Soil protists: a fertile frontier in soil biology research

Abd, 2003, Survival and growth of Francisella tularensis in Acanthamoeba castellanii, Curr Opin Plant Biol, 69, 135

Abd, 2005, Intracellular survival and replication of Vibrio cholerae O139 in aquatic free-living amoebae, Environ Microbiol, 7, 1003, 10.1111/j.1462-2920.2005.00771.x

Acosta-Mercado, 2003, The edaphic quantitative protargol stain: a sampling protocol for assessing soil ciliate abundance and diversity, J Microbiol Methods, 53, 365, 10.1016/S0167-7012(03)00042-3

Acosta-Mercado, 2004, Soil ciliate species richness and abundance associated with the rhizosphere of different subtropical plant species, J Eukaryotic Microbiology, 51, 582, 10.1111/j.1550-7408.2004.tb00295.x

Acosta-Mercado, 2006, Contrasting soil ciliate species richness and abundance between two tropical plant species: A test of the plant effect, Microb Ecol, 51, 453, 10.1007/s00248-006-9067-3

Adl, 2006, Protists in soil ecology and forest nutrient cycling, Can J For Res, 36, 1805, 10.1139/x06-056

Adl, 2003, The Ecology of Soil Decomposition, 10.1079/9780851996615.0000

Adl, 2005, Dynamics of soil protozoa using a direct count method, Biol Fertil Soils, 42, 168, 10.1007/s00374-005-0009-x

Adl, 2006, Slow recovery of soil biodiversity in sandy loam soils of Georgia after 25 years of no-tillage management, Agriculture, Ecosystems & Environment, 114, 323, 10.1016/j.agee.2005.11.019

Adl, 2014, Amplification primers of SSU rDNA for soil protists, Soil Biol Biochem, 69, 328, 10.1016/j.soilbio.2013.10.024

Adl, 2007, Diversity, nomenclature, and taxonomy of protists, Syst Biol, 56, 684, 10.1080/10635150701494127

Adl, 2012, The revised classification of eukaryotes, J Eukaryot Microbiol, 59, 429, 10.1111/j.1550-7408.2012.00644.x

Agler, 2016, Microbial hub taxa link host and abiotic factors to plant microbiome variation, PLoS Biol, 14, e1002352, 10.1371/journal.pbio.1002352

Aguilar, 2014, Using environmental niche models to test the “everything is everywhere” hypothesis for Badhamia, ISME J, 8, 737, 10.1038/ismej.2013.183

Ben Ali, 2002, Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA, Protist, 153, 123, 10.1078/1434-4610-00091

Alphei, 1996, Protozoa, Nematoda and Lumbricidae in the rhizosphere of Hordelymus europeaus (Poaceae): faunal interactions, response of microorganisms and effects on plant growth, Oecologia, 106, 111, 10.1007/BF00334413

Altermatt, 2015, Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution, Methods Ecol Evol, 6, 218, 10.1111/2041-210X.12312

Amaral Zettler, 2002, Microbiology: eukaryotic diversity in Spain's River of Fire, Nature, 417, 137, 10.1038/417137a

Amaroli, 2015, The effects of temperature variation on the sensitivity to pesticides: a study on the slime mould Dictyostelium discoideum (Protozoa), Microb Ecol, 70, 244, 10.1007/s00248-014-0541-z

Amblard, 1991, Activité hétérotrophe des microalgues et des cyanobactéries vis-a-vis du carbone: implications écophysiologiques, L’Année Biol, 30, 73

Anderson, 2000, Abundance of terrestrial Gymnamoebae at a Northeastern U. S. Site: a four-year study, including the El Nino Winter of 1997-1998, J Eukaryotic Microbiology, 47, 148, 10.1111/j.1550-7408.2000.tb00024.x

Anderson, 2016, Experimental evidence for non-encysted, freeze-resistant stages of terrestrial naked amoebae capable of resumed growth after freeze- thaw events, Acta Protozool, 55, 19

Antonelli, 2017, On the potential for terrestrial diatom communities and diatom indices to identify anthropic disturbance in soils, Ecol Indic, 75, 73, 10.1016/j.ecolind.2016.12.003

Aoki, 2007, Silica and testate amoebae in a soil under pine–oak forest, Geoderma, 142, 29, 10.1016/j.geoderma.2007.07.009

Azam, 1983, The ecological role of water-column microbes in the sea, Mar Ecol Prog Ser, 10, 257, 10.3354/meps010257

Azovsky, 2013, Do microbes have macroecology? Large-scale patterns in the diversity and distribution of marine benthic ciliates, Glob Ecol Biogeogr, 22, 163, 10.1111/j.1466-8238.2012.00776.x

Balderrama-Carmona, 2014, Occurrence and quantitative microbial risk assessment of Cryptosporidium and Giardia in soil and air samples, Int J Infect Dis, 26, 123, 10.1016/j.ijid.2014.05.002

Bamforth, 1973, Population dynamics of soil and vegetation protozoa, Am Zool, 13, 171, 10.1093/icb/13.1.171

Bamforth, 2008, Protozoa of biological soil crusts of a cool desert in Utah, J Arid Environ, 72, 722, 10.1016/j.jaridenv.2007.08.007

Barker, 1994, Trojan Horses of the microbial world: protozoa and the survival of bacterial pathogens in the environment, Microbiology, 140, 1253, 10.1099/00221287-140-6-1253

Barker, 1999, Survival of Escherichia coli 0157 in a soil protozoan: implications for disease, FEMS Microbiol Lett, 173, 291, 10.1111/j.1574-6968.1999.tb13516.x

Barthlott, 1998, First protozoa-trapping plant found, Nature, 392, 447, 10.1038/33037

Bass, 2004, Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa), Int J Syst Evol Microbiol, 54, 2393, 10.1099/ijs.0.63229-0

Bass, 2016, Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists, Environ Microbiol, 18, 1604, 10.1111/1462-2920.13235

Bates, 2013, Global biogeography of highly diverse protistan communities in soil, ISME J, 7, 652, 10.1038/ismej.2012.147

Beisser, 2017, Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships amongst chrysophytes, Peer J, 5, e2832, 10.7717/peerj.2832

Belasky, 1992, Assessment of sampling bias in biogeography by means of a probabilistic estimate of taxonomic diversity: application to modern Indo-Pacific reef corals, Palaeogeogr Palaeoclimatol Palaeoecol, 99, 243, 10.1016/0031-0182(92)90018-Z

Berg, 2014, Unraveling the plant microbiome: Looking back and future perspectives, Front Microbiol, 5, 148, 10.3389/fmicb.2014.00148

Berger, 1979, The feeding behavior of Didinium nasutum on an atypical prey ciliate (Colpidium campylum), Trans Am Microsc Soc, 98, 487, 10.2307/3225898

Bernasconi, 2011, Chemical and biological gradients along the damma glacier soil chronosequence, Switzerland, Vadose Zo J, 10, 867, 10.2136/vzj2010.0129

Berney, 2015, Expansion of the ‘reticulosphere’: diversity of novel branching and network-forming amoebae helps to define Variosea (Amoebozoa), Protist, 166, 271, 10.1016/j.protis.2015.04.001

Berney, 2013, Vampires in the oceans: predatory cercozoan amoebae in marine habitats, ISME J, 7, 2387, 10.1038/ismej.2013.116

Berney, 2017, UniEuk: time to speak a common language in protistology!, J Eukaryot Microbiol, 64, 407, 10.1111/jeu.12414

Bhattacharya, 1995, Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent rhizopod lineage containing the Euglyphina and the Chlorarachniophyta, J Eukaryotic Microbiology, 42, 65, 10.1111/j.1550-7408.1995.tb01541.x

Bischoff, 2016, Winter abundances of naked amoebae in the soil system of the invasive species Japanese knotweed (Fallopia japonica) with comparative data from adjacent sites, Acta Protozool, 55, 155

Bjørnlund, 2012, Nematodes and protozoa affect plants differently, depending on soil nutrient status, Eur J Soil Biol, 50, 28, 10.1016/j.ejsobi.2011.11.012

Blandenier, 2017, Mycamoeba gemmipara nov. gen., nov. sp., the first cultured member of the environmental Dermamoebidae clade LKM74 and its unusual life cycle, J Eukaryot Microbiol, 64, 257, 10.1111/jeu.12357

Boenigk, 2002, Food concentration-dependent regulation of food selectivity of interception-feeding bacterivorous nanoflagellates, Aquat Microb Ecol, 27, 195, 10.3354/ame027195

Boenigk, 2005, High diversity of the ‘Spumella-like’ flagellates: an investigation based on the SSU rRNA gene sequences of isolates from habitats located in six different geographic regions, Environ Microbiol, 7, 685, 10.1111/j.1462-2920.2005.00743.x

Bonkowski, 2004, Protozoa and plant growth: the microbial loop in soil revisited, New Phytol, 162, 617, 10.1111/j.1469-8137.2004.01066.x

Bonkowski, 2002, Do soil protozoa enhance plant growth by hormonal effects?, Soil Biol Biochem, 34, 1709, 10.1016/S0038-0717(02)00157-8

Bonkowski, 2012, Stimulation of plant growth through interactions of bacteria and protozoa: testing the auxiliary microbial loop hypothesis, Acta Protozool, 51, 237

Bonkowski, 2000, Substrate heterogeneity and microfauna in soil organic ‘hotspots’ as determinants of nitrogen capture and growth of ryegrass, Applied Soil Ecology, 14, 37, 10.1016/S0929-1393(99)00047-5

Bonkowski, 2001, Contrasting effects of microbial partners in the rhizosphere: interactions between Norway Spruce seedlings (Picea abies Karst.), mycorrhiza (Paxillus involutus (Batsch) Fr.) and naked amoebae (protozoa), Applied Soil Ecology, 18, 193, 10.1016/S0929-1393(01)00165-2

Bonnet, 1984, Le signalement écologique des Thécamoebiens du sol, Bull la Société d’Histoire Nat Toulouse, 120, 103

Brown, 1998, Biogeography

Brown, 2012, Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria, Curr Biol, 22, 1123, 10.1016/j.cub.2012.04.021

Brown, 2013, The non-dictyostelid sorocarpic amoebae, Dictyostelids: Evolution, Genomics and Cell Biology, 219, 10.1007/978-3-642-38487-5_12

Brown, 2010, A morphologically simple species of acrasis (Heterolobosea, Excavata), Acrasis helenhemmesae n. sp, J Eukaryot Microbiol, 57, 346, 10.1111/j.1550-7408.2010.00481.x

