Dec 182013

Early last year, the mayor of Salzburg proudly announced the creation of a new conservation zone around this “globally unique ‘natural monument'”:


Click image for source,

The newly protected feature is not that rocky bluff, Festungsberg hill, or the 11th-century fortress that sits on top of it. It is the long, narrow puddle in the foreground.  This is Krauthügel Pond, an ephemeral body of water barely 30 cm deep where researchers have found 121 species of ciliates, ten of them previously undescribed. Because of these organisms–five of which have not been found elsewhere–Salzburg now possesses the world’s first second “Natural Monument for Single-celled Organisms.” A protist wildlife sanctuary!

The pond comes and goes during the year, appearing after heavy rains on a raised agricultural plot known as Krauthügel, or “cabbage hill.” The bed in which it lies is thought to be the remains of an old stream, whose natural course might have been altered by agriculture during the middle ages. Since then, roadwork and urban development have isolated the body from other surrounding channels.

From 1789 until 1960, the field was used for raising vegetables.  After that, it became a pasture. For about thirty years, cows trampled the soft turf and nourished the local microbes with their  manure, creating what ecologists call a “eutrophied pond.” In other words, a cattle wallow, or slough.

This is not what you could call a pristine natural environment. It doesn’t shelter any large, charismatic animals. It is not particularly scenic, when it can be seen at all (much of the year, the “pond” is dry). In short: it’s hard to imagine a patch of ground less likely to be singled out for conservation.

However, Krauthügel Pond has something your local ditches and mudholes lack: proximity to Wilhelm Foissner, an astonishingly productive ciliatologist who happens to live and work in Salzburg.


Wilhelm Foissner (Click Image for Source)

Arguably, the “natural wonder” here is not so much Krauthügel pond as Professor Foissner, whose vast body of work looms over modern ciliate systematics like the Festungsberg itself. With five or six hundred publications to his name–at least three hundred in peer-reviewed journals–Foissner, working alone or in collaboration, has discovered and described over 500 new protist species.  If there were new ciliates in your cow field, he would be the man to find them.

Actually, to see a new species is not that unusual.  Likely, we all run across undescribed organisms, from time to time, without knowing it. The little red bug that alights on your arm might be something never before recorded in the literature, if only you knew. Place samples of local mud under the microscope, and you are quite likely to find organisms that don’t yet have names. Of course, it’s one thing to see something new as it paddles by, and quite another to know what you have seen. To properly document your discovery, and publish the news of it, requires skills and technology that are in extremely short supply.

So, these ciliates were pretty lucky to have been born in Salzburg, near one of the few people in the world with the ability (and inclination) to see them for what they are and lobby for their protection. It raises some interesting questions.

First, how exceptional is the microbe diversity that has been preserved in Krauthügel?  In a report on the the pond, published earlier this year, Fenton P.D. Cotterill and his co-authors compare the ciliate species count at their location to various “well-investigated ephemeral waters” in other parts of the world: two meltwater ponds in Southwestern Ontario, a roadside puddle in Namibia, a rock pool in Venezuela, a meadow in Hungary, and several other choice spots.  They find that the Salzburg pond is in the “upper range” for total number of species, but only in the “middle range” for the number of new species.

Evidently, the old cabbage field supports a high–but far from unique–diversity, and when closely probed by the best protistologists in the business, it yields about the expected number of new organisms. A rich but fairly ordinary body of water, it seems.  Why single it out for protection?

Three species only found at Krauthügel  e)  Semispathidium pulchrum f) Papillorhabdos multinucleatus g) Fuscheria nodosa salisburgensis

Three species only found at Krauthügel e) Semispathidium pulchrum f) Papillorhabdos multinucleatus g) Fuscheria nodosa salisburgensis

There are a couple of reasons. First, as the authors point out, appeals for conservation are usually based “on the narrow distribution of one or several species and their habitat, or of species and habitats endangered by human activities.”  If a forest supports the only known population of Sibree’s Dwarf Lemur, we have reason to preserve it, because if we don’t, we can expect to lose that species forever. By that standard–provided we suppress the size-bias that can make us indifferent to the fate of a microbial species–the case for protecting Krauthügel is pretty strong.  As of April, 2013, five of the the ten new species found there had “not been reported from any other locality.”  Until they turn up elsewhere, those five species are assumed to be “endemic” to Salzburg (that is, restricted to that area).  Given the scarcity of competent ciliatologists in other parts of the world, they may remain so for quite a while.

