BACKGROUND: Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a 2-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses. RESULTS: Following the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transitions from a homogeneous community to distinct strata-specific communities. A prevalence of auto- and mixotrophic protists dominated by cryptophytes was associated with spring algal bloom-specialized bacteria in the epilimnion. In contrast, the meta- and hypolimnion showcased a development of a protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans, telonemids and excavate protists (Kinetoplastida), co-occurring with bacteria associated with lake snow. CONCLUSIONS: Our high-resolution sampling matching the typical doubling time of microbes along with the combined microscopic and molecular approach and inclusion of all main components of the microbial food web allowed us to unveil depth-specific populations' successions and interactions in a deep lentic ecosystem.

Biology Centre of the Czech Academy of Sciences Institute of Hydrobiology Na Sádkách 7 37005 Ceske Budejovice Czech Republic

Biology Centre of the Czech Academy of Sciences Institute of Soil Biology and Biogeochemistry Na Sádkách 7 37005 Ceske Budejovice Czech Republic

Department of Ecology Environment and Plant Sciences Stockholm University Stockholm Sweden

Faculty of Science University of South Bohemia 37005 Ceske Budejovice Czech Republic

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Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE, Keeling PJ. Environmental science. Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science. 2015;347:1257594. doi: 10.1126/science.1257594. PubMed DOI

Caron DA, Countway PD, Jones AC, Kim DY, Schnetzer A. Marine protistan diversity. Ann Rev Mar Sci. 2012;4:467–493. doi: 10.1146/annurev-marine-120709-142802. PubMed DOI

Arndt H, Dietrich D, Auer B, Cleven E-J, Grafenhan T, Weitere M, Mylnikov AP. Functional diversity of heterotrophic flagellates in aquatic ecosystems. Syst Assoc Spec. 2000;59:240–268.

Zubkov MV, Tarran GA. High bacterivory by the smallest phytoplankton in the North Atlantic Ocean. Nature. 2008;455:224–226. doi: 10.1038/nature07236. PubMed DOI

Caron DA, Hu SK. Are we overestimating protistan diversity in nature? Trends Microbiol. 2019;27:197–205. doi: 10.1016/j.tim.2018.10.009. PubMed DOI

Piwosz K. Weekly dynamics of abundance and size structure of specific nanophytoplankton lineages in coastal waters (Baltic Sea) Limnol Oceanogr. 2019;64:2172–2186. doi: 10.1002/lno.11177. DOI

Šimek K, Grujčić V, Mukherjee I, Kasalický V, Nedoma J, Posch T, Mehrshad M, Salcher MM. Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes. FEMS Microbiol Ecol. 2020;96:fiaa121. doi: 10.1093/femsec/fiaa121. PubMed DOI PMC

Boenigk J, Arndt H. Bacterivory by heterotrophic flagellates: community structure and feeding strategies. Antonie Van Leeuwenhoek. 2002;81:465–480. doi: 10.1023/A:1020509305868. PubMed DOI

Massana R, Terrado R, Forn I, Lovejoy C, Pedros-Alio C. Distribution and abundance of uncultured heterotrophic flagellates in the world oceans. Environ Microbiol. 2006;8:1515–1522. doi: 10.1111/j.1462-2920.2006.01042.x. PubMed DOI

Obiol A, Muhovic I, Massana R. Oceanic heterotrophic flagellates are dominated by a few widespread taxa. Limnol Oceanogr. 2021;66:4240–4253. doi: 10.1002/lno.11956. DOI

Lopez-Garcia P, Rodriguez-Valera F, Pedros-Alio C, Moreira D. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature. 2001;409:603–607. doi: 10.1038/35054537. PubMed DOI

Moon-van der Staay SY, De Wachter R, Vaulot D. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature. 2001;409:607–610. doi: 10.1038/35054541. PubMed DOI

de Vargas C, Audic S, Henry N, Decelle J, Mahe F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, et al. Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348:1261605. doi: 10.1126/science.1261605. PubMed DOI

Pasulka A, Hu SK, Countway PD, Coyne KJ, Cary SC, Heidelberg KB, Caron DA. SSU-rRNA gene sequencing survey of benthic microbial eukaryotes from Guaymas basin hydrothermal vent. J Eukaryot Microbiol. 2019;66:637–653. doi: 10.1111/jeu.12711. PubMed DOI

Giner CR, Pernice MC, Balague V, Duarte CM, Gasol JM, Logares R, Massana R. Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean. ISME J. 2020;14:437–449. doi: 10.1038/s41396-019-0506-9. PubMed DOI PMC

