Who is hiding behind these square scales? or The mystery of the origin of square shell plates in testate amoebae

Contributed by Anush Kosakyan


It would be hard to find a testate amoeba lover who does not know the genus Quadrulella. These vase-shaped species are a very unique group within family Hyalospheniidae (Arcellinida) since they are capable of secreting their own square or rectangular shell scales (or plates). These scales are characterisstic only for this genus, while most other members of the family are predators that build their shell by using mainly recycled plates taken or scavenged from other testate amoebae (i.e. kleptosquamy, Lahr et al. 2015).


My story started in the summer of 2013, when Edward Mitchell returned from his holiday in South Africa with a bag of Sphagnum samples. The samples were full of Quadrulella shells, including species that had never been seen since their original description back in 1957. And that was it….”the right time” for single-cell barcoding of this group. From this material, we obtained very interesting results that have been published recently (Kosakyan et al., 2016).

The most surprising result was that organisms presenting square shell plates appeared not to be monophyletic: two different groups of taxa with square scales (genus Quadrulella and newly established genus Mrabella) were indeed placed far from each other on the mtCOI-based phylogenetic tree. We thought of two possible evolutionary scenarios to explain this situation. These two hypotheses depend on whether the square-shaped plates in an organism have an autogenous or exogenous origin. This is a relevant aspect because hyalospheniids are known to engage in the behaviour of kleptosquamy, or recycling of shell plates produced by other organisms (Lahr et al., 2015).

Assuming that all amoebae that present square-shaped plates in their shells have produced them autogenously, the phylogenetic hypothesis presented here indicates homoplasy:

1) either the ability to produce square plates is an ancestral character that has been lost in a number of lineages (reversion); or

2) this character has evolved more than once independently (convergence).

We have assumed that convergence is the most parsimonious alternative (see the detailed discussion in the paper for further detail), with only two steps required – one event in genus Quadrulella and another independent event in genus Mrabella. Although we should not forget another unrelated group of organisms that are capable of producing square plates: the shelled amoeba Paraquadrulla is capable of producing calcareous square plates (the genus has not been sequenced yet, but while it is almost certainly an Arcellinid it is most likely unrelated to hyalosphenids or at best branches in a basal position to the whole group).

Alternatively, considering the fact that majority of hyalosphenids have the ability to scavenge plates from prey and use them to make the shell (kleptosquamy), a possible scenario is that Mrabella is in fact using scales from preyed Quadrulella, or scavenging these scales from the environment to construct the shell. And indeed, this was our first guess when we saw the description of Nebela galeata (current name Gibbocarina galeata) from Africa by Gauthier-Lièvre (1957). It is almost identical to Q. subcarinata in general shape and dimensions of the test (L=180-200, B=98-144, A=31-41 μm) (see Figure). Gauthier-Lièvre, 1957 (in her Fig. 10A) showed that square plates typical for Quadrulella can be integrated in the shell of N. galeata.  This is very easy to explain since Gauthier-Lièvre (1957) documented other Quadrulella species from the same locality where she found N. galeata and Q. subcarinata. Thus, other Quadrulella species could have provided the square plates use by these two species.


Legend: A- Line drawing of Gibbocarina (Nebela) galeata from Congo by Gauthier-Lievre, 1957. B and C– Scanning electron microscopy and light microscopy micrographs of Mrabella subcarinata from South Africa. Scale bars =50 µm (in A) and 20 µm (in B). Modified from Kosakyan et al. 2016.


However,  things are not that easy in our case for two reasons:

1) Mrabella would specifically select these plates, a trait that is not known for any other hyalosphenid presenting kleptosquamy; these species generally use a mixture of plates from different origins to build their shell (see for instance: Apodera vas in Fig. 69 in Meisterfeld 2002);

2) if not specifically selecting, then Quadrulella would have to be the most abundant prey organism, or Quadrulella plates would have to be the most abundant in the environment, both options are likely not true since Quadrulella tends to be present in low abundance in comparison to Euglypha (although Euglypha was not abundant in our sample where we found Mrabella subcarinata), a genus of filose testate amoebae which is generally abundant and produces oval and ornamented siliceous plates.

Additionally, there are a number of other described species in genus Quadrulella that differ from the tear-shaped morphology of Quadrulella s.str. These also present similar shapes to other genera: Quadrulella vas, Q. constricta Apodera vas, Q. lageniformis Padaungiella lageniformis, Q. tubulata P. tubulata. These “mirror” species could either be a result of convergent evolution or alternatively represent cases of the “classical” hyalosphenids (A. vas, Padaungiella ssp.) that live in environments where euglyphids are rare but Quadrulella are abundant enough to provide material for building their shells. We have suggested that at this point these Quadrulella species must be treated as incertae sedis, and their sequencing will certainly illuminate the conundrum of the evolution of square-shaped plates.