Brown, 2009, Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta, Mol Biol Evol, 26, 2699, 10.1093/molbev/msp185

Brüssow, 2007, Bacteria between protists and phages: from antipredation strategies to the evolution of pathogenicity, Mol Microbiol, 65, 583, 10.1111/j.1365-2958.2007.05826.x

Brussaard, 2016, Immediate ecotoxicological effects of short-lived oil spills on marine biota, Nat Comms, 7, 11206, 10.1038/ncomms11206

Buée, 2009, The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors, Plant Soil, 321, 189, 10.1007/s11104-009-9991-3

Bukovská, 2016, Organic nitrogen-driven stimulation of arbuscular mycorrhizal fungal hyphae correlates with abundance of ammonia oxidizers, Front Microbiol, 7, 711, 10.3389/fmicb.2016.00711

Bulgarelli, 2013, Structure and functions of the bacterial microbiota of plants, Annu Rev Plant Biol, 64, 807, 10.1146/annurev-arplant-050312-120106

Bulman, 2001, A phylogenetic analysis of the SSU rRNA from members of the Plasmodiophorida and Phagomyxida, Protist, 152, 43, 10.1078/1434-4610-00042

Burgess, 2017, Parasitic protozoa and interactions with the host intestinal microbiota, Infect Immun, 85, 1, 10.1128/IAI.00101-17

Burki, 2016, Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista, Proc R Soc B, 283, 20152802, 10.1098/rspb.2015.2802

Busch, 2017, The cytoskeleton architecture of algivorous protoplast feeders (Viridiraptoridae, Rhizaria) indicates actin-guided perforation of prey cell walls, Protist, 168, 12, 10.1016/j.protis.2016.10.004

Carlson, 2010, Community development along a proglacial chronosequence: are above-ground and below-ground community structure controlled more by biotic than abiotic factors?, J Ecol, 98, 1084, 10.1111/j.1365-2745.2010.01699.x

Caron, 2009, Past president's address: protistan biogeography: why all the fuss?, J Eukaryot Microbiol, 56, 105, 10.1111/j.1550-7408.2008.00381.x

Caron, 2009, Protists are microbes too: a perspective, ISME J, 3, 4, 10.1038/ismej.2008.101

Cateau, 2011, Acanthamoeba sp. promotes the survival and growth of Acinetobacter baumanii, FEMS Microbiol Lett, 319, 19, 10.1111/j.1574-6968.2011.02261.x

Cavalier-Smith, 1996, Oikomonas, a distinctive zooflagellate related to Chrysomonads, Archiv für Protistenkunde, 146, 273, 10.1016/S0003-9365(96)80014-5

Cavender, 2016, New species of Polysphondylium from Madagascar, Mycologia, 108, 80, 10.3852/14-313

Chacín-Bonilla, 2008, Transmission of Cyclospora cayetanensis infection: a review focusing on soil-borne cyclosporiasis, Trans R Soc Trop Med Hyg, 102, 215, 10.1016/j.trstmh.2007.06.005

Chadfield, 2012, Phytophthora ramorum in England and Wales: which environmental variables predict county disease incidence?, For Pathol, 42, 150, 10.1111/j.1439-0329.2011.00735.x

Chao, 2006, A statistical approach to estimate soil ciliate diversity and distribution based on data from five continents, Oikos, 114, 479, 10.1111/j.2006.0030-1299.14814.x

Cirillo, 1994, Growth of Legionella pneumophila in Acanthamoeba castellanii enhances invasion, Infect Immun, 62, 3254, 10.1128/IAI.62.8.3254-3261.1994

Clarholm, 1981, Protozoan grazing of bacteria in soil—impact and importance, Microb Ecol, 7, 343, 10.1007/BF02341429

Clarholm, 1985, Possible roles for roots, bacteria, protozoa and fungi in supplying nitrogen to plants, Ecol Interact Soil, 4, 355

Clarholm, 1985, Interactions of bacteria, protozoa and plants leading to mineralization of soil nitrogen, Soil Biol Biochem, 17, 181, 10.1016/0038-0717(85)90113-0

Clarholm, 2002, Bacteria and protozoa as integral components of the forest ecosystem – their role in creating a naturally varied soil fertility, Antonie Van Leeuwenhoek, 81, 309, 10.1023/A:1020543424098

Clarholm, 2005, Soil protozoa: an under-researched microbial group gaining momentum, Soil Biol Biochem, 37, 811, 10.1016/j.soilbio.2004.11.002

Clarke, 2014, The thermal limits to life on Earth, Int J Astrobiol, 13, 141, 10.1017/S1473550413000438

Cohen, 2016, Nocturnal fanning suppresses downy mildew epidemics in sweet basil, PLoS One, 11, e0155330, 10.1371/journal.pone.0155330

Cohen, 2013, Light suppresses sporulation and epidemics of Peronospora belbahrii, PLoS One, 8, e81282, 10.1371/journal.pone.0081282

Corno, 2008, Structural and functional patterns of bacterial communities in response to protist predation along an experimental productivity gradient, Environ Microbiol, 10, 2857, 10.1111/j.1462-2920.2008.01713.x

Corsaro, 2014, Microsporidia-like parasites of amoebae belong to the early fungal lineage Rozellomycota, Parasitol Res, 113, 1909, 10.1007/s00436-014-3838-4

Curry, 1991, Opportunistic protozoan infections in human immunodeficiency virus disease: review highlighting diagnostic and therapeutic aspects, J Clin Pathol, 44, 182, 10.1136/jcp.44.3.182

Dado, 2012, Detection of zoonotic intestinal parasites in public parks of Spain. Potential epidemiological role of microsporidia, Zoonoses Public Health, 59, 23, 10.1111/j.1863-2378.2011.01411.x

Das, 1970, Virulence and identification of free-living soil amoebae of the Naegleria-Hartmanella type, Trans R Soc Trop Med Hyg, 64, 20

Dassen, 2017, Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity, Mol Ecol, 26, 4085, 10.1111/mec.14175

Dawson, 2002, Novel kingdom-level eukaryotic diversity in anoxic environments, Proc Natl Acad Sci, 99, 8324, 10.1073/pnas.062169599

Deng, 2014, Grazing of heterotrophic flagellates on viruses is driven by feeding behaviour, Environmental Microbiology Reports, 6, 325, 10.1111/1758-2229.12119

Díaz, 2006, Evaluation of heavy metal acute toxicity and bioaccumulation in soil ciliated protozoa, Environ Int, 32, 711, 10.1016/j.envint.2006.03.004

Dick, 2001, Straminipilous Fungi, 10.1007/978-94-015-9733-3

Dixon, 2009, The occurrence and economic impact of Plasmodiophora brassicae and clubroot disease, J Plant Growth Regul, 28, 194, 10.1007/s00344-009-9090-y

Dumack, 2016, A bowl with marbles: revision of the thecate amoeba genus Lecythium (Chlamydophryidae, Tectofilosida, Cercozoa, Rhizaria) including a description of four new species and an identification key, Protist, 167, 440, 10.1016/j.protis.2016.08.001

Dumack, 2017, Rhogostomidae (Cercozoa) from soils, roots and plant leaves ( Arabidopsis thaliana ): description of Rhogostoma epiphylla sp. nov. and R. cylindrica sp. nov, European Journal of Protistology, 60, 76, 10.1016/j.ejop.2017.06.001

Dunthorn, 2015, Ciliates — protists with complex morphologies and ambiguous early fossil record, Mar Micropaleontol, 119, 1, 10.1016/j.marmicro.2015.05.004

Dunthorn, 2014, Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context, Mol Biol Evol, 31, 993, 10.1093/molbev/msu055

Dupont, 2016, Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs, Environ Microbiol, 18, 2010, 10.1111/1462-2920.13220

Ehrenkaufer, 2013, The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation, Genome Biol, 14, R77, 10.1186/gb-2013-14-7-r77

Ehrmann, 2012, Testate amoebae in 31 mature forest ecosystems – densities and micro-distribution in soils, European Journal of Protistology, 48, 161, 10.1016/j.ejop.2012.01.003

Ekelund, 2002, Estimation of protozoan diversity in soil, Eur J Protistol, 37, 361

Ekelund, 2004, Phylogeny of Heteromita, Cercomonas and Thaumatomonas based on SSU rDNA sequences, including the description of Neocercomonas jutlandica sp. nov., gen. nov, European Journal of Protistology, 40, 119, 10.1016/j.ejop.2003.12.002

Ekelund, 1994, Notes on protozoa in agricultural soil with emphasis on heterotrophic flagellates and naked amoebae and their ecology, FEMS Microbiol Rev, 15, 321, 10.1111/j.1574-6976.1994.tb00144.x

Ekelund, 2009, The “soil microbial loop” is not always needed to explain protozoan stimulation of plants, Soil Biol Biochem, 41, 2336, 10.1016/j.soilbio.2009.08.019

Elmore, 2010, Toxoplasma gondii: epidemiology, feline clinical aspects, and prevention, Trends Parasitol, 26, 190, 10.1016/j.pt.2010.01.009

Essig, 1997, Infection of Acanthamoeba castellanii by Chlamydia pneumoniae, Appl Environ Microbiol, 63, 1396, 10.1128/AEM.63.4.1396-1399.1997

Fasoli, 2008, Simkania negevensis in community-acquired pneumonia in Italian children, Scand J Infect Dis, 40, 269, 10.1080/00365540701642146

Fenchel, 1982, Ecology of heterotrophic microflagellates. IV Quantitative occurrence and importance as bacterial consumers, Mar Ecol Prog Ser, 9, 35, 10.3354/meps009035

Fenchel, 2014, Protozoa and oxygen, Acta Protozool, 53, 3

Fenchel, 1990, Anaerobic free-living protozoa: growth efficiencies and the structure of anaeorobic communities, FEMS Microbiol Lett, 74, 269, 10.1111/j.1574-6968.1990.tb04073.x

Fenchel, 2004, The ubiquity of small species: patterns of local and global diversity, Bioscience, 54, 777, 10.1641/0006-3568(2004)054[0777:TUOSSP]2.0.CO;2

Fernández, 2016, Water-energy balance, past ecological perturbations and evolutionary constraints shape the latitudinal diversity gradient of soil testate amoebae in south-western South America, Global Ecol Biogeogr, 25, 1216, 10.1111/geb.12478

