Flying amoebae

Contributed by Edward A. D. Mitchell

Laboratory of Soil Biology, University of Neuchâtel

I’m learning to fly but I ain’t got wings

Coming down is the hardest thing

Jeff Lynne/ Tom Petty

Since the early days of protistology it has been known that testate amoebae can be transported passively by wind. Darwin had collected dust that had fallen on the Beagle while sailing off the coast of Africa. He sent the sample to Ehrenberg who observed it under his microscope and found many protists (Darwin, 1846). Observations such as this have led to the idea that microscopic organisms could travel far and colonise all potentially favourable habitats (i.e. everything is everywhere, but, the environment selects; (Baas Becking, 1934, de Wit and Bouvier, 2006)). It is therefore perhaps surprising that not much experimental research has been done to quantify the amoebae that are transported by wind. A recent modelling study showed that the medium to large sized testate amoebae (i.e. 40-60µm diameter) were unlikely to travel over large distances and certainly incapable of crossing oceans while the smaller ones (e.g. 9 µm diameter) could potentially do so (Wilkinson et al., 2012). But, to my knowledge, observational and experimental studies on wind dispersal of testate amoebae are very rare. An elegant recent study by Wanner and colleagues contributed to filling this important gap (Wanner et al., 2015).

Wanner and colleagues used sticky traps: 15cm diameter plastic petri dishes in which filter paper was attached using a paraffin-based balm, which also covered the filters. The petri dishes were used as passive, sticky traps for airborne organisms and contained no growth media. The system was initially designed to study seed dispersal but proved to also be useful to study microorganisms. They exposed traps for periods ranging from 16 to 42 days and recorded 12 testate amoeba species (excluding unidentifiable specimens): Centropyxis aerophila, C. elongata, C. sphagnicola, C. ambigua, C. eurystoma, Difflugia lucida, Phryganella acropodia, Tracheleuglypha dentata, Trigonopyxis arcula, Trinema complanatum, Trinema lineare, and Trinema penardi. The two most commonly found species were respectively ca. 40µm and 60µm in diameter (Phryganella acropodia and Centropyxis sphagnicola). The overall abundance was low with little over 80 specimens recorded in total. Therefore although this study shows that amoebae can “fly”, they don’t do so in massive numbers even close to the ground and near source populations. The probability for long-distance (e.g. across 100-1000km of ocean) passive dispersal must therefore be extremely low.

Also it is rather surprising that the dominant taxa recorded on the traps were not small euglyphids but mid-size arcellinids. Indeed small euglyphids are likely to be more numerous in the upper soil horizons and the better drained and exposed microsites from which they can be expected to have more chances to be lifted up by the wind. Their small size and lighter shells should potentially allow them to be transported more easily than larger taxa, but this is not what Wanner and colleagues observed.

Extrapolating form their results, Wanner and colleagues estimated that on average 61 individual amoebae (living + dead) were deposited per square meter each day. Therefore a viable population can become established rather rapidly on a newly exposed surface, provided that a source population is present nearby. These results also suggest that initial colonisation will be rather stochastic but that as more and more amoebae are deposited on a given place the full potential community will soon be present and community composition will therefore soon be controlled by local processes such as environmental filtering. The authors estimated that the shift from stochastic to deterministic community pattern takes place after ca. seven years of soil development and therefore concluded that testate amoebae are valuable indicators of initial ecosystem development and utilisation.

Such research is important at the local as well as global scales. Locally it informs on the mechanisms that determine primary and secondary colonisation of soil and other habitats and at which temporal scale testate amoebae can be used as bioindicators. Globally it provides useful data on actual wind dispersal of amoebae. The first step is indeed for an amoeba to become airborne and this may not be trivial depending where the species live.

The study of Wanner and colleagues also shows that it is not straightforward to design traps for studying aerial dispersal of testate amoebae. The traps were indeed initially not designed for such a study but were nevertheless useful. However it may be possible to develop an optimal type of trap for studying aerial dispersal of testate amoebae. This study clearly gives food for thoughts and hopefully will stimulate the community of testate amoeba researchers to further explore how amoebae colonise new habitats.


Baas Becking, L.G.M. (1934) Geobiologie of inleiding tot de milieukunde. W.P. Van Stockum & Zoon The Hague, the Netherlands.

Darwin, C. (1846) An account of the fine dust which often falls on vessels in the Atlantic Ocean. Quartely Journal of the Geological Society, 2, 26-30.

de Wit, R. & Bouvier, T. (2006) “Everything is everywhere, but, the environment selects”; what did Baas Becking and Beijerinck really say? Environmental Microbiology, 8, 755–758.

Wanner, M., Elmer, M., Sommer, M., Funk, R. & Puppe, D. (2015) Testate amoebae colonizing a newly exposed land surface are of airborne origin. Ecological Indicators, 48, 55-62.

