which are well-known antibiotic producers and whose genomes are rich in information coding for the synthesis of potentially useful metabolites. The scientists cultured the microorganism under a variety of conditions: they tried both standard and unusual ones (starvation, sub-optimal temperatures or culture media, etc.). However, no antibiotic activity was ever detected.

So, they tried to "stress" Rhodo by adding another microbe in the same flasks: the name of the second partner was Streptomyces padanus ("Strepto", for short). Strepto produces a potent antibiotic (actinomycin) that kills bacteria such as Rhodo. So, what was the point? Rhodo died in all flasks, didn't it? Well, not in all of them. In one particular flask (out of hundreds), Rhodo not only survived but actually exterminated Strepto! The "Super-Rhodo" did this by producing a new antibiotic substance, never seen before. Moreover, Super-Rhodo was able to do this thanks to a piece of DNA that Rhodo stole from Strepto!

Both documentaries refer to the same story, but they use remarkably different styles. Please watch both of them, and post a comment if you want to share your thoughts (about them or about the story).

The first video is War in a Petri Dish, by Grace Chua, Allyson Collins, and Lissa Harris:

Click To Play

The second video is Shot in the Dark, by Andrew Moseman, Rachel VanCott, Megan Rulison, and Ashley Yeager:

Click To Play

There are some scientific aspects that may need some clarification. The initial idea was that Rhodo contained the genetic potential to make antibiotics, and the genes responsible for this were only "switched on" under certain unknown circumstances. This might be correct, but the mentioned results don't clearly validate it. When Rhodo faced a Strepto attack, it simply died. The only survivor (and now a killer itself), Super-Rhodo, had acquired genetic material from its enemy. This extra piece of DNA was essential for production of the new compounds. Although full details have yet to be published, it is not clear if the transferred DNA contained all, or some, of the genes coding for biosynthetic enzymes for antibiotic production. The new antibiotics are not related to actinomycin; however, it is possible that Strepto is able to produce them, in addition to actinomycin (again, under certain unknown circumstances...). Alternatively, the real effect of the extra DNA might be just regulatory, coding for some factor that induced the "switching on" of Rhodo's own genes. We'll wait for the answers to these doubts.

Scholar article:
K. Kurosawa, I. Ghiviriga, T.G. Sambandan, P.A. Lessard, J.E. Barbara, C. Rha, A.J. Sinskey (2008). Rhodostreptomycins, Antibiotics Biosynthesized Following Horizontal Gene Transfer from Streptomyces padanus to Rhodococcus fascians Journal of the American Chemical Society, 130 (4), 1126-1127 DOI: 10.1021/ja077821p

Related link:
Deadly mycelia: predatory streptomycetes. Twisted Bacteria (Jan. 15, 2008).

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Women scientists, sixty years ago

New York City, 1949. During the last three years, Elizabeth Hazen had been isolating hundreds of microbes from dirt samples taken at different locations. Many microbiologists at the time were following a path open by Alexander Fleming, Selman Waksman and others, who discovered that some soil microbes produced certain substances—antibiotics—with powerful activities against bacteria. However, rather than looking for a new agent against prokaryotic microbes, Elizabeth searched for a medicine to fight fungal infections. For this purpose, she grew the soil microbes and tested the cultures against disease-causing fungi (Cryptococcus neoformans, Candida albicans [see image]). Whenever a culture showed an interesting activity, she put it in a glass Mason jar and mailed it to Albany, 250-km away. Here, Rachel Brown—a chemist—used the culture for purification and characterization of the active compound. Then, Rachel mailed the fruit of her efforts back to New York, where the microbiologist tested the sample again for fungicidal potency. Through this collaboration, the two scientists isolated several antifungal compounds that, unfortunately, were too toxic when tested in laboratory animals.

But, finally, Elizabeth and Rachel found a useful fungicidal agent with a lower toxicity. It was produced by a soil bacterium isolated from a sample that Elizabeth had collected, while on holiday, in Warranton, Virginia. She had taken a bit of soil at the edge of a cow pasture, near a dairy barn, at the farm of a certain Walter B. Nourse. Because the microbe appeared to be a new species of streptomycetes, it received the name Streptomyces noursei, in honor of Mr. Nourse. The fungicidal agent was initially named fungicidin, but it was soon renamed nystatin, as both Elizabeth and Rachel worked for the New York State Department of Health (although in different locations). Since then, nystatin has been widely used to treat candidiasis and other fungal infections.


Related links:

• Elizabeht Hazen, seeker. Arts of Innovation.
• Elizabeth Hazen and Rachel Fuller Brown, Pharmaceutical Achievers. Antibiotics in Action.
• News of Science: Scientists in the News (on E. Hazen). Science (1955) 122, 914.
• Women in Microbiology, Microbes and Society: A Closer Look.
• Elizabeth Hazen Biography. World of Microbiology and Immunology.
• Elizabeth Lee Hazen and Rachel Fuller Brown. Inventor of the Week, Lemelson-MIT Program.