Figueroa-Martínez, 2015, When the lights go out: the evolutionary fate of free-living colorless green algae, New Phytol, 206, 972, 10.1111/nph.13279

Findenig, 2010, When the lights go out: the evolutionary fate of free-living colorless algae, J Phycol, 46, 868, 10.1111/j.1529-8817.2010.00892.x

Finlay, 2002, Global dispersal of free-living microbial eukaryote species, Science, 296, 1061, 10.1126/science.1070710

Finlay, 1996, Global diversity and body size, Nature, 383, 132, 10.1038/383132a0

Finlay, 1992, An anaerobic ciliate as a natural chemostat for the growth of endosymbiotic methanogens, European Journal of Protistology, 28, 127, 10.1016/S0932-4739(11)80041-6

Fiore-Donno, 2010, Deep phylogeny and evolution of slime moulds (Mycetozoa), Protist, 161, 55, 10.1016/j.protis.2009.05.002

Fiore-Donno, 2016, Metacommunity analysis of amoeboid protists in grassland soils, Sci Rep, 6, 19068, 10.1038/srep19068

Flechtner, 1998, Algal composition of microbiotic crusts from the Central Desert of Baja California, Mexico, West North Am Nat, 58, 295

Flues, 2017, Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function, Environ Microbiol, 19, 3297, 10.1111/1462-2920.13824

Foissner, 1993, Colpodea (Ciliophora). Protozoenfauna 4/1: i-x, 1

Foissner, 1987, Soil protozoa: fundamental problems, ecological significance, adaptation in ciliates and testaceans, bioindicators, and guide to the literature, Prog Protozool, 2, 69

Foissner, 1997, Protozoa as bioindicators in agroecosystems, with emphasis on farming practices, biocides, and biodiversity, Agriculture, Ecosystems & Environment, 62, 93, 10.1016/S0167-8809(96)01142-5

Foissner, 1998, An updated compilation of world soil ciliates (Protozoa, Ciliophora), with ecological notes, new records, and descriptions of new species, European Journal of Protistology, 34, 195, 10.1016/S0932-4739(98)80028-X

Foissner, 1999, Soil protozoa as bioindicators: pros and cons, methods, diversity, representative examples, Agriculture, Ecosystems & Environment, 74, 95, 10.1016/S0167-8809(99)00032-8

Foissner, 1999, Description of two new, mycophagous soil ciliates (Ciliophora, Colpodea): Fungiphrya strobli n. g., n. sp. and Grossglockneria ovata n. sp, J Eukaryotic Microbiology, 46, 34, 10.1111/j.1550-7408.1999.tb04581.x

Foissner, 1999, Protist diversity: estimates of the near-imponderable, Protist, 150, 363, 10.1016/S1434-4610(99)70037-4

Foissner, 2006, Biogeography and dispersal of micro-organisms: a review emphasizing protists, Acta Protozool, 45, 111

Foissner, 2008, Protist diversity and distribution: some basic considerations, Biodivers Conserv, 17, 235, 10.1007/s10531-007-9248-5

Foissner, 2009, Morphology and ciliary pattern of some rare haptorid ciliates, with a description of the new family Kamburophryidae (Protists, Haptoria), European Journal of Protistology, 45, 205, 10.1016/j.ejop.2008.11.002

Fontaneto, 2006, Patterns of diversity in microscopic animals: are they comparable to those in protists or in larger animals?, Global Ecol Biogeography, 15, 153, 10.1111/j.1466-822X.2006.00193.x

Fournier, 2016, A legacy of human-induced ecosystem changes: spatial processes drive the taxonomic and functional diversities of testate amoebae in Sphagnum peatlands of the Galápagos, J Biogeogr, 43, 533, 10.1111/jbi.12655

Fournier, 2012, Toward the use of testate amoeba functional traits as indicator of floodplain restoration success, Eur J Soil Biol, 49, 85, 10.1016/j.ejsobi.2011.05.008

Franklin, 2002, Effect of initial cell density on the bioavailability and toxicity of copper in microalgal bioassays, Environ Toxicol Chem, 21, 742, 10.1002/etc.5620210409

Fránková, 2009, The structure and species richness of the diatom assemblages of the Western Carpathian spring fens along the gradient of mineral richness, Fottea, 9, 355, 10.5507/fot.2009.035

Friman, 2014, Phages can constrain protist predation-driven attenuation of Pseudomonas aeruginosa virulence in multienemy communities, ISME J, 8, 1820, 10.1038/ismej.2014.40

Friman, 2008, Availability of prey resources drives evolution of predator-prey interaction, Proceedings of the Royal Society B: Biological Sciences, 275, 1625, 10.1098/rspb.2008.0174

Friman, 2013, Effects of predation on real-time host-parasite coevolutionary dynamics, Ecol Lett, 16, 39, 10.1111/ele.12010

Gabilondo, 2015, The effects of experimental increases in underground carbon dioxide on edaphic protozoan communities, Int J Greenhouse Gas Control, 41, 11, 10.1016/j.ijggc.2015.06.015

Gaston, 2000, Pattern and Process in Macroecology, 10.1002/9780470999592

Geisen, 2016, Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists, Environ Microbiol, 18, 1669, 10.1111/1462-2920.13309

Geisen, 2016, The bacterial-fungal energy channel concept challenged by enormous functional versatility of soil protists, Soil Biol Biochem, 102, 22, 10.1016/j.soilbio.2016.06.013

Geisen, 2017, Methodological advances to study the diversity of soil protists and their functioning in soil food webs, Appl Soil Ecol

Geisen, 2015, Heterogeneity in the genus Allovahlkampfia and the description of the new genus Parafumarolamoeba (Vahlkampfiidae; Heterolobosea), European Journal of Protistology, 51, 335, 10.1016/j.ejop.2015.05.003

Geisen, 2014, Soil water availability strongly alters the community composition of soil protists, Pedobiologia, 57, 205, 10.1016/j.pedobi.2014.10.001

Geisen, 2016, The soil food web revisited: diverse and widespread mycophagous soil protists, Soil Biol Biochem, 94, 10, 10.1016/j.soilbio.2015.11.010

Geisen, 2015, Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa, Mol Ecol, 24, 4556, 10.1111/mec.13238

Geisen, 2017, Soil protistology rebooted: 30 fundamental questions to start with, Soil Biol Biochem, 111, 94, 10.1016/j.soilbio.2017.04.001

Geisen, 2015, Pack hunting by a common soil amoeba on nematodes, Environ Microbiol, 17, 4538, 10.1111/1462-2920.12949

Geisen, 2015, Metatranscriptomic census of active protists in soils, ISME J, 9, 2178, 10.1038/ismej.2015.30

Gelman, 2001, Amoebic encephalitis due to Sappinia diploidea, JAMA, 285, 2450, 10.1001/jama.285.19.2450

Gentil, 2017, Review: origin of complex algae by secondary endosymbiosis: a journey through time, Protoplasma, 254, 1835, 10.1007/s00709-017-1098-8

Giangaspero, 2015, Molecular detection of Cyclospora in water, soil, vegetables and humans in southern Italy signals a need for improved monitoring by health authorities, Int J Food Microbiol, 211, 95, 10.1016/j.ijfoodmicro.2015.07.002

Gilbert, 1998, Short-term effect of nitrogen enrichment on the microbial communities of a peatland, Hydrobiologia, 373/374, 111, 10.1023/A:1017091926454

Gilbert, 1998, The microbial loop at the surface of a peatland:structure, function, and impact of nutrient input, Microb Ecol, 35, 83, 10.1007/s002489900062

Gilbert, 2000, Le régime alimentaire des Thécamoebiens (Protista, Sarcodina), L’Année Biologique, 39, 57, 10.1016/S0003-5017(00)80001-X

Gilbert, 2006, Chapter 13 Microbial diversity in Sphagnum peatlands, Developments in Earth Surface Processes. Vol 9, 287

Glücksman, 2010, Closely related protist strains have different grazing impacts on natural bacterial communities, Environ Microbiol, 12, 3105, 10.1111/j.1462-2920.2010.02283.x

Gomaa, 2013, Amphitremida (Poche, 1913) is a new major, ubiquitous labyrinthulomycete clade, PLoS One, 8, e53046, 10.1371/journal.pone.0053046

Gomaa, 2012, SSU rRNA phylogeny of Arcellinida (Amoebozoa) reveals that the largest Arcellinid genus, Difflugia Leclerc 1815, is not monophyletic, Protist, 163, 389, 10.1016/j.protis.2011.12.001

Gómez, 2011, Bacteria-phage antagonistic coevolution in soil, Science, 332, 106, 10.1126/science.1198767

Graczyk, 2007, Human-virulent microsporidian spores in solid waste landfill leachate and sewage sludge, and effects of sanitization treatments on their inactivation, Parasitol Res, 101, 569, 10.1007/s00436-007-0515-x

Greub, 2004, Microorganisms resistant to free-living amoebae, Clin Microbiol Rev, 17, 413, 10.1128/CMR.17.2.413-433.2004

Griffiths, 1994, Microbial-feeding nematodes and protozoa in soil: their effectson microbial activity and nitrogen mineralization in decomposition hotspots and the rhizosphere, Plant Soil, 164, 25, 10.1007/BF00010107

Grossmann, 2016, Protistan community analysis: key findings of a large-scale molecular sampling, ISME J, 10, 2269, 10.1038/ismej.2016.10

Grytnes, 2007, Elevational trends in biodiversity., Encyclopedia of Biodiversity, 10.1016/B978-012226865-6/00503-1

Guillou, 2013, The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy, Nucleic Acids Res, 41, D597, 10.1093/nar/gks1160

Guimaraes, 2016, Acanthamoeba spp. as a universal host for pathogenic microorganisms: one bridge from environment to host virulence, Microbiol Res, 193, 30, 10.1016/j.micres.2016.08.001

Gustafsson, 1989, Acanthamoeba spp. as a universal host for pathogenic microorganisms: one bridge from environment to host virulence, Can J Microbiol, 35, 1100, 10.1139/m89-184

Häder, 1979, Growth and survival of four strains of Francisella tularensis in a rich medium preconditioned with Acanthamoeba palestinensis, Photochem Photobiol, 29, 1157, 10.1111/j.1751-1097.1979.tb07834.x

Hanson, 2012, Beyond biogeographic patterns: processes shaping the microbial landscape, Nat Rev Micro, 10, 497, 10.1038/nrmicro2795

Harder, 2016, Local diversity of heathland Cercozoa explored by in-depth sequencing, ISME J, 10, 2488, 10.1038/ismej.2016.31

