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.

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. [http://www.nature.com/ismej/journal/v8/n5/abs/ismej2013209a.html]

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.