Gauther-Lievre L. 1957.  Additions aux Nebela d’Afrique. Bull. Soc. Hist. Nat. l’Afrique du Nord 48, 494-523.

Kosakyan, A., Lahr, D. J. G., Mulot, M., Meisterfeld, R., Mitchell, E. A. D. and Lara, E. 2016. Phylogenetic reconstruction based on COI reshuffles the taxonomy of hyalosphenid shelled (testate) amoebae and reveals the convoluted evolution of shell plate shapes. Cladistics, 32: 606-623. doi:10.1111/cla.12167


What’s in a name? Something (completely different) to be said about taxonomic nomenclature

By Edward A. D. Mitchell,

Laboratory of Soil Biodiversity, University of Neuchâtel, Switzerland

With the advent of high throughput sequencing, estimates of global diversity are being totally revised as well.  For us protistologists – arguably much more importantly – so is the picture of how diversity is distributed among the different branches of the tree of life. The image that emerges is one that shows a huge unknown diversity among protists, at all levels, from major groups (i.e. “environmental clades”) and within known groups (i.e. from more or less divergent groups to complexes of cryptic and pseudo-cryptic species). This is fascinating and to say the least mind-boggling and a much welcome development for making a case about the need to study protists more intensively. It is indeed impossible today to ignore this diversity and the many functional roles that protists play in all ecosystems.

But this unknown diversity also calls for a massive investment in taxonomy. And as we all know there are only few active protist taxonomists. We therefore need to train a new generation of taxonomists to meet the huge challenge of keeping up with the novel discoveries resulting from molecular studies. And indeed, combining molecular and traditional microscopy approaches is the key to doing this job properly.

But there is also an often overlooked but important aspect of taxonomy, besides the critically important fact that descriptions need to be done correctly in order not to make a huge mess of nomenclature: naming a species. Choosing an appropriate name is indeed not always easy. Should we name a species after an esteemed colleague, the geographical location where the species was found, a morphological feature of the species, or should we try to find a name that also allows non-specialists to relate to the species – thus providing an excellent opportunity to increase the impact of the finding and making a broader audience aware of the sheer existence of our beloved amoebae?

I firmly believe that witty names are useful. They make us happy, allow many lively discussions to take place among colleagues and are much appreciated by journalists always keen to report on “something completely different” (Monty Python, 1971).

The choice of names tells a lot about the personality and cultural references of the author. Here are a three recent examples among testate amoebae:


Padaungiella Lara & Todorov 2012.

This genus of hyalosphenid testate amoebae is characterised by an elongated neck (Kosakyan et al., 2012). The idea for this name came to me while riding my bicycle (a great source of inspiration!). I knew about the existence of some African tribes that used metal necklaces to elongate the necks of woman (allegedly, if the woman cheated on her man he would remove the necklaces and she would die due to cervical spine injury). I did a bit of research on this and found out that there were two unrelated tribes using such necklaces, one in Africa, with independent circular necklaces piled on top of each other and one in Asia (Padaung – https://en.wikipedia.org/wiki/Kayan_people_(Myanmar)), with a single spiral necklace. The latter corresponded much better to the shape of the amoeba shell and hence we decided to choose this name.

At the time of writing this post there were 1’110 hits for Padaungiella in Google.



Padaungiella wailesii (left, picture by E. Mitchell) and a Padaung woman (right, source: http://www.chiangdao.com/chiangmai/karenlongneck.htm)


Nebela gimlii Singer & Lara 2015.

This species was named after Gimli (http://lotr.wikia.com/wiki/Gimli), a dwarf in Tolkien’s Lord of the Rings saga (Singer et al., 2015). This dwarf wanders in forests during the saga, something dwarfs are not supposed to do much. This species being the smallest of the species complex and being found in forested bogs the name seemed appropriate. Newspapers as far as Austria wrote about this. http://www.krone.at/wissen/amoebenart-nach-figur-aus-herr-der-ringe-benannt-in-torfmoor-entdeckt-story-497678.

At the time of writing this post there were 188 hits for “Nebela gimlii” in Google.


Arcella gandalfi Féres, Porfírio-Sousa, Ribeiro, Rocha, Sterza, Souza, Soares & Lahr 2016.