Whether they turn out to be truly endemic or not, it is indisputable that the organisms in the pond were “endangered by human activities”. In 2010, as part of an art project, somebody filled it in with earth. Imagine the alarm of researchers who had been studying the site for decades when they found out their protists had been buried! It was this event that prompted investigators to call for protection, resulting in the restoration of the pond to its previous condition and the creation of a buffer zone around it:

Buffer zone around Krauthügel Pond

Protected zone around Krauthügel Pond

And that brings us to the second reason for conserving this puddle: thanks to the work that had already been done there, it has become the “type locality” for some eighteen species (eight new species, and ten redescribed taxa). The significance of this might require a bit of explanation.

amblyodus taurus

Amblyodus taurus (click image for source)

When a biologist names a new taxon, the usual practise is to select a particular fixed specimen, or group of specimens, as the “type,” and (ideally) to deposit that specimen in a permanent collection somewhere, available to other researchers.  This provides a permanent concrete reference, so there can be no ambiguity about what we really mean when we say Utricularia floridana (a species of carnivorous plant), or Amblyodus (a genus of beetle).  If need be, we can point to a certain bug on skewered on a certain pin and say, “There! Amblyodus means that.”

The site at which the type specimen was collected becomes the “type locality,” where one might expect to find others of the same breed.  That locality is especially important to protist taxonomists. Protists are small and fragile, and fixed type specimens of older named organisms are rarely available.  Even when permanent slides exist, they can be lost, or simply deteriorate over time.  If we know the type location where our guys were originally found, we can go look for them there. In theory. But if the place at which the work was done has been drained or paved, and no type material exists, the identities of the species found there can be lost in taxonomic noise.

What is being conserved at Krauthügel is, at least in part, the scholarly work that has already been done there.  It is a body of acquired biological knowledge, and not just the organisms themselves, that is being protected.  From this point of view, environmental conservation can be similar to task that museum and art conservators do, preserving the best products of human effort for future generations.

Where does that leave all the ponds that haven’t been, and likely never will be, studied?  In spring, when I drive through the countryside where I live, I see ephemeral pools by the hundreds and thousands. They flash by in the car window, mile after mile: beaver ponds, ditches, mill pools, flood plains, and wide shallow puddles in fields where cows dip their muzzles and drop their nutritious poops. Some will have less protist diversity than Krauthügel, a few may have more, but none will ever enjoy the benign oversight of Wilhelm Foissner.

But what if more research were being done on these bodies of water–a protistologist for every puddle!–and more ponds found worthy of conservation? It is not clear where that road goes. If the Krauthügel initiative stirred up any controversy in Salzburg, there’s no record of it in the article, or the press release, but it’s not hard to anticipate the kind of pushback we’d see if similar initiatives were tried here.  Attempts to control the use of private land arouse deep and incredibly long-lived resentments.  Twenty-five years after efforts to conserve habitat for the Northern Spotted Owl in the PNW, anti-environmentalists are still seething and sneering. In some circles, the words “spotted owl” have become a kind of shorthand for “meddlesome tree-hugging morons who place a higher value on a stupid bird than the lives and livelihoods of hardworking humans.” Imagine the volcano of outrage that might erupt over the mandated protection of a one-celled organism! We would never hear the end of it.

All the same, the idea of protecting protist habitat has a lot of appeal for me.  Down the road from my house in the Gatineau hills, there’s a group of ephemeral ponds where I like to gather samples. Within a few years, they will almost certainly be filled in, as the land is subdivided for new housing. I’ve watched those ponds for several seasons, and hate the idea of losing their amazing microscopic diversity. If, as is statistically probable, they contain a few new species, there might even be grounds for conservation. However, it is pretty certain that the bulldozers will get to any new organisms before I gain the competence and resources to find and describe them.

