Small bacterivorous flagellates have been the focus of intense research. However, medium sized (5-20 μm) flagellates with more complex feeding behaviors (e.g. predators or omnivores with active/passive feeding on both bacteria and other flagellates) are much less understood. Such trophic interactions of these highly diverse, medium sized protists can significantly modulate current views on a simplistic energy transfer in microbial food chains. We propose a novel model of considerably more complex energy transfer patterns through aquatic food webs. To test our hypothesis, food web manipulation experiments and sampling will be conducted by Czech-Polish research team on two contrasting ecosystems: Římov reservoir (freshwater) and the Baltic Sea (brackish). We will analyze population dynamics and food preference of individual protistan groups using a battery of existing methods and newly developed single-cell techniques, likely revealing hidden trophic interactions. The results will allow refinement of current concepts of carbon and energy transfer in aquatic microbial food webs.

The overarching aim of the proposed project is shedding light on the role of the middle-sized (5- 20 μm) heterotrophic flagellates in freshwater and brackish microbial food webs, and by this to enhance our current understanding of the carbon cycle and energy transfer in aquatic ecosystems.

PREDATOR - PREvent, Detect and combAT the spread Of SiluRus glanis in south european lakes to protect biodiversity

Project No.: 101074458

Co-principal Investigator: Martin Čech

Financial support: European Commission – program LIFE-2021-SAP-NAT

Duration: 2022 - 2027

Project in research consortium Italy – Portugal – Czech Republic aims at monitoring of the spread and preventing the further introductions of the invasive European catfish (Silurus glanis) contributing to the application of the EU IAS (Invasive Alien Species) Regulation No. 1143/2014 in southern European lakes and reservoirs. An early detection system based on environmental DNA (eDNA) will be tested and developed in 50 lakes and reservoirs (23 in Italy, 25 in Portugal and 2 in Czech Republic; later two serving as control localities) and integrated with citizen science records. In 10 selected lakes where the species is widespread and abundant, different capture methodologies are tested to select the best selective (i.e. with lowest by-catch) and effective capture method, which will be then applied to reduce the catfish biomass by 90 % in 5 small and isolated Natura 2000 lakes, at least 10 % in large lakes and reservoirs, 50 % in small reservoirs and involving in these activities at least 130 commercial fishermen and 100 anglers. Massive awareness-raising campaigns are organized targeting specifically anglers (at least 400,000) but also the general public, expecting to reach 1 million people at the end of the project, including 12,000 school children. Protocols and best practices are transferred to at least 15 management authorities to be integrated into their management plans, particularly of Natura 2000 sites. For the replication of the project results, a South European catfish Management Group (SEMG) is created. Additionally, to sustain the project goals where the catfish invasion is more advanced (i.e., northern Italy), the creation of a local circular economy is proposed, looking for the best solution to make the catfish more palatable and thus increasing the fishing pressure on catfish by encouraging its consumption as food.

Project aim is to reduce the impact of catfish on local freshwater ecosystems, to reduce and control the spreading of the species, to avoid the new introductions and thanks to that to reduce the effect on biological diversity.

According to the decision of the regional self-government, Italy, Portugal and European Union itself, this kind of species will be intensively subdued. Even eradicated within some protected areas. The most suitable and processes will be tested.

FERRO - Fostering European lakes Restoration by nutrient removal, RecOvery, and reuse: integrated catchment and in-lake scale approach

Project No.: 101157743

Coordinator: Helmholtz-Zentrum Fur Umweltforschung Gmbh - UFZ

Co-principal Investigator: Petr Porcal

Financial support: European Commission – program HORIZON-MISS-2023-OCEAN-01-04

Duration: 2024 - 2028

Eutrophication is a major problem causing poor ecological status of European lakes with its severe impacts being enhanced by climate change. However, at the same time, eutrophication could be the potential solution to the depletion of global phosphate (P) reserves, threatening global food security. A vast amount of P and other nutrients are lost from the catchment and transported into lakes, making most lakes a nutrient-rich reserve, as observed by the frequent occurrence of massive, devastating algal blooms in many lakes. FERRO bridges the nutrient enrichment problem to the depletion of P problem to create a sustainable solution to both challenges by circular management. We will develop a next-generation lake restoration approach by combining targeted restoration techniques with nutrient recovery and recycling to achieve multi-benefits: improved ecological status of lakes, support a circular economy, climate adaptation, support food production, promote biodiversity, and boost ecosystem services provision. The multiple environmental and socio-economic co-benefits extend beyond the scale of intervention, supporting wider sustainability and accounting for social and economic ambitions.

FERRO supports the natural recovery of lakes (after many years of nutrient enrichment) through four transdisciplinary pillars: 1) classification and prioritization of lakes for restoration (integrated in-situ and remote sensing-based techniques); 2) implementation of sustainable catchment-oriented solutions (biotechnology to prevent nutrient losses in agriculture and nutrient recovery at lake inflows and reuse in agriculture), 3) implementation of sustainable in-lake restoration solutions (nutrient recovery from lakes and reuse in agriculture); and 4) knowledge transfer. FERRO marks a major shift in how lake restoration will be done for ages.

PROCLEANLAKES - Integrated emerging approaches for joint protection and restoration of Natural Lakes in the spirit of European life heritage support

Project No.: 101157886

Coordinator: University of Natural Resources and Life Sciences, Vienna (BOKU)

Principal Investigator: Anca-Lulia Stoica (BOKU)

Co-principal Investigator: Jiří Peterka

Financial support: European Commission – program HORIZON-MISS-2023-OCEAN-01

Duration: 2024 - 2028

ProCleanLakes targets to combat the combined impact of various disruptive factors that generate continuous pressure on the lake's ecosystem status and facilitate the accumulation of emerging, non-regulated, chemical contaminants and nutrient enrichment. The project will design and demonstrate the feasibility of integrated nature-based emerging approaches for joint protection and restoration of European Natural Lakes (ENL) and their biodiversity, considering scenarios which imply the presence of various pressures that affect the aquatic ecosystems' status. The holistic transdisciplinary approaches that are to be used in the project, based on the synergic effect of the economic-environment-social nexus, targets to support the improvement of ENL ecological and chemical status in association with major EU instruments, sustainable development goals and policies related to freshwater ecosystems. The project engages multiple sites affected by the presence of various pressures and stressors, that will be the subjects for the demonstration of integrated protection and restoration solutions efficiency.

www.proclenlakes.eu

REA - ProtectFish

Project No.:

Coordinator:

Principal Investigator:

Co-principal Investigator: Martin Čech

Financial support: European Commission – program ...

Duration: 2024 - 2028

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Interreg

Living jewels under the water surface of Šumava

Project No.: BYCZ01-020

Principal Investigator: Petr Blabolil

Financial support: Programme INTERREG Bavaria - Czechia 2021–2027

Duration: 2023 - 2026

The project aims to make a significant contribution to the coordinated protection of surface waters by studying the populations of brown trout in the programme area. The flagship species brown trout is a popular and also commercially important keystone species for the stability of aquatic ecosystems (top predator and key link in the life cycle of the endangered river pearl mussel). Detailed ichthyological monitoring is being carried out in the Šumava region, with genetic analyses of brown trout populations and analysis of environmental DNA in sediment for the presence of fish parasites. Since water and fish do not respect national borders, areas with different management (protected areas and sport fishing areas) in both states will be covered. The aim is to identify those populations that deserve special protection (original genotypes in their natural habitat) and those populations that are heavily affected by stocking with non-native origins (areas with high pressure from sport fishing). In the programme area, there will be a significant streamlining of fisheries management and exchange of experience between area managers, conservationists, fisheries owners and stakeholder organisations.

Information letter

Ministry of Education, Youth and Sport of the Czech Republic

Impacts of climate change on nutrient availability in soils and waters of mountainous areas

Project No.: LUAUS24268

Principal Investigator: Eva Kaštovská (JČU), co-PI: Jiří Kopáček

Financial support: INTER-ACTION-LUAUS24

Duration: 3/2024 - 12/2027

The project focuses on understanding the mechanisms causing the increase in nutrient concentrations, especially phosphorus (P) and nitrogen (N), as well as dissolved organic carbon (DOC) in the surface waters of natural, human-unaffected mountainous areas. Increased nutrient availability significantly contributes to the productivity growth of these naturally oligotrophic waters, reducing their biodiversity, landscape value, and usability as drinking water reservoirs. These undesirable changes are closely related to climate change, which has been escalating in the last decade and significantly affecting the functioning of ecosystems in mountainous areas of Europe and America.

Alongside the increase in average annual temperatures, there is a shortening of the winter period, during which microbial processes in alpine soils are limited by low temperatures, and a lengthening of the growing season, when intensive decomposition of organic matter and nutrient recycling occur in soils, significantly supported by plant activity. Additionally, the frequency of torrential rains and the possibility of summer droughts are increasing. These factors accelerate rock weathering and nutrient cycles in soils, leading to the subsequent leaching of mobile forms of N, P, and DOC into the surface waters of mountainous systems. In addition to the climate change manifestations described above, other factors contribute to the eutrophication of waters in mountainous systems. In the mountainous areas of Central Europe, this is primarily due to increased leaching of P and DOC from soils recovering from acidification. In the alpine areas of the USA (and southern Europe), the increasing concentration of P in mountain lakes is likely due to increased dust deposition resulting from drier and windier weather in recent years.

The project's goal is to study and quantify the actual impacts of the combined manifestations of climatic and environmental changes on the cycles of C, N, and P and their availability in soils, retention/leaching, and concentrations in alpine lakes along the altitudinal gradient in two different mountain ranges with different historical and geographical contexts. We selected the High Tatras (Slovakia) and Uinta (Utah, USA) mountain ranges, for which we have long-term climatic data, dust deposition data, and a 30-40 year series of water quality data for mountain lakes. We hypothesize that in the alpine zone of the High Tatras, the behavior of soils and water quality is influenced by the combination of an extraordinary (globally unique) decline in acidic deposition along with a significant increase in temperatures and the frequency of torrential rains, accelerating the mechanical weathering of rocks. In contrast, in the Uinta mountain range (Utah, USA), which has been affected by acidification to a low extent, we expect that changes in the availability of N and P and the mobility of DOC in alpine soils are primarily caused by increased dust deposition and the significant external input of P, in addition to rising temperatures.

