Projects

The various interactions between bacteria, cyanobacteria and unicellular eukaryotes (protists) in freshwater systems are in focus of our studies. Our research site is primarily Lake Zurich where we also follow the tradition of long-term monitoring (for 60 years). Food webs in lakes and ponds are based on the quantitative importance (biomass) of a tremendous diversity of prokaryotes and protists. Both organismic entities include heterotrophic, (photo)autotrophic and mixotrophic representatives. Prokaryotes are often seen only as potential prey for protists, but interactions are manifold. Firstly, prokaryotes can be efficient competitors of protists in aquatic systems due to overlapping lifestyles and nutrient requirements (e.g., cyanobacteria versus algae). Secondly, prokaryotes and unicellular eukaryotes can be linked to each other through various symbiotic interactions (ranging from parasitism to mutualism). Thirdly, interactions between heterotrophic bacteria and bloom-forming cyanobacteria can influence all higher trophic levels in freshwater food webs. In addition to the importance of these relationships for the functioning of aquatic systems, we investigate why and how interactions have developed and will continue to evolve in times of ecosystem change (climate change).

The harmful cyanobacterium Planktothrix rubescens can get a dominant primary producer in especially mesotrophic, large temperate lakes (e.g., Lakes Zurich & Hallwil, CH). The cyanobacterial species is favored by effects of lake warming, thus the number of lakes affected by blooms increases, with now occasional reports of mass developments in even ‘atypical’ habitats, e.g., both small shallow (e.g., Lake Hütten, CH) and large eutrophic lakes (e.g., Lake Zug, CH). In terms of food web structure, P. rubescens seems to be rather a sink of nutrients owing to competitive advantages over algae and reduced edibility (via morphology and toxins) for predators. However, the collapse of former population biomass and toxins during mixing events (e.g., to 1% of biomass in Lake Zurich) may lead to a boost (link) of available nutrients via heterotrophic bacteria or parasites to higher trophic levels. Although the annual decline of P. rubescens biomass in large lakes and breakdowns in smaller systems are well documented, degradation processes of P. rubescens biomass are widely unknown, as well as the importance of decaying biomass for carbon distribution in food webs.

Lake Zurich (Switzerland) serves as the major source of drinking water for >1 million people and is thus of great economic importance. A 60-year long-term dataset of the Limnological Station provides strong evidence, that changes in the mixis regime due to warming is coupled to an increasing importance of the filamentous cyanobacterium Planktothrix rubescens. In our weekly to biweekly monitoring of the lake multiple physical and microbial parameters are determined. The goal of this project is to explain current patterns of P. rubescens growth dynamics and predict expected changes in Lake Zurich. We apply a holistic limnological approach based on fine-scale temporal and spatial samplings. A detailed genetic characterization of P. rubescens (in terms of gas vesicle and microcystin genotypes, and entire genomes) gives new scientific aspects for the long-term dataset.

Selected publications on this topic

Knapp, D., et al. (2021). The red harmful plague in times of climate change: Blooms of the cyanobacterium Planktothrix rubescens triggered by stratification dynamics and irradiance. Frontiers in Microbiology 12:2366. https://doi.org/10.3389/fmicb.2021.705914

Knapp, D., and Posch, T. (2021). Burgunderblutalge im Zürichsee. Populationsdynamik und Einfluss des Klimawandels. Aqua & Gas 4:14-21. https://www.aquaetgas.ch/wasser/gew%C3%A4sser/20210330_ag4_burgunderblutalge-im-z%C3%BCrichsee/

Posch, T., et al. (2012). Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming. Nature Climate Change 2:809-813. https://doi.org/10.1038/nclimate1581

Our work was and is supported by several grants of the Swiss National Science Foundation, AWEL (Amt für Abfall, Wasser, Energie und Luft - Kanton Zürich), Water Supply Zurich and the University of Zurich.

The filamentous cyanobacterium Planktothrix rubescens is generally considered toxic for eukaryotes. Intact cyanobacterial cells contain cyclic heptapeptides (microcystins - MCs) which are potent hepatotoxins and potentially act as tumor promoters on a molecular base. MCs also act as efficient inhibitors of eukaryotic serine/threonine-specific protein phosphatases. Potential consumers (zooplankton and -benthos) get in direct contact with the endotoxins when cyanobacterial filaments are ingested and digested.

Although cyanobacteria are often considered unsuitable or toxic food by most consumers, various protists (e.g., within Amoeboza, Ciliophora, Nucleariidae) have been described as efficient predators of cyanobacterial blooms. It is of particular interest to better understand how these protists, being eukaryotic organisms, can survive a toxic diet. Former detailed studies about the amoeboid Nucleariidae and their interactions with symbiotic bacteria and filamentous cyanobacteria gave us a good scientific background about this topic. Future studies on already cultivated ciliate and other amoeboid species will follow. This knowledge will be of great relevance for a better understanding of natural degradation processes of MCs in Lake Zurich.