Havlicek, Soils supporting biodiversity, Interactions in soil: promoting plant growth, biodiversity, community and ecosystems., 27

Heal, 1961, The distribution of testate amoebae (Rhizopoda: Testacea) in some fens and bogs in Northern England, J Linn Soc London, Zool, 44, 369, 10.1111/j.1096-3642.1961.tb01621.x

Heger, 2016, Testate amoebae like it hot: species richness decreases along a subalpine-alpine altitudinal gradient in both natural Calluna vulgaris litter and transplanted Minuartia sedoides cushions, Microb Ecol, 71, 725, 10.1007/s00248-015-0687-3

Heger, 2014, A resurgence in field research is essential to better understand the diversity, ecology, and evolution of microbial eukaryotes, J Eukaryot Microbiol, 61, 214, 10.1111/jeu.12095

Heger, 2009, The curse of taxonomic uncertainty in biogeographical studies of free-living terrestrial protists: a case study of testate amoebae from Amsterdam Island, J Biogeogr, 36, 1551, 10.1111/j.1365-2699.2009.02094.x

van der Heijden, 2015, Root surface as a frontier for plant microbiome research: Fig. 1, Proc Natl Acad Sci USA, 112, 2299, 10.1073/pnas.1500709112

Held, 1981, Rozella and Rozellopsis: naked endoparasitic fungi which dress-up as their hosts, Bot Rev, 47, 451, 10.1007/BF02860539

Van der Henst, 2016, An intracellular replication niche for Vibrio cholerae in the amoeba Acanthamoeba castellanii, ISME J, 10, 897, 10.1038/ismej.2015.165

Herdler, 2008, Interactions between arbuscular mycorrhizal fungi (Glomus intraradices, Glomeromycota) and amoebae (Acanthamoeba castellanii, Protozoa) in the rhizosphere of rice (Oryza sativa), Soil Biol Biochem, 40, 660, 10.1016/j.soilbio.2007.09.026

Hess, 2012, Shedding light on vampires: the phylogeny of vampyrellid amoebae revisited, PLoS One, e31165

Higgs, 2000, Population biology of Eimeria (Protozoa: Apicomplexa) in Apodemus sylvaticus: a capture/recapture study, Parasitology, 120, 355, 10.1017/S0031182099005545

Hill, 2002, Toxoplasma gondii: transmission, diagnosis and prevention, Clin Microbiol Infect, 8, 634, 10.1046/j.1469-0691.2002.00485.x

Hillebrand, 2001, Body size determines the strength of the latitudinal diversity gradient, Ecography (Cop), 24, 251, 10.1034/j.1600-0587.2001.240302.x

Hodge, 2015, Arbuscular mycorrhiza and nitrogen: implications for individual plants through to ecosystems, Plant Soil, 386, 1, 10.1007/s11104-014-2162-1

Holtkamp, 2008, Soil food web structure during ecosystem development after land abandonment, Applied Soil Ecology, 39, 23, 10.1016/j.apsoil.2007.11.002

Holtkamp, 2011, Modelling C and N mineralisation in soil food webs during secondary succession on ex-arable land, Soil Biol Biochem, 43, 251, 10.1016/j.soilbio.2010.10.004

Holzinger, 2013, Desiccation stress and tolerance in green algae: consequences for ultrastructure, physiological and molecular mechanisms, Front Plant Sci, 4, 327, 10.3389/fpls.2013.00327

Honigberg, 1964, A revised classification of the phylum Protozoa*, J Protozool, 11, 7, 10.1111/j.1550-7408.1964.tb01715.x

Hortal, 2011, Ice age climate, evolutionary constraints and diversity patterns of European dung beetles, Ecol Lett, 14, 741, 10.1111/j.1461-0248.2011.01634.x

Howe, 2011, New genera, species, and improved phylogeny of Glissomonadida (Cercozoa), Protist, 162, 710, 10.1016/j.protis.2011.06.002

Howe, 2009, Phylogeny, taxonomy, and astounding genetic diversity of Glissomonadida ord. nov., the dominant gliding zooflagellates in soil (Protozoa: Cercozoa), Protist, 160, 159, 10.1016/j.protis.2008.11.007

Hu, 2015, Estimating protistan diversity using high-throughput sequencing, J Eukaryot Microbiol, 62, 688, 10.1111/jeu.12217

Hughes, 1983, A natural source of infection due to Pneumocystis carinii, J Infect Dis, 147, 595, 10.1093/infdis/147.3.595

von Humboldt, 1805, Essai Sur La Géographie Des Plantes: Accompagné D’un Tableau Physique Des Régions Équinoxiales, Fondé Sur Des Mesures Exécutées, Depuis Le Dixiéme Degré de Latitude Boréale Jusqu’au Dixiéme Degré de Latitude Australe, Pendant Les Années 1799, 1800, 1801

Hünninghaus, 2017, Changes in bacterial community composition and soil respiration indicate rapid successions of protist grazers during mineralization of maize crop residues, Pedobiologia, 62, 1, 10.1016/j.pedobi.2017.03.002

Hunt, 1987, The detrital food web in a shortgrass prairie, Biol Fertil Soils, 3, 57

Huws, 2008, Interactions of some common pathogenic bacteria with Acanthamoeba polyphaga, FEMS Microbiol Lett, 282, 258, 10.1111/j.1574-6968.2008.01123.x

Hwang, 2006, Effect of intracellular resuscitation of Legionella pneumophila in Acanthamoeba polyphaga cells on the antimicrobial properties of silver and copper, Environ Sci Technol, 40, 7434, 10.1021/es060412t

Imparato, 2016, Stimulation of bacteria and protists in rhizosphere of glyphosate-treated barley, Applied Soil Ecology, 98, 47, 10.1016/j.apsoil.2015.09.007

Inglis, 2000, Interaction between Burkholderia pseudomallei and Acanthamoeba species results in coiling phagocytosis, endamebic bacterial survival, and escape, Infect Immun, 68, 1681, 10.1128/IAI.68.3.1681-1686.2000

Jadin, 1975, Amibes Limax vecteurs possibles de mycobacteries et de M. leprae, Acta Leprol, 59, 57

Jassey, 2014, Plant functional diversity drives niche-size-structure of dominant microbial consumers along a poor to extremely rich fen gradient, J Ecol, 102, 1150, 10.1111/1365-2745.12288

Jassey, 2015, An unexpected role for mixotrophs in the response of peatland carbon cycling to climate warming, Sci Rep, 5, 16931, 10.1038/srep16931

Jentschke, 1995, Soil protozoa and forest tree growth: non-nutritional effects and interaction with mycorrhizae, Biol Fertil Soils, 20, 263, 10.1007/BF00336088

Jiao, 2010, Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean, Nat Rev Micro, 8, 593, 10.1038/nrmicro2386

de Jonckheere, 1991, Ecology of Acanthamoeba, Rev Infect Dis, 13, S385, 10.1093/clind/13.Supplement_5.S385

de Jonckheere, 2006, Isolation and molecular identification of free-living amoebae of the genus Naegleria from Arctic and sub-Antarctic regions, European Journal of Protistology, 42, 115, 10.1016/j.ejop.2006.02.001

de Jonckheere, 2014, What do we know by now about the genus Naegleria?, Exp Parasitol, 145, S2, 10.1016/j.exppara.2014.07.011

de Jonckheere, 2011, A new thermophilic heterolobosean amoeba, Fumarolamoeba ceborucoi, gen. nov. sp nov., isolated near a fumarole at a volcano in Mexico, Acta Protozool, 50, 41

Jones, 2011, Discovery of novel intermediate forms redefines the fungal tree of life, Nature, 474, 200, 10.1038/nature09984

Jousset, 2012, Ecological and evolutive implications of bacterial defences against predators, Environ Microbiol, 14, 1830, 10.1111/j.1462-2920.2011.02627.x

Jousset, 2010, The model predator Acanthamoeba castellanii induces the production of 2,4, DAPG by the biocontrol strain Pseudomonas fluorescens Q2-87, Soil Biol Biochem, 42, 1647, 10.1016/j.soilbio.2010.05.018

Jousset, 2010, Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil, Sci Total Environ, 408, 1221, 10.1016/j.scitotenv.2009.09.056

Jousset, 2006, Secondary metabolites help biocontrol strain Pseudomonas fluorescens CHA0 to escape protozoan grazing, Appl Environ Microbiol, 72, 7083, 10.1128/AEM.00557-06

Jousset, 2009, Predators promote defence of rhizosphere bacterial populations by selective feeding on non-toxic cheaters, ISME J, 3, 666, 10.1038/ismej.2009.26

Kahane, 1998, High prevalence of “‘Simkania Z,’” a novel Chlamydia-like bacterium, in infants with acute bronchiolitis, J Infect Dis, 177, 1425, 10.1086/517830

Kang, 2017, Between a pod and a hard test: the deep evolution of amoebae, Mol Biol Evol, 34, 2258, 10.1093/molbev/msx162

Kanyuka, 2003, Polymyxa graminis and the cereal viruses it transmits: a research challenge, Mol Plant Pathol, 4, 393, 10.1046/j.1364-3703.2003.00177.x

Karpov, 2014, Morphology, phylogeny, and ecology of the aphelids (Aphelidea, Opisthokonta) and proposal for the new superphylum Opisthosporidia, Front Microbiol, 5, 112, 10.3389/fmicb.2014.00112

Kennedy, 1993, Water as a limiting factor in the Antarctic terrestrial environment: a biogeographical synthesis, Arct Alp Res, 25, 308, 10.2307/1551914

Kidder, 2005, Impact of grassland radiation on the nonmarine silica cycle and Miocene diatomite, Palaios, 20, 198, 10.2110/palo.2003.p03-108

Kinealy, 1994, This Great Calamity: The Great Irish Famine: The Irish Famine 1845–52

King, 1988, Survival of coliforms and bacterial pathogens within protozoa during chlorination, Appl Environ Microbiol, 54, 3023, 10.1128/AEM.54.12.3023-3033.1988

Koch, 2005, Strains of the heterotrophic flagellate Bodo designis from different environments vary considerably with respect to salinity preference and SSU rRNA gene composition, Protist, 156, 97, 10.1016/j.protis.2004.12.001

Koenig, 2015, Comparative ecology of vascular plant, bryophyte and testate amoeba communities in four Sphagnum peatlands along an altitudinal gradient in Switzerland, Ecol Indic, 54, 48, 10.1016/j.ecolind.2015.01.043