This large Arcella species bears striking resemblance to Gandalf’s hat and thus logically was named after this even more famous character of the Lord of the Rings (Féres et al., 2016; Tolkien, 1954) (http://lotr.wikia.com/wiki/Gandalf).


Arcella gandalfi (left, from Féres et al., 2016) and Gandalf, as played by Ian McKellen in The Lord of the Rings triology, (right, source: http://lotr.wikia.com/wiki/Gandalf).

The media picked up on this story even more and this illustrates again how a well-chosen name can significantly contribute to making our field of research more visible.

Arcella gandalfi” has 31’600 hits on Google at the time of writing this post. To this date, news agencies in more than 15 countries reported on this, including: Brazil, USA, Germany, France, Russia, India, Mexico, Spain, Turkey, Argentina, Hungary, Indonesia, Croatia, South Korea, Ukraine.

Gandalf clearly wins! Well done fellows!

Who’s next? There’s no end to the fun!



Féres, J.C., Porfírio-Sousa, A.L., Ribeiro, G.M., Rocha, G.M., Sterza, J.M., Souza, M.B.G., Soares, C.E.A., Lahr, D.J.G., 2016. Morphological and Morphometric Description of a Novel Shelled Amoeba Arcella gandalfi sp. nov. (Amoebozoa: Arcellinida) from Brazilian Continental Waters Acta Protozool. 55(4).

Kosakyan, A., Heger, T.J., Leander, B.S., Todorov, M., Mitchell, E.A.D., Lara, E., 2012. COI Barcoding of Nebelid Testate Amoebae (Amoebozoa: Arcellinida): Extensive Cryptic Diversity and Redefinition of the Hyalospheniidae Schultze. Protist 163, 415-434.

Monty Python, 1971. And Now for Something Completely Different, in: MacNaughton, I. (Ed.), Monty Python’s Flying Circus. Columbia Pictures, United Kingdom, p. 95 minutes.

Singer, D., Kosakyan, A., Pillonel, A., Mitchell, E.A.D., Lara, E., 2015. Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida, Hyalospheniidae), a new species described from a Swiss raised bog. European Journal of Protistology 51, 79-85.

Tolkien, J.R.R., 1954. The Fellowship of the Ring, The Lord of the Rings, Boston. Ballantine Books, New York.


A new approach to testate amoeba paleoecology: reconstructing past environmental conditions from morpholological traits

Contributed by Edward A. D. Mitchell

Laboratory of Soil Biodiversity, University of Neuchâtel, Switzerland

Testate amoebae are well known to be good indicators of micro-environmental gradients and especially soil moisture, water table depth and pH. This has been known since the early 20th century (Harnisch, 1925). The predictable distribution patterns of many species not only systematically result in seeing these variables emerge as being significantly correlated to testate amoeba community data in ecological studies but also allow the development of inference models – so called “transfer functions” – based on testate amoeba community data to reconstruct (infer) these variables either from modern samples or more generally from subfossil communities extracted from peat deposits or lake sediments. As there are few proxies to reconstruct past hydrological changes, testate amoebae have become part of the standard toolbox of palaeoecologists (Charman, 2001; Mitchell et al., 2008). Indeed, developing and using such transfer function has been the main reason to study testate amoebae and indeed most papers dealing with testate amoebae published in the last couple of decades. These organisms were thus being used as tools using correlative approaches rather than considered as study subjects in their own right.
Simon van Bellen and colleagues have just published a paper in which they present a new approach for palaeo-environmental inference based on testate amoeba morphological traits rather than community data (van Bellen et al., 2017). They used nine different traits and related them to the depth to the water table (DWT), the variable most commonly inferred from testate amoebae. Their data set is from Tierra-del-Fuego, but could almost be from anywhere in the World where Sphagnum peatlands occur. The list of traits includes morphological traits such as biovolume, aperture position, test compression, aperture size and test composition, a binary physiological trait (mixotrophy vs. heterotrophy) and two phylogenetic traits (Arcellinida and Euglyphida – there were no Amphitremids in the data). Most traits showed a relationship to DWT. For example, Arcellinida show an almost perfect negative linear correlation to DWT (i.e. the propostion of Arcellinida decreases with increasing DWT, in other words, the wetter the habitat, the more Arcelinida dominate the community). By contrast Euglyphida show a positive correlation to DWT (so the drier it gets the more the testate amoeba community is dominated by Euglyphida).


