Small Things Considered

Of Terms in Biology: Neuston

by Merry

A water strider. Surely handsome, albeit not microbial.
Source.

When I stumbled across the term bacterioneuston, I discovered a whole new world where the air meets the sea. I found that marine neuston had long been used to refer to the diverse flora and fauna inhabiting the topmost 5 cm of the oceans—a distinctly different assemblage than found in the waters below. This broad grouping had been further subdivided. Floating organisms, such as Physalia, the Portuguese Man o' War, make up the pleuston (the small organisms floating on or near the surface of a body of water, from the Greek pleustikos, fit for sailing). The 40-some species of water striders are part of the epineuston (the organisms living in the air on the surface film of a body of water). Just beneath them, living immediately below the surface film, are the organisms of the hyponeuston. There are no hard and fast lines here. A diving epineustonic water strider finds itself briefly a hyponeuston. The planktohyponeuston gather near the surface at night but spend their days below. And, of course, the plankton float or drift throughout the rest of the water column. (For these neustonic terms and more, click here.)

Notice how those definitions shifted from the topmost 5 cm to the surface microlayer film as our focus of interest shifted. Today, unadorned neuston is often used to mean the organisms in the surface film. Its etymology? From the Greek neustos swimming, from nein to swim.

The presence of a gelatinous surface microlayer film had been proposed in 1983, based partly on observations of the slick associated with blooms in the Sargasso Sea of the filamentous cyanobacterium Trichodesmium. (It struck me that the surface microlayer might be a most desirable location for a filamentous, nitrogen-fixing, photosynthetic cyanobacterium.)

What about the ocean surface film from the microbial neustonian point of view? It might appear to be an immense biofilm stretching from horizon to horizon. Thickness? The authors of one paper wryly note: In most investigations, the surface microlayer is operationally defined based on the depth of the sample layer collected, which is in turn dependent on the sampling method employed. Estimates of its thickness range from 1 to 50 µm, with some of the difference likely due to the variable layers of bacteria present. Surface layer bacterial concentrations are commonly said to be 10³−10⁵ times higher than in the underlying water column. One study of the North Sea found that the surface layer microbes were predominantly from two genera, Vibrio and Pseudoalteromonas, both of which have characteristics suggestive of adaptation to life in biofilms.

Oh, what about the bacterioneuston, where this article began? This is—of course—the bacterial component of the neuston. So far Google finds no mention of an archaeaneuston. The poor Archaea, ignored and neglected yet once again.

All for One, and One for All!

by Mark Martin

Panic grass growing well at a soil temperature
of over 50 °C (123 °F). Source.

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 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—was able to survive intermittent high temperatures in geothermal soils (up to 65 °C.) due to its association with an endophytic fungus, Curvularia protuberata. 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 derives from the Latin panicum, referring to foxtail millet.

The thermal areas of Yellowstone National
Park are home to thermotolerant microbes,
and even a few “macrobes”! Source.

Endophytic fungi are quite common among plants and have been implicated in a number of mutualistic associations that display enhanced stress tolerance. But the story was far stranger than this. It turns out that the "thermal tolerance" trait conferred by the endophytic fungus is actually due to a specific RNA virus onboard. (See the 2007 report in Science.) This dsRNA virus is aptly named "Curvularia thermal tolerance virus" (CThTV). Infected fungal mycelia contain two viral dsRNA molecules: a 2.2 kb dsRNA molecule that encodes two ORFs related to viral replication and a 1.8 kb dsRNA molecule with two ORFs with no similarity to any protein of known function.

It has long been known that viruses can modulate the ability of a fungus to interact pathogenically with a host organism, but this is the first report showing a clear-cut mutualistic interplay. Isolates of C. protuberata "cured" of CThTV by freeze-thaw and desiccation cycles conferred no thermal tolerance on the host plant; re-infection of the virus-free fungus with CThTV restored its ability to confer thermal tolerance to the panic grass.