This post modestly celebrates March 8th, International Women's Day. The discovery of nystatin seems a good example of an important contribution of women scientists to microbiology, natural product chemistry, and medicine. A related story is that of Alma Whiffen, who discovered cycloheximide—also known as actidione—around the same time (1947). She isolated the compound from cultures of a soil microbe, Streptomyces griseus. Cycloheximide has antifungal activity, and was employed to treat fungal infections in plants; however, it is not useful for human treatment. The compound is better known as a general inhibitor of protein synthesis in eukaryotes, and it is widely used for research purposes. Read more here:

• Antibiotic for Plants. Time (Nov. 22, 1948).
• Alma Whiffen Barksdale Records. The New York Botanical Garden.

More related links:

• Microbiology pioneer dies (Esther Lederberg, discoverer of the lambda phage). Aetiology (Nov. 30, 2006).
• Committee on the Status of Women in Microbiology, American Society for Microbiology.
  
• Women in Science, the blog.
• Iraq's women scientists. BBC News, Middle East (Sept. 22, 2004). The dark side of microbiology...

Image credits: Wikipedia.

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A medicine cabinet in her ears

Image: European beewolf carrying a honeybee towards its tunnel. Source: Wikipedia.

In a previous post (Intertwined lives: symbiosis), I mentioned the friendship between beewolf wasps and their pet microbes: female beewolves carry live cultures of fungicide-producing streptomycetes in specialized glands of their antennae. The insect spreads a secretion from these glands all over its underground nest, just before leaving an egg. The secretion (rich in streptomycetes) protects the beewolf offspring against fungal infections.

The symbiosis seems to be quite specific for this particular kind of wasps (Philanthus species) and the corresponding streptomycetes (‘Candidatus Streptomyces philanthi’). Other wasps do not have these bacteria, nor the special glands. Therefore, the relationship between beewolves and their microbes probably started around the time of origin of the first Philanthus. According to genetic studies made with the streptomycetes found in different beewolves (isolated from Europe, America and Africa), the time of origin dates back about 26-67 million years.

Now, how would you like to have a medicine cabinet in your ears?


Links from the University of Würzburg (Germany):

• Biology of the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae)
• Symbionts for pathogen defense – Beewolves and their antennal bacteria
• Morphology, ultrastructure and phylogeny of beewolf exocrine glands

Other links:

• Beewolf (Philanthus), at Wikipedia
• David Element's Wildlife Web Page Hymenoptera 1 - Bee Wolves

Related link (added April 17th, 2011):
Streptomyces en las antenas, antibióticos en el capullo [in Spanish] por Manuel Sánchez. Curiosidades de la Microbiología (April 17th, 2011).

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Deadly Mycelia: Predatory Streptomycetes

Streptomycetes are often viewed as friendly, soil-dwelling saprophytic bacteria —feeding on dead or decaying matter. But, actually, some of them are pathogenic agents. For instance, Streptomyces scabies is responsible for the common scab of potatoes and other root crops. And some streptomycetes are able to cause human diseases called actinomycetomas, or actinomycotic mycetomas. An example is Bouffardi's white mycetoma, produced by Streptomyces somaliensis. Nevertheless, most actinomycetomas are generally caused by other, non-Streptomyces actinomycetes such as Nocardia and Actinomyces.

Despite their potential negative effects on our health or our economy, streptomycetes are mostly notable because of their ability to produce useful compounds (antibiotics, antitumor, immunosuppressive drugs...) and industrial enzymes (proteases, xylanases, cellulases...). Of course, the term "useful" can be understood only under our human point of view. Imagine that you are a soil microbe, living in close proximity to a streptomycete. You probably don't like your neighbor: it produces antibiotics and other substances that may affect your growth or even kill you and, if the worse happens, the damned streptomycete is well equipped with digestive enzymes to feed on your carcass. It is really an awful neighbor. Under your point of view, the word "saprophyte" does not make it justice at all. But, would you call it a "predator"?

A recent report, available from Nature Precedings [1] although not yet published in a peer-reviewed journal, suggests that actinomycetes, and streptomycetes in particular, are non-obligate predators of bacteria in soil. This assertion is based on the following evidences:

• Ability to grow on live bacterial cells as a sole source of nutrients.
• Prey cell lysis accompanying growth.
• Probable involvement of diffusible molecules (antibiotics, enzymes?).

The report proposes that predatory abilities are widespread within the Streptomyces genus. Previous studies described predatory activities for a few actinomycetes, including some streptomycetes [2-6]. In one of the early studies [6], Micrococcus luteus cells (the "prey") were applied to slides which were then buried in natural soil, either outdoors or in the laboratory. At different times, the slides were stained and observed microscopically, searching for natural soil predators. The M. luteus cells were attacked by two different bacteria from soil: one of them was a gram-negative one (later known as Ensifer adhaerens), while the other one was a streptomycete, which was named "strain 34". The following description derives from the microscopic observations of soil-buried slides (see picture) [6]:

"Under nutritionally poor conditions in soil, strain 34 sought out host cells [Micrococcus luteus] by extending a slender filament of mycelium. If this mycelium found host cells, it attacked them. If it did not, it lysed. Only one strand of mycelium actually connected any two packets of M. luteus cells under attack, although more than one strand could radiate from a given packet to other packets. This would appear to represent some sort of conservation of mycelium."