Still,  I find it a little comforting to remind myself of the very different scale and speed of life at the microscopic level. When you are a hundred microns long, from tip to tail, a puddle is a lake, and a pond is an ocean. An hour is a year!

In a few days, a rain-filled tire rut can burst into startling diversity, like a miniature coral reef. Species bloom in quick succession, replacing and displacing one another. Each one changes the chemistry, light-permeability and nutrient load of the water, conditioning the environment to suit certain organisms, all of whom, in turn, will alter the water around them. Accidents of geography (a floating leaf,  a ball of dung) make opportunities for some organisms, and extinguish all hope for others. Things progress quickly. If you return to the tire-rut every day and follow its progress with the help of a microscope, it can seem like looking at a time-lapse film. In the “big” world, environments change in much the same way, but over longer periods of time: forests encroach on prairies, then recede; wetlands take shape, silt up and vanish; animals come and go.  At the microscopic level, shifts in populations may happen in hours, instead of years, and change is unremitting. “Ecological balance” is never achieved: things happen, then more things happen. Some species flourish, others fade from view. Then one day the hot sun dries it all up, and the little creatures climb back into their resting cysts, as their habitat reverts to grass.


Cotterill, Fenton PD, et al. “Conservation of Protists: The Krauthügel Pond in Austria.” Diversity 5.2 (2013): 374-392.
Dec 112013
Ferry Siemensma at his Microscope

Ferry Siemensma at the microscope

Ferry Siemensma is an independent researcher in the Netherlands, and a leading expert on several groups of amoeboid and heliozoan organisms. For the past two years he’s been building a website devoted to his favourite creatures: Microworld: world of Amoeboid Organisms. This was an ambitious project from the beginning, but over time it has gradually turned into something that hasn’t been seen since the comprehensive texts of Cash, Wailes and Hopkinson, or Eugène Penard: a wide-ranging illustrated guide, featuring good formal descriptions, keys for identification, and up-to-the minute taxonomy. Ferry kindly agreed to answer my questions, in the first of what I hope will be a regular series of “Meet the Protistologist” interviews.

Your enthusiasm for your research reminds me of Joseph Leidy’s recorded remark: “How can life be tiresome so long as there is still a new rhizopod undescribed?”   He was not raised in natural science (his father was in the hat business), but even in childhood he was driven “to see how plants and animals are made.” What was your upbringing like?

I grew up in a rural community in the northern part of the Netherlands. My father was a carpenter and I was the oldest of nine children. We always played on our uncle’s farm around the corner, and there I got my first interest in nature. I became a voracious reader of popular books about science and biology and in one of them I read the word “amoeba”. For me it was such a magic word, I don’t know why. From then on I was determined to find such a creature once. I was 14 years old when I bought a cheap Japanese microscope for about $10, which was pretty expensive in 1962. I could recognize some moving protists with it, but no amoebae. Many years later, at the age of 22, I became a teacher in a primary school, where I worked with 11-12 year old children. I also took a study to become a biology teacher and during that study we were offered to buy a Lomo microscope. This Russian instrument was really great, and it had a wonderful 70X water-immersion. From the day I got that scope, my life changed completely!

So, you were a schoolteacher, like Alfred Kahl! What changed in your life after you acquired the Lomo?  

From then on, for more than 12 years, I looked through the microscope nearly every evening. My three daughters were very young at that time and went to bed very early, which was a great advantage ;-). Very soon I got in contact with Rob Wellner, who was looking for a microscope friend. We worked together for two days a week for many years. He taught me a lot, but his main interest was algae and I shifted to amoebae and heliozoa. In that time I got in contact with Dr. De Groot, a well known Dutch amoeba specialist. We smoked a lot of cigars together and had nice talks about our shared interest.


Frederick C. Page at Cambridge, 1980 (Source: Ferry Siemensma)

When he died in 1981, he left me his scientific literature, with the books of Leidy, Penard and Cash, which was a great luck for me, because in that time it was very difficult to get any papers. There was no internet, which is very hard to imagine now. In the meantime I also got in contact with Fred Page in Cambridge. He is such a pleasant man and we wrote each other a lot of letters. I went twice to Cambridge to see him.

