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

1.1 Species used


Species generally used for protist microcosm experiments cover several major domains of life and a large part of eukaryotic phylogenetic diversity (Adl et al. 2005; Adl et al. 2012). Generally, and also in the following, the term “protist” covers free-living, unicellular eukaryotes that are not purely autotrophic (Fig. S1). This mostly includes species within the Cryptophyta, Foraminifera, Alveolata, Chloroplastida and Tubulinea (incl. Amoebozoa (Adl et al. 2005; Adl et al. 2012). Very typical and commonly used representatives are species of the genera Paramecium, Tetrahymena, and Colpidium (all Alveolates, used in >80 studies), as well as species of the genera Bodo, Colpoda, Euplotes and Spirostomum (all used in at least 30–50 studies). These species cover different trophic levels (purely bacterivorous heterotrophs, mixotrophs and predatory heterotrophs feeding also or exclusively on other protists). Table S1 gives a comprehensive list of species that have been used in microcosm experiment studies as discussed here. Many of the methods described in the following are also not restricted to protists, but can (and have been) also applied to single-celled autotrophic species (i.e., algae) or metazoans of similar size and ecological functional (e.g., rotifers).

Fig. S1. Examples of different protist species used in microcosm experiments. A) Blepharisma sp., B) Euglena gracilis, C) Paramecium bursaria, D) Colpidium sp. All pictures by F. Altermatt/R. Illi.

Some of the species used can be cultivated in axenic conditions. However, most of the species thrive better when bacteria (see section 1.3) or microflagellates are present.

The selection of species is often a combination of practical reasons, such as distinctness, cultivability or availability, and the respective question of interest (e.g., functional types or size). All species can in principle be collected directly from natural populations in ponds, phytotelmata or other aquatic habitats (see detailed protocol below). This approach allows the use of co-evolved, potentially genetically diverse populations of natural co-occurring species. However, the difficulties faced during the isolation, cultivation and identification of naturally collected species often preclude this approach. Many studies have thus been based on species either already available in laboratory stocks or commonly available from culture collections. The most commonly used sources to order protist species are:

A difficulty/shortcoming of field collected species/strains is the often imprecise/vague identification of species. Most ecologists and evolutionary ecologists conducting protist microcosm experiments have relatively little taxonomic expertise regarding protists, and thus identifications and naming of species has to be taken with care. A set of identification manuals (Foissner & Berger 1996; Lee, Leedale & Bradbury 2000; Patterson 2003) as well as genetic barcoding techniques (Pawlowski et al. 2012), which are nowadays commonly available, should allow an identification at least to the genus level.

The advantage of the use of a common set of species across studies and laboratories is the availability of prior information (such as species traits, Table S2), and the possibility to link findings across studies. In this context, some species from a set of about 20 protist species originally isolated by Peter Morin from a pond at Rutgers University (McGrady-Steed, Harris & Morin 1997) have been very widely used across >50 studies, exemplifying the use of “model organisms” in ecology. The wider range of phylogeny, traits and trophic levels covered allows to select species for specific experiments, e.g., to study predator-prey relationships (e.g., Holyoak 2000b; Vasseur & Fox 2009), compare trait-related relationships across orders of magnitude (Giometto et al. 2013), or to study how phylogenetic relationships are affecting competitive interactions (Violle et al. 2011). Importantly, it needs to be considered that A) many trait values are phenotypically plastic and can vary easily within one order of magnitude given the specific experimental conditions. B) protists often do not fall easily into well-defined categories that “higher” organisms do, and that are often used as inspiration for models and concepts to be tested with protists. For example, many protists may switch between different trophic roles, from heterotroph/mixotroph to autotroph (e.g., Euglena gracilis) or from autotroph to predatory (e.g., Paramecium bursaria). Thus, some of the classifications may be stricter than the actual behaviour/life history of the protists. C) Protists as used here cover the widest phylogenetically range possible within the Eucaryotes (Adl et al. 2012). Thus, comparisons that include phylogeny as an explanatory variable may be only meaningful within sub-groups (such as Alveolates, see for example Violle et al. 2011), as phylogenetic signals across major taxonomic groups may be mostly lost through multiple convergences.

The use of protists in ecology and evolutionary biology can be traced back to Gause (1934b; 1934a) and Dallinger (1878; 1887), who looked at ecological and evolutionary dynamics respectively. Both of them have been very much inspired by the work of Charles Darwin (1859), and are among the first experimental studies testing Darwin’s ideas. In the 1950ies to 1970ies, a whole school of American Ecologists used protist experiments, and especially Paramecium aurelia, to address questions of species-coexistence, population dynamics and predator-prey interactions (e.g., Sonneborn 1950; Nelson 1958; Nelson & Kellermann 1965; Nelson 1967; Salt 1967; Gill 1972a; Gill 1972b; Gill & Nelson 1972; Vandermeer et al. 1972; Luckinbill 1973; Luckinbill 1974; Luckinbill & Fenton 1978; Luckinbill 1979; Veilleux 1979). This work was later on revived, especially by Peter Morin and colleagues (e.g., Lawler & Morin 1993; McGrady-Steed, Harris & Morin 1997; Petchey et al. 1999; McGrady-Steed & Morin 2000; Fox & Morin 2001; Fukami & Morin 2003; Jiang & Morin 2004; Morin & McGrady-Steed 2004; Jiang & Morin 2005; Steiner et al. 2006). It has been ever since used by a growing number of ecologists and evolutionary biologists (e.g., Lawler & Morin 1993; Warren 1996b; Warren 1996a; Fox & Smith 1997; Petchey et al. 1999; Fox, McGrady-Steed & Petchey 2000; Holyoak 2000b; Holyoak 2000a; Petchey 2000; Fukami 2001; Donahue, Holyoak & Feng 2003; Kneitel & Miller 2003; Laakso, Loytynoja & Kaitala 2003; Jiang & Kulczycki 2004; Kneitel & Chase 2004; Holyoak & Lawler 2005; Cadotte et al. 2006; Östman, Kneitel & Chase 2006; Cadotte 2007b; Fjerdingstad et al. 2007; Friman et al. 2008; Haddad et al. 2008; Jiang & Patel 2008; Davies et al. 2009; Schtickzelle et al. 2009; Worsfold, Warren & Petchey 2009; Chaine et al. 2010; Hammill, Petchey & Anholt 2010; Petchey, Brose & Rall 2010; TerHorst 2010; Violle, Pu & Jiang 2010; Altermatt et al. 2011; Altermatt, Schreiber & Holyoak 2011; Friman & Laakso 2011; Limberger & Wickham 2011; Violle et al. 2011; Altermatt & Holyoak 2012; Carrara et al. 2012; Limberger & Wickham 2012; Mächler & Altermatt 2012; Clements et al. 2013a; Clements et al. 2013b; Giometto et al. 2013; Pennekamp & Schtickzelle 2013; Carrara et al. 2014; Clements et al. 2014; Fronhofer, Kropf & Altermatt 2014; Giometto et al. 2014; Pennekamp et al. 2014; Seymour & Altermatt 2014), and the types of questions addressed diversified extensively. Research areas now include the phylogenetic limiting similarity hypothesis (e.g., Violle, Pu & Jiang 2010), effects of disturbance and productivity on diversity (e.g., Haddad et al. 2008; Altermatt, Schreiber & Holyoak 2011), the significance of trade-offs (e.g., Cadotte 2007a; Violle, Pu & Jiang 2010), synchrony in population dynamics (e.g., Vasseur & Fox 2009), effects of environmental change on food web structure and species interactions (e.g., Petchey et al. 1999; Fox & Morin 2001), the study of predator-prey interactions and inducible defences (Kratina et al. 2009; Kratina, Hammill & Anholt 2010), the regulatory effects of biodiversity on ecosystem processes (e.g., McGrady-Steed, Harris & Morin 1997), invasion dynamics (e.g., Mächler & Altermatt 2012; Giometto et al. 2014), the significance of spatial dynamics on diversity and species interactions (e.g., Holyoak & Lawler 1996; Carrara et al. 2012), scaling laws in ecology (e.g., Fenchel 1974; Giometto et al. 2013), epidemiological dynamics (e.g., Fellous et al. 2012) and evolutionary and eco-evolutionary dynamics (e.g., Dallinger 1887; Schtickzelle et al. 2009; Hiltunen et al. 2014).

