Captured in this time-lapse video taken by one Nick Lariontsev (see here for pictures of the camera setup) is a sampler of fungal growth. In a few cases, it begins with single spores, which would require higher magnification to see. Then, individual fungal threads, or hyphae, sprout and branch in all directions, crossing and recrossing each other. Finally, the group of hyphae becomes a full-fledged mycelium (my-SEAL-ee-um), and then inflates or pinches off certain tips to make spores and sporangia, or spore houses. When the mold changes color from a distance, it is because it is producing colored spores with sunscreen.

You should think of these white fuzzy masses not in sterile petri plates, but in nature. When you turn over a log and see a white mat underneath, you are seeing these filaments. When a fungus attacks a tree, the filaments infiltrate the tree’s cells with a prickly, probing fingers. And when a fungus partners with a tree as a mycorhiza, its hyphae (high-fee) wrap around or penetrate the root — all the way through cell walls to the cell membranes, where they stop so as not to harm the tree. And of course, when takeout spends a bit too long at the Frigidaire spa, it too feels the caress of fungi.

Finally, you see fungus mites briefly at about 3:22, and then again at the very end, where they’re mowing down mold like cows that got into the corn field. In the comments at César’s post, Psi Wavefunction comments that in order to terrorize a mycologist, all one has to do is point and shout “fungus mite!”. I don’t recall every having troubles with them when I was in school, but I can easily believe it. I’ve had enough trouble with aphids and powdery mildews on my plants . . .

Mites are arachnids like spiders and ticks. In fact, mites are in the same taxon (Acari) as ticks. Here’s a close-up of the fungus mites featured in our film:

Courtesy U.S. Department of Agriculture

As for the molds, I don’t know which mold species are which, exactly, except that the tiny black pinheads are probably Mucor, and the grey stuff is likely Botrytis. But for what it’s worth, here are close-ups of conidiophores and conidia (asexual spore houses and spores) of the fungi the author names in the notes as the subjects of the film. All of these molds are extremely common in the environment. Odds are you are breathing in a few of their spores at this very moment. And it’s not cause for panic. Mold spores are everywhere.

Aspergillus fumigatus

Courtesty CDC

Botrytis sp. — so named for the grape-like clusters of spores, and also called “grey mold” for its outward appearance. Ironically, it is also used to produce extremely sweet dessert wines referred to as “Botrytized”. The Germans call it “Trockenbeerenauslese”. Of course.

Creative Commons ninjatacoshell. Click for link.

Mucor — the only zygomycete here. Conidia are housed in a sporangium that looks like a Q-tip (sorry — “cotton swab”).

US Department of Agriculture, Agricultural Research Service, Systematic Botany and Mycology Laboratory

Trichoderma. Conidia (asexual spores) are at tips of “phialades”. They blow them up like balloons. In the photo below you can see them in various stages of inflation.

Courtesy U.S. Department of Agriculture

Cladosporium

Creative Commons keisotyo. Click for link.

First, a refresher. Lichens are fungus/algal collectives in which it may be a partnership or may be something more sinister on the part of the fungus. The algae are trapped in tangles of fungal filaments and sandwiched between two protective cortices (sing. cortex). To whit:

A and D are the upper and lower cortices. B is the algal layer. C is the medulla. And E are the root-like structures called rhizines. For you botanists out there, this should remind you of something — the cross section of a leaf. Convergent evolution in action again, my friends.

The algae photosynthesize and make the food. The fungus provides a place to live that protects the algae from death by dryness and sometimes provides sunscreen. Though “lichen usually” means one fungus and one alga (conservatives would be happy), it sometimes means one fungus and a few algae (not so happy). The following is one such case.

Here we have the common freckle pelt, Peltigera apthosa. These things can range from bright green when they’re wet to greyish brown when dry and sad. In most of the lichen, the green eukaryotic (nucleated) algae Coccomyxa

Photo by Oregon State University

holds sway, but the second spouse photosymbiont Nostoc

Creative Commons Kristian Peters

gets its own little house (the freckles on the freckle pelt in the photo above, also called cephalodia) because apparently partner 1 and partner 2 don’t play nicely together. Notice the bigger cells in the chains of the cyanobacterium Nostoc. Those are called heterocysts and those particular cells can do something most living things cannot: fix nitrogen. Something like 70% of the air you breathe is nitrogen (N2) but turning it into a form living things can use (like NH4, ammonia) is difficult.

Thus nitrogen is a limiting nutrient in most biological systems, and creatures that can make it get extra street cred and often special cushy living arrangements. The nitrogen-fixing bacteria that live with legumes are one such case (thus the invention of crop rotation to keep fields fertile), and so can Nostoc. Hence the quirky living arrangements in Peltigera. If someone made a TV show about this thing, it would have to be called “Big Lichen”. When reached for comment, Coccomyxa admitted the relationship was strange but said it was sometimes fun to sneak out for algae-nights-out with Nostoc and that having more than one alga in the relationship really helped relieve the pressure to put out glucose. But I digress.

The reddish-brown curvy things on the common freckle pelt are the apothecia, or disc-like reproductive strucutres of the fungus. This is where the fungus half of the lichen gets busy, making its ascopores (sexual spores) in sac-like structures called asci (ass-eye). Here’s a cross section of one in an un-lichenized cup fungus:

So these little cups, or apothecia, are a visible demonstration that a fungus is part of the lichen mix.

Here’s our next subject:

This is Leprocaulon — the “cottonthread lichens” –– either Leprocaulon gracilescens or Leprocaulon subalbicans, probably the former. I had never seen this lichen before in my life and it was an odd one. Ann described it as being “barely lichenized”, and it is a collecting of threadlike granular fibers that stand up from the surface they’re growing on by a centimeter or so. It’s soft. Really soft. The upright fibers move back and forth easily, and when I gave it a pet it was not unlike touching dryer lint. Not like the typical crusty, papery, or fibery lichen at all.

