Trophic guild data for microbial eukaryotes

Data on trophic guilds of microbial eukaryotes derived from the following sources:

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

Aleoshin, V.V., Mylnikov, A.P., Mirzaeva, G.S., Mikhailov, K.V. and Karpov, S.A., 2016. Heterokont Predator Develorapax marinus gen. et sp. nov.–A Model of the Ochrophyte Ancestor. Frontiers in microbiology, 7, p.1194. https://doi.org/10.3389/fmicb.2016.01194

Ann PJ, Huang JH, Wang IT, Ko WH, 2006. Pythiogeton zizaniae, a new species causing basal stalk rot of water bamboo in Taiwan. Mycologia 98: 116e120. https://doi.org/10.1080/15572536.2006.11832717

Azevedo C., Hine P.M. (2016) Haplosporidia. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_16-1

Baldauf S.L., Strassmann J.E. (2017) Dictyostelia. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_14-1

Beakes G.W., Thines M. (2016) Hyphochytriomycota and Oomycota. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_26-1

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

Bennett R.M., Honda D., Beakes G.W., Thines M. (2017) Labyrinthulomycota. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_25-1

Bernard, Catherine, Alastair G. B. Simpson & David J. Patterson (2000) Some free-living flagellates (protista) from anoxic habitats Ophelia 52(2):113-142. https://doi.org/10.1080/00785236.1999.10409422

Bigelow, D. M., Olsen, M. W., & Gilbertson, R. L. (2005). Labyrinthula terrestris sp. nov., a new pathogen of turf grass. Mycologia 97:185–190. https://doi.org/10.1080/15572536.2006.11832852

Boltovskoy D., Anderson O.R., Correa N.M. (2017) Radiolaria and Phaeodaria. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_19-2

Bourland, W. A. & Struder-Kypke, M. C. 2010. Agolohymena aspidocauda nov. gen., nov. spec., a histophagous freshwater tetrahymenid ciliate in the family Deltopylidae (Ciliophora, Hymenostomatia), from Idaho (northwest USA): morphology, ontogenesis and molecular phylogeny. Eur. J. Protistol. 46:221–242. https://doi.org/10.1016/j.ejop.2010.04.003

Bower, S. M., McLean, N., & Whitaker, D. J. (1989). Mechanism of infection by Labyrinthuloides haliotidis (Protozoa, Labyrinthomorpha), a parasite of abalone (Haliotis kamtschatka) (Mollusca, Gastropoda). Journal of Invertebrate Pathology, 53, 401–409.

Buaya, A. T., Ploch, S., Inaba, S., & Thines, M. (2019). Holocarpic oomycete parasitoids of red algae are not Olpidiopsis. Fungal systematics and evolution 4:21–31. https://doi.org/10.3114/fuse.2019.04.03

Bulman S., Neuhauser S. (2016) Phytomyxea. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_24-1

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

Carr, M., Leadbeater, B. S., Hassan, R., Nelson, M., & Baldauf, S. L. (2008). Molecular phylogeny of choanoflagellates, the sister group to Metazoa. Proceedings of the National Academy of Sciences of the United States of America, 105(43):16641–16646. https://doi.org/10.1073/pnas.0801667105

Cavalier-Smith, T., & Chao, E. E. (2004). Protalveolate phylogeny and systematics and the origins of Sporozoa and dinoflagellates (phylum Myzozoa nom. nov.). European Journal of Protistology 40(3):185-212. https://doi.org/10.1016/j.ejop.2004.01.002

Cavalier-Smith, T., 2018. Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. Protoplasma 255, 297–357. https://doi.org/10.1007/s00709-017-1147-3

Cavalier-Smith, T., Chao, E.E.-Y., 2006. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). J. Mol. Evol. 62, 388–420. https://doi.org/10.1007/s00239-004-0353-8

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

Cho, Anna, Denis V. Tikhonenkov, Elisabeth Hehenberger, Anna Karnkowska, Alexander P. Mylnikov, and Patrick J. Keeling. 2022. Monophyly of Diverse Bigyromonadea and their Impact on Phylogenomic Relationships Within Stramenopiles. Molecular Phylogenetics and Evolution 171: 107468. https://doi.org/10.1016/j.ympev.2022.107468

Cook, M.E., Graham, L.E., 2016. Chlorokybophyceae, Klebsormidiophyceae, Coleochaetophyceae, 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. 1–20. https://doi.org/10.1007/978-3-319-32669-6_36-1

Cook, W.I., 1932. On the life-history and systematic position of the organisms causing dry top rot of sugar cane. The Journal of Agriculture of the University of Puerto Rico, 16(4):409-418.

Dorrell, R.G., Azuma, T., Nomura, M., Audren de Kerdrel, G., Paoli, L., Yang, S., Bowler, C., Ishii, K., Miyashita, H., Gile, G.H., Kamikawa, R., 2019. Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes. Proceedings of the National Academy of Sciences 116, 6914–6923. https://doi.org/10.1073/pnas.1819976116

Dykstra M, Olive L. 1975. An unusual sorocarp-producing Protist. Mycologia 67 (4):873–879. https://doi.org/10.1080/00275514.1975.12019815

Eikrem W. et al. (2017) Haptophyta. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_38-2

Eliáš, M., Amaral, R., Fawley, K.P., Fawley, M.W., Němcová, Y., Neustupa, J., Přibyl, P., Santos, L.M.A., Ševčíková, T., 2017. Eustigmatophyceae, 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. 1–39. https://doi.org/10.1007/978-3-319-32669-6_39-1

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

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., López-García, P., Torruella, G., Karpov, S. and Moreira, D., 2021. Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota. Nature communications, 12(1), pp.1-14. https://doi.org/10.1038/s41467-021-25308-w