Wilkinson, D.M., Koumoutsaris, S., Mitchell, E.A.D. & Bey, I. (2012) Modelling the effect of size on the aerial dispersal of microorganisms. Journal of Biogeography, 39, 89-97.

Tropical testate amoebae as hydrological indicators?

Sampling testate amoebae in a tropical peatland. A recent paper in Microbial Ecology by Swindles et al. suggests that testate amoebae have potential as hydrological indicators in tropical peatlands.

Sampling testate amoebae in a tropical peatland. A recent paper in Microbial Ecology by Swindles et al. suggests that testate amoebae have good potential as hydrological indicators in tropical peatlands.

Testate amoebae have been successfully used as indicators of past changes in peatland hydrology, particularly ombrotrophic (i.e., nutrients derived exclusively from precipitation) peatlands of north-temperate and boreal regions.  Over the past couple decades, many ecological studies of testate amoebae have been performed in these northern bogs, allowing empirical relationships between community composition and surface moisture to be described. Because the shells of testate amoebae preserve well in the acidic and anaerobic environment of bogs, these modern relationships have been used to infer past changes in the relative wetness of the bog surface from the composition of subfossil communities.  Much recent work has focused on the validation and interpretation of testate amoeba paleohydrological records from bogs, and their application to pressing global change questions.

Surveying along a transect across the peatland.

Surveying along a transect across the peatland.

However, very little is known regarding the potential paleoenvironmental applications of testate amoebae in tropical peatlands.  Peatlands in this region contain a large reservoir of soil carbon, and are extremely vulnerable to environmental changes including changes in land use (e.g., drainage, deforestation) as well as ongoing climate change. How have these peatlands responded to past environmental changes? How similar are communities of testate amoebae in these systems to those of northern bogs? Can testate amoebae be used as indicators of past hydrological changes in tropical peatlands? A recent study by Swindles et al. published in the journal Microbial Ecology set out to find preliminary answers to some of these questions.

One of 100 sampling sites.  Testate amoeba communities and several environmental variables were examined at each site.

Testate amoeba communities and several environmental variables were examined at 100 sites.

The study examined the present-day testate amoeba communities on a ombrotrophic peatland in Peruvian Amazonia. Surface samples of testate amoeba communities and measurements of water-table depth, pH, litter-moisture content, vegetation, and loss-on-ignition were taken along a transect across the peatland. The field work sounds like it was challenging, as the authors succinctly noted that the orientation of the transect had to be a bit flexible given certain obvious constraints:

A slight change in direction was needed half-way along the transect to avoid working in an area containing snakes.

Clearly the work was not well suited for ophidiophobes.

The research group also collected a peat core from the site and assessed changes in testate amoeba communities for the last several thousand years, using the results of their modern survey to inform their interpretation of the paleoecological record.

Tropical testates!

Tropical testates!

Results of the study indicated that the species composition of testate amoebae on this tropical peatland was most strongly related to measurements of water-table depth, with secondary relationships to pH. Forty-seven testate amoeba taxa were encountered, including one species only found in the southern hemisphere. Some taxa were clearly diagnotic of particular habitats (e.g., pools on the peatland surface). Testate amoebae were also preserved in the peat core,  and the authors applied the results of their modern study to infer changes in past water-table depth for approximately the last 3000 years. Although there is clearly much more work needed to describe the ecology of testate amoebae in peatland systems of the tropics, the results of this work indicate good potential to use testate amoebae in paleoenvironmental studies of these important, vulnerable, and unique peatland systems. Hopefully more work will follow soon.



Hotel Testate Amoebae

Imagine, after a long journey, you arrive alone in a hotel. The radio is playing a nice song…

“On a dark desert highway, cool wind in my hair

Warm smell of colitas, rising up through the air

Up ahead in the distance, I saw a shimmering light

My head grew heavy and my sight grew dim

I had to stop for the night”

You’re lucky, all of the rooms are free, and you can choose the one you like. You try all of the rooms and choose the largest, most comfortable room, with the best view and a well-stocked fridge.

“Welcome to the Hotel Testate Amoebae

Such a lovely place (Such a lovely place)

Such a lovely face

Plenty of room at the Hotel Testate Amoebae

Any time of year (Any time of year)

You can find it here”

After some time, you realize you start getting bored alone in this hotel and call some friends to share your room and your fridge. Your friends delight greatly in your hotel and thus call their own friends to continue parties, reducing the space and resources available.

“They livin’ it up at the Hotel Testate Amoebae

What a nice surprise (what a nice surprise)”

You decide to move with your friends in another hotel, nicely situated in the mountains. Here again, the local food is great and parties abundant… decreasing food and drinks quickly after few weeks… Why not moving again? Seems a good choice and you move not so far in new hotel.

