Thomas WeisseThomas Weisse

Present position:

retired Senior scientist

Research area:

Plankton Ecology



Research topics · Study objects · Current group members · Projects · Recent publications  · CV


Research topics 

  • Functional ecology and diversity of eukaryote freshwater microorganisms
  • Sensitivity of planktonic protists to climate change
  • Adaptations to extreme environments

We combine field studies with experimental laboratory investigations to address the above research topics.

Banner Microorganisms

Study objects 

  • Heterotrophic protists (ciliates and flagellates)
  • Phytoplankton (picocyanobacteria and eukaryotic algae)
  • Rotifers

study objects


Former group members  

  • Sabrina Seywald (2023). Does connectivity affect phytoplankton species and functional diversity? Sabrina investigated in her Master's project if hydrologic connectivity affects phytoplankton species richness and functional diversity in lakes. Her goal was to allocate suitable functional traits to the phytoplankton species to characterize their eatability for ciliates and other microzooplankton (mainly copepods and cladocerans). The thesis was carried out within the FWF project Functional Diversity of planktonic ciliates, MSc thesis, University of Innsbruck. 
  • Xiaoteng (Leo) Lu (2021). Functional ecology and biodiversity of planktonic ciliates. Leo conducted field and experimental work to test general ecological theories such as those related to the effect of connectivity on diversity of planktonic ciliates. In his experimental work, the emphasis was on the interaction of intrinsic and environmental factors on the  FE of ciliates. His work was supported by a grant from China Scholarship Council. PhD thesis, University of Innsbruck.

  • Astrid Beckmann (2020). "Top-down control of the planktonic peritrich ciliate Pelagovorticella natans" MSc thesis, University of Innsbruck.

  • Christina Wirth (2018). "Auswirkungen von Temperatur- und Lichtveränderungen auf planktische Algenarten" MSc-thesis, pp. 95, University of Innsbruck. Christina investigated the interactive effect of temperature, light, and nutrients on temperature-sensitive algae in laboratory experiments 

  • Adam Cieplinski (2018). Within the project ‘Rotifer cryptic diversity along alitutude (RotiAlti; PI: Ulrike Obertegger)’ Adam investigated in his PhD the influences of spatial versus environmental processes on the genetic diversity of the rotifer Keratella cochlearis; he was employed with a grant by the Fondazione Edmund Mach (Trentino, Italy;

  • Victoria Bergkemper (2018). Phytoplankton community responses to short-term meteorological extremes – improved analysis using advanced optical methods. In her PhD thesis, Victoria used an imaging flow cytometer, FlowCAM (Flow-Cytometer-And-Microscope), to study the protist community in situ (mainly in Lake Mondsee) and experimentally in the laboratory. University of Innsbruck

  • Patrick Kaspar (2016). Size and Volume Estimations of Polystyrene Beads and Algae with Optical and Electronical Methods, MSc-thesis, pp. 79, University of Applied Sciences Upper Austria (FH)
group-photo 2017

P. Stadler – P. Kaspar – X. Lu – V. Bergkemper – T. Weisse – A. Cieplinski



  • Functional Diversity of Planktonic Ciliates, funded by the Austrian Science Fund (FWF P 32714; T. Weisse), Oct 2019 – Sept 2022

    Ciliates are a dominant group of unicellular microorganisms (protists) that occurs in virtually all water bodies. Ciliates are key elements of aquatic food webs, acting as predators of bacteria, algae, other protists and even some metazoans. Planktonic ciliates are important food for zooplankton, and mixotrophic and functionally autotrophic species may significantly contribute to primary production in lakes and in the ocean. Therefore, the question of whether ciliate functional diversity and their ecosystem roles differ between marine and freshwater ecosystems is of fundamental importance for the global biodiversity debate and water management. To this end, this project will provide the first rigorous analysis to test if the functional diversity differs between marine and freshwater ciliates. It is based upon an established cooperation between four research laboratories located in Austria, the UK and China. This research takes an interdisciplinary approach, integrating the project partners’ expertise from classical and molecular taxonomy, phylogeny, ecology, and modelling, building bridges between the traditionally separated disciplines Biological Oceanography and Limnology.


