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.
High-throughput host detection and cultivation of freshwater CRPs (‘Ca. Patescibacteria’)
Project No.: 24-12912M
Principal Investigator: Cecilia Chiriac
Financial support: Czech Science Foundation
Duration: 2024-2028
Team Members: Paul Layoun, Michaela Salcher, Rohit Ghai, Paul Bulzu, Monika Okrouhlíková, TBA
One of the most important discoveries in microbiology in the last decade was Candidate Phyla Radiation (CPR) or ‘Ca. Patescibacteria’, a recently described phylum of mostly episymbionts that include up to 26% of bacterial diversity. Although >2400 representative genomes are available, less than a dozen members were cultivated to date, belonging to just two out of 24 CPR classes. Because of their prevalence in the environment, cultivating ‘Ca. Patescibacteria’ is important, but notoriously difficult due to their complex nutrition needs and reliance on other microorganisms, and new strategies and techniques are needed to understand their ecophysiology. In our project, we propose to target both partners with metatranscriptomics and EpicPCR to assess the functional potential and host range of CPRs. Further, we aim to obtain episymbionts - hosts co-cultures by combining reverse metagenomics and high-throughput cultivation. These approaches represent the necessary steps that will advance the understanding of CPRs biology.
The project aims 1) to understand the functional potential of ‘Ca. Patescibacteria’ members in the environment; 2) to assess the host range of these epi- and endo-symbiotic bacteria; and 3) to obtain new enrichment cultures and co-cultures.
MATISSE: Microbial Activity in Time and Space during Spring Ecological Succession
Project No.: 24-11998S
Principal Investigator: Rohit Ghai
Financial support: Czech Science Foundation
Duration: 2024 - 2026
The phytoplankton spring bloom in freshwaters, dominated by cryptophytes and diatoms, is a recurring ecological spectacle with fast-changing microbial assemblages in response to environmental conditions. Many main players (prokaryotes, protists, viruses) are known and genome-sequenced, but fundamental gaps exist in linking genomic potential to gene activity. Complex community interactions also remain unresolved, e.g., temporal fluctuations and microdiversity in prokaryotic gene expression or factors affecting major events e.g. bloom collapse. To connect genomic potential, gene activity and organismal interactions to large scale ecosystem outcomes, we propose a high-frequency metatranscriptomic approach. Furthermore, isolation of giant viruses of the dominant cryptophyte, transcriptomics under nutrient limitation and viral infection will reveal the role of abiotic factors and biotic interactions regulating the fate of these blooms. Collectively, we expect the results to have broad repercussions for understanding coordinated biological responses of planktonic microbial communities
We aim to link genomic potential of the freshwater phytoplankton spring bloom microbial community to gene activity by high-frequency metatranscriptomics and experimental approaches to reveal cellular mechanisms behind the responses of microbes and their interactions in environmental conditions.
EPIC - Epibiont-mediated Induction of cyanopeptides
Project No.: 24-10743S
Principal Investigator: Dr. Kumar Saurav, Institute of Microbiology Czech Academy of Sciences, Co-PI: Klara Rehakova
Financial support: Czech Science Foundation
Duration: 2025 - 2027
The widespread occurrence of cyanopeptides beyond microcystins demonstrates the need to further understand their overall impact on aquatic and other organisms including humans. Our knowledge on interspecies interaction between cyanobacteria and their epibionts within their phycosphere is scarce. EPIC will undertake a comprehensive study based on quorum sensing mediated interaction and demonstrate its role in inducing cyanopeptide production. Our objective is to design a bottom-up reconstruction of the multipartite interactions within the microbial community, mediated by exchange of molecules and inducing certain secondary metabolite production. The question of when and how a bacterium ‘chooses’ to induce given biosynthetic gene cluster is fascinating and yet unresolved. Understanding the regulatory mechanisms behind triggering and maintenance of CNP (including cyanotoxins) production in natural phytoplankton communities can provide crucial background data for future considerations in ecotoxicology and water quality management.
The aim of the EPIC is to identify the cyanobacterial epibionts community by using metagenomics and study the role of epibionts in regulating cyanopeptide production using metatranscriptomics and metabolomics.
Factors driving the global diversification of cosmopolitan cyanobacterium Microcoleus
Project No.: 23-06507S
Principal Investigator: Petr Dvořák, Faculty of Science, Palacky University Olomouci
Co-principal Investigator: Kateřina Čapková
Financial support: Czech Science Foundation
Duration: 2023 - 2025
The processes of species emergence (speciation) are still enigmatic especially in prokaryotes, although it is one of the fundamental questions in biology. Methods to study the speciation on a genomic, transcriptomic, and epigenomic level have only recently been developed, and they are mostly applied to animals and plants, although the species diversity of microbes is much larger. In this project, we will investigate the patterns of speciation in cyanobacterium Microcoleus. The objectives, we propose, will provide a detailed insight into the diversity of Microcoleus at four levels – genome, transcriptome, epigenome, and phenotype. We will focus on the genome-wide distribution of nucleotide diversity and divergence, selection, adaptation, and base modification. This will be investigated on closely related species and populations on both small and large geographical scales. We will observe how all these factors concert evolutionary divergence, adaptation, and speciation in cyanobacteria by the integration of all omic layers.
We will investigate the diversity of Microcoleus (cyanobacteria) species at four levels –genome, transcriptome, epigenome, and phenotype – on both small and large geographical scales. We will observe how all these factors concert evolutionary divergence and speciation in cyanobacteria.
SoWaFUN - Fungal ecology at the soil-water interface
Project No.: 23-06429S
Principal Investigator: Jiří Bárta, Faculty of Science, South Bohemia University in Ceske Budejovice
Co-principal Investigator: Dagmara Sirová
Financial support: Czech Science Foundation
Duration: 2023 - 2025
Understanding the processes involved in organic matter (OM) degradation at the interface between terrestrial and aquatic ecosystems is key for understanding of energy flow at landscape level. Fungi produce a wide variety of extracellular enzymes and break down diverse forms of complex plant-derived OM, and thus are one of the main regulators of carbon balance. We hypothesize that, contrary to the so-far accepted paradigms, many fungal taxa colonizing plant matter under terrestrial conditions remain important players in the transfer of energy to higher trophic levels in standing freshwaters. To unravel the complex interactions that accompany fungal lifestyle at the soil-water interface at a sufficient level of resolution, we assembled a team of collaborators with multidisciplinary backgrounds and will employ a combination of modern molecular methods, advanced bioinformatic analyses, and state-of-the-art approaches in analytical chemistry to close some of the pressing knowledge gaps in the newly emerging field of microbial ecology.
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 Markwitz, Vojtěch Kasalický, Geyby Carrillo Apolo, Ievgen Lebeda, Alžběta 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., Fonsibacter, Methylopumilus, Planktophila). 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
Fresh
water 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 www.fytoplankton.cz
