I would like a fascinator made in this shape. The dinoflagellate Oxyrrhis marina with its transverse and longitudinal flagella. Creative Commons Census of Marine Life E&O

Life on Earth is full of weird convergences. For example, the cell walls of fungi are made of chitin, as are the shells of insects and arthropods like lobsters and crabs. Why? Whether due to chance or something deeper, I have never heard a good explanation.

Similarly, the proteins called rhodopsins are found in two seemingly completely unrelated places: the retina of your (and all vertebrate) eyes, and in some photosynthetic archaea and bacteria. We use ours for detecting light (it’s in the rod cells used for low-light vision); they use theirs to pump protons (as illustrated and discussed recently here) to make food.

And now, scientists have discovered a predatory dinoflagellate that has apparently stolen a bacterial photorhodopsin from one of its meals — and is using it (see also here).

The protein in question is called rhodopsin (Greek root “rhodo” = rose and “opsis” = sight) because it absorbs blue-green light and so appears purplish-red. Rhodopsins have seven protein coils called alpha helices that pass through membranes the protein is embedded in. In turn, embedded inside the helices is retinal, a light-sensitive pigment. As a result, the whole structure changes shape in response to light. In vertebrates, rhodopsin has another subunit called a “G protein“. G protein acts as signal transducer, or on-off switch in a signaling cascade — just like a switch in an electrical circuit. Vertebrates use it to relay information to the brain about what the eyes are seeing. Bacteria use their rhodopsin simply for pumping protons, not for signalling, so they have no need for G protein section.

The bacterial protein — still seven alpha helices and a retinal — resembles overall shape of vertebrate protein, so scientists suspect they may be distantly related. Proteorhodopsin — the bacterial version, was only discovered in 2000, but the (now ironically named) bacteriorhodpsin found in archaea was discovered much earlier, in archaea living and photosynthesising in sun-drenched salt flats, brackish pools, or salt marshes.

The dinoflagellate Oxyrrhis marina (ox-EE-ris MARE-i-na, I think) is neither a vertebrate nor a prokaryote (bacterium/archaeon). And yet O. marina makes so much rhodopsin it has turned pink. How? Scientists believe the gene for the proteorhodopsin was acquired by what biologists call horizontal gene transfer — that is, O. marina was happily digesting its photosynthetic bacterial prey when the gene for this protein somehow wandered off and found its way into the nucleus (where DNA is stored) and slipped, spliced, or got sliced into the chromosome.

This appears to be a case of “hedging your bets” because O. marina is now both photosynthetic and predatory. So in this case, you can make your own cake and stalk it too. Scientists believe they use this protein not only to make energy by pumping protons and passing them back down a chemical gradient via an ATP synthase, but also to help digest the very prey they stole it from. As they say, all too easy.

But before I say more, a few words on what dinoflagellates are are in order.

The dinoflagellate Ceratium longipes, in all it's tricorne glory. One, and possibly two flagella visible. Creative Commons Census of Marine Life E&O

In short, 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).

Dinoflagellates (from the roots for “whirling whip”) are also alveolates like ciliates (including the paramecia I wrote about here) and apicomplexans (which include Plasmodium, the protist that causes malaria). That means they often have sacs called alveoli under their cell membranes, trichocysts (defensive spikes that shoot out like harpoons), and tubular mitochondrial folds, or cristae. Some even produce structures like the nematocysts of jellyfish. You can explore how dinoflagellates fit into the life family tree here (use the black arrows to move toward the root).

Some dinoflagellates cause the poisonous red tides infamous for sickening fish and swimmers alike. Others build up in tropical fish or shellfish and cause ciguatoxin or paralytic shellfish poisoning in people. Others become the zooxanthellae, the green algal symbionts found in coral and other animals and protists. These photosynthetic dinoflagellates vastly increase the speed at which corals can build their skeletons. And finally, some dinoflagellates (including some red tiders) are bioluminescent, emitting short flashes of light when disturbed, and are responsible for the unearthly glow of the wakes of ships passing through tropical waters in the night.

Bioluminescent red tide dinoflagellates getting all bright and bothered by rolling surf. Creative Commons Catalano82. Click for link.

Dinoflagellates have some interesting quirks; their chromosomes stay condensed throughout the cell cycle and down relax into a spaghetti pile of chromatin (individual DNA threads) between cell divisions. And they don’t wrap their DNA around proteins called histones as most of the rest of us upstanding eukaryotes do. They prefer instead to attach it to the inside of the nuclear membrane. Also, they tend to eschew the reliable DNA base thymine in favor of the boutique 5-hydroxymethyluracil.

