Selected publications:
Šafařík I., Angelova R., Baldíková E., Pospíšková K., Šafaříková M. (2017) Leptothrix sp. sheaths modified with iron oxide particles: Magnetically responsive, high aspect ratio functional material Materials Science & Engineering C-Materials for Biological Applications 71: 1342-1346.
Raschmanová N., Žurovcová M., Kováč Ĺ., Paučulová L., Šustr V., Jarošová A., Chundelová D. (2017) The cold-adapted population of Folsomia manolachei (Hexapoda, Collembola) from a glaciated karst doline of Central Europe: evidence for a cryptic species? Journal of Zoological Systematics and Evolutionary Research 55: 19-28.
DOI: 10.1111/jzs.12150
Wozniak E., Špírková M., Šlouf M., Garamus V., Šafaříková M., Šafařík I., Štěpánek M. (2017) Stabilization of aqueous dispersions of poly(methacrylic acid)-coated iron oxide nanoparticles by double hydrophilic block polyelectrolyte poly(ethylene oxide)-block-poly(N-methyl-2-vinylpyridinium iodide) Colloids and Surfaces A: Physicochemical and Engineering Aspects 514: 32-37.
DOI: 10.1016/j.colsurfa.2016.11.044

Current research projects

Behaviour of pharmaceuticals in water-soil-plant system

Abstract: The presence of human and veterinary pharmaceuticals in the environment has been recognized as a potential threat. Pharmaceuticals may contaminate soils and consequently a food. The main objective of the project is better understanding of selected pharmaceuticals behaviour in various soils and a bioaccumulation in plants. The project should attain several aims: a) Evaluation of competitive/cooperative sorption of selected pharmaceuticals in different soils; b) Evaluation of degradation rates of selected pharmaceuticals, production rates and stability of their metabolites /transformation products in different soils; c) Evaluation of pharmaceuticals impact on soil microbial biomass, activity and structure and vice versa influence of microbial conditions on pharmaceuticals dissipation from soils; d) Evaluation of selected pharmaceuticals root uptake by various plants from diverse soils; e) Evaluation of the root uptake coupled with a transient water and contaminant transport in soils; f) Numerical modelling of observed water and pharmaceuticals transports and their root uptake.

Aims of the project: Goals are: 1) link behaviour of pharmaceuticals to soil physical, chemical and microbial conditions; 2) link microbial community behaviour to type and degree of soil contamination; 3) link bioaccumulation of pharmaceuticals (metabolites) in plants to soil conditions; 4) root-uptake modelling.

Funding: GA ČR (2017-2019), No. 17-08937S

Principal investigator: prof. Ing. Radka Kodešová, CSc., Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Praha


doc. Roman Grabic, PhD., University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, Vodňany
RNDr. Alica Chroňáková, PhD., Biology Centre CAS, Institute of Soil Biology, České Budějovice

Project team (ISB):

RNDr. Alica Chroňáková, PhD., 

MSc. Zuzana Frková, PhD.,

Tomáš Chrudimský, PhD.,

RNDr. Anna Koubová, PhD.,

Ing. Martina Petrlíková

We are seeking for motivated students to attend our team!

Linking functional traits of three organism levels as driving mechanisms of ecosystem functions in the Arctic

There is an increasing evidence that functional traits of biota may serve as important indicators of ecosystem services. Although it is known that different organism levels interact in providing ecosystem services, there are so far only few studies linking functional traits of several trophic levels together. Here we propose to interconnect functional traits of three organism levels – plants, soil fauna and soil microorganisms – to ecosystem functions underlying ecosystem services in the Arctic terrestrial ecosystem, representing a less complex, model system. Several ecosystem functions will be approached (C sequestration potential and soil stability, fertility and water retention) in a set of manipulative experiments. We expect that joining relevant functional traits across organism levels into “multitrophic” trait clusters will allow us to identify key traits underlying the ecosystem functions.

Funding: GA ČR (2017-2019), No. 17-20839S

Principal investigator: Petr Macek, University of South Bohemia in České Budějovice, Faculty of Science

Co-investigator: Miloslav Devetter, Biology Centre CAS, Institute of Soil Biology, České Budějovice

Unique biosynthetic enzymes as the key to novel bioactive compounds

Effective search for producers of novel, pharmaceutically attractive natural compounds requires application of new screening techniques using genomic data. Growing information on the genetics of biosynthesis of natural compounds and their structural components, brings the possibility to use newly characterized enzymatic systems as markers in genetic screening of potential producers of structurally and functionally unique active metabolites, which may find it application as novel antibiotics, immunomodulators and cancerostatics.  Two model enzymes of actinomycetes, the cyclizing aminolevulinate synthase and a novel type II polyketides synthase specific for short linear polyketide chains, will be employed in the project.