Running national projects

Ministry of Education, Youth and Sport of the Czech Republic, the support provided from EU funds

Ministry of the Environment of the Czech Republic

Engaging youth in the conservation of critically endangered fish species as part of landscape water retention measures

Project No. 5230200002

Principal investigator: Marek Šmejkal

Financial support: MŠMT

Duration: 2024-2025

Human activity in the landscape brings a decline in diversity, which can also be demonstrated in previously common species of organisms. Freshwater ecosystems are currently facing changes related to climate change, invasive species, or loss of original habitat. In this project, students will become familiar with the general issue of declining diversity in freshwater ecosystems and will be able to participate in a rescue program for two critically endangered fish species, the crucian carp (Carassius carassius) and sunbleak (Leucaspius delineatus). These species have practically disappeared from our waters due to the aforementioned problems and at the same time represent umbrella species of ecosystems that are disappearing from our country due to landscape drainage, climate change, and the presence of invasive species. The project will involve students in mapping the diversity in their surroundings and reintroducing critically endangered fish species.

Awareness of the decline in freshwater biodiversity and its causes (habitat change, invasive species, fragmentation, impacts of climate change, etc.)
Involvement of 7th and 8th grade students in mapping freshwater diversity in their surroundings
Involvement of 7th and 8th grade students in the reintroduction program of critically endangered fish species.
Creation of educational materials for the project and raising awareness beyond the six participating schools.

Ministry of Agriculture of the Czech Republic

Pikeperch fry production, their adaptability and optimalization of their stocking into open waters

Project No. QK23020002

Principal investigator: Tomáš Jůza

Financial support: Applied Research Program of the Ministry of Agriculture for the period 2017–2025

Duration: 2023 – 2025

The main aim of the project is an optimization of pikeperch production and stocking in open waters to reach the best survival and growth rates for this economically and ecologically valuable species. The main outputs of the project will be impacted publications focused on optimal conditions of pikeperch fry production in intensive aquaculture, on comparison of stocking effectiveness of pikeperch originated in intensive aquaculture (RAS) and pond-cultured pikeperch, on the optimal timing of stocking to open waters with regards to survival rate, growth, and conditions. The influence of the extreme overstocking by the predatory fish on the whole reservoir fish community and the water, quality will be also studied. The trophic position will be estimated via stable isotopes analysis.

Inovative fisheries management of a large reservoir

Project No. QK 22020134

Principal investigator: Jan Kubečka

Financial support: Applied Research Program of the Ministry of Agriculture for the period 2017–2025

Duration: 2022 – 2024

The project maps the dynamics (abundance, biomass, growth, survival, behaviour) of the mainmfish species of the Lipno model reservoir under the influence of anthropogenic stressors (climate change, recreational and illegal fishing, stocking, water level manipulation), protective measures and limnology. Based on quantified relationships, mathematical models of population dynamics and energy and matter flows will be parameterized, including simulations of management and climate scenarios till 2050. Simulations will anticipate risks and show possible mitigation to sustain yield, biodiversity, and ecological and recreational quality. An optimal management and stocking plan will be proposed. The solutions and management software developed here will find use in the management of other waters.

Optimization of the management in carp ponds with 1-year production cycle in terms of co-feeding methods and mass balance

Project No. QK21010131

Principal investigator: Milan Říha

Financial support: Applied Research Program of the Ministry of Agriculture for the period 2017–2025

Duration: 2021 – 2025

Technology Agency of the Czech Republic

Algal meadows: bioremediation technology for ecological restoration of aquatic habitats

Project No. SS07020018

Principal investigator: Klára Řeháková

Financial support: TACR

Duration: : 4/2024-6/2026

The utilization of underwater macroalgal meadows, occurring in post-mining lakes of northern Czechia, for the bioremediation of nutrients and pollutants in aquatic biotopes. The project focuses on implementing ecologically appropriate and economically sustainable methods to preserve water quality in various aquatic biotopes. The project’s aim is to obtain macroalgal strains capable of nutrient and pollutant accumulation from the water and utilize them in the processes of remediation and bioaccumulation. The bioremediation abilities of macroalgae will serve as a valuable basis for the management of existing and newly emerging mining lakes. The focus will be on ensuring the long-term ecological, socio-economic, and recreational value of these exceptional aquatic ecosystems.

Reducing the input of pollutants into the aquatic environment, particularly those that prevent achieving a good status of surface water bodies, including those that enter the aquatic environment exclusively through human activities.

New risks are coming, but old ones remain: Assessing Pollutant Contamination in Aquatic Biota and Its Potential Impact on Human Health, Including Tracing Routes from Historical and Present Sources. A Model Study of the Ohre River Basin

Project No. SS07010132

Principal investigator: Lukáš Vejříká

Financial support: TACR

Duration: : 4/2024-12/2026

The Ohře River, due to its geological position and history of industry and mining, serves as an ideal model of a river heavily burdened by a wide range of pollutants from both historical and contemporary sources. Additionally, it flows through the Karlovy Vary and Ústí Regions, areas that have been neglected in terms of research and environmental care. To minimize the risks associated with bioaccumulative (micro)pollutants, it is crucial to identify their presence and understand their behavior in the aquatic environment and food chain. These substances mainly enter the aquatic environment through insufficiently purified wastewater, landfill leachates, poorly insulated industrial production, and runoff from agricultural or urban areas. In addition to new sources, pollutants are often released into surface waters from historical deposits. For example, heavy metals can enter the water from historical sources such as former mines or defunct factories. These pollutants are often stored in river sediments and can be remobilized during floods or increased water flows. The proposed project aims to develop and optimize a comprehensive methodology, including the sampling and analysis of aquatic biota, to evaluate the contamination of watersheds with bioaccumulative (micro)pollutants. By applying this methodology in the Ohře Basin, the project seeks to identify the main sources of pollution and assess the risk to humans associated with fish consumption. As part of this methodology, monitoring will include organic (micro)pollutants (such as polychlorinated biphenyls, brominated flame retardants, per- and polyfluorinated compounds, selected pharmaceuticals, and personal care products) and toxic metals, including mercury and uranium. The departments involved in the project are the Institute of Hydrobiology of the Biological Center of the Academy of Sciences of the Czech Republic (HBÚ BC) and the Institute of Microbiology of the Academy of Sciences of the Czech Republic (MBÚ).

To develop methodology for the evaluation of the contamination of aquatic ecosystems with emergent pollutants with bioaccumulative potential. A systematic combination of innovative biota sampling and advanced analytical methods will create a methodology that can be used by the state administration to determine both historical and present watershed loads. The main attention will be paid to toxic metals (including uranium and mercury) and organic (micro)pollutants with a bioaccumulative and biomagnifying characters. Through detailed optimization and validation of the procedures, it will be possible to assess the anthropogenic drainage of the site and to reveal the various routes of introduction of the pollutants into any watershed, thus minimizing risks for the environment and humans.

Czech Science Foundation EXPRO

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

Project No.: 20-12496X

Principal Investigator: Rohit Ghai

Financial support: Czech Science Foundation

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.

Czech Science Foundation

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.

Nitrogen fixation in polluted Czech peat bogs: Reconciling high N accumulation rates based on 210Pb dating with low 15N2 uptake and low P availability

Project No.: 24-12596S

Principal Investigator: Martin Novák (Czech Geological Survey), co-PI: Jiří Kopáček

Financial support: Czech Science Foundation

Duration: 2024 - 2026

Availability of reactive nitrogen (Nr) is a key control of carbon sequestration in wetlands. To complement the metabolic demands of Sphagnum in pristine bogs, diazotrophs supply additional Nr via biological nitrogen fixation (BNF). Since breaking the triple bond of atmospheric N2 is energy-intensive, it is reasonable to assume that high inputs of pollutant Nr will lead to BNF downregulation. Yet, recent work has documented measurable BNF rates in Sphagnum bogs also in N-polluted regions. Our study, performed at 3 highly polluted bogs in Central Europe and 1 pristine bog in Svalbard, will attempt to statistically tease apart the role of 10 parameters potentially controlling BNF. Special attention will be paid to phosphorus limitation, but also to sulfate and molybdenum availability. Excess N observed by us in 210Pb dated peat profiles will be attributed to BNF if BNF rates directly measured over 2 seasons and 3 depths by 15N2 experiments are high enough, and if we document immobility of 210Pb as a prerequisite of 210Pb dating at sites with fluctuating water table/redox conditions.

The rates of biological nitrogen fixation (BNF) estimated from excess N in accreting peat will be compared to BNF rates directly measured by 15N2 moss incubations and constrained by P availability. 10 parameters will be measured to statistically tease apart the strength of individual BNF controls.

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.

Contamination of European aquatic ecosystems by organofluorine pollutants: levels and driving factors of bioaccumulation in the trophic web

Project No.: 24-11430K

Principal Investigator: Tomáš Cajthaml (Institute of Microbiology CAS, Praha), Co-PI: Lukáš Vejřík

Financial support: Czech Science Foundation

Duration: 04/2024-3/2027

Freshwaters are the most affected ecosystems by anthropogenic pollutants worldwide. The main goal of the proposed project will be to unravel the fate of classical and new organofluorine pollutants in aquatic ecosystems of Europe and to assess the driving factors of their accumulation in fish. Using advanced analytical technics, several tens of anthropogenic chemicals will be determined across the aquatic food web in different lotic and lentic localities. Physiological assessment together with chemical analysis of pollutants in various biota (from plankton to top predators) and trophic position determined using stable isotope analysis will also bring light to the biomagnification in the food chain and will provide needed data for human health risk assessment. Moreover, preselected localities will be representing various conditions to discover driving factors of bioaccumulation of organofluorine contaminants. Finally, the redundancy analysis of such a large set of collected data will point out the most relevant factors of selected pollutants transport in the environment and food web.

The main aim of this project is to describe the driving factors of organofluorine pollutants bioaccumulation in various fish feeding guilds and food web. The next aim is to evaluate the contamination of European aquatic ecosystems to bring the light in human exposition towards fillet consumption.

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

Duration: 2024 - 2026

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.

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.

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

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.

Phage host hunt: finding hosts for freshwater phages

Project No.: 23-06806S

Principal Investigator: Markus Haber

Financial support: Czech Science Foundation

Duration: 2023 - 2025

Phages (viruses infecting bacteria) are present in all ecosystems and structure microbial communities through the regulation of host populations and the release of host-bound nutrients through lysis. Metagenomics revealed a huge phage diversity in nature but often failed to assign hosts to phages. Especially in freshwater environments, this is partly due to the lack of cultured reference phages and their hosts. Recent advances in bacterial cultivation enabled the isolation of abundant freshwater bacteria (e.g., Fonsibacter, Methylopumilus) and we have a large culture collection of such strains. Here we propose to use these bacteria and established high throughput phage isolation protocols to isolate new phages and to bona-fide identify phage-host pairs. We will study the host range, natural abundances and dynamics of newly isolated phages. Finally, we will identify prophages 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.

