For instance, this slinky and mysterious creature is a heteropod (“different foot”), or sea elephant:

It’s called a sea elephant because of that sausage-esque proboscis it holds aloft. I wrote about these a few years ago after my night pelagic dive in Hawaii. Quoting me:

[Heteropods] are phenomenally cool mollusks that have forsaken their snail shells to swim naked and free in the ocean like vicious little hippies. They look for the other pelagic creatures from which to take bites using their saw-like radulas at the tip of a Futurama-esque eye-stalk (but it’s not — the eyes are at its base). The larval forms still possess coiled mollusk shells, but they lose them when they become adults. They also possess a single “dorsal fin” — which is actually totally inaccurate because it is really ventral (stomach side — they swim “upside-down”) and was originally the mollusc’s foot –  which they undulate and paddle about with. For some reason, when moving, they remind me of Sir Hiss tooling about  in that ridiculous balloon at the tournament in the 1973 Disney “Robin Hood” (see 2:15 here, and :20 here for the Sir Hiss Version). Some species possess a sucker on their “fin” which the heteropod no doubt uses to hold its prey still while it savages it alive.

Then there is the sea butterfly.

Sea butterflies, the Thecosomata (“encased bodies” also sometimes called “pteropods”), possess fluttery, flappy wings (“parapodia”) that are actually yet another modified gastropod foot — the slimy, crawly part of a snail. They use these wings to haul themselves and their shells — when they have them — through the water column. They seem to be omnivorous, but spend at least part of their time making and dragging a mucus net through the water with which to snag food. They don’t seem to be sentimental about their gooey blankets, though. If disturbed, they’ll drop them and flap away.

Sea butterflies are also, strangely enough, one of the creatures scientists are most concerned about as the oceans acidify due to rising carbon dioxide concentrations. Here’s a clip from a BBC documentary (the new climate change one?) that shows both sea butterflies’ flappy wonderfulness and explains their sad expected fate.

Strangely enough, sea butterflies are the sole menu item for some species of sea angels (the Gymnosomata, or “naked bodies”), their possible close relatives in the informal gastropod taxon called “pteropods”. These would be the flying slugs. And I imagine if I were a slug, this is what I would dream of evolving into one day (torrid slug love scene in “Life in the Undergrowth” notwithstanding). They actually do hatch with tiny shell on their backs, like many heteropods, and then sever the connection to it and cast it aside not long into their development. In this way, you might say they have a vestigial shell that reveals their gastropod ancestry just as whales have vestigial leg bones that reveal their terrestrial ancestry.

Here’s an excerpt from a National Geographic documentary (perhaps the recent one on climate change?) that shows sea angels snacking on sea butterflies nicely.

I bring all this up because two of these three strange gelatinous mollusks (a sea elephant, or heteropod; and sea butterfly, or Thecosomatan, slides 1 and 4 respectively) are highlighted in a beautiful slideshow of deep sea oddities taken by Duke University optical biologist Sonke Johnson over at Duke Today. In the slide show are other delights as well, such as what a jellyfish parasitized by amphipods looks like (I’ve never seen that before), a beautiful plant-animal living fossil called a stalked crinoid, a gawky mantis shrimp larva which takes the concept of eye stalks to a whole new level (is it possible to overdo it, really?), and finally, what a baby flounder looks like before its weirdo eye migrates to the other side of its head (its pretty!).

Hit the button in the bottom right corner of the slide show menu to make the art as big as possible, and make sure to take time to study the photographs for a good long while both before and after reading the text. I’m often guilty of reading the captions and barely glancing at photos in slide shows. Don’t make that mistake. Savor.

Happy weekend!

When I was in North Carolina last month for the meet-and-greet-and-learn-exhausto-freneti-thon of ScienceOnline 2012, I procured for myself a sampling kit for a citizen science project being conducted by the lab of Rob Dunn, Sci Am Guest Blogger and author of the wonderful book The Wild Life of our Bodies.

He’s doing a new study called “The Wild Life of Our Homes“, and for the low, low price of nothing*, I got a sampling kit with two neato dual-pronged sterile Q-tips, instructions, a questionnaire about the characteristics of my pad, and a mailing address to send it back to.

All I had to do is carefully swab down my upper door sills with the respective swabs, reseal them, and mail them back to North Carolina. Then they analyze what molds, mildews, yeasts, and other assorted fungi; pollen (aka plant sperm!), algae, bacteria, archaea, viruses, are in the dust on the top of my inner and outer front door sill and tell me about it FOR FREE! Bio nerd nirvana achieved. It’ll be in the mail on Monday, boys!

It’s my understanding they did a similar study of belly button microbiota at ScienceOnline last year, but for sheer non-yuck factor this beats that hands down. And this time, you too can participate. To find out more and sign up, click here. It looks like there may be a waiting list, but they’re working to find the funding to help everyone sample their home who wants to. And who wouldn’t want to!? If you’re reading this blog, I know you do.

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*OK, technically the of U.S. postage and return envelope for your samples. But still!

The slinky rods of Legionalla pneumophila. If you didn't know better, you might assume these were extruded by a Play-Doh Fun Factory. CDC Public Health Image Library Image #11151. CDC/ Margaret Williams, PhD; Claressa Lucas, PhD;Tatiana Travis, BS

In July 1976, a convention of members of the American Legion — a veterans’ group — was meeting in Philadelphia at the Belleville Stratford Hotel in honor of America’s bicentennial. Soon, 221 attendees would be sickened and 34 dead of an illness it was believed no one had ever seen before. Swine flu was suspected, as were toxic chemicals or terrorism of some sort. None of these proved to be the cause.

The CDC sprang into action and by January of 1977 the culprit was identified: Legionella pneumophila. The bacteria had been living in the warm water of the hotel’s air conditioning cooling tower, whence they were aerosolized and spread through the building via air ducts.

Just yesterday, these bacteria made headlines again when they were discovered to have infected at least three and killed one last year at the Luxor Hotel and Casino in Las Vegas, where the bacteria were dwelling in “water samples” — most likely the plumbing or A/C system. Although this sounds scary, you have to put things in perspective: Legionnaire’s Disease, or legionellosis, already sends up to 18,000 people a year to the hospital in the United States, and doctors may overlook the diagnosis in others. But most of these infections do not take place at high-profile pyramidal Las Vegas casinos.

L. pneumophila, a gammaproteobacterium like E. coli or Salmonella, is actually quite an interesting organism in and of itself. It is related to no other respiratory pathogen, and in fact, its usual host is not a bird or a pig or a human. It’s an amoeba. Legionella live within and, in fact, parasitize free-living amoebae in nature*. We are accidental hosts.

Their preferred home in amoebas may explain why they like invading our macrophages so much. Macrophages are amoeba-like immune cells that wander through your body at will — often slithering between tissue cells — looking for invading microbes to engulf and digest, just as amoebas feed. Legionella bacteria get taken up by our macrophages and then parasitize them — and in turn us — just as they do wild amoebas.

If the infection progresses (which in many healthy people it does not), the consequences for a human shake out in one of two delightfully-named ways. The first is Pontiac Fever (I actually have this, but it’s because I drive a suh-weet Pontiac), a flu-like syndrome that usually resolves on its own. It was named for an outbreak in Pontiac, Michigan, that pre-dated that the Philadelphia outbreak and was identified ex post facto. The second option is Legionnaire’s Disease, which also begins with flu-like symptoms before progressing to pneumonia accompanied by sky-high fevers of up to about 107F. This option kills somewhere between 5 and 30% of the people who develop the symptoms. People sickened by the bacteria are typically middle-aged or older, and often have weakened immune systems.

In addition to water towers used in industrial air-cooling systems, the bacteria-parasitized amoebae can also hang out in shower heads, medical respiratory devices, spas, hot tubs, large central air conditioning systems, fountains, swamp coolers, ice machines(!), misting equipment, domestic plumbing, swimming pools, and humidifiers (another reason you should use only boiled or distilled water in them). The bacteria (and of course, their amoeba hosts) also thrive in freshwater ponds and creeks.

Legionella get into the air after an infected water source is disturbed mechanically. Any fine droplets produced may evaporate quickly, leaving the bacteria suspended and easily inhaled. The bacteria thrive between 77 and 112 F, so one simple strategy for keeping water free of the disease is to maintain a temperature hotter or colder than that.

It used to be thought the Legionella bacteria couldn’t travel far by air. But the investigation into an epidemic in Pas-de-Calais, northern France in 2003-2004 traced 86 confirmed cases and 18 resulting deaths to a cooling tower in a petrochemical plant, and found that some of the victims lived as far as 7 km from it. Once airborne, those bacteria can really move — or at least can survive a long time as the wind moves them. Perhaps it is a natural dispersal strategy for reaching new amoeba hosts.

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*In fact, the first amoeba-parasitizing giant viruses were found by scientists investigating a local pneumonia outbreak and looking for Legionella in amoebas found in an area water tower. They found large particles inside amoebas in the cooling tower they assumed were bacteria. It was only when the “bacteria” failed to respond to bacteria-specific molecules (PCR primers) that the scientists realized they had a new (and entirely harmless to humans) super-giant virus on their hands.

Ernst Haeckel around Christmas 1860, when he was 26, the year after he returned from Italy.

Ernst Haeckel had spent an unhappy year practicing medicine when his parents finally consented to pay for a year of scientific study and travel in Italy. It was 1859, and he was 25. He had discovered a passion for biology and a talent for art during his college years, but his parents had pushed for practicality. If there was ever an antidote for practicality, it’s Italy.

Once there, the lure of the lush Neapolitan landscape and hot weather that pushed the ocean microbes he’d hope to study far north conspired to draw the young scientist toward landscape painting. He was finding very little in his ocean samples, and began to lose faith that he had a talent for science. As he spent weeks living with other artists and enjoying the perks of the non-starving artists’ lifestyle, he seriously pondered leaving science for good.

Then he traveled to Messina, Sicily, where ocean currents and the geometry of the harbor captured tiny ocean protists called radiolarians in abundance. Haeckel was enchanted. Science had him. But so did art — he would go on to paint or draw thousands of radiolarians and scores of every other sort of living creature known to 19th century science.

This the crux of the story told in the documentary “Proteus“, the 22-year labor of love of filmmaker David Lebrun, which I have long known about as an ardent fan of Haeckel’s art and had long planned to see. This week I finally did. I approached it with trepidation because although the IMDB reviews were favorable, the reviews at Netflix were decidedly not.

Here are a few clips to give you a taste:

What was it he saw in the radiolarians that drew Haeckel back to science? “Every morning I am newly amazed at the inexhaustible richness of these tiny and delicate structures,” he wrote. “That I thrust myself with sheer passion on these scientific treasures, which are simultaneously so pleasing to the aesthetic eye, you can well imagine.” Haeckel had two passions. Radiolarians satisfied both.

Radiolaria with algal symbionts inside. By, of course, Haeckel.

Radiolarians are tiny protists that live inside intricate silica shells. Because silica is impervious to the acids that often dissolve shells made of calcium carbonate at great depth, they make up a huge proportion of the sludge found on deep sea beds. They extend tiny pseudopods out from their shell to capture food, and sometimes they house algae to help feed them.

They were among the earliest eukaryotes to evolve at the end of the Pre-Cambrian, 550 million years ago, and their shells have varied so much over time that they are useful for dating petroleum beds and geological formations. But why do they have those shells, and what force could be selecting for the endless variety in their structure? I do not know.

The film describes how Haeckel, raised a Christian, was torn as a youth between two powerful forces: his love of science, which seemed to be reducing nature to a system of soulless laws, and his love for the romanticism of the early 19th century German philosophers. That included, in particular, Goethe, who believed that (I’m, obviously, paraphrasing here) God is not a discrete being, but is found as an ineffable and intangible presence in all parts of nature, no matter how tiny — the “God in Nature”. Radiolarians, filmmaker David Lebrun argues, were what first resolved the tension in Haeckel between those two conflicting forces. In their endless variety and enchanting beauty, Haeckel felt he was seeing and touching — and by drawing them, sharing — a part of God.

Later in Haeckel’s life, the Challenger expedition dredged up thousands of new deep-sea radiolarian species from the depths of the Mariana Trench, site of Challenger Deep, the deepest spot on Earth, some five miles beneath the surface. Haeckel spent a decade studying the sediments brought back by the expedition and drawing the 3,000 new species he found, and it is these images that you see flipping by in black and white in “Proteus”, by director David Lebrun.

On nights and weekends over two decades while he often supported a family with other jobs, Lebrun labored to bring this film to the screen. He commissioned an original score and spent thousands of hours photographing Haeckel’s work (today with digital technology the same work would take only a few days).The film is illustrated like a Ken Burns film exclusively with beautiful period artwork, and whoever was the foley artist deserves a gold star: the sound effects bring them alive.

Lebrun likes to play with repetition of pattern, but I felt that the radiolarian animation sequences would have better achieved the point he was trying to make much better if he slowed down the switching of images a bit and never once repeated one. From watching bonus material, I know his goal was to make the radiolarians appear to dance. But I found it distracting and, strangely, almost boring after a certain point, and felt it got in the way of the point he was trying to make. Considering that Haeckel drew thousands of radiolarians, there was no need to repeat. If I’d never seen the same radiolarian twice, I think I would have felt more awe.