Lepere C, Boucher D, Jardillier L, Domaizon I, Debroas D. Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin) Appl Environ Microbiol. 2006;72:2971–2981. doi: 10.1128/AEM.72.4.2971-2981.2006. PubMed DOI PMC

Grossmann L, Jensen M, Heider D, Jost S, Glucksman E, Hartikainen H, Mahamdallie SS, Gardner M, Hoffmann D, Bass D, Boenigk J. Protistan community analysis: key findings of a large-scale molecular sampling. ISME J. 2016;10:2269–2279. doi: 10.1038/ismej.2016.10. PubMed DOI PMC

Simon M, Lopez-Garcia P, Deschamps P, Moreira D, Restoux G, Bertolino P, Jardillier L. Marked seasonality and high spatial variability of protist communities in shallow freshwater systems. ISME J. 2015;9:1941–1953. doi: 10.1038/ismej.2015.6. PubMed DOI PMC

Simon M, Lopez-Garcia P, Deschamps P, Restoux G, Bertolino P, Moreira D, Jardillier L. Resilience of freshwater communities of small microbial eukaryotes undergoing severe drought events. Front Microbiol. 2016;7:812. doi: 10.3389/fmicb.2016.00812. PubMed DOI PMC

Khomich M, Kauserud H, Logares R, Rasconi S, Andersen T. Planktonic protistan communities in lakes along a large-scale environmental gradient. FEMS Microbiol Ecol. 2017;93:fiw231. PubMed

Mukherjee I, Hodoki Y, Nakano S. Seasonal dynamics of heterotrophic and plastidic protists in the water column of Lake Biwa, Japan. Aquat Microb Ecol. 2017;80:123–137. doi: 10.3354/ame01843. DOI

Mukherjee I, Salcher MM, Andrei AS, Kavagutti VS, Shabarova T, Grujčić V, Haber M, Layoun P, Hodoki Y, Nakano SI, et al. A freshwater radiation of diplonemids. Environ Microbiol. 2020;22:4658–4668. doi: 10.1111/1462-2920.15209. PubMed DOI

Lepere C, Masquelier S, Mangot JF, Debroas D, Domaizon I. Vertical structure of small eukaryotes in three lakes that differ by their trophic status: a quantitative approach. ISME J. 2010;4:1509–1519. doi: 10.1038/ismej.2010.83. PubMed DOI

Mukherjee I, Hodoki Y, Okazaki Y, Fujinaga S, Ohbayashi K, Nakano SI. Widespread dominance of kinetoplastids and unexpected presence of diplonemids in deep freshwater lakes. Front Microbiol. 2019;10:2375. doi: 10.3389/fmicb.2019.02375. PubMed DOI PMC

Lepère C, Domaizon I, Hugoni M, Vellet A, Debroas D. Diversity and dynamics of active small microbial eukaryotes in the anoxic zone of a freshwater meromictic lake (Pavin, France) Front Microbiol. 2016;7:171591. doi: 10.3389/fmicb.2016.00130. PubMed DOI PMC

Monjot A, Bronner G, Courtine D, Cruaud C, Da Silva C, Aury J, Gavory F, Moné A, Vellet A, Wawrzyniak I. Functional diversity of microbial eukaryotes in a meromictic lake: coupling between metatranscriptomic and a trait-based approach. Environ Microbiol. 2023;25:3406–3422. doi: 10.1111/1462-2920.16531. PubMed DOI

Oikonomou A, Pachiadaki M, Stoeck T. Protistan grazing in a meromictic freshwater lake with anoxic bottom water. FEMS Microbiol Ecol. 2014;87:691–703. doi: 10.1111/1574-6941.12257. PubMed DOI

Šimek K, Grujčić V, Hahn MW, Horňák K, Jezberová J, Kasalický V, Nedoma J, Salcher MM, Shabarova T. Bacterial prey food characteristics modulate community growth response of freshwater bacterivorous flagellates. Limnol Oceanogr. 2018;63:484–502. doi: 10.1002/lno.10759. DOI

Moreira D, Lopez-Garcia P. Time series are critical to understand microbial plankton diversity and ecology. Mol Ecol. 2019;28:920–922. doi: 10.1111/mec.15015. PubMed DOI PMC

Šimek K, Nedoma J, Znachor P, Kasalický V, Jezbera J, Hornňák K, Sed’a J. A finely tuned symphony of factors modulates the microbial food web of a freshwater reservoir in spring. Limnol Oceanogr. 2014;59:1477–1492. doi: 10.4319/lo.2014.59.5.1477. DOI