Table S1. List of species used in protist microcosm experiments (alphabetically sorted from higher to lower taxonomic levels). The name of each species as well as its higher and lower taxonomic classification (after Adl et al. 2012) is given. For each species, we give one or few representative references of studies that have been using it. SAR is a clade including the groups Stramenopiles, Alveolata, and Rhizaria.

Species name Higher taxonomic group Lower taxonomic group Reference examples
Adercotryma glomerata SAR Foraminifera Gross 2000
Allogromia sp. SAR Foraminifera Gross 2000
Ammonia beccarii SAR Foraminifera Gross 2000
Ammoscalaria pseudospiralis SAR Foraminifera Gross 2000
Amoeba proteus Amoebozoa Tubulinea Davies et al. 2009, Holt et al. 2002, Holyoak 2000, Lawler & Morin 1993, Livingston et al. 2013, Naeem & Li 1998
Amoeba radiosa Amoebozoa Tubulinea Östman et al. 2006, Fox et al 2000, Krumins et al, 2006
Amphicoryna scalaris SAR Foraminifera Gross 2000
Ankistrodesmus falcatus Archaeplastida Chloroplastida Jin et al. 1991, McGrady-Steed et al. 1997 (genus), Davies et al. 2009 (genus), Fox et al. 2000 (genus)
Arcella vulgaris Amoebozoa Tubulinea Li & Stevens 2010 Oikos, Li & Stevens 2010 CommEcol
Askenasia sp. SAR Alveolata Lawler 1993, McGrady-Steed & Morin 1996
Aspidisca sp. SAR Alveolata Fox et al 2000, Kneitel & Perrault 2006, McGrady-Steed & Morin 2000, Warren et al. 2003
Asterionella formosa SAR Stramenopiles Fox 2004, Robinson & Edgemon 1998 (genus)
Atractomorpha echinata Archaeplastida Chloroplastida Livingston et al. 2013
Bigenerina nodosaria SAR Foraminifera Gross 2000
Blepharisma americanum SAR Alveolata Fox & Morin 2001, Holyoak 2000, Krumins et al. 2006, Livingston et al. 2013, Olito & Fukami 2009
Blepharisma japonicum SAR Alveolata Clements et al. 2013 JAnim Ecol, Holt et al. 2004, Law et al. 2000, Spencer & Warren 1996 Oecologia, Weatherby et al 1998
Bodo designis Excavata Discoba Fitter & Hillebrand 2009, Burkey 1997 (genus), Cochran-Strafira & von Ende 1998 (genus), Scarff & Bradley 2002 (genus)
Bodo saltans Excavata Discoba Giometto et al 2013, Jürgens & Sala 2000, Kneitel & Perrault 2006, Östman et al. 2006
Boldia erythrosiphon Archaeplastida Rhodophyceae Livingston et al. 2013
Bulimina marginata SAR Foraminifera Gross 2000
*Campylomonas reflexa * Cryptophyta Cryptophyta Livingston et al. 2013
Cassidulina leavigata SAR Foraminifera Gross 2000
Chilomonas paramecium Cryptophyta Cryptophyta Balciunas & Lawler 1995, Burkey 1997, Holt et al. 2004, Naeem & Li 1998, Warren & Gaston 1997, Scholes et al. 2005
Chilomonas spp. Cryptophyta Cryptophyta Giometto et al. 2013 PNAS, McGrady-Steed et al. 1997, Davies et al. 2009, Fox et al. 2000, Robinson & Dickerson 1987
Chlamydomonas microsphaera Archaeplastida Chloroplastida Jin et al. 1991
*Chlamydomonas moewusii * Archaeplastida Chloroplastida Dickerson & Robinson 1985, Dickerson & Robinson 1986
Chlamydomonas noctigama Archaeplastida Chloroplastida Rboinson & Edgemon 1988
Chlamydomonas reinhadrtii Archaeplastida Chloroplastida Fox & Olson 2000, Fox 2004, Livingston et al. 2013, Naeem & Li 1998
Chlamydomonas terricola Archaeplastida Chloroplastida Filip et al. 2012
Chlorella autotrophica Archaeplastida Chloroplastida Hiltunen et al. 2013, Fox 2008 (genus), Hulot et al. 2001 (genus), Kurihara 1978 (genus), Li & Stevens 2012 (genus)
Chlorella pyrenoidosa Archaeplastida Chloroplastida Jin et al. 1991
Chlorella vulgaris Archaeplastida Chloroplastida Fox 2004, Mueller et al. 2012, Nakajima et al. 2009
Chlorogonium euchlorum Archaeplastida Chloroplastida Giometto et al. 2013
*Chlorokybus atmophyticus * Archaeplastida Chloroplastida Livingston et al. 2013
Chloromonas clathrata Archaeplastida Chloroplastida Livingston et al. 2013
Chroomonas pochmanii Cryptophyta Cryptophyta Livingston et al. 2013
Chrysopsis sp. Archaeplastida Glaucophyta Krumins et al. 2006
Cibicidoides flordanus SAR Foraminifera Gross 2000
Closterium acerosum Archaeplastida Chloroplastida Livingston et al. 2013, Robinson & Edgemon 1988 (genus)
Closterium libellula Archaeplastida Chloroplastida Li & Stevens 2010 Oikos, Li & Stevens 2010 CommEcol
*Colacium vesiculosum * Excavata Discoba Livingston et al. 2013, Cadotte et al. 2006 (genus),
Coleps hirtus SAR Alveolata Have 1993, Cadotte et al. 2006 (genus), Fukami 2004 (genus), Mata et al. 2013 (genus)
Collodictyon triciliatum Collodictyonidae Collodictyonidae Petchey 2000
Colpidium campylum SAR Alveolata Have 1990, Luckinbill & Fenton 1978, Östman et al. 2006
Colpidium cf. striatum SAR Alveolata Balciunas & Lawler 1995, Holyoak & Lawler 1996 Ecology
Colpidium colpidium SAR Alveolata Scholes et al. 2005
Colpidium colpoda SAR Alveolata Have 1993
Colpidium kleini SAR Alveolata Jiang & Patel 1993, Livingston et al. 2013, Violle et al. 2010
Colpidium striatum SAR Alveolata Cadotte & Fukami 2005, Fox & Barreto 2006, Jiang & Morin 2005, Leary & Petchy 2009, Warren & Weatherby 2006
Colpoda cucullus SAR Alveolata Bretthauer 1980, Fukami 2004, Jiang & Morin 2005, Krumins et al. 2006
Colpoda inflata SAR Alveolata Cadotte & Fukami 2005, Krumins et al. 2006, Steiner 2005
Condylostoma sp. SAR Alveolata Warren 1996 Oikos
Cosmarium sportella Archaeplastida Chloroplastida Li & Stevens 2010 Oikos, Li & Stevens 2012, Robinson & Edgemon 1988 (genus)
*Cryptomonas curvata * Cryptophyta Cryptophyta Giometto et al. 2013, Filip et al. 2012 (genus)
Cryptomonas erosa Cryptophyta Cryptophyta Livingston et al. 2013