Just get in the hotel,     “You called up the Captain, ’Please bring me French red wine’

He said, ‘We haven’t had such wine here since nineteen sixty nine’

Some voices are calling from far away,

‘They only have Coca Cola there…’

Just to hear them say…”

What do you do? You have some good old whiskey in stock and therefore decide to mix it with Coca Cola… Unfortunately, this mixture is not good enough for your friends forcing them leaving one by one…

“Last thing I remember, they were

Running for the door…”

 What do testate amoebae do when different nutrient resources are available? This is the question posed by Krashevska et al. (2014). These authors found that testate amoebae from tropical mountain rainforests significantly responded to moderate nutrient additions. They investigated rainforests along an altitudinal transect to get insight into variations in the effects of nutrient inputs with altitude. They found that both diversity and density of testate amoebae benefited from the addition of N (e.g. French red wine), whereas the addition of P detrimentally affected their diversity and density (e.g. Whiskey-Coca Cola mixture). They also found that Nutrient-mediated changes in microbial PLFA community structure contributed only little to these changes, suggesting that testate amoebae communities are structured predominantly by abiotic factors rather than by the availability of food, but a more detailed analysis of microbial communities are needed to test these suggestions.

In conclusion, the results of Krashevska et al. suggest that testate amoebae communities of tropical mountain rainforests are structured by both positive and negative interactions via both biotic and abiotic factors, and that the response of testate amoebae to nutrient addition is dependent from altitude.


Krashevska, V., Sandmann, D., Maraun, M., & Scheu, S. (2014). Moderate changes in nutrient input alter tropical microbial and protist communities and belowground linkages, The ISME Journal 8(5), 1126–1134. []

Testate amoeba CSI

Now here is something you don’t see everyday. In fact, I am pretty sure this has never been done before.  Ildiko Szelecz and colleagues set out to answer a question that very few of you must have already pondered: could testate amoebae be used in forensic studies?

This should in fact be a very ordinary question if you know something about soil biology and protists. A dead body is a huge influx of carbon and nutrients  into the soil that it is sitting atop.  The bacterial communities will basically go wild, and all of that must influence very heavily the community of eukaryotic microorganisms that used to inhabit there.  Interestingly enough, it appears that the idea of checking out what happens to testate amoebae communities has never popped into anyone’s head before.  Testate amoebae are abundant, somewhat easily recognizable micro-eukaryotes, which despite a few taxonomic issues are quite useful as indicators of environmental conditions.  Well, I think we have to thank Miss Szelecz for kindly looking into this gory issue!

Basically, the authors hung pig cadavers of approximately 20 kilos each in a nicely setup experiment.  For each pig replicate, there were two controls – a similar sized are with nothing in it, and an area where they added a plastic bag filled with 20 kg of soil to mimic possible micro-climatic effects that do not come form decomposition itself.  They then sampled soil from beneath the cadavers at regular intervals and counted testate amoebae – what could be more fun?


What happens then is truly incredible.  At first, the testate amoebae die.  The changes introduced in soil chemistry are simply not tolerable to the amoebae and by the 22nd, all amoebae under the dead body are also dead.  The two controls behaved different from each other, presumably because microclimatic conditions (evaporation, etc) are quite different under a plastic bag filled with litter.

Screen Shot 2014-03-12 at 4.54.55 PMIn the image above straight from the paper, the plain line indicates live amoebae, the short-dashed line indicates encysted amoebae, and the long-dashed line indicates dead amoebae.

After the massive amoeba genocide caused by the dead pig body, it is apparently very difficult to recolonize and rebuild the original community.  Even after almost one year, the effects of the cadaver were still noticeable in the composition of the testate amoeba community.

The authors conclude that testate amoebae may actually be good forensic tools to estimate post-mortem intervals.  I’ve heard a bigger experiment exploring distinct types of habitats is in the works.  Perhaps the authors shouldn’t be surprised if they receive a phone call from the producers of CSI or another forensic show where they are looking for some kind of new forensic evidence…


Testate amoebae from the end of the earth!

Contributed by Matt Amesbury

The moss banks on Green Island on the Antarctic Peninsula provide a vivid green splash amidst the surrounding ice caps, glaciers and icebergs (Photo: Matt Amesbury)

The moss banks on Green Island on the Antarctic Peninsula provide a vivid green splash amidst the surrounding ice caps, glaciers and icebergs (Photo: Matt Amesbury)

The use of testate amoebae as a proxy for past changes in the hydrological status of peatlands has become ever more popular over the past two decades. Studies have been carried out over an increasing geographical range covering most major areas of northern hemisphere peatlands as well as in Patagonia and New Zealand amongst other places south of the equator. Despite this pushing of “amoebal” boundaries, there is one place you might certainly expect to be able to rule out moss-based testate studies: Antarctica.