(Image from reference [6]. Credits: American Society for Microbiology)

Analogous observations were made with a pure culture of strain 34 (isolated from the soil-buried slides) and agar media containing M. luteus cells [6]:

"On Noble agar, strain 34 mycelium attacked M. luteus cells in a manner similar to that in soil. However, it would seem that although there was mycelial contact with the host cells, the actual mechanism of lysis was through elaboration of a soluble, diffusible lytic agent. This was inferred because on nutritionally richer media lysis of the M. luteus cells occurred at a distance beyond the limit of mycelial extension"

Therefore, it is possible that many soil actinomycetes (particularly, streptomycetes) are predators of bacteria. It may well be that streptomycetes are able to recognize some diffusible substances secreted by their possible preys. Growth of a (specialized?) filament of mycelium may be stimulated by such substances; as a result, the filament approaches the target microbe. Then, the predator secretes its own diffusible poisons (antibiotics, enzymes?) that, eventually, lyse the prey cells. The released cellular contents are now ready to be degraded and taken up by the streptomycete.

Evidently, further research is needed for a better understanding of the ecological role of actinomycetes in soil, and the natural function of antibiotics (and other secondary metabolites). Under an applied point of view, it suggests a possible way to induce the expression of "silent" gene clusters in streptomycetes and, hence, discover new secondary metabolites: by co-culturing with potential preys.


Links:

Predatory actinomycetes
[1] Streptomyces sp. as predators of bacteria. Charushila Kumbhar and Milind Watve. Available from Nature Precedings (2007).
[2] Nonobligate bacterial predation of bacteria in soil. LE Casida Jr. Microbial Ecology (1988) 15, 1-8.
[3] Gram-negative versus gram-positive (actinomycete) nonobligate bacterial predators of bacteria in soil. LR Zeph, LE Casida Jr. Appl Environ Microbiol (1986) 52, 819-823.
[4] Interaction of Agromyces ramosus with other bacteria in soil. LE Casida Jr. Appl Environ Microbiol (1983) 46, 881-888.
[5] Ensifer adhaerens predatory activity against other bacteria in soil, as monitored by indirect phage analysis. JJ Germida, LE Casida Jr. Appl Environ Microbiol (1983) 45, 1380-1388.
[6] Bacterial predators of Micrococcus luteus in soil. LE Casida Jr. Appl Environ Microbiol (1980) 39, 1035-1041.

Predatory bacteria
- Predatory Behaviors in Bacteria - Diversity and Transitions. Edouard Jurkevitch. Microbe (2007) 2, 67-73.
- Top Bug. Lori Oliwenstein. Discover Magazine (03.01.1993).
- Martin’s Microbial Menagerie. Mark O. Martin. University of Puget Sound.

Pathogenic streptomycetes
- Streptomyces: not just antibiotics. Rosemary Loria, Madhumita Joshi and Simon Moll. Microbiology Today, May 2007 - Actinobacteria.
- Streptomyces scabies. Brooke Edmunds. North Carolina State University.
- Common Scab of Potato. Michigan Potato Diseases.
- Actinomycetoma and Mycetoma. Medical Dictionary at TheFreeDictionary.
- Bouffardi's white mycetoma. MedicineWord.
- Actinomycetoma vs. Melanoma. In Tropical Diseases vs. Cosmopolitan Diseases: IX. Mycetomas. Dr. K. Salfelder & Dr. E. Sauerteig.
- Mycetoma : a review. V. Lichon, A. Khachemoune. Am J Clin Dermatol (2006) 7, 315-321.
- Mycetoma. DermNet NZ.
- Pathogenic Microbiology: Actinomycetes. University of Maryland.

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Microbial Astronauts

Do you want to increase your productivity? Buy a ticket for the next spaceflight!

It may work... if you are a microbe with the ability to produce an interesting metabolite, such as an antifungal agent. The treatment involves some kind of unknown mutation, but that's OK as long as you become a better producer with a stable behavior.

Scientists from Zhejiang University and Shandong Lukang Pharmaceutical Co. (China), recently published the following article (open access):

Jingle, L., Jianping, L., Zhinan, X., Wei, S., Peilin, C. (2007). Space-flight mutation of Streptomyces gilvosporeus for enhancing natamycin production. Chinese Journal of Chemical Engineering, 15(5), 720-724. Link to publication.

Streptomyces gilvosporeus is a bacterium that produces natamycin (also known as pimaricin), which is an antifungal agent used as a treatment for fungal keratitis and also as a food preservative. Tubes containing spores of this microbe were placed in a sample module of a returnable satellite, which was launched from the Jiuquan Satellite Launching Center in Gansu Province, China. After orbiting the earth for 18 days, the bacterial taikonauts landed safely in a returning module. Then, ground-based scientists grew these spores and studied their colony morphology, survival rate, and natamycin production. As compared to similar spores that had never left the Earth, some of the space travelers behaved differently. This was expected, and most likely due to mutations produced by the spaceflight conditions (including cosmic radiation, microgravity, and vacuum). After selecting for the best natamycin producers, a stable overproducer strain was isolated.

