Department of Aquatic Microbial Ecology (AME)

Research at the Department of Aquatic Microbial Ecology is focused on freshwater microscopic organisms. Of interest are two main groups of aquatic microorganisms that differ in function. The first group, the autotrophs, consist of microscopic algae and cyanobacteria which are jointly referred to as phytoplankton. They are responsible for creating new organic matter via photosynthesis. The second group, the heterotrophs, are the bacteria and the protozoa which, on the contrary, co-operate on the decomposition of organic matter.


Research projects

Phylogeography and ecogenomics of ‘Ca. Fonsibacter’ (SAR11-IIIb)

Project No.: 22-03662S

Principal Investigator: Michaela Salcher

Financial support: Czech Science Foundation (GACR)

Duration: 2022-2024

Team Members: Clafy Fernandes, Markus Haber, Cecilia Chiriac, Rohit Ghai, Ievgen Lebeda, Alžběta Férová

Microbes affiliated to SAR11 (‘Ca. Pelagibacterales’) dominate in marine (SAR11-I, II, IV, V), brackish (SAR11-IIIa) and freshwater (SAR11-IIIb) systems and are challenging to cultivate due to their oligotrophic lifestyle and unusual nutrient requirements. A first culture of freshwater SAR11-IIIb was described only 2 years ago (‘Ca. Fonsibacter’). We have recently isolated 13 SAR11-IIIb strains by high-throughput dilution-to-extinction and aim at 50 additional cultures. State-of-the-art genomics will be combined with experiments to tackle their microdiversity, topdown control by protists and interactions with other microbes (WP1). Sampling of lakes on the southern hemisphere will counterbalance the uneven global sampling of mainly northern countries. Long-read metagenomics will enable sophisticated phylogeographic analyses of highquality genomes of metagenomes (MAGs) and cultures (WP2). The evolution of freshwater SAR11 will be addressed with SAR11 MAGs originating from freshwaters branching within marine lineages and strains gained from the brackish Baltic Sea (WP3).

We aim to characterize the ecology, microdiversity, global biogeography and evolutionary history of ‘Ca. Fonsibacter’ (freshwater SAR11-IIIb) by using high-throughput dilution-toextinction cultivation, experimental characterization, and whole-genome-sequencing together with long-read metagenomics.

Effects of warming and pollutants on nutrient flows and lower trophic levels in freshwater communities: from microbes to Daphnia

Project No.: 24-11779S

Principal Investigator: David Boukal, co-PI: Michaela Salcher

Financial support: Czech Science Foundation (GACR)

Duration: 2024-2026

Team Members: Tanja Shabarova, Ievgen Lebeda, TBA

Freshwater ecosystems face multiple human-induced environmental stressors including climate warming and chemical pollution. We do not have enough evidence to fully understand and predict community responses to these combined stressors. Using laboratory and mesocosm experiments and state-of-the-art analyses of micropollutants and microbial communities, we will
focus on the effects of warming and environmentally relevant concentrations of pharmaceutically active compounds and pesticides on nutrient flows and lower trophic levels from microbes to zooplankton in small standing waters. We will investigate the effects of
warming and pollution on Daphnia individuals from multiple populations and on simple trophic chain dynamics, and study long-term effects of pollutants and warming on nutrient cycling and pelagic food webs from microbial communities to zooplankton. We will also quantify if warming alters the emergence of antimicrobial resistance genes in freshwater habitats contaminated with antibiotics.

Project aims: We aim to unravel the combined impacts of climate change and pollution by pharmaceuticals and pesticides on freshwater ecosystems. Using lab and mesocosm experiments, we will study their effects on nutrient flows and microbial, phyto- and zooplankton communities across multiple temporal scales.

EcoFAct – Ecology of abundant freshwater actinobacteria

Principal Investigator: Markus Haber

Financial support: Czech Science Foundation; Project No.: 21-21990S

Duration: 2021 - 2023

Actinobacteria of the acI lineage (Ca. Nanopelagicales) are ubiquitously present and often among the most abundant microbes in freshwater lakes around the globe. While several hypotheses for their success have been advanced based on culture independent approaches, most remain untested owing to a lack of cultures. Isolation efforts based on the recently reported first successful cultivation of acI strains enabled us to isolate more strains from this group. Here we propose to expand this culture collection and test isolates for physiological and genomic differences related to environmental factors to determine their ecological niches and ecotype diversity. We will address hypotheses pertaining to protection against eukaryotic grazing and phage infection and their interactions with co-occurring auto- and heterotrophic bacteria. Finally, we will examine if their success can be explained by their ability to use light as energy source and its effects on their physiology. Our results will greatly enhance our understanding of the ecological role of this important group.