My plans to take over my neighborhood swimming pool are now complete . . . Dinoflagellate blueprints. Creative Coimmons Shazz. Click image for link.

Their two flagella — which emerge from the same point — are often set in grooves. One is a belt-like transverse groove called the cingulum, and the other is a longitudinal groove called the sulcus. You can see those grooves in a beautiful scanning electron micrograph here. (See also here and here for a dinoflagellate that I swear resembles Baron Harkonnen in his fat suspensor suit). The flagellum set in the cingulum wraps all the way around, while that set in the sulcus trails off the back like a rudder. Strangely, the transverse flagellum is responsible for most of the forward motion and is what sets dinoflagellates whirling, while the longitudinal chiefly helps steer.

Dinoflagellates are also really good at engulfing photosynthetic organisms and endosymbi-izing them. Most of their chloroplasts have three membranes, suggesting they came from an ingested alga, not a bacterium, and are the result of a secondary engulfment, or endosymbiosis. Others have chloroplasts of different color, shape and form, some still with nuclei. Thus we can infer that dinoflagellates are really good at finding themselves new photosynthetic dates by hook or crook — definitely crook, in the case of Oxyrrhis.

Flexibility and Finding a way seem to be themes with dinoflagellates. O. marina, for example, is common in shallow tide pools around world; it will go so far as to cannibalize its own species if it comes to it and can take down prey almost as big as it is. Photosynthesis. . . hunting . . . cannibalism — this thing is the MacGyver of protists. It’s going to survive with whatever comes to hand. So if you’re ever doing O. marina research, please do us all a favor: do not keep bubble gum, paper clips, or high explosives anywhere near your experimental organisms. Thank you.

I’m torn here. On the one hand, this is really cool. On the other, it somehow feels horribly wrong. I mean I’m sure it’s not much more wrong than what I do to baker’s yeast every time I bake bread. But . . . I don’t toy with the yeast before I incinerate them. Yeesh.

Anywho, for those who are unfamiliar, paramecia are classic organisms used to teach high school and college students about microbes. But they’re not simply boring microbial lab rats. They’re fascinatingly formed, filled, and operated little creatures. They are often described as “slipper-shaped”, or, as van Leeuwenhoek would have it, “slipper animalcules”. In this video, watch for the little cilia beating all over the cell’s pellicle, or membrane+submembrane shell.

So let’s have a tribute to the humble Paramecium today — we’ll take a closer look at a microbe you might think you already know. Think again. Take a look at the basic paramecium formula here (I can’t post it because I don’t have copyright). I’ll refer to the various parts of this diagram as we go along.

Paramecia are ciliates, protists coated in little beating hairs called cilia for at least part of their life cycle. In photographs where only their cilia are stained or photographed with scanning electron microscopy, paramecia look like ovoid shag rugs (or see here or here). These cilia can beat in forward or reverse with extreme precision — much more precise than large flagellae or lumbering pseudopods. When beating in foward or reverse, the paramecium moves in a spiral motion around an invisible axis — and they can throw it into reverse in a ciliumbeat to avoid obstacles or “negative stimuli” (cough).

Inside the cell is a contractile vacuole used to bail out water against the perpetual osmotic gradient (the inside of the cell has a higher solute concentration than its watery surroundings, leading water to constantly seep through the membrane by osmosis, like a leaky ship), various vacuoles (spherical storage vessels) for digesting food and excreting waste, and at least one micronucleus and macronucleus.

The micronucleus, of which there may be as few as one or as many as 80, is diploid, or contains two copies of all the DNA, just like all of your cells. But the macronucleus may contain 50-500 times as much DNA as the micronucleus (the Paramecium aurelia macronucleus is 860-ploid, according to one of my biology texts). The micronucleus is all about passing DNA to mating partners for sexual reproduction (aka swapping genes), while the macronucleus is in the business of pumping out messenger RNA and getting it translated into proteins.If you remove the micronucleus, the cell can divide asexually another 350 or so times before dying of no sex (yes, in ciliates, this can apparently happen). But if you remove the macronucleus, the cell immediately dies.

On the surface of the cell is a funnel-shaped oral groove that guides food particles toward a pocket where food vacuoles are created. Enzymes get pumped inside to digest whatever hapless bacteria, yeast or “other” finds its way inside. Many paramecia may contain symbiotic bacteria living within them or even within their macronucleus, perhaps providing vitamins or other growth factors that would otherwise be hard to get. One paramecium even has photosynthetic symbionts. Paramecium bursaria, which has ingested and partnered with the green alga Zoochlorella.

