It Came from the Pond – Page 2 – Do-It-Yourself Protistology

The Internet Discovers a New Organism

May 032015

Tulodens. I ran across them while skimming the Wikipedia article on Protozoa, and the name didn’t ring a bell. However, the free encyclopedia assured me that there are “an estimated 30,000 protozoan species,” so it wasn’t too surprising that I’d missed these guys.

Apparently, there are at least two of them, or two kinds, and they move slowly, with the help of flagella. Or cilia, or possibly pseudopods.

A suspicious Wikipedian had already pinned a “citation needed” tag to that first sentence, so I thought I’d better corroborate the claim. A Google search turned up hundreds of references to these Tulodens. The organism was mentioned in a 24-page brochure on the most common causes of calf diarrhea. It was listed among the germs on All About Germs. On a Q&A site, somebody asked for the name of a protozoan that moves “by lashing one or more of its whiplike parts,” to which a user named 1Jazz helpfully responded: “Tulodens are a form of protozoa that move using a whip-like tail.” That’s the internet for you, always ready to help a guy with his homework.

World Renowned Parasitologist Dr. Omar Amin. [Click Image for Source]

A bit further down the Google search page, I found a British company offering parasite-testing services. They’ve posted some general background literature on protozoa, reaffirming what everyone but me seems to know, which is that “Tulodens are one of the slow-moving form of protozoans.” This company is fortunate in being able to draw on the expertise of “world renowned parasitologist” Dr. Omar Amin, Ph.D, who also mentions Tulodens on the website of his Parasitology Center, Inc., located in Scottsdale, Arizona. If you visit the site, consider buying some expensive herbal cleanses to help rid you of various totally real diseases, such as Morgellons. You can trust these guys, they have a picture of a microscope on their homepage.

So, are Tulodens parasitic? We already suspect that they cause calf diarrhea, but what else is known? All sources agree that they are very slow. Evidently they are also common, and possibly heterotrophic. If you like, you can read about them in a book called Fundamentals of Plant Pathology, by N. G. Ravichandra. The paperback isn’t cheap, but the Kindle edition is a very affordable CDN $7.32. Ravichandra discusses Tulodens briefly on page 254, but unfortunately does not add to what we already know. They are “slow moving.” Well, sure.

Are these Tulodens?

But it would be nice to know what they look like. A search in Google Images called up all kinds of sciencey pictures: stained mounts, petri dishes, an Asian-looking guy peering into a microscope. Google Images also threw up a pretty cool papier-mâché model of a Vorticella made by a schoolboy in Spain as a science fair project. The boy’s blog post includes another passing reference to the famously slow-moving Tulodens, and he is careful to cite Wikipedia as his source (which makes him a more conscientious scholar than “world renowned parasitologist” Dr. Amin).

Tulodens are also known to the Germans, the Portuguese and the Russians, so presumably their distribution is cosmopolitan. Curiously, all these sources seem to have pulled their information from the same place: the English Wikipedia article on Protozoa.

Not a Tuloden, but quite a nifty Vorticella. Well done, Álvaro! [Click Image for Source]

I wasn’t learning anything new, so I turned to the biodiversity databases. I checked the Catalogue of Life, the Encyclopedia of Life, Algaebase and WoRMS. I’m happy to say that Tulodens did not appear in any of them. Perhaps some Wikipedia editor had simply misspelled the name of some legitimate protist? I ran my eye down a few alphabetized species lists, but didn’t see any likely candidates.

At this point, I decided to see what I could learn about the Wikipedian who had introduced this organism to the world. Luckily, Wikipedia discards almost nothing: every version of every page is saved, so it is easy to retrace the entire history of an article back to the very moment it was created. The protozoa article has been edited thousands of times since it was created on May 3, 2001, but it did not take me long to find the original appearance of Tulodens, on Feb 21, 2010. It read:

Tulodens are one of the slow moving form of protozoans. They are mainly found in Leyte, Philippines. Treatment would be axing, retrenching and other form of lay away operations. Exposure usually takes two years to get rid of and are usually costly to the host.