The Roossinck group went on to show that C. protuberata carrying CThTV could colonize eudicots such as tomato, and even provide some thermal tolerance to the new host plant. However, colonization was not as extensive and the thermal tolerance was not as pronounced as with panic grass. As one might guess, work is continuing to determine the mechanism by which the uncharacterized ORFs within the 1.8 dsRNA of CThTV confer the thermal tolerance in this fungal-plant mutualism.

Panic grass phenotype after laboratory testing of thermotolerance (soil temperature cycling between 65 °C for ten hours a day and 37 °C for fourteen hours a day, for two weeks). Legend: Wt = plant infected with virus-bearing fungi. An = plant infected with previously “cured” fungi carrying reintroduced virus. VF = plant infected with virus-free fungi. NS = plant not infected by fungi. Source.

This kind of fungal-conferred stress tolerance may be much more that a rare oddity. In fact, there is some evidence that the ability of fungi (with or without viral modification) to increase stress tolerance is fairly common, and evolutionarily ancient. The existence of multiple "partners" involved in a mutualism has been described for ants, leeches, and many other associations. This relationship between Dichanthelium lanuginosum, Curvularia protuberata, and CThTV is reminiscent of the interrelationships between bacteriophage, Wolbachia, and insects described here.

Clearly, in what appears to be a warming world, understanding how plants can tolerate and prosper at elevated temperatures is an intriguing topic. To a "symbiophile" like myself, learning that the plant has a fungal partner, and that the fungal partner has a viral passenger—and all are working together in a finely tuned mutualistic dance—is a hot topic indeed!

Mark is associate professor in the Department of Biology, University of Puget Sound, an Associate Blogger for STC, and a passionate advocate for the Small Things.

Of Terms in Biology: Planktonic

by Elio

The image of a diatom chain previously displayed here was used without permission of the photographer and has been removed. If any blog visitors have downloaded that image, they should be aware that it is under copyright and that permission and payment of a fee is required for its use. Our apologies to the photographer.

Phase contrast image of diatoms. Source.

The word planktonic is widely used in microbiology for organisms that are floating in bodies of water. It may be worthwhile to ponder its meaning. According to Wikipedia: plankton consist of any drifting organisms (animals, plants, archaea, or bacteria) that inhabit the pelagic zone of oceans, seas, or bodies of fresh water. So, what does pelagic mean? Wiktionary says: Living in the open sea rather than in coastal or inland waters. Clearly, microbiologists use the term planktonic without the “pelagic” restriction, and include any body of water, even that in a test tube. The word plankton is derived from the Greek word πλαγκτος ("planktos"), meaning wanderer or drifter (thus also related to planet).

What is the antonym of planktonic? Sessile comes to mind (i.e., permanently attached or established, not free to move about). Its etymology? From the Latin sessilis, from sessus, past participle of sedēre, to sit. But attached or clinging would do as well. Not relevant here but of linguistic interest, the antonym of sessile is vagile, having freedom to move about. I had never heard of it. I stopped being vagile years ago.

If sessile does not appeal to you, perhaps adhering would do. Or maybe we should invent a new term. How about biofilmic or biofilmatic? Want to vote it in or out? Let us know.

Talmudic Question #53A

In recent years, the use of radioactive isotopes has diminished considerably in microbiological research. What has been lost in the process?

Commentary by Elio

Source.

This is a nostalgia trip. Molecular microbiologists of my generation relied on the use of radioactive isotopes for much of their research. Those days, the size of a department’s research effort could be measured by the number of scintillation counters it had at its disposal. Radioactivity was a convenient way of detecting and quantitating very small amounts of cell constituents. This has now been superseded by fluorescence and other non-radioactive methods. However, there are some things that radioactive isotopes do best. Thus, they are still in use. Here are two such uses.

