Logo university of Turku
Logo of Academy of Finland


Phytoplankton-Parasite interactions along a salinity gradient

Phytoplankton play a crucial role in providing approximately 50% of the Earth’s available oxygen, serving as a vital food source for higher trophic levels, and acting as a significant carbon sink in the atmosphere. Consequently, changes in phytoplankton abundance and productivity due to parasite infections can have a profound impact on Earth’s climate. Our project aims to address fundamental questions concerning an enigmatic group of fungal phytoplankton parasites known as Chytridiomycota within the broader ecological context of harmful algal blooms and global climate change. We use the Baltic Sea, with its unique salinity gradient, as a model ecosystem to answer fundamental questions: Which species of parasites are present? What is their abundance? What is their potential to control phytoplankton blooms? How might climate-related changes in marine salinity influence the interactions between fungal parasites and their phytoplankton hosts?
To answer these questions, classical cultivation methods are combined with advanced molecular techniques and live cell imaging approaches. This comprehensive approach allows us to characterize biodiversity, identify environmental host refuges, and determine the conditions that are optimal or detrimental for parasite transmission along the salinity gradient of the Baltic Sea.

This research is funded by the Academy of Finland.

Virtual lab: web-based platform for Agent Based Modeling

In this project, we are developing a platform-independent virtual lab dedicated to microbial interactions. This tool features 3D visualization, plotting and intuitive user interface. The primary goal is to conduct virtual experiments for the theoretical validation of hypotheses. Additionally, we want to make this also an educational tool to illuminate key concepts in aquatic microbial ecology and evolution.

Specific expertise

Chytridiomycota taxonomy, isolation and cultivation of zoosporic parasites together with their phytoplankton host, light and fluorescence microscopy, individual based modeling

Software and Simulation


A virtual lab in your web browser

screenshot uglylab.app
screenshot uglyCounter


A multi counter web app


Thomé, P. C., J. Wolinska, S. Van Den Wyngaert, A. Reñé, D. Ilicic, R. Agha, H.-P. Grossart, E. Garcés, M. T. Monaghan, and J. F. H. Strassert. (2024) Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum. Molecular Phylogenetics and Evolution 197:108103. https://doi.org/10.1016/j.ympev.2024.108103

Hyde KD, Abdel-Wahab MA, Abdollahzadeh J, Abeywickrama PD, Absalan S, Afshari N,…Van den Wyngaert S,…et al. (2023) Global consortium for the classification of fungi and fungus-like taxa. Mycosphere 14: 1960–2012. DOI:10.5943/mycosphere/14/1/23

Bilik, S., Batrakhanov, D., Eerola, T., Haraguchi, L., Kraft, K., Van den Wyngaert, S., Kangas, J., Sjöqvist, C., Madsen, K., Lensu, L., Kälviäinen, H. & Horak, K. Toward phytoplankton parasite detection using autoencoders. Machine Vision and Applications 34, 101 (2023). https://doi.org/10.1007/s00138-023-01450-x

Klawonn, I., S. Van den Wyngaert, M. H. Iversen, T. J. W. Walles, C. M. Flintrop, C. Cisternas-Novoa, J. C. Nejstgaard, M. Kagami, and H.-P. Grossart. 2023. Fungal parasitism on diatoms alters formation and bio–physical properties of sinking aggregates. Communications Biology 6:1–14.

Silke Van Den Wyngaert, Martin J Kainz, Robert Ptacnik, Mucilage protects the planktonic desmid Staurodesmus sp. against parasite attack by a chytrid fungus, Journal of Plankton Research, 2022;, fbac071, https://doi.org/10.1093/plankt/fbac071

Ilicic D, Woodhouse J, Karsten U, Zimmermann J, Wichard T, Quartino ML, Campana GL, Livenets A, Van den Wyngaert S and Grossart H-P (2022) Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones. Front. Microbiol. 13:805694. doi: 10.3389/fmicb.2022.805694