These are *not* chloroplasts, or rather, they are not homologous to (share a common ancestry with) the chloroplasts in plants. Plant chloroplasts are ingested cyanobacteria. Zoochlorella are chloroplasts in the sense that they are internal photosynthetic symbionts, but they were free-living eukaryotic (nucleated — not bacterial) algae before ingestion. But here’s the mind-twister: the chloroplasts within the Zoochlorella are homologous to plant chloroplasts, because plants evolved from green algae.
This is the only Paramecium known to do this. To what extent the Zoochlorella could pop out of that paramecium and get along on its own or is degenerate and helpless I do not know.

Paramecium bursaria, a rare symbiotic photosynthetic paramecium. Love the gorgeous detail. Creative Commons PROYECTO AGUA**/**WATER PROJECT

Some large ciliates may hold the land-speed record for all protists. They can cruise at a blinding 2 millimeters per second, which, assuming a 250-micrometer paramecium and a 5.5-foot human [calculator tapping noises], is the equivalent our 5.5-foot human swimming  a blazing 30 miles per hour*. And they are backstroking at these speeds through a medium that has the viscosity (to a proist) of molasses.(See the middle of Psi Wavefunction’s post here, or for the physics-buff bionerds out there, the original 1977 paper “Life at [a] Low Reynolds Number” here).

Paramecia are also armored with a built-in defense system. Their pellicle is laced with dart-tipped harpoon-esque “trichocysts” (a specific type of a more general organelle called an “extrusome“, which is clearly another case of convergence (independent invention of the same structure) with jellyfish nematocsyts), which deploy explosively within milliseconds if the paramecium feels threatened, is feeling peckish, or perhaps needs a convenient anchor while it tucks in to dinner. See how they look retracted here, and how they look once fully-expelled here, which this site describes as the “disheveled porcupine” look. The bottom photo is of undeployed trichocysts in the pellicle**.

Known diversity in ciliates, ca. 1904, by the incomparable Haeckel

Paramecia are, as mentioned, ciliates. There are something like 9,000 species in fresh and salt water, and their complexity and diversity of form is astounding. Some of the most complex species come close to replicating the digestive systems, muscles, exoskeletal systems and even vertebrae so characteristic of multicellular life within a single cell. According to one of my biology texts, ciliates have produced the greatest specialization of subcellular organelles of any protist. Rest assured you will read more about the creatures in this group at this blog.

Ciliates fit into the larger taxon (group) called alveolates, a term you may recognize from high school biology as the name for the little sacs at the ends of the passages of your lungs. The structures are similar; the Latin just means “little cavities”, and in ciliates like Paramecium they are little membranous sacs found just below the cell surface engulfing the roots of cilia. Though the ciliates like Paramecium and the dinoflagellates and parasitic apicomplexans may seem worlds apart, they all share this feature and several others*** that reveal their common ancestry. See how the ciliates fit into the alveolates, and how the alvaeolates fit into the eukaryotes here and here.

Before I leave you today (or is it the other way around?), enjoy this video of some more active paramecia tooling around with a bunch of nerdy Euglena (the little guys). Because before you allow your little microbial minions to be devoured by Pac-Mecium or taunt them with a chemical blast, remember: were they your size (or you theirs), you’d never survive the hairpin extrusome assault mechanism, and they’d be gone before you knew what hit you. : )

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*or 48 km/hr for you metric users. According to the intertubes, the fastest human swimmers can go is around 5 miles/hr over very short distances. Of course, their bodies are not covered in highly-efficient propulsive cilia (and more’s the pity).

**With all this weaponry, forget Pac-mecium. Helloooooo Ultimate Paramecium Fighting League.

***including, for the bionerds out there, tubular mitochondrial christae, “closed mitosis” in which the micronuclear membrane doesn’t dissolve during mitosis and the mitotic spindle forms inside it, and similar “extrusive organs” like trichocysts

Repeat after me: “The penitent protist shall pass . . .the penitent protist shall pass . . . ”

As you can see rotifers (literally “wheel bearers”) are so called from the accessories on their foreheads involved in hoovering up dinner. And they are truly amazing creatures. To learn more about bdelloid rotifers (including some gorgeous SEM shots of their jaws) and their alternative lifestyles, see two posts from early in this blog’s life: Lesbian Necrophiliac Bdelloid Rotifers (and the Scientists who Love Them)Parts 1 and 2. The above video provides a good illustration of why they are called “bdelloid”, or leech-like rotifers. They move just like inchworms or leeches**:

Psi Wavefunction did point out, however, that rotifers are *not* the smallest animals. Rotifers are animals (not protists), but as for what the smallest animals might be, I will leave for another day.