Close up of Polytrichum strictum moss growing on Green Island (Photo: Matt Amesbury)

Close up of Polytrichum strictum moss growing on Green Island (Photo: Matt Amesbury)

Only a tiny 0.3% of the Antarctic continent is ice free, yet in parts of this seemingly minute slither, the climate is just about amenable enough to have permitted the formation of deep moss banks; accumulations of moss that grow a few millimetres each year and are then frozen stiff over the winter months only to thaw out in the short Austral summer and accumulate a little further. The most extensive moss banks are to be found on Elephant Island, located just off the northern tip of the Antarctic Peninsula. Here, the banks are almost three metres deep and around four to five thousand years old. At the other end of the scale, almost ten degrees of latitude further south at Lazarev Bay on Alexander Island as the Antarctic Peninsula begins to merge into the continental mass, comparatively tiny moss banks of only 40 cm depth still cling on to a dubious existence.

The rugged surface topography of a moss bank on Green Island (Photo: Matt Amesbury)

The rugged surface topography of a moss bank on Green Island (Photo: Matt Amesbury)

Work is currently underway to exploit these moss banks as a palaeoclimatic archive. The Antarctic Peninsula has warmed by 3°C since the 1950s making it one of the most rapidly warming parts of the globe, but there is comparatively little terrestrial palaeoclimate data to put this temperature rise into a longer-term perspective. Could this be where testate amoebae step into the fray once more?

The pioneering work of the British Antarctic Survey’s Humphrey Smith laid the foundations of knowledge on Antarctic testate amoeba throughout the 1970s and 80s. His work painstakingly analysed and recorded the distribution and ecology of moss bank Protozoan communities from the sub-Antarctic Islands (mainly on Signy and Elephant Islands) as well as the Antarctic Peninsula itself and latterly in sites spanning the entire circumference of the Antarctic continent. Taxonomic diversity was relatively low with the same few familiar faces cropping up over and again, perhaps most frequently the taxa Corythion dubium.

Campsite on Green Island with blue-eyed cormorants and the creaking icebergs just offshore as our only companions (Photo: Matt Amesbury)

Campsite on Green Island with blue-eyed cormorants and the creaking icebergs just offshore as our only companions (Photo: Matt Amesbury)

So when we began working in the region in 2012 we were faced with a lot of testate unknowns, especially in terms of their abundance, diversity and distribution in core samples; all of Smith’s work had been on surface samples. To date, we’ve counted assemblages from a range of locations ranging from the southerly extent of moss banks at Lazarev Bay to Elephant Island in the north. In some locations the concentration of tests is low enough to make counting rather unfeasible but in other places we have been able to produce records with relatively high diversity (for Antarctica!) and evidence of switching between taxa, suggesting that the method can be applied in the traditional sense that it is in more temperate regions. Corythion dubium remains the best friend of the Antarctic testate counter, being abundant and dominant in most profiles. But it is joined by Assulina, Difflugia, Euglypha, Pseudodifflugia, Trinema and Valkanovia taxa, as well as some as yet unidentified tests (pictures included – please get in touch if you recognise any!)

The ubiquitous Corythion dubium, found in abundance in most Antarctic Peninsula sites.

The ubiquitous Corythion dubium, found in abundance in most Antarctic Peninsula sites.

In our work at Lazarev Bay, recently published in Current Biology, we used the testate concentration profile as part of a multi-proxy record alongside carbon stable isotope discrimination and measures of moss growth rates and accumulation. The testate profile here, at the limits of moss bank growth, was swamped with C. dubium to the almost complete exclusion of other taxa but concentration values showed a rapid increase coherent with changes in the other proxies and with the recorded temperature changes in the region since the 1950s. C. dubium is a taxa that shows a wide range of recorded sizes in the literature, but morphometric work we have embarked on suggests it may be possible to consistently split these size fractions, perhaps offering more information on past changes than we currently realise.

Three examples of an a yet to be confirmed test from Ardley Island, Antarctic Peninsula.

Three examples of a yet to be confirmed test from Ardley Island, Antarctic Peninsula.

With such a relatively blank canvas of testate research in the Antarctic Peninsula and so much still to learn, there is a lot left to do and there are certainly more questions than answers at present. But even so, it is a remarkable testament to these fascinating organisms that they survive and flourish at the end of world (well, give or take a few degrees of latitude!).


Royles, J., Amesbury, M. J., Convey, P., Griffiths, H., Hodgson, D. A., Leng, M. J. and Charman, D. J. 2013. Plants and soil microbes respond to recent warming on the Antarctic Peninsula. Current Biology 23, 1702-1706.

