DOI: 10.5281/zenodo.13320567
title: Microbe Ecomorphological Guilds

description: Ecomorphological guild data for microbial organisms compiled from the following sources:

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Adl, S.M., Bass, D., Lane, C.E., Lukeš, J., Schoch, C.L., Smirnov, A., Agatha, S., Berney, C., Brown, M.W., Burki, F., Cárdenas, P., Čepička, I., Chistyakova, L., Campo, J. del, Dunthorn, M., Edvardsen, B., Eglit, Y., Guillou, L., Hampl, V., Heiss, A.A., Hoppenrath, M., James, T.Y., Karnkowska, A., Karpov, S., Kim, E., Kolisko, M., Kudryavtsev, A., Lahr, D.J.G., Lara, E., Gall, L.L., Lynn, D.H., Mann, D.G., Massana, R., Mitchell, E.A.D., Morrow, C., Park, J.S., Pawlowski, J.W., Powell, M.J., Richter, D.J., Rueckert, S., Shadwick, L., Shimano, S., Spiegel, F.W., Torruella, G., Youssef, N., Zlatogursky, V., Zhang, Q., 2019. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. https://doi.org/10.1111/jeu.12691

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Baumgartner, M., Eberhardt, S., De Jonckheere, J. F., & Stetter, K. O. (2009). Tetramitus thermacidophilus n. sp., an amoeboflagellate from acidic hot springs. Journal of Eukaryotic Microbiology 56:201–206. https://doi.org/10.1111/j.1550-7408.2009.00390.x

Bell, E.M. and Laybourn‐Parry, J., 2003. Mixotrophy in the antarctic phytoflagellate Pyramimonas gelidicola (Chlorophyta: Prasinophyceae). Journal of Phycology, 39(4), pp.644-649. https://doi.org/10.1046/j.1529-8817.2003.02152.x

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Bishop, A. (1935). Observations upon a “Trichomonas” from pond water. Parasitology 27:246–256. https://doi.org/10.1017/S0031182000015110

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Bovee, E.C. and Sawyer, T.K., 1979. Marine Flora and Fauna of the Northeastern United States: Protozoa, Sarcodina, Amoebae (Vol. 419). Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service.

Bovee, E.C., 1953. Oscillosignum nov. gen. proboscidium nov. sp., type form of its genus, family Mayorellidae, order Amoebida. Transactions of the American Microscopical Society, 72(4):328-332. https://doi.org/10.2307/3223477

Bovee, E.C., 1985. The lobose amebas: III. Descriptions of nine new conopodous amebas of the genus Vexillifera Schaeffek, 1926, emd. Bovee 1951, 1970, with comments on the genus. Archiv für Protistenkunde, 129(1-4):101-118. https://doi.org/10.1016/S0003-9365(85)80013-0

Brown, M.W., Silberman, J.D. (2013). The Non-dictyostelid Sorocarpic Amoebae. In: Romeralo, M., Baldauf, S., Escalante, R. (eds) Dictyostelids. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38487-5_12

Brown, M.W., Silberman, J.D., Spiegel, F.W., 2012. A contemporary evaluation of the acrasids (Acrasidae, Heterolobosea, Excavata). Eur J Protistol 48, 103–123. https://doi.org/10.1016/j.ejop.2011.10.001

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Burki, F., Roger, A.J., Brown, M.W., Simpson, A.G.B., 2020. The New Tree of Eukaryotes. Trends in Ecology & Evolution 35, 43–55. https://doi.org/10.1016/j.tree.2019.08.008

Bursa, A.S., 1970. Din Amoebidwm Coloradense Spec. Nov. and Katodinium Auratum Spec. Nov. in Como Creek, Boulder County, Colorado. Arctic and Alpine Research, 2(2), pp.145-151. https://doi.org/10.2307/1550349

Cavalier-Smith, T., Chao, E.E., Lewis, R., 2015. Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. Molecular Phylogenetics and Evolution 93, 331–362. https://doi.org/10.1016/j.ympev.2015.07.004

Cavalier-Smith, T., Chao, E.E., Lewis, R., 2016. 187-gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution. Molecular Phylogenetics and Evolution 99, 275–296. https://doi.org/10.1016/j.ympev.2016.03.023

Cavalier-Smith, T., Chao, E.E., Lewis, R., 2018. Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria. Protoplasma 255, 1517–1574. https://doi.org/10.1007/s00709-018-1241-1