An extract from Figure 3 of van Bellen et al. 2017. Relationship between the community weighed means of Arcellinida (top) and Euglyphida (bottom) vs depth to water table (DWT, horizontal axis – left is wet, right is dry). The two phylogenetic groups clearly show opposite responses to the humidity gradient.

Interestingly this pattern corresponds to a ratio used in mineral soil, the LF index (Bonnet, 1976), where “L” stands for Lobosea (Arcellinida) and “F” stands for Filosa (Euglyphida). By analogy to MacArthur and Wilson’s concept of r (ruderal) and K (competitors) life history classification (MacArthur and Wilson, 1967), Euglyphida are considered as r strategists while Arcellinida are on average more K strategists. Euglyphids are on average smaller and thus more likely to feed on smaller prey such as bacteria. Being smaller also means that they may tolerate dry conditions better than the generally larger arcellinids that require a thicker water film to move.

The study of testate amoebae functional traits is clearly rapidly becoming a dynamic field of research within our community (Arrieira et al., 2015; Fournier et al., 2016; Fournier et al., 2015; Fournier et al., 2012; Jassey et al., 2016; Jassey et al., 2015; Lamentowicz et al., 2015; Marcisz et al., 2016; Marcisz et al., 2014). It will be interesting to follow the next developments in this area!


Arrieira, R.L., Schwind, L.T.F., Bonecker, C.C., Lansac-Toha, F.A., 2015. Use of functional diversity to assess determinant assembly processes of testate amoebae community. Aquatic Ecology 49, 561-571.

Bonnet, L., 1976. Le peuplement thécamoebien édaphique de la Côte-d’Ivoire. Sols de la région de Lamto. Protistologica 12, 539-554.

Charman, D.J., 2001. Biostratigraphic and palaeoenvironmental applications of testate amoebae. Quaternary Science Reviews 20, 1753-1764.

Fournier, B., Coffey, E.E.D., van der Knaap, W.O., Fernandez, L.D., Bobrov, A., Mitchell, E.A.D., 2016. A legacy of human-induced ecosystem changes: spatial processes drive the taxonomic and functional diversities of testate amoebae in Sphagnum peatlands of the Galapagos. Journal of Biogeography 43, 533-543.

Fournier, B., Lara, E., Jassey, V.E.J., Mitchell, E.A.D., 2015. Functional traits as a new approach for interpreting testate amoeba palaeo-records in peatlands and assessing the causes and consequences of past changes in species composition. Holocene 25, 1375-1383.

Fournier, B., Malysheva, E., Mazei, Y., Moretti, M., Mitchell, E.A.D., 2012. Toward the use of testate amoeba functional traits as indicator of floodplain restoration success. Eur. J. Soil Biol. 49, 85-91.

Harnisch, O., 1925. Studien zur Ökologie und Tiergeographie der Moore. Zoologisch Jahrbuch (Abteilung Systematik) 51, 1-166.

Jassey, V.E.J., Lamentowicz, M., Bragazza, L., Hofsommer, M.L., Mills, R.T.E., Buttler, A., Signarbieux, C., Robroek, B.J.M., 2016. Loss of testate amoeba functional diversity with increasing frost intensity across a continental gradient reduces microbial activity in peatlands. European Journal of Protistology 55, Part B, 190-202.

Jassey, V.E.J., Signarbieux, C., Haettenschwiler, S., Bragazza, L., Buttler, A., Delarue, F., Fournier, B., Gilbert, D., Laggoun-Defarge, F., Lara, E., Mills, R.T.E., Mitchell, E.A.D., Payne, R.J., Robroek, B.J.M., 2015. An unexpected role for mixotrophs in the response of peatland carbon cycling to climate warming. Scientific Reports 5, 16931.

Lamentowicz, M., Gałka, M., Lamentowicz, Ł., Obremska, M., Kühl, N., Lücke, A., Jassey, V.E.J., 2015. Reconstructing climate change and ombrotrophic bog development during the last 4000 years in northern Poland using biotic proxies, stable isotopes and trait-based approach. Palaeogeography, Palaeoclimatology, Palaeoecology 418, 261-277.

MacArthur, R.H., Wilson, E.O., 1967. The Theory of Island Biogeography. Princeton University Press.

Marcisz, K., Colombaroli, D., Jassey, V.E.J., Tinner, W., Kołaczek, P., Gałka, M., Karpińska-Kołaczek, M., Słowiński, M., Lamentowicz, M., 2016. A novel testate amoebae trait-based approach to infer environmental disturbance in Sphagnum peatlands. Scientific Reports 6, 33907.