Koller, 2013, Protozoa enhance foraging efficiency of arbuscular mycorrhizal fungi for mineral nitrogen from organic matter in soil to the benefit of host plants, New Phytol, 199, 203, 10.1111/nph.12249

Koller, 2013, Protozoa stimulate N uptake and growth of arbuscular mycorrhizal plants, Soil Biol Biochem, 65, 204, 10.1016/j.soilbio.2013.05.020

Kolman, 2015, Effects of developmental temperature on gametocysts and oocysts of two species of gregarines Blabericola migrator and Blabericola cubensis (Apicomplexa: Eugregarinida: Blabericolidae) parasitizing blaberid cockroaches (Dictyoptera: Blaberidae), J Parasitol, 101, 651, 10.1645/14-673

Kosakyan, 2013, Using DNA-barcoding for sorting out protist species complexes: a case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae), European Journal of Protistology, 49, 222, 10.1016/j.ejop.2012.08.006

Kota, 1999, Influence of protozoan grazing on contaminant biodegradation, FEMS Microbiol Ecol, 29, 179, 10.1111/j.1574-6941.1999.tb00609.x

Kramer, 2016, Resource partitioning between bacteria, fungi, and protists in the detritusphere of an agricultural soil, Front Microbiol, 7, 1524, 10.3389/fmicb.2016.01524

Krashevska, 2007, Testate amoebae (protista) of an elevational gradient in the tropical mountain rain forest of Ecuador, Pedobiologia, 51, 319, 10.1016/j.pedobi.2007.05.005

Krashevska, 2010, Carbon and nutrient limitation of soil microorganisms and microbial grazers in a tropical montane rain forest, Oikos, 119, 1020, 10.1111/j.1600-0706.2009.18169.x

Krashevska, 2012, Consequences of exclusion of precipitation on microorganisms and microbial consumers in montane tropical rainforests, Oecologia, 170, 1067, 10.1007/s00442-012-2360-6

Krashevska, 2014, Moderate changes in nutrient input alter tropical microbial and protist communities and belowground linkages, ISME J, 8, 1126, 10.1038/ismej.2013.209

Kreuzer, 2006, Grazing of a common species of soil protozoa (Acanthamoeba castellanii) affects rhizosphere bacterial community composition and root architecture of rice (Oryza sativa L.), Soil Biol Biochem, 38, 1665, 10.1016/j.soilbio.2005.11.027

Krishna-Prasad, 1978, Preliminary report on engulfment and retention of mycobacteria by trophozoites of axenically grown Acanthamoeba castellanii Douglas, 1930, Curr Sci, 47, 245

Krome, 2009, Grazing of protozoa on rhizosphere bacteria alters growth and reproduction of Arabidopsis thaliana, Soil Biol Biochem, 41, 1866, 10.1016/j.soilbio.2009.06.008

Krome, 2010, Soil bacteria and protozoa affect root branching via effects on the auxin and cytokinin balance in plants, Plant Soil, 328, 191, 10.1007/s11104-009-0101-3

Kuikman, 1990, Protozoan predation and the turnover of soil organic carbon and nitrogen in the presence of plants, Biol Fertil Soils, 10, 22, 10.1007/BF00336120

Lahiri, 2008, The role of free-living pathogenic amoeba in the transmission of leprosy: a proof of principle, Lepr Rev, 79, 401, 10.47276/lr.79.4.401

Lahr, 2015, The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems, PeerJ, 3, e1234, 10.7717/peerj.1234

Lahr, 2012, Time to regulate microbial eukaryote nomenclature, Biol J Linn Soc Lond, 107, 469, 10.1111/j.1095-8312.2012.01962.x

Lamentowicz, 2013, Seasonal patterns of testate amoeba diversity, community structure and species–environment relationships in four Sphagnum-dominated peatlands along a 1300 m altitudinal gradient in Switzerland, Soil Biol Biochem, 67, 1, 10.1016/j.soilbio.2013.08.002

Lamentowicz, 2015, Hydrological dynamics and fire history of the last 1300 years in western Siberia reconstructed from a high-resolution, ombrotrophic peat archive, Quat Res (United States), 84, 312

Lamothe, 2004, Burkholderia cepacia complex isolates survive intracellularly without replication within acidic vacuoles of Acanthamoeba polyphaga, Cell Microbiol, 6, 1127, 10.1111/j.1462-5822.2004.00424.x

Lanzén, 2016, Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient, Sci Rep, 6, 28257, 10.1038/srep28257

Lara, 2012, A molecular perspective on ciliates as soil bioindicators, Eur J Soil Biol, 49, 107, 10.1016/j.ejsobi.2011.11.001

Lara, 2011, SSU rRNA reveals major trends in oomycete evolution, Fungal Diversity, 49, 93, 10.1007/s13225-011-0098-9

Lara, 2007, Molecular comparison of cultivable protozoa from a pristine and a polycyclic aromatic hydrocarbon polluted site, Soil Biol Biochem, 39, 139, 10.1016/j.soilbio.2006.06.017

Lara, 2007, Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil, FEMS Microbiol Ecol, 62, 365, 10.1111/j.1574-6941.2007.00387.x

Lara, 2006, Andalucia (n. gen.)-the deepest branch within jakobids (Jakobida; Excavata), based on morphological and molecular study of a new flagellate from soil, J Eukaryotic Microbiology, 53, 112, 10.1111/j.1550-7408.2005.00081.x

Lara, 2011, COI gene and ecological data suggest size-dependent high dispersal and low intra-specific diversity in free-living terrestrial protists (Euglyphida: Assulina), J Biogeogr, 38, 640, 10.1111/j.1365-2699.2010.02426.x

Lara, 2011, Highly diverse and seasonally dynamic protist community in a pristine peat bog, Protist, 162, 14, 10.1016/j.protis.2010.05.003

Lara, 2016, Soil microorganisms behave like macroscopic organisms: patterns in the global distribution of soil euglyphid testate amoebae, J Biogeogr, 43, 520, 10.1111/jbi.12660

Ledeganck, 2003, Plant functional group diversity promotes soil protist diversity, Protist, 154, 239, 10.1078/143446103322166536

Lee, 2013, Cysteine protease inhibitor (AcStefin) is required for complete cyst formation of Acanthamoeba, Eukaryotic Cell, 12, 567, 10.1128/EC.00308-12

Leigh, 2011, Growth and symbiotic effectiveness of an arbuscular mycorrhizal fungus in organic matter in competition with soil bacteria, FEMS Microbiol Ecol, 76, 428, 10.1111/j.1574-6941.2011.01066.x

Lejzerowicz, 2010, Molecular evidence for widespread occurrence of Foraminifera in soils, Environ Microbiol, 12, 2518, 10.1111/j.1462-2920.2010.02225.x

Lentendu, 2014, Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach, Mol Ecol, 23, 3341, 10.1111/mec.12819

Lepère, 2013, Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems, FEMS Microbiol Ecol, 85, 85, 10.1111/1574-6941.12100

Lesaulnier, 2008, Elevated atmospheric CO 2 affects soil microbial diversity associated with trembling aspen, Environ Microbiol, 10, 926, 10.1111/j.1462-2920.2007.01512.x

Levine, 1980, A newly revised classification of the Protozoa, J Protozool, 27, 37, 10.1111/j.1550-7408.1980.tb04228.x

Lewin, 1953, Heterotrophy in diatoms, J Gen Microbiol, 9, 305, 10.1099/00221287-9-2-305

Lewis, 2012, Survival of Protosiphon botryoides (Chlorophyceae, Chlorophyta) from a Connecticut soil dried for 43 years, Phycologia, 51, 662, 10.2216/11-108.1

Li, 2016, Contrasting elevational diversity patterns for soil bacteria between two ecosystems divided by the treeline, Sci China Life Sci, 59, 1177, 10.1007/s11427-016-0072-6

Li, 2005, Impact of grazing on soil biota in a Mediterranean grassland, Land Degrad Dev, 16, 581, 10.1002/ldr.680

Liu, 2015, Species diversity of myxomycetes associated with different terrestrial ecosystems, substrata (microhabitats) and environmental factors, Mycol Progress, 14, 27, 10.1007/s11557-015-1048-9

Lloyd, 2017, The myxobacterium Myxococcus xanthus can sense and respond to the quorum signals secreted by potential prey organisms, Front Microbiol, 8, 439, 10.3389/fmicb.2017.00439

Logares, 2013, Biogeography of bacterial communities exposed to progressive long-term environmental change, ISME J, 7, 937, 10.1038/ismej.2012.168

López-García, 2017, Symbiosis in eukaryotic evolution, J Theor Biol, 434, 20, 10.1016/j.jtbi.2017.02.031

López-García, 2001, Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton, Nature, 409, 603, 10.1038/35054537

Lorenzo-Morales, 2007, Early diagnosis of amoebic keratitis due to a mixed infection with Acanthamoeba and Hartmannella, Parasitol Res, 102, 167, 10.1007/s00436-007-0754-x

Lueders, 2006, Identification of bacterial micropredators distinctively active in a soil microbial food web, Appl Environ Microbiol, 72, 5342, 10.1128/AEM.00400-06

Lukešová, 1996, Soil algae from acid rain impacted forest areas of the Krušné hory Mts. 1. Algal communities, Vegetatio, 125, 123, 10.1007/BF00044646

Lundberg, 2012, Defining the core Arabidopsis thaliana root microbiome, Nature, 488, 86, 10.1038/nature11237

Ly, 1990, Interactions of Listeria monocytogenes, Listeria seeligeri, and Listeria innocua with protozoans, J Gen Appl Microbiol, 36, 143, 10.2323/jgam.36.143

MacArthur, 1967, The Theory of Island Biogeography

Mahé, 2017, Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests, Nat ecol evol, 1, 91, 10.1038/s41559-017-0091

Makiuchi, 2014, Highly divergent mitochondrion-related organelles in anaerobic parasitic protozoa, Biochimie, 100, 3, 10.1016/j.biochi.2013.11.018

Marcos, 2013, Intestinal protozoan infections in the immunocompromised host, Curr Opin Infect Dis, 26, 295, 10.1097/QCO.0b013e3283630be3

Martiny, 2006, Microbial biogeography: putting microorganisms on the map, Nat Rev Micro, 4, 102, 10.1038/nrmicro1341

Martiny, 2015, Microbiomes in light of traits: a phylogenetic perspective, Science, 350, aac9323, 10.1126/science.aac9323