1. Determining which molecules are made anew. Adding radioactive precursors of macromolecules to a growing culture will result in selective labeling of the newly synthesized molecules. If the labeled compound is added for a short time ("pulse labeling"), the radioactivity is found in the portion of the molecule most recently made. Among many other things, such methods were used to elucidate the direction of synthesis of proteins (from N- to C-terminus) and of nucleic acids (5'- to 3'-terminus). Moreover, with this strategy you could estimate the speed with which such macromolecules are synthesized.
2. Measuring the stability of a molecule. Adding a labeled precursor for some period of time, then replacing it with its non-radioactive counterpart (“pulse-chase”) lets us measure the stability of synthesized molecules. If the molecules are stable, they will retain the radioactive label; if unstable, the label will be lost. This method enabled us to determine the half-life of high-turnover molecules such as mRNA and certain regulatory proteins.

These days, when I mention radioactive isotopes, the response I get tends to focus on the dangers of working with them. Well, in the past we were not only careful but also aware of what constitutes danger. Mostly, we worked under safe conditions. Or so we thought. And I'm still around, many millicuries of P³² later.

The Three Stages of My Experience in Discovering the Mode of Action of Penicillin

Once penicillin came into common use, it became imperative to figure out how it works. This knowledge might be expected to lead to the development of better antibiotics or a more effective use of their therapeutic power. In actuality, the research effort directed to understanding the mode of action of penicillin led to major insights into basic biological phenomena. We are delighted to be able to share this personal perspective by one who made many of the key discoveries in this field.

by Ted Park,
aka James T. Park

Ted Park is Professor Emeritus, Department of Molecular Biology and Microbiology, Tufts University.

Act 1: Precursors of an unknown, and presumably essential, metabolic process accumulate in penicillin-treated Staphylococcus aureus cells.

The scene opens in 1943. I was a graduate student in fermentation biochemistry at the University of Wisconsin in Madison. As this was at the height of World War II, most research projects were war-related. My first assignment was no different: to identify mutants of Aerobacter aerogenes that produced improved yields of 2,3-butylene glycol (2,3-butanediol), a potential candidate for conversion to synthetic rubber. It was not a terribly exciting project.

My fortune changed when a new assignment came to the lab. Penicillin had recently been shown to be a miracle drug. Production had started in England by growing the mold, Penicillium notatum, as mycelial mats on the surface of media in individual bottles—hardly an efficient method for mass production. The new project was to produce penicillin by growing the mold in submerged culture in large vats, and I was able to sign on to the team. My job was to develop a turbidometric assay for penicillin. It was easy enough to produce a beautiful standard curve of final turbidity versus penicillin concentration using Staphylococcus aureus 209P. However, the fermentation broths varied in their effects—because, as we learned much later, they contained multiple penicillins with different fatty acid side chains with different potencies. Somewhere along the way I managed to pick up an S. aureus 209P infection in my eye. It was treated successfully with a mercury salt cream, penicillin not yet being available for the general public.

Source.

The next year, I volunteered to become an officer in the Navy, which seemed preferable to being drafted as a private into the Army. I soon found myself one of 900 at the 'Ship of the Desert' in Tucson, Arizona. Two months later, as a freshly minted ensign, I was almost the last of the 900 to receive orders! I was to report to Camp Detrick, Maryland, a place I'd never heard of. It turned out that a fair number of Navy personnel with scientific backgrounds, myself included, were assigned to this Army research unit studying biological warfare. I spent the remainder of my 2 years in the Navy trying to develop a vaccine to protect against one of the organisms under study.

During this time, I came across an interesting article by Chain and Duthie about the mode of action of penicillin. Their results indicated that, contrary to prevailing thought, penicillin did not interfere with respiration and the production of ATP. In the back of my mind I stored the naïve—and at that time unlikely—notion that maybe penicillin interfered with some essential biosynthetic process. Towards the end of my tour of duty, I learned that money was available from the US Army to support education and research. I wrote to my former thesis adviser, Marvin Johnson, and told him that I would like to return to study under him, but that I wanted to investigate the mode of action of penicillin. Would he agree to this if I supported myself with a small grant from the Army?