Although the reviewers on Netflix complained that the film was boring and repetitive, I found it to be engrossing, beautiful to look at and listen to (if a bit slow at times), and completely coherent.  Lebrun does a great job tracing the historical, scientific, and literary forces that shaped Haeckel’s world, from the influence on romantics of Samuel Taylor Coleridge’s Rime of the Ancient Mariner, to the unexpected spur to oceanography that the laying of the first trans-Atlantic telegraph cable by the SS Great Eastern proved to be. At one point, it even moved me to tears. I recommend.

More radiolaria, again by Haeckel. Notice icosahedral structures at top that evolved convergently with some virus capsids.

Though Haeckel went on to become one of the most influential and widely-read biologists of the 19th century, championing evolutionary theory, drawing the first evolutionary tree to incorporate all known life, coining the terms phylum”, “phylogeny”, “ecology”, and “protist”, and being among the first to boldly, publicly, state that humans evolved from apes and life evolved from non-living matter, he embraced some controversial, and in several cases, incorrect theories about evolution. Perhaps as a result, he is little known today.

Probably his biggest blunder was his belief in Recapitulation Theory, often expressed as “ontogeny recapitulates phylogeny“. He believed the embryonic forms of animals literally expressed their evolutionary history, and that humans pass through all the stages of their past evolution as embryos. This is not correct; at best, we might say that embryos pass through many, but not all, of the embryonic forms of our ancestors, but certainly not their adult forms.

Instead of natural selection, he also believed a form of Lamarckism was the driver of evolution. He also succumbed to racial prejudices common during his time and used science to back his views, sullying his reputation today, and he held controversial and mystical religious ideas that drew attacks from contemporary scientists and clergy alike.

“Everything now came before me in new and beautiful and remarkable forms,” he wrote of the radiolarians in Messina. “I began to see and hear not only the outer forms, but also the inner content, the nature and the history of things.” The astute reader will recognize this as an early expression of his Goethe-driven mystical nature philosophy as well as ultimately flawed belief in Recapitulation Theory.

But he had this virtue: an unadulterated sense of wonder at the diversity of life, and a burning passion to share this wonder with others through his art. Indeed, he believed the universe was an infinite unfolding work of art, and that it was a scientist’s job to portray with both precision and passion what he had found.

If his personal philosophy led him astray scientifically, the romantic artist in him was able to depict the diversity of life in a way so moving that it is alluring to non-scientists even today. Personally, I will never get enough of Haeckel’s art, which helped inspire my beloved Art Nouveau. I’ve seriously considered decorating a room, or possibly every room, in my house with them.

Indeed, I’m not the first person with this impulse. Lebrun discovered during his research that Haeckel’s home in Jena, Germany — the aptly named Villa Medusa — was adorned with such features as chairs carved with radiolarians and a chandelier surrounded by a painted jellyfish mandala. WANT.

You can buy a copy of his 1904 masterwork “Artforms of Nature” here at Amazon, originally issued in 10 sets of 10 between 1899 and 1904, of which at least one print in almost every set was of radiolarians. Or you can buy individual prints of them to hang on your wall here (or just search for “Haeckel” at your favorite art prints webseller). And if you’re interested in “Proteus” and don’t have Netflix or similar, look for it at Amazon.

Whatever his faults as a scientist and biologist, to me his legacy as science illustrator is his highest and greatest. In my opinion, the best science communicators — Carl Sagan, Richard Feynman, Rachel Carson, or Jane Goodall, to pick a few — understand that speaking to people’s hearts about science is as important as speaking to their brains. In this mission, I believe Haeckel was an unqualified success.

Purple packages of pain: false colored (no, they’re not purple in real life) transmission electron micrograph of human norovirus. CDC/Charles D. Humphrey. CDC Public Health Image Library ID 10708, click for link.

If there is a central circle of hell, I now know what’s there: endless glasses of water spiked with norovirus that you must drink for eternity. Yet incredibly, some persons of Achilles-class bravery/stupidity actually signed up for this punishment of their own free will, and did so in the name of science. Brave souls, I salute you.

Because what these people helped discover is nothing short of spine-tingling: norovirus can survive at least 61 days in well water. Considering it takes only the number of virus particles that you can count on two hands to  make you wish for death for about 24-48 hours, this is not good news. However, there is some good news, too, in the world of norovirus defense. More on that in a minute.

OK, so many of you are no doubt wondering: What the heck is norovirus?

A Pain in the Gut

Norovirus is Norwalk Virus, named for the Ohio town which in 1968 was home to the virus’s first identified outbreak and which no doubt do not include this information in its Chamber of Commerce literature. Often called “stomach flu” or “24-hour flu”, this awful malady has no relation to influenza virus, but has gained a reputation no less sinister in recent years. It is the agent responsible for innumerable cruise-ship “gastroenteritis” outbreaks and outbreaks at camps, state fairs, nursing homes, schools, and yes, even NBA locker rooms.

Anyone who’s experienced it can tell you it’s a bit like having all of your intestines’ pain receptors activated at once, with uncontrollable nausea and/or diarrhea added as a special bonus. When I was in high school, every so often I’d experience twelve hours of intense pain along with nausea so powerful that I’d feel the urge to hurl even when nothing was left. This was followed by 12 hours of utter exhaustion. Then, I’d feel pretty much normal again and go right back to school, no doubt perpetuating the cycle since victims shed virus for several days after they recover. I’m pretty sure that it was norovirus.

I’ve never given birth, but if I ever do, it will be interesting to make the comparison. So far, the only other thing that’s come close to the pain of norovirus infection is an unfortunate incident in which I was told that some people didn’t need anaesthesia during their flexible sigmoidoscopy (aka colonoscopy lite) and I chose this option in a misguided money-saving move. Once they blew the air into my colon (I know, I know, TMI), it was like someone had flipped all the norovirus pain switches again. Needless to say, the next 5 minutes were among the longest of my life.

This virus is responsible for about nine out of 10 “stomach flu” cases in the U.S., and is probably responsible for about 50% of the cases of what people call “food poisoning”. It takes fewer than 10 virus particles to make you sick, and the virus can be spread by sick people handling your food or water, or shaking your hand, or by you touching surfaces they’ve touched, or even by (I know, ewwww) aerosolization of their bodily fluids when they flush the toilet after a visit to the necessary room.

At one Boy Scout Jamboree in the Netherlands, scientists calculated each sick person infected 14 others before anything was done. After strict hygeine was imposed, each sick person infected a mere two others, which, the scientists soberly noted, was still not few enough to contain such an outbreak. In the NBA outbreak mentioned above, the CDC concluded there were at least two occasions on which norovirus was likely to have been transmitted to a new victim during a game.

A Simple Formula for Suffering

Let’s back up a bit and look at what viruses are in general, so you can understand what noroviruses in particular actually are. Viruses are little packages of DNA or DNA’s henchman RNA wrapped in a protein and/or fatty lipid coat. The protein coat, if it exists, is referred to as a “capsid”, and individual virus particles are “virions”. When present, lipid coats are more or less like our own cell membranes, and are often stolen from them by the virus.

Noroviruses are in the family Caliciviridae, whose members seem to specialize in making hits on terrestrial vertebrates — everything from frogs on up. Another calicivirus — Rabbit Hemorrhagic Disease Virus — has been used for bio-control in Australia and New Zealand, while other viruses in the family — like the beautiful hexagonal icosohedral Sapovirus, below, cause other forms of gastroenteritis in people. Norovirus has a more or less amorphous spherical capsid. You can see this in the photo at the top, where a few viruses that happen to have been sliced in half during the preparation for microscopy reveal the cross section of the virus.

The ghostly, graceful icosahedrons of Sapporo Virus, also called Sapovirus, in the Calicivirus family. Creative Commons GrahamColm. Click image for source and license.

“Calicivirus”, which I so hope is pronounced “ka-leaky-virus” — not unlike the titular greeting in this totally unrelated but awesome ditty — name comes from calyx, which means a cup or goblet. The botanists in the room will recognize the term as the same one that refers collectively to the sepals of a flower, the sometimes, but not always, cup-shaped green leaves at the base of a flower. Some species apparently have a cup-shaped depression on their capsid surfaces.

Caliciviruses contain one single piece of single-stranded RNA in a protein capsid with no lipid envelope. Norovirus is the same, and its RNA encodes a mere two proteins, both used in making the capsid. It is utterly amazing to me that something so inconsequentially small and simple could cause such profound misery from such an efficient little package. If someone calculated a misery per base pair per person infected index, I think norovirus would be right at the top, considering Ebola virus clocks in at just under 19,000 RNA base pairs and might cause a few hundred cases a year at most (thank god), while norovirus contains a mere 7,500 but infects 21 million, hospitalizes 70,000 and kills more than 500 people in the U.S. alone every year. In developing countries, the virus kills about 200,000 children under age five annually. Not Cool, norovirus, Not Cool.

Unfortunately, norovirus also has a high mutation rate even by RNA-virus standards. The further bad news here is that having no fatty-lipid membrane means that the virus isn’t killed very well by alcohol or detergents (which break down fats), though bleach and old-fashioned handwashing supposedly work well (Oh, old-fashioned handwashing, is there anything you can’t do?). This is not good news for those that rely on alcohol-based hand sanitizers and wipes (something to think about next time you blithely swipe an alcohol-based wipe across the handle of your grocery cart or rub your hands with hand sanitizer). Obviously, this is one insidious virus.

Which brings us to the findings of two new studies.

Norovirus. Bar=50 nm. F.P. Williams, U.S. EPA

Viral Survivor

Scientists wondered how long well water — from which about half the U.S. population draws its water — would support noroviruses. The viruses could and have gotten into such water through leaking septic tanks or sewer lines, and in fact, when I was a reporter in Wyoming, I covered just such a case at a remote kids’ camp. The results of this study were jaw-dropping. The scientists spiked water from an Atlanta well with a known quantity of the virus. Then they had (the sado-masochistic?) volunteers drink this water on day one, 4, 14, 21, 27, and 61. Volunteers were sickened by the water on each of these days, including day 61.

They didn’t have enough money to subject the poor people to “testing” longer than that. But they did store and test the water for viral RNA contained in intact capsids up to 1,266 days later. That’s nearly 3 1/2 years after spiking the water. There was no change in RNA levels over a year later, and only a small reduction after 3 1/2. That is one tenacious virus.

Since most ground and well water in the U.S. isn’t treated prior to drinking, the scientists suggested we might want to start doing that.

In lieu of that (this country is home to a hatred of government regulation neatly encapsulated in New Hampshire’s motto “Live Free or Die“), scientists are working on another approach: a vaccine. This is also important, as I’ve already mentioned, because a lot of people pick up the virus in other places, and seniors with weakened immune systems in long-term care facilities are particularly vulnerable.

As covered in Science late last year (original New England Journal of Medicine paper here), scientists have discovered that when one of the two viral proteins is produced by cultured cells, they spontaneously assemble (as they do in nature) into “virus-like particles” that contain no viral RNA payload and are thus non-infectious. But they look like norovirus from the outside (check out the photo in the Science article), and apparently look enough like it to our immune system that they can generate a partially-effective response.

Symptoms of norovirus infection appeared in just over two out of three of people exposed to both the virus and a placebo vaccine, but in only one in three of people given the real vaccine. Their symptoms were also less intense and took longer to develop. Well, it ain’t perfect, but it’s a good start. Porcelain-god worshipers everywhere will no doubt greet the news with the greatest relief.

Riftia pachyptila, the weird, iconic giant of hydrothermal vents. Creative Commons Sabine Gollner et al.; click image for link and license.

In 1977, scientists and the world were shocked to discover the first deep-sea hydrothermal vent community at the Galapagos Rift in the eastern Pacific (see a great story on this at NPR here). At this site, chimneys spewing black, superheated and chemically supersaturated water towered over fields of blood-red tube worms encased in white sheaths, giant deep-sea clams, mussels and anemones. Biologists, who had long considered the deep, sunless places of earth to be lifeless death zones, were flabbergasted.

Since then, when you think “black smokers” or “hydrothermal vents”, you probably think “tube worms”. And with reason: the gutless, endosymbiotic, spectacular 7-foot+ deep-sea worms are iconic.

But that would be very, very wrong. For the majority of deep-sea vents are not home to vent worms, which as best as I can tell from this Encyclopedia of Life map and from my own reading are right now only known from the east Pacific. The dominant species at all the vents along the mid-Atlantic ridge, for example, are shrimp and mussels. And in the last two years scientists probing the East Scotia Ridge — some 8500 feet from the surface — stumbled into a deep-sea black smoker system encrusted with, of all things, yeti crabs.

The ultimate in high-density housing. Credit: Oxford University, used with permission; Click image for link to source paper

Yup. Yeti crabs (In case you’re at a loss as to how they got their name, see this). The impressively (and hairily) armed denizens of the South Pacific were only discovered in 2005. The news was announced yesterday in an article in PLoS One, and was also covered here at Scientific American.

Along with the yeti crabs was a community the likes of which has never been seen before at a deep sea vent. In the picture above at right, those aren’t seaweeds or even coral. They are stalked barnacles new to science. There were new anemones (look for the photos of them in Figure 3 here) and a new snail, and a new seven-armed predatory sea star. And there was a ghostly ocotopus species, also new to science, that seemed to be attracted — out of curiosity? — to the ROV’s lights.

I'm ready for my closeup, ROV Isis. Credit: Oxford University, used with permission; click image for link to source paper.