The authors cite other reports on the use of spaceflight for obtaining improved microbial strains. But, more generally, the relationship between microbes and space is fascinating, involving different aspects such as:

• physiological responses of microbes to spaceflight conditions (affecting growth, pathogenicity, production of interesting metabolites...),
  
• health of astronauts (microgravity weakens the immune system, which might make astronauts prone to infections),
• microbial contamination of spaceships (terrestrial microbes landing on other worlds, and vice versa?),
  
• panspermia theory and the origin of life,
• etc.

Some links:

- NASAexplores: Microbes in Space!
- Microbes May Threaten Lengthy Spaceflights, washintonpost.com.
- NASA Study Will Help Stop Tiny Stowaways To Mars, ScienceDaily.
- Russian rocket carries experiment to be analyzed at MSU, Montana State University.
- Spaceflight shown to alter ability of bacteria to cause disease, Biology news Net.
- Microbial responses to microgravity and other low-shear environments, Microbiol Mol Biol Rev.

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The froth of the liquid jade

Thirteen centuries ago, Tibetans started to enjoy the drinking of tea. However, the tea plant (Camellia sinensis) did not grow on the Tibet plateau, so the product had to be brought from the neighbor regions of Sichuan and Yunnan (present southwest China). Around the year 1000, a large-scale commerce was already established: tea, sugar and salt came in exchange of horses, furs and other Tibetan goods. All these products were transported through a very mountainous terrain, with mules and horses following a path known as the Ancient Tea and Horse Caravan Road, or the Ancient Tea-Horse Road, which was heavily used until mid 20th century. Given the difficulties of the trip, merchants compressed the tea leaves as much as possible, so fewer horses were needed for the transport. With time, instead of loose leaves, tea started to be traded in the form of hard, dry cakes of various shapes, including tea bricks (which were used as tea money in several Asian regions).

A renowned area of tea production was Pu-Erh county, in Yunnan. Today, Pu-Erh tea (or just “pu-erh”) is generally compressed into cakes or bricks, and has become very appreciated among tea connoisseurs all over the world. Pu-erh is made from a “broad leaf” variety of Camellia sinensis (var. assamica), and the best tea is said to come from old wild trees growing in the Famous Tea Mountains. Many wild and cultivated trees, known as “Tea Tree Kings,” are more than a thousand years old. The traditional elaboration converts pu-erh into an unusual tea, because it can be stored for years and its quality improves with aging (if conditions are adequate). In other words, pu-erh is a “living” tea, which matures with age due to the activity of certain microorganisms. The custom of aging the tea is most likely reminiscent from the times of caravans, when tea cakes had to endure several months of transport across the mountains and were traded as highly valuable goods for years. Similarly to other teas, pu-erh might have some beneficial effects on human health: antioxidant, anticancer, and lowering cholesterol, blood pressure and blood sugar. Concerning its flavor, some experts say that it is “strongly earthy but clean, reminiscent of the smell of rich garden soil or an autumn leaf pile, sometimes with roasted or sweet undertones.”

In a less poetical tone, a group of researchers from Taiwan has studied the effect of microbial fermentation on the quality and chemical composition of pu-erh. First, they isolated a number of fungi and bacteria from two types of high-quality pu-ehr, which were 20-25 years old. They used these microbes to inoculate fresh tea leaves (previously sterilized), which were then fermented under controlled conditions for 7 months. Next, the teas were evaluated by a group of experts, assessing flavor and quality. As a result, a number of bacterial strains, belonging to the Actinoplanes and Streptomyces genera, were found to contribute to pu-erh characteristic taste and flavor. The researchers observed that the fermentation of fresh tea leaves with some of the Streptomyces microbes produced a tea with at least some of the characteristics typical of aged pu-erh. The characteristics included color of tea infusion, antioxidant activity and content of several compounds (statins, GABA, polyphenols) that may be involved in the alleged health benefits of tea. These studies will contribute to a better understanding of the process of pu-erh aging, and eventually might lead to a controlled production of teas with healthier properties.


Reference:
Jeng, K., Chen, C., Fang, Y., Hou, R.C., Chen, Y. (2007). Effect of Microbial Fermentation on Content of Statin, GABA, and Polyphenols in Pu-Erh Tea. Journal of Agricultural and Food Chemistry, 55(21), 8787-8792. DOI: 10.1021/jf071629p



Link list:

• Tea, Wikipedia. There you can read: "Laozi (ca. 600-517 BC), the classical Chinese philosopher, described tea as "the froth of the liquid jade" and named it an indispensable ingredient to the elixir of life".
• Tea plant (Camellia sinensis), Wikipedia.
• The "Ancient Tea and Horse Caravan Road," the “Silk Road” of Southwest China. By: Yang Fuquan. The Silk Road Foundation Newsletter.
• Ancient Tea-Horse Road, at TuochaTea.com
• Tea bricks, Wikipedia.
• Tea money of China. By: Ken Bressett.
• Pu-Erh tea, Wikipedia.
• The Famous Tea Mountains of Southern Yunnan, at The Tao of Tea.
• Puer Cafe, a site devoted to Puer tea.
• Statins and polyphenols, from Wikipedia.
• GABA (gamma-aminobutyric acid), from Vitamins & Health Supplements Guide.
• Puerh history, from "Pu-erh, A Westerner's Quest." Includes collection of related links.
• Potential effects of tea on health, Wikipedia.
• Ancient Tea Horse Road (A Pu-erh Tea Lover's Journey). Nice pictures and videos: harvesting leaves, manufacturing tea bricks, preparing and tasting the infusion.
• Images from Wikipedia: tea plant (Köhler's Medizinal-Pflanzen in naturgetreuen Abbildungen mit kurz erläuterndem Texte, 1887), cake of pu-erh (Xia Guan Tuo Cha), and Chinese teapot (yixing zisha teapot).
  

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This post is my contribution to Science Linked: Bacteria, a Group Writing Project at Science in Review.
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Twisted Picks

This is the first of a series of posts where I plan to gather some links from my Connotea library that other people (you?) might find interesting. They'll mainly consist of links to research news or original articles, but don't expect many big headlines (that you can read anywhere). Links to research news will be preferred, as they are more readable by a wider audience. Most of the links will be microbe-centric but others may be related to biology fields beyond microbiology. So, there we go.

Microbes and spaceships, great combination! I thought that microorganisms were too small to be bothered by terrestrial gravity, but I was wrong. For instance, Salmonella can get more virulent during a space trip (not very good news for astronauts): Spaceflight shown to alter ability of bacteria to cause disease. Other researchers are studying the effects of microgravity on mutation and DNA recombination rates in microbes (including some streptomycetal astronauts!): Russian rocket carries experiment to be analyzed at MSU. No wonder that NASA workers do their best to avoid bacterial contamination of spaceships, which are assembled at specially clean rooms; but the tiny bugs are still there: NASA Study Will Help Stop Tiny Stowaways To Mars.

In relation to endurance, it seems that ancient microbes can be detected and resuscitated from ice samples ranging in age from 100,000 to 8 million years old: Locked in glaciers, ancient ice may return to life as glaciers melt (news release), Fossil genes and microbes in the oldest ice on Earth (original article). Yes, this is the story about "gene popsicles" (a new meme?). From the article:
"The community DNA immobilized in Antarctic ice is essentially a "gene popsicle," which can potentially be acquired by extant organisms upon thawing (...). Our analysis suggests that melting of polar ice in the geological past may have provided a conduit for large-scale phage-independent LGT [lateral gene transfer], potentially scrambling microbial phylogenies and accelerating the tempo of microbial evolution. Finally, the preservation of microbes and their genes in icy comets may have allowed transfer of genetic material among planets. However, given the extremely high cosmic radiation flux in space, our results suggest it is highly unlikely that life on Earth could have been seeded by genetic material external to this solar system."

By the way, lateral gene transfer seems to be more frequent than previously thought, even from prokaryotes to eukaryotes: Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. The whole genome of a bacteria has been naturally transferred to one of the chromosomes of a fruit fly... what shall we find next? Perhaps published genome sequences from eukaryotic organisms (such as us) should be fully reanalyzed, searching for prokaryotic sequences (previously removed as "contaminations").

And, finally... sex, sex, sex! There is a review article titled Bacterial solutions to the problem of sex. But don't misunderstand: bacteria don't have sexual problems (except when in pure culture at laboratories, I guess) (wait... "sexual microtherapist" could be a new job option for microbiologists, treating sexual dysfunctions in microbes...?) (oops, sorry about that!) The review highlights a research article reporting the use of bacteria in carefully designed experiments to study the possible advantages of sexual vs. asexual reproduction: Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli. So, "the problem of sex" is ours (we feel the need to answer "why sex?"), not theirs (bacteria just don't care).

Image credits:
Spacecraft (Soyuz TMA-6), NASA.
Glacier (Grosser Aletschgletscher, Alps) by Dirk Beyer.
Fruit fly (Drosophila melanogaster) by André Karwath.
Bacterial conjugation by Mike Jones.

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Beauty on the surface

In my previous post (Beauty inside a cell) I showed an application of a powerful microscopy technique for studying the inner structure of cells. Here I comment on the results of applying a different technique to obtain wonderful images of the surface of cells.

Researchers from University of Wales Swansea (UK) used atomic force microscopy to study the surfaces of growing hyphae during the life cycle of Streptomyces. If you're not much interested in the scientific details, just admire the textures and shapes of the pictures in large format (see fig. 1, fig. 2, fig. 3).

In addition to be visually captivating, the images support previous reports on cell differentiation processes which are characteristic of these bacteria. Young vegetative mycelium has a smooth surface and is attached to the substrate by an extracellular matrix. Then, older hyphae get covered with fibers, while loosing the extracellular matrix. Finally, the dense fibrous layer completely covers the surface of aerial mycelium and, especially, that of spores. The fibers are probably formed by the assembling of hydrophobic proteins called chaplins and rodlins; these proteins are essential for transforming the substrate-attached, vegetative mycelium into the reach-for-the-sky, aerial hyphae.