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*for which I am endebted to the twitter feed of Chris Mah at the Echinoblog

**which are, by the way, annelids (from the last post — see the tree at the bottom) in the Clitellata — look for the Hirudinea. Look for the earthworms just above them in the Lumbricidae. And, just below them but also in the Clitellata (and hence annelids) is the sludge worm Tubifex Tubifex in the Tubificidae — from here, remember?)

Creative Commons Thorney¿?

Fly fisher(wo)men everywhere are mourning the loss of a cherished piece of equipment: their felt-soled waders. All too often now, clinging to the felt fibers are the tenacious strands of Didymosphenia geminata (did-em-o-sfeen’-ee-a jem-i-na’-ta), or, for the rest of us, rock snot.

The stuff looks like pre-owned toilet paper and apparently feels like wet cotton, and it’s slowly taking over the freshwater streams of the temperate world, smothering fish, insects, and other aquatic life. It spreads by hitchhiking on the gear of flyfishers, challenging slime molds, dandelions, and jellyfish for the non-human Plans for World Domination Cup. You can read all the gory details in New York Times articles here and here. But hidden inside that slimy brown mass is a work of remarkable beauty.

This.

With the lines of a Stradivarius and the detailing of a Fabergé egg, this baby is a microscopic work of art. If only its macroscopic manifestations could be so beautiful. As you may have guessed, it is a diatom (as covered here), a microscopic glass house (literally (littorally?) made of silicon dioxide) enclosing a little photosynthesizing alga.

At left you see two interesting features: The two long slits, or raphes, through which the diatom can secrete mucilage (aka slime) with which it slides over surfaces, and the porefield, through which it can secrete a mucopolysaccharide (aka slime) stalk that attaches it to a surface. The secretion and aggregation of these stalks is what causes the brown mess of rock snot, not the beautiful fiddle-like head.

In beauty, destruction. In destruction, beauty. This particular destruction brought to you by the otherwise largely upstanding diatoms, conveniently located in this sector of the tree of life. For all the scientific, er, dirt, on rock snot, including a beautiful scanning electron micrograph of the trouble-causing stalks, check out this EPA White Paper.

In Russia, amoeba study YOU.

OK, giant deep-sea amoebae that roll around like possessed dust bunnies? AWESOME. The 411. Though this group had just been discovered in the Arabian Sea in 2000, it seems it was still a surprise to find them *leaving tracks* (although I should emphasize no one can actually see them move in real time. This sounds like a job for the BBC’s magic time-lapse camera). They are testate amoebae, or ameobae that make shells called tests (a few other deep sea protists like foraminifera also make shells called tests, and I just discovered that Chris Taylor over at Catalogue of Organisms just happens to have coincidentally published on the foram version yesterday.). This species, Gromia sphaerica, fits into the Gromiidea on this tree. Just look at all the uncharted territory and things you’ve never heard of. Space is not the final frontier. . . not by a long shot. Not yet.

The bigger, non-motile existing deep-sea protozoans Matz refers to in the video are probably xenophyophores, an outrageously bizarre group alluded to here before. You’ll just have to wait on a post about those another day. And there’s probably lots more giant deep sea protists I don’t know about yet. Readers?

The big take-home message of Matz’s discovery (or at least what they’d like us to take home) seems to be that we could really be misinterpreting Pre-Cambrian fossil trackwaves — that is, the fossil tracks of organisms that predate the blossoming of most modern animal groups in an event called the Cambrian Explosion, ca. 550 million years ago. These tracks can be found in fossils as old as 1.8 billion years (yes, that’s billion with a pinkie to the corner of the mouth). These tracks were for many years interpreted as early modern animals for whom we just didn’t happen to have fossils. But what if they were giant protists? Or something else? Possible, and probably not surprising given the fossils we do have of Ediacaran creatures, they bizarre early animal(?) forms that predate the Cambrian explosion and are the first fossils of complex multicellular organisms we have. They all seem to be soft and, for lack of a better term, pillowy. Yes, like Charmin.

Will we ever know? Probably not. But you never know. A fossil of a recognizable ancestor of a modern animal keeled over at the end of one of these tracks might settle things. On the other hand, simple tracks do tend to look alike. And with hundreds of millions of years on hand, there’s plenty of time for lots of really weird things we’ll never know about to have made them.

You know what this video reminds me of, of course . . .

Punk rockers are clearly dinoflagellate posers. Is it just me or does (a) appear to be a member of the House Harkonnen? Dinoflagellate micro-plankton of Atlantic tropical waters. P. 75. In: "Aus den Tiefen des Weltmeeres" by Carl Chun, 1903. NOAA Photo Library.