But just as surprising as what was there, was what wasn’t. There were none of the tubeworms, polychaetes (bristly worms), clams, mussels, predatory crabs, or shrimp typically found at other deep sea vents in the Pacific, Indian, and Atlantic Oceans. At the same time, there were a few species that overlapped with vents in the west, south, and east Pacific, and the Mid-Atlantic Ridge. Though the yeti crab species is new, it has relations on the Pacific-Antarctic Ridge and at cold seeps off Costa Rica. In particular, the chemosynthetic (making food from inorganic chemicals) bacteria and other microbes at the base of the food chain at the Antarctic vents were similar to those found elsewhere.

The take home here, then, is not that this new vent system is from another planet (although it’s definitely more unusual than most, for reasons gone into in the Sci Am article), but that there are actually *many* different kinds of vent community on Earth, and that most don’t involve tube worms. The authors made an attempt to calculate just how many types there are. When their new data from the Southern Ocean were added to existing data, computers calculated that there are most likely 11. Here’s a map they made showing this; the two new East Scotia Ridge vents are shown as blue circles. As you’ll note, there’s a lot of different vent communities out there. Probably only about 2 or 3 host tube worms, though the rest, to be sure, are home to their own set of fascinating weirdos.

A model of global deep-sea vents that presents 11 types. The two new East Scotia vents are shown as blue dots. Figure 6 in Rogers et al. Creative Commons license. Click image for link to article.

In a commentary that alongside the article, Steven Chown from Stellenbosch University in South Africa notes that although the new vents are well protected by Antarctic treaty, many of the other vents on Earth are not, and, given their uniqueness and rarity, that is a problem. As it turns out, the very thing that makes them hospitable to life — the hot water precipitating minerals — also creates rich metallic sulfid ore veins in the vents. In fact, most of the ore veins found on Earth are ancient hydrothermal vent systems, although these can form on dry land, too, at places like Yellowstone, or deep within the earth. But deep sea hydrothermal vents seem to be particularly good at concentrating metals. Chown points out that at the Solwara Vent off Papua New Guinea, ore deposits may contain 7% copper by weight. Ore at copper mines on land contain about a tenth of that.

In the absence of rules or protection, mining deep-sea vent system will happen (see this enlightening article from the Economist in 2009), and indeed is about to happen. Nautilus Minerals of Canada plans to start mining the Solwara Vent in 2013, although, Chown notes, “environmental impacts at this site will, apparently, be well managed.” Neptune Minerals of Australia was granted exploration licenses for sites off Papua New Guinea, Micronesia, and Vanuatu, and in 2008 applied for mining licenses for two site off New Zealand, according to the Economist. Russia has its eye on four sites on the Mid-Atlantic Ridge, and China is exploring the Indian Ocean.

Chown also points out that in July 2011, the International Seabed Authority approved four new applications for mineral exploration of polymetallic sulfides in association with hydrothermal vents. The current plan is to explore only inactive vent systems devoid of vent life, but all these developments obviously make some nervous that in international waters, in the absence of a conservation policy agreed to by all, all bets could be off. It’s not as if there’s anyone else down there watching what’s going on. And satellites can’t see the seabed, or at least not in the way you can check out the contents of your neighbor’s backyard via Google Earth.

Now I’m not trying to villainize mining companies here. Let’s not be naive about where the metals and rare earth elements in your iPad, iPhone, laptop, and flat-screen TV come from (although you should, perhaps, consider buying used when possible, and recycling them responsibly when you’re done playing with them). The lifestyle you enjoy is made possible by mining (and farming and logging). But in a world where the Chinese entertain semi-serious thoughts of strip-mining the moon (not to mention the seabed), perhaps we as a global society should formally set certain sites — some suggest all active vents; others most — off-limits to mining. It’s our responsibility — not theirs — to set clear, uniformly enforced rules for the mining companies to play by. If you’re interested in learning more about this issue, InterRidge, a non-profit international conservation organization, is heavily involved in it.

One final note. Buried at the end of the new PLoS paper was an aside mentioning that in 1966, a seafloor photograph was taken 7,800 feet down at the East Scotia Ridge. The photograph clearly shows animals similar to the ones scientists just (re?)discovered at East Scotia. So it seems the first hydrothermal vent community was actually discovered — but not recognized — in 1966, 11 years before the legendary descent to the Galapagos Rift. Who knows if anyone ever looked at the picture in detail. One would assume someone at least glanced at it. Perhaps because that person didn’t expect, and couldn’t conceive of, anything so wonderful as deep sea hydrothermal vents, they weren’t able to see the magic right in front of their eyes.

But what if you live somewhere between, in a zone where, dependent on the weather, the time of day, or the soupiness of the water, you may be better off being transparent or colored? Well, if you’re an octopus or squid, the shape and color shifters of the aquatic world, this is one solution:

These octopuses are expanding and contracting pigmented chromatophores to produce the effect. According to new research in Current Biology by scientists at Duke University, the octopus Japatella heathi and squid Onychoteuthis banksii will produce the effect when a blue light is shined on them or they’re physically touched, but not when an object passes in front of or overhead of the animal. The scientists could see that the octopus could see the objects (and were not amused), however, because they followed them with their eyes.

They also used spectrophotometers and probes to test reflectance; they found that octopuses with chromatophores deployed reflected half as much light as in transparent mode, and similar amounts of light to other deep sea fish and invertebrates.

This species shows a depth preference change as they age; the young prefer shallower, daylight waters, and adults prefer deeper, darker waters. So being able to shift between evasive strategies would make a lot of sense for these creatures. Furthermore, most deep sea predators have blue light searchlights. When the scientists tested these octopus with red light, they got no reaction either. I think there’s a joke about a Red Light District wandering around here somewhere . . .

In any case, whether your own chromatophores were deployed or contracted this past year, or a mixture of both, I wish you a sunny, tranquil 2012. Happy New Year!

Zylinski, S., & Johnsen, S. (2011). Mesopelagic Cephalopods Switch between Transparency and Pigmentation to Optimize Camouflage in the Deep Current Biology, 21 (22), 1937-1941 DOI: 10.1016/j.cub.2011.10.014

But the strangest sight of all were the lichens I noticed peppering the railings of the boardwalk that led us through the swamp, and the bark of the occasional tree. They had bright red borders and sometimes speckled centers on either a white or green ground. I had to know what they were. When I got home and looked them up, I discovered they were called “Christmas lichens“, or Christmas wreath lichens”. And so I use these photographs to wish you a happy Christmas, should you happen to celebrate it. Here they are (along with a fascinating assembly of other lichens and mosses that leave no wooden surface uncovered in the heart of the swamp):

Here’s a closeup of a slightly different section of the railing:

What a spectacular and unexpected sight! Here we have another strange red pigment, like the prodigiosin produced by Serratia marcescens that I wrote about earlier this year. This red pigment is chiodectonic acid, which like many lichen chemicals likely serves as a UV protectant. Beta-carotene (which might help with DNA repair after exposure to UV) and chlorophyll are also found in the bright red areas. For some more lovely photographs of Cryptothecia rubrocincta (the species epithet means “red-girdled” or “red-wreathed”) that show the green of the red/green Christmas lichen a little better, see here.

Merry Christmas!

Yes, algae. The filmy red/brown/green/golden stuff that washes up along many a beach and occasionally serves as the draperies of the underwater world. And not just any algae. British algae. I know. You can catch your breath now.

But what you may not realize is that algae are, in fact, quite beautiful, and never more so than when their diaphanous delights are on full display in a cyanotype, the type of photograph employed by Anna Atkins, the author of “Photographs of British Algae”. That’s right. Not only did the first book of photographs contain cyanotypes of algae, it was produced by a woman. Her book is part of a collection in the Royal Society, which has just put on an exhibit of some of its choicest works called “Treasures of the Royal Society Library”.

Anna Atkins was the daughter of John George Children, a scientist who worked in the British Museum’s Natural History Department. He taught her more about science that most girls could expect to learn in those days, and it seems to have sparked a life-long love in her. She and her father knew Sir John Herschel, the inventor of the cyanotype, and he, or someone who knew him, *cough*, exposed her to the new technique in about 1842 or 43.

Cyanotype is a photographic medium that uses ferric ammonium citrate, potassium ferricyanide, and simple sunlight to make an image. On exposure to ultraviolet light, the compounds react to form a dye called Prussian Blue, or ferric ferrocyanide. Ever wonder where cyanide got its name? This is it. Essentially, you put whatever you want to photograph on top of the paper. You expose it to the sun for 10-20 minutes. Then you rinse the paper in water to wash off the unreacted solution. Dry carefully. Art complete.

You can still make your own cyanotypes today, I believe, using kits like this one, which are often marketed to children as art projects. There is absolutely no reason they couldn’t be art projects for adults as well.

From what I can gather, Atkins simply took her collection of pressed, dried algae and cyanotyped them. Voila. The first book of photography. But what an inspired choice for the medium: because many algae are translucent to some degree, even when dried, her photographs of these life forms have a beautiful, ethereal elegance. With any object that is not translucent, the cyanotype process simply yields a sillhouette. With algae, or anything similarly thin, the cyanotype gives information about its thickness and translucency — to beautiful effect.

Treasures of the Royal Society Library contains at least 30 selections of real rare books from the library’s 350 years of collecting. [begin cheesy infomercial music]It’s a Greatest Hits of Science from 1504 on,  including works by  Albrecht Durer, Gailleo Galilei, Robert Boyle (“The Sceptical Chymist”), Robert Hooke (“Micrographia”), Isaac Newton (“Philosophiae Naturalis Principia Mathematica”), Charles Lyell (“Principles of Geology”), Charles Darwin (“On the Origin of Species by Means of Natural Selection”), and MANY more!! Act now — time is limited. This special exhibit ends June 21, 2012 .

It’s enough to make a girl wish plane tickets between DIA and Heathrow didn’t cost nearly four figures [ducks shoes being thrown by readers in the Southern Hemisphere].

In any case, if you live anywhere in the vicinity of the Greater Europe Area, you have no excuse not to visit the Royal Society exhibit in the next few months and pay homage to some of the pillars of science in their original printed form, including “Photographs of British Algae”, and a fascinating table of the causes of death for Londoners from the mid-1600s (“itch” and “frighted” were apparently ways to go back then). For the rest of us, here are a selection of scanned images of Atkins’s book at the British Library and the New York Public Library. Of those, this one and this one are among my favorites. Enjoy.

And on a personal note, Merry Christmas, Happy Yule/Kwaanza/Hannukah/Festivus, and Ex-Post Facto Joyous Solstice. There was a small bright spot in my life recently: one of my posts was selected for inclusion in next year’s published blog anthology “The Open Laboratory”, which you may have seen over at Jennifer Ouellette’s and Bora Zivkovic’s blogs. Yay! I’ll be a published author soon. That’s something to be thankful for.

This summer saw a micro-burst of brain-eating amoeba attacks (well, only three, but that was plenty for the press to get its panties in a bunch over it. How could you not about “brain-eating amoebas”?) in people who swam in U.S. freshwater lakes, ponds, etc. You’d think the commencement of North American winter would preclude further possibility of attack. Alas, it does not. For this is the “amoeba’s” new secret weapon: the neti pot.

The notorious neti pot. Creative Commons image by Kurt Yoder, 2004. Click image for license and link.

Yes, the Neti pot. For those of you unfamiliar with this contraption, the idea is that instead of honking your way to kingdom come into a scratchy paper tissue, you can gracefully irrigate your way to an obstruction-free breathing by pouring the contents of a Neti pot into one nostril and out the other. Exhibit A:

A neti pot in action. Creative Commons image by Aikhan. Click for license and link.

Although I’ve never tried this, I’d say it’s probably easier said than done, at least to start. But it does seem to be effective, once mastered, based on what I’ve read.

Unless, that is, the tap water you use to fill the pot is home to some wayward “amoebas” called Naegleria fowleri. Somehow they can slip through the microbial Fort Knox of some U.S. water treatment plants and make it into tap water (at least in Louisiana).

This is not a problem if you drink the water and they end up in your stomach, where they are digested. This is very much is a problem if you dribble them through your sinus system, where they seem to occasionally find their way brainward with the same efficacy they display in unlucky swimmers who accidentally inhale some protist-infested pond water while swimming. Once they wander into your brain, death is almost certain.

There’s an easy solution, though. Just boil your neti pot water first, or use store-bought distilled water. And in any event, only two people in Louisiana have died from infested neti pots this year. So don’t panic. This rates nowhere near the level of concern that should be inspired by, say, getting in your car and driving it down the street. These amoebas don’t seek out humans. They just go sightseeing when they happen to be in the neighborhood. Unfortunately, the sight they’re seeing is your gray matter.

For those of you who missed it and are curious exactly what Naegleria fowleri is (it’s not actually a true amoeba), I’m reprinting my post from August on this very subject below:

Cyst, trophozoite ("amoeba"), and flagellate forms of the protist Naegleria fowleri. Photos by CDC.

In the press this week were reports (see here and here and here) that the brain-eating amoeba Naegleria fowleri has killed three people this summer, as it does in a typical year. The only trouble is, Naegleria isn’t a true amoeba.