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

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.

Harnessing iEcology and culturomics to advance invasion science

Project No.: 23-07278S

Principal Investigator: Ivan Jarič

Financial support: Czech Science Foundation

Duration: 2023 - 2025

The introduction of invasive alien species (IAS) represents a key stage in the invasion process and one where management measures, if applied early enough, are most cost-effective. Improved understanding of socioeconomic and ecological factors that are driving introduction events can improve IAS risk assessments and management effectiveness. However, the data on these early phases of invasion process are often not available, and obtaining them is costly, time-consuming and often impossible. The proposed project will focus on harnessing large digital data sources with approaches from the emerging fields of culturomics and iEcology, and on integrating them with existing data on species life history, biodiversity, introductions and invasions, and habitat and climatic data to develop an IAS introduction model. Main focus will be on species from the list of IAS of Union Concern. By integrating biological, socioeconomic and cultural factors, this project will yield novel insights into the mechanisms influencing the invasion process.

Using approaches of iEcology and conservation culturomics the project will collect large bodies of digital data about invasive alien species of Union Concern and develop an IAS introduction model to test the impact of biological, socioeconomic and cultural factors on invasion process.

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.

Performance of mountain ecosystems along elevation gradients under changing environmental conditions

Project No.: 23-06379S

Co-Principal Investigator: Jiří Kopáček

Financial support: Czech Science Foundation

Duration: 2023 - 2025

Changes in the chemical and biological composition of mountain lakes are currently accelerating, being more pronounced at higher elevations. These trends reflect differences in not only nutrient pools and microbial biomass (decreasing with increasing elevation), but also in the increasing intensity of responses of terrestrial systems to environmental changes (recovery from acidification and climate) with elevation. Our study along the elevation gradient of the Tatra Mts. will evaluate the responses of different soil types (from forest, through alpine meadows, to till soils in scree) to current changes in temperature and precipitation regimes (differences in the rapidity and temperature sensitivity of microbial processes involved in C, N, and P cycling). Using field and laboratory experiments, we will identify differences in key processes of nutrient retention, mobilization, and leaching from soils. The leaching mechanisms will be used to understand long-term trends in chemical and biological composition of lakes and their current differences along the elevation gradient.

The aim of the project is to quantify (1) the effects of climate change on nutrient (C, N, P) cycles and microbial community in soils along a mountain gradient from forest to scree area, and (2) the effects of related changes in nutrient leaching on lake chemistry, biota and trajectories of their recovery from acidification.

Environmental changes caused by extraterrestrial impacts and volcanism: Evidence from lake sediments

Project No.: 23-06075S

Principal Investigator: Evžen Stuchlík

Financial support: Czech Science Foundation

Duration: 2023 - 2025

Impact events are potential triggers of abrupt environmental changes as their direct destructive power influences atmospheric and geochemical processes. A multiple evidence from many sites in both hemispheres of Earth shows that a major cosmic impact occurred 12,800 years ago and triggered the Younger Dryas cooling (YD). We propose an interdisciplinary study of lake sediments of YD onset age to evaluate (1) responses of lake-catchment ecosystems to this event. Our study sites are located in the Bohemian Forest (Czechia) and the Tatra Mts (Poland) which allows to disentangle effects of the impact from effects of the preceding eruption of the Laacher See volcano (13,000 years ago) that caused deposition of a volcanic ash in the Bohemian Forest. We will also focus on (2) testing of presence of extraterrestrial admixture in melt grains that we have found in lake sediments of YD onset age and on (3) developing a new method for identification of circannual cycles of sediment deposition. Such a method would considerably improve dating of environmental changes in non-varved lake sediments.

The aim of the project is to evaluate: (1) responses of lake-catchment ecosystems to the Younger Dryas (YD) onset including changes in pedogenesis; (2) presence of extraterrestrial admixture in melt grains of YD onset age; (3) a new method for identification on circannual sedimentation changes in nonvarved lake sediments.

Water scarcity hotspots in Central Europe based on the composition of water isotopesin lakes: hydrological, climatic, and socio economic determinants

Project No.: 23-07152S

Principal Investigator: Yuliya Vystavna

Financial support: Czech Science Foundation

Duration: 2023 - 2025

Climate change and water scarcity in Central Europe have a significant impact on the availability of water resources. The overall aim of the project is to develop a new approach to identify water scarcity hotspots in Central Europe and their determinants based on the isotopic composition of lakes and water balance model using isotopes. The project is focused on: (i) identification of best variables and methods of the data collection and treatment for use in isotope water balance in lake catchments and (ii) quantification of water scarcity using composition of water isotopes in lakes and isotope water balance modelling and assessment of hydrological, climatic and socio-economic determinants of water scarcity using machine learning tools (Random Forest, Gaussian Mixing Model). The novelty of the project relates to unresolved questions on the factors affecting water scarcity and the prediction of water scarcity based on a multidisciplinary approach including environmental and socio-economic variables.

The overall aim of the project is to develop a new approach to identify water scarcity hotspots in Central Europe and their determinants based on the isotopic composition of lakes, isotope- enabled water balance modelling, citizen science and machine learning tools.

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 farreaching 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 composition, structure and phenology of plankton assemblages.

The aim of the project 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.

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

Project No.: 22-03662S

Principal Investigator: Michaela Salcher

Financial support: Czech Science Foundation

Duration: 2022 - 2024

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 nitrogen availability and forest status on soil microbiome, nutrient cycling, and biological recovery of acidified waters in mountain ecosystem

Project No.: 22-05421S

Principal Investigator: Jiří Kopáček

Financial support: Czech Science Foundation

Duration: 2022 - 2024

The dominant Norway spruce vegetation was to different extents disturbed by bark beetle infestation in the unmanaged Bohemian Forest (BF) catchments during the last two decades. All dead tree biomass remained on site and stands began to regenerate naturally, providing wide gradients of vegetation, soil properties, and surface water composition within individual catchments, as well as among them. We propose an integrated study in the BF catchment-lake systems on effects of natural forest regeneration on chemical and microbial soil composition and function, element (primarily N) cycles and leaching, and recovery of receiving waters from acidification. We plan to evaluate (1) effects of gradual decomposition of dead biomass on a cascade of compositional and functional changes in soil microbial communities, and element availability and leaching; (2) how their fluctuations are affected by density of regenerating trees and their growth rates (both related to microclimate conditions); and (3) how seasonality of postdisturbance element leaching affects biological recovery of waters.

The aims of the project are to evaluate links among (1) climate, soil properties, and spruce forest regeneration after disturbances in mountain catchments; (2) forest re-grow, soil microbiome composition and function, and element leaching; and (3) seasonality of water chemistry and biological recovery from acidification.

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

Project No.: 22-05478S

Principal Investigator: Pavel Hrouzek

Co-principal Investigator: Jan Mareš

Financial support: Czech Science Foundation

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.

The aims are 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

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 are: 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.

EcoFAct – Ecology of abundant freshwater actinobacteria

Project No.: 21-21990S

Principal Investigator: Markus Haber

Financial support: Czech Science Foundation

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.

Finished projects

EU Horizon 2020

Co-creating a decision support framework to ensure sustainable fish production in Europe under climate change (ClimeFish)

Project No.: 677039

Principal Investigator: Prof. Michaela Aschan, University of Tromso, Norway

Co-principal Investigator: Prof. Jan Kubečka, Ph.D.

Financial support: EU Horizon 2020

Duration: 2016-2020

Scientist from 16 countries join forces to help ensure that the increase in seafood production comes in areas and for species where there is a potential for sustainable growth, given the expected climate changes. In ClimeFish they will provide a support framework for decision makers, thus contributing to robust employment and sustainable development of rural and coastal communities. In Czech part of the project we intend to rationalize the angling use of fish production under changing environment.

Why: Climate changes are real, they are happening right now and they are threatening sustainable growth in aquaculture and fisheries worldwide. The world population is growing, and the demand for food is increasing. Forecasts indicate an overall decline in food production due to climate change. ClimeFish addresses the necessity of changes, both when it comes to utilizing opportunities and mitigating risks under climate change. ClimeFish will help ensure that the increase in seafood production comes in areas and for species where there is a potential for sustainable growth. IN Czech
conditions the growth of production is complicated by the changes of nutrient concentrations and angling effort. All these factors will be considered.

What: ClimeFish will provide guidelines for how to make climate-enabled management plans to prepare and adapt to climate change while minimizing economic losses and social consequences. Thus, based on the expected climatic challenges, ClimeFish will contribute to robust employment and sustainable development of rural and coastal communities. The output of the project will be the ClimeFish Decision Support Framework (DSF), which contains guidelines, databases and the ClimeFish Decision Support System (DSS). The results of the project will be used for optimization of fishery in Lipno reservoir and other waterbodies.

How: ClimeFish will develop forecasts for production scenarios that will serve as input to socio-economic analysis and identify risks and opportunities regarding climate changes. Strategies to mitigate risk and utilize opportunities will be identified in co-creation with stakeholders, and will serve to strengthen the scientific advice and to improve long term production planning and policymaking. The project addresses three production sectors: marine aquaculture, marine fisheries and lake and pond production in a total of 16 case studies, involving more than 25 species. For Czech fisheries, the main target species are wells, Silurus glanis, pikeperch, Sander lucioperca and carp, Cyprinus carpio.

ClimeFish

Spanish Ministry of Environment, in the frame of the cooperative research programme called “PROGRAMA NACIONAL DE INVESTIGACIÓN CIENTÍFICA, DESARROLLO E INNOVACIÓN TECNOLÓGICA”

Calibration of sampling methods for Spanish fish populations in reservoirs

Project No.: IT

Principal Investigator: Jan Kubečka

Co-principal Investigator: ECOHYDROS, S.L., Spain, Department of Ecology of the Universidad de Sevilla, Spain

Financial support: Spanish Ministry of Environment, in the frame of the cooperative research programme called “PROGRAMA NACIONAL DE INVESTIGACIÓN CIENTÍFICA, DESARROLLO E INNOVACIÓN

Duration: 2009-2010

The project is aimed at improvement of ecological potential of Spanish reservoirs and enhancement of fisheries management by improving the methods of assessment of qualitative and quantitative composition of the fish stock. The project includes introduction of active methods of monitoring, namely new hydroacoustic and trawling approaches. Active methods should mitigate the main weaknesses of the current monitoring based predominantly on passive methods. Managing of the use of active trawling gear for fish capture would represent the revolution both in monitoring and the management of reservoirs. The project follows the philosophy of the EC water framework directive 2000/60/EC and promises to create new fish monitoring methodology and to bring new crucial knowledge to the methods of fish capture in general.

