Supplementary information for Altermatt et al. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12312

“Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution”

Altermatt F, Fronhofer EA, Garnier A, Giometto A, Hammes F, Klecka J, Legrand D, Mächler E, Massie TM, Pennekamp F, Plebani M, Pontarp M, Schtickzelle N, Thuillier V & Petchey OL

3.6 Temperature manipulation


Manipulating the temperature of microcosms is relatively straightforward, with the most important considerations concerning good experimental design. E.g., avoiding or accounting for pseudoreplication, avoiding systematic non-independence of other treatments within controlled temperature environments, choice of appropriate temperature levels and regimes.

Previous studies include effects of temperature on individual metabolic rate (Fenchel & Finlay 1983), movement speed (e.g., Beveridge, Petchey & Humphries 2010), cell size (Atkinson, Ciotti & Montagnes 2003) and competition (Nelson & Kellermann 1965). These individual level effects cause altered population and community dynamics (e.g., Petchey 2000; Leary & Petchey 2009; Fussmann et al. 2014) via changes in interaction strengths (Jiang & Kulczycki 2004). Temperature dependent changes in community dynamics can affect ecosystem processes, such as net primary production (Petchey et al. 1999).



  • Multiple, ideally identical, controlled temperature environments (CTE) such as incubators or water baths.


  • None


  1. Design experiment, including exactly where in each CTE each microcosm will be placed.

  2. Thoroughly test the temperature control of the CTEs across the range of planned experimental temperatures. Include testing for spatial variation of temperature within CTEs

  3. Ideally, test for difference in ecological dynamics (e.g., single species dynamics) across CTEs that are set at the same temperature (to test for CTE effects).

  4. Start the experiment.

  5. Remove microcosms from CTEs on when needed and for as short periods as possible (e.g., for sampling).

  6. Monitor temperature in the CTEs during the experiment, ideally with an independent probe in a dummy microcosm.

  7. Finish the experiment.

  8. Check the actual temperatures in the CTE closely match the desired temperatures.


Microcosms can experience significant evaporation even with caps on, if these are not tightened. Be aware of and monitor for differential evaporation across temperatures, with higher evaporation rates at higher temperatures. Replace evaporate with distilled or reverse osmosis water. If microcosms are not covered, or if the CTE has strong air circulation, evaporation will be faster.


Beveridge, O.S., Petchey, O.L. & Humphries, S. (2010) Mechanisms of temperature-dependent swimming: the importance of physics, physiology and body size in determining protist swimming speed. Journal of Experimental Biology, 213, 4223-4231.

Fenchel, T. & Finlay, B.J. (1983) Respiration rates in heterotrophic, free-living protozoa. Microbial Ecology, 9, 99-122.

Fussmann, K.E., Schwarzmueller, F., Brose, U., Jousset, A. & Rall, B.C. (2014) Ecological stability in response to warming. Nature Climate Change, 4, 206-210.

Jiang, L. & Kulczycki, A. (2004) Competition, predation and species responses to environmental change. Oikos, 106, 217-224.

Leary, D.J. & Petchey, O.L. (2009) Testing a biological mechanism of the insurance hypothesis in experimental aquatic communities. Journal of Animal Ecology, 78, 1143-1151.

Nelson, G.H. & Kellermann, S.L. (1965) Competition between Varieties 2 and 3 of Paramecium Aurelia: The Influence of Temperature in a Food-Limited System. Ecology, 46, 134-139.

Petchey, O.L. (2000) Environmental colour affects aspects of single-species population dynamics. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 267, 747-754.

Petchey, O.L., McPhearson, P.T., Casey, T.M. & Morin, P.J. (1999) Environmental warming alters food-web structure and ecosystem function. Nature, 402, 69-72.