Kavagutti VS, Bulzu PA, Chiriac CM, Salcher MM, Mukherjee I, Shabarova T, Grujcic V, Mehrshad M, Kasalicky V, Andrei AS, et al. High-resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome. 2023;11:15. doi: 10.1186/s40168-022-01451-4. PubMed DOI PMC

Shabarova T, Salcher MM, Porcal P, Znachor P, Nedoma J, Grossart HP, Sedá J, Hejzlar J, Šimek K. Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession. Nat Microbiol. 2021;6:479–488. doi: 10.1038/s41564-020-00852-1. PubMed DOI

Sommer U, Gliwicz ZM, Lampert W, Duncan A. The PEG-model of seasonal succession of planktonic events in fresh waters. Arch Hydrobiol. 1986;106:433–471. doi: 10.1127/archiv-hydrobiol/106/1986/433. DOI

Sommer U, Adrian R, Domis LDS, Elser JJ, Gaedke U, Ibelings B, Jeppesen E, Lürling M, Molinero JC, Mooij WM, et al. Beyond the Plankton Ecology Group (PEG) model: mechanisms driving plankton succession. Annu Rev Ecol Evol Syst. 2012;43:429–448. doi: 10.1146/annurev-ecolsys-110411-160251. DOI

Park H, Shabarova T, Salcher MM, Kosová L, Rychtecký P, Mukherjee I, Šimek K, Porcal P, Sedá J, Znachor P, Kasalický V. In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model. Microbiome. 2023;11:112. doi: 10.1186/s40168-023-01522-0. PubMed DOI PMC

Zeder M, Peter S, Shabarova T, Pernthaler J. A small population of planktonic Flavobacteria with disproportionally high growth during the spring phytoplankton bloom in a prealpine lake. Environ Microbiol. 2009;11:2676–2686. doi: 10.1111/j.1462-2920.2009.01994.x. PubMed DOI

Eckert EM, Salcher MM, Posch T, Eugster B, Pernthaler J. Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom. Environ Microbiol. 2012;14:794–806. doi: 10.1111/j.1462-2920.2011.02639.x. PubMed DOI

Neuenschwander SM, Ghai R, Pernthaler J, Salcher MM. Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria. ISME J. 2018;12:185–198. doi: 10.1038/ismej.2017.156. PubMed DOI PMC

Piwosz K, Mukherjee I, Salcher MM, Grujčić V, Šimek K. CARD-FISH in the sequencing era: opening a new universe of protistan ecology. Front Microbiol. 2021;12:640066. doi: 10.3389/fmicb.2021.640066. PubMed DOI PMC

Grujčić V, Nuy JK, Salcher MM, Shabarova T, Kasalický V, Boenigk J, Jensen M, Šimek K. Cryptophyta as major bacterivores in freshwater summer plankton. ISME J. 2018;12:1668–1681. doi: 10.1038/s41396-018-0057-5. PubMed DOI PMC

Šimek K, Mukherjee I, Nedoma J, de Paula CCP, Jezberová J, Sirová D, Vrba J. CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes. Environ Microbiol. 2022;24:4256–4273. doi: 10.1111/1462-2920.15846. PubMed DOI PMC

Šimek K, Mukherjee I, Szöke-Nagy T, Haber M, Salcher MM, Ghai R. Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores. ISME J. 2023;17:84–94. doi: 10.1038/s41396-022-01326-4. PubMed DOI PMC

Znachor P, Nedoma J, Hejzlar J, Seda J, Kopacek J, Boukal D, Mrkvicka T. Multiple long-term trends and trend reversals dominate environmental conditions in a man-made freshwater reservoir. Sci Total Environ. 2018;624:24–33. doi: 10.1016/j.scitotenv.2017.12.061. PubMed DOI

Sherr EB, Sherr BF. Protistan grazing rates via uptake of fluorescently labeied prey. In: Handbook of methods in aquatic microbial ecology. CRC Press; 2018, pp. 695–701.