Cryptomonas ovata Cryptophyta Cryptophyta Bretthauer 1980, Elstad 1986, Fox 2004, Östman et al. 2006
Crytolophosis sp. SAR Alveolata Fukami 2001
Cyclidium glaucoma SAR Alveolata Giometto et al. 2013, Fox 2007, Davies et al. 2009 (genus), Kneitel & Perrault 2006 (genus)
Cyclotella sp. SAR Stramenopiles Krumins et al. 2006
*Dexiostoma campylum * SAR Alveolata Giometto et al. 2013, Riblett et al. 2003
Dictyosphaerium planctonicum Archaeplastida Chloroplastida Dickerson & Robinson 1985, Dickerson & Edgemon 1988
Didinium nasutum SAR Alveolata Veilleux 1979, Holyoak & Sachdev 1998, Luckinbill 1979, Warren 1996 Oikos
Dileptus anser SAR Alveolata Davies et al. 2009, Petchey 2000
Dileptus monilatus SAR Alveolata Jiang et al. 2011, Livingston et al. 2013
Dinobryon cylindricum Archaeplastida Chloroplastida Dickerson & Robinson 1986, Robinson & Edgemon 1988
Entosiphon sulcatum Excavata Discoba Fitter & Hillebrand 2009, Holt et al. 2004 (genus), Scholes et al. 2005 (genus), Warren & Weatherby 2006 (genus)
Eremosphaera viridis Archaeplastida Chloroplastida Robinson & Edgemon 1988
Eudorina elegans Archaeplastida Chloroplastida Dickerson & Robinson 1985
*Euglena gracilis * Excavata Discoba Altermatt & Holyoak 2012, Davies et al. 2009, Dickerson & Robinson 1985, Kawambata et al. 1995
*Euglena mutabilis * Excavata Discoba Giometto et al. 2013
*Euplotes aediculatus * SAR Alveolata Altwegg et al. 2004, Carrara et al. 2012, Jiang & Morin 2005, Kratina et al. 2007
Euplotes affinis SAR Alveolata Bretthauer 1980
Euplotes cf. eurystomus SAR Alveolata Mata et al. 2013
Euplotes daidaleos SAR Alveolata Filip et al. 2012
Euplotes eurystomus SAR Alveolata Li & Stevens 2010 Oikos, Li & Stevens 2012, Naeem & Li 1998
Euplotes octocarinatus SAR Alveolata Altwegg et al. 2004
Euplotes patella SAR Alveolata Balciunas & Lawler 1995, Fox et al. 2013, Holyoak & Sachdev 1998, Spencer & Warren 1996 Oecologia
Euplotes plumipes SAR Alveolata Altwegg et al. 2004
Euplotes surystomus SAR Alveolata Li & Stevens 2010 CommEcol
Fragilaria capucina SAR Stramenopiles Filip et al. 2012, Fitter & Hillebrand 2009
Frontonia angusta SAR Alveolata Filip et al. 2012, McGrady-Steed et al. 1997 (genus), Fox et al. 2000 (genus), Have 1993 (genus)
Gavelinopsis praegeri SAR Foraminifera Gross 2000
Gavelinopsis translucens SAR Foraminifera Gross 2000
Glaucoma myriophylli SAR Alveolata Bretthauer 1980
Glaucoma scintillans SAR Alveolata Have 1990, Livingston er al. 2013, Violle et al. 2011
Glaucoma sp. SAR Alveolata Jiang & Patel 2008
Globobulimina affinis SAR Foraminifera Gross 2000
Globocassidulina subglobosa SAR Foraminifera Gross 2000
Gonium pectorale Archaeplastida Chloroplastida Dickerson & Robinson 1985, Dickerson & Robinson 1986
Haematococcus lacustris Archaeplastida Chloroplastida Fox 2004, Livingston et al. 2013
Halteria grandinella SAR Alveolata Have 1993, Jiang et al. 2009, Livingston et al. 2013, Violle et al. 2010,
*Heliozoa sp. * SAR Chromista McGrady-Steed et al. 1997 (genus), Davies et al. 2009, Fox et al. 2000
Keronopsis sp. SAR Alveolata Have 1993
Lacrymaria olor SAR Alveolata Have 1993, Jiang et al. 2009, Cadotte & Fukami 2005 (genus)
Lenticulina cultrata SAR Foraminifera Gross 2000
Leptopharynx sp. SAR Alveolata Fukami 2001
Litonotus sp. SAR Alveolata Östman et al. 2006
Loxocephalus simplex SAR Alveolata Have 1990, Clements et al. 2013 JAnimEcol (genus), Jiang & Morin 2005 (genus), Steiner 2005 (genus)
Loxophyllum helus SAR Alveolata Have 1993
Mallomonas caudata SAR Stramenopiles Robinson & Edgemon 1988
Mayorella sp. Amoebozoa Tubulinea Kneitel & Perrault 2006 (genus)
Micrasterias rotata Archaeplastida Chloroplastida Li & Stevens 2010 CommEcol
Monas sp. SAR Chromista Bretthauer 1980
Nassula sorex SAR Alveolata Filip et al. 2012
Navicula pelliculosa Archaeplastida Stramenopiles Filip et al. 2012, Limberger & Wickham 2011 PLoSOne, Limberger & Wickham 2010
Netrium sp. Archaeplastida Chloroplastida Fox et al. 2000, McGrady-Steed et al. 1997, McGrady-Steed & Morin 2000
Nitzschia sp. Archaeplastida Chloroplastida Fitter & Hildebrand 2009, Jin et al. 1991, Robinson & Edgemon 1988
Nonion commune SAR Foraminifera Gross 2000
Ochromonas danica Archaeplastida Stramenopiles Dickerson & Robinson 1985, Dickerson & Robinson 1986, Robinson & Edgemon 1988
Ochromonas sociabilis Archaeplastida Stramenopiles Bretthauer 1980
Onychodromopsis flexilis SAR Alveolata Limberger & Wickham 2011 Oecologia, Limberger & Wickham 2012
Oocystis apiculata Archaeplastida Chloroplastida Robinson & Edgemon 1988
Ophiocytium maius SAR Stramenopiles Robinson & Edgemon 1988
Oxyrrhis marina SAR Alveolata Hiltunen et al. 2013
Oxytricha sp. SAR Alveolata Fox et al. 2000, Krumins et al. 2006
Pandorina morum Archaeplastida Chloroplastida Li & Stevens 2010 CommEcol, Robinson & Edgemon 1988
Paradileptus sp. SAR Alveolata Have 1993
Paramecium aurelia SAR Alveolata DeLong & Vasseur 2012, Fox 2008, Luckinbill 1973, Petchey 2000
*Paramecium bursaria * SAR Alveolata Altermatt et al. 2011, Cadotte 2006 Ecol, Vandermeer 1969, Violle et al 2011 EcoLet
Paramecium caudatum SAR Alveolata Fellous et al. 2012 PLoSOne, Duncan et al. 2011, Fels et al. 2008, Lunn et al. 2013
Paramecium multimicronucleatum SAR Alveolata Dickerson & Robinson 1986, Naeem & Li 1998, Robinson & Dickerson 1987
Paramecium primaurelia SAR Alveolata Luckinbill & Fenton 1978, Luckinbill 1979 AmNat
Paramecium tetraurelia SAR Alveolata Cohen et al. 1998, Gonzales & Holt 2002, Jiang & Kulcycki 2004, Long & Karel 2002
Paramecium trichium SAR Alveolata Östman et al. 2006