Marcisz, K., Lamentowicz, L., Slowinska, S., Slowinski, M., Muszak, W., Lamentowicz, M., 2014. Seasonal changes in Sphagnum peatland testate amoeba communities along a hydrological gradient. European Journal of Protistology 50, 445-455.

Mitchell, E.A.D., Charman, D.J., Warner, B.G., 2008. Testate amoebae analysis in ecological and paleoecological studies of wetlands: past, present and future. Biodivers. Conserv. 17, 2115-2137.

van Bellen, S., Mauquoy, D., Payne, R.J., Roland, T.P., Hughes, P.D.M., Daley, T.J., Loader, N.J., Street-Perrott, F.A., Rice, E.M., Pancotto, V.A., 2017. An alternative approach to transfer functions? Testing the performance of a functional trait-based model for testate amoebae. Palaeogeography, Palaeoclimatology, Palaeoecology 468, 173-183.

Fashionable testate amoebae!

Fashion phenomena strongly influence our societies. These phenomena mostly affect young people and can be very worrysome. Many sociological studies seek to understand these phenomena, based on community background, culture and society tendencies but none seem to have considered a simple possibility: are our young people not just copying nature?

Recently, a very interesting study highlighted an intriguing fashion phenomenon within the testate amoeba community. Gomaa et al. (1) indeed revealed that all mixotrophic testate amoebae dressed up with the same algal-underwear!

Mixotrophic testate amoebae are species able to combine two nutrition modes; phototrophy and phagotrophy (predation). Using light energy thanks to their algal symbionts, mixotrophic testate amoebae are able to fix inorganic carbon through photosynthesis, whilst in parallel they are also able to assimilate organic carbon by feeding on prey items such as bacteria, fungi and other protists (2-5). This mixotrophic energetic mode thus gives them an important trophic advantage when food resources are low.

Some mixotrophic testate amoebae we can find in mosses : Placocista spinosa (A), Archerella flavum (B), Amphitrema wrigthianum (C), Hyalosphenia papilio (D) and Heleopera sphagni (E). Scale bar on E = 50 μm

Figure 1| Some mixotrophic testate amoebae we can find in mosses : Placocista spinosa (A), Archerella flavum (B), Amphitrema wrigthianum (C), Hyalosphenia papilio (D) and Heleopera sphagni (E). Scale bar on E = 50 μm

Most mixotrophic testate amoebae show different characteristics, with for instance, different body sizes, shape and test composition. However, visually under the microscope, it seems that all of these species choose their algal symbionts in the same shop, copying each other! Probably intrigued by such fashion phenomena, Gomaa et al. (1) investigated the genetic diversity of the algal symbionts harboured by several mixotrophic testate amoeba species such as Archerella flavum, Hyalosphenia papilio, Heleopera sphagni and Placocista spinosa. These analyses showed that most algae found in testate shells shared the same kind of gene sequence (ribulose- 1,5-bisphosphate carboxylase/oxidase), thus revealing a close genetic proximity (1). The phylogenetic analysis further placed all surveyed testate amoebae symbionts close to Chlorella variabilis, a species known for forming symbiotic relationships with the ciliate Paramecium bursar (6). However, the authors also underlined that it is probable that some other endosymbiotic species occur in mixotrophic testate amoebae. Some symbionts morphologically clearly differ from C. variabilis in shape and colour, in particular within genus Placocista (Figure 1).

The modalities of symbiont acquisition by mixotrophic testate amoebae are still poorly kown and would require more investigations. Who is copying whom? Did Archerella flavum make Hyalosphenia papilio jealous with such nice colours in its shell leading the latter to feed on it to steal these nice coloured symbionts (Figure 2)? Is Placocista spinosa a weak copy of Archerella flavum and Hyalosphenia papilio, selecting its symbionts from a cheaper shop? Many questions remain unanswered. Could some of these require a sociological approach?


Hyalosphenia papilio taking its revenge on Archerella flavum H. papilio feeding on A. flavum.

Figure 2 | Hyalosphenia papilio taking its revenge on Archerella flavum.



