Thomas WeisseThomas Weisse

Present position:

Head of Research institute

Research area:

Microbial Ecology


+43 512 507-50200
+43 512 507-50299

Employment History · Research · Staff · Projects · Teaching · Publications ·
Professional Memberships and Honours · Editorial Advisorship/Editorial Board Service

Employment History

  • Sept 1, 2012: Senior Scientist and head of the Research Institute for Limnology, Mondsee of the University of Innsbruck, and Adjunct (Honorary) Professor for Limnology at the University of Salzburg

  • 1998-Aug 31, 2012: Senior Scientist and director at the Institute for Limnology of the Austrian Academy of Sciences, Mondsee, Austria, and Adjunct (Honorary) Professor for Limnology at the University of Salzburg

  • 1995-1998: Senior scientist (Associate Professor level) and head of working group Microbial Ecology' at the Max-Planck-Institute for Limnology, Plön, Germany

  • 1995: University lecturer (Privatdozent, Venialegendi for Limnology) at the Christian-Albrechts-University at Kiel

  • 1993-1995: Guest researcher at the West Vancouver Laboratory,Fisheries & Oceans Canada (hosted by Dr. J. G. Stockner)

  • 1992: University lecturer (Privatdozent, Venia legendi for Hydrobiology) at Konstanz.

  • 1988-1993: Assistant Professor (Wissenschaftlicher Assistent, C1) at the Limnological Institute Konstanz

  • 1986-1988: Research Scientist at the Limnological Institute Konstanz

  • 1980-1985: Research Associateat the Institute for Marine Research Kiel and the Biological Station Helgoland at List/Isle of Sylt



My research focuses on microbial food webs and microbial diversity in aquatic ecosystems (see Weisse 2003, 2006a, 2006b, 2008 for reviews). Lately, I studied niche separation among sympatric freshwater ciliates, flagellates, and microeukaryotes (rotifers); in particular, I investigated the effect of temperature, pH, food, competitors and predators on growth and production rates of key species in different habitats. Our laboratory experiments revealed that interaction of the various abiotic and biotic variables usually strongly narrows the realized niche width of photoautotrophic (i.e., algae) and heterotrophic protists. We use electronic particle counting, flow cytometry and image analysis to analyze population dynamics of bacteria, picocyanobacteria, and protists. I am intrigued by the ecological significance of clonal variability among asexually reproducing microbes. Recent projects (see Projects and Publications, below) investigated the significance of local adaptation among globally, respectively locally, dispersed protists and rotifers. We study the specific adaptations that enable protists and microeukaryotes to survive in extreme habitats such as acid mining lakes (pH ≈2.6) and tank bromeliads. We also investigate the consequences of global warming for biodiversity in alpine lakes. To this end, we perform microcosm experiments to mimic ongoing change in the temperature regime and nutrient load to our study lakes in the Austrian Salzkammergut area.


Our long-term goal is to assess phenotypic flexibility relative to genotypic variability in relation to environmental conditions, i. e. we want to measure microbial diversity and understand the inherent processes (microevolution) creating and maintaining the diversity. Graduate students, Postdocs and guest researchers are welcome to join our working group.



  • Peter Stadler (Laboratory technician) - Culture collection, flow cytometry, image analysis
  • Birgit Gröschl (Master student)



  • Morphology and ecology of endemic ciliates from bromeliads, funded by the Austrian Science Fund (together with W. Foissner, Univ. of Salzburg, Project no. P20360-B17) (Summary)

  • "DEcadal deTECTion of biodIVErsity in alpine lakes, DETECTIVE - Global warming threatens biodiversity in (ultra)-sensitive Alpine lakes: an assessment of past, present and future scenarios" funded by the Alpine Research Programme of the Austrian Academy of Sciences (Dec 2009 - Dec 2012), National and International Research Programme (together with R. Kurmayer)

  • Patterns and processes of adaptation and tolerance to low pH of freshwater plankton. FWF project P 20118 (Summary and publications)

  • Ecological significance of phenotypic and genotypic variability in freshwater protists – a test case using the oligotrich ciliate Meseres corlissi (together with W. Foissner, Univ. Salzburg; H. Müller, Konstanz; D. Lynn & M. Strüder-Kypke, Univ. Guelph, Ontario, Canada) FWF project P 16796 finished; (Summary of final report and publications)

  • Ecophysiological impact of pH on aquatic protists (Weisse & Stadler 2006) PDF

  • Distribution, diversity, and population dynamics of autotrophic picoplankton in the lakes of the 'Salzkammergut' area (Austria) , funded by the Austrian Science Fund (Project no. P14238-Bio, finished (Summary)



  • Field and laboratory courses, lecture courses and seminars in Limnology, Biological Oceanography and Protozoology at the Universities in Kiel, Konstanz, Freiburg and Salzburg.

