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.

Opened PhD position in aquatic Protist Ecology supervised by Karel Šimek and Indranil Mukherjee

Current research projects

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

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.

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.

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.

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.

From dark to dark: do bacterial ‘seeds’ from subsurface habitats find their place in lake hypolimnia?

Principal Investigator: Tanja Shabarova

Financial support: Czech Science Foundation; Project No.: 20-23718Y

Duration: 2020 - 2022

The mechanisms underlying species distribution in metacommunities represent a challenging topic in microbial ecology. Although the interactions between species-sorting, mass-effects and neutral processes in planktonic communities of surface waters are well understood, both the microbial communities in deeper lake strata (hypolimnion) and mechanisms influencing their assembly are largely unknown. Moreover, the role of groundwaters in formation of freshwater communities remains enigmatic. We aim to uncover microbial community composition and assembly mechanisms during transfers from soil to soil water and along continua of subsurface vs surface streams to a deep lake using amplicon sequencing and metagenomics. Additionally, compositional and functional differences between bacterial assemblages from subsurface vs surface flows, along with accompanying environmental alterations will be investigated. We hypothesize that communities formed by surface and subsurface streams are distinct and subsurface streams provide successful ‘seed’ phylotypes for aphotic, deep lake strata.

The aims of the project are: (i) To test microbial community assembly concepts known for surface waters on subsurface counterparts. (ii) To quantify the contribution of bacterial communities of surface and subsurface flows to communities of different lake strata. (iii) Expand these results to different karst regions in Europe.

Who eats whom and when? Zooming-in on alternative energy transfer pathways in planktonic food webs of shallow lakes

Principal Investigator: Dagmara Sirová

Financial support: Czech Science Foundation; Project No.: 19-16554S

Duration: 2019 - 2021

Freshwater planktonic food webs (FW) are crucial for understanding of energy and material flow among organisms in the water column. Though theory on FW structure and function is advancing rapidly, it remains poorly resolved and based on relatively simple systems in stratified lakes. Shallow polymictic ecosystems such as hypertrophic fishponds, however, seem to support more complex communities of immense biodiversity. Based on our preliminary results, we hypothesise that, contrary to the widely accepted plankton ecology paradigms, methane-oxidising bacteria, picocyanobacteria, and fungal zoospores are important players in the transfer of energy to higher trophic levels in hypertrophic lakes. The flow of energy from primary producers to higher trophic levels through the ‘classical FW’ is reduced here, the microbial FW is the main component, although likely less efficient due to more trophic levels and consequent energy losses. To unravel these complex interactions at a sufficient level of resolution, a combination of modern molecular methods and multidisciplinary skills is planned.

We will use a unique combination of molecular, epifluorescence, and chemical methods to unravel complex interactions in planktonic food webs of the underexplored but important aquatic ecosystems at an unprecedented level of resolution.

The effect of periphyton assemblages on productivity and phosphorus cycling in oligotrophic post-mining lakes

Principal Investigator: Klára Řeháková

Financial support: Czech Science Foundation; Project No.: 19-05791S

Duration: 2019 - 2021

Periphyton is ubiquitous in aquatic habitats and performs numerous environmental functions such as nutrient cycling and self-purification of aquatic ecosystems. Less attention has been paid to the investigation of periphyton than of plankton, although in many ecosystems periphyton forms higher biomass. One of the less studied ecosystems are oligotrophic lakes, especially those founded antropogenetically. In the Czech Republic, there is a unique series of 3 anthropogenic oligotrophic lakes of gradual successional age, which were created during the recultivation after coal mining. Even though one of them, Medard, is the largest lake in the Czech Republic, data on primary production, diversity and functions of periphytic community are missing. The proposed project will investigate the rate of primary production during the season and along the successional chronosequence of the lakes, species diversity and dynamics of the development of periphyton, its functions in the nutrient cycling, with a special focus on the fate of phosphorus, which is the limiting nutrient in investigated lakes.

Aim of the study is to explore periphyton diversity and dynamics in the oligotrophic anthropogenic lakes. To estimate the primary production during the season and along successional gradient of lakes. To estimate the phosphorus uptake efficiency by periphyton under various environmental conditions.