  1. Gomaa, F. et al. One alga to rule them all: unrelated mixotrophic testate amoebae (amoebozoa, rhizaria and stramenopiles) share the same symbiont (trebouxiophyceae). Protist 165, 161–176 (2014).
  2. Gilbert, D., Amblard, C., Bourdier, G., Francez, A.-J. & Mitchell E. A. D. Le régime alimentaire des thécamoebiens (Protista, Sarcodina). L’année Biologique 39, 57–68 (2000).
  3. Gilbert, D., Mitchell, E. A. D., Amblard, C., Bourdier, G. & Francez, A.-J. Population dynamics and food preferences of the testate amoeba Nebela tincta major-bohemica-collaris complex (Protozoa) in a Sphagnum peatland. Acta protozoologica 42, 99–104 (2003).
  4. Jassey, V. E. J., Shimano, S., Dupuy, C., Toussaint, M.-L. & Gilbert, D. Characterizing the feeding habits of the testate amoebae Hyalosphenia papilio and Nebela tincta along a narrow ‘fen-bog’ gradient using digestive vacuole content and 13C and 15N isotopic analyses. Protist 163, 451–464 (2012).
  5. Wilkinson, D. M. & Mitchell, E. A. D. Testate Amoebae and Nutrient Cycling with Particular Reference to Soils. Geomicrobiology Journal 27, 520–533 (2010).
  6. Hoshina, R., Iwataki, M. and Imamura, N. (2010) Chlorella variabilis and Micractinium reisseri sp nov (Chlorellaceae, Trebouxiophyceae): Redescription of the endosymbiotic green algae of Paramecium bursaria (Peniculia, Oligohymenophorea) in the 120th year. Phycological Research, 58, 188-201.

Testate amoebae on fire

Contributed by Katarzyna Marcisz

How do testate amoeba communities respond to fire? How does burning affect this group of microorganisms and the environment where they occur in exceptionally high abundance – Sphagnum peatlands?

Answering these questions is crucial, as fire has a significant impact on peatland ecosystems. Peatlands are an important carbon pool, containing 1/3 of the global soil carbon (Parish et al., 2008). It has been shown that even a moderate drop in water table influences vegetation composition in peatlands and disturbs carbon accumulation (Kettridge et al., 2015). Peatlands experiencing drying are also more often ignited, and the frequency of fire and the extent of peat fires often increases (Turetsky et al., 2015). Peat fires can be deceptive: peat often burns by smouldering combustion that can persist for long periods of time rather than by more visible large fires as in the case of forests. The consequence is nevertheless that this burning affects the peat carbon stock.

The relationships between testate amoebae and fire are still quite a mystery. In studies from North America, Clifford and Booth (2013) and Clifford and Booth (2015) revealed peaks in microscopic charcoal accumulation rates that corresponded to drought periods as reconstructed with the use of a testate amoeba-based transfer function. However, these charcoal peaks were likely primarily derived from regional, upland fires rather than fire on the peatlands themselves. The effects of peatland fires on testate amoeba communities, and the response of individual species, have not been adequately examined. For example, Trigonopyxis arcula was suggested to be a possible fire indicator by Warner (1990) and Turner et al. (2014), and Hyalosphenia subflava was correlated with fire in the work by Turner and Swindles (2012). However, Turner et al. (2014) later suggested it should rather not be regarded as a reliable local fire indicator.

Fig. 1. Linje mire in the spring 2013.

Fig. 1. Linje mire in the spring 2013.

Recently the relationships between individual testate amoeba species and fire were examined in a study by Marcisz et al. (2015), which was conducted within the RE-FIRE Sciex project (http://www.swissuniversities.ch/en/topics/sciex) and CLIMPEAT project (www.climpeat.pl), in northern Poland at a beautiful Linje mire (Fig. 1).

The analyses revealed that the peatland was wet before the onset of the Little Ice Age (ca. AD 1300-1850), when a rapid drop in water table occurred. Drying was also correlated with human migrations in the region, and with changing agricultural practices. Anthropogenic fires preceded hydrological changes on the mire; the response of the mire recorded as hydrological changes towards drier conditions was delayed in relation to the surrounding fire-related vegetation changes.

Fig. 2. Cross-correlation diagrams between testate amoeba species and macroscopic charcoal particles (from Marcisz et al., 2015)

Fig. 2. Cross-correlation diagrams between testate amoeba species and macroscopic charcoal particles (from Marcisz et al., 2015)

Individual testate amoeba species were correlated with macroscopic charcoal particles recorded in the peat profile (Fig. 2). Testate amoebae indirectly responded to vegetation removal in the catchment driven by fire. While all the wet indicator species were negatively correlated with fire activity, most of the dry indicators (as well as Arcella discoides) were positively correlated. Although no explicit local fire indicator was found, from all the testate amoeba species Nebela tincta s.l. had the highest positive correlation recorded (Fig. 3)…..


Fig. 3. Nebela tincta s.l. on fire.

Fig. 3. Nebela tincta s.l. on fire.