So why are they called amoebas if they are not? The organisms in question — which, like true amoebas are microbes called protists — do alternate between cysts, flagellate (swimming) forms, and amoeba-like (blobby, crawling) forms that are more properly called “trophozoites”. When times are good, these trophozoites crawl through the mud in search of bacteria to eat. When times are bad, they sprout tails and swim off like guided missiles in search of happier hunting grounds. Either of these forms can rarely, accidentally infect humans, typically in warm, shallow water in the southern U.S. in summertime. When times get *really* bad, they encyst. Click here for a CDC graphic of their life cycle (on the left). But the trophozoite forms only superficially resemble amoebas; their DNA tells us they are something much different indeed.

Naegleria, it turns out, is only a distant relative of the Amoebozoa, the true amoebae, which generally lack flagella. In fact, the true amoebae seem to be more closely related to fungi and animals than it they are to Heterolobosea, the phylum that includes Naegleria. Naegleria, in turn, seem to be much more closely related to Euglena — the flagellated (tailed) photosynthetic single-celled organisms from high school and college biology lab — and Trypanosoma, the causal organisms of sleeping sickness and Chagas disease. Take a look at this family tree of eukaryotes (nucleated organisms – everything except bacteria and archaea) for the groups Amoebozoa and Heterolobosea to see what I mean.

Heterolobosea are difficult to define in a sentence, since they have evolved into so many niches. What tells us they are related is their DNA. But generally speaking, the phylum that includes Naegleria is made up of organisms that alternate between amoeboid and swimming forms, and that, like the Euglenozoa, have “discoid” cristae, or folds, in their energy-producing mitochondria. In contrast, most animals, I believe, have sheet-like or laminar cristae. How exactly discoid is different from laminar I have not been able to discover. For extra randomness, the Heterolobosea also includes a group of slime molds that’s completely unrelated to the big showy ones most people (if they ever think of them) think of as slime molds.

The proposed kingdom to which the Heterolobosea belong — the Excavata — are even more of a mixed bag, although again one might say they are almost exclusively protists with either no or unusual mitochondria, two or more flagella for swimming, and a characteristic underside feeding groove supported by fibers called microtubules.

There are true amoebas that infect humans. Entamoeba histolytica comes to mind, the cause of the vastly more prevalent disease amoebic dysentary, which infects some 50 million worldwide. Naegleria, on the other hand, are not parasites of humans; they prefer bacteria and don’t seek out people. They only infect us when we swim into their habitat and happen to bump into them nose-first. Hungry and far from home, they crawl into our brains and start eating like crazy, killing the unfortunate host 95% of the time.

But as a result of its accidental nature, Naeglaria infection is quite rare in the United States — happening perhaps 2-3 times a year — especially compared to organisms that do seek us out in water. As a blog post at the L.A. Times points out:

According to the Centers for Disease Control and Prevention, the most commonly reported recreational water illness (RWI) is diarrhea, which can be caused by germs such as Cryptosporidium, Giardia, Shigella, norovirus and E. coli. These can be introduced into the water through trace amounts of fecal matter that cling to people’s bodies. The agency reports:

Swimmers share the water — and the germs in it — with every person who enters the pool. On average, people have about 0.14 grams of feces on their bottoms which, when rinsed off, can contaminate recreational water. In addition, when someone is ill with diarrhea, their stool can contain millions of germs. This means that just one person with diarrhea can easily contaminate the water in a large pool or water park.

I think I could have gone my whole life without knowing each and every bottom in the pool contains 0.14 grams of feces. It certainly makes a hard sell for the bidet. This fact alone should be *much* more frightening than the chance that a little, lost, hungry protist might somehow find its way into your brain, no matter how food-crazed it might be once it gets there. And if you’re still worried, there’s always nose clips.

The red tide dinoflagellate Karenia brevis. Public Domain, photo by Florida Fish and Wildlife Conservation Commission

Last week as I sat in a beach-side open-air restaurant in southwest Florida, I started coughing. Hard. I couldn’t stop, and I apologized repeatedly. Yet I hadn’t felt sick before, and the suddenness of the coughing was very weird.

Our waitress came by as I was expressing my bewilderment. She said, “Oh, it’s the red tide.” She said she had coughed all day too, and that some people were more sensitive than others (many people in the restaurant seemed unaffected), and that all that was necessary to relieve the symptoms was to go inland.

I stared out at the darkening Gulf of Mexico. A strong breeze blew into my face. Was this really possible? Was the irritation in my throat and my unstoppable coughing really the result of a microscopic sea creature? I had never heard that red tide could affect people on land. Since the algae that cause red tide, in spite of their menace, are still algae, and therefore a topic near and dear to my heart, I had to know what was going on.

After doing a little digging, I discovered I had indeed had an unexpected run-in with Karenia brevis (see here for pretty pictures), a dinoflagellate* that is the Gulf of Mexico’s very own purveyor of red tide neurotoxins.

In a post I did last summer I wrote about what dinoflagellates are:

Dinoflagellates are two-tailed plankton. They are also protists, the loose association of single-celled organisms with DNA inside nuclei and cellular organelles that are usually much bigger than bacteria or archaea. About half are predatory, half make their own food, and obviously, now we know some do both. The photosynthetic lot are the second most abundant constituent of the photosynthetic marine plankton after diatoms (which I covered here).

So, it is worth emphasizing, most dinoflagellates don’t cause red tides, nor are they inherently evil. Even Karenia, which does cause red tide, is not an infectious organism. It’s photosynthetic and makes its own food. It only causes problems when dies or gets eaten.

Gulf of Mexico red tides have always come. When conditions are right, the dinoflagellate blooms in smothering but sometimes patchy patchy clouds near shore. Karenia has been wreaking havoc since the days of the conquistadors and well before. But red tides in southwest Florida seem to have been more frequent and intense in recent years (see also here for the global perspective), and the intensity of respiratory disease in coastal Floridians may be worsening. This may be partly our doing, perhaps due to a combination of phosphate and nitrogen pollution from overfertilized yards and farms, detergent-laden sewage, and warming seawater.

This is the very real result. This video was taken in October just miles north of where I was last week (warning: graphic decay images):

During my stay, on the beach I saw dozens of dead horseshoe crabs, brittle stars (some still alive), crab bits, and a few fish washed ashore after a storm.These were also likely red-tide casualties.

The chemical that made me sick and killed all these fish and crabs is a neurotoxin called brevetoxin. Here’s Brevetoxin A, which, you must admit, is quite beautiful:

A deadly neurotoxin, or the Very Hungry Caterpillar? YOU decide.

When fish eat Karenia, they may accumulate this toxin in their bodies. When enough has accumulated, they die, but before that happens, they may in turn be eaten by a bottlenose dolphin or manatee. These, too, have been fatal victims of red tides. Shellfish also accumulate brevetoxin from Karenia they eat, and unfortunate diners who consume them in turn may acquire Neurotoxic Shellfish Poisoning, a charming combination of nausea, vomiting, and slurred speech.

K. brevis that die near shore or get smashed to bits in the surf somehow have their brevetoxins aerosolized, possibly carried on bits of sea salt or dust. When blown ashore, they can cause a suite of symptoms called “Red Tide Tickle” by tongue-in-cheek locals. For those of us who are sensitive, they include watering eyes, sore throat, and uncontrollable coughing. These effects stop pretty quickly once you get out of the breeze. The symptoms may be worse and far more prolonged in asthmatics, and may even contribute to more pneumonia, bronchitis, and asthma-related ER visits, if this 2009 study in Environmental Health Perspectives is to be believed. All told, the respiratory effects of red tide in Florida may cost up to $4 million a year. Some people report that swimming in red tides can cause irritated skin, too. I recommend you Don’t Try That at Home.

As early as 2005, a massive outbreak of Red Tide Tickle made headlines in papers as far away as Boston, where the Globe did a nice article for its science section. But obviously, tourism officials and local chambers of commerce are not eager for tourists to be scared off, and efforts by local health officials to spread the word to tourists resulted in canceled bookings and many unhappy local businesspeople. So perhaps it’s not surprising I never heard aerial red tide assault was possible, when Florida’s tourism dollars depend on it not being a big deal.

To me, it wasn’t especially, and it probably isn’t to most tourists. I left the restaurant and went home. The coughing stopped as soon as I got out of the sea breeze, and my sore throat was gone by morning. But I can’t help but think about that poor waitress — stuck there for an entire shift, all day every day she works, in red tide or no. For her, as for the fish and mammals of southwestern Florida waters, there is no easy escape.

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*Dinoflagellate literally means “whirling scourge”, and if you watch one, it’s easy to see why. Here is a video of a dinoflagellate waving one flagellum and twirling its other, inexplicably paired with Billie Holiday. The flagellum twirling and Billie Holiday are both cool, I just don’t get why they go together.

Smooth Operator: the slinky placozoan Trichoplax adhaerans. Creative Commons Oliver Voigt. Click image for license and link.

Author’s Note: This post is being entered in the National Evolutionary Synthesis Center ScienceOnline 2012 Travel Award contest. Enjoy!

Hidden away in calm, sheltered coastal waters is a remarkable little animal: a tiny transparent sheet of cells called a placozoan. Though composed of only a few thousand cells and no more than 25 micrometers thick (a bacterium is about 1 micromter thick), it’s an animal — the simplest we know of.

Here’s one in action:

And hidden inside it, scientists found recently, may be a clue to the Cambrian Explosion.

The Cambrian Explosion, you will recall, was the sudden appearance of the major modern groups of complex animals around 550 million years ago after several billion years of unmolested microbial partying on Planet Earth. Then, suddenly, Big Life crashed the party. What happened?

Placozoans, which may resemble the first animals, wander about eating algae and other detritus. Both upper and lower surfaces bear flagella that the creature uses to swim around. The whole organism can glue itself to a feeding surface and arch upward to form a makeshift stomach into which it excretes digestive enzymes. It then swallows the resulting goo through cellular drinking called pinocytosis.

Here’s a diagram (in French)*:

Public Domain. Click image for link.

And here is Trichoplax feeding behavior in action. Whatever genius thought to put this music with this video, well, I salute you.

The Atavism had a great post on placozoans a few months ago that is well worth reading if you’d like to learn more about their basic biology.

Though these little creatures look about as dissimilar to humans as can be, we do, in fact, share quite a few similarities. Nearly 87% of its 11,500+ protein-coding genes are identifiably similar to genes in other animals. And interestingly enough, scientists have just discovered that Trichoplax contains something else in common with us and all other animals, but not any other life: special oxygen sensors.

While the Cambrian explosion was under way, oxygen concentrations were rising. For most of Earth’s history, atmospheric oxygen concentrations had not exceeded perhaps 3%. Early single-celled organisms just absorbed oxygen by diffusion. That made it hard for organisms that dared form layers of cells greater than one or two thick to breathe, because there was no way enough oxygen could diffuse to interior cells.

But in a world where atmospheric oxygen concentrations were busy rising from 3% to near-modern levels of about 21%, oxygen could diffuse much further. That in of itself  may have helped drive the appearance of multicellular life. But that solution only goes so far.

A related problem for any such multicellular organism is how to know whether the cells inside are starving for oxygen or in danger of overload. Unattended oxygen is a bit like a bad drunk: it staggers around and breaks things. Too much of it in the cell can lead to a buildup of toxic reactive oxygen chemicals. On the other hand, hypoxia, or oxygen starvation, is a bad situation too. Without an oxygen-sensing system, cells have no way of taking action to prevent suffocation or poisoning.

Trichoplax adhaerens, stained and under the confocal microscope, by Karolin von der Chevallerie (Schierwater lab, University of Hannover). Used with permission.

But this is just what scientists in the UK and Germany have discovered in placozoans. In animals studied so far, scientists have found three critical oxygen-sensing proteins: an oxygen sensing protein called proline hydroxylase domain enzyme (PHD), a hypoxia response protein called hypoxia-inducible transcription factor (HIF) that can be switched on or off by PHD, and a trash-tagging protein called von Hippel Lindau protein (VHP — love that name).

When PHD senses oxygen, it switches off HIF by adding -OH (hydroxyl) units to certain proline amino acids near the end of the protein and VHP then tags it for trashing(by ubiquitination). When PHD does not sense oxygen, it doesn’t tag HIF, and HIF — a transcription factor — is transported back to the nucleus where it promotes the production of a gene that shuts off the Citric Acid Cycle (a system that cells use to harness oxygen to extract lots of energy from glucose) along with a host of other oxygen-related genes. As a result, glucose is shunted from the Citric Acid cycle into the energetically-less-productive but undoubtedly-preferable-to-starving process of fermentation.

What Loenarz et al. found and published in EMBO Reports last January was that the basic components of this system — present in more elaborate forms in humans and all other animals tested — is present even in placozoans, and still functioning much as it does in humans.

Stained, fluorescent T. adhaerans under the confocal microscope. Staining is for the Hox-Para-Hox gene Trox-2. Image by Karolin von der Chevallerie (Schierwater lab, University of Hannover).

In fact, when they inserted the placozoan version of the oxygen sensor PHD into human cells, it worked just as well as human forms in shutting off the hypoxia-response protein HIF. Think about that: the functioning of these proteins is so conserved (read: important) that they still work in species separated by at least 550 million years of evolution. Wow.

So what could this mean? The HIF system is not found in single-celled protists or the choanoflagellate Monosiga brevicollis, which, as I mentioned in my last post on sponges, are probably animals’ closest relatives. That means that early on, animals came up with a way to maintain oxygen homeostasis within their enlarging bodies. Such a system gave them a way to sense whether cells inside them needed oxygen, and then take appropriate measures.