Matz, 2005, Off the hook – how bacteria survive protozoan grazing, Trends Microbiol, 13, 302, 10.1016/j.tim.2005.05.009

Mazur, 1995, The duration of the cyst stage and the viability and virulence of Acanthamoeba isolates, Trop Med Parasitol, 46, 106

Mazzola, 2009, Protozoan-induced regulation of cyclic lipopeptide biosynthesis is an effective predation defense mechanism for Pseudomonas fluorescens, Appl Environ Microbiol, 75, 6804, 10.1128/AEM.01272-09

McCain, 2010, Elevational gradients in species richness, Encyclopedia of Life Sciences, 1, 10.1002/9780470015902.a0022548

McGeogh, 1998, The selection, testing and application of terrestrial insects as bioindicators, Biol Rev, 73, 181, 10.1017/S000632319700515X

Meisterfeld, 2002, Order Arcellinida Kent, 1880, The Illustrated Guide to the Protozoa, 827

Meisterfeld, 2002, Testate amoebae with filopodia, The Illustrated Guide to the Protozoa, 827

Meisterfeld, 2001, Morphological and Molecular characterization of a new terrestrial allogromiid species: gen. et spec. nov. (Foraminifera) from Northern Queensland (Australia), Protist, 152, 185, 10.1078/1434-4610-00058

Mergeryan, 1991, The prevalence of acanthamoeba in the human environment, Rev Infect Dis, 13, S390, 10.1093/clind/13.Supplement_5.S390

Michel, 1995, Acanthamoeba, naturally intracellularly infected with Pseudomonas aeruginosa, after their isolation from a microbiologically contaminated drinking water system in a hospital, Zentralbl Hyg Umweltmed, 196, 532

Michel, 1997, Isolation of an Acanthamoeba strain with intracellular Burkholderia pickettii infection, Zentralblatt für Bakteriologie, 285, 541, 10.1016/S0934-8840(97)80116-8

Minetti, 2016, Giardiasis, BMJ, 355, i5369, 10.1136/bmj.i5369

Mitchell, 2007, The evolution of eukaryotic cilia and flagella as motile and sensory organelles, Adv Exp Med Biol, 607, 130, 10.1007/978-0-387-74021-8_11

Mitchell, 2004, Response of testate amoebae (Protozoa) to N and P fertilization in an Arctic wet sedge tundra, Arctic, Antarctic, and Alpine Research, 36, 78, 10.1657/1523-0430(2004)036[0078:ROTAPT]2.0.CO;2

Mitchell, 2015, Pack hunting by minute soil testate amoebae: nematode hell is a naturalist's paradise, Environ Microbiol, 17, 4145, 10.1111/1462-2920.13025

Mitchell, 2004, Testate amoebae (protista) communities in (Hedw.) B.S.G. (Bryophyta): relationships with altitude, and moss elemental chemistry, Protist, 155, 423, 10.1078/1434461042650334

Mitchell, 2008, Testate amoebae analysis in ecological and paleoecological studies of wetlands: Past, present and future, Biodivers Conserv, 17, 2115, 10.1007/s10531-007-9221-3

Mitchell, 2005, Taxonomic confusion blurs the debate on cosmopolitanism versus local endemism of free-living protists, Protist, 156, 263, 10.1016/j.protis.2005.07.001

Mitchell, 2013, The performance of single- and multi-proxy transfer functions (testate amoebae, bryophytes, vascular plants) for reconstructing mire surface wetness and pH, Quat res, 79, 6, 10.1016/j.yqres.2012.08.004

Miura, 2000, Light affects cAMP signaling and cell movement activity in Dictyostelium discoideum, Proc Natl Acad Sci, 97, 2111, 10.1073/pnas.040554497

Molmeret, 2005, Amoebae as training grounds for intracellular bacterial pathogens, Appl Environ Microbiol, 71, 20, 10.1128/AEM.71.1.20-28.2005

Moon-van der Staay, 2001, Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity, Nature, 409, 607, 10.1038/35054541

Moon, 2011, Microarray analysis of differentially expressed genes between cysts and trophozoites of Acanthamoeba castellanii, Korean J Parasitol, 49, 341, 10.3347/kjp.2011.49.4.341

Mora, 2011, How many species are there on earth and in the ocean?, PLoS Biol, e1001127

Morgan, 2010, Comparative analysis of myxococcus predation on soil bacteria, Appl Environ Microbiol, 76, 6920, 10.1128/AEM.00414-10

Moussa, 2015, Soil is the origin for the presence of Naegleria fowleri in the thermal recreational waters, Parasitol Res, 114, 311, 10.1007/s00436-014-4197-x

Mueller, 1970, Colpoda cucullus: a terrestrial aquatic, American Midland Naturalist, 84, 1, 10.2307/2423721

Müller, 2010, Tolerance of the resting cysts of Colpoda inflata (Ciliophora, Colpodea) and Meseres corlissi (Ciliophora, Spirotrichea) to desiccation and freezing, European Journal of Protistology, 46, 133, 10.1016/j.ejop.2009.12.004

Mura, 2006, Replication and long-term persistence of bovine and human strains of Mycobacterium avium subsp. paratuberculosis within Acanthamoeba polyphaga, Appl Environ Microbiol, 72, 854, 10.1128/AEM.72.1.854-859.2006

Murase, 2007, A methane-driven microbial food web in a wetland rice soil, Environ Microbiol, 9, 3025, 10.1111/j.1462-2920.2007.01414.x

Murase, 2006, Impact of protists on the activity and structure of the bacterial community in a rice field soil, Appl Environ Microbiol, 72, 5436, 10.1128/AEM.00207-06

Mylnikov, 2008, The main cell morphology of the freshwater colorless chrysomonad Spumella sp. (Ochromonadales, Chrysophyceae), Inland Water Biol, 1, 32, 10.1007/s12212-008-1006-1

Nagington, 1974, Amoebic infection of the eye, Lancet, 2, 1537, 10.1016/S0140-6736(74)90285-2

Neff, 1957, Purification, axenic cultivation, and description of a soil amoeba, Acanthamoeba sp, J Protozool, 4, 176, 10.1111/j.1550-7408.1957.tb02505.x

Neuhauser, 2010, Plasmodiophorids: the challenge to understand soil-borne, obligate biotrophs with a multiphasic life cycle, Molecular Identification of Fungi, 51, 10.1007/978-3-642-05042-8_3

Neuhauser, 2014, Cross-kingdom host shifts of phytomyxid parasites, BMC Evol Biol, 14, 33, 10.1186/1471-2148-14-33

Niederberger, 2015, Microbial communities composition of transiently wetted Antarctic Dry Valley soils, Frontiers Microbiol, 6, 9

Nikolaev, 2005, The Testate lobose amoebae (Order Arcellinida Kent, 1880) finally find their home within Amoebozoa, Protist, 156, 191, 10.1016/j.protis.2005.03.002

Nikul'shin, 1992, Associations of the soil amoeba Hartmannella rhysodes with the bacterial causative agents of plague and pseudotuberculosis in an experiment, Zh Mikrobiol Epidemiol Immunobiol, 9-10, 2

Not, 2009, New insights into the diversity of marine picoeukaryotes, PLoS One, e7143

Olive, 1980, Aerial sorocarp development by the aggregative ciliate, Sorogena stoianovitchae, 27, 293

Olson, 1999, Giardia cyst and Cryptosporidium oocyst survival in water, soil, and cattle feces, J Environ Qual, 28, 1991, 10.2134/jeq1999.00472425002800060040x

Opperman, 1989, Changes in microbial populations following the application of cattle slurry to soil at two temperatures, Soil Biol Biochem, 21, 263, 10.1016/0038-0717(89)90103-X

Opravilová, 2006, The variation of testacean assemblages (Rhizopoda) along the complete base-richness gradient in fens: A case study from the Western Carpathians, Acta Protozool, 45, 191

Özkayhan, 2006, Soil contamination with ascarid eggs in playgrounds in Kirikkale, Turkey, j helminthol, 80, 15, 10.1079/JOH2005311

Page, 1977, The genus Thecamoeba (Protozoa, Gymnamoebia) species distinctions, locomotive morphology, and protozoan prey, J Nat Hist, 11, 25, 10.1080/00222937700770031

Parfrey, 2014, Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity, Front Microbiol, 5, 298, 10.3389/fmicb.2014.00298

Parry, 2004, Protozoan grazing of freshwater biofilms, Adv Appl Microbiol, 54, 167, 10.1016/S0065-2164(04)54007-8

Pawlowski, 2013, The new micro-kingdoms of eukaryotes, BMC Biol, 11, 40, 10.1186/1741-7007-11-40

Pawlowski, 2012, CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms, PLoS Biol, 10, e1001419, 10.1371/journal.pbio.1001419

Payne, 2013, Seven reasons why protists make useful bioindicators, Acta Protozool, 52, 105

Payne, 2016, Significance testing testate amoeba water table reconstructions, Quat Sci Rev, 138, 131, 10.1016/j.quascirev.2016.01.030

Pedersen, 2010, Interaction of bacteria-feeding soil flagellates and Pseudomonas spp, Biol Fertil Soils, 46, 151, 10.1007/s00374-009-0417-4

Pedersen, 2011, Protozoan growth rates on secondary-metabolite-producing Pseudomonas spp. correlate with high-level protozoan taxonomy, FEMS Microbiol Lett, 316, 16, 10.1111/j.1574-6968.2010.02182.x

Penard, 1902, Faune Rhizopodique Du Bassin Du Leman, 10.5962/bhl.title.1711

Peñuelas, 2014, The foliar microbiome, Trends Plant Sci, 19, 278, 10.1016/j.tplants.2013.12.007

Pérez, 2016, Bacterial predation: 75 years and counting!, Environ Microbiol, 18, 766, 10.1111/1462-2920.13171

Petz, 1997, Ecology of the active soil microfauna (Protozoa, Metazoa) of Wilkes Land, East Antarctica, Polar Biology, 18, 33, 10.1007/s003000050156

Petz, 1989, The effects of mancozeb and lindane on the soil microfauna of a spruce forest: a field study using a completely randomized block design, Biol Fert Soils, 7, 225, 10.1007/BF00709653

Ploch, 2016, High diversity revealed in leaf-associated protists (Rhizaria: Cercozoa) of Brassicaceae, J Eukaryot Microbiol, 63, 635, 10.1111/jeu.12314