The next two lichens got me really excited.

These dark patches are jelly lichens, and they are what happens when Nostoc rules the roost. I’m not sure of the genus, but it may be Collema or Leptogium. Their fungi are monogamously lichenized to cyanobacteria, and this gelatinous, brown mass is the result. True to their name, they were rubbery and fun to squish gently between the fingers. Interestingly, when Nostoc makes giant colonies of itself on its own, it doesn’t look much different.

Creative Commons Lairich Rig

So I guess we know who’s wearing the pants in this relationship.

Next we have what Ann called the most spectacular lichen in Colorado, and I agree. To give you a sense of scale, I could easily sit on the rock in the center of this photo.

This is rock tripe, also called Umbilicaria americana. It is unique to our hemisphere. Generally speaking, when the rock looks like its gotten a really bad sunburn and is sloughing its skin, that’s rock tripe. I think it’s called tripe because it was what one could eat when there was nothing better left. True to its generic name, it is an umbilicate lichen. You had an umbilicus once too; it attached you to your mother. Umbilicaria keeps its umbilicus thorughout life. It attaches it to its substrate — in this case, a rock. Look carefully at the photo below. This Umbilicaria is about three or four inches across, or more than 15 cm. The white raised portion overlies the umbilicus underneath.

You probably wouldn’t guess it from looking, but the underside is pitch black and fuzzy.

And, of course, something has found a way to rain on even Umbilicaria‘s parade.

It’s another lichen growing on top of it. This reminds me of one of my favorite lines from Jurassic Park: “Life finds a way.” (although obviously, not always, or we wouldn’t be facing an extinction crisis of staggering proportions that makes me feel both blindingly angry and supremely helpless).

Speaking of de-motivational events, on our way out, we saw this:

Yes, those are two giant sets of bear claw scratch marks on that tree. Though bears aren’t known to eat lichens, I believe they are known to eat hikers. Time to go find some hot chocolate . . .

Rozella sp., a previously discovered internally parasitic cryptomycete totally devoid of a chitin cell wall. I think they're the brown truffley balls. Click to enlarge. Creative Commons Timothy Y. James. License at http://tolweb.org/Rozella_spp./103935

To listen to news reports, you might have thought the big news was that the fungi have an interesting new set of oddball relatives. But these news reports completely missed what I consider the most earth-shattering news in the paper in Nature announcing the discovery, cleverly hidden at the end of this sentence:

Our analyses also recovered a highly diverse clade of environmental sequences branching with the fungi and demonstrated that current models of fungal evolution and biodiversity, which are largely based on cultured microbes, have missed a huge fraction of the kingdom (perhaps even approaching half).

Wait– hold up. HALF?!! Thus, the news isn’t that there’s some new oddball fungal relatives out there. It’s that the new oddball fungal relatives may make up half of Kingdom Fungi. And the first sample of this huge, undiscovered and massively diverse group came from none other than one of the scientists’ very own university pond. In spite of our best efforts to survey life, we had virtually no idea these things were out there — in virtually every environment we have now looked.

To understand how we may have been ignorant of half of Kingdom Fungi, you must think back to the time before DNA. To discover new life that couldn’t be seen with a hand lens, you had two options:

1. Take some dirt or water. Wash and dump said sample onto a microscope slide. Apply various dyes as desired. Squash under coverslip. Place under microscope and stare intensely, searching for something that might be alive. Repeat thousands of times. See doctor about eyestrain.
2. Take some dirt or water. Dump said sample into a petri dish containing some food-like substance. Wait. Pray the smell is not too bad. Place sample of stuff that grows on microscope slide. Squash under coverslip. Place under microscope and stare at similar-looking blobs. Repeat thousands of times. See doctor about eyestrain.

As you can see, this system left a lot to be desired. And it’s how hundreds of groups of organisms got mis-classified with other groups, because all biologists had to go on was the way the microbes looked and — in some cases, behaved — under a microscope. In addition, many groups of life on Earth are not culturable in a petri dish, or have evolved to look and behave in very similar ways, regardless of their ancestry.

Enter DNA. With this molecule, we can detect true heredity by comparing how the unique sequence of four letters in the code have gradually changed over time in related organisms. With millions of positions for letters in a defined order (like a cryptokey or license plate), it is easy to tell who is related to who and what is unique. By doing massive sampling of all the DNA in the environment, we can now easily sample for and pick out new variations of known genes (and the new organisms they must represent) in dirt and water samples, because they will look unique even if the organisms that make them do not*. And we can compare those new sequences** to sequences of organisms whose appearances and taxonomies we understand — in this case, a broad selection of fungi and their closest relatives.

AND we can use sequences unique to new groups as organismal metal detectors (scientists call them “probes”) to finger them under the microscope so we can see what they actually look like. Since DNA is a pair of complementary strands that bind to each other, you can make a probe that’s complementary to the particular sequence you’re looking for*** and attach that bit of DNA to a fluorescent molecule. Then you stick it in your hopelessly confusing sample of water or dirt and turn out the lights. Voila! Your organism lights up like a Christmas tree! No more eyestrain.

And that is just what a group of enterprising mycologists did. Biologists have sampled many different environments for DNA from all sources. In this study, scientists accessed online records of those sequences and looked for any that seemed to fit in with the fungi. They were in for a shock. As it turned out, there was an enormous group of organisms that branched with the fungi, that apparently no one had ever seen or cultured before, with the exception of one genus. Here is what they found:

This figure is actually much simpler than it looks. All the branches at the top with the colored dots represent organisms new to science in the new group, dubbed the “Cryptomycota”, or “hidden fungi”. There is one exception: a group of strange parasites called Rozella, which was already known. Everything else with the exception of the “opisthokont outgroup” — the group most closely related to Cryptomycetes and Fungi — are organisms from the known Kingdom Fungi. The rainbow of colors give you a feel for all the environments from which they found this new group. The only place they did not find cryptomycetes was seawater, although they did find them in mud on the seabed. The branch lengths should give you a feel for the diversity. It is incredible. The breadth of ribosomal DNA molecular diversity shown in they cryptomycetes here is similar to that of the known fungal kingdom.