Good Guys, Bad Guys

by Merry

The Good Guy. Aphidius wasps are commonly used for
for biocontrol of aphids. Here, a female wasp hits
her mark. Source.

Because it prefers to dine on some of our valued crop plants, the pea aphid (Acyrthosiphon pisum) 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, 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 wasp emerges from the aphid "mummy." Agriculturally speaking, parasitoid wasps are Good Guys, important partners in our integrated pest management 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 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. (What makes a symbiont a primary rather than a secondary symbiont? That depends on who you ask. Some distinguish based on the evolutionary age of the symbiosis, others mention the obligate nature of the relationship for both partners.)

The Bad Guy. SEM of an aphid, sure to have
Buchnera on board. Source.

The nutritional role of the Buchnera endosymbionts is well known. Aphids feed on phloem—a high sugar, low amino acid plant sap. The Buchnera genome encodes the genes required to make all the essential amino acids needed by the aphids. The Buchnera live within specialized aphid cells (called bacteriocytes) along with a variable number of secondary symbionts. The secondary symbionts characterized so far include three γ-proteobacteria, a Rickettsia, and a Spiroplasma. In order for these maternally-inherited symbionts to persist or spread in aphid populations, they must confer some benefit, at least under some conditions. Of the three γ-proteobacteria, the presence of one (Regiella insecticola) improves the survival rate of pea aphids infected by a major aphid fungal pathogen (the Entomophthorales fungus Erynia neoaphidis). For the other two (Hamiltonella defensa and Serratia symbiotica), the presence of either one confers some resistance to the parasitoid wasp—thus making them Bad Guys on the side of the aphid.

We now know quite a bit more about H. defensa, thanks to work carried out in Nancy Moran's lab. Some insights came from their recent sequencing of its complete genome. At 2.1 Mb, H. defensa has undergone significant genome reduction compared to its free-living close relatives such as Yersinia and Serratia with their 4.6 – 5.4 Mb genomes. On the other hand, it has suffered far less gene loss than Buchnera, whose genome is a mere 640 Kb. However, H. defensa lacks the genes needed to synthesize eight essential amino acids. For those, it relies—like its aphid host—on synthesis by Buchnera. What H. defensa does contribute is defense against the wasp. It earns its keep when parasitoids are present but otherwise carries a fitness cost. As the result, H. defensa occurs only sporadically in these aphids, its infection frequency fluctuating in concert with parasitoid pressure.

Accomplices. TEM of aphid bacteriocyte showing the
larger Buchnera primary symbionts (arrowheads) and
the smaller H. defensa secondary symbionts (arrows).
Bar = 10 μm. Source.

The story becomes even more complex because not all strains of H. defensa are defenders. Those effective in blocking development of the wasp larvae carry a λ-like phage known as APSE. (The source of this acronym? A. pisum secondary endosymbiont.) Even among the phage-carrying H. defensa, some are better defenders than others, likely due to differences between their phage. All of the ASPE phage studied so far have been found to have 95% or more sequence identity and to encode some nasty toxins. Some of their toxin genes are homologous to those found in well-known mammalian pathogens, e.g., genes for Shiga and Campylobacter jejuni toxins. The particular toxin-encoding genes present differ from one phage strain to another, likely accounting for the variable effectiveness of their H. defensa hosts.

That H. defensa's defense of its aphid host requires the ASPE phage does not mean that H. defensa doesn't play a part—only that it can't do it alone. H. defensa comes from a line of pathogens and has retained abundant weaponry, including type-III secretion systems, putative toxin genes, and related regulatory factors. Nevertheless, it seems clear that the phage is an essential partner. To quote the investigators, …the evolutionary interests of phages, bacterial symbionts, and aphids are all aligned against the parasitoid wasp that threatens them all.