Pediastrum sp. Archaeplastida Chloroplastida Livingston et al. 2013, Robinson & Edgemon 1988
Pelomyxa carolinensis Amoebozoa Archamoebae Naeem & Li 1998
Peranema trichophorum Excavata Discoba Spencer & Warren 1996 Oikos
Peridinium cinctum f. ovoplanum SAR Alveolata Dickerson & Robinson 1985, Fox 2008 (genus), Robinson & Edgemon 1988 (genus)
Petalomonas sp. Excavata Discoba Spencer & Warren 1996 Oikos
Phacus sp. Excavata Discoba Fox et al. 2000
Planorbulina mediterranensis SAR Foraminifera Gross 2000
Platydorina sp. Archaeplastida Chloroplastida Dickerson & Robinson 1985
Pleodorina californica Archaeplastida Chloroplastida Livingston et al. 2013
Polytomella sp. Archaeplastida Chloroplastida Kneitel & Perrault 2006
Poterioochromonas malhamensis SAR Stramenopiles Kadowaki et al. 2012, Saleem et al. 2012 (genus), Saleem et al. 2013 (genus)
Poterioochromonas stipitata SAR Stramenopiles Östman et al. 2006
Pseudocyrtolophosis alpestris SAR Alveolata terHorst 2010 AmNat, terHorst 2010 JEB
Pyrgo murrhina SAR Rhizaria Gross 2000
Quuinequeloculina lamarckiana SAR Foraminifera Gross 2000
Rhynchomonas nasuta Excavata Discoba Fitter & Hillebrand 2009
Rosalina cf. bardyi SAR Rhizaria Gross 2000
Rubrioxytricha ferruginea SAR Alveolata Limberger & Wickham 2011 Oecologia
Saccammina sp. SAR Foraminifera Gross 2000
Scenedesmus gladiosum Archaeplastida Chloroplastida Livingston et al. 2013
Scenedesmus obliquus Archaeplastida Chloroplastida Jin et al. 1991
Scenedesmus opoliensis Archaeplastida Chloroplastida Li & Stevens 2010 ComEcol, Li & Stevens 2010 Oikos, Li & Stevens 2012
Scenedesmus quadricauda Archaeplastida Chloroplastida Dickerson & Robinson 1985, Dickerson & Robinson 1986, Robinson & Edgemon 1988
Selenastrum capricornutum Archaeplastida Chloroplastida Jin et al. 1991
Sellaphora pupula SAR Stramenopiles Livingston et al. 2013
Spathidium sp. SAR Alveolata Fukami 2001, McGrady-Steed & Morin 1996
Sphaerocystis schroeteri Archaeplastida Chloroplastida Robinson & Edgemon 1988
*Spirogyra occidentalis * Archaeplastida Chloroplastida Livingston et al. 2013, Robinson & Edgemon 1988 (genus)
Spiroplectinella wrightii SAR Foraminifera Gross 2000
Spirostomum ambiguum SAR Alveolata Have 1990, Kratina et al. 2007, Krumins et al. 2006, Naeem & Li 1998, Spencer & Warreb 1996 Oikos
Spirostomum teres SAR Alveolata Holt et al. 2004, Violle et al. 2011, Warren & Gaston 1997
Spumella sp. Archaeplastida Chloroplastida Jürgens & Sala 2000, Riblett et al. 2008
Staurastrum gladiosum Archaeplastida Chloroplastida Livingston et al. 2013, McGrady-Steed et al.1997 (genus), Davies et al. 2009 (genus), Fox 2008 (genus)
Staurastrum pingue Archaeplastida Chloroplastida Robinson & Edgemon 1988
Steinia sp. SAR Alveolata Lawler 1993
Stentor coeruleus SAR Alveolata Bretthauer 1980, Cadotte & Fukami 2005, Jiang & Morin 2005, Spencer & Warren 1996 Oecologia
Stentor polymorphus SAR Alveolata Have1993, Östman et al. 2006
Stephanodiscus sp. SAR Stramenopiles Robinson & Edgemon 1988
Stichococcus sp. Archaeplastida Chloroplastida Scraff & Bradley 2002
Stigeoclonium sp. Archaeplastida Chloroplastida Jin et al. 1991
Stylonychia mytilus SAR Alveolata Bretthauer 1980, Fox et al. 2000 (genus), McGrady-Steed et al. 1997 (genus), Filip et al. 2009 (genus)
Stylonychia pustulata SAR Alveolata Limberger & Wickham 2012 Oecologia, Limberger & Wickham 2011 PLoSOne
Suctoria sp. SAR Alveolata Fukami 2001
Synedra sp. SAR Stramenopiles Robinson & Edgemon 1988
Synura sp. SAR Stramenopiles Robinson & Edgemon 1988
Tachysoma pellionellum SAR Alveolata Östman et al. 2006, Limberger & Wickham 2012 PLoSOne, McGrady-Steed & Morin 1996 (genus)
Tetrahymena pyriformis SAR Alveolata Amezuca & Holyoak 2000, Glaser 1988, Olito & Fukami 2009, Vasseur & Fox 2009
*Tetrahymena thermophila * SAR Alveolata Fjerdingstad et al. 2008, Fryxell et al. 2005, Chaine et al. 2009, Laakso et al. 2003, Nakajima et al. 2009
Tetrahymena vorax SAR Alveolata Fox 2008, Holyoak & Sachdev 1998, Jiang & Patel 2008, Livingston et al. 2013
Textularia porrecta SAR Rhizaria Gross 2000
Tillina magna SAR Alveolata Scholes et al. 2005, Warren & Weatherby 2006, Holt et al. 2004 (genus), McGrady-Steed & Morin 1996 (genus)
Trachelomonas grandis Excavata Discoba Dickerson & Robinson 1985, Dickerson & Robinson 1986
Trachelomonas hispida Excavata Discoba Robinson & Edgemon 1988, Robinson & Dickerson 1987 (genus)
Trochammina shannoni SAR Rhizaria Gross 2000
Urocentrum turbo SAR Alveolata Have 1993
Uroleptus sp. SAR Alveolata Kneitel & Perrault 2006
Uronema sp. Archaeplastida Chloroplastida Cadotte 2006, Kuppardt et al. 2010, Lawler 1993, Livingston et al. 2013
Urostyla grandis SAR Alveolata Limberger & Wickham 2012 PLoSOne, Fox et al. 2000 (genus), Lawler 1993 (genus)
Uvigerina mediterranea SAR Foraminifera Gross 2000
Vischeria helvetica SAR Stramenopiles Livingston et al. 2013
Volvox aureus Archaeplastida Chloroplastida Li & Stevens 2012 Oikos, Robinson & Edgemon 1988
Volvox carteri Archaeplastida Chloroplastida Li & Stevens 2010 CommEcol, Li & Stevens 2010 Oikos
Volvox rousseletti Archaeplastida Chloroplastida Livingston et al. 2013
Vorticella campanula SAR Alveolata Ollason 1977, Fox 2008 (genus), Fukami 2001 (genus), Kneitel & Perrault 2006 (genus)
Vorticella convallaria SAR Alveolata Ollason 1977
Vorticella microstoma SAR Alveolata Östman et al. 2006
Vorticella similis SAR Alveolata Spencer & Warren 1996 Oikos
*Zygnema circumcarinatum * Archaeplastida Chloroplastida Livingston et al. 2013