What did these critters look like once fluorescently tagged by DNA? So far, the cells found in samples were 3-5 micrometers long — not much bigger than bacteria — and capable of making a microtubule-based flagellum like other good eukaryotes. In two of the three groups of cyrptomycetes they studied with probes, they found more than half of the cells had single flagella. Other, non-flagellate examples seemed to like latching onto — of all things — diatoms, the algae that make glass pillbox houses in a blinding array of uber-cute shapes. In addition, though they clearly group with the fungi, the Cryptomyctes — including Rozella — lack a very important marker of fungus-hood: they have no chitin/cellulose-rich cell wall.

For fungi as we know it, this is about as elemental as it gets. Their distinctive tubular, chitinous cell walls have enabled them to infiltrate a variety of foodstuffs that other creatures cannot and digest them osmotically. That is, grow into food that is concentrated in sugars or other nutrients that would make other cells shrivel up and die thanks to osmosis if they attempted it. We humans exploit this effect to preserve our food. Pickles, preserves, and peanut butter are so rich in salt, sugar, and general osmotic potential respectively that no bacteria or fungi can survive. But in nature, there’s a gray area where only fungi are bold enough to tread. They grow into their food (i.e. log, leaf, leftovers, etc.) They excrete digestive enzymes. They absorb the resulting goo. Life is good.

But the cryptomycetes have no such chitinous cell wall. The researchers know this because they stained the cells that probes identified as cryptomycetes with chemicals that bind to chitin and cellulose, the stuff of fungal cell walls, and they lit up like a Christmas tree during a power outage. Which is to say, they did not.

This is a problem for our definition of Fungi. As I learned it, to be a fungus requires five things:

• you are eukaryotic (you have a nucleus where you keep your DNA and various other cute organelles orbiting it)
• you are heterotrophic (you get food by taking it, rather than making it)
• you are absorptive (we already covered this)
• you reproduce with spores (a much better method than that used by mammals, IMO)
  
• you possess a tubular body with a chitin cell wall

Yeast are somewhat exceptions to these last two; they are spherical and reproduce by budding. But they do not make up the majority of the fungi, by far, and so far, no one has ever bucked the chitin rule.

Hmmmm.

This brings us to the real questions wrought by this study: Are the Cryptomycota truly fungi? Or are they a larger group to which the fungi belong? Or are they a sister group of fungi? Did they ever have chitin cell walls or have they lost them? Are there vestiges of chitin in ephemeral life stages the researchers may have missed? There has already been some commentary on these questions in the comments here. We may learn a lot about the evolution of fungi based on the answers. One thing seems clear: if we decide they are “Fungi”, our definition — and our perceptions of the group — must change.

Aside from these important questions, we also have the delicious prospect of discovering how the contents of this new clade — the Cryptomycota — look and behave. There is almost no telling what we might find among some of the more eccentric members, though based on their fluorescence experiments so far, the paper’s authors suggest a saprophytic or parasitic lifestyle for the majority of species based on what they’ve actually seen under the microscope: a free swimming zoospore stage with a single tail, a resting cyst stage, and period of attachment and feasting upon a “second-party cell”, a.k.a. a helpless diatomic host or rotting microbial corpse (like leeches — or hyenas). But the group is so genetically diverse there are probably many, many ways of life. Based on what we know of the fungi, the authors suggest, there may be many life stages and accessories yet to discover: germ tubes, root-like food-harvesting devices called rhizoids, and spore-making houses called sporangia, filter-feeding structures, DirectTV dishes, etc.

Without a cell wall, they may even be phagocytic — that is, able to engulf, swallow, and digest prey internally. Outside the Cryptomycota, fungi’s closest sister group is the nucleariids, a group of amoebae with filamentous (hmmm . . . ) pseudopods that feed, as amoebae do, by phagocytosis. Makes a girl think.

As the biologists say, this is an exciting time to study life. When reports like this come along, I feel a bit like a mapmaker in 16th Century Portugal hungrily studying the blank spots on the map. Can’t. Wait.

_________________________________________________________________

* because those groups will have two very different evolutionary histories, and thus, genetic patterns.

** in this case, of ribosomal RNA genes, a commonly sampled subject because they change so slowly and are present in everything

*** in this study, they used ten 18-base pair long clade-specific probes for taxonomic analysis fluorescent tagging purposes

Jones MD, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, & Richards TA (2011). Discovery of novel intermediate forms redefines the fungal tree of life. Nature PMID: 21562490

The Many Ways to Be a Fungus (in Colorado) from Jennifer Frazer on Vimeo.

Creative Commons Jeans_photos, photo by Fred Hort. Click for link to license.

In 1928, a farmer in Western Australia named Jack Trott was plowing a field newly carved from the Outback by fire. An unusual crack in the soil caught his attention. In it was something extraordinary — a sweet-smelling pallid little flower of the first known completely subterranean plant: the Western Underground Orchid, Rhizanthella gardneri*.

Strange things are known to lurk under Australia’s soils (these come once again to mind), and these flowers must surely be counted among their ranks (although not perhaps for much longer — fewer than 50 individuals are known to exist). Obviously, living your entire life underground is weird for a group of organisms (i.e., plants) known for its sun worship. True to their underground creds, these orchids never break the surface. Or rather, they do break it (crack it, usually), but they never break on through, in the Doors-ensian sense. The flowers form within a few inches of the surface, but get no further. The sweet smell is clearly a lure for pollinators — identity still TBD — to their underground digs.