Puerto Rico department of Natural and Environmental Resource

Freshwater sport fish management and enhancement

Project No.: -001577

Principal Investigator: J. Wesley Neal, Robert Kroger, Craig G. Lilyestrom

Co-principal Investigator: Marie Prchalová

Financial support: Puerto Rico department of Natural and Environmental Resource

Duration: 2009-2011

Much of the research and management decisions for largemouth bass Micropterus salmoides in Puerto Rico have been based on the assumption that prey availability is not limiting, yet conclusive data to this end are not available. Threadfin shad are the primary prey species for sport fish in Puerto Rico reservoirs, yet directed research has never effectively quantified threadfin shad abundance or annual production. Threadfin shad appear to reproduce year-round, but the extent of reproduction in not known. Whereas effective largemouth bass management requires consideration of both predator and prey, improved understanding of prey population dynamics is required for reservoirs in Puerto Rico. The subcontract comprises two jobs - comparison of active versus passive gears for sampling threadfin shad in Puerto Rican reservoirs and population dynamics of threadfin shad in Puerto Rico.

Ministry of Education, Youth and Sport of the Czech Republic administrate the support provided from EU funds

Biomanipulation as a tool for the improvement of reservoir water quality

Project No.: CZ.02.1.01/0.0/0.0/16_025/0007417

Principal Investigator: Jan Kubečka, Tomáš Jůza

Financial support: Ministry of Education, Youth and Sport of the Czech Republic administrate the support provided from EU funds

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.

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Palaeoecological reconstruction of global environmental changes at the Younger Dryas onset

Project No.:

Principal Investigator: Evžen Stuchlík

Financial support: Ministry of Education, Youth and Sport of the Czech Republic

Duration: 2019 - 2022

Scientific goals of the project:
1. To test the hypothesis that the Laacher See volcanic explosion (12900 calibrated years BP) changed freshwater communities in the Bohemian Forest lakes.
2. To test the hypothesis that the Younger Dryas Boundary (YDB) layer (well-known from many North American sedimentary sequences) is also present in sediments of the Bohemian Forest lakes. If yes, this layer has characteristic geochemical and geophysical signal, contains impact-related micro-spherules (MSPs), and could be used as an important tool for regional chronostratigraphy.
3. To test the hypothesis that YDB is present in selected Alaska lakes. If yes, YDB will be compared with YDB found at the Czech sites.
4. To test the hypothesis that the Younger Dryas (YD) onset was characterized by changes in environmental chemistry, a decrease in biota abundances and biodiversity, or a shift in composition of ecological groups in the studied palaeoecosystems. If yes, which factors were responsible for the ecosystem damage and transformation? Was the YD onset more pronounced in Alaska lakes or in the Czech lakes?
5. To determine the timing of the presumed sudden environmental changes at the YD onset in both regions (central Europe and Alaska) and compare the results with the geochemical data from the Greenland ice (especially with the North Greenland Ice Core Project record).

Centre for Ecological Potential of Fish Communities in Reservoirs and Lakes (CEKOPOT)

Project No.: .07/2.3.00/20.0204

Principal Investigator: Josef Matěna, Jan Kubečka

Financial support: Ministry of Education, Youth and Sport of the Czech Republic administrate the support provided from EU funds

Duration: 2012–2015

Fish communities in reservoirs and lakes are highly valuable from genetic, ecological and economical point of view. They have also substantial influence on the water quality in these ecosystems. The project enables support of a top quality team for the synthesis of functions mentioned above and for the definition of ecological potential of fish communities. We assume improvement and widening of methods presently used and investigation of fish stock of the most important and interesting reservoirs in the Czech Republic. At the same time, the Czech activities will be interconnected with European initiatives in order to publicize the huge effort of the Czech limnological school for explaining the true picture of the fish communities and their role in the ecosystem. The complex specification of the ecological potential (faunistic, fish- productive and biomanipulative value, equilibrium of the population dynamics a trophic interactions) will be possible by enhancement of inland human resources, support of external stays on top institutions, integration into European structures and close cooperation with an external expert. The engagement of a top expert in the field of hydroacoustics As./Prof. Helge Balk from Norway enables the improvement of methods especially the data collection in shallow water layers (0-5 m).

A new methodological approach have been planned – the analysis of stable isotopes in fish which should help us to clarify the role of particular species and its ontogentical stage in the food webs of ecosystems studied.

In the framework of the project a field course and one world conference dealing with the function of fish in the reservoir ecosystem will be organized.

The outputs of the project will be as follows: i) final establishment and stabilization of the working group FISHECU, ii) involvement of the Czech Republic into the European intercalibration net (JRC-EEWAI intercalibration forum, Lake-Fish Intercalibration Group LFIG), iii) production of scientific papers, iv) external stays of our scientists and students oriented on hydroacoustics and methods of stable isotopes studies.

Landesamt für Verbraucherschutz, Landwirtschaft und Flurneuordnung Frankfurt/O., Germany

Estimation of fish yield potential in lakes, fish assessment in Lake Werbellinsee

Project No.: 09-14

Principal Investigator: Jan Kubečka

Co-principal Investigator: Institut für Binnenfischerei e.V. Potsdam-Sacrow

Financial support: Landesamt für Verbraucherschutz, Landwirtschaft und Flurneuordnung Frankfurt/O., Germany

Duration: 2009-2010

The investigations were be carried out on Lake Werbellinsee in September 2009 by using the following methods:

1) Hydroacoustic survey by scientific echosounder (two day and night surveys)

2) Survey of the open water fish by fry trawls (approximately 20 trawlings by 3x3 m trawl)

The emphasis of the survey work was on the population assessment (abundance, spatial and vertical distribution, species and size composition) of vendace (Coregonus albula)
and smelt (Osmerus eperlanus).

EEA Grant/Norway

Drinking WAter Readiness for the Future

Project No.: TO01000202

Principal Investigator: doc. Ing. Petr Porcal, Ph.D.

Financial support: TAČR and Norway Grants

Duration: 2021 - 2024

Increasing levels of Dissolved Organic Matter (DOM) is a large challenge for Drinking Water Treatment Plants. Surface water is the source for more than 50% of drinking water in the Czech Republic. In the region of South Bohemia surface water supports drinking water for more than 350 thousand people from the reservoirs (Římov, Husinec, Jordán) and Otava River. Catchments of these sources will be characterized with respect to the sources of DOM and their temporal and spatial variability resulting in a map of DOM sources with future predictions. A methodology for outflow control in reservoirs to minimize the effect of flood events with high DOM levels will be developed. A cooperation among basin authorities, drinking water producers and Czech and Norway research partners will be established.

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Size estimation and taxonomical identification of European freshwater fishes using a broadband echosounder

Project No.: EHP-BFNU-OVNKM-2-093-01-2019

Principal Investigator: RNDr. Michal Tušer, Ph.D.

Financial support: EEA and Norway Grants

Duration: 2019 - 2023

Environmental assessment, monitoring and management is an important societal concern as the quality of human living and health depends to a large extent on a favorable state of ecosystems providing a multitude of ecosystem services to mankind. This is specifically true for freshwater ecosystems providing essential drinkable water to large parts of the human population. To assess and monitor aquatic ecosystems and specifically those organisms serving as water-quality indicators, fishes in the case, echosounding has become an important, integral monitoring technique in most countries worldwide.

The development of broadband echosounders represents a technological leap compared to conventional narrowband (single-frequency) echosounders. The broadband echosounder is an echosounder that can emit a wide spectrum of frequencies in a single acoustic pulse, providing much richer information on fish. For instance, a different size, spatial orientation or species of fish can provide different frequency responses. Deciphering the receiving signals will provide the clue to size and taxonomical identification of observed fish.

Every new technology, nevertheless, requires groundtruthing of its capabilities. Therefore, the recent spreading of broadband echosounders among fish biologists urges for a thorough performance analysis of such systems in order to exploit their merits and a possibility as replacement for the conventional narrowband echosounders. We aim to explore the application potential of the broadband echosounder for estimation of the true fish size and taxonomic group identification of common European fish species.

For the investigation, a new broadband echosounder EK80 (SIMRAD, Norway), owned by the applicant, will be utilized in controlled experiments with common European freshwater fishes. The controlled experiments will be executed in a special experimental cage, situated in the Rimov reservoir (the Czech Republic). Different sizes of several fish species will be observed. The shape of receiving sound signals will be extracted, inspected and processed into classification algorithms.

Both the biologically and methodologically oriented applicant has experiences in field experiments and acoustic data recording, will realize all experimental work connected to cage experiments in the Czech Republic. Data processing will require a profounded knowledge of sound physics and detailed analysis of acoustic sound shapes, which will be provided by the Norwegian partner. Data processing and analyses will be equally shared between both the participants.

The combination of both participants’ expertise is essential in reaching ambitions of this project. Besides that the results of this initiative will be published in an open-access journal, the outcome of this collaboration will be to maintain a long-term mutual relationship between the institutes.

Web

Monitoring of the fish stock of Czech reservoirs

Project No.: 91

Principal Investigator: Jan Kubečka

Financial support: EEA Grant/Norway

Duration: 2008-2010

The project is aimed at improvement of ecological potential of Czech reservoirs and enhancement of fisheries management by improving the methods of assessment of qualitative and quantitative composition of the fish stock. The project includes introduction of active methods of monitoring, namely new hydroacoustic and trawling approaches. Active methods should mitigate the main weaknesses of the current monitoring based predominantly on passive methods. Managing of the use of active trawling gear for fish capture would represent the revolution both in monitoring and the management of reservoirs. The project follows the philosophy of the EC water framework directive 2000/60/EC and promises to create new fish monitoring methodology and to bring new crucial knowledge to the methods of fish capture in general.

Monitoring the environment of man-made lakes: what can fisheries data and models tell us?

Project No.: 0046/2/0029

Principal Investigator: David Boukal

Co-principal Investigator: Jan Kubečka

Financial support: EEA Grant/Norway

Duration: 2009-2010

Research and development of a comprehensive database on fish population dynamics and history of exploitation in selected man-made reservoirs in the Czech Republic. Development of mathematical models to identify exploitation strategies that take into account stakeholder interests along with the ecological and evolutionary consequences of the exploitation, with the aim to identify the 'best' strategies and identify data/parameters/processes whose measurement can greatly improve the quality of the monitoring of the status of fish stocks in Czech man-made reservoirs. Communication of the main scientific findings to the key stakeholders identified during this study.