The rascal who inserted that did not leave his name, but Wikipedia records the IP address of everyone who alters a page. In this case, the editor’s IP was 66.196.163.70, which (according to WHOIS) belongs to a company called Apac Customer Services, in Bannockburn, Illinois. Apparently, somebody at that IP used to edit Wikipedia from time to time, in a desultory and occasionally mischievous way, between 2008 and 2010. Whoever it was, he seems to have had a recurring interest in both parasites and the Phillipines, and was once blocked for editing the Wikipedia article (since deleted) on Apac Customer Services.

The treatment for Tulodeniasis

A couple of weeks later, another editor came along and removed the scary bit about the “axing and retrenching” treatment needed to cure a Tulodens infection. Within the month, somebody else edited out the observation that Tulodens were “mainly found in Leyte, Phillipines.” Now, nothing stood between Tulodens and the claim that these little fellows “move around with whip-like tails called flagella.” There was still a certain awkwardness in the passage, though, which described the “Tulodens” (plural, presumably) as “one of the slow moving form of protozoans.” It was two years before another editor solved that problem by ingeniously changing the phrase to read “Tulodens are 2 of the slow-moving form of protozoa.” Recently, that was changed again, to read “two of the slow-moving form of protozoa.” Wikipedia’s Manual of Style stipulates that integers below nine should be spelled out as words, and Wikipedians are very careful about things like that. Somewhere along the way, somebody added a hyphen between “slow” and “moving.”

Having satisfied myself that Tulodens don’t exist outside the internet, I removed them from the original article. There’s no way to delete them from all those other sites, though, and it will be interesting to see how long they last, now that the source is gone. During their five year run on Wikipedia Tulodens managed to wriggle into hundreds of other hosts. They’re informational parasites, you could say. They may be slow, but they get around.

Sometimes, it happens automatically. Web bots and data scrapers find these tasty scraps of knowledge as they’re scuttling around the net, and simply scoop up the content and repackage it. It’s nothing remarkable, just the machinery of the internet babbling to itself. More troubling, I think, is the way this fanciful critter–dreamed up, apparently, by a bored employee at a mid-western customer services company–has found its way into so many credible-looking commercial and educational sites. Some of these sources appear, at a glance, more professional and authoritative than Wikipedia, with better web design and nicer pictures, and none of them can be edited by their readers. That last point is the important one, I think. Some might think the moral of this little story is something along the lines of “don’t trust Wikipedia,” but that isn’t it at all. Anyone can change Wikipedia for the better, if they feel like it, but there’s not much we can do about diploma mills and fake textbooks and quack doctors who are quite happy to resell the information they picked up for free, but can’t be bothered to check its veracity. I think that tells us who the real parasites are.

More on Calyptotricha pleuronemoides

Ciliates, Protistology No Responses »

Feb 182015

In my previous post on the lorica-dwelling scuticociliate Calyptotricha pleuronemoides, I mentioned that only two substantial articles have been written about the species since its discovery (apart from brief descriptions in various places). Until yesterday, I’d been unable to find the second article, which appeared in the German microscopy journal Mikrokosmos in 1999. Luckily, one of the co-authors, Martin Kreutz, was kind of enough to send me a copy!

Calyptotricha pleuronemoides. Image by Martin Kreutz. Source: micro*scope. Click on image for link to source.

Martin tells me he sees the organism frequently in water from the sphagnum ponds of Simmelried, a system of bog lakes, like the one in Ottawa’s Mer Bleue where I sometimes find Calyptotricha. He and Philipp Mayer provide a good redescription of the ciliate, with morphometrics. Their measurements match those of the specimens I’ve found, and agree with those of Phillips and D.S. Kellicott. (All sources give a size range somewhat smaller than that recorded by Alfred Kahl, who gives 50 µm for the length of the cell, and 85 µm for the lorica).

The Mikrokosmos article is difficult to find, so I thought I might give a brief redescription of the species, based on the information collected by Kreutz and Mayer:

Calyptotricha pleuronematoides: Pleuronematid ciliates, in spindle-shaped hyaline lorica 56-75 µm long, tubular with narrowed openings at either end, 9-13 µm in width. Lorica broadens in the middle to a width of 23-24 µm. Cell body resembling Cyclidium, slightly flattened back to front, 22-35 µm long, 15-24 µm wide, somewhat concave on the ventral surface, where oral apparatus occupies 3/4 of body length. L-shaped undulating membrane, made up of fused cilia, 14 µm long. Caudal cilium 10-12 µm long; roughly 17 somatic kineties, spaced 2-3 µm apart. Most specimens with 8-15 zoochlorellae, colorless examples rare. Single oval macronucleus, with small spherical micronucleus. CV in posterior.