    Ciliaten sind eine dominante Gruppe von einzelligen Mikroorganismen (Protisten), die in nahezu jedem Wasserkörper vorkommen. Ciliaten sind als Räuber von Bakterien, Algen, anderen Protisten und sogar einigen Mehrzellern (Metazoen) Schlüsselglieder in aquatischen Nahrungsnetzen. Planktische Ciliaten sind wichtige Nahrungsorganismen für das Zooplankton, und mixotrophe Arten (die sich sowohl „tierisch“, d.h. heterotroph, als auch „pflanzlich“, d.h. autotroph, ernähren können) sowie funktionell autotrophe Ciliaten können signifikant zu der Primärproduktion in Seen und im Ozean beitragen. Das Projekt wird erstmals analysieren, ob sich die funktionelle Diversität der Ciliaten in den aquatischen Lebensräumen (Meer und Süßwasser) signifikant unterscheidet. Diese Frage ist von grundsätzlicher Bedeutung für die Beurteilung der globalen Biodiversität und das Gewässer-Management. Das Projekt basiert auf einer etablierten Zusammenarbeit zwischen vier Forschungsgruppen in Österreich, Großbritannien und China. Die geplante Forschungsarbeit ist interdisziplinär und wird die Expertise der Projektpartner, die von klassischer und molekularer Taxonomie bis hin zu Phylogenie, Ökologie und Modellierung reicht, integrieren. 

  • Species and functional diversity of planktonic ciliates: Does connectivity make a difference?, funded by the Tyrolian Science Fund (Tiroler Wissenschaftsförderung ,TWF; Xiaoteng Lu, T. Weisse), March 2019 – Sept 2020 

    We analyze species diversity (SDiv) and functional diversity (FDiv) of planktonic ciliates among several connected and disconnected lakes in the Austrian Salzkammergut area in relation to major environmental variables, i.e. we link ciliate FDiv to major ecological drivers (i.e., bottom-up via food and temperature, top-down via predation and competition). We postulate that due to functional redundancy, FDiv of planktonic ciliates is similar between connected and similar (with respect to trophic status, depth, altitude, etc.) lakes; however, SDiv may differ between connected and disconnected lakes. We combine imaging cytometry (FlowCAM), acoustic flow cytometry, microscopy and protargol staining, and single-cell molecular analyses to characterize and quantify the ciliates. 

  • Top-down control of the planktonic peritrich ciliate Pelagovorticella natans, funded by the University of Innsbruck, Aktion D. Swarowski KG 2018; Xiaoteng Lu, T. Weisse), Jan 2019 – Sept 2020 

    Unicellular ciliates play a central role in all aquatic food webs as predators of bacteria and small algae on the one hand, and as food for larger zooplankton (mainly crustaceans) on the other hand. However, thus far, only a handful of studies quantified ciliate predation by small crustaceans. We use the free swimming ciliate Pelagovorticella natans as model to decipher ciliate population dynamics and their role in the lake food web. To this end, we will quantify production rates of the ciliates and their loss rates by crustacean predation.

    Die einzelligen Ciliaten ("Wimpertierchen") haben in allen aquatischen Nahrungsnetzen als Räuber von Bakterien und kleinen Algenarten und sowie als Beute für das größere Zooplankton (v. a. Kleinkrebse) eine zentrale Rolle. Die Frage, inwieweit die Ciliaten tatsächlich von Kleinkrebsen gefressen werden, ist bisher jedoch nur in wenigen Fällen beantwortet worden. Wir verwenden den frei schwimmenden Ciliaten Pelagovorticella natans als Modellart, um die Populationsdynamik der Ciliaten und ihre Rolle im Nahrungsnetz aufzuklären. Dazu sollen die Produktionsraten des Ciliaten sowie die Verlustraten durch den Fraßdruck der Kleinkrebse quantifiziert werden. 



 Recent Publications


  • Weisse T., Scheffel U., Stadler P. (2023). Temperature-dependent resistance to starvation of three contrasting freshwater ciliates, European Journal of Protistology 88: 125973,

  • Weisse T., Scheffel U., Stadler P. (2023). Functional ecology of planctonic ciliates: Measuring mortality rates in response to starvation, J. Eukaryot. Microbiol. 00:e12969,


  • Lukić D., Limberger R., Agatha, S. Montagnes D.J.S, Weisse, T. (2022). Thermal performance of planktonic ciliates differs between marine and freshwaters: a case study providing guidance for climate change studies. Limnology and Oceanography Letters,7: 520-526.

  • Lu X., Weisse, T. (2022) Top-down control of planktonic ciliates by microcrustacean predators is stronger in lakes than in the ocean. Scientific Reports 12:10501,  

  • Weisse T., Montagnes D.J.S. (2022). Ecology of planktonic ciliates in a changing world: Concepts, methods, and challenges. Journal of Eukaryotic Microbiology, 69: e12879.