Brussaard CP. Optimization of procedures for counting viruses by flow cytometry. Appl Environ Microbiol. 2004;70:1506–1513. doi: 10.1128/AEM.70.3.1506-1513.2004. PubMed DOI PMC

Lund JWG, Kipling C, Le Cren E. The inverted microscope method of estimating algal numbers and the statistical basis of estimations by counting. Hydrobiologia. 1958;11:143–170. doi: 10.1007/BF00007865. DOI

Hillebrand H, Dürselen C-D, Kirschtel D, Pollingher U, Zohary T. Biovolume calculation for pelagic and benthic microalgae. J Phycol. 1999;35:403–424. doi: 10.1046/j.1529-8817.1999.3520403.x. DOI

McCauley E. The estimation of the abundance and biomass of zooplankton in samples. In A manual on methods for the assessment of secondary productivity in fresh waters 1984.

Koste W. Rotatoria. Die Rädertiere Mitteleuropas, begründet von Max Voigt. Überordnung Monogononta. Gebrüder Borntraeger, Berlin, Stuttgart. I. Text (673 pp) u II Tafelbd; 1978.

Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–1414. doi: 10.1111/1462-2920.13023. PubMed DOI

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–12. doi: 10.14806/ej.17.1.200. DOI

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–583. doi: 10.1038/nmeth.3869. PubMed DOI PMC

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–596. doi: 10.1093/nar/gks1219. PubMed DOI PMC

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glockner FO. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res. 2014;42:D643–648. doi: 10.1093/nar/gkt1209. PubMed DOI PMC

Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2013;41:D597–604. doi: 10.1093/nar/gks1160. PubMed DOI PMC

Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14:927–930. doi: 10.1111/j.1654-1103.2003.tb02228.x. DOI

Hu A, Ju F, Hou L, Li J, Yang X, Wang H, Mulla SI, Sun Q, Burgmann H, Yu CP. Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community. Environ Microbiol. 2017;19:4993–5009. doi: 10.1111/1462-2920.13942. PubMed DOI

Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. In: Proceedings of the international AAAI conference on web and social media. 2009, pp. 361–362.

Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28:1823–1829. doi: 10.1093/bioinformatics/bts252. PubMed DOI PMC

Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar A, Buchner A, Lai T, Steppi S, Jobb G, et al. ARB: a software environment for sequence data. Nucleic Acids Res. 2004;32:1363–1371. doi: 10.1093/nar/gkh293. PubMed DOI PMC

Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188–7196. doi: 10.1093/nar/gkm864. PubMed DOI PMC

Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 2005;21:456–463. doi: 10.1093/bioinformatics/bti191. PubMed DOI

Yilmaz LS, Parnerkar S, Noguera DR. mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization. Appl Environ Microbiol. 2011;77:1118–1122. doi: 10.1128/AEM.01733-10. PubMed DOI PMC

Sherr BF, Sherr EB, Fallon RD. Use of monodispersed, fluorescently labeled bacteria to estimate in situ protozoan bacterivory. Appl Environ Microbiol. 1987;53:958–965. doi: 10.1128/aem.53.5.958-965.1987. PubMed DOI PMC

Šimek K, Grujčić V, Nedoma J, Jezberová J, Šorf M, Matoušů A, Pechar L, Posch T, Bruni EP, Vrba J. Microbial food webs in hypertrophic fishponds: omnivorous ciliate taxa are major protistan bacterivores. Limnol Oceanogr. 2019;64:2295–2309. doi: 10.1002/lno.11260. DOI

Jezbera J, Horňák K, Šimek K. Food selection by bacterivorous protists: insight from the analysis of the food vacuole content by means of fluorescence in situ hybridization. FEMS Microbiol Ecol. 2005;52:351–363. doi: 10.1016/j.femsec.2004.12.001. PubMed DOI

Posch T, Eugster B, Pomati F, Pernthaler J, Pitsch G, Eckert EM. Network of interactions between ciliates and phytoplankton during spring. Front Microbiol. 2015;6:1289. doi: 10.3389/fmicb.2015.01289. PubMed DOI PMC

Risse-Buhl U, Scherwass A, Schlüssel A, Arndt H, Kröwer S, Küsel K. Detachment and motility of surface-associated ciliates at increased flow velocities. Aquat Microb Ecol. 2009;55:209–218. doi: 10.3354/ame01302. DOI

Gómez F, Wang L, Lin S. Morphology and molecular phylogeny of peritrich ciliate epibionts on pelagic diatoms: Vorticella oceanica and Pseudovorticella coscinodisci sp. Nov. (Ciliophora, Peritrichia) Protist. 2018;169:268–279. doi: 10.1016/j.protis.2018.03.003. PubMed DOI

Grossart HP, Simon M. Limnetic macroscopic organic aggregates (lake snow): occurrence, characteristics, and microbial dynamics in Lake Constance. Limnol Oceanogr. 1993;38:532–546. doi: 10.4319/lo.1993.38.3.0532. DOI