It was a system so successful we are all still using it, and with genes so similar to our animal relatives — even to shimmying microbial sheet animals — we could all basically still trade with each other. You could probably swap in the T. rex oxygen sensing system, were you to know it, and get along just fine (and impress every five-year-old on the planet).Thus, the first animals, whatever they looked like, probably cobbled together this system during the oxygen-fueled Cambrian bloom, and in the process, helped propel themselves to half a billion years of evolutionary success.

Loenarz C, Coleman ML, Boleininger A, Schierwater B, Holland PW, Ratcliffe PJ, & Schofield CJ (2011). The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens. EMBO reports, 12 (1), 63-70 PMID: 21109780

Rytkönen KT, & Storz JF (2011). Evolutionary origins of oxygen sensing in animals. EMBO reports, 12 (1), 3-4 PMID: 21109778
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*I hereby move that a suitable French restaurant in New York City be renamed “Chez Trichoplax”. In order to dine, however, you have to hover over your food and digest it by absorption. I’d eat there.

Way, way cool, boys. In addition to Serratia, which provides the delightful red coloring of the biohazard symbols and the lettering of the board on the right (handy bio-nerd tip: If you want to keep your roommates away from your leftovers, use those cute biohazard marked zip-loc bags to store them. Expensive, but effective!), they also appear to have innoculated several species of mold (Pennicillium? Cladosporium?) into the lettering of the board on the left. Notice that the mold starts out white, and doesn’t darken until the very end, when it starts making its melanin-laced spores (the melanin is sunscreen to protect the spores from UV damage).

I would not, however, have wanted to be the unfortunate whose job it was to remove these things after they’d, um, served their purpose. Speaking of uses for biohazard bags . . .

Well, it just so happens it probably looked a lot like a sponge, because they, or something very like them, were likely the first. And this is what they look like today:

A tube sponge, a vase sponge, a rope sponge, and a crust sponge all walk into a bar. Wait, scratch the bar part. Sponges come in lots of shapes! The yellow tube sponge, Aplysina fistularis, the purple vase sponge, Niphates digitalis, the red encrusting sponge, Spiratrella coccinea, and the gray rope sponge, Callyspongia sp. in the Caribbean Sea, near the Cayman Islands. May 23, 2007. Creative Commons Twilight Zone Expedition Team 2007, NOAA-OE. Click for link.

Some sort of vertebrate hides inside a gorgeous blue barrel sponge off Bonaire in the Caribbean. Creative Commons Chris Coccaro, NOAA-OE. Click image for link.

A sponge is, in essence, a multicellular organism with no organs or tissues, but with specialized cells, which distinguishes it from small multicellular protists. Like algae, the thinness of the sponge body plan and the fact that most of its cells are exposed to circulating water (provider of oxygen and food, remover of wastes) makes organs like hearts, kidneys, and digestive tracts unnecessary.

A typical barrel or tube sponge is in essence a perforated sac. Click here for a nice diagram that helps illustrate the following text. The exterior of sponges is coated with epidermal cells; in the wall of the sponge are wandering amoeboid cells that perform some immune-system like duties and secrete crystalline spicules (usually calcium carbonate or silicic acid) or proteinaceous fibers that support the sponge; special cells called porocytes can encircle the inflowing wall pores; and distinctive choanocytes, or collared cells, line the interior spaces of the sponge. The spicules can have any number of points; the fossils of the glass sponge Hydnoceras from the Devonian (390-360 mya) look for all the world like they’re wrapped in plaid thanks to their six-pointed spicules which appear four-pointed in the two dimensions apparent on its exterior.

Sponge spicules. Some can be four- or six- pointed; others are hooked. Public domain, click for link.

The collars that give choanocytes their name are made up of finger-like cytoplasmic membrane extensions called microvilli (like the ones that line your small intestine) surrounding tail-like flagella. The beating flagella create a current that draws water in through the porocytes or intercellular pores (in either case, the holes are called “ostia”) and out through the central hollow of the sponge, called the osculum. Food particles that bump into the microvilli stick to them and are either engulfed and digested, or passed off to amoeboid cells who get the job done.

You can see the flow of water choanocytes generate most easily when sponges spawn. In this video, the divers capture sponges spawning at the Flower Garden Banks National Marine Sanctuary, in the Gulf of Mexico, some 70 to 115 miles off the coasts of Texas and Louisiana.

The sponges at the end of the video are undoubtedly releasing sperm. The first set of sponges may be females releasing eggs, but they are more likely hermaphrodites (most sponges are) and are releasing fertilized eggs or larvae. Sperm — formed from a transmogrification of choanocytes — must find another sponge of the proper species and fuse with a choanocyte inside. This is where it gets trippy. Once there, the sperm-bearing choanocyte metamorphoses into an amoeba and crawls toward an egg. The egg itself was formed when either a choanocyte or an amoebocyte engulfed special “nurse” cells to form a yolk. Sperm-bearing amoeboid choanocyte and engorged egg fuse. How the proper chromosomes find each other to form a single diploid nucleus in all this mess without ending up with five or six copies of the genome is a subject for another day.

The sponge can then release the fertilized eggs, or it can retain them. Either way, the zygote develops into a larva that consists of a ball of cells with external flagella or cilia drive the whole thing around. They tool about for a while praying they don’t get eaten while looking for a suitable site to set up their choanoflagellate condo, and presto chango, the larva lands and grows into a sponge.

Sponges are often considered colonial organisms like the alga Volvox. The cells are so loosely associated that if you run a sponge through a filter and scramble the cells, they will re-associate easily to form another sponge. Slime molds, though evolved out of a completely different amoeboid lineage, can perform this trick too (Try *that* with any supposedly “higher” animal).

This brings us to the meat of this blog post, and the reason I include it in today’s “Friends in Groups” Blog-a-thon. Ancestors of today’s sponges may have been the the first truly multicellular animals. Over at S.E. Gould’s Lab Rat blog is a nice definition of multicellularity, which says, essentially, cells of multicellular organisms must stick together, communcate with each other, depend on each other for survival, and specialize. Sponges seem to qualify by all these measures. To be fair, the placazoans, a fascinatingly simple roving cellular film, are also in the running for that honor, but I must save discussing them for another day.

How long ago this happened is a subject for debate, but it seems it was at least 543 million years ago during the Proterozoic from whence we know of the first fossil sponge spicules, and it could be much more. Early sponges may not have made spicules or any other traces likely to fossilize. Whenever they appeared, they must have cleaned up considerably what was probably becoming some pretty soupy seawater as they were and are, in essence, little ocean filtration units, the first of many filter feeders to come.

Regardless of which was the first multicellular animal, sponges and placozoans were probably not the first animals. That distinction may belong to protists called Choanoflagellates, which are single or multicellular bouquets or spheres of what look just like the choanocytes inside sponges. At least one free-living spherical choanoflagellate colony (coincidentally named Sphaeroeca volvox) looks not unlike a sponge larva.

Sphaeroeca sp., a colonial choanoflagellate. Public domain, click image for link.

In still other choanoflagellate species, the flagellate cells face *inward* into a cavity, much like, well, an adult sponge.

But, you may be saying, how do we know that such sedentary beings are animals at all, though? Well, their DNA sequences tells us nowadays. But biologists have known sponges are animals for much longer than we have known about DNA. Remember those proteinacious, elastic skeletons? (if you’ve ever squeezed a true bath sponge, you are familiar with this) Among other similarities, these fibers are made of a form of the protein collagen — the very same protein in your tendons, ligaments, and skin, where, when it breaks down, you get wrinkles. And although no other animal groups have true choanocytes, most major groups (phyla) have “collar cells”, and some of these may well have evolved from choanocyte ancestors. And your immune system also contains amoeboid “macrophages” that wander about your body at will, slipping in and out of tissues as they please, seeking invaders. No doubt there are other similarities.

Sponges were the first animal multicellular cooperatives, then. Some of these loose cellular federations, when subject to strong selection and other evolutionary forces, transformed into tightly knit multicellular cooperative machines like you: the rest of the animals. Their cells have become so bound up together that we no longer think of them as cellular co-ops. Animals are spoken of as one “organism”. Yet when you shed skin cells or digestive cells, or when any cells in your body voluntarily die without offspring, they are sacrificing themselves for the good of this larger, albeit genetically identical, entity.

Before we leave the sponges, let’s briefly look at some of the more entertaining types.

One of the three major groups of sponges are the glass sponges, distinguished by their glassy, six-pointed silicious spicules and sometimes-delicate, sculpted appearances. Here is one preserved in the Sant Ocean Hall at the Smithsonian. Notice its long rooting spicules, a feature many sponges share. These would be covered in mud in the ocean.

The Venus's Flower Basket, a glass sponge. They look pretty much like this in the water, too. Creative Commons Ryan Somma. Click Image for link.

When sponges live deep — really deep — beyond the domain where filter feeding is a profitable business, they tend to become, amazingly, carnivorous. One might not expect such a feat for an organism that typically has all the mobility of a potted plant, but then again, plants have produced more than a few carnivores themselves.

One of the most bizarre-looking organisms on the planet is a carnivorous sponge. Don’t believe me? Behold the ping-pong tree sponge, Chondrocladia lampoglobalis, a deep-sea dweller that resembles a 60′s-retro chandelier popular among hipster home decorators. These curiosities are typically about 50 cm (20 in) high and live at 2600 to 3000 m (8,500 to 9800 ft) deep. Small crustaceans or worms so unfortunate as to land on the ping-pong tree sponge find themselves velcroed to it by tiny grappling-hook-like spicules. This triggers digestive cells to migrate to the site and spend the next few days chowing down.When supper is finished, they return to their original locations.

Other carnivorous sponges deploy similar weaponry. In addition to hooked spicules, they may use sticky threads to entangle and digest prey. Most carnivorous sponges have lost their choanocytes and resulting hydraulic systems, as these would be pointless in the absence of filter feeding. Chondrocladia has not. It uses a highly-modified hydraulic system to inflate the ping-pong balls at the ends of its branches.

A few sponges — perhaps 50 species — live in freshwater. My friend George Watson, a technical diver, snapped beautiful photos of this freshwater sponge deep — probably beyond the reach of light — in a small but *very deep* lake in, of all places, New Mexico. It is likely a species of Spongilla (and if anyone knows the exact species, George would like to know), the same genus as this specimen of Spongilla lacustris captured in the upper reaches of the Columbia River in Washington state:

A photosynthetic, symbiotic freshwater sponge, Spongilla lacustris. Creative Commons Kurt L. Onthink. Click image for link.

You will notice that it is green. That is because it, like many freshwater sponges, hosts a green algal symbiont. Some marine species partner with blue-green algae (also called cyanobacteria) or even photosynthetic dinoflagellates (a kind of protist), which can provide over half of their energy demands in places where the filter feeding is not so hot. Ahh, biology. How I love you.

Finally, I cannot end this post without mentioning the plague of potato sponges that washed ashore following Hurricane Irene this year. The poor homely things seem to have been scoured from the seabed by the storm, whence they drifted, dying, ashore, only to be accused of being foul-smelling and disgusting. If your corpse were floating for several days in Chesapeake Bay, I’ll wager it would not be so sweet-smelling either.

The many colors of Serratia marcescens. Image courtesy Dr. Robert Shanks, the University of Pittsburgh.

Over on the news side today is an article I put together for Scientific American Online on some mysterious, ubiquitous, and sometimes-deadly red bacteria that are probably at this moment living in your shower grout and contact lens case. Plus, when slime molds eat them, their plasmodia turn red like flamingoes eating shrimp turn pink. How cool is that! Check it out!

A short while after I posted it I received an astonishing letter about it from a man named John MacDougal. He wrote,

[I] was shocked to see your article on passionflowers in SciAmer because those specimens were collected by me, and each has a truly special inner personal story which all came flooding back. It was hard to concentrate on the rest of your story, though the Rynchospora that started Duke’s slide show is a truly beautiful specimen, and the close-up of the fern is… iconic.

Then he added with good humor

I thought you would enjoy seeing a photo of the flower before I killed it

And here it is:

You can even see the coiled tendrils so carefully preserved on the pressed specimen above.

According to MacDougal, this is a very rare passionflower originally discovered by botanist William Jameson and duly named Passiflora jamesonii. He mentioned that I should look up Volcán Mojando and Jameson to discover an interesting story about the species but my google-fu was not up to the task and I couldn’t find it (if anyone knows it and wants to share, please do!).

He continued on to point out that the flower is big, and its sex parts at the business end of the flower are asymmetric. That is, the pollen-making stamens (yellow things), or male parts, are all on one side of the flower. There’s a good reason for this: it helps deposit pollen specifically on the underchin of the flower’s hummingbird pollinators. Since flowers compete for pollen-porting real estate on their pollinators, this would be a way of selecting a uniform spot that is unlikely to be used by another flower.

But that asymmetry would be hard to tell from a pressed herbarium specimen, he noted, and there are many other things that cannot be guessed. For this species, no one knows the natural appearance or taste of the fruit, or even who eats it (and thereby “spreads” it seeds) in the wild. It’s a good reminder that although herbarium sheets are be good “manmade fossils”, they are not the final word on plants. For that, you must observe them growing in nature.

Where, unfortunately, MacDougal notes this flower may not last much longer. It lives at treeline, he noted, on the volcano where it grows, and is likely to be pushed up and out of existence by climate change.