Additional work is needed to better quantify the relationships between testate amoebae, hydrological change, and fire, and experimental work is needed to assess the causes of these relationships. Such work may provide insight into the underlying processes controlling microbial community responses to fire and hydrological change. However, fire activity likely affects peatland microbial food webs, both directly (combustion of surface Sphagnum and peat layers) and indirectly (surrounding vegetation and surface run-off changes).

Literature cited

Clifford, M.J., Booth, R.K., 2013. Increased probability of fire during late Holocene droughts in northern New England. Climatic Change 119, 693–704.

Clifford, M.J., Booth, R.K., 2015. Late-Holocene drought and fire drove a widespread change in forest community composition in eastern North America. The Holocene 25, 1102-1110.

Kettridge, N., Turetsky, M.R., Sherwood, J.H., Thompson, D.K., Miller, C.A., Benscoter, B.W., Flannigan, M.D., Wotton, B.M., Waddington, J.M., 2015. Moderate drop in water table increases peatland vulnerability to post-fire regime shift. Scientific Reports 5.

Marcisz, K., Tinner, W., Colombaroli, D., Kołaczek, P., Słowiński, M., Fiałkiewicz-Kozieł, B., Łokas, E., Lamentowicz, M., 2015. Long-term hydrological dynamics and fire history over the last 2000 years in CE Europe reconstructed from a high-resolution peat archive. Quaternary Science Reviews 112, 138-152.

Parish, F., Sirin, A., Charman, D.J., Joosten, H., Minayeva, T., Silvius, M., Stringer, L., 2008. Assessment on peatlands, biodiversity and climate change: main report. Global Environment Centre, Kuala Lumpur and Wetlands International, Wageningen 179 pp.

Turetsky, M.R., Benscoter, B., Page, S., Rein, G., van der Werf, G.R., Watts, A., 2015. Global vulnerability of peatlands to fire and carbon loss. Nature Geosci 8, 11-14.

Turner, T.E., Swindles, G.T., 2012. Ecology of Testate Amoebae in Moorland with a Complex Fire History: Implications for Ecosystem Monitoring and Sustainable Land Management. Protist 163, 844-855.

Turner, T.E., Swindles, G.T., Roucoux, K.H., 2014. Late Holocene ecohydrological and carbon dynamics of a UK raised bog: impact of human activity and climate change. Quaternary Science Reviews 84, 65-85.

Warner, B.G., 1990. Testate amoebae (Protozoa). Methods in Quaternary ecology no. 5. Geosci. Can. 5, 65-74.

Testate amoebae and their influence on (global) silicon cycling

Contributed by Daniel Puppe

Silicon is the second most common element in the Earth’s crust (after oxygen) and the seventh most abundant element in the universe. That means we can find silicon almost everywhere. Silicon plays a pivotal role in diverse living organisms comprising pro- and eukaryotes accumulating biogenic silicon in various siliceous structures (= biosilicification) – like idiosomic testate amoeba shells. In soils of terrestrial ecosystems we can find a lot of biogenic silicon forming different silicon pools. These pools can be separated into zoogenic, phytogenic, microbial and protistic ones (Fig. 1).

Fig. 1: Biogenic silicon (Si) pools in terrestrial ecosystems (from Puppe et al. 2015).

Fig. 1: Biogenic silicon (Si) pools in terrestrial ecosystems (from Puppe et al. 2015).

While scientific research has been focused especially on the phytogenic silicon pool (represented by so-called phytoliths), little is known about zoogenic, microbial and protistic silicon pools. The protistic silicon pool in soils comprises mainly terrestrial diatoms and idiosomic testate amoebae (some testates are shown in Fig. 2).

Fig. 2: Scanning electron microscope (SEM) micrographs of various idiosomic (a - c) and xenosomic (d) testate amoebae: a) Euglypha rotunda-like amoeba, b) Puytoracia bonneti (first record for Germany), c) Corythion dubium and d) two individuals of Centropyxis sphagnicola. Scale bars in all micrographs = 20 µm. Source: Puppe et al. 2014.

Fig. 2: Scanning electron microscope (SEM) micrographs of various idiosomic (a – c) and xenosomic (d) testate amoebae: a) Euglypha rotunda-like amoeba, b) Puytoracia bonneti (first record for Germany), c) Corythion dubium and d) two individuals of Centropyxis sphagnicola. Scale bars in all micrographs = 20 µm. Source: Puppe et al. 2014.