Van den Wyngaert, S., Ganzert, L., Seto, K., Rojas-Jimenez, K., Agha R., Berger SA., Woodhouse J., Padisak J., Wurzbacher C., Kagami M., Grossart H-P. Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits. ISME J (2022). https://doi.org/10.1038/s41396-022-01267-y

Klawonn I, Dunker S, Kagami M, Grossart H-P, Van den Wyngaert S. Intercomparison of Two Fluorescent Dyes to Visualize Parasitic Fungi (Chytridiomycota) on Phytoplankton. Microb Ecol (2021). https://doi.org/10.1007/s00248-021-01893-7

Klawonn I., Van den Wyngaert S., Parada A-E., Arandia-Gorostidi N., Whitehouse M-J., Grossart H-P, Dekas A-E. (2021). Characterizing the “fungal shunt”: Parasitic fungi on diatoms affect carbon flow and bacterial communities in aquatic microbial food webs. Proceedings of the National Academy of Sciences. 118(23). https://doi.org/10.1073/pnas.2102225118

Beng K., Wolinska J., Funke, E., Van den Wyngaert S., Gsell A., & Monaghan M. (2021). Temporal dynamics of freshwater planktonic parasites inferred using a DNA metabarcoding time-series. Parasitology. 1-10. doi:10.1017/S0031182021001293

Yoneya K, Miki T., Van den Wyngaert S., Grossart H-P., Kagami M. (2021). Non-random patterns of chytrid infections on phytoplankton host cells: mathematical and chemical ecology approaches. Aquatic Microbial Ecology. 87:1–15. https://doi.org/10.3354/ame01966

Van den Wyngaert S. & Kagami M. (in press) Fungi and chytrids. In: Encyclopedia of Inland Waters 2nd Edition

Rasconi S., Ptacnik R., Dannera S., Van den Wyngaert S., Rohrlack T., Pileckya M. and Kainz M.J. (2020) Parasitic chytrids upgrade and convey primary produced carbon during inedible algae proliferation. Protist. https://doi.org/10.1016/j.protis.2020.125768

Sánchez Barranco, V., Van der Meer, M.T.J., Kagami, M., Van den Wyngaert, S., Van de Waal, D.B., Van Donk, E., Gsell, A.S. (2020) Trophic position, elemental ratios and nitrogen transfer in a planktonic host–parasite–consumer food chain including a fungal parasite. Oecologia. https://doi.org/10.1007/s00442-020-04721-w

Seto, K., Van den Wyngaert, S., Degawa, Y. & Kagami, M. (2020). Taxonomic revision of the genus Zygorhizidium: Zygorhizidiales and Zygophlyctidales ord. nov. (Chytridiomycetes, Chytridiomycota). Fungal Systematics and Evolution, 5, 17-38. doi.org/10.3114/fuse.2020.05.02

Wurzbacher, C., Kreiling, A.-K., Svantesson, S., Van den Wyngaert, S., Larsson, E., Heeger, F. et al. (2020). Fungal communities in groundwater springs along the volcanic zone of Iceland. Inland Waters, 1-10. https://doi.org/10.1080/20442041.2019.1689065

Taube, R., Fabian, J., Van den Wyngaert, S., Agha, R., Baschien, C., Gerphagnon, M. et al. (2019). Potentials and limitations of quantification of fungi in freshwater environments based on PLFA profiles. Fungal Ecology, 41, 256-268.

Grossart H.-P., Van den Wyngaert S., Kagami M., Wurzbacher C., Cunliffe M., and Rojas-Jimenez K. (2019). Fungi in aquatic ecosystems. Nature Reviews Microbiology. 10.1038/s41579-019-0175-8.