Most people have only seen plankton in crappy, fuzzy photos in college textbooks, if they’ve seen it at all. If you have heard of it, it’s probably in the context of the stuff baleen whales eat, and that’s about it. I personally was lucky enough to see an entire jar of the delicacy when I visited the Smithsonian’s Sant Ocean Hall last fall. It looked a lot like the larvae of the neural parasites that took over the brains of the Federation’s top brass in the first season of Star Trek: TNG. Mmmm, mmmm good!

Plankton is not a taxonomic/phylogenetic group like most of the things I write about on this blog. Plankton instead refers to any sea creatures that drift. That can include things as large as jellyfish, but typically plankton are much smaller and include things as small as the bacteria, archaea, and viruses with which the oceans teem. The phytoplankton, or photosynthesizing component, are responsible for half of the oxygen you breathe.

Well, someone’s finally taken some skillful, beautiful pictures of the plankton and they’ve gone on display at the London Zoo in honor of the Royal Society’s 350th Anniversary (Dang! That Society’s been around over 100 years longer than my country!). Over at the BBC there is a don’t-miss slide show of the exhibit, narrated by the scientist photographer, Dr. Richard Kirby. Let me repeat that: DON’T MISS THIS SLIDE SHOW.

You’ll get to see how evolution has taken body plans on some interesting trips, as larvae that retain ancestral forms metamorphose into sea creatures you are more likely to recognize. The squid-like larval origin of starfish, in particular, is a fascinating thing.

One final note — Dr. Kirby mentions that plankton are responsible for the characteristic smell of the sea. That is not surprising to me. When I was a grad student in plant pathology at Cornell, I was startled one day to discover that dirt doesn’t smell like dirt. Dirt smells like the bacteria that are living in dirt. In one lab we were allowed to sniff (I believe “waft” is the preferred term) a pure culture of soil bacteria. It was a clear agar dish with opaque colonies of bacteria. But it smelled just like fresh topsoil or a cave — dirty, earthy, wonderful.

Discovered thanks to the fine staff of Deep Sea News.

Efficiency in Motion: A wild slime mold clambers over soil and moss looking for bacteria and protists to eat. Note the dead leaf for scale. http://www.flickr.com/photos/deliciousblur/ / CC BY-NC 2.0 Not for commercial use.

Behold, the artful amoeba itself — a slime mold. In this case, it is Physarum polycephalum, the lab rat of plasmodial slimes. Scientists in Japan have been leading the world in creative slime mold research, demonstrating about 10 years ago (when I was first learning about these creatures) that slime molds could solve mazes. If you’ll recall, slime molds can also remember. We’re talking about an oversized bag of multinucleate cytoplasm here, folks. (Cytoplasm being, of course, everything inside a cell membrane, and multinucleate because it contains lots of nuclei, or DNA packets) So it was no surprise to me to see the latest juicy morsel of slime mold research last week, once again from Japan, showing that not only can slime molds efficiently design rail networks, they can do it for a budget comprised of a $2.99 box of oats. Planning engineers, prepare for Japanese outsourcing.

The slimes managed a decent reproduction of the actual Tokyo rail network when scientists put a piece of the mold where Tokyo would be inside a Japan-shaped corral with oat flakes placed at the location of major cities. To simulate mountains or other barriers that slime molds have no way of knowing about, they illuminated portions of the map. Slime molds, like vampires, trolls, and college students, hate light. In just over a day, the slime mold had taken in the lay of the land and laid down its solution to the problem. The similarities were striking. For a map of the actual Tokyo rail network versus a slime-mold-designed network, see here (scroll down).

Slimes do it by spreading out in all directions, moving on from areas without food and pumping more cytoplasm into the ones that do. For a great video of the slime mold doing its thing in the experiment, see here.

So you see, slime molds would never miss that left turn at Albuquerque. They’d take both turns. : ) Boringly, the scientists designed a computer program to replicate the effect that they hope could help design mobile and computer networks without human help. I don’t understand why they don’t just stick with slime molds, though. “Will work for oats — prefer nights” makes for a pretty attractive employee in my opinion.

By the way, the “oat flakes” they talk about in this study are just regular rolled oats. Though you might be tempted to think the slime molds are eating the oats, they are not. They eat the bacteria that live on the oats. Yes, your oats have bacteria on them. No, this is not cause for panic. In spite of what the makers of Chlorox would have you believe, germs are a normal part of our world. More on that another time . . .

To see how most slime molds fit in to their section of the tree of life, go here and look for “Amoebozoa”.