Selected publications on this topic

Dirren, S., et al. (2017). Grazing of Nuclearia thermophila and Nuclearia delicatula (Nucleariidae, Opisthokonta) on the toxic cyanobacterium Planktothrix rubescens. European Journal of Protistology 60:87-101. https://doi.org/10.1016/j.ejop.2017.05.009

Dirren, S. and Posch, T. (2016). Promiscuous and specific bacterial symbiont acquisition in the amoeboid genus Nuclearia (Opisthokonta). FEMS Microbiology Ecology 92:fiw105. https://doi.org/10.1093/femsec/fiw105

Dirren, S., et al. (2014). Ménage-à-trois: The amoeba Nuclearia sp. from Lake Zurich with its ecto- and endosymbiotic bacteria. Protist 165:745-758. https://doi.org/10.1016/j.protis.2014.08.004

Our work was and is supported by several grants of the Swiss National Science Foundation and the University of Zurich.

Planktonic freshwater ciliates are still our ‘favorite’ protists. In course of our monitoring programs on Lake Zurich, we also focus on fine-scale temporal and spatial dynamics of the ciliate assemblage. However, most planktonic ciliates have short-lived maxima and many species seem to be rare or ephemeral. The classical morphospecies based methods have limitations concerning the amount and volume of samples that can be processed. Thus, for high sampling frequencies at large scales, high throughput sequencing (HTS) and metagenomes of freshwater ciliates seems to be one promising tool. However, planktonic ciliate taxa are still poorly represented in public databases. Through linking operational taxonomic units (OTUs) with known morphospecies, we can use the deep knowledge about the autecology of these species. In addition, we developed a suitable protocol for the fluorescence in situ hybridization of planktonic ciliates. By this technique larger sample volumes at high sampling frequencies can be evaluated with species-specific probes for even closely related, similar looking as well as very tiny ciliates.

Selected publications on this topic

Schalch-Schuler, M., et al. (2025). The planktonic freshwater ciliate Balanion planctonicum (Ciliophora, Prostomatea): A cryptic species complex or a "complex species"? Journal of Eukaryotic Microbiology 72(1):e13084. https://doi.org/10.1111/jeu.13084

Dirren-Pitsch, G., et al. (2022). FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates. Frontiers in Microbiology 13. https://doi.org/10.3389/fmicb.2022.1070232

Pitsch, G., et al. (2019). Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts? Frontiers in Microbiology 10:248. https://doi.org/10.3389/fmicb.2019.00248

Our work was and is supported by several grants of the Swiss National Science Foundation and the University of Zurich.

The first real green Tetrahymena species – Tetrahymena utriculariae:

Mostafa, K. M., et al. (2025). Environment-dependent mutualism–parasitism transitions in the incipient symbiosis between Tetrahymena utriculariae and Micractinium tetrahymenae. The ISME Journal, 19: wraf203. https://doi.org/10.1093/ismejo/wraf203

Pitsch, G., et al. (2017). The green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with its endosymbiotic algae (Micractinium sp.), living in traps of a carnivorous aquatic plant. Journal of Eukaryotic Microbiology, 64:322-335. https://doi.org/10.1111/jeu.12369

Interesting bacteria from Lake Zurich and other lakes:

Salcher, M.M., et al. (2025). Bringing the uncultivated microbial majority of freshwater ecosystems into culture. Nature Communications 16:7971. https://doi.org/10.1038/s41467-025-63266-9

Alfreider, A., et al. (2025). Depth-dependent distribution patterns of ammonia- and nitrite-oxidizing microorganisms in the water column of stratified lakes. Scientific Reports 15:42232. https://doi.org/10.1038/s41598-025-26324-2

Resilience of planktonic freshwater ciliates:

Schalch-Schuler, M., et al. (2024). Variability of winter cooling affects intensity of phytoplankton spring blooms – how resilient is the ciliate assemblage composition to changes in food availability? Frontiers in Protistology 2. https://doi.org/10.3389/frpro.2024.1428985

1. Bacteria-protists interactions illustrated by the amoebae Nuclearia spp. and their bacterial symbionts

Sebastian Dirren, Thomas Posch
Collaboration: Dr. Michaela Salcher (Institute of Hydrobiology, Czech Republic)
SNF project 31003A_159842 (2015-2018)

All animals and plants live in symbiosis with several, up to thousands of prokaryotic species, however, this phenomenon is not restricted to multicellular organisms. Protists (unicellular eukaryotes) live in intimate contact with bacteria, and this co-occurrence is a potential playground for symbioses (from mutualism to parasitism). Bacteria interacting with protists are either attached to extracellular structures (ectosymbionts) or inside the host itself (endosymbionts). In this project we study the diverse symbioses of amoeboid species of the genus Nuclearia (Opisthokonta, Dirren et al. 2014) with their endo- and / or ectosymbiotic bacteria, also in view of the fact that a few Nuclearia representatives may have no (or lost) symbionts. Nucleariidae are placed at the animal-fungal boundary, and they are unique in that their ectosymbionts (when present) are loosely arranged in a mucous layer, without a direct contact to hosts. Thus, Nucleariidae are an ideal model group to study the basic principles of symbioses between opisthokonts and prokaryotes.