The authors mention that specimens are seldom seen outside of their loricas. Free-swimming individuals move quickly, but not as jerkily as Cyclidium. I happen to have recorded a free-swimming Calyptotricha, last year, so I might as well post it here:

References:

Kreutz, Martin, and Philipp Mayer. “Artikel-Calyptotricha pleuronemoides-Ein Ciliat in einer Rohre.” Mikrokosmos 88.1 (1999): 27-30.

Protist Homes 2 — Calyptotricha pleuronemoides

Ciliates, Protist Homes, Protistology 1 Response »

Feb 132015

A few years ago, I looked in a sample of water from a bog lake, and saw something like a hyperactive avocado shifting around inside in a tiny kerosene lamp:

The architect of that pretty dwelling is the ciliate Calyptotricha pleuronemoides. The species and genus were discovered in 1882, in samples from a pond near Hertford, England, by an amateur naturalist named Frederick W. Phillips. Not much is known about him. During the 1880s, he was an active member of the Hertfordshire Natural History Society and Field Club, to whom he occasionally read essays on “The Protozoa of Hertfordshire,” based largely on the classification scheme in William Saville Kent’s Manual of the Infusoria. He was a Fellow of the Linnean Society of London, and he found and named a few new taxa.

In his very first glimpse of the creature, Phillips was lucky enough to catch it in the act of building its lorica. “At first sight,” he writes, “I thought it was an embryonic or encysted stage of some monad; but upon applying a magnifying power of some 900 diameters, I observed that it possessed a singular vibratile membrane, closely resembling that which characterizes the members of the family Pleuronemidae.” A week later, Phillips looked at it again, and discovered that “the lorica had increased in size, and that one end was elongated into a teat-like form.” At this stage, he accidentally allowed the sample to dry out, leaving the organism’s empty, half-finished lorica still attached to a strand of pond-weed. He made a nice drawing of what he’d seen.

Calyptotricha pleuronemoides from Phillips resized

A. First stage B. The same, further developed C. End view of lorica D. The perfect animal E. Ventral view (adapted from Phillips)

To modern readers, accustomed to the impersonal, passive style of scientific writing–“samples were collected,” “living cells were isolated and observed”–there is something pleasingly candid about the way Victorian naturalists report their findings. Phillips doesn’t just describe his new genus, he spins us the tale of its discovery, including the mishap that destroyed his first specimen, and his initial misreading of the oval shell, after which he takes us to the very moment of discovery when he exposed the creature’s true nature by “applying a magnification of 900 diameters.” Something about that reminds me of the exploration literature of the same period. It’s probably not just an accident of style: Victorian microscopists were explorers. Superior lenses and stains had opened up a miniature Dark Continent on their laboratory benches, and a gentleman adventurer from somewhere like Hertfordshire could now penetrate these hidden realms, returning with breathless accounts of what he had seen. A session at the microscope was an expedition into the unknown.

In our time, researchers are expected to pile up some data before going to print, and nobody would attempt to erect a new ciliate genus on the basis of a brief observation of a few specimens. No doubt that is a good thing: the 19th century left a big legacy of poorly defined taxa, many of which are still desperately in need of revision. But this kind of field work, as sketchy and dilettantish as it might seem now, has largely been put to one side without really being replaced by anything better. Outside of a few centers of activity, ciliate field work has slowed to a crawl. Consider the fact that 132 years after Phillips wrote his three-page note on Calyptotricha pleuronemoides it is still one of only two substantial treatments of the species, and the only source that describes the construction of its curious lorica. Anyone who wants to know more about this ciliate than its name, has to travel back to the 19th century.

A straw poke-bonnet, from the early 19th century. (Click for source)

Needless to say, the old information is not always reliable.