As orchids go, they are odd in in that their “flower” is actually a cluster of flowers in a cup called a “capitulum”, or “little head”. If you look at the picture, you’ll see a bunch of upside-down teardrop shapes; those are the flowers, in which orchid afficianados can no doubt see a faint resemblance to more conventional orchids that this “flower” as a whole quite lacks.

But also weird for orchids, these flowers subvert the usual fungus-orchid BFF relationship. Many, if not most orchids, have what is usually euphemistically termed an “intimate” relationship with fungi. That starts on day one: germination. Orchids are notoriously difficult to start from seed because they store no food of their own and must be in the presence of their preferred fungal partner — under Goldilocks conditions — to sprout. For most wild orchids, your best source of information on what that fungus and those conditions might be would be your nearest Magic 8-Ball.

Not actually natural size (anymore).

Most photosynthetic, self-sufficient orchids seem to associate with saprophytic or parasitic fungi. But R. gardneri has found a different niche: myco-heterotrophy, or exploiting the mycorrhizal fungi of other plants. In this case, it gets all up in the business of the fungal partners of Melaleuca uncinata, the broom bush. Mycorrhizae are fungi that encase or invade the roots of nearly every land plant. This is good; without them, plants would have a considerably rougher go of it. The usual exchange is sun-made plant glucose in exchange for a vastly improved water and mineral uptake thanks to the exponential surface area increase made possible by a network of fungal filaments extending well beyond the roots. Mycoheterotrophic plants break into the mycorrhizal associaton of a fungus and another plant and steal some of the goodies for themselves.

R. gardneri is not the first plant to have figured this sweet deal out. Here in Colorado there are at least two pale pink spiky plants terrorize our fungi: the Heath-family pinedrops, and the Orchid-family spotted coralroot. I often see pinedrops and spotted coralroot on hikes in the mountains, where the former associates with (probably parasitizes) mycorrhizal truffle fungi in the genus Rhizopogon (related to the bolete genus Suillus for those who care) and the latter goes after mycorrhizal Russula, which make the majority of the red-capped, white-stalked (and usually poisonous and/or disgusting) mushrooms found in the temperate forest.  I wrote about another Heath-family floral parasite that I used to encounter often here. In spite of exceptions like pinedrops, almost all mycoheterotrophs are orchids.

In all these cases, these plants have lost their chlorophyll. But none have taken the admittedly drastic step (for a plant) of entirely forsaking wind and rain, sun and cloud.

Chloroplasts: Not Just for Photosynthesis Anymore

The Western Underground Orchid has, and in the process, has gone farther toward forsaking its planthood (if its planthood can be tied to the vir(d)ility of its chloroplasts — the cell bits responsible for photosynthesis) than any other plant.

Chloroplasts — as first understood with genius by Lynn Margulis — are what remains of a fateful meal billions of years ago. A bigger cell engulfed a smaller photosynthetic one, probably a cyanobacterium, or blue-green alga. But the alga didn’t go quietly. It managed to survive and thrive in its would-be predator. It became its partner instead. Already in that cell were the remains of bacterial cells who had long ago struck a similar bargain: mitochondria, the power-packs of the cell. You have these ancient bacteria still in nearly every cell of your body. Plants have both mitochondria (which is how we know that endosymbiotic event happened first) and chloroplasts, the descendants of the world’s luckiest alga. And both still have DNA, the remains of their bacterial chromosomes.

Chloroplasts inside a true moss -- each one a descendant of an alga that gave a predatory cell indigestion billions of years ago. Its offspring (and that of a few other lucky photosynthetic microbes cum organelles) blanket the planet. Creative Commons Krisitian Peters, click image for license link.

But in R. gardneri, 70% of its expected chloroplast genes are gone, according to a new paper in Molecular Biology and Evolution. And the total length of the R. gardneri’s chloroplast chromosome (which is still circular like all most good bacteria) is just 59,190 base pairs, also the smallest for a land plant on record.

Chloroplasts are where the proteins and other cogs of photosynthesis are manufactured. They’re where photosynthesis takes place too. But it seems that even chloroplasts must have some functions in the cell aside from harnessing light. Because Rhizanthella has gone as far as any plant in ditching their chloroplasts since they spend their entire lives underground, ensuring zero photosynthesis takes place. So maybe the news isn’t that they’ve shed 70 % of their chloroplasts genes. It’s that they still have 30% of them. What are those genes still doing there? And what can they tell us about how other parasites operate?

Even in your garden-variety plant, the chloroplast genome is sharply reduced compared to its cyanobacterial ancestor. When a cell goes from going it solo to living in a co-op, there’s a lot of genes it doesn’t pay to make in-house. There may be genes already doing the same thing in the host cell’s nucleus, or just not usable from inside another cell anymore. Over time, natural selection will prune these genes away, since they are costly to make if not being used. Other genes, perhaps because it’s more efficient to regulate and transcribe them there, get shuttled to and permanently housed in the nucleus. What’s left is chiefly what’s essential for the business of turning light into sugar, Job #1 for the choroplast.

But in Rhizanthella, which has clearly boarded up the photosynthetic apparatus, there remain 37 genes coding for 20 proteins, 4 ribosomal RNAs (an important constituent of ribosomes), and 9 transfer RNAs (essential tools for turning RNA into proteins within the ribosome; they ferry the appropriate amino acid to the appropriate RNA codon). Scientists checked DNA made from the messenger RNA they found in the chloroplasts; they were all being spliced and edited correctly, implying they were, in fact, still being used, in spite of the strip mining of the rest of the genome.

Toxoplasma gondii motherships constructing new invasion craft. Creative Commons Ke Hu and John Murray. Click image for license link.