Reference:
Del Sol, R., Armstrong, I., Wright, C., Dyson, P. (2007). Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells. Journal of Bacteriology, 189(6), 2219-2225. DOI: 10.1128/JB.01470-06

Images: reproduced from the same article, copyright 2007, American Society for Microbiology. Left, initial stages of assembly of a fibrous layer, prior to aerial growth. Right, an aerial hypha prior to sporulation septation, showing complete coverage of the tip by the fibrous layer.

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Streptomyces: they're twisted!

I'm back from vacation, and trying to catch up. Perhaps this is a good moment for a brief, personal overview of Streptomyces biology, summarizing some important aspects.


Although they may look like molds, Streptomyces organisms are bacteria (eubacteria). There are essential differences at the cell and molecular levels between fungi (which are eukaryotes) and bacteria (which are prokaryotes). The similarities found between streptomycetes and fungi are the result of convergent evolution, adapting to similar environments as saprophytic soil microorganisms.


Streptomyces has a complex life cycle that includes formation of spores and other cell types. Typically, a spore germinates under the right conditions to generate a vegetative or substrate mycelium. This consists of a net of branching hyphae that grow and "dig" into the substrate to reach nutrients. Remarkably, there are few partition walls in the substrate mycelium: as a result, several copies of the genome are contained in every "cell". When nutrients are scarce (or in response to other signals), some hyphae start growing away from the substrate and into the air. In the new kind of hyphae (or aerial mycelium), partition walls are more frequently formed. At the same time, the substrate mycelium suffers a process of programmed cell death and its content is reused by the growing aerial mycelium. Finally, on the distal parts of aerial hyphae, the partition process is complete and yields beautiful chains of spores. Each spore contains a single copy of the genome.

Streptomyces and their close relatives became famous thanks to their ability to produce (among other stuff):

• antibiotics (antibacterials): streptomycin, erythromycin, tetracycline, neomycin, chloramphenicol, vancomycin, gentamicin
• antifungals: nystatin, amphotericin
  
• anticancer drugs: doxorubicin, bleomycin, mitomycin
• immunosuppressants: rapamycin
• herbicides: bialaphos

The biosynthesis of these nasty compounds is carefully co-regulated with the processes of cell differentiation, starting during the transition to aerial mycelium (on agar plates) or in late exponential phase (in liquid cultures).

However, "under standard laboratory conditions", the production of these metabolites is not essential for Streptomyces: mutants lacking the ability to produce the compounds are viable and not impaired in growth. This criterion distinguishes secondary metabolism ("reactions are not essential for viability") from primary metabolism ("reactions are essential"). That's why the mentioned compounds are called secondary metabolites.

But, if these funny bugs can live without secondary metabolites, why do they produce them? What's the use for a soil bacterium to produce an anticancer drug (for instance)? Are they spending valuable resources just to make something they don't need? Sure they're not. Of course, the microorganisms have not evolved "under standard laboratory conditions". But discussing about putative functions of secondary metabolites deserves a new post.

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Images:

(a) Several Streptomyces isolates growing on agar plates. (b) A close look at the colonies of Streptomyces coelicolor. Both images by Tobias Kieser, Celia Bruton and Jennifer Tenor, reproduced from Genome Biology 2002, 3:reviews1020.1-1020.4.

Life cycle of Streptomyces coelicolor, reprinted by permission from Macmillan Publishers Ltd:
Esther R. Angert. Alternatives to binary fission in bacteria. Nature Reviews Microbiology 3, 214-224 (copyright 2005).

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Romans, dried figs and Streptomyces

In the year 79 AD, the Roman towns of Herculaneum and Pompeii were devastated by a terrible eruption of Mount Vesuvius. As a result, the towns were buried under many meters of volcanic ash, which left buildings, food remains and human bodies in a remarkable state of preservation. This allows to study the state of health of ancient Romans and its relationship to nutrition and other environmental conditions. For instance, analysis of human remains from Herculaneum showed lesions typically produced by tuberculosis and, especially, brucellosis. The high frequency of brucellosis has been related to the eating of contaminated cheese: Herculaneum had an important production of goat's milk and cheese. Remarkably, the study of carbonized cheese showed particles of the right size and shape, suggesting that they were bacteria of the Brucella group.

However, the Herculaneum inhabitants appeared to suffer few non-specific infections, which were common in antiquity due to poor sanitary conditions. A recent study suggests that people were protected against these infections due to consumption of dried fruits contaminated by antibiotic-producing Streptomyces!

The author of the work arrived to this conclusion through two kinds of experimental evidences:

First, examination of food remains under the microscope (both light and scanning electron) revealed the presence of virus and possible Salmonella on eggshells, and Saccharomyces in wine and bread. More important for us was the observation, under the skin of pomegranate seeds and figs, of a dense net of branching filaments resembling those of Streptomyces. These fruits were originally dried as a mode of preservation: Romans buried them in straw under a weight to achieve dehydration. This technique may explain the proliferation of Streptomyces. And we all know that Streptomycetes are prolific producers of antibiotics, right?