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

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

Glockling, S.L., Marshall, W.L., Gleason, F.H., 2013. Phylogenetic interpretations and ecological potentials of the Mesomycetozoea (Ichthyosporea). Fungal Ecology 6, 237–247. https://doi.org/10.1016/j.funeco.2013.03.005

Gomaa F, Mitchell EAD, Lara E. 2013. Amphitremida (Poche, 1913) Is a New Major, Ubiquitous Labyrinthulomycete Clade. PLoS ONE 8(1): e53046. https://doi.org/10.1371/journal.pone.0053046

Gómez, F. and Skovgaard, A., 2015. The molecular phylogeny of the type-species of Oodinium Chatton, 1912 (Dinoflagellata: Oodiniaceae), a highly divergent parasitic dinoflagellate with non-dinokaryotic characters. Systematic parasitology, 90(2), pp.125-135. https://doi.org/10.1007/s11230-014-9538-8

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

Grant J, Tekle YI, Anderson OR, Patterson DJ, Katz LA. Multigene evidence for the placement of a heterotrophic amoeboid lineage Leukarachnion sp. among photosynthetic stramenopiles. Protist. 2009 Aug;160(3):376-85. https://doi.org/10.1016/j.protis.2009.01.001

Graupner, N., Jensen, M., Bock, C., Marks, S., Rahmann, S., Beisser, D., Boenigk, J., 2018. Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics. FEMS Microbiology Ecology 94, fiy039. https://doi.org/10.1093/femsec/fiy039

Hall J.D., McCourt R. (2017) Zygnematophyta. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_41-2

Hampl V. (2016) Preaxostyla. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_8-1

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

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

Horiguchi T. (2016) Raphidophyceae (Raphidophyta). In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_37-1

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

Huang, J.-H., Chen, C.-Y., Lin, Y.-H., Ann, P.-J., Huang, H.-C., & Chung, W.-H. (2012). Six new species of Pythiogeton in Taiwan, with an account of the molecular phylogeny of this genus. Mycoscience, 54:130–147. https://doi.org/10.1016/j.myc.2012.09.007

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

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

Jaskowska, E., Butler, C., Preston, G., Kelly, S. 2015. Phytomonas: Trypanosomatids Adapted to Plant Environments. PLOS Pathogens 11 (1): e1004484. https://doi.org/10.1371/journal.ppat.1004484

Jee HJ, Ho HH, Cho WD, 2000. Pythiogeton zeae sp. nov. causing root and basal stalk rot of corn in Korea. Mycologia 92: 522e527. https://doi.org/10.1080/00275514.2000.12061188

Johnston, M.R.L. and Davies, A.J., 1973. A Pirhemocyton-like parasite of the blenny, Blennius pholis L.(Teleostei; Blenniidae) and its relationship to Immanoplasma Neumann, 1909. International Journal for Parasitology, 3(2), pp.235-241. https://doi.org/10.1016/0020-7519(73)90028-3

Joubert, J.J. and Rijkenberg, F.H.J., 1971. Parasitic green algae. Annual Review of Phytopathology, 9(1):45-64. https://doi.org/10.1146/annurev.py.09.090171.000401

Kai, A., Yoshii, Y., Nakayama, T. and Inouye, I., 2008. Aurearenophyceae classis nova, a new class of Heterokontophyta based on a new marine unicellular alga Aurearena cruciata gen. et sp. nov. inhabiting sandy beaches. Protist, 159(3), pp.435-457. https://doi.org/10.1016/j.protis.2007.12.003

Kamikawa, R., Yubuki, N., Yoshida, M., Taira, M., Nakamura, N., Ishida, K., Leander, B.S., Miyashita, H., Hashimoto, T., Mayama, S., Inagaki, Y., 2015. Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae): Evolution of colorless Nitzschia. Phycol Res 63:19–28. https://doi.org/10.1111/pre.12072

Kawai H., Henry E.C. (2016) Phaeophyta. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_31-1

Keeling, P.J., 2004. Diversity and evolutionary history of plastids and their hosts. American journal of botany, 91(10), pp.1481-1493. https://doi.org/10.3732/ajb.91.10.1481

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

Kostka M. (2016) Opalinata. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_4-1

Kostygov, A.Y., Karnkowska, A., Votýpka, J., Tashyreva, D., Maciszewski, K., Yurchenko, V., Luke, J., 2021. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biology 11:200407. https://doi.org/10.1098/rsob.200407

Kristiansen, J., Škaloud, P., 2016. Chrysophyta, 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. 1–38. https://doi.org/10.1007/978-3-319-32669-6_43-1

Kühn, S., Medlin, L. and Eller, G., 2004. Phylogenetic position of the parasitoid nanoflagellate Pirsonia inferred from nuclear-encoded small subunit ribosomal DNA and a description of Pseudopirsonia n. gen. and Pseudopirsonia mucosa (Drebes) comb. nov. Protist, 155(2), pp.143-156. https://doi.org/10.1078/143446104774199556

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

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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

Lester R.J.G., Hine P.M. (2017) Paramyxida. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_21-1

Lhee, D., Ha, J. S., Kim, S., Park, M. G., Bhattacharya, D., & Yoon, H. S. (2019). Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species. Scientific reports, 9(1), 2560. https://doi.org/10.1038/s41598-019-38621-8

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Lynn, D.H., 2016. Ciliophora, 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. 1–52. https://doi.org/10.1007/978-3-319-32669-6_23-1

Maistro S., Broady P., Andreoli C., Negrisolo E. (2016) Xanthophyceae. In: Archibald J. et al. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_30-1

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