Table S2. Overview on traits of some of the most commonly used species. The trait measurements for individual species may depend on the specific experimental conditions (e.g., temperature and nutrient levels affecting both growth rates as well as size). This table, however, is mostly aiming at showing overall patterns in traits and exemplifying the range of trait values (often over orders of magnitudes). The original source of the trait value is given for each trait. Size gives the diameter. If not indicated differently, trait values on size, growth rate and carrying capacity are from Carrara et al. 2012, and velocity is from Altermatt et al. 2012. When possible, mean and ±standard deviations of trait values are given.

Species name Size (µm) Growth rate r (1/d) Carrying capacity K (Ind/ml) Velocity (µm/s) Trophic status
Blepharisma sp. 471.3 ± 57.1 0.67 ± 0.07 59.5 ± 4.7 predator
Chilomonas sp. 23.3 ± 3.7 0.98 ± 0.13 1572.4 ± 278.3 168.1 heterotroph
Colpidium sp. 81 ± 7.8 1.5 ± 0.08 1379.2 ± 76.6 470.2 heterotroph
Euglena gracilis 36.7 ± 6.4* 0.87* 84578* 69.1 mixotroph
Euplotes aediculatus 85.4 ± 8.6* 0.43* 359* 591.9 mixotroph
Paramecium aurelia 111.6 ± 15.1 0.86 ± 0.02 111.1 ± 2.6 1280.8 heterotroph
Paramecium bursaria 101.3 ± 12.9 0.23 1639 1090.2 mixotroph
Spirostomum sp. 843.8 ± 149.7 0.57 ± 0.15 13.6 ± 4.2 418.2 heterotroph
Tetrahymena cf. pyriformis 26.7 ± 4.8 2.24 ± 0.15 2996.8 ± 196.1 148.8 heterotroph

* data from Haddad et al. 2008



For the isolation of protists the following equipment is needed:

  • Stereomicroscope (see section 2.2) and general apparatus for cultivation (section 1.4).