Porras-Alfaro, 2011, Hidden fungi, emergent properties: endophytes and microbiomes, Annu Rev Phytopathol, 49, 291, 10.1146/annurev-phyto-080508-081831

Preisig, 1982, Ultrastructure and taxonomy of Paraphysomonas (Chrysophyceae) and related genera 1, Nord J Bot, 2, 397

Prosser, 2015, Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology, Nat Rev Micro, 13, 439, 10.1038/nrmicro3468

Pruesse, 2007, SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res, 35, 7188, 10.1093/nar/gkm864

Puppe, 2014, Dynamics and drivers of the protozoic Si pool along a 10-year chronosequence of initial ecosystem states, Ecol Eng, 70, 477, 10.1016/j.ecoleng.2014.06.011

Qian, 2013, Latitudinal gradients in phylogenetic relatedness of angiosperm trees in North America, Global Ecol Biogeogr, 22, 1183, 10.1111/geb.12069

Qvarnstrom, 2009, Molecular confirmation of Sappinia pedata as a causative agent of amoebic encephalitis, J Infect Dis, 199, 1139, 10.1086/597473

Rasmussen, 2001, Group-specific PCR primers to amplify 24S alpha-subunit rRNA genes from Kinetoplastida (Protozoa) used in denaturing gradient gel electrophoresis, Microb Ecol, 42, 109, 10.1007/s002480000120

Reyes-Batlle, 2016, Isolation and molecular identification of Vermamoeba vermiformis strains from soil sources in El Hierro Island, Canary Islands, Spain, Curr Microbiol, 73, 104, 10.1007/s00284-016-1035-7

Rivadeneira, 2011, An inverse latitudinal gradient of diversity of peracarid crustaceans along the Pacific Coast of South America: out of the deep south, Glob Ecol Biogeogr, 20, 437, 10.1111/j.1466-8238.2010.00610.x

Robson, 2005, Solar UV-B influences microfaunal community composition in a Tierra del Fuego peatland, Soil Biol Biochem, 37, 2205, 10.1016/j.soilbio.2005.04.002

Rodriguez-Zaragoza, 1997, Species richness and abundance of naked amebae in the rhizoplane of the desert plant Escontria chiotilla (Cactaceae), J Eukaryotic Microbiology, 44, 122, 10.1111/j.1550-7408.1997.tb05948.x

Rodriguez-Zaragoza, 2005, vertical distribution of the free-living amoeba population in soil under desert shrubs in the Negev Desert, Israel, Appl Environ Microbiol, 71, 2053, 10.1128/AEM.71.4.2053-2060.2005

Rodriguez, 2009, Fungal endophytes: diversity and functional roles, New Phytol, 182, 314, 10.1111/j.1469-8137.2009.02773.x

Rojas, 2016, Bacterial and eukaryal diversity in soils forming from acid mine drainage precipitates under reclaimed vegetation and biological crusts, Applied Soil Ecology, 105, 57, 10.1016/j.apsoil.2016.03.012

Rojas, 2017, Oomycete species associated with soybean seedlings in North America—Part II: diversity and ecology in relation to environmental and edaphic factors, Phytopathology, 107, 293, 10.1094/PHYTO-04-16-0176-R

Ros Die, 2017, Isospora belli, Clinical Microbiology and Infection, 24, 43, 10.1016/j.cmi.2017.07.009

Rosenberg, 2009, Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana, ISME J, 3, 675, 10.1038/ismej.2009.11

Rowbotham, 1980, Preliminary report on the pathogenicity of Legionella pneumophila for freshwater and soil amoebae, J Clin Pathol, 33, 1179, 10.1136/jcp.33.12.1179

Ruggiero, 2015, A higher level classification of all living organisms, PLoS One, e0119248

de Ruiter, 1995, Energetics, patterns of interaction strengths, and stability in real ecosystems, Science, 269, 1257, 10.1126/science.269.5228.1257

Šabacká, 2006, Response of cyanobacteria and algae from Antarctic wetland habitats to freezing and desiccation stress, Polar Biol, 30, 31, 10.1007/s00300-006-0156-z

Saleem, 2012, Predator richness increases the effect of prey diversity on prey yield, Nat Commun, 3, 1305, 10.1038/ncomms2287

Saleem, 2013, Diversity of protists and bacteria determines predation performance and stability, ISME J, 7, 1912, 10.1038/ismej.2013.95

Samuelson, 2011, A simple fibril and lectin model for cyst walls of Entamoeba and perhaps Giardia, Trends Parasitol, 27, 17, 10.1016/j.pt.2010.09.002

Sanders, 2012, The patterns and causes of elevational diversity gradients, Ecography, 35, 1, 10.1111/j.1600-0587.2011.07338.x

Santamaría, 2003, Enteric pathogens and soil: a short review, Int Microbiol, 6, 5, 10.1007/s10123-003-0096-1

Sauvant, 1999, Tetrahymena pyriformis: a tool for toxicological studies. A review, Chemosphere, 38, 1631, 10.1016/S0045-6535(98)00381-6

Savory, 2015, The role of horizontal gene transfer in the evolution of the oomycetes, PLOS Pathog, e1004805

Scanlan, 2014, The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota, FEMS Microbiol Ecol, 90, 326, 10.1111/1574-6941.12396

Scherber, 2010, Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment, Nature, 468, 553, 10.1038/nature09492

Schleuning, 2015, Predicting ecosystem functions from biodiversity and mutualistic networks: an extension of trait-based concepts to plant-animal interactions, Ecography, 38, 380, 10.1111/ecog.00983

Schmidt, 2016, Photoautotrophic microorganisms as a carbon source for temperate soil invertebrates, Biol Lett, 12, 20150646, 10.1098/rsbl.2015.0646

Schoch, 2012, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi, Proc Natl Acad Sci, 109, 6241, 10.1073/pnas.1117018109

Schroeder, 2013, Molecular detection and quantification of pythium species: evolving taxonomy, new tools, and challenges, Plant Disease, 97, 4, 10.1094/PDIS-03-12-0243-FE

Schulz-Bohm, 2017, The prey's scent – volatile organic compound mediated interactions between soil bacteria and their protist predators, ISME J, 11, 817, 10.1038/ismej.2016.144

Schulze-Lefert, 2011, A molecular evolutionary concept connecting nonhost resistance, pathogen host range, and pathogen speciation, Trends Plant Sci, 16, 117, 10.1016/j.tplants.2011.01.001

Schuster, 2008, Current world status of Balantidium coli, Clin Microbiol Rev, 21, 626, 10.1128/CMR.00021-08

Schuster, 2004, Free-living amoebae as opportunistic and non-opportunistic pathogens of humans and animals, Int J Parasitol, 34, 1001, 10.1016/j.ijpara.2004.06.004

Schuster, 2004, Amebae and ciliated protozoa as causal agents of waterborne zoonotic disease, Vet Parasitol, 126, 91, 10.1016/j.vetpar.2004.09.019

Schwarz, 2003, Population dynamics and ecology of ciliates (Protozoa, Ciliophora) in an anoxic rice field soil, Biol Fertil Soils, 38, 245, 10.1007/s00374-003-0644-z

La Scola, 2005, Mimivirus in pneumonia patients, Emerg Infect Dis, 11, 449, 10.3201/eid1103.040538

La Scola, 2001, Survival of Coxiella burnetii within free-living amoeba Acanthamoeba castellanii, Clin Microbiol Infect, 7, 75, 10.1046/j.1469-0691.2001.00193.x

Seppey, 2013, Euglyphid communities under a pig (Sus scrofa) cadaver assessed by high-throughput sequencing: A new post mortem interval bioindicator?

Seppey, 2016, Response of forest soil euglyphid testate amoebae (Rhizaria: Cercozoa) to pig cadavers assessed by high-throughput sequencing, Int J Legal Med, 130, 551, 10.1007/s00414-015-1149-7

Seppey, 2017, Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling, Soil Biol Biochem, 112, 68, 10.1016/j.soilbio.2017.05.002

Serna-Chavez, 2013, Global drivers and patterns of microbial abundance in soil, Global Ecol Biogeogr, 22, 1162, 10.1111/geb.12070

Shadwick, 2009, Eumycetozoa = Amoebozoa?: SSUrDNA Phylogeny of protosteloid slime molds and its significance for the Amoebozoan supergroup, PLoS One, e6754

Shen, 2014, Contrasting elevational diversity patterns between eukaryotic soil microbes and plants, Ecology, 95, 3190, 10.1890/14-0310.1

Sherr, 1983, Grazing, growth, and ammonium excretion rates of a heterotrophic microflagellate fed with four species of bacteria, Appl Environ Microbiol, 45, 1196, 10.1128/AEM.45.4.1196-1201.1983

Shields, 1964, Algae in relation to soil fertility, Bot Rev, 30, 92, 10.1007/BF02858614

Shmakova, 2015, Viable eukaryotes of the phylum Amoebozoa from the Arctic permafrost, Paleontol J, 49, 572, 10.1134/S003103011506012X

Shmakova, 2016, Viable species of Flamella (Amoebozoa: Variosea) isolated from ancient Arctic permafrost sediments, Protist, 167, 13, 10.1016/j.protis.2015.11.001

da Silva, 2016, Spatial distribution and enteroparasite contamination in peridomiciliar soil and water in the Apucaraninha Indigenous Land, southern Brazil, Environ Monit Assess, 188, 217, 10.1007/s10661-016-5216-4

Singer, 2016, High-throughput sequencing reveals diverse oomycete communities in oligotrophic peat bog micro-habitat, Fungal Ecology, 23, 42, 10.1016/j.funeco.2016.05.009

Singh, 1941, Selectivity in bacterial food by soil amoebae in pure and mixed culture in sterilized soil, Ann Applied Biology, 28, 52, 10.1111/j.1744-7348.1941.tb07536.x

Singh, 1942, Selection of bacterial food by soil flagellates and amoebae, Ann Applied Biology, 29, 18, 10.1111/j.1744-7348.1942.tb06917.x

Smirnov, 2004, Guide to the methods of study and identification of soil gymnamoebae, Protistology, 3, 148

Smirnov, 2011, A revised classification of naked lobose amoebae (Amoebozoa: Lobosa), Protist, 162, 545, 10.1016/j.protis.2011.04.004

Smith, 1985, The colonization of volcanic tephra on Deception Island by protozoa - long-term trends, Br Antarct Surv Bull, 66, 19

Smith, 2007, Not all free-living microorganisms have cosmopolitan distributions? the case of Apodera (Nebela) vas Certes (Protozoa: Amoebozoa: Arcellinida), J Biogeography, 34, 1822, 10.1111/j.1365-2699.2007.01733.x