Compare those 37 genes to a standard photosynthetic orchid, in this case Phalaenopsis aphrodite, whose chloroplast genome has 110 genes. Even the parasite Toxoplasma gondii, notorious for its mind-control abilities (which chiefly involve making hosts — including accidental hosts like humans — do risky things to increase their odds of predation, or from the parasite’s point of view, getting to the next host), actually seems to have been photosynthetic in a previous life, and even it still contains 53 genes on its presumed remnant chloroplast genome, according to the authors.

Thus ex-photosynthetic plants of all sorts seem to share a minimum set of chloroplast genes, and they must be doing so because the chloroplast performs some sort of important non-photosynthetic function that can’t be transferred to the nucleus.

In fact, the scientists compared the reduced gene sets found in parasite ex-chloroplasts from a variety of groups. As mentioned above, they found strong similarities, suggesting that when photosynthetic parasites of any ancestry — related or not — give up free-living, they tend to lose and retain the same sorts of chloroplast genes. This knowledge could provide us with lines of attack in ex-photosythetic parasites that go after us or our crops or livestock. The bare-bones Rhizanthella genes could tell us which genes are most essential — and thus the best targets.

Thanks to convergent evolution, loss of similar genes in parasitic chloroplasts makes it look like Toxoplasma gondii (cause of Toxoplasmosis in humans and cats) is closely related to the plant parasites beechdrops and Western Underground Orchid. Ummm, no.

But wait. Does that mean the chloroplast — the sugar-making machine of plants — does things other than just photosynthesize? Yes. And parasitic plants like R. gardneri are how we know what those things are.

Of the genes that are left on the R. gardneri chloroplast genome, almost all of them encode proteins needed for translation (getting from RNA to protein). Five of the remaining transfer RNAs seem to have remained because either they must interact with many other chloroplast proteins and versions from the main cell would not necessarily recognize the appropriate proteins, or because they have quirky physical modifications that make the chloroplast translation machinery unable to recognize their cellular equivalents. In other words, for these genes, evolution’s backed itself into a corner it’s not easy to get out of with simple chance mutation and natural selection, so instead, it preserves the status quo.

But all these translation-related genes are probably still there for a larger reason: they are necessary to translate the four remaining non-translation related genes on the genome: one making a protein essential for membrane synthesis and two others likely involved in making it, and a fourth gene that makes a protein that seems to have a hand in a variety of important plant processes, at least one of which must be essential. Mutations in the chloroplast’s translation genes are probably fatal because the chloroplast can then no longer make this handful of genes.

Why must these four genes be expressed in the chloroplast and not in the nucleus? The authors hypothesize it has to something to do with a wonderfully vague term called “control by epistasy of synthesis”. As far as I can tell, that means the compartmentalization of these proteins in the chloroplast is essential to their proper synthesis and integration into large protein complexes. So there you have it: the chloroplast may stick around in parasitic plants because it’s handy as a clean manufacturing facility for making parts of a few complicated proteins.

________________________________________________________

* According to the poster of the flickr photograph I used to illustrate this post, Trott donated his specimen to an herbarium for identification and offered £100 to anyone who could find another. Although many looked, none was found until 1979, the year after Trott died. His widow, however, paid up.

Delannoy E, Fujii S, des Francs CC, Brundrett M, & Small I (2011). Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes. Molecular biology and evolution PMID: 21289370

A microsporidian like this is one-half of the perp identified as the cause of Honeybee Colony Collapse Disorder. This isn't the exact species, but is instead another microsporidian called Fibrillanosema that infects amphipods. Neat rows of polar filament cross sections line either side like cannon on a British Man o' War. In 3D, these coil around in a big spiral. Creative Commons Leon White

For the last several years, honeybee colonies have been emptying out like keggers at which the cops have arrived — and the bees show every sign of being just as out of it as drunk college kids. They abandon their hives to die alone and cold in the wild, striking a huge blow to North American apiculture and, until now, anyway, leaving everyone scratching their heads.

Well, no longer. Though early reports identified an Israeli virus as one possible cause, a serendipitous bioinformatics project taken on by, of all people, the military, along with Montana researchers, has identified a dual cause of colony collapse: a previously unidentified DNA-virus, and a fungus called Nosema ceranae.

For those who’ve been paying attention, a Nosema parasite of bees has been around quite a long time — Nosema apis. But the new species, Nosema ceranae, appears to have come from Asia. Is this yet another introduced species decimation story? ( See Elm, American; Chestnut, American; and White Pine, Western) Or did we just never notice it here before? (the species can only be separated by DNA or scanning electron microscope — not by light microscope) Too early to tell. And still, no one knows what the fungus and virus combo is doing to make the bees lose it:

Still unsolved is what makes the bees fly off into the wild yonder at the point of death. One theory, Dr. Bromenshenk said, is that the viral-fungal combination disrupts memory or navigating skills and the bees simply get lost. Another possibility, he said, is a kind of insect insanity.

Translation: Zombification, a well known problem for insects under the influence of parasites (see Parasitoid wasps, and Cordyceps fungi)

Here’s the critical bit from the NYT article announcing the discovery:

Dr. Bromenshenk’s team at the University of Montana and Montana State University in Bozeman, working with the Army’s Edgewood Chemical Biological Center northeast of Baltimore, said in their jointly written paper that the virus-fungus one-two punch was found in every killed colony the group studied. Neither agent alone seems able to devastate; together, the research suggests, they are 100 percent fatal.

Since a 100 percent correlation seems pretty convincing, so let’s go with the assumption these guys are right for now. And since the virus is as yet unidentified and undescribed, let’s take a bit of a closer look at Nosema. Because Nosema is interesting. Really interesting. As recently as 10 years ago this group of organisms — colloquially known as microsporidia — was classified with next to Giardia, the most ancestral (aka primitive) nucleated (aka eukaryotic) organism known. Seriously. This would be like putting Homo sapiens at the base of the eukaryotic family tree*, because it turns out Nosema is a seriously evolved fungus.   And in this case, as you’ll see, that crucial bit of taxonomic information makes a big practical difference in attacking this problem.