  • Current courses at the Univ. of Salzburg: Applied Limnology, Evolution and Diversity

  • Supervisor of 12 Diploma (masters) and 6 Doctorate (PhD) students.




  • Weisse, T., Scheffel, U., Stadler, P. & Foissner, W. (2013). Functional ecology of the ciliate Glaucomides bromelicola, and comparison with the sympatric species Bromeliothrix metopoides. J. Eukaryot. Microbiol. 60: (in press).

  • Weisse, T., Scheffel, U., Stadler, P. & Foissner, W. (2013). Bromeliothrix metopoides, a boom and bust ciliate (Ciliophora, Colpodea) from tank bromeliads. Eur. J. Protistol. 49: 406-41, [doi: 10.1016/j.ejop.2013.02.001].

  • Weisse T (2013). Editorial. Eur. J. Protistol. 49: 327, [doi: 10.1016/j.ejop.2013.04.008]

  • Weisse, T., Laufenstein, N. & Weithoff, G. (2013). Multiple environmental stressors confine the ecological niche of the rotifer Cephalodella acidophila. Freshwater Biol. 58: 1008-1015 [doi:10.1111/fwb.12104]

  • Weisse T., Moser M., Scheffel U., Stadler P., Berendonk T., Weithoff G., Berger H. (2013). Systematics and species-specific response to pH of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) from acid mining lakes. Eur. J. Protistol. 49: 255-271 [doi: 10.1016/j.ejop.2012.08.001].


  • Weisse T. (2012). Editorial. Eur. J. Protistol. 48: 95.


  • Jersabek, C., Weithoff, G. & Weisse, T. (2011). Cephalodella acidophila n. sp. (Monogononta: Notommatidae), a new rotifer species from highly acidic mining lakes. Zootaxa 2939: 50-58.

  • Moser, M. & Weisse, T. (2011c). The most acidified Austrian lake in comparison to a neutralized mining lake. Limnologica doi:10.1016/j.limno.2011.01.002

  • Moser, M. & Weisse, T. (2011b). Combined stress effect of pH and temperature narrows the niche width of flagellates in acid mining lakes. J. Plankton Res. 33: 1023-1032.

  • Moser, M. & Weisse, T. (2011a). The outcome of competition between the two chrysomonads Ochromonas sp. and Poterioochromonas malhamensis depends on pH. Eur. J. Protistol. 47: 79-85.


  • Weisse, T. (2010). Editorial. Eur. J. Protistol. 46: 253.

  • Weithoff, G., Moser, M., Kamjunke, N., Gaedke, U., and Weisse, T. (2010): Lake morphometry and wind exposure may shape the plankton community structure in acidic mining lakes. Limnologica. 40: 161-166.


  • Weisse, T. (2009): The European Journal of Protistology – Changes, chances and challenges. Eur. J. Protistol. 45: 163–164 .

  • Weisse, T., Boenigk, J. and Müller, H. (2009): Ecological methods for the study of heterotrophic nano- and microplankton of fresh and marine waters. In: A course in Protozoology, Röttger, R., Knight, R. & Foissner, W. (eds), Protozool. Monographs 4: 232-242.

  • Moser, M., Callieri, C. and Weisse, T. (2009):. Photosynthetic and growth response of freshwater picocyanobacteria are strain-specific and sensitive to photoacclimation. J. Plankton Res. 31: 349-357. LINK: PDF


  • Montagnes, D.J.S., Morgan, G., Bissinger, J. E., Atkinson, D. and Weisse, T. (2008): Short-term temperature change may impact freshwater carbon flux: a microbial perspective. Global Change Biology 14: 2810-2822.

  • Weisse, T., Strüder-Kypke, M., Berger, H. & Foissner, W. (2008): Genetic, morphological, and ecological diversity of spatially separated clones of Meseres corlissi Petz and Foissner, 1992 (Ciliophora, Spirotrichea). J. Eukaryot. Microbiol. 55: 257-270.