Czech-Norwegian Research Programme (CZ09)

Structuring effect of submerged macrophytes on trophic relationships and distribution of fish in deep lakes (MacFish)

Project No.: 316

Principal Investigator: Jiří Peterka

Co-principal Investigator: Karl Oysten Gjelland, Norwegian Institute for Nature Research

Financial support: Czech-Norwegian Research Programme (CZ09)

Duration: 2014-2017

Predation by fish is the primary top-down structuring force in aquatic ecosystems, and a change in predator-prey interactions involving fish may cause a change in the strength of trophic cascades and finally result in ecosystem shifts. Submerged macrophytes play an important role beyond that of primary production, as they provide increased structural complexity and niche potentials for fish. However, most of the scientific attention on habitat use in fish and the influence of macrophytes have been given to small and shallow lakes, where the vegetated areas are well-developed and the availability of a large deep water refugium is absent or limited. Our goal is to gain a detailed understanding of the structuring effect the submerged macrophytes have on fish communities in deep lakes. In order to achieve this, we will contrast two newly formed deep lakes of similar size and colonization history, but one with and the other without submerged macrophytes. We will use the latest developments in high-resolution positioning telemetry to assess individual habitat use and activity patterns in the different species of the multispecies assemblages in the two lakes. This will be combined with other sampling techniques, such as echosounding, acoustic cameras, video cameras, electrofishing, trawling and gillnetting, with an emphasis on the non-lethal methods and covering all ontogenetic stages from fish larvae to mature adults. Individual trophic position will be assessed by diet studies and stable isotope analyses. We will use the resulting data to study intra- and interspecific overlap in habitat and trophic niche use, as well as activity patterns with high spatiotemporal resolution. Combined with consumption estimates in piscivorous predator fishes and life-history characteristics such as growth and age at maturation in prey fish, a comprehensive and detailed insight into the effect of submerged macrophytes on the fish community structures and dynamics will be reached. The project will provide novel basic research results that will have important relevance for the management and restoration of water bodies, and it will strengthen the cooperation and knowledge transfer between Czech and Norwegian aquatic ecosystem research.

Technology Agency of the Czech Republic

The enhancement of rheophilous fish reproduction in the artificial river environment

Project No.: TJ02000012

Principal Investigator: Marek Šmejkal

Financial support: Technology Agency of the Czech Republic

Duration: 2019 - 2021

We will aim to increase substantially the reproductive success of asp in the studied system. The specific aims of this project are to quantify the hydropeaking effect on the egg mortality and to evaluate the mortality caused by egg-predating cyprinid fishes. We will test technical solutions mitigating the hydropeaking and egg-predation impact. More than 2000 asp individuals are migrating yearly in the tributary and altogether, more than 100 kg asp eggs are laid. Due to hydropeaking and egg predation is natural recruitment absent and it is necessary to sustain the population by stocking of artificially reared fish.

Floating green islands, a perspective alternative for improvement of ecological potential and support of littoral habitats in water reservoirs

Project No.: TH02030633

Principal Investigator: Jan Kubečka, Josef Hejzlar

Financial support: Technology Agency of the Czech Republic

Duration: 2017 - 2020

The aim of this project is to develop floating islands technology for reservoirs application (construction design, substrate, composition of plants and field tests of mechanics and ecosystem benefits). The target of the project is the littoral habitat, which is normally the richest habitat of natural lakes. In most of our reservoirs it is eco-hydrologically degraded due to water level fluctuations. Aquatic macrophytes are destroyed here by drying and freezing or due to shading by low transparency. Project outputs will enhance the ecological potential of reservoirs by supporting species diversity of aquatic organisms, the structure of the fish stock, nesting of waterfowl, nutrient reduction, water quality and aesthetic value.

Development of technical measure for protection of natural riverine fish stock against masive migration of undesirable fish species from Lipno reservoir as encouragement of population of brown trout and freshwater pearl mussel Margaritifera margaritifera

Project No.: TH02030709

Principal Investigator: Milan Muška, Jan Kubečka

Financial support: Technology Agency of the Czech Republic

Duration: 2017 - 2020

The aim of the project is to select suitable location and develop mobile migration barrier above the Lipno reservoir. The barrier must not influence either the river flow or transport of debris, but have to effectively prevent reservoir fish from migrating into upper Vltava river catchment. Effectively operating barrier assures undisturbed development of indigenous salmonid assemblage in upper Vltava river improving hereby the essential requirements for reproduction of critically endangered Pearl mussel. Simultaneously, the location of the barrier should allow finding suitable spawning habitats for desirable fish species from the reservoir. Developed technology will be applicable to many similar places where regulation of fish migration is necessary and building weirs is not possible.

Sediments of water bodies - identification, quantification, characterisation, sanitation - new approaches

Project No.: 021342

Principal Investigator: Jakub Borovec

Financial support: Technology Agency of the Czech Republic

Duration: 2015 - 2017

Ministry of Agriculture, National Agency for Agriculture Research

Methodology of predatory fish quantification in drinking-water reservoirs to optimize the management of aquatic ecosystems

Project No. QK1920011

Principal investigator: Petr Blabolil

Financial support: Applied Research Program of the Ministry of Agriculture for the period 2017–2025

Duration: 2019–2021

The aim of the project is to develop a methodology for quantification of predatory fish to optimize the management of drinking-water reservoirs using data from the investigator s comprehensive database and practical field tests. This main output together with the other outputs (proven technologies to use environmental DNA from water, longlines to determine the populations of European catfish and universal antenna systems, and prototype fish picking equipment from a large fyke-net) are the key for the effective planning of the fisheries management aiming to influence the food chain by predation on planktivory fish. This will positively affect water quality.

Aquaculture of rheofilous fish

Project No. QK1920326

Principal investigator: Peter Podhorec, South Bohemian University, Faculty of Fisheries and Protection of Waters

Co-investigator: Marek Šmejkal

Financial support: Applied Research Program of Ministry of Agriculture for the period 2017–2025

Duration: 2019–2021

The impacts of anthropogenic changes on the river environment lead to decrease of abundance and diversity in rheophilous fish communities. One of the possibilities to enhance native populations, especially where natural recruitment is not successful, is stocking of trained fish with high probability of their survival. Fish produced in aquaculture environment are formed by different selection pressure than fish in the natural environment. Although it seems impossible to maintain whole spectrum of natural behaviour in aquaculture while keeping the efficiency on the same level, it is at least possible to improve condition of stocked fish and escape reactions to predators. Production of rheophilous fish in conditions with enhanced emphasis on their condition and with acquired reaction to predation may potentially improve the stocking efficiency of rheophilous fish. Model fish species used in this study is the rheophilous asp (Leuciscus aspius). This species is produced as important community component of water drinking reservoirs, where it decreases the number of omnivorous fish species. Asp reared in artificial conditions will be divided in four groups and we will test the effect of condition (water speed during rearing) and presence/absence of alarm cues from predation on the survival rates of stocked fish in natural environment. We will assess relative survival rates three times a year (spring, summer and autumn) and the impact of improved conditions of rearing to survival will be evaluated.

Optimalisation of the biomanipulative effect of predatory fish in ecosystems of water reservoirs

Project No.: 046

Principal Investigator: Jan Kubečka

Financial support: National Agency for Agriculture Research

Duration: 2008-2012

The project is aimed on reduction of eutrophistaion of surface waters by increasing of efficiency of top-down controll through the enhacement of predatory fish. We plan to improve technologies of egg incubation and culture of larval and juvenile predators (both mono- and polyculture). The survival of stocked fry will be studied with respect to their size and stocking strategy. The predation immediatelly after stocking will be studied. The attention will be paid to the ratio between abundance of stocked fish and the fish from natural reproduction. The population dynamics of predatory fish will be studied during five years on four reservoirs.

Czech Science Foundation

Paleo-records of global range events from lake sedimentary sequence

Project No.: 20-08294S

Principal Investigator: Evžen Stuchlík

Financial support: Czech Science Foundation

Duration: 2020 - 2022

A multiple evidence from increasing number of sites shows that a major cosmic impact occurred at the end of the Pleistocene. The so-called Younger Dryas Boundary layer (YDB) supports the hypothesis that a fragmented cosmic body slammed into the Earth ~12,800 cal. BP at the time of the Younger Dryas cooling onset. This layer contains a characteristic assemblage of impactrelated particles and elemental composition. Simultaneously, megafaunal extinctions, changes in vegetation cover, human population cultural shifts, and widespread wildfires were documented. In Europe, YBD records are still rare and most of them are known from paleosoils. We have focused on lake sediment sequences and identified the presence of YDB markers in Bohemian Forest lakes, Czech Republic. Our first results suggest environmental contamination of the region by long-range atmospheric transport of pollutants. In the proposed project, we will study history of three selected lake-catchment ecosystems with focus on the YDB transition and identification of Late Glacial and Early Holocene tephra layers.

The aims of the project are: 1) Testing of uniqueness of the YBD proxies within the postglacial sedimentary records. 2) Identification of volcanic ash (tephra) layers in lake sediments of Late Glacial and Early Holocene age. 3) Reconstruction of ecosytems' reaction on the YDB environmental contamination.

Phosphorus leaching from undeveloped alpine soils: Biotic or abiotic control?

Project No.: 20-19284S

Principal Investigator: Jiří Kaňa

Financial support: Czech Science Foundation

Duration: 2020 - 2022

We will identify major environmental factors controlling P leaching from undeveloped soils in natural, unmanaged areas. We will evaluate effects of soil recovery from acidification, increasing dust deposition, and climate-accelerated physical erosion of rocks on chemistry and ability of soils to retain/release P. The most pronounced increases in lake water P concentrations (besides USA) have occurred in the Tatra Mountains, mainly in catchments with high proportion of scree and undeveloped till soils. Using local rocks, we will experimentally assess effects of climate change on their physical erosion. Then, we will evaluate effect of increased rock weathering on soil chemistry and P retaining ability. Special attention will be paid to composition of microbial community of till soils, and activity and role of its major components in P mobilization from rock and dust. Using long-term trends in chemistry and biology of lakes, we will evaluate individual and synergetic effects of recovery from acidification and climate change on the ongoing changes in their nutrient status and trophy.

The aims of the project ate to evaluate effects of (1) chemistry and microbial community of till and alpine meadow soils on P cycling, and (2) climate changes (increasing physical erosion and dust deposition) and recovery from acidification on increasing P leaching from soils and the related eutrophication of receiving waters.

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

Project No.: 20-23718Y

Principal Investigator: Tanja Shabarova

Financial support: Czech Science Foundation

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.