But the wasp, too, is an essential partner, bringing the count of participants so far up to five: wasp, aphid, Buchnera, H. defensa, and ASPE phage. Without the wasp, H. defensa would disappear from the aphid population like so much excess baggage. Without H. defensa and its phage, the aphids would be more vulnerable to the wasps. Without Buchnera, the aphids would starve and the wasp would have to look for some other host to nourish its young. In this pentangle, there are neither Good Guys or Bad Guys, only an interwoven ménage à cinq.

Fine Reading: The Good-Enough Clockus of Prochlorococcus

by Elio

Source.

The very first post on this blog (It Don't Mean a Thing If It Ain't Got That Swing) 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. 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! (I've used up my allotment of exclamation marks!)

A cyanobacterial lineup. (left) Five diverse
Synechococcus strains. (right) Two Prochloro
coccus strains, the first one being a sample
from the Mediterranean Sea and the subject
of the clock study. Courtesy of Ilka Axmann.

Most of this wonderland has been studied in a strain of Synechococcus elongatus. A recent report from Ilka Axmann's lab in Berlin concerns the marine cyanobacterium Prochlorococcus, likely the most abundant photosynthetic organism there is. These bacteria have KaiB and Kai C, but they have recently lost their gene for KaiA. Nevertheless, they still exhibit some diurnal patterns. But unlike the case with Synechococcus, if you put Prochlorococcus in continuous light, those patterns do not persist beyond the current cycle. The authors liken the Prochlorococcus system to an hourglass, which can measure a 24-hour period, but then has to be reset by being overturned before it can time the next day. Click here for a commentary: The Rolex and the Hourglass: a Simplified Circadian Clock in Prochlorococcus?

Ilka Axmann.

The authors propose that their data provide biochemical support for the observed evolutionary reduction of the clock locus in Prochlorococcus and are consistent with a model in which a mechanism that is less robust than the well-characterized KaiABC protein clock of Synechococcus is sufficient for biological timing in the very stable environment that Prochlorococcus inhabits. This makes for an interesting variation on the theme, expanding the established notions about biological clockworks.

Postscript: No sooner did we post this piece than the new issue of Microbe (the magazine of the American Society for Microbiology) arrived, including a review by Carl Hirschie Johnson entitled From Skepticism to Prominence: Circadian Clocks in Bacteria. We heartily recommend it. To access it, click here.

Exciting Resolution

by Jennifer Gutierrez

Fluorescence microscopy of bacteria has long been a challenge due to the size of the organisms and the diffraction limit of visible-light microscopy. Although much valuable data has been collected by refining optical systems, automating microscopy setups, and using deconvolution algorithms, localization of single molecules inside cells has rarely been possible. With the advent of PALM and STORM microscopy, however, single-molecule resolution inside live cells has the potential to become routine!

In principle, a point of light, as emitted by a single fluorescent molecule, should define its location. However, if there are several close light emitters, the optical microscope cannot resolve them and sees them as one. This is due to diffraction of light and the fact that microscopes can only 'see' a portion of the radiated light through the lens. (To learn more about this point spread function, click here.) Several methods have been developed to get around this problem, generating a whole alphabet soup of abbreviations: SIM, SSIM, STED, and others. The two that may gain great acceptance are PALM (PhotoActivation Localization Microscopy) and STORM (STochastic Optical Reconstruction Microscopy).

These super-resolution, light microscopy techniques can provide information below the limit of resolution determined by the Rayleigh criterion (about 200 nanometers in near-ultraviolet light). Both systems achieve this resolution by sequentially and randomly turning on and off a small number of fluorescent molecules. This way, two adjacent molecules are unlikely to turn on at the same time. The molecules used must be capable of photoswitching, meaning that after being activated by light of one wavelength, they can then be excited by a different wavelength and their resulting fluorescence detected. Also, excitation must irreversibly photobleach them so that they can be activated/excited only once. By hitting a sample with a very small dose of activation light, only a small number of fluorophores will become activated. The sample is imaged by hitting it with excitation light, which also bleaches the activated/excited fluorophores. This process is then repeated many times until all the fluorescent molecules have been imaged and bleached.