  • Sterile petri dishes.

  • Sterile capillary glass-pipettes (glass Pasteur pipettes with latex bulbs).


  • Autoclaved and bacterized culture medium (see section 1.2).

  • 80% Ethanol for sterilizing surfaces and equipment.


The following procedure is for isolating species from natural communities or from species purchased from culture collections that are not pure:

  1. Collect a water sample (100–200 mL) from the natural source of interest (pond, tree hole, pitcher plant etc.).

  2. Bring the sample as quickly as possible to the laboratory, avoid warming of the sample (store and transport it in a cooler box at 10°C) and avoid strong exposition to sunlight.

  3. Take a subsample of about 5 mL into a petri dish, dilute with 10 mL of the chosen culture medium, in order acclimate the species to the new osmotic conditions and to dilute densities of the protists.

  4. Separately place five 0.5 mL drops of the culture medium in a petri dish.

  5. Using the stereomicroscope, collect from the natural community sample (step 3) one individual of the focal species with a glass capillary pipette with as little water as possible.

  6. Place this isolated individual into the first of the separate drops (step 4).

  7. Take a new sterile pipette and isolate the focal individual from the drop and place it into the next one, again transporting it with as little medium as possible (\<5% of the total drops volume).

  8. Repeat at least five times, such that with each isolation step, the individual and potential co-occurring other individuals are diluted and “washed”, eventually isolating the focal individual from all other cells.

  9. From the final drop, transport the washed individual into a culture vessel containing up to 10 mL of bacterized medium.

  10. Label the vessel with the name of the species isolated (or morphospecies), source of origin (site) and date.

  11. Allow the isolated individuals to grow and reproduce (1 to 5 days)

  12. Check for survival and potential contaminations. If the isolated individual survived and replicated, and no contaminations are present, the species is now present in a pure (monoclonal) culture and can be used for further experiments.

  13. Add it to your long-term stock culture collection (section 1.6)

Timing: Collection of the sample >1 h, reparation all equipment: 0.5 h, isolating 1 h, growing the isolated individuals for 24 to 48 h, checking for success 0.5 h.

Troubleshooting (Tips and Tricks)

The two most common problems are: 1) the isolated species does not grow; 2) the isolation procedure was not successful and the isolated species is contaminated with other (mostly very small) protists species. It is advised to independently isolate at least 5 to 10 individuals, to ensure a higher success. Sometimes, isolated species grow better when they are initially placed in relatively little medium (1 mL, use microwell-plates), and only later on be transferred into more medium volume when the populations have reached a few dozen cells. Some species may not be cultivable within the chosen medium or the chosen medium concentration/laboratory conditions. Try different media (section 1.2) and different laboratory conditions, staying as close to the natural environmental conditions as possible. When using bacterized medium, ensure that the bacteria concentrations are not so high that anoxic conditions occur. Using 10-fold diluted medium may solve this.

Often, the isolation process is not 100% perfect, and other species (bacteria and mostly protists smaller than \<10 µm, such as “microflagellates”), are inadvertently isolated together with the focal species. To remove bacteria, the use of antibiotics is needed (see axenic cultures in section 1.2), while to remove microflagellates, steps 4 to 8 need to be repeated for another 5 to 10 times.

It is important to switch to new, sterilized pipettes for each serial dilution/washing step. However, the same pipette may be used multiple times to independently isolate several individuals/species in parallel. That is, use one pipette for each serial step, but the same pipette can be used multiple times for parallel isolations at the same step.

During the isolation process, individuals may die or get lost (e.g., get stuck to the glass of the pipette), thus to isolate one new species, it is generally necessary to go through the whole isolation process multiple times with independent individuals.

The above-described procedure can also be used to create monoclonal populations of already established and well-running laboratory cultures, which may have accumulated genetic diversity by mutations over time.

Anticipated results

The goal is to have a well-growing culture of the isolated species, which can then be added to the stock culture collection (section 1.3) and for which species traits etc. can be measured. It is important to remember that a culture isolated from one single cell is initially a monoclonal population, and may only accumulate genetic diversity over time by mutations. An initially potentially higher genetic diversity can be achieved by isolating several individuals a time. However, it is then not known if this includes different cryptic species or different cells that are genetically identical as they originated from the same mother cell in the natural environment already.


Adl, S.M., Simpson, A.G.B., Farmer, M.A., Andersen, R.A., Anderson, O.R., Barta, J.R., Bowser, S.S., Brugerolle, G., Fensome, R.A., Fredericq, S., James, T.Y., Karpov, S., Kugrens, P., Krug, J., Lane, C.E., Lewis, L.A., Lodge, J., Lynn, D.H., Mann, D.G., McCourt, R.M., Mendoza, L., Moestrup, O., Mozley-Standridge, S.E., Nerad, T.A., Shearer, C.A., Smirnov, A.V., Spiegel, F.W. & Taylor, M. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology, 52, 399-451.

Adl, S.M., Simpson, A.G.B., Lane, C.E., Lukeš, J., Bass, D., Bowser, S.S., Brown, M.W., Burki, F., Dunthorn, M., Hampl, V., Heiss, A., Hoppenrath, M., Lara, E., le Gall, L., Lynn, D.H., McManus, H., Mitchell, E.A.D., Mozley-Stanridge, S.E., Parfrey, L.W., Pawlowski, J., Rueckert, S., Shadwick, L., Schoch, C.L., Smirnov, A. & Spiegel, F.W. (2012) The Revised Classification of Eukaryotes. Journal of Eukaryotic Microbiology, 59, 429-514.

Altermatt, F., Bieger, A., Carrara, F., Rinaldo, A. & Holyoak, M. (2011) Effects of connectivity and recurrent local disturbances on community structure and population density in experimental metacommunities. PLoS ONE, 6, e19525.

Altermatt, F. & Holyoak, M. (2012) Spatial clustering of habitat structure effects patterns of community composition and diversity. Ecology, 93, 1125-1133.