About the author

Matt Amesbury is a Research Fellow at the University of Exeter.  He is a testate amoebae analyst with broad interests in Holocene climate change and peatland palaeoecology.  He is currently working on peat from New Zealand as well as moss banks in Antarctica. He is co-founder of the website Bogology which aims to share the science of peatlands and past climate change in a light-hearted and accessible way. He’d love you to visit him there.

Opening the Pandora box of community ecology – The value of long-term data sets and collaborative research

Community ecologists study how communities of plants, animals and other organisms vary in space and time, how they interact and what controls these patterns. To do this they usually either observe (more or less) natural communities or conduct experimental manipulation in the field (in situ experiments) or in controlled conditions (mesocosms, microcosms). Observational studies of natural communities have the longest history and have contributed to major (and often controversial) theories in ecology such as the intermediate disturbance hypothesis (IDH). Starting with the more easily studies taxonomic groups such as vascular plants observational studies of natural communities have expanded to covering numerous taxonomic groups, including microbes and of course testate amoebae.

In order to describe the ecological preferences of species numerous plots need to be studied, typically in the range of 50-100 or more if possible. And even so, most studies end up with a fair number of rare species, which are found in few samples and are usually excluded from the data analyses. A further complication is that patterns observed at a single site (where many plots may be sampled) may be misleading and it is clearly preferable to study fewer plots in multiple sites to circumvent the problem of spatial autocorrelation (pseudo-replication within individual sites).

Studying numerous sites and ideally distant ones means that it is all but impossible to visit these sites on many occasions with the budget limitations most ecologists have to live with. Community ecologists therefore often collect their data and samples during a single visit. The timing of such field campaigns inevitably ends up being a compromise between ideal season and weather and the agenda of the various participants. The problem with this approach is that as many environmental factors vary over time -and this is clearly the case for soil pH, temperature, moisture content, water table depth, which are key ecological factors in terrestrial ecosystems – the available data will only represent a snapshot of what happens over the growing season or the year. This raises the questions: how representative is this snapshot of longer-term patterns? Are the relative values of the measured variables comparable among samples at different times?

As species may respond to environmental factors over more or less long-time periods patterns of community structure may not necessarily be best explained by one-time measurements of environmental variables but rather by more or less long-term averages or some measure of variability as done recently by Sullivan and Booth in a study of the relationship between the relative humidity of mosses and testate amoeba communities (Sullivan and Booth, 2011). The fact that some organisms are able to enter dormancy (e.g. encystment) during part of the year further complicated the story. However, only a small proportion of community ecology studies have addressed these longer-term patterns. This is of course understandable as the collection of long-term data at dozens of sites bears a cost that cannot be covered by classical funded research projects (i.e. typically 3 years) or regular budget of research groups (if they have any at all).

Community ecologists are usually taxonomically competent in one or two groups of organisms and therefore community ecology studies are typically limited to one of very few taxonomic groups. This makes it very difficult to assess how different communities respond to ecological gradients or perturbations as studies always differ in one aspect or another (e.g. slightly different methodologies used either to record the species data or the environmental variables). Yet sound comparative studies of multiple taxonomic groups would allow addressing important ecological questions such as how life history traits (e.g. dispersal potential, generation time) determine the responses of communities to ecological factors. This of course requires collaborative research efforts. And these are surprisingly rare!

A recent study published in the journal “Freshwater Biology” by Martin Jirousek and colleagues (Jiroušek et al., 2013) from the Czech Republic stands out by its focus on both long-term (15 years) environmental data and the comparative analysis of community patterns for four taxonomic groups, vascular plants, bryophytes, diatoms and (last but not least for this blog!) testate amoebae in 51 plots located in 12 Czech peat bogs in two mountain ranges.

Taxonomic groups included 1) short-lived microscopic organisms (diatoms and testate amoebae) and long-lived macroscopic organisms (vascular plants and bryophytes), 2) organisms dispersing easily (diatoms, testate amoebae and bryophytes) and less easily (vascular plants), and 3) photosynthetic (vascular plants, bryophytes, diatoms) and heterotrophic (testate amoebae – with a few mixotrophic exceptions) organisms.

The long-term ecological data also offered a unique opportunity to conduct a study on the effects of aerial liming (Ca, Mg), which has been used in the study area since the 1980’ as a forest amelioration practice (following damage caused by acid rain) and influenced the studied bogs. Such unintentional experiments can be highly valuable for ecologists, for example, as in this case to untangle ecological gradients that are usually strongly correlated (e.g. pH and calcium gradients in peatlands).

Martin Jirousek and colleagues hypothesised that long-term data would overall explain the community data better than short-term or one-time measurements and that this would be especially true for the longer-lived vascular plants and bryophytes. Following this they further hypothesised that the newly established pH and Calcium gradients would be better reflected in the shorter-lived communities of diatoms and testate amoebae. They compared the significance of environmental variables for different time spans: single time point, three, five, 10 and 15-year averages.