The proposed research investigates the ecology of acI actinobacteria, one of the most abundant group of freshwater bacteria. Specifically, we will examine niche separation between strains; their interaction with grazer, phages, and sympatric bacteria; and its potential for photoheterotrophy.

Phage host hunt: finding hosts for freshwater phages

Project No.: 23-06806S

Principal Investigator: Markus Haber

Financial support: Czech Science Foundation (GACR)

Duration: 2023-2025

Team Members: Pawel MarkwitzVojtěch KasalickýGeyby Carrillo ApoloIevgen LebedaAlžběta Férová

Phages are present in all ecosystems. They impact them by structuring microbial communities through the regulation of host populations and the release of host-bound nutrients through lysis. Metagenomics and -transcriptomics revealed a huge phage diversity in nature but often fail to assign hosts to phages. Especially in freshwater environments, this is partly due to the lack of cultured reference phages. Recent advances in bacterial cultivation enabled the isolation of abundant freshwater bacteria (e.g., FonsibacterMethylopumilusPlanktophila). We established a freshwater bacteria culture collection that includes members of these lineages. Here we propose to use these isolates and established high throughput phage isolation protocols to bona-fide identify phage-host pairs. We will study the host range, natural abundance and dynamics of the isolated phages. Finally, we will identify prophage in the genomes of isolates and by long-read metagenomics in environmental bacteria. Our proposed project hence plans to close an important gap in viral ecology by assigning hosts to phages.

Project aims: This project aims to identify phage-bacteria host pairs and investigate their natural dynamics in a freshwater reservoir using cultivation-dependent and -independent methods.

Effects of extreme weather events on seasonal dynamics of planktonic assemblages and reservoir water quality

Project No.: 22-33245S

Principal Investigator: Petr Znachor

Financial support: Czech Science Foundation

Duration: 2022 - 2024

Extreme weather events, e.g. heavy rainfalls or droughts, are predicted to increase in frequency and intensity due to climate change. These events represent disturbances that have far-reaching consequences on the functioning of aquatic ecosystems and water quality. Their impacts on reservoirs have been poorly addressed, in part because field logistics and statistical issues complicate sampling, replication, and mechanistic attributions to drivers. Such methodological challenges can be circumvented by using long-term data sets produced by routine monitoring programs. We intend to use a unique detailed long-term dataset starting in 1983 that includes weather conditions, hydrodynamic, chemistry and taxonomically resolved biological data on plankton assemblages in the Římov Reservoir. In the proposed project, the Římov Reservoir will be used as a model to evaluate the sensitivity of the reservoir ecosystems to extreme weather events. We will explore how weather extremes affect environmental conditions that alter the composition, structure and phenology of plankton assemblages.

Our goal is to evaluate the impact of weather extremes on reservoir conditions that result in compositional, structural and functional changes and phenological shifts in plankton. We will analyse especially differences between dry and rainy years and the impact of flood events on the reservoir ecosystem.

Iron monopolization versus community service: the two faces of cyanobacterial beta-hydroxy aspartate lipopeptides

Project No.: 22-05478S

Co-Principal Investigator: Jan Mareš (PI: Pavel Hrouzek, Institute of Microbiology CAS)

Financial support: Czech Science Foundation (GAČR)

Duration: 2022 - 2024

Iron is an essential nutrient, yet generally present in poorly bioavailable form (Fe3+) on Earth´s surface. Siderophores are low molecular compounds that scavenge the precipitated Fe, providing an advantage in resource competition on one side and important community service (Fe2+ supply) on the other side. We have recently found siderophores with a double beta-OHAsp Fe-chelating motif in cyanobacteria and postulated their wide occurrence by genome mining. Hereby, we aim to assess the occurrence of these siderophores in natural communities by targeted field sampling followed by analytical and metagenomics survey. Microbial strains isolated from the samples will be co-cultivated with beta-OH-Asp siderophore producers under manipulated UV treatment and Fe2+/Fe3+ source to determine the ratio between Fe monopolization and benefit provided to other microbes. Bioengineered biosynthetic gene clusters will be assembled to generate structural variability to assess the role of siderophore structure fine-tuning in uptake by specific transporters present in the siderophore producing strains.