Altermatt, F., Schreiber, S. & Holyoak, M. (2011) Interactive effects of disturbance and dispersal directionality on species richness and composition in metacommunities. Ecology, 92, 859-870.

Cadotte, M.W. (2007a) Competition-colonization trade-offs and disturbance effects at multiple scales. Ecology, 88, 823-829.

Cadotte, M.W. (2007b) Concurrent niche and neutral processes in the competition-colonization model of species coexistence. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 274, 2739-2744.

Cadotte, M.W., Mai, D.V., Jantz, S., Collins, M.D., Keele, M. & Drake, J.A. (2006) On Testing the Competition-Colonization Trade-Off in a Multispecies Assemblage. The American Naturalist, 168, 704-709.

Carrara, F., Altermatt, F., Rodriguez-Iturbe, I. & Rinaldo, A. (2012) Dendritic connectivity controls biodiversity patterns in experimental metacommunities. Proceedings of the National Academy of Sciences, 109, 5761-5766.

Carrara, F., Rinaldo, A., Giometto, A. & Altermatt, F. (2014) Complex interaction of dendritic connectivity and hierarchical patch size on biodiversity in river-like landscapes. American Naturalist, 183, 13-25.

Chaine, A.S., Schtickzelle, N., Polard, T., Huet, M. & Clobert, J. (2010) Kin-based recognition and social aggregation in a ciliate. Evolution, 64, 1290-1300.

Clements, C.F., Collen, B., Blackburn, T.M. & Petchey, O.L. (2014) Effects of directional environmental change on extinction dynamics in experimental microbial communities are predicted by a simple model. Oikos, 123, 141-150.

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

Clements, C.F., Worsfold, N.T., Warren, P.H., Collen, B., Clark, N., Blackburn, T.M. & Petchey, O.L. (2013b) Experimentally testing the accuracy of an extinction estimator: Solow's optimal linear estimation model. Journal of Animal Ecology, 82, 345-354.

Dallinger, W.H. (1878) On the Life-History of a Minute Septic Organism: With an Account of Experiments Made to Determine Its Thermal Death Point. Proceedings of the Royal Society of London, 27, 332-350.

Dallinger, W.H. (1887) The President's Address. Journal of the Royal Microscopical Society, 7, 185-199.

Darwin, C. (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London.

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.

Donahue, M.J., Holyoak, M. & Feng, C. (2003) Patterns of Dispersal and Dynamics among Habitat Patches Varying in Quality. The American Naturalist, 162, 302-317.

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

Fenchel, T. (1974) Intrinsic rate of natural increase: The relationship with body size. Oecologia, 14, 317-326.

Fjerdingstad, E., Schtickzelle, N., Manhes, P., Gutierrez, A. & Clobert, J. (2007) Evolution of dispersal and life history strategies - Tetrahymena ciliates. BMC Evolutionary Biology, 7, 133.

Foissner, W. & Berger, H. (1996) A user-friendly guide to the ciliates (Protozoa, Ciliophora) commonly used by hydrobiologists as bioindicators in rivers, lakes and water waters, with notes on their ecology. Freshwater Biology, 35, 375-482.

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.

Fox, J.W. & Morin, P.J. (2001) Effects of intra- and interspecific interactions on species responses to environmental change. Journal of Animal Ecology, 70, 80-90.

Fox, J.W. & Smith, D.C. (1997) Variable outcomes of protist-rotifer competition in laboratory microcosms. Oikos, 79, 489-495.

Friman, V.-P. & Laakso, J. (2011) Pulsed-Resource Dynamics Constrain the Evolution of Predator-Prey Interactions. The American Naturalist, 177, 334-345.

Friman, V.P., Hiltunen, T., Laakso, J. & Kaitala, V. (2008) Availability of prey resources drives evolution of predator-prey interaction. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 275, 1625-1633.

Fronhofer, E.A., Kropf, T. & Altermatt, F. (2014) Density-dependent movement and the consequences of the Allee effect in the model organism Tetrahymena. Journal of Animal Ecology, in press.

Fukami, T. (2001) Sequence effects of disturbance on community structure. Oikos, 92, 215-224.

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

Gause, G.F. (1934a) Experimental analysis of Vito Volterra’s mathematical theory of the struggle for existence. Science, 79, 16-17.

Gause, G.F. (1934b) The Struggle for Existence. Dover Publications, Mineaola, N.Y.

Gill, D.E. (1972a) Density dependence and population regulation in laboratory cultures of Paramecium. Ecology, 53, 701-708.

Gill, D.E. (1972b) Intrinsic rates of increase, saturation densities, and competitive ability. I. An experiment with Paramecium. The American Naturalist, 106, 461-471.

Gill, D.E. & Nelson, G.H. (1972) The dynamics of a natural population of Paramecium and the rôle of interspecific competition in community stucture. Journal of Animal Ecology, 41, 137-151.

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.

Giometto, A., Rinaldo, A., Carrara, F. & Altermatt, F. (2014) Emerging predictable features of replicated biological invasion fronts. Proceedings of the National Academy of Sciences, 111, 297-301.

Haddad, N.M., Holyoak, M., Mata, T.M., Davies, K.F., Melbourne, B.A. & Preston, K. (2008) Species’ traits predict the effects of disturbance and productivity on diversity. Ecology Letters, 11, 348-356.

Hammill, E., Petchey, O.L. & Anholt, B.R. (2010) Predator Functional Response Changed by Induced Defenses in Prey. American Naturalist, 176, 723-731.

Hiltunen, T., Hairston, N.G., Hooker, G., Jones, L.E. & Ellner, S.P. (2014) A newly discovered role of evolution in previously published consumer–resource dynamics. Ecology Letters, 17, 915-923.

Holyoak, M. (2000a) Effects of nutrient enrichment on predator-prey metapopulation dynamics. Journal of Animal Ecology, 69, 985-997.

Holyoak, M. (2000b) Habitat Patch Arrangement and Metapopulation Persistence of Predators and Prey. The American Naturalist, 156, 378-389.

Holyoak, M. & Lawler, S.P. (1996) The role of dispersal in predator-prey metapopulation dynamics. Journal of Animal Ecology, 65, 640-652.

Holyoak, M. & Lawler, S.P. (2005) The contribution of laboratory experiments on protists to understanding population and metapopulation dynamics. Advances in ecological research, 37, 245-271.