  • Gächter, E. and Weisse, T. (2008): Long-term acclimation of growth rates in the oligotrich freshwater ciliate Meseres corlissi. Verh. Internat. Verein. Limnol. 30: 218-222.

  • Weisse, T. (2008): Distribution and diversity of aquatic protists: an evolutionary and ecological perspective. Biodivers. Conserv. 17: 243-259. Link PDF

  • Weisse, T. (2008a): Limnoecology - The Ecology of Lakes and Streams (Book review of Lampert, W. u. Sommer, U., 2nd edition 2007). J Plankton Res. doi: 10.1093/plankt/fbn013 PDF

  • Weisse, T. (2008b): Wilhelm FOISSNER and the German Society for Protozoology. Denisia 23: 9. PDF

  • Weisse, T. (2008c): The meaning of protist diversity: ecology meets taxonomy. Denisia 23: 297-306. PDF


  • Weisse, T. (2007): Limnology in Austria and at Mondsee - Going Against the Trend? SILnews 51: 7-8. PDF

  • Weisse, T., Scheffel, U., Stadler , P. and Foissner, W. (2007): Local adaptation among geographically distant clones of the cosmopolitan freshwater ciliate Meseres corlissi. II. Response to pH. Aquat. Microb. Ecol. 47: 289-297. PDF

  • Weisse, T. (2007a): Der Artbegriff bei Bakterien, Ein- und Vielzellern (The Species concept of bacteria, protists and metazoa). Denisia 20: 149-154 (in German, with English abstract). PDF


  • Weisse, T. (2006 c): Biodiversity of aquatic protists – what can we learn from bacteria and Daphnia? Endocytobiosis Cell Res. 17: 154-163. PDF

  • Weisse, T. (2006b): Biodiversity of freshwater microorganisms - achievements, problems, and perspectives. In: Gliwicz, Z. M. Mazurkiewicz-Boron, G. & Rouen, K. (eds.): Reviewing European Freshwater Sciences, 2005. Pol. J. Ecol. 54: 633-652. PDF

  • Foissner, W., Pichler, M., Al-Rahsheid, K. and Weisse, T. (2006): The unusual, Lepidosome-coated resting cyst of Meseres corlissi (Ciliophora: Oligotrichea): encystment and genesis and release of the lepidosomes. Acta Protozool. 45: 323-338.

  • Gächter, E. and Weisse, T. (2006): Local adaptation among geographically distant clones of the cosmopolitan freshwater ciliate Meseres corlissi. I. Temperature response. Aquat. Microb. Ecol. 45: 291-300. PDF

  • Weisse, T. (2006a): Freshwater ciliates as ecophysiological model organisms - lessons from Daphnia, major achievements, and future perspectives. Arch. Hydrobiol. 167: 371-402. PDF

  • Weisse, T. and Stadler, P. (2006a): Effect of pH on growth, cell volume, and production of freshwater ciliates, and implications for their distribution. Limnol. Oceanogr. 51: 1708-1715. PDF

  • Müller, H., Foissner, W. and Weisse, T. (2006): The role of soil in the life cycle of Meseres corlissi (Ciliophora: Oligotrichea): experiments with two clonal strains from the type locality, an astatic meadow pond. Aquat. Microb. Ecol. 42: 199-208. PDF

  • Weisse, T. and Rammer, S. (2006): Pronounced ecophysiological clonal differences of two common freshwater ciliates, Coleps spetai (Prostomatida) and Rimostrombidium lacustris (Oligotrichida), challenge the morphospecies concept. J. Plankton Res. 28: 55-63. PDF


  • Callieri, C., Moro, S., Crosbie, N.D. and Weisse, T. (2005): Strain-specific photosynthetic response of freshwater picocyanobacteria. Verh. int. Ver. Limnol. 29: 777-782.

  • Foissner, W., Müller, H. and Weisse, T. (2005): The unusual, Lepidosome-coated resting cyst of Meseres corlissi (Ciliophora: Oligotrichea) 1. Light and scanning electron microscopy, cytochemistry. Acta Protozool. 44: 201-215.


  • Weisse, T. (2004): Meseres corlissi : a rare oligotrich ciliate adapted to warm water and temporary habitats. Aquat. Microb. Ecol. 37: 75-83. PDF


  • Weisse, T. (2003): Pelagic Microbes - Protozoa and the Microbial Food Web. In: O'Sullivan, P. & Reynolds, C.S. (eds.), The Lakes Hand­book, Vol. I, Blackwell Scientific Publ., Ox­ford, pp. 417-460.