2. Co-occurrence networks in aquatic food webs: ciliates as models

Gianna Pitsch, Thomas Posch
Collaboration: Dr. Bettina Sonntag + Dr. Barbara Kammerlander (Institute for Limnology, Mondsee, Austria), Prof. Dr. Thorsten Stoeck (University of Kaiserslautern, Germany)
SNF D-A-CH project 310030E-160603/1 (2015-2018)

Aquatic food webs have always fascinated freshwater ecologists and relationships among the involved key players are extraordinary complex networks. Food webs consist of microscopic organisms, including viruses, bacteria, protists and small metazoans that co-occur in seasonal cycles. Elucidating the functional traits of individual planktonic organisms, their food preferences and their potential predators require a close monitoring of their dynamics in a habitat.

The major goal of this project is to identify factors that trigger the variability in ciliate assemblages (Posch et al. 2015) in time (seasonality) and space (spatial distribution) in two lakes. We base our observations upon ciliates because their morphotypes are relatively easy to identify, they have short generation times making them ideal experimental models, and current research on taxonomic marker genes has progressed far compared to other heterotrophic protists. Our international cooperation (D-A-CH) includes three experts on ciliate taxonomy, molecular ciliate ecology, aquatic ecology and computational biology. Through this integrative approach by combining classical morphological analyses with next generation sequencing, a much deeper look into microbial communities will be possible.

3. Interactions between global change, biodiversity, and feedback mechanisms

Yana Yankova, Thomas Posch, Jakob Pernthaler
Collaboration: Prof. Dr. Owen Petchey + Aurélie Garnier (University of Zurich)
Funding: University of Zurich, URPP – University Research Priority Programs

Climate warming affects the seasonal dynamics of important organisms in Lake Zurich, such as the toxic cyanobacterium Planktothrix rubescens (Posch et al. 2012). There is evidence that spring phytoplankton blooms will become shorter, with knock-on consequences for system-wide biogeochemical processes, e.g. sedimentation rates and lake net heterotrophy. Moreover, changes in environmental conditions might alter competitive relations, allow increased dominance of P. rubescens, and further alter ecosystem processes. The goal of this subproject is to predict system- (i.e., Lake-) wide changes in biodiversity patterns and associated ecosystem processes, by novel coupling of remote and in-situ sensing.

4. Long-term monitoring of Lake Zurich + Planktothrix rubescens

Thomas Posch, Daniel Marty, Eugen Loher
Collaboration: Dr. Oliver Köster (Water Supply Zurich), Dr. Michaela Salcher (Institute of Hydrobiology, Czech Republic)

Lake Zurich (Switzerland) serves as the major source of drinking water for >1.5 million people and is thus of great economic importance. A 40 years long-term dataset of the Limnological Station provides strong evidence, that changes in the mixis regime due to warming is coupled to an increasing importance of the filamentous cyanobacterium Planktothrix rubescens (Posch et al. 2012). In our biweekly monitoring of the lake multiple physical and microbial parameters are determined (Salcher et al. 2011).

5. Feeding of ciliates (Ciliophora) on toxic filamentous cyanobacteria

Thomas Posch, Bettina Eugster
Funding: SNF 31003A_138473 (2012-2015)

The filamentous cyanobacterium Planktothrix rubescens is generally considered toxic for eukaryotes. Intact cyanobacterial cells contain cyclic heptapeptides (microcystins - MCs) which are potent hepatotoxins and potentially act as tumour promoters on a molecular base. MCs also act as efficient inhibitors of eukaryotic serine/threonine-specific protein phosphatases. Potential consumers (zooplankton and -benthos) get in direct contact with the endotoxins when cyanobacterial filaments are ingested and digested.

Although cyanobacteria are often regarded as inappropriate or toxic food for most consumers, protists and in particular ciliates have been described as efficient predators of cyanobacterial blooms. It is of particular interest to better understand how these ciliates, being eukaryotic organisms, are able to survive a toxic diet. This knowledge will be of great relevance for a better understanding of natural degradation processes of MCs in Lake Zurich.