The results only partly supported the hypotheses. Micro and macro-organisms were correlated to both short- and long-term water chemistry variables (but not the same ones). Water table was correlated to all four communities but in agreement with the hypothesis, only the short-lived organisms reflected the recently established pH and Ca gradients. The results therefore generally support the idea that life-history traits condition the response of species communities to environmental gradients.

Although long-term ecological data sets such as the one used by Martin Jirousek and colleagues are not very common, they are perhaps not that rare. Ecologists would be well inspired to search for such data sets and if the monitoring program that generated them is still in place they should try to conduct similar studies (and encourage the monitoring program to continue!). Despite all technological advances we still can’t go back in time and therefore such data sets should be considered as a highly valuable asset. Although they involve some costs these can be very well justified if ecologists make good use of the data to address currently debated ecological questions such as the factors controlling community assembly and other questions related to metacommunity theory. This study also shows how valuable multi-taxa studies can be and hence how much added value there is to collaborative research!


Jiroušek, M., Poulíčková, A., Kintrová, K., Opravilová, V., Hájková, P., Rybníček, K., Kočí, M., Bergová, K., Hnilica, R., Mikulášková, E., Králová, Š. & Hájek, M. (2013) Long-term and contemporary environmental conditions as determinants of the species composition of bog organisms. Freshwater Biology, 58, 2196-2207.

Sullivan, M.E. & Booth, R.K. (2011) The Potential Influence of Short-term Environmental Variability on the Composition of Testate Amoeba Communities in Sphagnum Peatlands. Microbial Ecology, 62, 80-93.

How shall I build my test?

How do testate amoebae build their tests? How they chose the components to build it? How do they assemble organic or inorganic particles that shape their shell? These are questions I’m often asked. Unfortunately, these questions are very difficult to answer using common tools like the light microscope.

During the last couple decades, testate amoebae have been increasingly used as proxies for reconstructing Holocene environmental change in peatlands. Community composition primarily reflects surface wetness and pH, and can be used to study mire development, climate change and human impacts. However, little is known regarding the factors that may alter quantitatively or qualitatively the test composition of these organisms. Recently studies observed variations in shell composition of some testate amoebae in acidic environments, and suggested that a better understanding of how testate amoebae build their test may improve paleo-reconstruction models (Mitchell et al. 2008).

Historically, many researchers have worked on characterizing the shell of testate amoebae (e.g., Moraczewski 1971, Netzel 1972, Saucin Meulenberg et al. 1973, Eckert et al. 1974, Stout & Walker 1976, Hedley et al. 1976, Golemansky & Couteaux 1982, Ogden 1980a, b, 1983, 1984). Unfortunately, this line of research on testate amoebae has diminished over time.

Structural variability of the shell of testate amoebae (Source; Maxence Delaine)

Structural variability of the shell of testate amoebae (Source; Maxence Delaine)

So, when I heard that a PhD student – Maxence Delaine – had recently worked on this topic in France I was very curious. To satisfy my curiosity, I met Maxence Delaine and he explained me what they found in their recent paper (Armynot du Chatelet et al. 2013).

Across 14 sites situated in north-eastern France, Maxence collected samples from different microhabitats, such as mosses and soil, to study variations in testate amoeba shell composition.

Sites sampled for determination of shell construction of testate amoebae

Sites sampled for determination of shell construction of testate amoebae

3D representation of one species of testate amoebae, Difflugia oblonga. This picture is obtained by numerical recombination and correction of numerous 2D slides which are given by X-Ray microtomography. We can see on this picture the variability of the numerous grains constituting the shell: small vs big or smooth vs angular particules. (Source Maxence Delaine)

3D representation of one species of testate amoebae, Difflugia oblonga.
This picture was obtained by numerical recombination and correction of numerous 2D slides which are given by X-Ray microtomography.  The picture highlights the variability of the grains constituting the shell: small vs big or smooth vs angular particules. (Source Maxence Delaine)

The authors explored the potential application of 3D X-ray micro-tomography in addition to 2D techniques (Environmental Scanning Electron Microscope, Electron Probe Micro-Analysis, and cathodoluminescence) to characterize specimens such as Difflugia oblonga. The goal of this work was to test whether 3D morphology of testate amoebae in aqueous environments was governed by sediment size distribution and mineralogical composition.

From the 3D images, the authors calculated different parameters characterising the geometry of the specimens (size and mass) and of the individual grains forming the specimen (grain size distribution and volume). Combining chemical, mineralogical and morphological analyses allowed them to compare the grains forming the test with those of the sediment. Surprisingly, they found that Difflugia oblonga selectively picked up the small size fraction of the sediment with a preference for low-density silicates close to quartz density (~2.65). They also found that the maximum-sized grains are used for the pseudostome (i.e. shell aperture).