Second, histological study of bone samples from human remains (using a confocal microscope) showed presence of auto-fluorescence with characteristics typical of tetracycline-labeled bone occurring during life. Tetracycline antibiotics mark human bone, as it has been established for both modern and ancient humans. An example of tetracycline-labeled human bones was previously described from a cemetery in Sudanese Nubia dated 350-550 AD; in this case, a possible source of tetracycline was the grain stored in mud containers, which provided a proper environment for proliferation of Streptomyces.

I found that the paper and the whole story (mixing archeology and microbiology together) are fascinating. Of course, I'd certainly appreciate more experimental evidence concerning unequivocal identification of tetracycline in bones (could the fluorescence be due to any other molecule with similar properties but different to tetracycline?). And I wonder how common is tetracycline production among Streptomycetes. It would be very nice if the hypothesized conditions could be replicated, i.e. grow some figs and pomegranates (Roman style = "organically" produced?), and dry them using the Roman technique (ideally in the Herculaneum region). Then, try to detect tetracycline in the fruits. You can even isolate some Streptomycetes from the dried fruits, and screen the isolates for tetracycline production...

Reference:
Capasso, L. (2007). Infectious diseases and eating habits at Herculaneum (1st century AD, southern Italy). International Journal of Osteoarchaeology, 17(4), 350-357. DOI: 10.1002/oa.906

[Sadly, the author uses the word "mould" for Streptomyces, which is a bacterium, not a fungus. This mistake can still be found in medical and other technical literature]

(Image: Mosaic on a wall in the House of Neptune and Amphitrite, in Herculaneum, Italy. Source: Wikipedia)


UPDATE (September 3, 2010):
A scientific article has been published confirming the presence of tetracycline in the Nubian bones! The reference is:
Mass spectroscopic characterization of tetracycline in the skeletal remains of an ancient population from Sudanese Nubia 350–550 CE
Am. J. Phys. Anthropol. (2010) 143, 151-154.
DOI: 10.1002/ajpa.21340
(Found via Biounalm: Los antibióticos se usaban desde hace 2000 años?)


UPDATE (September 10, 2010):
See other blogs (in Spanish): Los nubios ya usaban antibióticos hace 2.000 años (Amazings.es), Una pinta de tetraciclina (Curiosidades de la Microbiología).

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Time travel

You may know Google News Archive Search. I enjoy using it to search for old, historical stories. Soon I noticed that the oldest (free) stories came from the archives of Time Magazine, which are fully available for searching and reading (don't miss the covers!). Looking for articles containing the words "Streptomyces" or "actinomycete" in the complete Time archive, I got only five hits. Remarkably, they were written on 1948, 1949, 1950 and 1963. (So sad, it seems nothing related to these terms has happened in almost 50 years!)

The Time articles, which deal with the discovery of antibiotics from actinomycetes, are:

• Antibiotic for Plants (Nov. 22, 1948). Actidione, now better known as cycloheximide, a product of Streptomyces griseus.
  
• Man of the Soil (April 4, 1949). Neomycin. You may have guessed that the "man" refers to Selman Waksman, the Father of Antibiotics.
• The Healing Soil (Nov. 7, 1949). Entertaining, long article about antibiotics (actinomycin, streptomycin, etc) and Waksman*.
• New Antibiotic (Feb. 6, 1950). Terramycin (oxytetracycline), produced by Streptomyces rimosus.
• Another Whisper, Another Wait (May 31, 1963). A brief piece on the discovery of a mysterious antitumor substance from Streptomyces. The active compound was later called anthramycin.

(*) Waksman was on the cover of this issue of Time magazine.

(Concerning the discovery of streptomycin, I very much recommend an article by Veronique Mistiaen: Time, and the great healer, The Guardian, Nov. 2, 2002)

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Size and shape in the genomes of actinomycetes

A new genome sequence of an antibiotic-producing actinomycete has been recently published in Nature Biotechnology. This seems to me a good excuse to highlight some peculiar aspects of genome evolution in this group of bacteria.

The mentioned microorganism is Saccharopolyspora erythraea, known as an industrial source for erythromycin. The size of the genome, 8.2 Mbp (Mbp = megabasepairs = million base pairs), is similar to that of Streptomyces coelicolor (8.7 Mbp) and Streptomyces avermitilis (9 Mbp). These are some of the largest genomes in bacteria, although much smaller genomes are found in other actinomycetes. An example of the latter is Bifidobacterium adolescentis, with only 2.1 Mbp (not to mention the obligate parasite Tropheryma whipplei, the causative agent of Whipple's disease, with a tiny 0.9-Mbp genome).

In the Sac. erythraea chromosome, the majority of conserved, essential genes are contained in a region extending either side of the origin of replication (the "core"). This genome organization consisting of core and "non-core" regions is also found in streptomycetes. The non-core region (3.8 Mbp in Sac. erythraea) includes most of the genes coding for conditionally adaptive functions, such as production of secondary metabolites (although the genes for erythromycin synthesis happen to be located in the core).

