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

2.10 Nutrient dynamics and litter-bags


Most microcosm studies manipulate the food availability by the concentration of the medium. Less frequently is the nutrient composition or elemental balance (i.e., stoichiometry) between carbon, nitrogen and phosphorus taken into account.

Decomposition is a critical ecosystem process due to its influence on nutrient cycling and availability (Ribblett, Palmer & Coats 2005). Microcosm studies of decomposition rate include the effects of biodiversity of non-decomposers affects (McGrady-Steed, Harris & Morin 1997), effects of temperature change (Petchey et al. 1999) or spatial habitat structure and composition of leave litter (Davies et al. 2009). Decomposition rate is estimated by measuring the weight loss of organic matter (e.g., of a wheat seed or leaf litter) over a specific amount of time, similar to use of leaf-litter bags for measuring decomposition in terrestrial ecosystems.

Individual wheat seeds can be identified, if required, by placing them in small, labelled bags. Since this may rarely be required, the protocol below is for measuring decomposition without identifying individual wheat seeds.



  • Microbalance (at least 0.001 g precision)

  • Drying oven


  • Wheat seeds or leaf litter (e.g., Alnus sp.)


  1. Decide how many wheat seeds/leaf litter pieces are required per microcosm and decide the period(s) over which decomposition will be measured (for time estimates, see Ribblett, Palmer & Coats 2005). This will determine the number of wheat seeds required in total, and per microcosm per measurement period.

  2. Select wheat seeds that are similar in size and weight, and that are not physically compromised.

  3. Dry the wheat seeds at 40 °C until their weight is stable (i.e., all moisture is removed).

  4. Weigh individual seeds or groups of seeds (depending on the decision made in step 1).

  5. Place each seed (or group of seeds) into a foil bag, labelled uniquely.

  6. Autoclave all the foil bags.

  7. Place the wheat seeds into the microcosms, noting the id of the bag that was put into each microcosm.

  8. Remove the wheat seeds from the microcosms, taking care to minimise chance of contamination, and taking care to remove material not part of the wheat seed (e.g., bacterial masses surrounding the wheat seed).

  9. Carefully rinse the wheat seeds, again to remove material that was not originally part of the wheat seed.

  10. Dry the wheat seeds, taking care to know which microcosm they came from / the unique id of the foil bag they came from.

  11. Weigh the wheat seeds over several days at 40 °C, until their weight stabilises.


Allow up to one week for drying before and after. Allow several hours for initial and final weighing, depending on the number of microcosms in the experiment.

Troubleshooting (Tips and Tricks)

Use preliminary experiments to ensure that treatments do not reach close to 100% weight loss during the experiment. This is to avoid lack of variation among treatments, due to complete decomposition in all treatments.

Anticipated results

Rate of decomposition, measured either as percentage weight loss, or the rate of exponential decline in weight (the latter is likely to be more generally appropriate).


Davies, K.F., Holyoak, M., Preston, K.A., Offeman, V.A. & Lum, Q. (2009) Factors controlling community structure in heterogeneous metacommunities. Journal of Animal Ecology, 78, 937-944.

McGrady-Steed, J., Harris, P.M. & Morin, P.J. (1997) Biodiversity regulates ecosystem predictability. Nature, 390, 162-165.

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.

Ribblett, S.G., Palmer, M.A. & Coats, D.W. (2005) The importance of bacterivorous protists in the decomposition of stream leaf litter. Freshwater Biology, 50, 516-526.