Phillips perceived immediately, and rightly, that Calyptotricha is closely related to the more common ciliate Pleuronema. Like its cousin, it is equipped with a large, billowing membrane that runs along the right side of its oral aperture. However, Phillips badly misunderstood the shape of this structure, describing it as “a membranous trap, or velum, which in form resembled the old-fashioned poke-bonnet.”

When I first read that passage, the comparison to a “poke-bonnet” confused me. The undulating membrane of pleuronematid ciliates is shaped something like a sail, or a flag: a sheet of fused cilia running along one side of the organism’s mouth. Phillips, however, interpreted this structure (which, admittedly, is very difficult to see clearly in the light microscope) as a sort of hood or canopy covering the oral aperture of the ciliate. If you look closely at his illustration, you can see that he has drawn it as a baggy tube.

Calyptotricha's undulating membrane resembles a sail or banner (image adapted from Colin R. Curds, British and Other Freshwater Ciliated Protozoa)

The true shape of Calyptotricha’s undulating membrane (image from Colin R. Curds, British and Other Freshwater Ciliated Protozoa, with arrows added)

Evidently, it was this imagined resemblance to a poke-bonnet that prompted him to give the genus its curious name, Calyptotricha, constructed from the Greek calyptos (“veiled” or “covered”) and trich (“hair”). It seems the “haired” holotrichous ciliate reminded him of a woman’s head, on top which the membrane sits like an old-fashioned hat!

It’s an example of how expectation shapes observation. In interpreting this membrane as an enclosed hood, he was deferring to an earlier error by his illustrious contemporary William Saville Kent. Writing about Pleuronema, Kent says: “[T]his membranous trap may be appropriately compared with the extensile hood of a carriage or an outside windowshade forming, when expanded, a capacious hood-shaped awning, and when not in use being packed away in neat folds close around the animalcule’s mouth.”

The “extensile hood” Kent mentions was a common convenience on carriages of his day, and provided a compelling mechanical analogy for the “neat folds” with which he imagined Pleuronema pulled back its velum.

Here, for comparison, is Kent’s illustration of Pleuronema chrysalis, which I’ve inverted to showcase its “extensile hood.”

Pleuronema chrysalis, from W. S. Kent's A Manual of Infusoria. Put wheels on it, and you have a chuck wagon.

With wheels, it would make a good chuck wagon.

To modern workers familiar with the morphology of hymenostome ciliates, as revealed in specimens that have been stained with silver, this is an implausible design. However, to Kent, who had done pioneering work on choanoflagellates, it seemed reasonable to speculate that Pleuronema’s hood might share “a distant homological relationship” with the “delicate funnel-shaped membranes” found in the collared flagellates, which really do wear something a bit like a straw poke-bonnet (but on the back end of the cell).

Finally, since we’ve been talking about Pleuronema and her sisters, I’ll post some footage of one, quietly browsing on bacteria in water taken from a tidal pool on the coast of Maine:

REFERENCES

Meet the Protistologist 3: an Interview with Eckhard Voelcker

Amoebae, Heliozoans, Meet the Protistologist No Responses »

Dec 092014

Eckhard Voelcker (right) with Steffen Clauß

It’s been less than half a year since Eckhard Voelcker and Steffen Clauß launched their enchanting online gallery of amoeboid organisms, www.Penard.de. Already, it has emerged as one of the best places to find micrographs of amoebae and heliozoans, and the collection is continuing to grow and improve. The site features some superb light microscopy, but also sumptuously clear and detailed scanning electron micrographs prepared in Eckhard’s own basement laboratory.

Eckhard is an unusual guy. A self-taught programmer, he spent several decades in software development (at the head of Völcker Informatik AG) before turning, in midlife, to the exploration of amoeboid protists. He has pursued the new discipline in a remarkably organized and self-assured way, and, in collaboration with Steffen Clauß, has begun to make real contributions to the field. As an amateur scientist working at a high level, Eckhard seemed like a perfect subject for ”Meet the Protistologist”. I contacted him a few weeks ago, and he agreed to answer some questions.

“The child is father of the man,” as the poet Wordsworth said. I would like to know something about your earlier life. Where did you grow up? Were you exposed to the natural sciences as a child?