How important is biogenic methane for secondary production in seasonally stratified freshwater reservoirs?

Project No.: 20-18005S

Principal Investigator: Mojmír Vašek

Financial support: Czech Science Foundation

Duration: 2020 - 2022

Methanogenesis followed by methane oxidation may provide a significant pathway of carbon and energy into aquatic food webs. This project aims at clarifying the potential importance of biogenic methane to secondary production in freshwater reservoirs. Our major objective is to examine the role of biogenic methane in food webs of three stratified, temperate reservoirs that represent a gradient of eutrophication and hypolimnetic oxygen availability. Basal organicmatter sources, methane, microbial communities, primary consumers (aquatic invertebrates), and top consumers (fishes) will be sampled in all principal habitats (littoral, pelagic, profundal) within each reservoir. Using stable isotopes as natural tracers, we will quantify within- and among-reservoir variation in the possible use of methane-derived carbon by primary and higherlevel consumers. We expect that biogenic methane can serve as a significant alternative source of energy, partially supporting production of invertebrate and fish biomass in reservoir ecosystems.

The aim of the project is to provide quantitative evaluation of the importance of biogenic methane to secondary production in stratified freshwater reservoirs. To examine how the relevance of methanederived carbon in the entire food web changes with reservoir trophic state and hypolimnetic oxygen availability.

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

Project No.: 19-16554S

Principal Investigator: Dagmara Sirová

Financial support: Czech Science Foundation

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.

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

Project No.: 19-23261S

Principal Investigator: Jitka Jezberová

Financial support: Czech Science Foundation

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.

Quantifying water and phosphorus fluxes in disturbed vs. intact mountain forest catchments by hydrological, isotopic and hydrochemical methods

Project No.: 19-22276Y

Principal Investigator: Yuliya Vystavna

Financial support: Czech Science Foundation

Duration: 2019 - 2021

Changes in catchment hydrology can result in nutrients losses from catchments with following reduction of soil fertility but increasing primary production and eutrophication of water bodies. Applying hydrological models, stable water isotopes (O-18, H-2) and hydrochemical measurements we will trace and quantify phosphorus fluxes in a pair of forest catchments - with a healthy stand and stand in early stage of recovery after deforestation. This paired catchment study is focused on (i) determination of recharge patterns and water balance, including snowmelt and rain runoff; groundwater-surface water interactions; partitioning of evaporation and transpiration by plants; estimation of water residence time; (ii) quantification of phosphorus leaching with different hydrological pathways under contrasted hydrological conditions. Results of these analyses will be demonstrated on modelled scenarios linking water and phosphorus fluxes. This multidisciplinary project will fill a gap in knowledge on possibilities of complex application of isotope hydrology, hydrology and hydrochemistry.

The project goal is to develop and apply multidisciplinary paired catchment study to quantify phosphorus fluxes under contrasted hydrological conditions and model scenarios to predict effects of hydrology on the nutrient dynamic in catchments.

Life on the edge: Biogeochemical factors driving transition from lotic to lentic microbial community in headwaters

Project No.: 19-00113S

Principal Investigator: Petr Porcal

Financial support: Czech Science Foundation

Duration: 2019 - 2021

Planktonic microbial communities of lotic and lentic headwater environments substantially differ. Until now, the transformation of bacterial community from lotic to lentic has been poorly studied and the role of stream-originated microbes in the formation of the lentic bacterial assemblies is not clear. Mechanisms of initial assembly of microbial communities in large water bodies are difficult to understand due to long water residence times and large pool of local species. Small lentic water bodies, with short water residence time, located on headwater streams represent promising model ecosystems of combined highly plastic characteristics of lotic vs. lentic microbial communities, depending on hydrological conditions and environmental (terrestrial & aquatic) chemistry. In our project, using such an ecosystem as a study site, we would like to address the general mechanisms driving microbial consortia transformation and reassembly, especially the role of alternation of hydrological conditions together with the changes in the pool of dissolved organic matter in this process.

This study will address the mechanisms responsible for assembly of lotic microbial communities by identification of: I) chemical and bacterial interactions relevant for their metabolic pathways; II) key environmental parameters driving the community shift; III) the role of stream microbial inoculum.

Life at the Edge: The Limits of Occurrence of Insect Larvae

Project No.: 20-00892L

Principal Investigator: Evžen Stuchlík

Financial support: Czech Science Foundation

Duration: 2020 - 2022

Survival of animals under extreme environmental conditions has always been intriguing to ecologists and physiologists. Examples for an extreme environment are brooks in mountainous areas with different degrees of harshness. Despite the harsh conditions, these rivers are densely populated by chironomids (Diptera: Chironomidae) who are even found close to the mouth of glaciers. We hypothesize that i) different pathways of metabolism are differently affected by very low temperature, ii) carbohydrate metabolism may be more flexible than e.g. lipid metabolism, and iii) these differences are based on subspeciation and not a pure metabolic phenomenon. The study sites for this project are high alpine streams with a harshness gradient located in the Alps and the Tatra Mts. We assume that the harshness gradient must be strong enough to limit the occurrence of chironomid larvae and energy stores of an animal are a good proxy for its health. To study thresholds for survival of the high alpine stream chironomids in the past, lake sediments cores from 3 sites in the Bohemian Forest will be used.

The aim of the project is the characterization of the harshness gradients; quantification of energy stores in individuals from different sites; tracing of selected genes from endocrine to metabolic regulation; characterization of genetic homogeneity; paleolimnological evidence of past populations' response to the deglaciation.

An interdisciplinary study on element cycling in mountain catchment-lake systems regenerating from tree dieback

Project No.: 19-16605S

Principal Investigator: Jiří Kopáček

Financial support: Czech Science Foundation

Duration: 2019 - 2021

Bark beetle outbreak killed many mature spruce trees in unmanaged, acidified catchments of the Bohemian Forest lakes (BF, Central Europe), with the most pronounced tree loss (>90% in 2004–2008) in the Plešné catchment. The tree dieback significantly changed element cycling in soils and waters and affected their biogeochemistry. At present, forest has been rapidly regenerating. Our >20-year long environmental research on the BF catchments (forest, soil, water, climate) provides a worldwide unique opportunity for a complex ecosystem study on the effects of natural forest dieback and regeneration of the individual ecosystem parts. We propose an integrated laboratory and field mass budget studies on (1) C and N cycling in soils and their effects on leaching of other elements (P, S, Ca, Mg, K, and Al) and (2) how these changes affect regeneration of forest and soil microbial community, and chemical and biological recovery of waters from acidification. Modelling will enable projection of these changes to other similarly affected mountain areas and different forestry practices.

We will evaluate (1) pools and fluxes of ecologically important elements (N, P, C, S, Ca, Mg, K, Al) in catchment-lake systems regenerating from natural tree dieback, (2) how nutrient availability in soil and deadwood affects tree grows, and (3) how this grow affects soil and water biogeochemistry.

Ecogenomics of genome-streamlined freshwater methylotrophs

Project No.: 19-23469S

Principal Investigator: Michaela Salcher

Financial support: Czech Science Foundation

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.

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

Project No.: 19-05791S

Principal Investigator: Klára Řeháková

Financial support: Czech Science Foundation

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.

Hunting down the Eagle Killer – Investigations into the cyanotoxin causing avian vacuolar myelinopathy

Project No.: 19-21649J

Principal Investigator: Jan Mareš

Financial support: Czech Science Foundation

Duration: 2019 - 2021

Avian vacuolar myelinopathy (AVM) is a fatal neurological disease of birds observed with an increasing frequency, threatening avian populations, including the iconic bald eagle. All evidence points at AVM being caused by a novel toxin produced by epiphytic cyanobacteria entering the food chain with water plants, finally causing the brain lesions in affected birds. We could isolate the toxigenic cyanobacterium in culture, purify the compound that is most likely causing AVM and determine its structure. In the current project we will confirm the identity of the AVM toxin, elucidate its biosynthesis, identify other coproduced cytotoxins, investigate environmental and anthropogenic factors driving the AVM toxin production, and design protocols for molecular detection of its producer. Localization of the toxin will be studied in a zebrafish model. The project will contribute to the understanding of AVM etiology, characterization of a novel cyanotoxin representing a potential threat for freshwater ecosystems or even human health, and development of techniques for its routine monitoring.

The aim of the project is to confirm the cyanotoxin causing avian vacuolar myelinopathy, elucidate its biosynthesis, and identify other coproduced cytotoxins. To find the factors driving the toxin production and design protocols for molecular detection of its producer. To study localization of the toxin in a zebrafish model.

Inside the leaf microbiome: bacterial and fungal endophytes in the context of ecosystem development

Project No.: 17-10493S

Principal Investigator: Dagmara Sirová

Financial support: Czech Science Foundation

Duration: 2017 - 2019

Microorganisms colonizing the interior of plant leaves are recognized to have enormous impact on all aspects of their host`s existence - from health to evolutionary diversification. Their specific function in plant ecology, however, is still largely unexplored. We will test the hypothesis that plant foliar endophytes, consisting of interacting fungi and bacteria, are extending the functional plasticity of their hosts and enhance their ability to adjust to changing environmental conditions during ecosystem development. We will employ in-situ screening of the endosphere in a taxonomically diverse selection of plants, along a gradient of vegetation succession. As our study system, we have chosen the unreclaimed areas of colliery spoil heaps formed by open cast coal mining in western part of Bohemia. We believe that unraveling the complex interactions of foliar endophytes with and within their plant hosts to generate unique biological and ecological entities will lead to our greater understanding of important aspects of biology and ecology, not only in our model plants, but in general.

The project goal is to explore the dynamics within microbial communities colonizing the interior of above-ground plant tissues, their role in plant adaptation to ecosystem changes, and their contribution to extending functional plasticity of plants, especially with regards to nitrogen acquisition.

Role of changes in environemntal chemistry on lake ecosystems at the Younger Dryas onset

Project No.: 17-05935S

Principal Investigator: Günther Kletetschka, Přírodovědecká fakulta, Univerzita Karlova v Praze

Co-principal Investigator: Evžen Stuchlík

Financial support: Czech Science Foundation

Duration: 2017 - 2019

Younger Dryas (YD) is well documented cold period. It began 12900 years ago and lasted 1200 years. The causes of this change are still not sufficiently resolved. According to recent new evidence multiple proxies support a major transient event. Finding of micro-particles containing iridium, microspherules, and nano-diamonds in a carbon rich black YD layer represent the new evidence. A transient episode initiated a sequence of catastrophic events including floods and fires that contributed to emissions of a dust containing toxic compounds. They became a part of global paleo-atmospheric pollution and contaminated paleo-ecology of undisturbed sites on continental scale (including America and Euroasia).