He gave me the address of a Danish microscopist, Niels Willumsen. I phoned him, he invited me and that was the beginning of a very long friendship. One day I got a letter from Rudi Roijackers, who worked at the University of Wageningen. He offered me the use of an electron microscope and that was an excellent chance to get new information about heliozoa. I hunted for heliozoa, isolated them, made dried preparations and once a week we looked at the results in the SEM. We discovered new species and published some papers. I also published two booklets in Dutch about heliozoa and naked amoebae. Than I was invited to write the heliozoan part of the German Protozoenfauna. Fred Page wrote the other part on naked amoebae. The book was published in 1991.


Ferry on a sampling excursion, 1981. (Photo by Niels Willumsen, who later capsized in the same boat)

Looking at your publications during this period, you were very active, especially with heliozoans. It must have been a thrill to be among the first to see EM images of the very intricate scales in certain groups! Were there certain organisms that you found particularly fascinating?


Ferry in the field with his Lomo, 1982. (Source: Ferry Siemensma)

I was intrigued by the scales of Rabdiophrys species, though they aren’t true heliozoans. Those scales had been studied ten years before by Thomsen and I found them very beautiful subjects to make drawings of. One problem was to interpret the information on the SEM photomicrographs and to form a 3-dimensional image of those scales, which was really a challenge, and very fascinating, which was also true for the base of many kind of spiculae of the true heliozoans.

If you don’t mind my asking, was it a struggle to find funding and free time for this research?  Did you continue to teach?

No, there was no funding, because the work at the university of Wageningen was part of the research of Rudi Roijackers. His interest was Mallamonas and he wanted to find out which scales belongs to heliozoans and which to Mallamonas species. He helped me with the SEM, I helped him with the identification.

Concerning my free time, I did all my research in the evening, the weekends and in my ample holidays. The latter was the big advantage of being a teacher! Schools were closed on Wednesday afternoon, so once a month on Wednesday I jumped into my car and drove to the SEM, one hour driving from my house! Teachers didn’t have a great salary, and they still don’t, so in that time I cleaned every cover glass in order to reuse it 😉

I still clean coverslips, unless they have immersion oil on them!:) In the decade between Nackte Rhizopoda und Heliozoea and the ISOP Illustrated Guide, you seem to have published less frequently. Were you pursuing other interests, or simply working quietly on your own?


At the British Museum in 1984, to look at Eugène Penard’s slides. (Source: Ferry SIemensma)

There came a moment that I didn’t find any more new heliozoans. Preparing them for the SEM was a lot of work. First I had to find one, then to decide if it could be a new species, then came the process of removing the cover glass, which was the most complicated part, isolating the specimen, drying it, marking it and finally cutting the slide for the SEM.

After some months without any positive hit, my interest faded. It was at that time, as my girls grew older and needed my attention, that I got very interested in computers and I had a chance to start a science magazine for children – all in my free time. For many years a layer of dust grew slowly on my microscope…

Did you make room for amoebae in your magazine?  It always seems to me that popular science publications have too many telescopes and not enough microscopes!

No, it was intended for 10-14 year old children, and they don’t usually own a microscope.

When did you decide to blow the dust off your microscope, and what brought you back?

Some years ago I got a letter from a woman working at a waterlaboratorium here in the Netherlands. They control the drinkwater quality and had problems with amoebae transporting Legionella bacteria through their filters. They needed my help for identification and had found my name with Google. And there I went to the lab and worked a whole day with a microscope…after so many years. I enjoyed it so much, it was a wake-up call. From that day on, I decided to start again. My first look through my Russian microscope taught me that it was unusable anymore: completely worn out. I bought a secondhand Zeiss standard and later an Orthoplan with DIC and phase contrast and other stuff on eBay. And so I came back home again!

In your website, your experience as an educator and your expertise with amoeboids have come together. How did this project begin?

I started this project about two years ago with the intention to make a survey of all the Dutch amoebae, and as replacement for the book of Hoogenraad & De Groot (1940). Here I could combine my interest in computers, nature, photography and drawing. But soon there came questions from people in the forums who asked for identifications of their findings and I started to publish their photographs also on my site. And then I realized it would be nice to cover the whole world. But it’s a huge project, in fact too much for one person. Every day there are new discoveries to document, new photomicrographs to edit and to archive and new email to answer. But I’m building my site stone by stone… uh.. shell by shell, without hurry and without any pressure. I love it!