PALM visualization of a main component of the E coli chemotaxis network. A photoactivatable fluorescent protein fusion was constructed for Tar, the high-abundance aspartate receptor. PALM images show numerous solitary Tar receptors (F), small clusters consisting of tens or hundreds of receptors (G), and large clusters with thousands of receptors (H) that can also be observed by conventional fluorescence microscopy. (mEos is the monomeric form of the photoactivatable fluorescent protein Eos.) Source.

A computer algorithm reconstructs the series of individual images into a composite that theoretically represents every fluorescently-tagged molecule within the cell. A key feature of these techniques is the low dose of activation energy. Because only one tagged molecule is activated within a relatively large area, this greatly reduces the possibility that one light source (fluorophore) masks another. In this way, single molecule (super) resolution can be achieved. Proteins can be counted and localized directly. The PALM/STORM techniques are nicely reviewed by Henriques and Mhlanga.

Recently, Greenfield et al. were the first to apply super-resolution PALM microscopy to a bacterium. The group labeled, counted, and localized components of the E. coli chemotaxis system to examine the dynamics of chemotaxis receptor clustering and localization. Both Tar, a transmembrane receptor that accounts for ~40% of all receptors inside the cell, and CheW, a response regulator that binds to all types of E. coli chemotaxis receptors, were fused with photoswitchable fluorescent proteins and imaged. Importantly, essentially the same localization pattern was obtained from each of the two fusion proteins: some single molecules, some small clusters of 10-1000 proteins, and one or two large clusters(over 1000 molecules) localized at the cell poles. The large clusters, but not the smaller ones, had also been previously seen using standard fluorescence microscopy and electron microscopy.

With the higher resolution afforded by PALM, the new data about small clusters and their subcellular location allowed the authors to directly test previously proposed models about how the chemotaxis receptor arrays localize to the poles. Specifically, they were able to address the question of whether or not an anchor is required for polar localization. Using computational modeling to accurately describe their experimental results, they provide direct evidence for a stochastic self-assembly mechanism for polar localization. No anchor required!

As this first published report of the application of PALM to bacteria demonstrates, the potential of PALM is hugely exciting! Imagine being able to see monomers of your favorite protein on their way to a specific subcellular address. How do they get there? Is the mechanism similar to the stochastic aggregation seen here? Now that we can see below the diffraction limit, we can ask if they are really co-localizing with their ‘partner.’ So many questions…and I can’t wait to learn the answers!

Jennifer is a microbiology graduate student in the Joint Doctoral Program of San Diego State University and University of California at San Diego. She works in Kit Pogliano’s lab.

Mycodiesel

This is the fourth (and final) post for this year's Week of the Fungi on STC, a sporadic undertaking. This annual festival is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

Colorized environmental SEM photo
of Gliocladium roseum. Source.

by Elio

Huge amounts of money and effort are going into making automotive fuels using biological processes, but a fully satisfactory answer is not yet at hand. Well, fungi may come to the rescue. Strobel et al. found that a fungus called Gliocladium roseum actually makes a complex mixture of volatile hydrocarbons and derivatives that resemble those found in diesel fuels. Not only that, this fungus decomposes cellulose without needing any help. It sounds just right, but before you talk to your broker about your Exxon Mobile stock, read on.

G. roseum culture plate. Source.

This fungus, a somewhat atypical member of its species, was found in a Northern Patagonian rainforest living as an endophyte of the tree Eucryphia cordifolia. Now, what are endophytic fungi? They are benign inhabitants of healthy plants and are quite common. Endophytic fungi are adroit chemists and make a large number of bioactive secondary metabolites. The most famous among these is the anticancer drug taxol, which is widely used in treatment. Incidentally, taxol can be isolated from both the plant and its fungi, suggesting the horizontal transfer of genes between them.

