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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From Aladdin’s Cave to Treasure Island

For a long time, it was thought that the land of actinomycetes was... well, land. I mean, they were supposed to be terrestrial creatures, even although some of them were isolated from samples taken in sea habitats (for instance, read this article from 1958). But these "marine" bacteria, generally found in shallow waters, were quite similar to their counterparts from land. For this reason, it was assumed that any actinomycetes obtained from the sea were just wash-offs from the shore.

Now this view is changing. But how can we say if a microbe isolated from a particular sea location is a true neighbor on the block (as opposed to be just derived from a passing-by or dormant spore, coming from land)? Ideally, it should be recognized by the following criteria: its ability to grow optimally at native conditions (salinity, pressure, temperature, nutrients); demonstration that the organism is really active on location; and the recognition of particular metabolic profiles, not found in terrestrial relatives. Nowadays, the existence of truly marine actinomycetes seems to be supported by solid data.

Similarly to their terrestrial relatives, marine microbes are a rich source of bioactive metabolites (antibiotics, antitumor drugs) and enzymes with different applications. For instance, cultivation of a marine actinomycete known as Salinispora tropica yielded a number of novel metabolites, not found before. One of these compounds, salinosporamide A, has antitumor properties and is currently being tested in humans for the treatment of cancer. Sequencing the genome of Salinispora tropica unveiled a number of genes coding for the synthesis of 17 potential metabolites; most of these compounds had not been detected in previous culturing of the microbe. Then, the researchers used the genetic information to guide a new chemical analysis of Salinispora cultures. The analysis uncovered an additional, novel compound (salinilactam), which had a structure corresponding to that deduced from the DNA sequence.

Let me finish with David Hopwood's words from Therapeutic treasures from the deep:

"In a recent book I likened the plethora of previously unknown genes in a newly sequenced Streptomyces genome to an Aladdin's Cave. Perhaps Treasure Island would be a more apt metaphor in this case [Salinispora]"

Neat.


List of links:
- Article from 1958: Grein A, Meyers SP, Growth characteristics and antibiotic production of actinomycetes isolated from littoral sediments and materials suspended in sea water. J. Bacteriol. 1958, 76, 457-463.
- Marine actinomycetes: Bull AT, Stach JE, Ward AC, Goodfellow M, Marine actinobacteria: perspectives, challenges, future directions. Antonie Van Leeuwenhoek, 2005, 87, 65-79.
- Salinosporamide A: Wikipedia.
- Sequencing the genome of Salinispora tropica: Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS, Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc. Natl. Acad. Sci. USA, 2007 , 104, 10376-10381.
- Therapeutic treasures from the deep: Hopwood DA, Nat. Chem. Biol. 2007, 3, 457-458.
- Aladdin's Cave: Aladdin - Wikipedia.
- Treasure Island: Wikipedia.


Images:
Left, Aladdin in the Magic Garden, an illustration by Max Liebert for Ludwig Fulda's Aladin und die Wunderlampe. Source: Wikipedia.
Right, Jim Hawkins and the treasure of Treasure Island, an illustration by Georges Roux for the 1885 edition of Treasure Island by Robert Louis Stevenson. Source: Wikipedia.

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This post is my contribution to Microbial Week, a collection of posts highlighting the many roles of microbes in deep-sea or marine environments. The event is organized by Christina Kellogg and the guys at Deep-Sea News.
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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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Natural products at Nature Chemical Biology

The current issue of Nature Chemical Biology is centered on natural products, with an emphasis on terpenes. I found the following articles most interesting:

• One pathway, many products, by M.A. Fischbach & J. Clardy [Nat. Chem. Biol. (2007) 3, 353-355]. Primary metabolic pathways make single products, while secondary pathways generally make a variety of products, not just one. Why?
  
• The function of terpene natural products in the natural world, by J. Gershenzon & N. Dudareva [Nat. Chem. Biol. (2007) 3, 408-414]. Terpenes are the largest class of natural products, and we are just beginning to understand the biological roles of a few of them.
  
• Mining and engineering natural-product biosynthetic pathways, by B. Wilkinson & J. Micklefield [Nat. Chem. Biol. (2007) 3, 379-386]. With the purpose of developing new therapeutic agents, recent advances in the field come from improved screening technologies, genome mining, expression of entire biosynthetic gene clusters in suitable hosts, gene synthesis, or directed evolution of enzymes.
  
• Plant endophytes as a platform for discovery-based undergraduate science education, by S.A. Strobel & G.A. Strobel [Nat. Chem. Biol. (2007) 3, 356-359]. Imaginative education projects have the potential to yield, as a bonus, direct scientific results. Superb.
  

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