However, what is the relevance of biogenic silicon pools for silicon cycling? To understand this, we have to look at biogeochemical cycles at a global scale. Globally, silicon and carbon cycles are connected by weathering processes and fluxes of dissolved silicon from terrestrial to aquatic ecosystems (e.g. Sommer et al. 2006). When silicon is washed away into the oceans, it is used by marine diatoms for frustule synthesis (frustules are the siliceous cell walls of diatoms). Due to their worldwide distribution in very high abundances, diatoms are able to fix carbon dioxide (CO2) on a large scale (about 20 % of the photosynthesis on Earth is carried out by diatoms! See, e.g., Armbrust 2009). By consuming atmospheric CO2, diatoms thus have an effect on climate change, which is mainly caused by increasing atmospheric concentrations of the greenhouse gas CO2 since 1750 (IPCC 2013). The fluxes of dissolved silicon are affected by organisms that synthesize siliceous structures and consequently accumulate and recycle biogenic silicon in soils. In other words, the more silicon that is fixed in terrestrial ecosystems, the less silicon that arrives in the oceans, and as a consequence diatom production in the oceans decreases. Let´s visualize the main aspects of the processes described so far (Fig. 3).

Fig. 3: Connections of global silicon (Si) and carbon (C) cycles and the influence of biogenic silicon pools (see descriptions in the text).

Fig. 3: Connections of global silicon (Si) and carbon (C) cycles and the influence of biogenic silicon pools (see descriptions in the text).

In two recent publications we analyzed protozoic silicon pools (represented by idiosomic testate amoebae) in initial (Puppe et al. 2014) and forested (Puppe et al. 2015) ecosystems. We found, that after (only!) 10 years of development idiosomic silicon pools in initial ecosystem states become comparable to the ones in forested ecosystems. In forest soils idiosomic silicon pools were relatively small (0.2 kg – 4.7 kg silicon per hectare in the upper 5 cm). Due to the fact that only intact shells were enumerated in our studies idiosomic silicon pools might be larger than calculated. However, there is no information on the quantity of this “platelet silicon pool”.

At the forested sites we further analyzed potential influences of abiotic factors (e.g. soil pH) and earthworms on idiosomic silicon pools. Surprisingly, no relationship between silicon supply (readily-available silicon in soils) and idiosomic silicon pools could be found, thus no silicon limitation for shell synthesis appeared in the field. Instead, idiosomic silicon pools showed a strong, negative relationship to earthworm biomasses. We concluded that earthworms control idiosomic silicon pools by direct (e.g. competition in the soil food web) and/or indirect mechanisms (e.g. change of habitat structure through burrowing activities). Earthworms themselves were strongly influenced by soil pH. Due to the fact that soil pH is a result of weathering and acidification, idiosomic silicon pools are indirectly, but ultimately controlled by soil forming factors, mainly parent material and climate. These results point to the potential relationships between soil fauna and the storage of biogenic silicon in terrestrial ecosystems. However, further research is needed to enlighten the complex biotic linkages in terrestrial biogeochemical silicon cycling and their importance for global silicon fluxes.

Annual biosilicification rates of living testate amoebae (17 kg – 80 kg silicon per hectare) in forested ecosystems were comparable to or even exceeded reported data of annual silicon uptake by trees. Just imagine it! Unicellular, microscopic organisms can out-compete multicellular, macroscopic ones in terms of annual silicon uptake. Given the worldwide distribution of testate amoebae, the importance of idiosomic silicon pools and corresponding biosilicification for (global) silicon cycling becomes clear.

Literature Cited

Armbrust, E.V. (2009). The life of diatoms in the world’s oceans. Nature, 459, 185-192.

IPCC, 2013: Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Stocker, T.F., D. Qin, G.-K. Plattner, M. Tignor, S.K. Allen, J. Boschung, A. Nauels, Y. Xia, V. Bex & P.M. Midgley (eds.). Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA, 1535 pp.

Puppe, D., D. Kaczorek, M. Wanner & M. Sommer (2014). Dynamics and drivers of the protozoic Si pool along a 10-year chronosequence of initial ecosystem states. Ecological Engineering 70, 477-482.

Puppe, D., O. Ehrmann, D. Kaczorek, M. Wanner & M. Sommer (2015). The protozoic Si pool in temperate forest ecosystems – Quantification, abiotic controls and interactions with earthworms. Geoderma 243-244, 196-204.

Sommer, M., D. Kaczorek, Y. Kuzyakov & J. Breuer (2006). Silicon pools and fluxes in soils and landscapes – a review. Journal of Plant Nutrition and Soil Science 169, 310-329.

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.