Source.

The problem with turning G. roseum into a fuel machine is that it grows slowly and its rate of production is far from overwhelming. However, who is to say that further work on this and other strains may not lead to significant improvements in production.

There may even be more to the story, as fungi may have participated in making petroleum and its products. To let the authors explain: In view of this work, perhaps it is not unreasonable to speculate that some hydrocarbons in the earth’s upper mantle may have arisen via the fermentation of plant material by fungi under conditions of limited oxygen. The endophytic microbes may be the first ones involved in the disintegration and utilization of plant material since, by definition, they are located in the plant tissues at the time of the demise of the plant.

How did these investigators come upon this unusual finding? What were they looking for? You may well find out by listening to a podcast in which Dr. Strobel talks about that.

Merry comments

When Strobel's paper was published last year, it was enthusiastically touted as reassurance that biofuel solutions are on the near horizon that will seemlessly replace fossil fuels and related petrochemicals. (Google "mycodiesel" and pick from the ~40,000 hits.) "Fill 'er up with mycodiesel" was the cry. While undoubtedly many biofuel options will prove useful at some scales, in some locales, at some point in time, significant issues arise when contemplating meeting the world's current energy needs in this fashion.

Let's assume for the sake of argument that, indeed, Strobel or others can grab the genes encoding the mycodiesel metabolic pathway, engineer them into a tractable microbe, and set up large-scale production. Among the many points that could be questioned, I'll focus on just one: the carbon input required. Strobel has a ready answer: the fungus can use cellulose. "That's the most common organic molecule on earth," he said. "It's all around us, everywhere."

Input could be grown as crops, which would potentially impact food supplies and costs, and could also increase greenhouse gas emissions. Or we could use agricultural or logging "wastes," thus accelerating the mining of our soils leading to further reductions in productivity. Again, it is a matter of scale.

To put this in perspective, consider how much of the photosynthetic output of terrestial ecosystems we already are using—in addition to our consumption of prior primary production in the form of fossil fuels. Currently, best estimates of HANPP (human appropriation of net primary production) stand a bit above 20%, with some oft-quoted values reaching as high as 40%. "People use this material directly or indirectly, it flows to different consumers and decomposers than it otherwise would, or it is lost because of human-caused changes in land use." (Source) "This is a remarkable level of co-option for a species that represents roughly 0.5% of the total heterotroph biomass on Earth."

The take home lesson here, stated in the most restrained and diplomatic of terms by Haberl: "An obvious implication of HANPP is that growth in the amount of biomass used by humans for their socio-economic metabolism must be envisaged with caution."

Fungal Stars in the Forest Dark

This is the third post for this year's Week of the Fungi on STC, a sporadic undertaking. This annual festival is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

Mycena lux-coeli, a Japanese fungus
photographed by its own light. Source.

by Elio

Fungi, along with selected bacteria and invertebrates, are included in the list of bioluminescent organisms. These fungi are pretty unique because, unlike the other light-emitting organisms, fungi don't walk, swim, or fly. Thus, the usual explanations for bioluminescence (e.g., attraction, repulsion, communication) do not seem to apply. Dispersing spores is a central preoccupation among mushrooms, so one can guess that the light may facilitate visits by animals that could help in this process. Plus, as Dennis Desjardin writes in a news item from the NSF, some may well glow to attract the predators of insects that eat the mushrooms...befriend the enemy of your enemy!

Mycena lucentipes, a Brazilian mushroom
photographed by its own light. Source.

So far, only 65 of the 85,000 species of fungi are known to glow. Looking for new bioluminescent species is something one does under the cloak of darkness and, in Desjardin's case, in deep Brazilian jungles. Just how you avoid getting bitten by who knows who, and, more importantly, how you keep from getting lost, is something that you need to read for yourself in this article. While you are worrying about that, ponder these other questions posed by the author: Why are there so few luminescent fungi? What is the mechanism of luminescence? When and how many times did luminescence evolve in the fungi? Why do they glow?”