The following diagram shows that Difflugia oblonga is able to select the grains based on size, because the grain-size of the sediment is completely different from the grain-size of the particles constituting these amoeba shells. Moreover, no particles exceed the limit ‘‘αβ’’, which corresponds to the maximal measured size of the pseudostome of these 2 individuals. It seems likely that all the particles must pass through the pseudostome before being distributed by the amoeba for the shell’s construction.

Histograms of the particles size which constitute the shell of 2 individuals (Difflugia oblonga), compared to the grain-size curve of the sediment (in which these amoebae lived).

Histograms of the particles size which constitute the shell of 2 individuals (Difflugia oblonga), compared to the grain-size curve of the sediment (in which these amoebae lived).

Amazing isn’t it? A single-celled organism selecting the “bricks” for its house! Research on this topic is very promising, and these results highlight that there is still much to learn shell composition of these amazing organisms.


ARMYNOT DU CHATELET E., NOIRIEL C., DELAINE M. (2013). 3D morphological and mineralogical characterisation of testate amoebae.  – Microscopy and Microanalysis, 19, 1511-1522.

ECKERT B.S., MCGEE-RUSSELL S.M., 1974, Shell structure in Difflugia lobostoma observed by scanning and transmission electron microscopy. – Tissue & Cell, 6, 215-221.

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Biogeography, cryptic species and amoebae

If you are lucky enough to know a protistologist, you have certainly heard her (or him) utter the statement: “not much is known about protist _________”, where the blank can be filled with your choice of a biological subject, such as “meiosis”, “ecology”, “paleontology”, and many others. The statement gets staggeringly truthful when the blank is filled with the word “biogeography”.

To me this has always been very interesting because biogeography is one of the most intuitive biological concepts: anyone knows that there are some biological species that simply won’t show up in their backyards. If you live in South America, you can expect to see a Capibara, even (or specially) in a large metropole like Sao Paulo. This is not true for London, Berlin, or Moscow, unless you are at the local Zoo. Similarly, people living in Sao Paulo know that they won’t see a Grizzly Bear, or any bears at all – leading to the very intuitive notion that animals have restricted geographical ranges. This is also true for plants, one of my personal dreams is to see a Baobab, but I would have to travel to one of the other pieces of Gondwana to see it.

Which brings us to the first thing that may influence how species are distributed on the planet: the geological history of the place where a given biological species had first appeared. If you check the following map, depicting what the supercontinent Gondwana must have looked like in the past, you can understand how different iconic fossils were distributed. The logical assumption by looking at these ancestral distributions is that the descendants of these biological species will inhabit the same places. The difference is that by now, those continents have moved apart.

ImageSource: Wikipedia

The same kid who knows that they won’t find a bear in Sao Paulo also knows that they will not find a Great White shark roaming the streets (although that would certainly be a cool sight). But that is because Great Whites are exclusively marine animals that can not survive on land. Although this may seem like a simplistic analogy, it illustrates a distinct issue altogher: ecological requirements. Besides the geological history of the biological species distributions, ecological requirements will also restrict the places on earth where a given species can be found.

Therefore, biological entities should be distributed across the globe according to geological history and ecological requirements, right? No. Protists are more difficult. Firstly, you generally can’t see them without a microscope. So, people need to get trained on microscopy to start seeing protists. Even then, it may be difficult to identify species among them. Take a look at the following images:


Source: micro*scope

Although very similar, these are two distinct genera of amoebae. If you know who they are, you certainly have a few of years of protistology under your belt. This is the first difficulty in protist biogeography – we must live with the possibility that different species live in different places, but we can’t tell them apart because trained morphologists are hard to come by [1]. To overcome this difficulty, people came up with the concept of “flagship species”: these would be easy to identify, large and abundant species [2]. That way, if the organisms are somewhere in the world that has ever been sampled by a human being, those organisms have a high probability of having been recorded. This is where the testate amoebae come into play. I use the following example in classes:


Quadrulella symmetrica. Source: Ferry Siemensma.

This is a Quadrulella symmetrica. If you can’t remember the look of an amoeba that lives inside a shell she made herself out of internally mineralized square pieces of glass, then maybe biology isn’t for you. Testate amoebae are really good models to ask biogeographical and ecological questions, because they are so conspicuous. The problem is that we do not know much about their taxonomy, but that is quickly changing.