Microsporidians are all single-celled parasites that can infect nearly any eukaryotic host, but most have specialized on insects. They have a bunch of crazy standard features. First off, Nosema has no mitochondria, which is usually a requirement for self-respecting nucleated cells. Such nucleated cells, called the eukaryotes — or all life that isn’t bacteria or the similar looking archaea — employ tiny intra-cellular organelles called mitochondria to make energy using food and oxygen in the air. For the purposes of this post, we will ignore mitochondria’s fascinating origin story and incredible biochemical gymnastics and simply focus on the utter necessity of these organelles to the business of being alive for air-breathing eukaryotes (cyanide is fatal because it stops up the energy-producing works inside mitochondria), and how utterly strange it is that the otherwise unrelated groups of microsporidia, the parasite Giardia, and the amoebic parasite Entamoeba histolytica all lack them.

Instead, they possess an organelle called a mitosome, which seems to be a vestigial mitochondrion — that is, what’s left after the mitochondria are no longer necessary for cell upkeep and they start to degenerate to save the organism energy. Another example of vestigial and remnant structures might be the tiny leg bones still produced inside some snakes and whales — though these creatures’ ancestors stopped using their legs millennia ago, there is still a part a part of their genome that makes a much reduced and apparently energetically inconsequential vestige of them.

The reason parasites like these can get away with dispensing with their mitochondria is that  precisely because they are parasites, they bathe in nutrients inside their host. They don’t need to breathe; their host does it for them. This seems to have happened several times in unrelated parasite groups. But because single-celled organisms possess few morphological characters, these groups were originally all placed together because they shared what few traits we could see: degenerate mitochondria (mitosomes), a double nucleus (microsporidia often have this, and Giardia always does — why is this adaptive for a parasite? No clue.), and a parasitic lifestyle. So a bunch of these funky parasites were thrown together into a classification called “archezoa“.

But someone must have studied these organisms’ DNA and found a very different story: microsporidia aren’t primitive protists, and aren’t related to Giardia and Entamoeba at all. They’re highly evolved fungi called zygomycetes — the same group that produces the bread mold Mucor and most snow molds that live at the foot of melting snowbanks that I wrote about in an August issue of High Country News. As recently as just 10 years ago, as printed in my copy of “The Variety of Life”, by Colin Tudge, they were still placed firmly at the base of the eukaryotic family tree — not near the tips of the branches, embedded in the fungi. It seems that the “archezoa” was really more of a niche than a true taxonomic grouping based on relatedness — these things evolved to occupy the same parasitic niches, and in the process, evolved similar adaptations, much as whales and fish look alike but come from very different sides of the tracks.

Zygomycetes are so called from the greek for “yoke” because they make a special sexual reproductive structure called a zygosporangium that yokes together two fungi of different mating types (=gender). As fungi, they follow the typical fungal body plan of being a bunch of thin filaments (aka mold). To look at a zygomycete, you would definitely think “fungus”. Not so with microsporidia! They tend to be single celled spores. But they also have cell walls made in part of chitin — another trait that unites the fungi.

But here’s the *really* weird thing about microsporidia. They are parasitic fungi that have evolved to look like protists and *act* like nematocytes (the stinging cells of jellyfish and anemones): Inside the spore is a coiled harpoon-like injection apparatus (go here to see it in 3D, rather than the 2D view at the top of this post) they use to get themselves into host cells. Just like nematocytes (covered in this post), the coiled “rope” of the harpoon turns inside out when the cell is triggered — and does so in less than 2 seconds. Once deployed, this long narrow filament (common size: .1-.2 micrometers in diameter by 50-500 micrometers long — click here to see one whose spring has sprung) inserts itself in a host cell and pumps the contents of the microsporidian inside. Pretty soon, the now zombified cell gets busy making little microsporidia.

Here’s the final important point, from the NYT:

They said that combination attacks in nature, like the virus and fungus involved in bee deaths, are quite common, and that one answer in protecting bee colonies might be to focus on the fungus — controllable with antifungal agents — especially when the virus is detected.

So without the taxonomic work to know these little jobbies are actually fungi and not protists, we wouldn’t know that we might have a chance of tackling the major threat to bees today with existing fungicides. Who says taxonomy is pointless?

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* OK, maybe not quite. Since Nosema is a severely reduced parasite, it’s more like putting mistletoes — severely reduced parasitic plants — down there.

Sad Stinkhorn. If only it had access to the little blue pill!

I covered a new species of African Lacy Stinkhorn in a post here before, but let’s face it: there’s no such thing as too many stinkhorn posts. For those of you who need a refresher, stinkhorns are fungi that hatch from “eggs” enveloped by a peridium (you can see the remains of the peridium at the tip of the head, or receptacle, and at the base of the stalk, above). Some brave souls profess to enjoy eating the eggs. Once the mushrooms hatch and reveal that they are, in fact, quite happy to see the world, they spread their spores by giving them that special odeur de corpse, thereby attracting flies who do the two-step in the sticky, slimy mass of spores at the tip. The flies eat some of the mess; some of the rest clings to their feet. When the flies land elsewhere (i.e. nearby soil, a garbage can, or your sleeping forehead) the spores are deposited  in a new, hopefully stinkhorn-friendly place. Then the spore germinates, and microscopic filaments called hyphae spread out through the soil to . . . I’m not exactly sure what. The one thing I cannot discover is whether stinkhorn fungi are wood rotters or symbionts (partners) with the roots of trees or other plants, the two chief fungal m.o.s.

