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. Because the methodology is different for each group of organisms, our department has two interlinked working groups, concerned with (1) the ecology of aquatic bacteria and protozoa, and (2) the ecology of phytoplankton.

The Ecology of aquatic bacteria group studies the taxonomy of freshwater bacteria, their biogeography, function, and their role in food chains. In aquatic bacterial taxonomy, we try to find out which of the few bacteria species or groups actually live in freshwater. We concentrate on two groups, betaproteobacteria and actinobacteria, which are typically found in freshwater (including those of Central Europe). We use molecular methods based on the study of the genetic information of the bacteria and have achieved considerable success in isolating and cultivating aquatic bacteria using unique methods developed by our researchers.

Aquatic bacterial biogeography is a very young field and basic investigations on where different bacterial groups occur and why only recently began. Our researchers are contributing significantly to its development. We also study the unique microbial communities in acidified Bohemian Forest lakes as well as the development of microbial populations in a lake emerging from a former brown-coal quarry which is being inundated.

The study of the functions of aquatic bacteria (the types of organic substances they decompose and utilise, and how quickly they grow) and of bacteria in relation to other organisms (protozoa and small animals that feed on them, and viruses attack them) is a classical field within aquatic microbiology. We have made significant contributions to the currrent general trend in this field: attempts at complete identification of the individual species or taxonomic groups of bacteria and protozoa involved in the processes studied. The work of professor Karel Šimek (one of the most cited Czech ecologists) in this field is especially valued by the international scientific community. He has contributed significantly to understanding the relationships between bacteria, protoza, and viruses; the protoza influence the composition of bacterial communities by preferential feeding on certain species, types or sizes of bacteria. This changes the rates of transfer of organic matter in the food chain via zooplankton all the way up to the fish.

The Phytoplankton ecology group focuses on the research of phytoplankton (consisting of microscopic algae and cyaonobacteria) including their taxonomy, ecology, ecophysiology, and interaction with bacteria. Internationally, our institute is one of the most respected research centers dealing with the taxonomy of cyanobacteria (also known as blue-green algae), which are known for their tendency to create unpleasant and dangerous water blooms. Our aim is to describe and reliably distinguish individual species using a combination of classical (microscopy) and modern (molecular) methods. Our institute hosts a unique collection of several hundred strains of cyanobacteria and algae isolated from various types of freshwaters.

In phytoplankton ecology we try to identify factors responsible for a species or group of algae or cyanobacteria being in a given place and time. We study competition for resources between phytoplankton species, the influence of extreme rainfall on the taxonomic composition of phytoplankton communities, and on the differences between phytoplankton composition in different reservoir areas. We also focus on long-term changes in phytoplankton composition caused by global climate change.

In algal and cyanobacterial ecophysiology, we concentrate on the relationship between the physiological traits of individual species and their occurence in an aquatic ecosystem. Here our development and implementation of modern fluoresecent methods has gained us considerable international recognition. The methods consist of marking cells using special fluorescent labels. This then enables microscopic comparison of the qualities of individual cells, such as producion of certain substances, growth rates, cell damage or vitality. Research on the interaction of phytoplankton and bacteria is focused on factors influencing the production of organic substances by phytoplanton and their impact on the composition, activity, and growth of bacteria.

Current research projects

Fishponds as models for exploring plankton diversity and dynamics of hypertrophic shallow lakes

Project No.: 17-09310S

Applicant: Jaroslav Vrba, Faculty of Science, University of South Bohemia in České Budějovice

Co-applicant: Jiří Nedoma

Financial support: Czech Science Foundation

Duration: 2017 – 2019

Aim of the project is to explore plankton diversity and dynamics, key players and their functional traits, and to estimate primary production, respiration, nutrient mobilisation, and production efficiency in the hypertrophic fishponds that allow refining and testing of general ecological hypotheses.

Fishponds are semi-natural, man-controlled, shallow ecosystems used for fish production. Different management results in different ecological states that predestine the fishponds as unique model systems. Nutrient loads and fish overstock have led to fishpond hypertrophy; however, interactions in the plankton communities under such extreme conditions remain unexplored. We are lacking data on primary production, community respiration, diversity and functions of heterotrophic microbial food webs in eutrophic freshwaters, as well as about the effects of fish on their food web structure. We hypothesise that hypertrophic conditions result in net ecosystem heterotrophy, an increase in heterotrophic microbial biomass and nutrient mobilisation, and a decrease in net ecosystem productivity and cost effectiveness. Under the conditions of high (auto- and heterotrophic) microbial biomass, intensive photosynthesis and respiration processes cause ecosystem imbalances and low resource use efficiency that results in higher plankton (mainly microbial) diversity due to niche diversification.