Smith, 2011, Roles of arbuscular mycorrhizas in plant nutrition and growth: new paradigms from cellular to ecosystem scales, Annu Rev Plant Biol, 62, 227, 10.1146/annurev-arplant-042110-103846

Snow, 2005, The global distribution of clinical episodes of Plasmodium falciparum malaria, Nature, 434, 214, 10.1038/nature03342

Sommer, 2013, Si cycling in a forest biogeosystem - the importance of transient state biogenic Si pools, Biogeosciences, 10, 4991, 10.5194/bg-10-4991-2013

Song, 2015, Molecular and chemical dialogues in bacteria-protozoa interactions, Sci Rep, 5, 12837, 10.1038/srep12837

Spiegel, 2017, Protosteloid Amoebozoa (Protosteliids, Protosporangiida, Cavostellida, Schizoplasmodiida, Fractoviteliida, and sporcarpic members of Vanellida, Centramoebida, and Pellitida), Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al

Spiegel, 2016, Unikonts, evolution and diversification of (with emphasis on fungal-like forms), Encyclopedia of Evolutionary Biology, Vol 4., 325, 10.1016/B978-0-12-800049-6.00248-1

Spiegel, 2004, Biodiversity of fungi: inventory and monitoring methods, Biodiversity of Fungi, Inventory and Monitoring Methods, 547, 10.1016/B978-012509551-8/50028-3

Stapleton, 2005, Microbial carbon dynamics in nitrogen amended Arctic tundra soil: measurement and model testing, Soil Biol Biochem, 37, 2088, 10.1016/j.soilbio.2005.03.016

Steinert, 1998, Mycobacterium avium bacilli grow saprozoically in coculture with Acanthamoeba polyphaga and survive within cyst walls, Appl Environ Microbiol, 64, 2256, 10.1128/AEM.64.6.2256-2261.1998

Stensvold, 2016, Current status of Blastocystis: a personal view, Parasitol Int, 65, 763, 10.1016/j.parint.2016.05.015

Suttle, 2007, Marine viruses — major players in the global ecosystem, Nat Rev Micro, 5, 801, 10.1038/nrmicro1750

Sutton, 2007, The effects of Rhododendron on testate amoebae communities in woodland soils in North West England, Acta Protozool, 46, 333

Swindles, 2009, A preliminary investigation into the use of testate amoebae for the discrimination of forensic soil samples, Science & Justice, 49, 182, 10.1016/j.scijus.2008.11.002

Szelecz, 2014, Can soil testate amoebae be used for estimating the time since death? A field experiment in a deciduous forest, Forensic Sci Int, 236, 90, 10.1016/j.forsciint.2013.12.030

Tansey, 1972, The upper temperature limit for eukaryotic organisms, Proc Natl Acad Sci, 69, 2426, 10.1073/pnas.69.9.2426

Taylor, 2003, Infection of Acanthamoeba castellanii with Mycobacterium bovis and M. bovis BCG and survival of M. bovis within the amoebae, Appl Environ Microbiol, 69, 4316, 10.1128/AEM.69.7.4316-4319.2003

Tedersoo, 2016, Tree diversity and species identity effects on soil fungi, protists and animals are context dependent, ISME J, 10, 346, 10.1038/ismej.2015.116

Thom, 1992, Association of Vibrio cholerae with fresh water amoebae, J Med Microbiol, 36, 303, 10.1099/00222615-36-5-303

Thomas, 1995, A stable Eimerian assemblage in Wyoming ground squirrels (Spermophilus elegans elegans): maintaining viability over winter, J Helminthol Soc Washingt, 62, 1

Tice, 2016, Sorodiplophrys stercorea: another novel lineage of sorocarpic multicellularity, J Eukaryot Microbiol, 63, 623, 10.1111/jeu.12311

Tiunov, 2015, Stable isotope composition (δ13C and δ15N values) of slime molds: placing bacterivorous soil protozoans in the food web context, Rapid Commun Mass Spectrom, 29, 1465, 10.1002/rcm.7238

Tiyo, 2008, Seasonal contamination of public squares and lawns by parasites with zoonotic potential in southern Brazil, JHL, 82, 1, 10.1017/S0022149X07870829

Todorov, 1998, Observation on the soil and moss testate amoebae (Protozoa: Rhizopoda) from Pirin Mountain (Bulgaria), Acta Zool Bulg, 50, 19

Torgerson, 2015, World Health Organization estimates of the global and regional disease burden of 11 foodborne parasitic diseases, 2010: a data synthesis, PLoS Med, 12, e1001920, 10.1371/journal.pmed.1001920

Torres-Machorro, 2010, Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny?, FEMS Microbiol Rev, 34, 59, 10.1111/j.1574-6976.2009.00196.x

Trap, 2016, Ecological importance of soil bacterivores for ecosystem functions, Plant Soil, 398, 1, 10.1007/s11104-015-2671-6

Tsvetkova, 2004, The identification of free-living environmental isolates of amoebae from Bulgaria, Parasitol Res, 92, 405, 10.1007/s00436-003-1052-x

Tsyganov, 2013, Flourish or flush: effects of simulated extreme rainfall events on Sphagnum-dwelling testate amoebae in a subarctic bog (Abisko, Sweden), Microb Ecol, 65, 101, 10.1007/s00248-012-0115-x

Tsyganov, 2013, Environmental factors influencing soil testate amoebae in herbaceous and shrubby vegetation along an altitudinal gradient in subarctic tundra (Abisko, Sweden), European Journal of Protistology, 49, 238, 10.1016/j.ejop.2012.08.004

de Vargas, 2015, Eukaryotic plankton diversity in the sunlit ocean, Science, 348, 1261605, 10.1126/science.1261605

Veresoglou, 2012, Arbuscular mycorrhiza and soil nitrogen cycling, Soil Biol Biochem, 46, 53, 10.1016/j.soilbio.2011.11.018

Vestergård, 2007, Decreasing prevalence of rhizosphere IAA producing and seedling root growth promoting bacteria with barley development irrespective of protozoan grazing regime, Plant Soil, 295, 115, 10.1007/s11104-007-9267-8

Villani, 2008, Evaluation of the possible role of ants (Hymenoptera: Formicidae) as mechanical vectors of nematodes and protists, Braz arch biol technol, 51, 923, 10.1590/S1516-89132008000500008

Vincke, 2007, Testacean communities in perturbed soils: the influence of the wandering albatross, Polar Biol, 30, 395, 10.1007/s00300-006-0196-4

Visvesvara, 2007, Pathogenic and opportunistic free-living amoebae: Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri, and Sappinia diploidea, FEMS Immunol Med Microbiol, 50, 1, 10.1111/j.1574-695X.2007.00232.x

Visvesvara, 1993, Balamuthia mandrillaris, N. G., N. Sp., agent of amebic meningoencephalitis in humans and other animals, J Eukaryotic Microbiology, 40, 504, 10.1111/j.1550-7408.1993.tb04943.x

Vohník, 2012, Testate amoebae communities in the rhizosphere of Rhododendron ponticum (Ericaceae) in an evergreen broadleaf forest in southern Spain, Acta Protozool, 51, 259

Vorholt, 2012, Microbial life in the phyllosphere, Nat Rev Micro, 10, 828, 10.1038/nrmicro2910

Wallace, 1876, Geographical Distribution of Animals

Walochnik, 2012, Protozoan Pathogens: Identification

Wanner, 2001, Biological activity of soils from reclaimed open-cast coal mining areas in Upper Lusatia using testate amoebae (protists) as indicators, Ecol Eng, 17, 323, 10.1016/S0925-8574(00)00148-8

Ward, 2016, Marine mixotrophy increases trophic transfer efficiency, mean organism size, and vertical carbon flux, Proc Natl Acad Sci USA, 113, 2958, 10.1073/pnas.1517118113

Wiens, 2004, Historical biogeography, ecology and species richness, Trends in Ecology & Evolution, 19, 639, 10.1016/j.tree.2004.09.011

Wilkinson, 2008, Testate amoebae and nutrient cycling: peering into the black box of soil ecology, Trends in Ecology & Evolution, 23, 596, 10.1016/j.tree.2008.07.006

Wilkinson, 2010, Have we underestimated the importance of humans in the biogeography of free-living terrestrial microorganisms?, J Biogeogr, 37, 393, 10.1111/j.1365-2699.2009.02236.x

Wilkinson, 2012, Modelling the effect of size on the aerial dispersal of microorganisms, J Biogeogr, 39, 89, 10.1111/j.1365-2699.2011.02569.x

Wilkinson, 2010, Testate amoebae and nutrient cycling with particular reference to soils, Geomicrobiol J, 27, 520, 10.1080/01490451003702925

Winiecka-Krusnell, 2002, Free-living amoebae promote growth and survival of Helicobacter pylori, Scand J Infect Dis, 34, 253, 10.1080/00365540110080052

Wintzingerode F, 1997, Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis, FEMS Microbiol Rev, 21, 213, 10.1111/j.1574-6976.1997.tb00351.x

Wuthrich, 1980, Les diatomées de la Tourbière du Cachot (Jura neuchâtelois) - III. Etude de l’apport éolien et du transport par les oiseaux et insectes aquatiques, Schweizerische Zeitschrift für Hydrol, 42, 269

Xiong, 2017, Soil protist communities form a dynamic hub in the soil microbiome, ISME J

Yang, 2006, Geographical distribution of testate amoebae in Tibet and northwestern Yunnan and their relationships with climate, Hydrobiologia, 559, 297, 10.1007/s10750-005-9400-8

Yang, 2013, Geographical sampling bias in a large distributional database and its effects on species richness-environment models, J Biogeogr, 40, 1415, 10.1111/jbi.12108

Yeates, 1995, Testate amoebae as predators of nematodes, Biol Fert Soils, 20, 1, 10.1007/BF00307834

Yeoh, 2017, Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence, Nat Commun, 8, 215, 10.1038/s41467-017-00262-8

Zancan, 2006, Soil algae composition under different agro-ecosystems in North-Eastern Italy, Agriculture, Ecosystems & Environment, 112, 1, 10.1016/j.agee.2005.06.018

Zuccaro, 2014, Broad compatibility in fungal root symbioses, Curr Opin Plant Biol, 20, 135, 10.1016/j.pbi.2014.05.013

Zuck, 1953, Alternation of Generations and the Mode of Nutrition, 41