I grew up in northern Germany. Natural sciences were always my favorite subjects and I wanted to study chemistry or biology. Somehow I ended up becoming a computer scientist and moved to Berlin. Here I started my own software firm a couple of years later. Biology became a hobby of mine and I enjoyed watching microbes with the microscope to relax after work. It was in the year 2010, after a large corporation bought my firm, that I started to think about my future. So I started to plan for an early retirement and went as often as possible to the university, where a friend of mine, Klaus Hausmann, was a professor teaching and researching protistology. After Klaus introduced me to the electron microscope, I was hooked. I planned and built a protistology laboratory with an electron microscope in my basement and decided to focus on this and not software anymore.

So, you had no formal training in protistology or microscopy, before you began to visit Klaus Hausmann’s lab at the Freie Universität Berlin? Did you do any work at his facility, or were you simply observing?

I had been a member of the Berlin Microscopic Society for some years and my microscopic interest was mainly protists. So I did spend many hours observing, reading papers and studying books. When I would find an amoeba unknown to me, I would try to identify at least the genus and then read the available literature about it. That was why I started with the EM in the first place. I found Cochliopodium amoebae and was interested in the scale structure that is invisible with the light microscope. Somehow I convinced Klaus Hausmann that this would be interesting and he promised to help me learning the EM preparation and operation. There was this magical day a couple of weeks later that I remember so well. I had brought a culture of Cochliopodium vestitum to the university and we put some cover slips in petri dishes and filled these with my culture. A couple of days later it was my birthday and I had decided to take the day off and prepare for the EM. In the afternoon, when the preparation was done, I went to Klaus’s office proudly holding 6 sputter-coated coverslips on EM stubs and together we went down to the SEM. It was a magic moment when I first saw those delicate scales – and it was my first very own preparation (Klaus said I was very lucky to be successful right away – oh boy, was he right). When I had dinner with my wife that evening, I told her, this is what I want to do when I am done with my job. It took me some years though to finalize my work and to build my lab, but now it is all done. Klaus Hausmann has retired two years ago and the lab at the university is not a hotspot for protistology anymore as his successor is focusing on evolution.

Cochliopodium vestitum (source: Eckhard Voelcker).

You’ve mentioned to me that you learn best on your own, outside an academic context. Could you elaborate on that?

It has nothing to do with the academic context. When I listen to a lecture on video, I will pause that lecture a dozen times or so and check something, often to dig deeper into a certain detail. After my curiosity is satisfied, I will continue the lecture. I cannot do this when somebody stands in front of a blackboard “live”.

How did you begin planning your home lab? You must have been acquiring new knowledge and skills at a prodigious rate.

Planning my lab was fairly easy. I knew what I needed for preparation and there was only one room available anyway. So basically it was just the question, how do you fit a fume hood, refrigerator and deep freezer for chemicals, a SEM, sputter coater and critical point dryer into one room. Originally I planned to leave the light microscopy at my old lab in my study, but this proved to be not practical. So I moved everything down into the lab, although it is a bit cramped now. But as my wife said, this removed the danger of me buying yet another microscope.

Eckhard’s home laboratory, with Zeiss Sigma Scanning Electron Microscope at the left. (Source: Eckhard Voelcker)

Did you have collaborators in the beginning? Were you already working with Steffen Clauß?

I got in contact with Ferry Siemensma pretty early. He helped me to identify some amoeba and we have spent many hours on the phone. It was Ferry who brought Steffen and me together. Steffen had found an undescribed testate amoeba and wanted to know how to prepare it for the EM. Eventually we met and got to know each other. We were in the same position, hobbyists working alone with an exotic (to say the least) passion for amoebae. In the spring of this year we came up with the idea to create a website about amoebae combining light- and electron-microscopic images.

So, even at the start you had a particular interest in amoebae. What attracts you to them?

When I had my first small microscope it did not take long to stumble across Arcella discoides. It looked so strange, so perfectly round, simply incredible, like a flying saucer. I realized that there was more to amoebae besides being a blob of slime. The more I looked into amoebae and heliozoans the more fascinated I became.

Have you singled out certain taxa or biological phenomena for closer study?