Schoenle A, Hohlfeld M, Rosse M, Filz P, Wylezich C, Nitsche F, Arndt H. Global comparison of bicosoecid Cafeteria-like flagellates from the deep ocean and surface waters, with reorganization of the family Cafeteriaceae. Eur J Protistol. 2020;73:125665. doi: 10.1016/j.ejop.2019.125665. PubMed DOI

Andrei AS, Salcher MM, Mehrshad M, Rychtecký P, Znachor P, Ghai R. Niche-directed evolution modulates genome architecture in freshwater Planctomycetes. ISME J. 2019;13:1056–1071. doi: 10.1038/s41396-018-0332-5. PubMed DOI PMC

Okazaki Y, Fujinaga S, Tanaka A, Kohzu A, Oyagi H, Nakano SI. Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes. ISME J. 2017;11:2279–2293. doi: 10.1038/ismej.2017.89. PubMed DOI PMC

Wiegand S, Jogler M, Jogler C. On the maverick planctomycetes. FEMS Microbiol Rev. 2018;42:739–760. doi: 10.1093/femsre/fuy029. PubMed DOI

Grossart H-P, Simon M. Significance of limnetic organic aggregates (lake snow) for the sinking flux of particulate organic matter in a large lake. Aquat Microb Ecol. 1998;15:115–125. doi: 10.3354/ame015115. DOI

Salcher MM, Posch T, Pernthaler J. In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake. ISME J. 2013;7:896–907. doi: 10.1038/ismej.2012.162. PubMed DOI PMC

van Grinsven S, Sinninghe Damste JS, Harrison J, Villanueva L. Impact of electron acceptor availability on methane-influenced microorganisms in an enrichment culture obtained from a stratified lake. Front Microbiol. 2020;11:715. doi: 10.3389/fmicb.2020.00715. PubMed DOI PMC

Piwosz K, Pernthaler J. Enrichment of omnivorous cercozoan nanoflagellates from coastal Baltic Sea waters. PLoS ONE. 2011;6:e24415. doi: 10.1371/journal.pone.0024415. PubMed DOI PMC

Kuhn S, Medlin L, Eller G. 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. 2004;155:143–156. doi: 10.1078/143446104774199556. PubMed DOI

Molmeret M, Horn M, Wagner M, Santic M, Abu Kwaik Y. Amoebae as training grounds for intracellular bacterial pathogens. Appl Environ Microbiol. 2005;71:20–28. doi: 10.1128/AEM.71.1.20-28.2005. PubMed DOI PMC

Watanabe K, Nakao R, Fujishima M, Tachibana M, Shimizu T, Watarai M. Ciliate Paramecium is a natural reservoir of Legionella pneumophila. Sci Rep. 2016;6:24322. doi: 10.1038/srep24322. PubMed DOI PMC

Ok JH, Jeong HJ, Lim AS, Lee SY, Kim SJ. Feeding by the heterotrophic nanoflagellate Katablepharis remigera on algal prey and its nationwide distribution in Korea. Harmful Algae. 2018;74:30–45. doi: 10.1016/j.hal.2018.03.011. PubMed DOI

Mukherjee I, Hodoki Y, Nakano S. Kinetoplastid flagellates overlooked by universal primers dominate in the oxygenated hypolimnion of Lake Biwa, Japan. FEMS Microbiol Ecol. 2015;91:fiv083. doi: 10.1093/femsec/fiv083. PubMed DOI

Caron DA. Grazing of attached bacteria by heterotrophic microflagellates. Microb Ecol. 1987;13:203–218. doi: 10.1007/BF02024998. PubMed DOI

Brate J, Klaveness D, Rygh T, Jakobsen KS, Shalchian-Tabrizi K. Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations. BMC Microbiol. 2010;10:168. doi: 10.1186/1471-2180-10-168. PubMed DOI PMC

Dokulil M, Skolaut C. Succession of phytoplankton in a deep stratifying lake: Mondsee, Austria. Hydrobiologia. 1986;138:9–24. doi: 10.1007/BF00027229. DOI

Mangot J-F, Debroas D, Domaizon I. Perkinsozoa, a well-known marine protozoan flagellate parasite group, newly identified in lacustrine systems: a review. Hydrobiologia. 2011;659:37–48. doi: 10.1007/s10750-010-0268-x. DOI