Wurzbacher, C., Larsson, E., Bengtsson‐Palme, J., Van den Wyngaert, S., Svantesson, S., Kristiansson, E., Kagami, M. and Nilsson, R. H. (2018), Introducing ribosomal tandem repeat barcoding for fungi. Molecular Ecology Resources. doi:10.1111/1755-0998.12944

Van den Wyngaert, S., Rojas-Jimenez, K., Seto, K., Kagami, M. & Grossart, H.-P. (2018). Diversity and Hidden Host Specificity of Chytrids Infecting Colonial Volvocacean Algae. Journal of Eukaryotic Microbiology. doi:10.1111/jeu.12632

Nilsson, R. H., A. F. S. Taylor, R. I. Adams, C. Baschien, J. Bengtsson-Palme, P. Cangren, C. Coleine, H.-M. Daniel, S. I. Glassman, Y. Hirooka, L. Irinyi, R. Iršėnaitė, Pedro M. Martin-Sanchez, W. Meyer, S.-Y. Oh, Jose P. Sampaio, K. A. Seifert, F. Sklenář, D. Stubbe, S.-O. Suh, R. Summerbell, S. Svantesson, M. Unterseher, Cobus M. Visagie, M. Weiss, J. H. C. Woudenberg, C. Wurzbacher, S. Van den Wyngaert, N. Yilmaz, A. Yurkov, U. Kõljalg, and K. Abarenkov. (2018). Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28:65-82.

Frenken, T., E. Alacid, S. A. Berger, E. C. Bourne, M. Gerphagnon, H.-P. Grossart, A. S. Gsell, B. W. Ibelings, M. Kagami, F. C. Küpper, P. M. Letcher, A. Loyau, T. Miki, J. C. Nejstgaard, S. Rasconi, A. Reñé, T. Rohrlack, K. Rojas-Jimenez, D. S. Schmeller, B. Scholz, K. Seto, T. Sime-Ngando, A. Sukenik, D. B. Van de Waal, S. Van den Wyngaert, E. Van Donk, J. Wolinska, C. Wurzbacher, and R. Agha. (2017). Integrating chytrid fungal parasites into plankton ecology: research gaps and needs. Environmental Microbiology 19:3802-3822.

Silke Van den Wyngaert, Kensuke Seto, Keilor Rojas-Jimenez, Maiko Kagami, Hans-Peter Grossart, A New Parasitic Chytrid,  (Rhizophydiales, Staurastromycetaceae fam. nov.), Infecting the Freshwater Desmid  sp., Protist, Volume 168, Issue 4, 2017, Pages 392-407, ISSN 1434-4610, http://dx.doi.org/10.1016/j.protis.2017.05.001.

Van den Wyngaert S., Möst M., Freimann R., Ibelings B.W., Spaak P. (2015) Hidden diversity in the freshwater planktonic diatom Asterionella formosa. Molecular Ecology (2015) 24, 2955–2972. doi: 10.1111/mec.13218

Van den Wyngaert S., Vanholsbeeck O., Spaak P. and Ibelings B. W. (2014), Parasite fitness traits under environmental variation: disentangling the roles of a chytrid’s immediate host and external environment. Microb Ecol:1-12. doi:10.1007/s00248-014-0434-1

Van den Wyngaert S., Gsell A. S., Spaak P. and Ibelings B. W. (2013), Herbicides in the environment alter infection dynamics in a microbial host–parasite system. Environmental Microbiology. doi: 10.1111/j.1462-2920.2012.02874.x

Ibelings, B.W., Gsell, A.S., Mooij, W.M., van Donk, E., Van den Wyngaert, S. & Domis, L.N.D. (2011). Chytrid infections and diatom spring blooms: paradoxical effects of climate warming on fungal epidemics in lakes. Freshwat. Biol., 56, 754-766.

Van den Wyngaert S, Salcher M.M., Pernthaler J., Zeder M. and Posch T. (2011). Quantitative dominance of seasonally persistent filamentous cyanobacteria (Planktothrix rubescens) in the microbial assemblages of a temperate lake. Limnol. Oceanogr. 56:97-109.

Zeder M., Van den Wyngaert S., Köster O., Felder K.M., Pernthaler J. (2010). Automated quantification and sizing of unbranched filamentous cyanobacteria by model based object oriented image analysis. Applied and Environmental Microbiology, 76(5):1615-1622.