Čepička I., Dolan M.F., Gile G.H. (2016) Parabasalia. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_9-1

Cepicka, I., Hampl, V., Kulda, J., 2010. Critical Taxonomic Revision of Parabasalids with Description of one New Genus and three New Species. Protist 161:400–433. https://doi.org/10.1016/j.protis.2009.11.005

Chardez D., Beyens L. (1988). Centropyxis gasparella sp.nov. and Parmulina louisi sp.nov., new testate amoebae from the Canadian High Arctic (Devon Island, NWT). Arch. Protistenkd. 136:337–344. https://doi.org/10.1016/S0003-9365(88)80014-9

Clarke, A., 2014. The thermal limits to life on Earth. International Journal of Astrobiology 13, 141–154. https://doi.org/10.1017/S147355041300043

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D’Amico, S., Collins, T., Marx, J.-C., Feller, G., Gerday, C., 2006. Psychrophilic microorganisms: challenges for life. EMBO Rep 7, 385–389. https://doi.org/10.1038/sj.embor.7400662

Dick, M.W., 2013. Straminipilous Fungi: systematics of the Peronosporomycetes including accounts of the marine straminipilous protists, the plasmodiophorids and similar organisms. Springer Science & Business Media.

Domozych, D., Popper, Z., Sorensen, I., 2016. Charophytes: Evolutionary Giants and Emerging Model Organisms. Frontiers in Plant Science 7:1470. https://doi.org/10.3389/fpls.2016.01470

Dyková, I., Kostka, M. and Pecková, H., 2010. Grellamoeba robusta gen. n., sp. n., a possible member of the family Acramoebidae Smirnov, Nassonova et Cavalier-Smith, 2008. European Journal of Protistology, 46(2), pp.77-85. https://doi.org/10.1016/j.ejop.2009.10.004

Farmer, M. A. (1993). Ultrastructure of Ditrichomonas honigbergii n. g., n. sp. (Parabasalia) and its relationships to amitochondrial protists. The Journal of Eukaryotic Microbiology 40:619–626. https://doi.org/10.1111/j.1550-7408.1993.tb06119.x

Febvre-Chevalier, C. & Febvre, J. 1984. Axonemal microtubule pattern of Cienkowskya mereschkovskyi and a revision of heliozoan taxonomy. Origins of Life 13:315–338. https://doi.org/10.1007/BF00927180

Figueroa‐Martinez, F., Nedelcu, A.M., Smith, D.R., Reyes‐Prieto, A., 2015. When the lights go out: the evolutionary fate of free‐living colorless green algae. New Phytol 206, 972–982. https://doi.org/10.1111/nph.13279

Frankovich, T.A., Ashworth, M.P., Sullivan, M.J., Theriot, E.C., Stacy, N.I., 2018. Epizoic and Apochlorotic Tursiocola species (Bacillariophyta) from the Skin of Florida Manatees (Trichechus manatus latirostris). Protist 169, 539–568. https://doi.org/10.1016/j.protis.2018.04.002

Galindo, L.J., Torruella, G., Moreira, D., Eglit, Y., Simpson, A.G., Völcker, E., Clauß, S. and López-García, P., 2019. Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi. Philosophical Transactions of the Royal Society B, 374(1786), p.20190094. https://doi.org/10.1098/rstb.2019.0094

Gao, F., Warren, A., Zhang, Q., Gong, J., Miao, M., Sun, P., Xu, D., Huang, J., Yi, Z., Song, W., 2016. The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata). Scientific Reports 6:24874. https://doi.org/10.1038/srep24874

Garstecki, T., Brown, S., & De Jonckheere, J. F. (2005). Description of Vahlkampfia signyensis n. sp. (Heterolobosea), based on morphological, ultrastructural and molecular characteristics. European Journal of Protistology 41:119–127. https://doi.org/10.1016/j.ejop.2005.01.003

Gast, R.J., 2017. Centrohelida and Other Heliozoan-Like Protists, in: Archibald, J.M., Simpson, A.G.B., Slamovits, C.H., Margulis, L., Melkonian, M., Chapman, D.J., Corliss, J.O. (Eds.), Handbook of the Protists. Springer International Publishing, Cham, pp. 1–17. https://doi.org/10.1007/978-3-319-32669-6_28-1