These easily identifiable, large and abundant species, are found everywhere that present their ecological requirements. So in the protist world, the sentence in bold above is generally translated to everything is everywhere, the environment selects. A simplistic way to explain this paradigm is that because protists are small, they should be able to disperse to all places, which seems to be a reasonable assumption [3]. This basically destroys the assumption that geological history must have an effect on the distributions of organisms, simply because they can potentially override this constraint. The second part of the paradigm, is quite similar to the shark analogy, and is to me the least understood part, not only in protist biology (well, not the extreme example of sharks on land, but more sutile things like pH gradients).

Recently, Thierry Heger and colleagues published a very intriguing study dealing with these questions [4]. They chose a single “morphospecies” to test some of these predictions — the testate amoeba Hyalosphenia papilio, a quite “flagshippy” species.


Hyalosphenia papilio. Source: Dan Lahr.

They sampled 42 Sphagnum dominated locations in 11 northern countries, obtaining over 300 individuals! They then went on to sequence a marker gene from each of these individuals and tried to correlate the genetic divergences with either geographical or ecological factors.

It may be surprising to some that even though Heger and colleagues sampled individuals that look almost exactly identical, they actually found 12 distinct genetic lineages. Now, the people who performed this work are experienced testate amoebae researchers, so we can rule out the possibility that they lumped together a bunch of morphologically distinct taxa. This may be a typical case of a “cryptic species”, lineages have diverged but the morphology has not yet changed. There is a small possibility that each of these 12 lineages actually have a distinguishing characteristic, but these would be so minimal that would not be of much help.

Even more surprising may be the fact that geographical distribution, or rather vicariance, cannot be an explanation to the divergence of these 12 distinct lineages. The following map is a figure from their paper, and shows how the different lineages were spread in the globe.

ImageAlthough you can already see that a particular place in the world doesn’t contain a single type of Hyalosphenia papilio, they went further ahead and tested this statistically, also testing if environmental variables they collected in specific sites could explain the distribution pattern.  They found out that climatic factors alone were responsible for 21% of the variation, while spatial factors (geography) were responsible for 3% of the variation.  The two combined factors explain an additional 13%.

Amazingly, this means that 63% of the variation is due to unkown factors.  In my view, this is solid proof that when a protistologist tells you that “not much is known about protist __________“, you should take them very seriously, because we can still learn a whole lot from the wee-beasties.


[1] Mitchell EAD, Meisterfeld R. 2005. Taxonomic confusion blurs the debate on cosmopolitanism versus local endemism of free-living protists. Protist 156(3): 263-267.

[2] Foissner, W. 2006. Biogeography and dispersal of micro-organisms: a review emphasizing protists. Acta Protozoologica 45(2): 111-136.

[3] Wilkinson, D. M., Koumoutsaris, S., Mitchell, E. A., & Bey, I. (2012). Modelling the effect of size on the aerial dispersal of microorganisms. Journal of Biogeography, 39(1), 89-97.

[4] Heger, T. J., Mitchell, E. A., & Leander, B. S. (2013). Holarctic phylogeography of the testate amoeba Hyalosphenia papilio (Amoebozoa: Arcellinida) reveals extensive genetic diversity explained more by environment than dispersal limitation. Molecular ecology, 22(20), 5172-5184.

50 million-year-old testate amoebae

Testate amoebae have an extraordinarily long fossil record, with the oldest known fossils 750 to 700 million years old (Porter and Knoll, 2000; Bosak et al. 2011; Corsetti et al. 2003); however, knowledge of the evolutionary history of these single-celled organisms is surprisingly spotty.  In a recent paper in the journal Protist, Barber et al. help to fill this knowledge gap by describing some beautifully preserved testate amoeba remains from a ~50-million year old lake deposit.

A 163-meter long core was recovered from a kimberlite diatreme within the Slave Craton in the Northwest Territories of Canada in the Northwest Territories of Canada.

A 163-meter long core was recovered from a kimberlite diatreme within the Slave Craton in the Northwest Territories of Canada in the Northwest Territories of Canada.

Eocene-age scales probably representing testate amoebae in the genus Scutiglypha (from Barber et al. 2013).

Fossil scales above show the denticulate margin commonly found on plates bordering the aperture (from Barber et al. 2013).

The fossils represent plates of Euglyphid testate amoebae (Rhizaria: Euglyphida), a group of testate amoebae that construct siliceous shells, or tests, out of secreted plates. The plates are arranged on the shell in an overlapping fashion, and the morphology of individual plates varies by species and by location on the test. Barber et al. recovered several different types of plates in the deposit, and the remarkable preservation and abundance allowed even fine-scale features, like denticulate plate margins and pitting in the central portions of some plates, to be examined. Some of the fossil plates were morphologically indistinguishable from modern species of the genus Scutiglypha, suggesting that little evolutionary change in plate morphology has occurred for the last 50 million years, and perhaps much longer. Read the paper here.

Image of a modern specimen of Scutiglypha acanthophora showing the arrangement and morphology of plates on the test (from