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

3.7 Manipulation of the biotic environment


Many aspects of the biotic environment can be manipulated. Thereby, the composition and dynamics of the biotic environment are not only studied as response variables (e.g., number of species, abundances), but are directly changed in order to study the consequences of specific aspects of the biotic environment on ecological dynamics (e.g., productivity, stability of the system). All of these manipulations are directly derived from the ecological question of interest and standardization is thus not directly possible or wanted, such that protocols cannot be given. However, we list below possible manipulations of the biotic environment and give a selection of representative references therefore.


Carrara, F., Giometto, A., Seymour, M., Rinaldo, A. & Altermatt, F. (2014) Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity. submitted.

Carrara, F., Giometto, A., Seymour, M., Rinaldo, A. & Altermatt, F. (2014) Experimental evidence for strong stabilizing forces at high functional diversity in aquatic microbial communities. Ecology, in press.

Clements, C.F., Warren, P.H., Collen, B., Blackburn, T., Worsfold, N. & Petchey, O. (2013) Interactions between assembly order and temperature can alter both short- and long-term community composition. Ecology and Evolution, 3, 5201-5208.

Fellous, S., Duncan, A., Coulon, A.l. & Kaltz, O. (2012a) Quorum Sensing and Density-Dependent Dispersal in an Aquatic Model System. PLoS ONE, 7, e48436.

Fellous, S., Duncan, A.B., Quillery, E., Vale, P.F. & Kaltz, O. (2012b) Genetic influence on disease spread following arrival of infected carriers. Ecology Letters, 15, 186-192.

Fox, J.W. (2007) Testing the mechanisms by which source-sink dynamics alter competitive outcomes in a model system. American Naturalist, 170, 396-408.

Fox, J.W., McGrady-Steed, J. & Petchey, O.L. (2000) Testing for local species saturation with nonindependent regional species pools. Ecology Letters, 3, 198-206.

Fukami, T. & Morin, P.J. (2003) Productivity-biodiversity relationships depend on the history of community assembly. Nature, 424, 423-426.

Giometto, A., Altermatt, F., Carrara, F., Maritan, A. & Rinaldo, A. (2013) Scaling body size fluctuations. Proceedings of the National Academy of Sciences, 110, 4646-4650.

Jiang, L. & Morin, P.J. (2005) Predator Diet Breadth Influences the Relative Importance of Bottom-Up and Top-Down Control of Prey Biomass and Diversity. The American Naturalist, 165, 350-363.

Lawler, S.P. & Morin, P.J. (1993) Food-web architecture and populatio-dynamics in laboratory microcosms of protists. American Naturalist, 141, 675-686.

Livingston, G., Jiang, Y., Fox, J.W. & Leibold, M.A. (2013) The dynamics of community assembly under sudden mixing in experimental microcosms. Ecology, 94, 2898-2906.

Mächler, E. & Altermatt, F. (2012) Interaction of Species Traits and Environmental Disturbance Predicts Invasion Success of Aquatic Microorganisms. PLoS ONE, 7, e45400.

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

McGrady-Steed, J. & Morin, P.J. (2000) Biodiversity, density compensation, and the dynamics of populations and functional groups. Ecology, 81, 361-373.

Morin, P.J. & McGrady-Steed, J. (2004) Biodiversity and ecosystem functioning in aquatic microbial systems: a new analysis of temporal variation and species richness-predictability relations. Oikos, 104, 458-466.

Petchey, O.L., Anna, E., Borrvall, C. & Ebenman, B. (2008) Trophically Unique Species Are Vulnerable to Cascading Extinction. The American Naturalist, 171, 568-579.

Seymour, M. & Altermatt, F. (2014) Active colonization dynamics and diversity patterns are influenced by dendritic network connectivity and species interactions. Ecology and Evolution, 4, 1243-1254.

Violle, C., Enquist, B.J., McGill, B.J., Jiang, L., Albert, C.c.H., Hulshof, C., Jung, V. & Messier, J. (2012) The return of the variance: intraspecific variability in community ecology. Trends in Ecology and Evolution, 27, 244-252.

Violle, C., Nemergut, D.R., Pu, Z. & Jiang, L. (2011) Phylogenetic limiting similarity and competitive exclusion. Ecology Letters, 14, 782-787.

Worsfold, N.T., Warren, P.H. & Petchey, O.L. (2009) Context-dependent effects of predator removal from experimental microcosm communities. Oikos, 118, 1319-1326.