Geisen, S., Bonkowski, M., Zhang, J. and De Jonckheere, J.F., 2015. Heterogeneity in the genus Allovahlkampfia and the description of the new genus Parafumarolamoeba (Vahlkampfiidae; Heterolobosea). European Journal of Protistology, 51(4), pp.335-349. https://doi.org/10.1016/j.ejop.2015.05.003

Gibson W. (2016) Kinetoplastea. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_7-1

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Gómez, F., Artigas, L.F. and Gast, R.J., 2019. Molecular phylogeny of the parasitic dinoflagellate Syltodinium listii (Gymnodiniales, Dinophyceae) and generic transfer of Syltodinium undulans comb. nov.(= Gyrodinium undulans). European Journal of Protistology, 71, p.125636. https://doi.org/10.1016/j.ejop.2019.125636

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Harding, T., Brown, M., Plotnikov, A., Selivanova, E., Park, J.S., Gunderson, J., Baumgartner, M., Silberman, J., Roger, A., Simpson, A., 2012. Amoeba Stages in the Deepest Branching Heteroloboseans, Including Pharyngomonas: Evolutionary and Systematic Implications. Protist 164(2):272-286. https://doi.org/10.1016/j.protis.2012.08.002

Hehenberger, E., Tikhonenkov, D.V., Kolisko, M., Del Campo, J., Esaulov, A.S., Mylnikov, A.P. and Keeling, P.J., 2017. Novel predators reshape holozoan phylogeny and reveal the presence of a two-component signaling system in the ancestor of animals. Current Biology, 27(13), pp.2043-2050. https://doi.org/10.1016/j.cub.2017.06.006

Heiss, A.A., Brown, M.W., Simpson, A.G.B., 2016. Apusomonadida, in: Archibald, J.M., Simpson, A.G.B., Slamovits, C.H., Margulis, L., Melkonian, M., Chapman, D.J., Corliss, J.O. (Eds.), Handbook of the Protists. Springer International Publishing, Cham, pp. 1–27. https://doi.org/10.1007/978-3-319-32669-6_15-1

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Hess, S. & Melkonian, M. 2013. The mystery of clade X: Orciraptor gen. nov. and Viridiraptor gen. nov. are highly specialised, algivorous amoeboflagellates (Glissomonadida, Cercozoa). Protist, 164:706-747. https://doi.org/10.1016/j.protis.2013.07.003

Hoef-Emden, K., Archibald, J.M., 2016. Cryptophyta (Cryptomonads), in: Archibald, J.M., Simpson, A.G.B., Slamovits, C.H., Margulis, L., Melkonian, M., Chapman, D.J., Corliss, J.O. (Eds.), Handbook of the Protists. Springer International Publishing, Cham, pp. 1–41. https://doi.org/10.1007/978-3-319-32669-6_35-1

Howe, A.T., Bass, D., Scoble, J.M., Lewis, R., Vickerman, K., Arndt, H., Cavalier-Smith, T., 2011. Novel Cultured Protists Identify Deep-branching Environmental DNA Clades of Cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia. Protist 162, 332–372. https://doi.org/10.1016/j.protis.2010.10.002

Ichinomiya, M., dos Santos, A.L., Gourvil, P., Yoshikawa, S., Kamiya, M., Ohki, K., Audic, S., de Vargas, C., Noël, M.-H., Vaulot, D., Kuwata, A., 2016. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J 10, 2419–2434. https://doi.org/10.1038/ismej.2016.38

Jain, S.K., Khan, A.A., Rai, M.K. (Eds.), 2016. Deep-sea Piezophilic Bacteria: Geomicrobiology and Biotechnology, in: Geomicrobiology. CRC Press, pp. 59–66. https://doi.org/10.1201/b10193-4

Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.\ https://doi.org/10.1101/2022.04.05.487141

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Keeling, P.J., 2016. Chlorarachniophytes, in: Archibald, J.M., Simpson, A.G.B., Slamovits, C.H., Margulis, L., Melkonian, M., Chapman, D.J., Corliss, J.O. (Eds.), Handbook of the Protists. Springer International Publishing, Cham, pp. 1–17. https://doi.org/10.1007/978-3-319-32669-6_34-1

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Kulda J., Nohýnková E., Čepička I. (2016) Retortamonadida (with Notes on Carpediemonas-Like Organisms and Caviomonadidae). In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_3-1

Leander B.S., Lax G., Karnkowska A., Simpson A.G.B. (2017) Euglenida. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_13-1

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