The aims of the project are: Characterize Younger Dryas Boundary proxies in sediments from 4 central European lakes; Characterize Laacher See tephra proxies from 4 central European lakes; Identify effect of catastrophic events on Central European lake ecosystems at the YD onset.

Phosphorus dynamics in unmanaged terrestrial ecosystems: Links with nitrogen and carbon cycling.

Project No.: 5229S

Principal Investigator: Jiří Kopáček

Co-principal Investigator: Jihočeská univerzita v Českých Budějovicích, Př.F.

Financial support: Czech Science Foundation

Duration: 2017 - 2019

Unmanaged central European ecosystems (the Bohemian Forest and Tatra Mountains) have been exhibiting world’s largest recovery from atmospheric acidification. Resulting changes in biogeochemical processes and P, N and C cycles in soils are further affected by rapid changes in climate and vegetation, resulting in undesired losses of these nutrients from terrestrial to aquatic ecosystems. The extent and rate of nutrient losses and water pollution differ between catchments, reflecting soil and bedrock composition and vegetation health. On the basis of our long-term research in these areas, we propose a set of integrated laboratory and field studies on effects of changing precipitation chemistry, climate, and vegetation on (1) soil microbial community at sites differing in P sources and availability, (2) P cycle in soils and its links with C and N cycles, especially effects of P availability on N-saturation of catchments and the role of organic C in P leaching, (3) weathering rate and P liberation from bedrock and soils, and (4) pollution of receiving waters with this key nutrient.

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

Project No.: 9310S

Principal Investigator: Jaroslav Vrba, Přírodovědecká fakulta, Jihočeská Univerzita v Českých Budějovicích

Co-principal Investigator: 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.: 4828S

Principal Investigator: 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.: 9381S

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

Co-principal Investigator: RNDr. Jan Mareš Ph.D., Biology Centre CAS, Institute of Hydrobiology

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.

Changes in fish isotopic signals: linking land use and reservoir food webs

Project No.: 1625S

Principal Investigator: Mojmír Vašek

Financial support: Czech Science Foundation

Duration: 2015 - 2017

Ecological functions of aquatic ecosystems have been negatively altered by various anthropogenic pressures. This project aims to evaluate how land use practices affect the functioning of reservoir food webs. Changes in fish community structure and stable isotope composition of key fish species will be investigated in Czech reservoirs across the gradient of land use. Unique time-series of archived fish scales will be analysed for carbon and nitrogen stable isotope ratios. We expect that isotopic composition of reservoir fish will reflect the intensity of anthropogenic nutrient loading and land use practices in reservoir catchments. The impacts of anthropogenic eutrophication on trophic relationships and energy flows through reservoir food webs will also be evaluated. Results of the project should clarify the consequences of land use for ecological structure and functioning of aquatic systems and can support formulation of sound catchment protection and management plans.

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

Project No.: 0243S

Principal Investigator: 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.

Do long-term zooplankton data in the Slapy reservoir reflect land use and/or climate changes in the past 50 years?

Project No.: 4034S

Principal Investigator: Jaroslav Vrba, Přírodovědecká fakulta, Jihočeská Univerzita v Českých Budějovicích

Co-principal Investigator: Josef Hejzlar

Financial support: Czech Science Foundation

Duration: 2015 - 2017

The project aims on so far unexplored legacy of the Czech reservoir limnology, such as unprocessed zooplankton samples and long-term data sets on stratification, chemistry and plankton of the Slapy reservoir, and will increase the understanding of important environmental drivers that influence freshwater ecosystems. Thorough analyses of the reservoir data sets will improve general understanding of the driving forces in plankton ecology, mainly the impacts of climate variability, hydrologic condition and temperature stratification, reservoir hydrodynamics, and nutrient loading on structure and plankton community succession. The detailed processing of zooplankton samples gathered during 60 years will allow to describe possible changes in species composition, phenology, biomass and size structure of copepods and cladocerans, and to determine the species-specific responses to both human-driven and climate-driven changes within the Vltava River basin since building the reservoir cascade. The project outputs will be relevant for other similar reservoirs in the temperate zone.

Long-term effect of fish reduction on Daphnia in a large reservoir

Project No.: 4309S

Principal Investigator: Jaromír Seďa:

Financial support: Czech Science Foundation

Duration: 2015 - 2017

Socio-economic changes in Europe in 90-ties caused changes in nutrient cycling in managed coutryside. Project goal is to explain the changes in the structure of reservoir trophic cascade nutrients-phytoplankton-zooplankton under long-term trends of decreasing phosphorus loads and in parallel increasing loads of terrestrial dissolved organic carbon.

Phytoplankton responses to environmental forcing

Project No.: 3750S

Principal Investigator: 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.

Factors regulating the phototrophic activity of freshwater community of Betaproteobacteria

Project No.: 2197S

Principal Investigator: Vojtěch Kasalický

Financial support: Czech Science Foundation

Duration: 2015 - 2017

This project investigates the factors influencing photosynthetic activity and autotrophic carbon assimilation of one of the key group of planktonic freshwater Betaproteobacteria, the genus Limnohabitans, in its typical habitat. We hypothesize that the synthesis of the light harvesting photosystem and the RuBisCO enzyme differs within the habitats of diverse trophic status. Taking into account, that the genus Limnohabitans is represented by bacteria of different metabolic types, we hypothesize that the ratio of photosynthetic or CO₂-fixing is related to the photosynthetic radiation and the oxygen concentration in the vertical profile of lakes and reservoirs. Manipulative experimental designs are proposed for testing the photosynthesis and CO₂-fixation contribution to the competitive success of photosynthetic genotypes during the naturally occurring events. Important new insights into distinct bacterial lifestyles are assumed, including the refinement of the existing concepts of bacterial life strategies.

The effect of solar light on key members of freshwater Betaproteobacteria

Project No.: 9721S

Principal Investigator: Petr Porcal

Financial support: Czech Science Foundation

Duration: 2015 - 2017

Planktonic bacteria are key players in biogeochemical processes, e.g. responsible for the transformation of dissolved organic matter (DOM) that represents crucial processes for the entire ecosystems. One of the key components of freshwater bacterioplankton is represented by Betaproteobacteria. Only two of its taxa have been identified as key players – genus Limnohabitans and species Polynucleobacter. Both taxa have been described as abundant parts of bacterioplankton, responding fast to changing environmental conditions. It is now accepted that photoproducts, generated by exposure of DOM to sunlight, are affecting growth of bacteria. In this proposal, we intend to widen our rapidly growing knowledge on two bacterial groups of interest. We will employ our world-wide unique culture collections of the target bacteria together with our specific expertise on DOM characterization by combining irradiation and incubation experiments.

Toxic potential, evolution of toxin synthesis, and factors driving anatoxin-a production in benthic and soil nostocacean cyanobacteria

Project No.: 8067S

Principal Investigator: Eliška Zapomělová

Financial support: Czech Science Foundation

Duration: 2014 - 2016

Disentangling the effects of changing environmental chemistry and climate on biogeochemistry and biodiversity of natural alpine soils and waters

Project No.: 9231S

Principal Investigator: Jiří Kopáček

Financial support: Czech Science Foundation

Duration: 2014 - 2016

The Tatra Mountains have been exhibiting world largest recovery of aquatic and terrestrial alpine ecosystems from atmospheric acidification due to unique declines in S (>60%) and N (40%) deposition since 1989. Resulting changes in biogeochemical processes and biodiversity are, however, confused by parallel effects of increasing temperature. Disentangling these effects is crucial for assessing future development of natural ecosystems under anticipated trends in atmospheric pollution and climate change. On the basis of our long-term research in this area, we propose an integrated study of effects of the chemical and climatic changes in natural alpine ecosystems on (i) weathering rates, soil chemistry, and leaching of nutrients (P, N, and C), base cations, and toxic Al forms to waters, (ii) in-lake processes responsible for P immobilization in waters and sediments, (iii) biological recovery (phytoplankton, zooplankton, and benthos) in lakes, and (vi) soil biodiversity (microbial composition and soil invertebrates) along gradients of soil pH and elevation (vegetation zones, temperature).

Functional diversity of soil microorganisms in spruce swamp forest and its effect on soil DOM

Project No.: 7398S

Principal Investigator: Tomáš Picek, Přírodovědecká fakulta, Jihočeská Univerzita v Českých Budějovicích

Co-principal Investigator: Jakub Borovec

Financial support: Czech Science Foundation

Duration: 2013 - 2016

The efffect of natural dieback of mountain spruce forest on microclimate

Project No.: /12/1218

Principal Investigator: Jiří Kopáček:

Financial support: Czech Science Foundation

Duration: 2012 - 2016

Windthrows and climatic factors have promoted bark beetle (Ips typographus) development and a large-scale dieback of Norway spruce in the unmanaged parts of the Bohemian Forest (central Europe). In 2004–2007, the defoliation killed>90% of forest in the Plešné Lake catchment. Windthrows occurred also in catchments of Čertovo and Laka lakes. All these areas have been subjects of our intensive long-term ecological research (water, climate, soil, and forest) since 1984–2002. Available pre-disturbance data, current research, and new proposed studies provide a worldwide unique opportunity for a complex ecological research on the effects of natural forest dieback on the individual ecosystem parts. We propose (1) mass budget study on changes in element fluxes and pools on a whole-catchment scale (forest, soil, waters); (2) evaluation of effects on microclimate, hydrology, and soil and aquatic chemistry and biodiversity; and (3) projection of the net effects to other mountain areas, for different forestry practices, and along the anticipated trends in climate and atmospheric pollution.

Hydroacoustical distinguishing between fish and bubbles, and quantification of methane bubble ebullition in freshwater reservoirs of temperate zone

Project No.: /12/1186

Principal Investigator: Jaroslava Frouzová

Co-principal Investigator: Petr Stanovský, Institute of Chemical Process Fundamentals of the ASCR, v. v. i.

Financial support: Czech Science Foundation

Duration: 2012-2015

The acoustic parameters of rising methane bubbles will be measured by echosounders at different frequencies at man-made bubbles. The special algorithms using multi-frequency record will be developed to distinguish the bubble echoes from the fish echoes having the same acoustic size. The obtained method will be used to estimate of fish abundance and biomass more accurately. Further, the model describing the bubble rise and dissolution in will be modified for freshwater lakes. The relation between bubble volume and acoustic echoes from experiments with m an-made bubbles will be used to gain more exact data about the amount of the methane bubbles ebullated from the chosen reservoirs in temperate zone. The spatiotemporal changes in their productions will be monitored also. At the end, the research should enlighten the correlation of the quantity and quality of ebullated methane bubbles with the environmental conditions.