They’re in the same general group as the gilled mushrooms, but in a special family all their own called the Phallaceae. (Fal-ace’-ee-ay) Some of their brethren are among the most striking fungi on the planet: the earth stars, earth cages, and the lacy stinkhorns, which have a demure, delicate skirt jarringly draped around the obscene fungus. This group, in turn, is in the Agaricomycetes (the mushrooms and friends) which is in turn in the Basidiomycota, which those of you who are *really* good will remember are the fungi that make their spores on club-shaped cells called basidia. Basidiomycota are one of the basic, top-level groups of fungi.

When I first spotted this particular specimen on Wednesday, it was standing tall and proud. But alas, by yesterday, it had toppled over into this sorry state. That wasn’t discouraging to a nearby retinue of flies, so perhaps the stinkhorn wasn’t so sad as I’m making out . . .

To see how the stinkhorns, et al, fit into to the life family tree, look for Phallomycetidae here. Click the arrow at left to back out, or follow the link of the group’s name to see a bit more about who they’re related to.

Little fungal bundles of joy: the sexual products (basidiospores) of the earthstar Geastrum triplex. The note in the lower left indicates that each increment on the scale bar is equal to one micrometer (the Greek letter mu is the bionerd abreviation for micrometer) -- which is one-thousandth of a millimeter. So each of these spores is 4-5 micrometers -- or 0.004 - 0.005 mm -- across. That's pretty typical for basidiospores, although the spiky spherical shape is not. Creative Commons Amadej Trnkoczy

In Killer Yeast from South America I briefly mentioned the strange sex lives of fungi, who have many different mating types instead of two genders. This, as you can imagine, makes it considerably easier to find a mate, among other advantages. My old mycology professor Kathie Hodge (who taught me just about everything I know about fungi) recently posted a more thorough exploration of the varieties of fungal sex and the implications thereof. She is a fabulous science writer too, and if you’re curious about the subject, check out her explanation “A Fungus Walks into a Singles Bar . . . “ at the Cornell Mushroom Blog. Or you could just go for the gratuitous Mutinus caninus dog stinkhorn video. Your choice. : )

The thick yeasty capsids (coats) of Cryptococcus gattii relative C. neoformans. C. gattii also has a thick capsid. CDC/Dr. Leanor Haley

It’s not every day you read about suggestions for potential health-related travel advisories to U.S. states. But such is the case for the Pacific Northwest, where an emerging fungal infection has — very unusually for fungi — begun felling otherwise healthy people. A growing number of cases of the potentially fatal disease cryptococcosis have been diagnosed in people who merely traveled to Washington, Oregon, or British Columbia.

There are several very scary things about this fungus, but foremost among them is that it a) was introduced somehow from the tropics, most likely South America/Brazil or also possibly Africa and is somehow not finding it a problem to survive in Canada; b) is actively spreading up and down the Pacific Northwest coast; c)hangs out in the environment, where it can get along apparently fine without us (and seems to particularly like the bark of and soil around trees like Eucalyptus); d) is acquired from the environment, that is, you don’t have to have contacted with an infected person or animal; e) doesn’t manifest itself symptomatically for 2-12 months after one picks it up and e) can kill otherwise healthy people.

So let’s review. This means that you can just be hiking along in the woods, minding your own business, and a few months later you’re dead. Now I’m not saying this is *common*. Only 200 people have been seriously affected in 10 years. And let’s face it, there are a lot of other things that can kill you while hiking along minding your own business, much, much quicker and more commonly than these fungi: bears, mountain lions, lightning, exposure, rockfalls, your own stupidity, deranged axe murderers, errant militias, etc. But the very fact that, like anthrax, you can pick it up for no apparent reason from the environment, and much more easily, is disturbing. (Histoplasmosis is also picked up by inhalation but it is well known you must spend time around bird or bat droppings. Aside: can you think of any other diseases that are picked up just by inhalation from the wild?)

This particular organism is Cryptococcus gattii, a relative of the Cryptoccoccus neoformans that gained some fame in infecting AIDS patients when the immune disease emerged in the ’80s. Cryptococcosis begins as a lung infection, but can progress to meningitis. C. gattii, a cousin of C. neoformans, first emerged on Vancouver Island in 1999, but in the last few years, two new strains have emerged that seem to be killing otherwise healthy people in numbers much higher than earlier strains.

There are anti-fungal drugs that can help show C. gattii the door, but the wikipedia article for C. gattii contains this ominous sentence:

Antifungals alone are often insufficient to cure C. gattii infections, and surgery to resect infected lung (lobectomy) or brain is often required.

Resectioning *brain*??! Oh hell no.

Fortunately, infection with this organism remains relatively rare, but that’s no guarantee of safety. Why? This fungus is having sex. And that is one possible origin of the two newly virulent strains that have emerged in the Pacific Northwest — and possibly the source of future, more dangerous strains. It is also possible that the two new strains were newly introduced from their tropical diversity centers. But the scientists *know* there’s a lot of C. gattii hanky-panky going on. They looked at a couple dozen genetic markers in this recent PLoS study, and compared which isolates had which markers and how they were organized in the genome. They also tried to reconstruct the evolutionary and geographic relationships between various North American isolates using these data. They found huge genetic diversity among their isolates, and that at least one north American strain came from Australia. They also that the fungus is bumping up its numbers by quick and easy asexual reproduction.

But the initial creation of the new hyper-virulent types, they concluded, was likely due to sex. Only sexual reproduction provides the opportunity for lots of large-scale genome reorganization; that’s one of sex’s main advantages. When two entire genomes get together, a process called “crossing over” takes place that allows all the various chromosomes to swap corresponding bits. The result is sometimes good, sometimes bad, but whatever the outcome, generation of diversity and evolution often happen a heck of a lot faster per generation with sex than without.