While developing your website, you are continuing to do original research.  Can you talk about that work?


Niels Willumsen at his country home in Sweden, in 1982. (Source: Ferry Siemensma)

I’m very interested in the variation within populations. Probably you know how difficult it is to distinguish between certain Centropyxis species, and the same is true for Difflugia, Euglypha, Cyphoderia and many other taxa. I’m measuring populations from different localities and will see what comes out. At the moment I have an Austrian sample with a population of Pseudonebela africana, which is new for Europe. It has been described from Africa and Brazil as having dimensions between 78 and 100 µm, but I find shells which are 85-185 µm long. That’s really interesting, and shows how little we know of populations in the wild. As these specimens are living, I also have the opportunity to observe their feeding behavior which is the same of that of Difflugia rubescens, and these specimens also have the same red color. They must be related. I’m fascinated by the behavior of amoeboids. I’m using a nice and simple, but very successful method for observations, the so-called “wet chambers” where I keep my wet mounts. It’s always a surprise, what comes up in such mounts after several days. Not seldom some species multiply rapidly and attach to the cover glass. which is excellent for observations. Mmm… I can go on for many hours…

It would be a pleasure to spend those hours with you, and I hope I will have the chance, one day.  Thank you so much for taking the time to do this.

Dec 082013

I’ve added a number to the title of this post, because I expect to make “Protist Homes” a regular feature. I had intended it to be an idea-free zone, devoted to uncomplicated wonderment (kind of like the tours of celebrity homes and stately residences on HGTV).  But I know some ideas and research will creep in, because it’s hard to feel wonderment without actually starting to wonder.

Difflugia acuminata

Difflugia acuminata, from a pond in Wakefield, Quebec


Consider the little shell in the image to the left.  Barely two tenths of a millimetre long, it was constructed by an amoeboid, using found materials: tiny grains of sand, glued together with some sort of proteinaceous cement.

How does a single-celled amoeba build such a perfect bottle, from such randomly-shaped material?  And why did my grade-school macaroni art projects turn out so much worse?


The organism that once lived in that test is dead (testate amoebae cannot leave their shells without dying). In life,  it would have looked and behaved like the one in this video, by my fellow protist-watcher, Francisco Pujante:

All members of the genus Difflugia build their shells–or tests, as they’re properly calledout of stuff they find lying around, such as grains of quartz or discarded diatom shells, binding them into a matrix of organic secretions. It turns out that they are quite selective about the particles they use for this work, and researchers have gone to a lot of trouble to figure out what criteria amoebae use when picking their building materials.

Difflugia 3D rendering 2

3D rendering of Difflugia oblonga, created by Châtelet et al. Click image to show source.

Recently, a group in France went so far as to create complete three-dimensional reconstructions of two specimens of Difflugia oblonga, using a process called x-ray microtomography. They calculated the volume, shape and orientation of each grain in their specimen tests, and gathered information about the density and composition of the individual particles. Yes, you read that correctly: they analyzed and modelled every micro-sandgrain in amoeba shells that are themselves smaller than the grains of sand you might find on an ordinary beach.

Using all this data, they compared the composition of the tests to the natural sediments in the ponds where they were collected. From their analysis, it appears that these amoebae really are selecting the smaller grains, and also showing a taste for certain minerals (quartz is preferred, while the more abundant calcite is shunned). What’s more, the amoebae seem to be selecting materials with a consistent density, which the authors speculate is to ensure the test will be perfectly balanced!

Difflugia grain sizes



The paper (du Châtelet et al, 2013), includes a handy graph, comparing the sizes of each of grain of sand in two Difflugia tests to a distribution plot of the size of sand particles in the surrounding pond sediment.