In any case, it goes without saying I was delighted by his letter, the coincidence, and the chance to compare an herbarium sheet’s occupant to its appearance at its former day job. Thanks so much for sharing, John!

This is the sperm of Zamia roezlii. It has a flapper dress-like fringe of tens of thousands of flagella to turbo-charge its way to eggs.* That a plant should possess sperm with such horsepower is all the more surprising given that most plants have sperm with no tails at all. A pollen grain is actually a tiny haploid plant called a male gametophyte. In most flowering and coniferous plants a pollen grain produces two tailless sperm who travel down a burrowing pollen tube to reach the female gametophyte buried inside a cone or flower — no tails needed.

Ancestral plants tend to have swimming sperm because land plants evolved from aquatic green algae, where the swimming — and fertilization — was easy. A few ancestral plants like mosses still have sperm with tails and rely on a watery film on the surface of the plant for the sperm to get from Point A to Point B. But they are such lousy swimmers that some mosses resort to Plan B: they make special leaves folded into little splash cups, and when a raindrop lands in them, their architecture blasts sperm inside skyward in an attempt to Fed-Ex them to the vicinity of a receptive female. So turbocharged swimming plant sperm is definitely an oddity.

To which plant does this impressively-endowed sperm belong? A cycad.

OK, so what’s a cycad? This is a cycad.

Not dinosaur eggs -- but something that the dinosaurs might have seen. Creative Commons kiryna. Click image for license and link.

Here’s what they typically look like in profile. These are mature, juvenile, and seedling cycads of the same species.

Creative Commons Esculapio; Click image for license and link.

Cycads are old. Way old. They were the dominant plants during the Mesozoic, the age of the dinosaurs, as seen in countless ancient murals. At least that was the dogma for many, many years. But recently a widely reported studied was published that undermines that idea — if you look at it in a certain way. But before we come to that, let’s look at what cycads are and at their surprising biology.

Sometimes called sago palms, cycads are in no way palms. Palms are flowering plants. Cycads, like pine trees and juniper bushes, are gymnosperms — “naked seed” plants. In other words, they make seeds, but they don’t make flowers or fruit as a way of bringing those seeds into the world or sending them on their way. Seeds were a great evolutionary innovation for plants, because they allowed them to package a little plant embryo that has already begun to develop — perhaps even a little root and a few small leaves — with a little stored food in a dessication-resistant shell.

A seed is a way of giving a young plant a jump start on life and a little food for the road, not unlike the relatively contemporaneous innovation of amniote eggs in land vertebrates. Microscopic spores — the previous dispersal method still employed by mosses, lycopods, and ferns today — are much more prone to drying out or landing in a place far too inhospitable for germination. Seeds help increase the chance of success.

A cycad plant is a column or trunk of old leaf bases surmounted by a cluster of new leaves. Cycad leaves are wonderful to touch, if you ever get the chance. Strappy, leathery, tough, and often blue-green, there’s something delightfully primeval in the way they feel (although, it should be said, the much-older mosses have delicate, thin leaves**).

Cycads also have an interesting symbiosis with cyanobacteria, also called blue-green algae, just like some lichens. They make special “coralloid roots” that grow upward in a very un-root-like fashion. In return for feeding, housing, and hoisting their cyanobacterial symbionts above-ground inside these structures, the cyanobacteria provide the cycad with that most limiting of bio-nutrients: fixed nitrogen.

In addition to having super-charged sperm, the pollen of cycads has another interesting habit that they share with their close relative, Gingko. When their pollen arrive on a female cone (usually via weevil, beetle, or wind), they start to grow into an ovule. Once there, they send out a long tube into a part of the ovule called the nucellus and send out a haustorial structure that sucks up nutrients from the host female.  Haustoria are also used by parasitic fungi that penetrate their plant hosts.

In cycads, the haustorial pollen tube ends up destroying most of the tissue into which it penetrates, although this tissue is a) not part of the future seed and b) technically expendable because once a cone is fertilized it is not used again. But imagine, if you will, that every time human sperm landed in a uterus, they implanted in the uterine wall, sucked up nutrients and grew into little organisms of their own for a while, and only then released the gametes that would go on to fertilize the egg. That should give you the general, somewhat unnerving idea.

Like most gymnosperms, cycads make both male and female cones, but unlike many conifers, they bear only male or female cones on a given plant. That is, there are girl cycads and boy cycads. The female cones make seeds and the male cones pollen. In the photo at top are female cones with seeds inside. When you break them open, you often find brightly colored seeds, like this, or this:

Disemboweling a cycad cone. One of the brightly colored seeds is visible in the subject's hand. Creative Commons Sharktopus; click for license and link.

Because cycads are gendered, that means it’s also possible to end up all alone. Indeed, as Robert Krulwich reported recently on his blog, that has been the sad fate of a cycad found in Africa 100 years ago and sent off to the Royal Botanic Gardens at Kew. It’s a boy. And unless someone finds a female to keep it company, it will be the last of its kind.

Cycads have received a bit of attention lately. Many cycads contain carcinogens or neurotoxins or both. In Oliver Sacks’s Island of the Colorblind, he relates his fondness for cycads (a love I share) and his frustrating investigation into a mysterious devastating neurological disease among the people of Guam that may be linked to their habit of pounding up seeds to make cycad flour. Lately, suspicion has fallen on the practice of eating bats who may have concentrated cycad neurotoxins in their bodies.

That brings us back to the question of their antiquity. Cycad fossils date back to at least the Permian, and possibly the Carboniferous, 320 million years ago, the age of giant coal-forming swamps and disturbingly large dragonflies. But they flourished during the Mesozoic — the “age of the dinosaurs” — and probably were dined upon, and certainly trod upon by dinosaurs. They may also have been the first insect pollinated plants when beetles took up the habit of eating — and generally living in, wallowing in, and spreading around — cycad pollen, a tradition they continue today. But a recent study in Science reported here, here, and here finds that, according to their DNA, the 300 modern species of cycad evolved a paltry 5-12 million years ago.

OK, so the species alive today were not those alive during the Mesozoic. I accept that. That, in of itself, that is interesting news — their diversity declined in the wake of the Big Impact, and seem to have rebounded and re-speciated during some sort of worldwide climatic change. But the authors make a big point about us not being able to call cycads “living fossils” because they are not the same species we find in fossils.

Hold up there. They still look like ancient cycads. They still make seeds like ancient cycads. Their tailed sperm still betray their ancient origin, and the ancestral condition of all land plants, presumably just like ancient cycads. Survey says: They’re still cycads. And cycads are still old. And so, in my opinion, when you visit cycads at botanic gardens or see them in someone’s yard, it’s still OK to think of them as ancient, and imagine these extraordinary creatures among the dinosaurs.

**OPTIONAL BIONERD TECHNICAL DIGRESSION AND SOAPBOX ALERT**

You learn quickly in biology, as in our lives, nearly everything is a gray area. Life is a continuum of form and function. We try to impose neat conceptual order on it to make it easier for us to understand and discuss, but no sooner have we done it than we find some (or many!) creatures that throw wrenches in the cogs.

Take, for example, the term “species”. If you really want to light a match in a room full of ideological fuel, ask a group of biologists to define that term. Better yet, study life long enough and you’ll realize “species” has completely different meanings among various groups of living things, and especially bacteria and archaea, where inter-species sex is common and species-defining mechanisms like reproductive or geographical isolation that work fairly well in animals are often meaningless.

I’m not saying we should ditch the concept “species” or even get rid of binomial nomenclature, the double-named system devised by Carolus Linnaeus for calling species by name (think: Homo sapiens). I think it still has great value for humans to think of living things in terms of species — many of which are easily discernable and very “real” — and to give them names and not (forgive the term) dehumanizing barcode numbers, as some have proposed.

BUT, perhaps we should not be so finicky about the term “living fossil” with regard to species. Perhaps cycads have changed a little bit from their days of the dinosaurs. Perhaps they’re not the same “species”. If they look more or less the same and are doing more or less the same things in the same ways, that’s good enough for me. They are still recognizable ancient forms, and they’re still alive.

I, for one, love “living fossils” because it helps make things vivid for non-scientists. It helps people engage their imaginations. Because unless you know their story, and their history, cycads might just seem like a boring palm-thingy, and a cycad fossil just “a leaf”. When you read that cycads are living fossils, and that something almost identical lived among dinosaurs and giant ancient dragonflies, and that today they possess perhaps the most well-endowed sperm on the planet, and that you can still touch their living, breathing descendants today, your eyes may be opened that they are so much more.

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*I’m sensing some latent flagella envy among some elements of my reading audience. Kinda reminds me of those guys with three or four outboard motors clamped to the back of their motorboats, if you know what I mean.

** Technically, “phyllids“. Only vascular plants (those possessing conducting tissues for water and sugars like xylem and phloem) have true leaves, according to botanists.

So far, we’re up to $110 so far here at Amoebas for a Better Science Tomorrow. Thank you SO MUCH if you’ve already given! But if you ever play cards with me, you’ll learn very quickly how competitive I am. Right now we’re in the middle of the pack on the Sci Am leader board. Let’s see if we can make it to #2. (#1 seems out of reach [shakes fist congenially in general direction of Jason Goldman]). Similarly, as a blog network, we’re trailing the Independent Science Bloggers and the Ocean and Geobloggers. I can’t resist the urge to try and chase them down at the finish line. Join me, and help out some deserving kids stiffed by short-sighted budget cuts — and perhaps even inspire someone who will go on to change the world for the better — in the process. : )

Click here to go to my donors page, read about some other readers who’ve given, select the microscope project that appeals to you the most, and give. You’ll be glad you did. Promise.

The geocarpic fruits of Spinelia genuflexa. Creative Commons Alex Popovkin, Bahia, Brazil. Click image for license and link.

The above plant is a sweet little creature, yet may not seem particularly noteworthy. But it did to a handyman named Jose Carlos Mendes Santos, who found it in the backyard of an amateur Russian botanist named Alex Popovkin in northeast Brazil, took the trouble to carefully uproot it, and shared it with his employer. He, in turn, planted it, placed it on a window sill, and shared photographs with botanists. After studying it at length, they determined it was a new species.

And it was a new species in, of all things, the strychnine family (Loganiaceae). Another genus in this family, Strychnos, contains many plants whose bark or seeds contain the poison strychnine, which has been a popular choice in many real and fictitious murders, in spite of the fact its bitter taste is obvious even at low concentrations. Spigelia, the genus of which this little plant proved a member, probably contains nothing of the sort.

The little plant (it’s only an inch high) does, however, have a distinguishing feature. It practices geocarpy. Once its flowers are pollinated and its fruit is ripening, they droop to the ground and deposit their payload, as you can see above. They may even gently bury the seeds in the mosses at the plant’s feet. Awwww. In case you don’t recognize this habit, it is the same one employed by a plant you probably know and love (especially if you are American): the peanut.

Spigelia genuflexa in bloom. Creative Commons Alex Popovkin, Bahia, Brazil. Click image for link and license.

But why should you really care about this obscure little plant? I found out about this story through a press release, and though I don’t normally quote press releases as the “quotes” are often, well, a bit suspicious, this one is too genuine not to. It is attributed to a scientist at Rutgers — Lena Struwe — who helped identify the plant:

“It is very easy to think we have found and described most plant species of the world already, but this discovery shows that there are so much left out there without name and recognition … [it] shows that the most amazing living things can be found when you least expect it, during times and places when you really aren’t looking for something new, and suddenly it is right there in front of you. How many of us haven’t had the most brilliant ideas in the shower? The art of taxonomy is finding as well as being able to recognize something as new or different, which is hard when the world is home to millions of species and very few species experts.”

With taxonomists in obscure groups of organisms a vanishing species due to a lack of funding, don’t think you can’t make a worthy contribution to biology just because you’re not a scientist. My friend Nathan Pieplow of earbirding.com has never trained formally in biology (he studied foreign language and speaks several of them) but is a recognized expert in bird song. Another friend, Michael Kuo, teaches english by day but is a university-class mushroom expert by night who’s making a huge contribution to morel taxonomy by helping to sort out the North American species. And then there’s Kerry Knudsen, a retired construction worker, who, after growing bored with retirement, got interested in lichens and decided to volunteer in the University of California at Riverside herbarium. In five years, he described more than 25 new species of lichen and lichenicolous fungi and published more than 70 peer-reviewed papers. He has no academic degrees.

But even if you’re not willing to devote hours to biology in your spare time, remember this next time you’re out in nature or even just in your own back yard: this little flower, now appropriately named Spigelia genuflexa, was discovered by an observant handyman.

The species description was eventually published in the journal Phytokeys; You can read the paper here.

This year, some intrepid divers changed that, stumbling onto a geological and biological treasure and capturing it on video. We’ll get to that in just a moment.

Don't drink the water: the Dead Sea. Creative Commons xta11. Click Image for License and link.

This is the Dead Sea. As you can see, it appears quite dead. There are no plants, fish, or any other visible life in the sea. Its salt concentration is a staggering 33.7%, 8.6 times saltier than ocean water, which is only about 3.5% salt. The stones at the water’s edge encrusted in salt are a good clue in that department. As a result, the Sea is famous for its body buoyancy properties, as people who take an exploratory dip generally find themselves riding high on its waters.

The Dead Sea is also the lowest point on earth, and getting lower every year, as water that would ordinarily fill it by flowing in from the Jordan River has been diverted to quench the thirst of Israel, Jordan, and Palestine. Every year, the lake drops over a meter per year. If this goes on long enough, the Sea could face Owens Lake’s and the Aral Sea’s fate: becoming a wind-swept salt flat. Yet, for now, life goes on.