Lest you think that’s the only worrying bit, it turns out that this fungus has a rather kinky sex life. Not only is it having sex with all the other mating types (fungi often have many “genders”, which for convenience scientists refer to as “mating types”), it can also, somewhat unusually for fungi, have sex (and I mean produce viable offspring) with its own type, a process called unisexual mating. Sheesh.

So that’s what was chiefly covered in the news reports. But it turns out there’s more to this story. Because this fungus is actually a yeast — an infectious yeast. Now I know what you may be thinking: yeast are the source of everything good and worthy on Earth: fresh, crusty, heavenly leavened bread, wine, beer, soy sauce, etc. And you’re right. But that doesn’t mean there aren’t evil yeast. Nasty yeast. Parasitic yeast. Because “yeast” is a lifestyle, not a taxonomic group or single species.

The yeast you’re probably most familiar with, Saccharomyces cerevisiae, commonly called baker’s yeast, is but one fungus that has adopted this way of life. And that way of life is: forsaking multicellularity for swingin’ single cellhood. In a way, yeast have devolved (although that’s a bit misleading; it doesn’t mean they’re less adapted or successful than they were before; just that being unicellular is more like their long-ago ancestors). The standard fungal body plan today is a multicellular filament, or tube. The tube branches, and the collection of branched tubes makes up the fungal body, or cottony “mycelium” we are familiar with from the surface of refrigerator contents gone rogue. Yeast are fungi that have given up this form, and have gone back to single celled living, a bit like a protist. It would be as if all your spleen cells decided that they’d rather just go off and live on their own in pond water — they’re sick and tired of cleaning up your bloodstream, thank you very much! — and they want out of the cooperative.

But it gets more complicated than that. Some fungi can go back and forth between their normal, filamentous lifestyle and the yeast lifestyle. Histoplasmosis, mentioned earlier, can do this. In the wild, it is a brownish mycelium that lives in bird droppings and bat guano. Once inhaled and installed in your lungs, it becomes a yeast. Cryptococcus neoformans and Cryptococcus gattii are among this group too. Sometimes they are filamentous. Sometimes not.

And here’s where it gets really weird. Because yeast is a lifestyle, not a taxonomic group (like a genus or family), yeast come from all over the fungal family tree. Baker’s yeast is an ascomycete like morels and truffles. But C. gattii is . . . a yeast evolved from the jelly fungi! Jelly fungi are super-awesome amazing organisms in the basidiomyctes (a major division in the fungi, like ascomycetes, that make their sexual cells on special pronged cells called basidia) that usually decay wood and produce fantastically fun-to-touch-and-play-with fruiting bodies that are gelatinous and sometimes quite colorful.For reference, here is what one looks like:

Ascocoryne sarcoides, Photo by Daryl Thomas, Mushroom Observer. Creative Commons Attribution-Unported 3.0 license

The jelly fungus you might be familiar with, if you are familiar with one at all, is the wood ear mushroom*, Auricularia auricula, commonly used in Asian cuisines — in particular, in hot and sour soup. Again, these fungi are perfectly innocuous. Some fungi produce very different forms when they live asexually or sexually. Because they’re so different, mycologists often give the sexual form a different name from the asexual form (an explanation of whether this is a good idea and why mycologists continue the practice could take up a book). The sexual jelly fungus form of C. gattii is Filobasidiella bacillispora, although it’s not necessarily the case that the jelly form would produce a structure big enough for you to see with your naked eye. I know of no jelly fungi that can hurt you either by touch or consumption. But the yeast form of these particular fungi apparently can. Weird!

A larger question might be: what are these fungi doing in us? Are they only accidental parasites? What are they doing out in the wild when they aren’t infecting us? As they say . . . further studies are needed.

But in the meantime, the weirdness parade goes on. C. gattii has *also* been isolated from a regular menagerie of other mammals, including koalas, llamas and. . . are you ready for this? . . . dolphins. How dolphins managed to spend time frolicking in the woods (or how the fungus managed to spend time frolicking with dolphins) is a subject for another blogger.

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*According to the Wikipedia article, the Japanese name for these jelly fungi is “tree jellyfish”(!) Sometimes literal foreign phrases smack you upside the head with a perfectly obvious insight you never thought of before.

Byrnes, E., Li, W., Lewit, Y., Ma, H., Voelz, K., Ren, P., Carter, D., Chaturvedi, V., Bildfell, R., May, R., & Heitman, J. (2010). Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii Genotypes in the Northwest United States PLoS Pathogens, 6 (4) DOI: 10.1371/journal.ppat.1000850

I didn’t get any guessers. But here’s what it reminds me of: another member of the ascomycetes/mycota (which, as you *all* recall, is one of the four or five major groups of fungi, and is distinguished by the way it makes its sexual spores in microscopic sacs called asci), whose contorted cups have become the whole fruiting body and who have gone completely underground —

Tuber melanosporum, dug up and cut in half. This species is not found in the wild in the USA -- but other smaller delicious species are. Haven't invested in a truffle rake yet, though.

Yes, the black truffle. Yours for a mere 1,000-3,000 Euros per kilo in the farmer’s markets and shops of Europe. The labrynthine flesh is hypothesized to represent the final stage in an evolutionary chain that started with a simple cup (see below), morphed into a compound cup like the head of the morel, and finally became twisted and dark and moved underground, relying on its pungent odeur to get itself noticed and propagated, thereby slowly taking over Europe today, tomorrow the world! And thusly a 30’s era radio villain is born:”The Black Truffle!”

So that single crazy morel shows how a mutation or two (should that be the cause of the odd shape, and should it be inheritable by the morel’s offspring) can get you from one form to the other rather quickly, and that evolution needn’t take millions or even thousands of years going about its business.

You can see how Ascomycota fit into the Fungi on a tree here.