I have a special interest in cells with scales. Some of the “naked” amoebae are really not naked, but covered with minute scales of a specific structure. Korotnevella and Cochliopodium are two nice examples. Also some heliozoans, especially Pterocystis fascinate me. When we sample in unspoiled environments, we will find species that have been more or less forgotten since over 100 years and that have never been imaged with an electron microscope. We also find many undescribed species. When I load a preparation into the electron microscope and I see an undescribed species, it really is some kind of golden moment. I am the first human who is seeing this species. But the challenge is to isolate and culture so molecular data can be obtained. Without molecular data you cannot describe new species these days. And publishing what we find is an important goal. I hope that next year we will be able to do this.

Korotnevella sp. looks like a “naked” amoeba in transmitted light, but SEM reveals its cloak of intricate scales. Source: Eckhard Voelcker.

Many of your micrographs are as aesthetically pleasing as they are informative. Do you have any thoughts about the role of art in science, or science in art?

This is a very interesting question. Most boys of my generation, as some generations before me, received at some point in their youth a microscope as a present. Looking into pond water to see the wonders of paramecium, euglena etc. was very common. Today internet gaming, social media etc. seems to be more popular and „young scientists“, who explore their surrounding nature with the microscope or a looking glass have become very rare. If we want to make people understand, that environmental protection is not only about rare plants and animals, but about unspoiled environments, swamps etc, we need to show them there is something wonderful living in these waters. If we want to make people excited about science, we need to make it visually attractive. I fully understand why most scientists don’t bother about aesthetics in their images. They have little time, are under pressure to produce papers etc. But this will create little public enthusiasm about their work. And this leads to less funding. For Steffen and me, if we can’t show an amoeba in a nice image, we won’t show it at all.

In many natural sciences, even in mathematics, very often the most fundamental equations are very aesthetic. Look at the mandelbrot set. Or look at some important equations like e = mc2, c2 = a2 + b2, or my favorite one, Euler’s eⁱ^π + 1 = 0 that combines 5 of the most important numbers. And the result is a circle!

Pterocystis, a very small centrohelid surrounded by spathe-like siliceous scales. (Source: Eckhard Voelcker).

The website you and Steffen Clauß have created to house these images was named for Eugène Penard, and features a touching biography of the great amoebologist. Do you see your research as a revival or continuation of the kind of work he did? Obviously, alpha taxonomy is less ambitious, these days, and proceeds more slowly; but you have tools at your disposal that can open doors that were closed to pioneers like Leidy and Penard…

I think it would be greatly overstating our capabilities and ambitions to call it a revival or continuation of Penard’s work. But we hope that we can fill a niche. We do groundwork, trying to find amoebae hotspots, and scrutinize them for new species etc.

Next year will be a big change. I have retired from my normal job and Steffen will be working in his normal job only 50%, spending the other 50% in protistology with me. This gives us opportunities to become more professional and to isolate species for further investigation and also for sequencing. When you come home from a normal job, your kids demand attention, the cultures demand attention, there are images that need to be processed, species need to be identified … This has been difficult for us and often when we found something that would require more attention and care we would fail due to time restrictions. Our families have been very supportive and understanding but ultimately, there is only so much you can do when you have a normal job and a family. So now that we made all those changes, we have high hopes for the future.

What is the most challenging hurdle to getting into protists, in your opinion?

Getting into protists is easy, the challenge is coming later: finding a job in protistology that is paying!

Given your professional background in computers and software, do you have any thoughts on how IT could provide more support for protist research?

This is something that constantly amazes me. How can a group of such highly intelligent and educated people live with so little IT infrastructure support? Where is our species database? I want to be able to search based on traits. I want to see images. I want to see the latest papers on this subject. I want to know who has seen it, who is interested in it, etc., etc. I think that protist research would greatly benefit from a certain shared infrastructure. If they all would work for the same institution they would have an infrastructure like this in place within in a short period of time. It would make the entire group so much more efficient and the ROI would be quick and high.

Any other thoughts?

Spend less time surfing the internet and more time in front of your microscope. 😉

I will try to follow that advice! Thanks for taking the time to do this.