What about shape? Most bacteria possess a circular chromosome, which is the case of Sac. erythraea and the majority of actinomycetes. On the other hand, at least some species of Streptomyces and Rhodococcus contain linear chromosomes. Given that actinomycetes more closely related to Rhodococcus (such as Nocardia) possess circular chromosomes, linearization may have occurred more than once during the evolution of this group of bacteria. Remarkably, genomic instability is frequently found in Streptomyces: the non-core region of the chromosome contains transposable elements and is prone to undergo rearrangements and deletions. This leads to large-scale variations, even among genomes of the same species. When the telomeres are lost, a circular chromosome results, and there are examples of the co-existence of linear and circular forms for a particular strain. It has been proposed that linear chromosomes arose from the recombination of linear plasmids with circular chromosomes, and that linear plasmids evolved from bacteriophages.

(Figure: Schematic representation of Saccharopolyspora erythraea chromosome. Reprinted by permission from Macmillan Publishers Ltd: Nat. Biotechnol. 25: 447-453, copyright 2007).

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Intertwined lives: symbiosis

Some actinomycetes are known for establishing symbioses with other organisms. A typical example is the formation of nodules on the roots of certain plants by soil bacteria of the genus Frankia. Although these microbes can also be found as free forms in the soil, the nodule constitutes a comfortable home for Frankia, with abundance of carbon sources. Additionally, it's an adequate environment for an activity that greatly benefits the plant: nitrogen fixation. This is a process by which atmospheric nitrogen is converted into ammonia, nitrate and other compounds. Hence, the actinomycete fixes nitrogen and fertilizes its host plant. Recently, the genomes of three Frankia strains have been sequenced, which will help to understand how different strains are able to select and colonize certain plant hosts but not others.
(Image: Nodule from Alnus incana subsp. rugosa, about 1.5 cm diameter; D. R. Benson)

In other actinomycetal symbioses, the second partner is an insect, for instance a beewolf. Beewolves are not wolves, but a type of wasps that hunt honeybees to feed their larvae. After digging a nest in sandy soil, the female beewolf deposits an egg together with one or several paralyzed bees. But the underground nest is humid and warm, and the wasp larva may easily get infested by pathogenic microorganisms. As an strategy to diminish larva infestation, beewolves cultivate and use their own antibiotic-producing actinomycetes. Antennae of female beewolves have specialized glands housing symbiotic Streptomyces bacteria. The wasp applies a secretion from these glands all over the nest before leaving its egg. Later, the larva takes the bacteria and applies them to its cocoon, resulting in lower risk of fungal infestation. Sequencing DNA from both symbiotic partners is beginning to yield interesting results.
(Image: Philanthus triangulum, a European beewolf)

But the story can get more complicated. Imagine a symbiosis with four co-evolving partners: three of them are engaged in a mutualistic relationship, while the fourth one is a parasite. That's the beautiful case of fungus-growing ants. In their underground nests, the ants grow a mushroom-like fungus by feeding it with plant materials or other organic matter. In turn, the fungus serves as food for the ants (yes, this is agriculture!). But every garden has its pests, and the ants' farm is home for the Escovopsis mold. Escovopsis is a specialized pest, found only on the crop of farming ants. To battle the parasite, the ants combine special behaviors and microbial symbionts. These insects carry a bunch of antibiotic-producing actinomycetes in elaborate cuticular crypts, supported by unique exocrine glands. The symbiotic bacteria produce substances that specifically inhibit Escovopsis growth. Although initially identified as Streptomyces, the actinomycete symbionts appear to belong to the Pseudonocardia genus. The case of the fungus-growing ants has become a textbook example for teaching evolution and symbiosis (educational materials are available from the University of Nebraska State Museum or from the PBS Evolution project)
(Image by Grey Wulf: leaf-cutter ants [a type of fungus-growing ants])

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Actinomycetes, natural drug factories

Actinomycetes are Gram-positive bacteria with a high GC-content in their DNA. Among others, representative genera include Corynebacterium, Micrococcus, Mycobacterium, Nocardia, Propionibacterium, and Streptomyces. Many actinomycetes, such as Streptomyces, grow as branching filaments and live in soil, as fungi do. Because of this resemblance, actinomycetes were originally classified as fungi. This was reflected on their name, where "mycetes" comes from the Greek for "mushroom, fungus".

Some actinomycetes are pathogenic, such as Mycobacterium tuberculosis. However, many others are extremely useful due to their ability to produce compounds with pharmaceutical properties (antibiotic, antifungal, antitumor, immunosuppressive). The genus Streptomyces is well known precisely for this ability.

In this blog, I intend to post mainly about the biology of actinomycetes, especially those aspects related to the biosynthesis of natural products of pharmaceutical interest. However, I may occasionally deviate from the primary theme. There might be some microbiology, some biochemistry, some chemical biology, some genetics...

Oh, about the title: "Twisted Bacteria". No, it's not that they are "perverted" (although some times we researchers in the field may think so...). The title was inspired by the word "Streptomyces", where "strepto" comes from the Greek for "twisted, twined".

(Image: Streptomyces sp. under the microscope. CDC/Dr. David Berd, Public Health Image Library)

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