Get out! she signalized: sex segregation of freshwater fish

Project No.: /12/P647

Principal Investigator: Marie Prchalová:

Financial support: Czech Science Foundation

Duration: 2012-2014

Sex segregation is widespread in animal kingdom. But it has not been investigated much in freshwater fishes. The guppy is the only aquatic vertebrate for which hypotheses of sex segregation were verified. In this project we will study sex segregation of the five most common fish species of lentic freshwaters of Europe. Using gillnet sampling and segregation coefficient we will be able to say whether fishes are sexually segregated and how (habitat vs. location segregation). Three potential reasons for segregation will be tested (predation pressure, water temperature, food availability). Sex dimorphism will be studied in detail as well. Parameters as life expectancy, growth, condition, length-weight relationship and morphology of branchial sieve will be compared between sexes. Females of the target species can be more active and have better condition, which could bias the representativeness of gillnet sampling. Thus we plan an easy experiment when we will perform gillnet sampling in a rented pond stocked with a completely known fish community in terms of sex ratio and condition.

Cyanobacterial competition mechanisms influencing species composition of the phytoplankton communities

Project No.: 09/0309

Principal Investigator: RNDr. Klára Řeháková, Ph.D.

Co-principal Investigator: RNDr. Ondřej Komárek, PhD., Jihočeská univerzita v Českých Budějovicích

Financial support: Czech Science Foundation

Duration: 2009-2013

The phytoplankton composition in European lakes and reservoirs has been investigated for decades. Dense populations of cyanobacteria often dominate phytoplankton. They can build water blooms in summer and autumn, and produce harmful toxins. Therefore, they present potential hazards to public and animal health worldwide, both via blooming of water reservoirs leading to toxin release in drinking water as well as to hypertrophy with consequent oxygen depletion in the natural environments. For these reasons it is necessary to reveal the details in biology of water blooms. The proposed project is focused on the study of competition among dominating species of water bloom. How the co-existence of the species can influence their ecophysiological and biochemical characteristics? How the changes in these characteristics can increase their successfulness to become dominant species of water bloom? Project will be unique in the interface of results from biochemical and physiological point of view.

Predator avoidance strategies in early life stages of percid fishes

Project No.: 09/P266

Principal Investigator: Martin Čech

Financial support: Czech Science Foundation

Duration: 2009-2011

The project is focused on predator avoidance strategies of early life stages of percid fishes – European perch Perca fluviatilis L., zander Sander lucioperca (L.), ruffe Gymnocephalus cernuus (L.) - in stratified canyon-shaped reservoir, non-stratified shallow reservoir and opencast mine lake. It follows up the recent finding that percid fry are able to create sympatric ecological groups with different behaviour (Čech et al. 2005). This is supposed to be an excellent strategy of the species to avoid predation pressure, which would be of different level in different main habitats and in different water bodies. A special attention will be paid to the newly discovered community of bathypelagic percid fry in stratified canyon-shaped reservoir (Čech et al. 2005, Čech & Kubečka 2006, Čech et al. 2007a, b, Kratochvíl et al. 2008), which most probably changes to bottom-dwelling community in case of non-stratified shallow reservoir and to dense deep water vegetation-dwelling community in opencast mine lake. The effectiveness of individual strategies will be evaluated using various new approaches including scientific sonars (SIMRAD), acoustic (DIDSON) and underwater camera for monitoring of behaviour of both prey and predator and SCUBA divers for quantitative fry sampling in dense vegetation.

Horizontal acoustic surveys and fish behaviour in the open water

Project No.: 07/1392

Principal Investigator: Jan Kubečka

Financial support: Czech Science Foundation

Duration: 2007-2010

Most fish of the open water of large reservoirs of Czech Republic (also applies to many lakes and reservoirs worldwide) inhabit surface layers where they can be studied quantitatively preferably by horizotal acoustic surveys. The aim is to solve main persistent problems of horizontal surveying like undefined behaviour of ultrasonic field, uncertainty of fish size estimates, microdistribution, discrimination between small fish and bubbles, influences of swimming behaviour and diurnal changes of behaviour. The emphasis is on improvement of quality of mobile surveys with large spatial coverage. The problems will be solved by the combination of (i) klassical split-beam echosounder, (ii) newest commercially available high frequency multibeam sonar Didson, which has theoretically a number of advantages (iii) direct fishing and optical approaches. Project should significantly improve horizontal detection of fish, interpretation of records and elucidate a number of patterns of pelagic behavoir of fish which is insufficiently known in fresh waters.

Patterns and reasons of different pelagic behaviour of perch fry: novel insight into the declared ecological plasticity of a species

Project No.: 06/1371

Principal Investigator: Martin Čech

Financial support: Czech Science Foundation

Duration: 2006-2008

The project follows up the recent finding that juvenile perch Perca spp. are able to create sympatric ecological groups with different behaviour. The epipelagic fry (EPF) spent the whole 24 hours in the epilimnion whereas the bathypelagic fry (BPF) performed diel vertical migrations (DVMs), being in the epilimnion during the night and migrating into the cold hypolimnion during the day. The project aims on better definition of newly discovered groups, temporal and spatial patterns of their separation, reasons of sympatric existence of EPF and BPF, profitability and fate of individual strategies, cues of DVMs, predation pressure on pelagic perch fry, gradients in perch fry abundance, age and size
distribution as well as perch egg strands deposition on the longitudinal profile of the reservoir. New approaches including more quantitative and extensive acoustic and net sampling, SCUBA diving, molecular genetics, histology and parasitology will be used. Grouping behaviour of juveniles of close relative, zander, Sander and ruffe, Gymnocephalus will be also investigated and the project is likely to bring new understanding into early behaviour of perciform fish.

Competition relationships among dominant species of phytoplankton in the reservoirs.

Project No.: 06/0462

Principal Investigator: RNDr. Klára Kaštovská, PhD, Hydrobiologický ústav AV ČR

Co-principal Investigator:

Financial support: Czech Science Foundation

Duration: 2006-2008

Suitable light and temperature conditions coupled with high nutrient concentrations in water lead to a mass development of cyanobacterial bloom in our reservoirs. Cyanobacterial blooms cause serious problems and their presences markedly impair water quality, produce broad range of toxins, which pose a relevant health risk in recreational and drinking water reservoirs. Although high attention is paid to this problem recently, the decisive mechanisms affected species compositions of particular bloom remain still unclear. Our knowledge about the competition and competitiveness of cyanobacterial and algal dominants is still unsatisfactory. The proposed project is focused on the study of ecological demands of water bloom dominants and their growth optima, on competition mechanisms among single dominant species of phytoplankton in the reservoirs and particular factors which favor the development of certain species in summer phytoplankton blooms in the laboratory and natural conditions.

Seasonal dynamics of food consumption, growth and production of 0+ fish and their impact on zooplankton in a reservoir with trophic gradient

Project No.: /06/P418

Principal Investigator: Mojmír Vašek

Financial support: Czech Science Foundation

Duration: 2006-2008

Deep-valley reservoirs are unique aquatic ecosystems characterized by a high degree of spatial and temporal variability. This project aimed to analyse how variable environmental conditions within a model reservoir influence seasonal dynamics of age-0 fish abundance, food consumption, growth and production. Dynamics of age-0 fish was studied in the Římov Reservoir during two subsequent years, 2006 and 2007, that differed markedly in hydrological and weather regimes. A few generalist species from two families, Percidae and Cyprinidae, dominated age-0 fish assemblages. At the start of growing season, percids were abundant in pelagic habitat, but later on they shifted to littoral zone. An opposite trend in habitat use was recorded for age-0 cyprinids. Flooded shoreline vegetation enhanced survival of age-0 fish in 2006, while increased spring temperatures in 2007 accelerated ontogenetic development of age-0 fish. Underyearling fish in the Římov Reservoir were largely planktivorous throughout the whole growing season of both years. In the pelagic zone of the reservoir, impact of age-0 fish on zooplankton of the genus Daphnia was quantified using bioenergetics modelling. The estimated consumption rates of age-0 fish assemblages were found too low to be responsible for the midsummer decline of Daphnia population. In summary, extensive data on abundance, distribution, growth, production and food consumption of age-0 fish were collated during this project. The data provided valuable information on the structure and functioning of a reservoir ecosystem and, in practice, they can be beneficial for management of fisheries and water resources.

Grant Agency of the Academy of Sciences of the Czech Republic

Effect of food quantity and quality on the reverse in competitive success between 0+ perch and roach

Project No.: 00960810

Principal Investigator: Jiří Peterka

Financial support: Grant Agency of the Academy of Sciences of the Czech Republic

Duration: 2008-2010

Young-of-the-year perch and roach dominate the 0+ fish communities of meso- to eutrophic temperate water bodies across Europe. General succession from dominance of perch to roach with increasing ecosystem productivity has been documented for lakes of different trophic status and when comparing fish community structure within reservoirs with pronounced longitudinal gradients. Better competitive abilities of juvenile roach for crustaceoplankton have been suggested as responsible for these changes. But recently, the higher efficiency of roach for copepod or cladoceran prey was doubted. This project aims to clarify the effect of intra- and interspecific foraging competition of juvenile roach on perch in manipulative enclosure experiments with larvae and juveniles of both species, and particularly, focuses on the effect of food quantity and quality (prey taxa, prey size, timing of diet shifts etc.) on the changes in competitive success (evaluated as realized growth) between both species.

The Czech Academy of Sciences

Strategy AV21 - Diversity of life and ecosystem health - Activity: Monitoring of cryptic species having indicative value using harmless sampling methods

Project No.: 00/991100

Principal Investigator: Petr Blabolil

Financial support: The Czech Academy of Sciences

Duration: 2015-2016

Monitoring changes of biota composition and abundances is important to evaluate changes in the environment. These environmetal shifts on scales from local catchment management to global changes are especially evident in water ecosystems. One of the most sensitive elements are fish integrating all lower parts of the trophic food-web. However, most of the current research is dedicated to dominant fish species, that can be easily captured using common sampling equipment. Cryptic species, sensitive to environmental changes, are often neglected. The aim of the project is to develop and verify new monitoring scheme using harmless sampling methods (electrofishing, fyke-nets, SCUBA diving) in reservoirs. Model species are burbot (Lota lota) and stone loach (Cobitis elongatoides). Both endangered species and good ecological quality elements.

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