Some choanoflagellates (Choanomonada Kent 1880), members of the protist group most closely related to us. (Source: Eckhard Voelcker)

A first attempt at silver carbonate staining

Ciliates, Silver Carbonate, Silver Staining 10 Responses »

Oct 092014

As I might have mentioned already, my favorite protists are the shaggy, shapely, fast-moving ciliates. They have a lot to offer the idle protist-ogler. As a group, they include some of the largest and most ridiculous-looking microbes in the pond. Many are easy to identify without expensive equipment or special techniques. Some, like the noodle-necked Lacrymaria olor, can be recognized at a glance in the light microscope, even at low magnification. Others, like the stately Stentors, may need closer inspection for a species-level classification, but can still be identified by prominent features such as the colour of the cell, or the shape and distribution of various organelles.

Unfortunately, not all ciliates are so easy to tell apart. Some are like the “little brown birds” that plague neophyte birders, and can only be distinguished from one another by very close observation under exacting conditions. And many, I’m sorry to say, are pretty much impossible to identify, even to genus level, without the help of special stains that expose distinctive patterns in the cilia on the surface of the cell body.

The classic technique for exposing these structures is to fix the cells in some noxious and foul-smelling substance and then soak them in solutions containing various compounds of silver. Certain parts of the organism–most conveniently, for our purposes, the ciliary rows and the nuclei–are “argentophilic,” which is to say they stain darkly when exposed to silver. The ability to selectively stain these organelles revolutionized ciliate taxonomy in the second half of the 20th century, and it is still the most important technique available to modern ciliatology.

Despite my particular interest in ciliates, I’d never tried it until just a few days ago.

I’ve been slow to get around to this, mainly because it’s hard to do. Even the easiest methods of silver staining call for a cupboard full of powders and solvents, none of which is available at Shopper’s Drug Mart, and some of which must be handled and stored very thoughtfully. To procure the ingredients I had to find suppliers willing to do business with an individual buyer, and in some cases I had to pay special transport fees.

Then, of course, I had to assemble the equipment required to use this stuff safely: graduated cylinders, flasks, funnels, fixing jars, an accurate scale, syringes, latex gloves, etc.

And finally, I had to acquire a bunch of new skills. I haven’t stood at a lab bench since the ninth grade (40 years ago, if you can believe it), so I had to learn how to do simple tasks, like weighing, pouring and mixing. Fortunately, before undertaking any of this, I had the foresight to culture a full-sized biochemist, which was quite expensive and took about 23 years. He is currently living in my basement, and was very helpful at several points.

Here, then, is my first attempt at staining a plain old Paramecium by one of the silver carbonate methods:

Yes, there’s a lot of room for improvement, but, frankly, I’m delighted that it worked at all.

Here’s one more from the same slide, a specimen of a common hymenostome ciliate with the curious name of Glaucoma:

The impregnation could be more uniform, the focus could be sharper and the hot spot from the microscope lamp is downright annoying. However, I can count the kineties and easily see the shape of the macronucleus. That’s a step forward, for me.

The protocol I followed is the one developed by Augustin, Foissner and Adam in 1984 (described in Foissner’s updated guide to basic methods for ciliate taxonomy). I’m told that the original Fernandez-Galiano method gives more consistent results, so I’ll try that next.

A New Thing in an Old Place

Biodiversity, Conservation, Testate Amobae No Responses »

Jun 042014

Common House Centipede (Scutigera coleoptrata) Click image for source.

My daughter slept on the couch last night because there was a “giant centipede” in her room. A search on “giant centipede” turns up exotic beauties like the fabulous foot-long Scolopendra gigantea, which eats mice, snakes, lizards, birds and frogs and has even figured out how to catch bats by dangling from cave ceilings . I doubt that my daughter’s centipede was really a giant–she only needed one hand to show me how big it was. But it’s another reminder, if we need one, that “nature” is not off in the woods somewhere, and you don’t have to paddle to it, or ride there on an ATV. It is under the floorboards and between the threads of our sheets. It’s us, and it’s all over us. As science writers like to remind us, our own skins are a fertile savannah to the microbes and mites that browse in its moist valleys and fungal thickets. Our intestines are as lush and biologically diverse as a jungle, an Amazon you can carry around.