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

Jiang, L. & Morin, P.J. (2004) Temperature-dependent interactions explain unexpected responses to environmental warming in communities of competitors. Journal of Animal Ecology, 73, 569-576.

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.

Jiang, L. & Patel, S.N. (2008) Community assembly in the presence of disturbance: A microcosm experiment. Ecology, 89, 1931-1940.

Kneitel, J.M. & Chase, J.M. (2004) Disturbance, predator, and resource interactions alter container community composition. Ecology, 85, 2088-2093.

Kneitel, J.M. & Miller, T.E. (2003) Dispersal rates affect species composition in metacommunities of Sarracenia purpurea inquilines. American Naturalist, 162, 165-171.

Kratina, P., Hammill, E. & Anholt, B.R. (2010) Stronger inducible defences enhance persistence of intraguild prey. Journal of Animal Ecology, 79, 993-999.

Kratina, P., Vos, M., Bateman, A. & Anholt, B.R. (2009) Functional responses modified by predator density. Oecologia, 159, 425-433.

Laakso, J., Loytynoja, K. & Kaitala, V. (2003) Environmental noise and population dynamics of the ciliated protozoa Tetrahymena thermophila in aquatic microcosms. Oikos, 102, 663-671.

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

Lee, J.J., Leedale, G.F. & Bradbury, P. (2000) Illustrated guide to the Protozoa. Society of Protozoologists, Lawrence Kansas.

Limberger, R. & Wickham, S. (2011) Competition-colonization trade-offs in a ciliate model community. Oecologia, 167, 723-732.

Limberger, R. & Wickham, S. (2012) Disturbance and diversity at two spatial scales. Oecologia, 168, 785-795.

Luckinbill, L.S. (1973) Coexistence in laboratory populations of Paramecium aurelia and its predator Didinium nasutum. Ecology, 54, 1320-1327.

Luckinbill, L.S. (1974) The effects of space and enrichment on a predator-prey system. Ecology, 55, 1142-1147.

Luckinbill, L.S. (1979) Selection and the r/K Continuum in Experimental Populations of Protozoa. The American Naturalist, 113, 427-437.

Luckinbill, L.S. & Fenton, M.M. (1978) Regulation and environmental variability in experimental populations of protozoa. Ecology, 59, 1271-1276.

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.

Nelson, G.H. (1958) Observations on the Ecology of Paramecium, with Comments on the Species Problem. Evolution, 12, 440-450.

Nelson, G.H. (1967) Studies on The Limitation of a Natural Population of Paramecium Aurelia. Ecology, 48, 904-910.

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.

Östman, Ö., Kneitel, J.M. & Chase, J.M. (2006) Disturbance alters habitat isolation's effect on biodiversity in aquatic microcosms. Oikos, 114, 360-366.

Patterson, D.J. (2003) Free-living freshwater protozoa: A colour guide. Manson Publishing Ltd, London.

Pawlowski, J., Audic, S.p., Adl, S., Bass, D., Belbahri, L.d., Berney, C.d., Bowser, S.S., Cepicka, I., Decelle, J., Dunthorn, M., Fiore-Donno, A.M., Gile, G.H., Holzmann, M., Jahn, R., Jirku, M., Keeling, P.J., Kostka, M., Kudryavtsev, A., Lara, E., Lukeš, J., Mann, D.G., Mitchell, E.A.D., Nitsche, F., Romeralo, M., Saunders, G.W., Simpson, A.G.B., Smirnov, A.V., Spouge, J.L., Stern, R.F., Stoeck, T., Zimmermann, J., Schindel, D. & de Vargas, C. (2012) CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms. PLoS Biol, 10, e1001419.

Pennekamp, F., Mitchell, K.A., Chaine, A. & Schtickzelle, N. (2014) Dispersal propensity in Tetrahymena thermophila ciliates—a reaction norm perspective. Evolution, 68, 2319-2330.

Pennekamp, F. & Schtickzelle, N. (2013) Implementing image analysis in laboratory-based experimental systems for ecology and evolution: a hands-on guide. Methods in Ecology and Evolution, 4, 483-492.

Petchey, O.L. (2000) Prey diversity, prey composition, and predator population dynamics in experimental microcosms. Journal of Animal Ecology, 69, 874-882.

Petchey, O.L., Brose, U. & Rall, B.r.C. (2010) Predicting the effects of temperature on food web connectance. Philosophical Transactions of the Royal Society B: Biological Sciences, 365, 2081-2091.

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.

Salt, G.W. (1967) Predation in an Experimental Protozoan Population (Woodruffia-Paramecium). Ecological Monographs, 37, 113-144.

Schtickzelle, N., Fjerdingstad, E., Chaine, A. & Clobert, J. (2009) Cooperative social clusters are not destroyed by dispersal in a ciliate. BMC Evolutionary Biology, 9.

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.

Sonneborn, T.M. (1950) Methods in the general biology and genetics of Paramecium aurelia. Journal of Experimental Zoology, 113, 87-147.

Steiner, C.F., Long, Z.T., Krumins, J.A. & Morin, P.J. (2006) Population and community resilience in multitrophic communities. Ecology, 87, 996-1007.

TerHorst, C.P. (2010) Experimental evolution of protozoan traits in response to interspecific competition. Journal of Evolutionary Biology, no-no.

Vandermeer, J., Addicott, J., Andersen, A., Kitasko, J., Pearson, D., Schnell, C. & Wilbur, H. (1972) Observations of Paramecium Occupying Arboreal Standing Water in Costa Rica. Ecology, 53, 291-293.

Vasseur, D.A. & Fox, J.W. (2009) Phase-locking and environmental fluctuations generate synchrony in a predator-prey community. Nature, 460, 1007-1010.

Veilleux, B.G. (1979) An Analysis of the Predatory Interaction Between Paramecium and Didinium. Journal of Animal Ecology, 48, 787-803.

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

Violle, C., Pu, Z. & Jiang, L. (2010) Experimental demonstration of the importance of competition under disturbance. Proceedings of the National Academy of Sciences, 107, 12925-12929.

Warren, P.H. (1996a) Dispersal and destruction in a multiple habitat system: an experimental approach using protist communities. Oikos, 77, 317-325.

Warren, P.H. (1996b) The effects of between-habitat dispersal rate on protist communities and metacommunities in microcosms at two spatial scales. Oecologia, 105, 132-140.

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