  • Weisse T., Lukić D., Lu X. (2021). Container volume may affect growth rates of ciliates and clearance rates of their microcrustacean predators in microcosm experiments, Journal of Plankton Research, fbab017, doi.10.1093/plankt/fbab017

  • Lu X., Gao Y., Weisse, T. (2021). Functional ecology of two contrasting freshwater ciliated protists in relation to temperature. J. Eukaryot. Microbiol. 68, e12823,

  • Weisse T., Jezberova J., Moser M. (2021). Picoplankton feeding by the ciliate Vorticella similis in comparison to other peritrichs emphasizes their significance in the water purification process. Ecol. Ind. 121:106992,


  • Weisse, T. (2020). Wilhelm Foissner and the European Journal of Protistology Eur. J. Protistol. 76:125739,
  • Kurmayer R., Entfellner E., Weisse T., Offterdinger M., Rentmeister A., Deng L. (2020). Chemically labeled toxins or bioactive peptides show a heterogeneous intracellular distribution and low spatial overlap with autofluorescence in bloom-forming cyanobacteria. Sci Rep 10, 2781,

  • Weisse T., Moser M. (2020). Light affects picocyanobacterial grazing and growth response of the mixotrophic flagellate Poterioochromonas malhamensis. J. Microbiol. Vol. 58, DOI 10.1007/s12275-020-9567-8


  • Cieplinski A., Weisse T., Obertegger U. (2019). First study on the male inducing signal in Keratella cochlearis, crowding is the key, Limnologica 77: article 125688,
  • Weithoff G., Neumann C., Seiferth J., Weisse T. (2019). Living on the edge - reproduction, dispersal potential, maternal effects and local adaptation in aquatic, acidophilic invertebrates. Aquat. Sci. 81:40, doi: 10.1007/s00027-019-0638-z

  • Wirth C., Limberger R., Weisse T. (2019). Temperature x light interaction and tolerance of high water temperature in the planktonic freshwater flagellates Cryptomonas (Cryptophyceae) and Dinobryon (Chrysophyceae). J. Phycol. 55:404-414, DOI: 10.1111/jpy.12826


  • Weisse T. (2018). Editorial. Eur. J. Protistol. 66: iii-iv.

  • Bergkemper V., Stadler P., Weisse T. (2018). Moderate weather extremes alter phytoplankton diversity - A microcosm study. Freshwater Biology 63(10):1211-1224 doi. 10.1111/fwb.13127 

  • Bergkemper V., Weisse, T. (2018). Do current European lake monitoring programmes reliably estimate phytoplankton community changes? Hydrobiologia 824: 143-162, DOI 10.1007/s10750-017-3426-6

  • Weisse T., Bergkemper V. (2018). Rapid detection and quantification of the potentially toxic cyanobacterium Planktothrix rubescens by in-vitro fluorometry and flow cytometry. Water research, 138, 234-240, doi. 10.1016/j.watres.2018.03.052

  • Cieplinski, A., Obertegger, U. & Weisse, T. (2018). Life history traits and demographic parameters in the Keratella cochlearis (Rotifera, Monogononta) species complex. Hydrobiologia, 811: 325-338. DOI: 10.1007/s10750-017-3499-2


  • Weisse, T. (2017). Functional diversity of aquatic ciliates. European Journal of Protistology EJOP 24492, 61B, 331-358, doi:10.1016/j.ejop.2017.04.001

  • Cieplinski A., Weisse T., Obertegger U. (2017). High diversity in Keratella cochlearis (Rotifera, Monogononta) - morphological and genetic evidence. Hydrobiologia, 796:145-159, doi: 10.1007/s10750-016-2781-z

  • Bergkemper V., Weisse T. (2017). Phytoplankton response to the summer heat wave 2015 – a case study from prealpine Lake Mondsee, Austria. Inland Waters 7:88-99. doi 10.1080/20442041.2017.1294352

  • Warren, A., Patterson, D.J., Dunthorn, M., Clamp, J.C., Achilles-Daye, U.E.M., Aescht, E., Al-Farraj, S.A., Al-Quraishy, S., Al-Rasheid, K., Carr, M., Day, J.G., Dellinger, M., El-Serehy, H.A., Fan, Y., Gao, F.,Gao, S., Gong, J., Gupta, R. Hu, X., Kamra, K., Langlois, G., Lin, X., Lipscomb, D., Lobban, C.S., Luporini, P., Lynn, D.H., Ma, H., Macek, M., Mackenzie-Dodds, J., Makhija, S., Manserg, R.I., Martin-Cereceda, M., McMiller, N., Montagnes, D., Nikolaeva, S., Ong’ondo, G.O., Perez-Uz, B., Purushothaman, J., Quintela-Alonso, P., Rotterová, J., Santoferrara, L., Shao, C., Shen, Z., Shi, X., Song, W., Stoeck, T., La Terza, A., Vallesi, A., Wang, M., Weisse, T., Wiackowski, K., Wu, L., Xu, K., Yi, Z., Zufall, R.& Agatha, S. (2017). Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora). J. Eukaryot. Microbiol., doi:10.1111/jeu.12391