Biologists have known since the 1930s the lake is “not dead yet”. Instead, it’s full of microbes that get along quite happily in the salty soup, for it keeps out competitors that would take over in a more hospital aqueous environment. In general, the water contains 1,000 to 10,000 archaea* per ml, a much lower concentration of life than in seawater, but quite respectable, all in all, for a place where one molecule in three is not water. Occasionally, when conditions are right, the sea blooms red with life. This happened in 1980 and 1992.

In any case, divers from Israel and Germany finally braved the waters this year to see what might have been causing the aforementioned  concentric-ringed ripples observed near shore. They were not disappointed. This is what they found (hit the button at the bottom right corner of the youtube player to watch it in uber-super-cool full screen mode):

These are freshwater springs, jetting into the bottom of the Dead Sea from inside craters. Found as deep as 100 feet from the surface, the springs lie at the base of craters as large as 50 feet wide and 65 feet deep.  As can be seen, a variety of interesting geological formations surround them.

The springs roil the waters they flow into in a phantasmal slipstream. Starting at about 2:00, you can see it coiling and mixing like it’s hundreds of degrees hotter or more sugary than the surrounding water. But no, it’s just that much less salty (and dense). (There’s a famous scene in the “Caves” episode of Planet Earth that vividly illustrates salinity gradients (haloclines) in the cenotes of Mexico too — go track down a copy if you can).

What makes this place biologically amazing was the life they found near the plumes.

A nice article on the discovery at National Geographic notes:

The top of the springs’ rocks are covered with green biofilms, which use both sunlight and sulfide—naturally occurring chemicals from the springs—to survive. Exclusively sulfide-eating bacteria coat the bottoms of the rocks in a white biofilm.

Bacterial mats or biofilms have never been found in the Dead Sea before. You can see the films of green photosynthetic bacteria on top of a rock and a film of white sulfide-oxidizing bacteria underneath it in the very last scene of the movie. Go have a peek.

Not only have the organisms evolved in such a harsh environment, Ionescu speculates that the bacteria can somehow cope with sudden fluxes in fresh water and saltwater that naturally occur as water currents shift around the springs.

Ionescu further pointed out that all known hard-core halophiles, or salt-loving microbes, die if you put them in freshwater, and vice versa. How these microbes are able to withstand what must be wicked shifts in salinity on an ongoing basis is anyone’s guess. This reminds me of the creatures at deep sea vents that must withstand massive fluctuations in temperature as ventwater hundreds of degrees hotter than the surrounding seawater shifts back and forth. I’ll say it along with Jeff Goldblum once more: “Life finds a way.”

Whatever they are — and scientists are planning to go back to find out more — they are not like the microbes found in the rest of the sea nor like the organisms that cause the sea to occasionally bloom red. And they are very diverse — much more so than their halophilic neighbors.

The article also notes that the Dead Sea’s waters are particularly caustic and difficult for divers, which, as a new diver myself, I found particularly interesting/horrifying. In addition to having to weight yourself down incredibly — on the order of 90 pounds; when I dove in Hawaii last year, I used about 12 pounds — Dead Sea water is not something you want coming into contact with your face. Ever.

Divers will also need to wear full face masks to protect their eyes and mouths. That’s because accidentally swallowing Dead Sea salt water would cause the larynx to inflate, resulting in immediate choking and suffocation.

Oh good.

Likewise, the intensely salty water would instantly burn and likely blind the eyes—both reasons why Dead Sea swimmers rarely fully submerge their bodies, Ionescu noted.

I well recall practicing losing, replacing, and clearing my mask of water at depth when I was getting certified. I guess in the Dead Sea, that’s more of the nuclear option in case of leak or “wardrobe malfunction”.

For more information on the springs (which have not be formally published in a journal yet), see the scientists’ press releases here and here.

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*Archaea are a fascinating and huge group of bacteria-like organisms that were only discovered in the 1970s by biologist Carl Woese (“Woes”). If you don’t know about archaea, you should learn more. Trust me.

The Artful Amoeba is proud to participate in this year’s Science Bloggers for Students science classroom fund drive (read more about this year’s project at Janet Stemwedel’s Doing Good Science blog). A number of Scientific American bloggers are participating, and we’re competing against each other and a whole bunch of other blog networks to raise cash for science supplies. If you’ve been paying any attention to what’s been happening to education budgets across the nation this year, you know how critical the situation is in some states.

The projects I chose for my giving page will all help buy microscopes for students with either old or obsolete microscopes or no microscopes at all. If you’ve experienced the magic of seeing living microorganisms right in front of your eyes, you know what an important experience this can be. I’ll never forget the first time I observed Vorticella in microbiology at Cornell, and was stunned to see it retract in an instant like a telephone cord when someone bumped the lab bench on which my microscope sat. That these little guys could respond to stimuli from our world, and in such an astounding way, opened my eyes to the beauty and complexity of the small. Here’s a sample for you; if you watch carefully, you can see roundworms (I think) swimming slinkily by as well, along with a host of other interesting beasties.

As awesome as this is, there’s nothing like seeing it live and in person (and being surprised by the spontaneous behaviors you see!), so microscopes for schools are a cause I can support with my whole heart.

I’ve kicked in $10 to get it started — I’d donate more, but I’m currently “underemployed” as I work on getting my freelance career off the ground and (shh) also on a book proposal. You may be in similar circumstances, but it doesn’t matter. Whatever you can give, no matter how small, is great. For the cost of a frozen pizza, you can help spread the magic of biology to kids who wouldn’t otherwise get the chance to experience it.

Have a look at the microscope projects I’ve chosen and select one of your desire. Or give to more than one, or just give at the top of my page to the projects I’m supporting in general. If you’re a reader of this blog, it’s a cause I know you can get behind. And if you have a competitive streak, you can track how Scientific American is doing against our competition (or you can see how this blog is doing against the other Sci Am bloggers here). Help us represent!

When I took botany and taxonomy of vascular plants in college, we spent many an hour poring over specimens under dissecting microscopes pulled with tweezers from smelly jars of preserving liquid. I was always a bit dubious about this prospect, although the result generally justified the effort. We also had some fresh specimens or live plants to examine, and on one occasion we even had frozen magnolia flowers to dissect. But the backbone of our laboratory learning program — since there was no way the greenhouses could contain good specimens of all of the dozens of plant families we were learning — were 11 x 17″ sheets of acid-free paper on which plants pressed flat had been taped, glued, and labeled. They were called herbarium sheets.

Often the plants were decades old. One day I looked down at a sheet I was examining and noticed the plant had been collected in 1902. That was the year my grandfather was born, and I gazed in wonder at a plant that had been alive and growing in that year. And yet, like all the plants in the herbarium, it looked like it could have been pressed just a few decades ago at most. Such is the magic of the herbarium sheet — manmade plant fossils that preserve color, detail, seeds, spores, and DNA in a way art cannot.

Herbarium sheets may also preserve the “type” specimen for a given species. This is usually the first specimen collected and named by a scientist. There’s often a piece of red tape or another indicator on the page to mark it as type. They are very valuable, since they are the specimen against which all future specimens — and the dividing lines between other species — will be judged.

Some herbarium sheets contain little treasure chests too — folded paper packets containing seeds or other structures that don’t press well or fall off too easily. I once even saw an herbarium sheet for a fir tree with a fir cone wired into its own snug little cage on the sheet (fir cones fall apart at maturity, which is why you never see one lying on the ground off the tree).

Duke University has created a charming little slideshow, whence the images on thsi page come, highlighting some of the 800,000+ sheets in their herbarium, or library of preserved botanical specimens, which they claim makes it the second largest in the nation. Put the slide show in full-screen mode to fully appreciate the details.

With a focus on passion flowers (arguably (when unpressed) the coolest flowers in the world and the source of my favorite tropical fruit — passion fruit) and a few neglected plants like sedges (at the top of this page — monocot flowering plants related to grasses; the brown clusters are either the flowers or the developing fruits) and ferns (in the slide show, note the sporangia (spore houses) at the edges of the leaflets of the maidenhair ferns, and in clusters called sori on the edges of the smaller leaflets of the Christmas fern), it’s a fun way to spend a few moments appreciating plants. And really, I think most people — perhaps even you — don’t do that enough. : )

A scanning electron micrograph of an unidentified rust spore from Alaska. Note the gorgeous projections that look like they've been turned on a lathe.

Author’s note: This is the last of a series of four posts in Fungi Month here at TAA. Enjoy!

Last month a mysterious orange film (“goo” in the media vernacular) washed up on the shores of a northwest Alaskan village called Kivalina. Experts suspected crustacean eggs; locals were unnerved. In retrospect, reports that the substance “dried into a powder” should have been suspicious, as should reports that the orange stuff also appeared on the water in rain buckets. Either the crustaceans really got around, or all was not as it seemed.

An orange powder seems an odd product for the drying of crustacean eggs, but could make perfect sense for fungi — specifically, the rust fungi. And indeed, that is what experts believe them now to be. And yet, for all the gumshoe work, they really still have no idea what they actually were — or what produced such an explosion in a place that had not seen such an event in the memory of anyone living.

Rusts are all plant parasites, but unlike the smuts — their close relatives, who I wrote about here earlier this month — they don’t specialize in hijacking plant parts for their nefarious purposes; instead they embed their reproductive structures in plant tissue in a system that can only be described as a byzantine dance of propagules. Some rusts have make up to five different sorts of spores in five different structures on two different hosts. It’s a bit dizzying keeping up with it all.

Before I fry your neurons with a rust life-cycle chart, let’s take a slightly larger view. There are thousands of species of rust, and all are plant parasites, many of which specialize in giving farmers — and biologists — headaches: coffee, asparagus, beans, snapdragons, carnations, roses, and wheat all have rusts that have achieved or are working on infamy. One rust — cedar-apple — makes distinctively alien orange goo starbursts on eastern red cedar (really a juniper) in the United States; its alternate host is apple.

A cedar-apple rust (Gymnosporangium juniperi-virginianae) gall on eastern red cedar after rain. When they're not wet, instead of looking like something your kids would enjoy eating or dropping down your shirt, they look like wooden balls with little satanic horns.

The reason they are called rusts is obvious: they make plants look rusty by discharging orange, powdery spores on leaves and stems during at least one of their many life stages. Here’s a photo I took of a rust dropping powdery orange spores in a rather undignified manner from a wild rose when I was on my boreal toad-hunting trip in July:

In completing their reproductive gymnastics, rusts produce some pretty interesting microscopic structures, or fruiting bodies, as mycologists sometimes call them.

Inside one of them, called a spermagonium or pycnium, sterile, stiff, tapering filaments called periphyses converge and push up on the plant epidermis. They rupture it, forming a little hole called an ostiole, and sometimes protrude through it like tentacles. Tailless male gametes called spermatia (or pycniospores) are formed inside and exuded in droplets of sweet, sticky nectar.

Nearby, “receptive hyphae” (high-fee — fungal filaments that make up their bodies) also protrude through the hole. Nectar-seeking insects land, get a sugar fix, and then take off with some hitchhiking spermatia stuck — in some embarrassing configuration, no doubt — to their feet or bodies. When they land on another spermagonium/pycnium, the spermatia/pycnia can then fuse with and fertilize the receptive hyphae. You know what this should remind you of, of course: a flower. A fungal flower, in fact, convergently evolved to suit the same purpose. And like some flowers, rusts have a rudimentary male/female system (mycologists boringly call the mating types A1 and A2) that ensures spermatia from a given spermagonium can’t fertilize their own receptive hyphae

OK. That is ONE of the FIVE possible life stages of a rust fungus. I’ve tried to shield you from this as long as possible. But I can’t hold back any more. Behold: the full horror of the life cycle of a heteroecious (two-host), macrocyclic (way too many spore-types) rust:

For the bionerds, delight in digesting this. For the rest of you, all that’s necessary is to notice what a headache it must have been getting this all figured out. For the record, not all rust fungi have life cycles this complex. Some have only one host, and some have only a few of the structures described above. But you get the idea.

This particular life cycle belongs to a rust fungus that is on my own personal ****-list. It is white pine blister rust — Cronartium ribicola — introduced to North America around 1900 and just now reaching Colorado after killing untold numbers of five-needle pines across the west. It has come south from Montana. And it is set to start killing our venerable limber and bristlecone pines, which I wrote about in June here. But I digress.

Each of those little cross sections in the drawing is a vertical section through a tiny cup-like structure on a stem or leaf. The potato-like objects inside are the spores. N is haploid(one copy of the chromosomes) and 2N is diploid, but N+N is a special fungal thing. It means the cells are dikaryotic — they have two nuclei from mating but they haven’t yet fused. Fungi have a tendency to have some part of their life cycle involve this odd-couple state. In humans, as you’ll recall, the nuclei of sperm and egg waste no time in fusing once the sperm makes its intentions known.

There is also a beautiful variety in the structure, color, and texture of rust teliospores — the resting stage for many rusts — which were traditionally used to classify them. They are often spiky or pegged dark brown visual confections of one to several cells, in chains, layers, or on stalks. At least one teliospore I looked at was a multicellular bundle with a striking resemblance to pattypan squash.

It is the urediospores (produced in the uredia) which are usually rusty orange (aeciospores can be orangey too), and these are the spores that scientists believe exploded into view in Alaska.

