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

1.4 Apparatus


A laboratory equipped with general microbiological apparatus is required for protist microcosm experiments (Fig. S1). Furthermore, general laboratory glassware is needed. Protists cultures can be maintained and handled with general laboratory equipment. Importantly, all equipment used must be inert with respect to chemical leaking into the medium (e.g., using silicon tubes or glass jars). Jars and pipettes used must be rinsed with deionized water before autoclaving/use, to get rid of detergents. For experiments, glass jars or polystyrol-multiwell plates have been proven successful. Care needs to be taken when vessels are self-made, as for example silicone glue used to seal containers mostly contains antifouling chemicals that leak into the medium and kill protists (even from silicone glue recommended for aquaria use).



For general lab-procedures, the following equipment is needed:

  • Labcoat.

  • Disposable gloves.

  • Labelling tape and water proof pens.

  • Autoclave bags (to autoclave/dispose biohazard waste).

  • 80% denaturated alcohol (to clean surfaces).

  • 2% bleach (to dispose cultures).

For the general procedures involving medium preparation, experimental set-up, and analyses of basic protist microcosm experiments, the following equipment is needed:

  • Microbalances (precision 0.1 mg).

  • Autoclave (Fig. S2).

  • Incubators (temperature range 5 to 40 °C, light controlled) (Fig. S3) or temperature controlled walk-in chamber (Fig. S4)

  • pH meter.

  • Stereomicroscopes with zoom and dark field illumination (i.e., dissection microscope, Fig. S5).

  • Sterile bench.

For the handling and culturing of protists in microcosms, the following equipment is needed:

  • 200 mL glass jars (e.g., Erlenmeyer jars) to grow protist cultures.

  • 2 L autoclavable containers to prepare the medium.

  • Measuring glass beakers.

  • Micropipettes (1–10 µL, 10–100 µL, 100–1000 µL, 1–5 mL).

  • Petridishes (Polystyrol).

  • Small vials to take subcultures (e.g., scintillation vials, 10 or 50 mL PP tubes).

Fig. S1. An exemplary laboratory in which protist microcosm experiments can be conducted. Photo by Florian Altermatt.

Fig. S2. Autoclave used to sterilize protist medium and equipment used for protist experiments. Photo by Florian Altermatt.

Fig. S3. Example of an incubator with individual protist microcosms (showing the experiment by Mächler & Altermatt 2012). The incubator is temperature-controlled (20 °C) and has constant fluorescent lighting. The position of the replicates of each treatment is randomized across the incubator to avoid biases due to position in the incubator. Photo by Elvira Mächler.

Fig. S4. Temperature controlled walk-in chambers in which protist experiments can be conducted. At each shelf, homogeneous light-sources are installed (note the insulation above each light to avoid warming of the shelf above it). Photo by Florian Altermatt.

Fig. S5. Two working spaces equipped with zoom stereomicroscopes and cameras. Microscopes are equipped with dark field illumination. Note: for working on the microscopes, blinds of the windows would be lowered to avoid reflections and uncontrolled illumination. Next to the microscopes, a calendar is given to reserve slots for individual work-projects. Photo by Florian Altermatt.