  • Ceríaco L.M.P., Gutiérrez E.E., Dubois A. et al. (2016). Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences. Zootaxa 4196(3): 435-445. org/10.11646/zootaxa.4196.3.9
  • Weisse, T. (2016). Editorial. European Journal of Protistology PDF

  • Weisse T. (2016). Current trends in protistology - results from the VII ECOP Joint Meeting 2015. Special Issue. Amsterdam [u.a.]: Elsevier (= European Journal of Protistology), 55, 101 pp.

  • Weisse T., Sonntag B. (2016). Ciliates in planktonic food webs: communication and adaptive response. In: Witzany, G. & Nowacki, M. (eds), Biocommunication of ciliates. Spinger, Berlin, 351-372.
  • Cieplinski A., Weisse T., Obertegger, U. (2016). High diversity in Keratella cochlearis (Rotifera, Monogononta) - morphological and genetic evidence. Hydrobiologia, doi: 10.1007/s10750-016-2781-z
  • Weisse T., Gröschl B., Bergkemper V. (2016). Phytoplankton response to short-term temperature and nutrient changes.
    Limnologica - Ecology and Management of Inland Waters 59, S. 78 - 89. doi:10.1016/j.limno.2016.05.002
  • Weisse T., Anderson R., Arndt H., Calbet A., Hansen P.J., Montagnes D.J.S. (2016). Functional Ecology of aquatic phagotrophic protists – concepts, limitations, and perspectives. J. Protistol., http://dx.
  • Weckström K., Weckström J., Huber K., Kamenik C, Schmidt R., Salvenmoser W., Rieradevall M., Weisse T., Psenner R.,  Kurmayer, R. (2016). Impacts of climate warming on Alpine lake biota over the last decade. Arctic, Antarctic, and Alpine Research 48, 361-376. Abstract


  • Dunthorn M, Lipps JH, Dolan JR, Abboud-Abi Saab M, Aescht E, Bachy C, Barría de Cao MS, Berger H, Bourland WA, Choi JK, Clamp J, Doherty M, Gao F, Gentekaki E, Gong J, Hu X, Huang J, Kamiyama T, Johnson MD, Kammerlander B, Kim SY, Kim Y-O, la Terza A, Laval-Peuto M, Lipscomb D, Lobban CS, Long H, Luporini P, Lynn DH, Macek M, Mansergh RI, Martín-Cereceda M, McManus GG, Montagnes DJS, Ong’ondo GO, Patterson DJ, Pérez-Uz B, Quintela-Alonso P, Safi LSL, Santoferrara LF, Sonntag B, Song W, Stoeck T, Stoecker DK, Strüder-Kypke MC, Trautmann I, Utz LRP, Vallesi A, Vd’ačný P, Warren A, Weisse T, Wickham SA, Yi Z, Zhang W, Zhan Z, Zufall R, Agatha S (2015). Ciliates  – protists with complex morphologies and ambiguous early fossil record. Marine Micropaleontology 119:1-6. Abstract

  • Weisse T. (2015). Editorial. European Journal of Protistology 51(2):A1-A2. doi 10.1016/j.ejop.2015.04.003

  • Mirtl M., Bahn M., Battin T., Borsdorf A., Dirnböck T., Englisch M., Erschbamer B., Fuchsberger J., Gaube V., Grabherr G., Gratzer G., Haberl H., Klug H., Kreiner D., Mayer R., Peterseil J., Richter A., Schindler S., Stocker-Kiss A., Tappeiner U., Weisse T., Winiwarter V., Wohlfahrt G., Zink R. (2015). Forschung für die Zukunft-LTER-Austria White Paper 2015 zur Lage und Ausrichtung von prozessorientierter Ökosystemforschung, Biodiversitäts- und Naturschutzforschung sowie sozio-ökologischer Forschung in Österreich. LTER-Austria Schriftenreihe, Vol. 2, 74pp., ISBN 978-3-9503986-0-1.

  • Nevalainen L., Luoto T. P., Manca M., Weisse T. (2015). A paleolimnological perspective on aquatic biodiversity in Austrian mountain lakes, Aquatic Sciences, 77:59-69. DOI 10.1007/s00027-014-0363-6



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