But the scientists at the NOAA lab in Charleston, South Carolina, that did the identification could not give the rust a species name. It didn’t match anything they had worked with before, they said, and they noted that there are many unidentified rust species lurking in Arctic tundra; as you can imagine, mycologists, a scarce resource in any climate, are not particularly abundant in northwest Alaska.

When I contacted the lab this week to find out if they had any further information on the rust’s identity, they said they did not. And unless some inquiring mycologist with time on their hands (ha!) has time to take a look, that is all we will probably ever know. And yet it gets a girl wondering: where *did* all those spores come from? What tundra plant could have possibly been so parasitized without anyone noticing? It’s not like rusts hide the fact they’re hanging out on plants — quite the opposite. And for an explosion of spores so profuse that they coated the ocean and washed ashore, there must have been something brewing on a biblical scale on the unfortunate hosts east of town. And what was it about this year that made them go crazy? If you’ve been paying to any news of the Arctic in the last five years, you can probably make an educated guess.

Before I close this post, though, I have a question about rusts I’d like to pose: if a rust has two hosts, they’re usually only distantly related. For instance, wheat stem rust’s hosts are common barberry and various grasses, straddling the gap between monocot and dicot flowering plants. White pine blister rust feeds on five-needle pines and various currants and gooseberries, shifting between the conifers and flowering plants. Uredinopsis osmundae shuttles between balsam fir and cinnamon ferns, crossing a huge taxonomic gap between seed-making and spore-making plants. Why?

And this leads to a larger question, which some of the wiser minds among you may understand, which is why so many parasites both of animals and plants seem to enjoy doing the host shuffle at all, much less across giant taxonomic gaps (there are many animal parasites, for instance, that shuttle between vertebrates and invertebrates like snails or annelid worms)? What benefit could having two sets of biologies and immune systems to navigate possibly offer when you could confine yourself to the comfy and familiar environs of just one host? I’m interested in your thoughts, so please feel free to share below. I should probably know the answer to this since I read Parasite Rex once upon a time, but I do not. Forgive me, St. Carl.

Reduviasporonites, an enigmatic end-Permian microfossil. Courtesy Cindy Looy

What seems apparent, and what everyone seems to agree on, is that they were once alive. Chemical signatures left in the rock by the fossils tell us this. But their appearance — darkened branching filaments divided into cells up to 24 units long — also seems very, well, lifey. What few agree on is their identity. Were they algae, thriving in ponds and swamps during some great deluge? Or were they wood-decay fungi feasting on the corpses of climate-felled conifer forests? Both have long been suggested, but here, the biochemical evidence is ambiguous. Whatever they were, something very strange was going on.

The Permo-Triassic Extinction, or Great Dying, that produced the rocks filled with these filaments seems to have been brought on by a massive slow-motion volcanic eruption in what is now Siberia 250 million years ago. According to the majority opinion, vast oozing plains of lava emitted catastrophic quantities of carbon dioxide and methane, poisoning the air for life. Other scenarios have been conjured involving ozone depletion, acidification, or the ever-popular asteroid impact¹. Whatever the scenario, the result was staggering extinctions. About 90% of ocean life and 75% of land life vanished. Forests died. Soils eroded. General chaos ensued.

And somehow, something that made chains of little, brown barrel-shaped cells managed to make a, well, killing in the process.

It should be said that these fossils — generally called Reduviasporonites — bear a variety of appearances, and may represent several species (here is a nice gallery of their variety — click “Galleries” at left). The filaments didn’t resemble the active filaments (or hyphae — high-fee) of known fungi, which are generally tubular and unpigmented. That led some to discount the fungal hypothesis. The key insight, it turned out, was that these were not normal fungal hyphae at all. They were something much more sinister.

A trio of scientists from Utrecht University, Imperial College, and the University of California-Berkeley recently noted that at least some Reduviasporonites from classic Permo-Triassic boundary rock in the Dolomites of northern Italy bear a striking resemblance to a pathogenic fungus: Rhizoctonia. And if this is the case, it raises a more ghoulish possibility: What if the fossil filaments are remnants of an orgy of fungal destruction, as pathogenic fungi feasted on helpless, dying trees in a noxious atmosphere lit from afar by endless plains of erupting lava? Interesting times, as they say.

If we’re going by appearance (which they are), you can judge for yourself. Here is living Rhizoctonia solani:

Living Rhizoctonia solani, image courtesy Lane Tredway, copyright of The American Phytopathological Society. Used with permission; click image for link.

Compare with image at top. Uncanny, no?

And for comparison, here are some images (and also here) of two of the genera of the Zygnemataceae, the group of algae generally considered the other chief suspect (I am not certain these are the genera Reduviapsoronites are considered to be most like, but they were the genera with photographs available on the internet). Interestingly, these genera have stunningly beautiful star-shaped and spiral chloroplasts, the little green structures where plant cells make sugar from light. Yet to the naked eye, you would know them as pond scum.

Modern Rhizoctonia are interesting beasts. They are really an amalgam (“form group”) of species united by their structure and M.O. When hyphae are young, they branch at almost perfect right angles. When mature, they make thickened, barrel-shaped short cells, as you can see at left, and the whole thing (mycelium, or my-seal-ee-um) is pigmented with the same stuff that darkens human skin.

Whether young or old, Rhizoctonia reproduce virtually without spores. For many years they were called “sterile fungi” by scientists because they were thought to never produce asexual spores called conidia (most fungi pump them out like they’re going out of style). Now we know some do so very rarely. Spores produced by sexual reproduction (aka meiosis) are rare too. Instead, they seem to reproduce by breaking into pieces that wash or blow away.

Although this is all interesting (to bionerds like myself, anyway), these sterile, tough fungi are notorious for a different reason: they are tenacious plant pathogens. Rhizoctonia are known for producing a variety of nasty diseases on vegetables, flowers, shrubs, and trees — from wilting newly sprouted seedlings to eating holes in the stems of grown plants in a botanical version of flesh-eating bacteria (these would be, of course, flesh-eating fungi). Root and stem rots are their specialties, and they especially like attacking anything in or near the soil, their base of operations.

Lots of seemingly unrelated things have evolved into this niche of sterile, plant pathogenic mycelium². Some of them fall into the huge group of fungi called ascomycetes that make their sexual spores in sacs; others are basidiomycetes that make their sexual spores on the outside of club-shaped cells (one of them, Rhizoctonia leguminicola produces a wonderfully-named chemical in clover called slaframine, or “slobber factor” because it causes livestock who eat the clover it to drool uncontrollably).

They were once all called Rhizoctonia, but since only genetically related things can share names in biological nomenclature, scientists are busy sorting and renaming them. Still, that tells you it’s a pretty popular niche, and convergent evolution — when genetically unrelated creatures evolve to look and behave similarly, like whales and fish, or hummingbirds and insects(in my opinion) — has been rife in it. We’ll get back to this momentarily.

The alga Zygnema, pond scum (literally) and namesake of the Zygnemataceae, the other group Reduviasporonites has been suggested to resemble. Note the star-shaped chloroplasts. Creative Commons Bob Blaylock; Click image for license and link.

When Rhizoctonia is facing hard times, it makes disks of hardened, fortified mycelium called sclerotia by twisting chains of its dark, squat resting cells together. They pack the thing full of fats and sugars — the fungal version of stocking your fallout-shelter with pallets of Dinty Moore — and darken the cell walls for UV protection. Then they darken the lights, put on fuzzy slippers and a movie, and wait.

Lots of other fungi make sclerotia too. You can find them in many places if you rake aside the leaf or needle litter. Just below the duff, you’ll find hard little structures sitting at the soil line. Sometimes they’re quite colorful. These hardened resting structures are a major way fungi — and even slime molds — survive what is rather delicately called “unfavorable conditions”. When conditions improve, they sprout.

Distinctively, the sclerotium of Rhizoctonia produces no rind or internal structure, and is basically a loosely-packed clump of mycelium. These are just the sort of structures that authors Visscher, Sephton and Looy found in their end-Permian Italian rock.

Putative Rhizoctonia-like sclerotium of Reduviasporonites. Courtesy Cindy Looy

So is this the smoking gun? Based on the resemblence of these fossil structures to the mature hyphae and sclerotia of modern pathogenic Rhizoctonia (the background image in this picture), the authors propose that Reduviasporonites sclerotia are “indistinguishable” from those of modern Rhizoctonia. From the presence of soilborne sclerotia, they also conclude Reduviasporonites are unlikely to have simply been wood-rotters. And previous studies have found that, in general, the more pathogenic sclerotia you find in soil, the more plant disease you find nearby. So in other words, according to the authors, finding samples of end-Permian sediments in which up to 90% of the ex-alive material in the rock is Rhizoctonia-like sclerotia as they did is like finding a smoking gun.

Modern Rhizoctonia often act as facultative pathogens. That is to say: they’re opportunists. They can grow into and live relatively quietly with living trees, held in check by their immune system while waiting for them to sicken or weaken. Once they do, they attack. One of the more amazing discoveries of the last few decades is how common that is. Many plants, it seems, can have fungi living in or on them patiently waiting for a good place in line at the decay buffet. Rhizoctonia, as a pathogen, seems to stand right at the front, and would have been well-positioned to capitalize on an arboreal windfall.

Another fossilized Reduviasporonites fliament. Courtesy Cindy Looy

The authors propose the following scenario: attack by volcanic gases like carbon dioxide and methane (or whatever massive, inescapable stressor precipitated the global extinctions) weakened forests and disrupted the host-pathogen equilibrium in a way that favored the fungi, hastening the trees’ already-inevitable declines. The fungi tucked in like zombies at a brains buffet.

As food dwindled and times got bad for fungi too, the massive fungal blooms went with their usual Plan B: make sclerotia. But they were storing up goods for a day that would never come. Most of their hosts were dead. No saplings could grow in the terrible conditions. Rain washed the killing fields clean, massively eroding the land, and carried the doomed sclerotia to the bottoms of watery graves, where they would be pressed into the rocks that were buried, lifted into mountains, and then finally collected by scientists who released them from their stony prisons at last. But 250 million years later, the Dinty Moore is long gone.

Let’s return to the authors’ original assumption, that comparing the structures of 250-million year old fossils to living creatures can help us identify them and infer what they were doing. Did the ancestors of Rhizoctonia at the dawn of the Triassic necessarily look like their descendants today? Our ancestors and the ancestors of flowering plants certainly did not.

On the other hand, they didn’t necessarily look different. Many organisms 300 or 400 million years old look essentially the same today as they did then (sharks are the classic example, but see my Sci Am Guest Blog post for some 600 million year-old critters that look similar to existing forms).

But even if they are not genetic ancestors of modern Rhizoctonia (which the authors never claim), the fact they they seem to have evolved into the same form (as, I mentioned above, so many other unrelated fungi have done today) implies that they were doing roughly the same thing that modern Rhizoctonia and their ilk do. We call this convergent evolution, and although it would mean that you couldn’t start calling Reduviasporonites “Rhizoctonia”, it wouldn’t change the picture the authors paint of the terrible endgame of Permian forests: global fungal apocalypse.

Visscher, H., Sephton, M., & Looy, C. (2011). Fungal virulence at the time of the end-Permian biosphere crisis? Geology, 39 (9), 883-886 DOI: 10.1130/G32178.1

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¹In this recent study, scientists claim that the rapid buildup of CO2 could have fatally acidified the oceans, leaving marine creatures unable to build their shells.

²Rhizoctonia aren’t always attacking plants; many are saprobes in soil, from which they launch their plant attacks. And the soil can be a launching place for other “deals” as well. Some can be cooperative, or “mycorrhizal” with orchids.

Tiny, nutrient-poor orchid seeds notoriously require very specific fungi to help them germinate and provide them food until they can produce their first green leaf, which may take two to 11 years (this is why growing orchids from seed outside the jungle can be, to say the least, challenging).

But, as in much of biology, all is not exactly as it seems. Though several soil fungi can colonize orchid seedlings, the Rhizoctonia (whose sexual forms are crust fungi) who can do so are also saprobes, and thus in possession of the nutrients to support a young orchid. The fungus penetrates root cortex cells and generates coils or “pelotons” in order to mediate nutrient exchange. Scientists who have watched this process have noticed that several things can happen. The seed may get colonized successfully by the appropriate fungus and grow up to be an orchid. Happy day. Or, the fungus may get out of hand and kill the seedling. Sad orchid. Finally, the fungal invasion may fail and the seedling stops growing and still dies without a fungus to launch it. This appears to be a symbiosis in the process of forming, where one false move on the part of either partner can result in death. In other words, the fungus and plant are still working out the mycorrhizal prenup. It’s a delicate balance, and as with the host-pathogen equilibrium, any perturbation in the relationship can lead to disaster.

As well, I was captured on film (although my last name was not quite captured in writing) in this story about mushroom hunting in Colorado in the New York Times. I’m the one in the hat holding the basket in the photo at top, and then you can see a nice photo of me holding up a mushroom like a diamond merchant at lower left. Oh, NYT, would it have killed you to check the spelling of my last name? I sent a correction but it must have been misfiled.

Though I wasn’t interviewed for the story, I thought they did a pretty good job. I did, however, note that the journalist showed up in running shorts and tennies on the day we forayed at 10,000 or so feet in the Colorado backcountry. Definitely a New Yorker. : )