Unveiling life strategies of uncultivated viruses in freshwater environments using metagenomics

Project No.: 17-04828S

Applicant: Rohit Ghai

Financial support: Czech Science Foundation

Duration: 2017 - 2019

Viruses are the most abundant biological entities on the planet, at least one order of magnitude more numerous than their host microbes in aquatic environments. Despite their abundance, studying viruses via cultured isolates remains challenging owing to the complexities in obtaining axenic cultures for the abundant microbial groups. The situation is even more acute for freshwaters where the availability of such pure cultures of the dominant phyla is still rather limited.

We propose a long-term metagenomics based approach in two well-studied freshwater habitats to enable a first glimpse of the important double-stranded DNA bacteriophages in freshwaters. We will link these uncultured phages to their host both using existing sequence based approaches and also develop novel methods. In particular we will focus on life strategies of free-living viruses developed in the process of co-existence with the host microbes. Moreover, important insights into factors affecting seasonal dynamics of phage and host populations and global biogeography of freshwater phages are expected.

Bioactive cyanobacterial lipopeptides: genome mining, detection, and structure-activity relationships

Project No.: 16-09381S

Applicant: RNDr. Pavel Hrouzek Ph.D., Institute of Microbiology, CAS

Co-principal Investigator: RNDr. Jan Mareš Ph.D.

Financial support: Czech Science Foundation

Duration: 2016 – 2018

The project is focused on the detection of bioactive lipopeptides and lipopeptide synthetase genes in cyanobacteria. Potential cyanobacterial lipopeptide producers will be identified based on genome database mining. Methods for molecular (PCR) and chemical detection (HPLC-HRMS/MS) of lipopeptides in laboratory strains and environmental samples will be designed and tested. Bioactivity of lipopeptides will be assessed by means of in vitro testing on human cancer cell lines and phytopathogenic fungi. Lipopeptides exhibiting strong bioactivity will be purified and their structures will be characterized. Structure-activity relationship and possible utility for pharmaceutical and biotechnological purposes will be evaluated. Whole genome sequencing will be performed in strains producing the most interesting compounds but lacking genomic data. This will enable identification of novel lipopeptide synthetase clusters and biosynthesis prediction. Phylogenetic and environmental distribution of cyanobacterial lipopeptide producers and evolution of lipopeptide synthetase genes will be investigated.

Phytoplankton responses to environmental forcing – lessons learned from 30-year monitoring of the Římov Reservoir

Project No.: 15-13750S

Applicant: Petr Znachor

Financial support: Czech Science Foundation

Duration: 2015 – 2017

Freshwater lakes and reservoirs are particularly sensitive to the ongoing climate change. Various long-term data studies have shown close coupling between climate and individual organism physiology, population abundance and community and food-web structure. Phytoplankton represent the base of aquatic food webs and their dynamics are linked to annual fluctuation of temperature, water column mixing, resource availability and consumption. The ongoing climate change and has been recognized as an important driver affecting these factors. In the proposed project, we wish to explore mechanisms underlying phytoplankton interannual variability in the Římov Reservoir using a 30-year data set including meteorological, physical, chemical and biological data. Our investigation will be focused on changes in the timing of seasonal events (phenology) using phytoplankton morpho-functional classification.

Unveiling life strategies of selected groups of planktonic Betaproteobacteria in relationship to carbon flow to higher trophic levels

Project No.: 13-00243S

Applicant: Karel Šimek

Financial support: Czech Science Foundation

Duration: 2013 – 2017

We propose investigations of life strategies related to genomic and ecophysiological traits of representative strains of the key groups of freshwater Betaproteobacteria, i.e. the genera Limnohabitans and Polynucleobacter, with contrasting lifestyles and frequently also different habitat preferences. We hypothesize that strains affiliated with these abundant groups differ in growth potential and grazing-induced mortality in situ, thus modulating the role of the groups in carbon flow to higher trophic levels. Notably, a large collection of representative strains from both groups is available that facilitates examination of diversity in ecophysiologic and genomic traits of these bacteria. Specific in situ experimental designs are proposed for testing of ecophysiological characteristics of the bacteria and estimating of their taxon-specific roles in carbon transfer to bacterivorous flagellates in five different habitats. Important new insights into distinct bacterial lifestyles are assumed, including implications for refinement of existing concepts of bacterial life strategies.


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

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