Building with quartz is fine, if you are lucky enough to live in the mud bottom of a pond where chunks of silicate minerals are available.  But what if your habitat is a floating clump of algae in a mineral-poor spagnum pool?  There, the best source of silicate particles might be the siliceous shells (frustules) of your fellow protists the diatoms, which have the ability to build their little glass canoes from dissolved silica (silicic acid) found in the water around them. The testate amoeba Difflugia baccillariarum–typically found in sphagnum pools, where sand is in short supply–has figured out how to glue diatoms around itself as a means of protection.  I find these guys, sometimes, in samples from the Mer Bleue bog,  and always stop to look at them.  They are truly amazing:

It is hard not to admire this crafty amoeboid, building its home from the bodies of other organisms.  Sitting here in my post-and-beam house, assembled from the trunks and branches of felled trees, I feel a certain kinship.


Dec 062013

The Last Eukaryote Common Ancestor–affectionately known to cellular evolution geeks as “LECA“– was almost certainly a predator.  Later in the history of the lineage, certain eukaryotes would form permanent symbiotic alliances with photosynthetic bacteria, and once that occurred, some lucky cells could just bask in the sunshine, drawing energy from light with the help of their chloroplasts. Until that happy day, however, all nucleated cells survived by using a bizarre trick that LECA must have known: the ability to ingest other cells by phagocytosis (literally, “cell-devouring”).

Another thing about LECA and its descendents is that, thanks largely to the mitochondria which give them a fairly generous energy budget, eukaryotes of all kinds have a real genius for evolving new and outlandish bodily structures. Unlike the prokaryotes, bacteria and archaea, which tend to have rather unimaginative body shapes, energy-rich eukaryotic cells have developed a huge (and hugely entertaining) diversity of organs, appendages and specialized equipment.

So, in the eukaryotes we have a population of ravenous cell-eating cells that also have a talent for morphological innovation. Clearly, this has the makings of an arms race, as prey and predator (and most eukaryotes are both!) hurry to develop new instruments for attack and self-defense. This race  is one of the likely drivers of their exceptional somatic diversity. There are other evolutionary drivers of eukaryote complexity–including some not directly tied to adaptive pressures–but the need to avoid being devoured  is certainly an important one.

There are many ways to avoid being eaten. One of the simplest strategies is to be too big to swallow. However, there is a cost to that.  Big bodies are expensive: they require a lot of energy to keep going, which means the organism has to gather more food.  But what if you can be big without having to maintain a large mass of living tissue?

One way to accomplish that is to congregate with others of your kind in close-knit (even clonal) colonies, as many flagellates do.  Take, for example, the planktonic heterokont Synura, which usually lives in big, rolling spherical clusters made up of many cells. If you want to eat a single Synura, you will need to be big enough to eat the whole sphere.

Obviously, there are plenty of creatures big enough to consume a whole colony (I’ve seen Stentor pyriformis gobbling Synura like popcorn balls); but the strategy of colonial aggregation does take some of the smaller predators out of the game.

There are a few downsides to colonial living (decreased freedom of movement, for one); but the tradeoffs can be acceptable, especially for those protists whose way of life doesn’t require much personal mobility. Not surprisingly, photosynthetic organisms, which don’t have to chase their dinner around, often live in colonies.  In the microworld, familiar examples are the filamentous green algae, or the great spherical death stars we call Volvox (which are not only colonial, but actually have some cellular specialization, like plants and animals).

Volvox by R. Wagner

Volvox aureus. Image by R. Wagner. Click on the picture to see more Volvox on Dr. Wagner’s site.

Another good survival strategy is to borrow “bigness” from your surroundings.  Mix yourself in with a pile of debris, or crawl into a hole in the mud, and your enemies will be unable to get their mouths around you.  In short: take shelter.  It is the same plan, here, whether you are a protist, a beetle, or a juicy human surrounded by bearsharks: position yourself inside something bigger, pricklier and tougher than your own delicious body, and you might survive.

One major disadvantage of opportunistic shelter-seeking, as practised by cautious organisms of all sizes, is that your fortress isn’t always located close to your preferred food source; and if you leave it to go foraging, you risk becoming a food source yourself. One good solution is to build (or secrete) your own shelter in an optimal location. This approach, often combined with the strategy of colonial living, has given rise to an amazing array of ingenious shells, houses, tube dwellings and domestic mucous piles which protists have created for their own protection. In my next couple of posts, I will look at some examples of protistan architectural achievements.