Jobard M, Wawrzyniak I, Bronner G, Marie D, Vellet A, Sime-Ngando T, Debroas D, Lepère C. Freshwater Perkinsea: diversity, ecology and genomic information. J Plankton Res. 2020;42:3–17. doi: 10.1093/plankt/fbz068. DOI

Park MG, Yih W, Coats DW. Parasites and phytoplankton, with special emphasis on dinoflagellate infections. J Eukaryot Microbiol. 2004;51:145–155. doi: 10.1111/j.1550-7408.2004.tb00539.x. PubMed DOI

Morrison DA. Evolution of the Apicomplexa: Where are we now? Trends Parasitol. 2009;25:375–382. doi: 10.1016/j.pt.2009.05.010. PubMed DOI

Rösel S, Grossart H-P. Contrasting dynamics in activity and community composition of free-living and particle-associated bacteria in spring. Aquat Microb Ecol. 2012;66:169–181. doi: 10.3354/ame01568. DOI

Paver SF, Hayek KR, Gano KA, Fagen JR, Brown CT, Davis-Richardson AG, Crabb DB, Rosario-Passapera R, Giongo A, Triplett EW, Kent AD. Interactions between specific phytoplankton and bacteria affect lake bacterial community succession. Environ Microbiol. 2013;15:2489–2504. doi: 10.1111/1462-2920.12131. PubMed DOI

Kagami M, Gurung TB, Yoshida T, Urabe J. To sink or to be lysed? Contrasting fate of two large phytoplankton species in Lake Biwa. Limnol Oceanogr. 2006;51:2775–2786. doi: 10.4319/lo.2006.51.6.2775. DOI

Müller H, Schlegel A. Responses of three freshwater planktonic ciliates with different feeding modes to cryptophyte and diatom prey. Aquat Microb Ecol. 1999;17:49–60. doi: 10.3354/ame017049. DOI

Liang D, Luo H, Huang C, Ye Z, Sun S, Dong J, Liang M, Lin S, Yang Y. High-throughput sequencing reveals omnivorous and preferential diets of the rotifer Polyarthra in situ. Front Microbiol. 2022;13:1048619. doi: 10.3389/fmicb.2022.1048619. PubMed DOI PMC

Gilbert JJ. Food niches of planktonic rotifers: diversification and implications. Limnol Oceanogr. 2022;67:2218–2251. doi: 10.1002/lno.12199. DOI

Devetter M, Seďa J. Regulation of rotifer community by predation of Cyclops vicinus (Copepoda) in the Římov Reservoir in spring. Int Rev Hydrobiol. 2006;91:101–112. doi: 10.1002/iroh.200510810. DOI

Šorf M, Brandl Z. The rotifer contribution to the diet of Eudiaptomus gracilis (GO Sars, 1863) (Copepoda, Calanoida) Crustaceana. 2012;85:1421–1429. doi: 10.1163/15685403-00003133. DOI

Kunzmann AJ, Ehret H, Yohannes E, Straile D, Rothhaupt K-O. Calanoid copepod grazing affects plankton size structure and composition in a deep, large lake. J Plankton Res. 2019;41:955–966. doi: 10.1093/plankt/fbz067. DOI

Šimek K, Bobková J, Macek M, Nedoma J, Psenner R. Ciliategrazing on picoplankton in a eutrophic reservoir during the summer phytoplankton maximum: a study at the species and community level. Limnol Oceanogr. 1995;40:1077–1090. doi: 10.4319/lo.1995.40.6.1077. DOI

Metfies K, Berzano M, Mayer C, Roosken P, Gualerzi C, Medlin L, Muyzer G. An optimized protocol for the identification of diatoms, flagellated algae and pathogenic protozoa with phylochips. Mol Ecol Notes. 2007;7:925–936. doi: 10.1111/j.1471-8286.2007.01799.x. DOI

Bochdansky AB, Huang L. Re-evaluation of the EUK516 probe for the domain eukarya results in a suitable probe for the detection of kinetoplastids, an important group of parasitic and free-living flagellates. J Eukaryot Microbiol. 2010;57:229–235. doi: 10.1111/j.1550-7408.2010.00470.x. PubMed DOI

Mangot JF, Lepere C, Bouvier C, Debroas D, Domaizon I. Community structure and dynamics of small eukaryotes targeted by new oligonucleotide probes: new insight into the lacustrine microbial food web. Appl Environ Microbiol. 2009;75:6373–6381. doi: 10.1128/AEM.00607-09. PubMed DOI PMC

Global freshwater distribution of Telonemia protists