Ecogenomics of genome-streamlined freshwater methylotrophs

Principal Investigator: Michaela Salcher

Financial support: Czech Science Foundation; Project No.: 19-23469S

Duration: 2019 - 2021

The most abundant planktonic microbes have reduced genomes and streamlining theory predicts that gene loss is caused by evolutionary selection driven by environmental factors. Yet the evolutionary path of streamlining remains unknown because of obstacles in establishing axenic cultures of such microbes. We developed a targeted isolation technique for abundant genome-streamlined freshwater methylotrophs: ‘Ca. Methylopumilus planktonicus’ (Betaproteobacteria, 1.3 Mbp genome size), that are ideal model organisms for studying microdiversification patterns and the evolution of genome-streamlining per se. The closest relatives of ‘Ca. M. planktonicus’ inhabit lake sediments and the pelagial of oceans, and we propose that the evolutionary origin of the family can be traced back to sediment microbes with medium-sized genomes. Whole genome sequencing of 150 strains and deep sequencing of metagenomes will allow comparative population genomics with the aim to disentangle the underlying ecological reasons for the widespread but yet enigmatic phenomenon of genomestreamlining in aquatic microbes.

The aim of the project is using targeted isolation and whole-genome-sequencing of oligotrophic freshwater ‘Ca. Methylopumilus planktonicus’ (Betaproteobacteria) together with metagenomics to study the evolution of genome-streamlining in planktonic microbes. Identifying microdiversification patterns in closely related taxa.

project site

Illuminating the ecology of freshwater picocyanobacteria through a genome-resolved taxonomic framework

Principal Investigator: Jitka Jezberová

Financial support: Czech Science Foundation; Project No.: 19-23261S

Duration: 2019 - 2021

Although picocyanobacteria (Pcy) are viewed as one of the quintessential players in the Global Carbon Cycle (through fueling World’s Oceans primary production), our apprehension of their ecology in freshwater ecosystems strongly lags behind. We reason that one of the main impediments in elucidating their impact and importance, in lacustrine habitats, stems from the lack of means necessary to delineate ecologically-relevant taxonomical units (e.g. species and subspecies). Thus, we intend to surpass the existing taxonomical bottleneck, of microscopybased taxa description and 16S rRNA gene-orientated species delineation, through developing a robust genomic-centered classification framework. We intend to build on our existing freshwater Pcy collection (already containing more than 120 strains) and to use state-of-the-art shotgun sequencing in order to obtain approx. 100 high-quality genomes. This extent of genomic data will also provide the means necessary to track discrete populations in the natural environment (through CARD-FISH targeting) and disentangle their food web role.

We intend to develop a robust genomic-centred classification framework for freshwater picocyanobacteria. Phylogenomic reconstructions and genomes composition will be confronted with in situ population dynamics and a link-or-sink role in the food-web to create ecologically coherent taxa.

project web

Biomanipulation as a tool for the improvement of reservoir water quality

Principal Investigator: Jan Kubečka, Tomáš Jůza... from AME: Petr Znachor & Vojtěch Kasalický

Financial support: Ministry of Education, Youth and Sport of the Czech Republic administrate the support provided from EU funds; Project No.: CZ.02.1.01/0.0/0.0/16_025/0007417

Duration: 2018–2022

     Water is the most important of global resources and therefore strong emphasis is placed on sustaining its high quality. Due to climatic changes, water resources are exposed to various climatic extremes and only healthy ecosystems with good ecological potential are able to withstand these changes. Surveys have shown that most of the reservoirs in the Czech Republic are in an unsatisfactory state and amendments to improve this situation will have to be implemented in the near future. Evaluation of the ecological potential has clearly shown that the cause of this negative state is eutrophication, stemming from increased loads of phosphorus and nitrogen into water bodies. A successful biomanipulation, or the achievement of better water quality through targeted changes in the food chain, requires interventions in the watersheds which lead to decreased nutrient loading into reservoirs as well as development of bulk reduction fishing. The aim of the project is a unique wholelake experiment with the monitoring of all of the important parts of the reservoir food chain before, during, and after a targeted manipulation. The project will evaluate the effect of reducing the stock of undesirable fish species and the proliferation of predatory fish species on specific trophic levels, and, ultimately on the improvement of water column transparency and water quality in selected reservoirs. The majority of the biomass of planktivorous fish will be removed from three model reservoirs differing in nutrient load (trophy). At the same time, predatory fish will be introduced. Detailed monitoring of the entire reservoir ecosystem from fish, zooplankton, fytoplankton, macrophytes, and bacteria to nutrients and reservoir metabolism will help uncover the effects of such a vigorous manipulation. The economic rentability of these biomanipulations will also be evaluated, with the aim to put into numbers the difference between the costs and the savings due to the improvement of ecological potential (Water Framework Directive). Other savings can include easier treatment of raw water in waterworks processing or an increase in the recreation potential. According to the Water Framework Directive, all European Union member states are expected to reach at least good ecological state of water bodies by the year 2027. Biomanipulation represents one of the important tools to fulfill this ambitious goal.

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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