Project aims:

To establish the role of cyanobacterial photolabile beta-hydroxyaspartate siderophores in microbial communities. To study the ratio between specific iron uptake by siderophore producers and benefit provided to other microbes using a combination of genetic transformation and manipulative experiments.

Consolidating cyanobacterial systematics through harmonization of polyphasic and genomic taxonomy

Project No.: 22-06374S 

Principal Investigator: Jan Mareš

Financial support: Czech Science Foundation (GAČR)

Duration: 2022 - 2024

Since 2000, criteria for recognition of cyanobacterial taxa utilizing the polyphasic approach have been developed. Due to the slow pace of phylum-wide revision, genome taxonomy approaches have been introduced to avoid a taxonomic bottleneck in metagenomic studies. Genome taxonomy has not been integrated into the existing taxonomy, which has caused substantial confusion between the fields. We will compare these approaches by collecting complementary data within the model group, Synechococcales, the best studied group in terms of both genomes assembled and recent polyphasic taxonomic effort. Direct comparison will allow us to integrate both approaches, evaluate taxonomic boundaries, and derive taxonomic concepts for cyanobacteria that will satisfy and be workable for all researchers. We will initiate the revision of higher hierarchical taxonomic ranks, and formulate recommendations for standard practice in taxonomic and metagenomics studies. Accomplishing this urgent task will provide a new milestone for a unified taxonomy acceptable by phycologists, microbiologists, and metagenomists.

Project aims:

1) To assemble a set of strains characterized by polyphasic data and whole genome sequence

2) To assess taxonomic boundaries among species, genera, families, and orders by both approaches

3) To propose a unified concept, based in phylogenomics but compatible with existing taxonomy and nomenclature

Pan-European Lake Sampling - Microbial Eco-genomics (PELAGICS)

Principal Investigator: Rohit Ghai & Michaela Salcher

Financial support: Czech Science Foundation; Project No.: 20-12496X

Duration: 2020 - 2024

     Freshwater habitats are critical for all terrestrial life, yet the vast majority of their microbial inhabitants (pro- and eukaryotes) remain enigmatic, outside the bounds of cultivation. The recent development of novel cultivation methods, coupled with advances in sequencing now provides an opportunity to finally unravel freshwater microbial diversity. The PELAGICS project plans a coordinated pan-European sampling campaign (70 lakes) with 24 collaborating scientists from 16 European countries. With novel media mimicking natural conditions and semiautomated high-throughput isolation we aim for stable cultivation and whole-genome sequencing of 500 prokaryotes and 50 unicellular eukaryotes. Moreover, terabyte scale deepmetagenomic sequencing (ca. 18 TB) will allow recovery of thousands of metagenomeassembled genomes for pro-, eukaryotes and viruses. This large-scale effort will finally uncover the microbial diversity (pro- and eukaryotes), their natural interactions and ecological roles in aquatic food webs.

A Pan-European microbial ecology network is proposed to sample 70 lakes towards the goal of stable cultivation, whole-genome sequencing (500 pro- and 50 unicellular eukaryotes) and terabyte-scale deep-metagenomic sequencing to obtain 1000s of genomes of freshwater pro-, eukaryotes and viruses.

Ecology of phytoplankton in freshwater reservoirs

Research is focused on freshwater microscopic algae and cyanobacteria (jointly referred to as phytoplankton) inhabiting lentic ecosystems, namely reservoirs. Freshwater reservoirs provide important ecosystem services such as the supply of drinking water, irrigation, transportation, industrial and cooling water supplies, power generation, flood control or recreation. They differ from natural lakes in several important aspects: elongated morphology, shorter water residence time, pronounced water level fluctuation and irregular water withdrawal, often from various strata.

Leading person: Petr Znachor

More at


Biology Centre CAS
Institute of Hydrobiology
Na Sádkách 702/7
370 05 České Budějovice

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