  • Crosbie, N.D., Pöckl, M. and Weisse, T. (2003): Rapid establishment of clonal isolates of freshwater autotrophic picoplankton by single-cell and single-colony sorting. J. Microbiol. Meth. 55: 361-370. PDF

  • Crosbie, N.D., Pöckl, M. and Weisse, T. (2003): Dispersal and phylogenetic diversity of non-marine picocyanobacteria, inferred from 16S rRNA gene and cpcBA -intergenic spacer sequence analyses. Appl. Environ. Microbiol. 69 : 5716-5721. PDF

  • Crosbie, N.D., Teubner, K. and Weisse, T. (2003): Flow-cytometric mapping provides novel insights into the seasonal and vertical distribution of freshwater autotrophic pico­plankton. Aquat. Microb. Ecol. 33.: 53-66. PDF

  • Lindström, E.S., Stadler, P. and Weisse, T. (2003): Live sorting and survival of unstai­ned and DAPI-stained ciiates by flow cyto­metry. Arch. Hydrobiol. 157 : 173-184.


  • Weisse, T. and Lettner, S. (2002): The ecological significance of intraspecific variation among freshwater ciliates. Verh. Internat. Verein. Limnol. 28: 1880-1884.

  • Weisse, T. (2002): The significance of inter- and intraspecific variation in bacterivorous and herbivorous protists. Antoine van Leeuwenhoek 81: 327-341. PDF

  • Weisse, T. and Mindl, B. (2002): Picocyanobacteria - sensitive bioindicators of contaminant stress in an alpine lake (Lake Traunsee, Austria). Water, Air, and Soil Pollution: Focus 2: 191-210.

  • Müller, H., Stadler, P. and Weisse, T. (2002): Seasonal dynamics of cyst formation of strombidid ciliates in alpine Lake Mondsee Austria. Aquat. Microb. Ecol. 29: 181-188. PDF

  • Weisse, T. Stadler, P., Lindström, E.S., Kimmance, S.A. and Montagnes, D.J.S. (2002): Interactive effect of temperature and food concentration on growth rate: A test case using the small freshwater ciliate Urotricha farcta. Limnol. Oceanogr. 47: 1447-1455. PDF

  • Weisse, T. Gomoiu, M.-T., Scheffel, U. and Brodrecht, F. (2002): Biomass and size composition of the combjelly Mnemiopsis sp. in the north-western Black Sea during spring and summer. Estuar. Cst. Shelf Sci. 54: 423-437 Abstract .

  • Lindström, E.S., Stadler, P. and Weisse, T. (2002): Quantification of small cultured ciliates by flow cytometry is superior to electronic particle counting and light microscopy. J. Microb. Methods 49: 173-182. PDF

  • Weisse, T. and Frahm, A. (2002): Direct and indirect impact of two common rotifer species (Keratella spp.) on two abundant ciliate species (Urotricha furcata, Balanion planctonicum). Freshwater Biology 47: 53-64. PDF

 Click here to get a full list of publications by T. Weisse


Professional Memberships and Honours

  • American Society of Limnology and Oceanography

  • German Society of Protozoologists (DGP [])
    • President (2008-2011)
    • Vice President (2005-2008)

  • International Society of Protistologists (ISOP)
    • Member of ISOP’s Strategic Planning Committee (2012-)

  • Member of the Peer Review College of the Danish Council for Independent Research (2012-)

  • International Association of Theoretical and Applied Limnology (SIL)

  • SIL-Austria ( - Member of the Managing Committee since (2007-2012)

  • Leipniz-Institut für Gewässerökologie und Binnenfischerei ( - Member of the Scientific Advisory Board (2004-2012), vice-chairman (2008-2012)

  • Wasser Cluster Lunz ( - Member of the Scientific Advisory Board (2007-2012)


Editorial Advisorship/Editorial Board Service

  • European Journal of Protistology (Editor, 2008-) LINK

  • Freshwater Biology (Editorial Board, 2009-)

  • Aquatic Ecosystem Health and Management Soc. (AEHMS, Editorial Board 2002-2006)

  • Journal of Eukaryotic Microbiology (Associate Editor, 2006-2009)

  • Journal of Plankton Research (Editorial Board 1998-2008, Assoc. Editor 2002-2003)

  • Limnologica (Editorial Board 2004-present) LINK

  • Protozoologiacal Monographs (Field Editor, 2001-present)


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