Too often, though, we think of nature as something that had better not be scrabbling up the leg of the bed. It belongs in certain places, and we do like to put things where they belong. The urge to sort things, to put them in their place, is strong in us and features prominently in lists of human universals. When things are in the “wrong” place, we tend to not see them properly, or to not see them at all. Take the contents of any contemporary art museum and put them out by the side of the road. I’m pretty sure some of the artwork will still be there the next day; and some of it will probably sit there long enough to be hauled away with the trash on Wednesday morning. Leaving aside the likelihood that the landfill is the right place for some of it, this is a small failure of perception, one that is so common and familiar that we design our public spaces to allow for it. We have trouble seeing the art, even when it is in front of our eyes. So, we label the art, or lift it off the ground on a slab of stone, or we build places like museums and galleries where the right kind of seeing and thinking is gently encouraged.

Seeing “nature” is almost as hard as seeing “art”. To make it possible to notice nature, we set some of it aside in special spots. These are our sanctuaries and conservation zones: places where we can look at what would be here if we were not. We choose a patch of ground, or pool of water–often, I’m sorry to say, one that nobody wants for anything else–and we do with it something that does not come naturally to us, something that is not “in our nature”: we leave it alone. We just leave it to itself, so that we can go there once in a while, and look at it to see what things are like when we are not around. Except that we are around, of course, stealthily watching. We are there and not there at the same time. This gives us a feeling we find so agreeable that we are willing to tax one other to pay for it all: the boardwalks and the picnic tables, the bilingual signs warning us not to interfere with it in any way.

A marsh in the Mer Bleue Conservation Area

For a couple of years, I’ve been going to one of those places as often as I can. It is the Mer Bleue Bog, a patch of subarctic peatland inside Ottawa’s city limits. At one time, the Ottawa River ran directly through it, but then the course of the river changed, leaving it hydrologically isolated, fed only by rainwater. For about 8,400 years, sphagnum moss has been accumulating there, to a depth of 6 metres in some places. It is an unbroken link to the end of the last ice age, and although the city and its commercial sprawl are not far away, it has an eerie–I was about to say “unnatural”–calm that seems to startle its many visitors into speaking very quietly, as if they were in a church.

There is still some open water attached to the bog, including a cattail marsh where I collect samples to look at under the microscope. It is what lake researchers–“limnologists”–call a “dystrophic lake.” The water is low in nutrients, highly acidic and steeped in humus. It is the colour of a weak tea, one that happens to be filled with the most wonderful algae, ciliates and amoebae.

The chemistry of the water, and the isolation of the entire system, give it a distinctive microlife, quite different from anything in the other lakes and rivers around here. It is much greener, for one thing. Perhaps because it is so poor in available nutrients, many of the organisms here make their own food by photosynthesis. In this water, I’ve found a surprising diversity of protists, including many that don’t turn up in my usual samples,and a few that have never been described before.

A new testate amoeba in the genus Arcella.

Some are different enough to deserve new names of their own. The most recent novelty to turn up in my jars is a testate amoeba of the genus Arcella, a creature that lives in a rather pretty proteinaceous shell. This one resembles an amoeba described in 1918 by Playfair, Arcella costata var. angulosa. However, it is distinct enough from anything previously described that, in the opinion of Arcella expert Ralf Meisterfeld (in personal communication), it is “certainly a new species.”

Ventral view showing crenulated pseudostome.

The main feature that sets it apart is the shape of the aperture at the bottom of the shell. This “pseudostome” (“false mouth”) is an opening in the shell through which the amoeba extends its pseudopods. In most Arcella it is smooth and round, but in these guys it has a frilly, “crenulated” shape, like a malformed flower. I wonder if this is a strictly local variation, or something that is found elsewhere in the world? I would like to think it arose locally in the Mer Bleue population, perhaps because of its isolation from the surrounding waters; however, it is likely that the feature is found in many other populations, but has rarely been recorded. This line of thought risks reanimating the perpetual debate about whether microbial species have a discernible biogeography, as lemurs and wombats do. I’ll leave that alone for now, but it deserves a post of its own.

In the meantime, here’s some video of this little jewel:

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