A Thing of Beauty

This is the second post for this year's Week of the Fungi on STC, a sporadic undertaking. This annual festival is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

The entombed springtail with numerous
conidiophores. Source.

by Elio

A thing of beauty is a joy for ever:
Its loveliness increases; it will never
Pass into nothingness…

      from Endymoin, by John Keats (1878)

Close-up of the conidiophores. Bar = 50 μm.
Source.

We can attest to these truths through a lone piece of amber. Between 50 and 35 million years ago, a springtail (Collembola) got stuck in some resin, probably from a conifer. Before it could free itself, more resin dripped on it, eventually entombing it completely. In time, the resin became amber, but before that happened, a fungus grew on the insect's cadaver, sprouting numerous spore-bearing structures (conidiophores). Fortunately, this piece of amber found its way to two paleomycologists, Heinrich Dörfelt and Alexander Schmidt, who readily identified the fungus as a member of the genus Aspergillus.

Amber has served up other fascinating glimpses of ancient fungi, including the oldest known fossil mushroom entrapped 100 million years ago. However, the preservation of these conidiophores is stunning, probably unmatched by any other piece of amber containing fungal material. The likely reason is that the fungus did indeed sprout these structures after the insect’s burial in the thick-but-still-liquid resin. Otherwise, little would have been preserved of its natural shape.

An especially illuminating article on the same subject by Cornell student Christine Layton appeared in the famed Cornell Mushroom Blog.

(right) A single conidiophore showing the radial chains of spores typical of Aspergillus. Bar = 50 μm. Source.

Myco-kleptomaniacs

This is the second annual Week of the Fungi on STC, a sporadic undertaking. It is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

by Elio

SEM micrograph of adult southern pine beetle. The
arrow indicates the location of a mycangium. Source.

Anyone who has gone out hunting for wild mushrooms and came back with a nearly empty basket has been tempted to "borrow" specimens from someone more lucky. This cardinal sin now has a name: mycoklepty.

Stealing fungi is not limited to humans. Beetles do it too. A graduate student at Michigan State, Jiri Hulcr, observed that small bark beetles in the forests of Papua New Guinea were consistently found in proximity of larger ones. These beetles make galleries in the bark of trees and, in this case, those made by these two particular beetle species, the larger and the smaller, were always adjacent to each other. How come?

First, something more about these beetles. Like leaf-cutting ants and termites, these insects depend on fungi for sustenance. They sow spores of specific fungi in the tunnels they make into the sapwood of healthy trees. The spores germinate, the fungus grows into a glistening mat known as "ambrosia," Food of the Gods. This ambrosia is Food of the Beetles. A pioneer student of these insects, H. G. Hubbard, wrote in 1897: All the growing parts of the fungus are extremely succulent and tender. The young larvae nip off the tender tips as calves crop the heads of clover, but the older larvae and the adult beetles eat the whole structure down to the base, from which it soon springs up afresh, appearing in white tesselations upon the walls. The growth of ambrosia may be compared to asparagus, which remains succulent and edible only when continually cropped, but if allowed to go to seed is no longer useful as food. The fungi provide the beetle not only with all nutrients but also with the steroids needed to make the hormones that regulate the beetle's metamorphosis, a most unusual relationship between nutrition and development.

Observing the beetle habits in Papua New Guinea, Hulcr suspected that the smaller beetles were sponging off the larger species rather than collecting and hauling their own spores. To check this out, he looked closely at their anatomy. Sure enough, the smaller species lacks a specialized fungus spore-carrying structure called a mycangium. Furthermore, DNA analysis of the fungi found in the galleries of the two kinds of beetles matched, leading to the conclusion that the smaller beetles did indeed appropriate their fungi from the larger ones. Mycoklepty indeed!