Aims of the project: 1) By means of genetic screening targeting two novel biosynthetic genes to search for potential producers of novel active compounds. 2) To analyse the biosynthetic gene clusters, which contain the target genes and identify the encoded compounds. 3) To assay biological activities of new metabolites.

Funding: Ministry of Healthcare of the Czech Republic (2017-2020), No. 17-30091A

Principal investigator: Mgr. Kateřina Petříčková, PhD., University of South Bohemia in České Budějovice, Faculty of Science, České Budějovice


  • RNDr. Alica Chroňáková, PhD., Biology Centre CAS, Institute of Soil Biology, České Budějovice

Project team (ISB):

RNDr. Alica Chroňáková, PhD., 

RNDr. Tomáš Chrudimský, PhD.,

Ing. Václav Krištůfek, CSc.,

Ing. Martina Petrlíková

We are seeking for motivated students to attend our team!

Fresh and stable carbon decomposition and sequestration in temperate coniferous forest soils

Soil organic carbon (SOC) is the largest carbon (C) pool in temperate coniferous forests. However, soil C pool is susceptible to changes in fresh C input, which can influence soil organic matter (SOM) decomposition and SOC sequestration. Nevertheless, our knowledge on the processes following fresh C input in temperate coniferous forest soils is largely limited mainly in the prospect of future climate change. This project aims to determine the rate of fresh and stable SOM decomposition and SOC sequestration, potential increase in fresh and stable SOM decomposition and SOC sequestration with increased labile C input, and the roles of soil microbial community in fresh and stable C flux through coniferous forest soils.

Poskytovatel: AVČR

Řešitel: Veronika Jílková

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

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.

Funding: GA ČR

Team member: Veronika Jílková

Organic matter decomposition and carbon sequestration on a natural gradient of labile carbon sources in coniferous temperate forest soils

This project will deal with the effect of labile carbon (C) from various sources (litter, rhizodeposition, honeydew) on soil organic matter (SOM) decomposition and C sequestration in temperate coniferous forest soils, which are of global importance in terms of organic C storage. The proposed project will mainly deal with: (i) the rate of SOM decomposition and C sequestration on a natural gradient of labile C sources; (ii) potential increase in SOM decomposition and C sequestration with increased labile C input; (iii) effect of microbial and faunal community on labile C flux; and (iv) the role of respective labile C sources in C fluxes through soil. Field samplings and observations will be combined with field and laboratory manipulation experiments, both followed by laboratory analyses.

Funding: GAČR

Principal investigator: Veronika Jílková

Tetracycline resistome in soil: Insight into networking of bacterial invaders, residents and environment

This project respects the need for better understanding the impact of environmental factors on movement of genes responsible for antibiotic resistance (ARG) between faecal (manure) and soil resident bacteria. A model situation, when soil is amended by cattle manure originated from dairy cows under prophylactic treatment of tetracycline (T) will be studied. Detailed processes of introduction, survival and establishment of manure tetracycline resistant bacteria (TRB), genes (TRG) and responsible mobile elements (TRME) in soil will be studied on the model of HOT-SPOT experiments. The project will bring complex information allowing an insight into networking between manure and soil T resistome. The project will show importance of three different factors on TR dissemination in soil impacted by manure: (i) survival of invading TRB, (ii) abiotic impact of manure on soil TR residents and (iii) horizontal transfer of TRG.


Principal investigator: Dana Elhottová

Funding: Czech Science Foundation 2017-2019

Telomeres and genome stability in lower plants.

Telomeres are nucleoprotein complexes forming chromosome ends. Besides their role in solving the end-replication problem, they protect chrom. ends from recognition as DNA damage sites. Surprisingly, DNA damage signaling and repair factors reside at telomeres. Not only they do not threaten tel. functions, but are actively recruited to telomeres and their absence results in tel. malfunction. Enigma of mutually beneficial coexistence of telomeres and repair factors was found in yeasts, mammals and flowering plants with model-specific differences. We will analyse the problem in algae and moss. While algae are attractive by evolutionary diverse tel. composition and maintenance, moss Physcomitrella is unique by high efficiency of homol. recombination, availability or easy preparation of knock-out mutants and high proportion of apical dividing (presumably telomerase-positive) cells in early protonema development. Elucidation of the interplay between telomeres and DNA repair in simple eukaryotic systems provides a chance to discover principles valid (but hidden) in models explored so far.
The aim is to describe structure, functions and evolution of telomeres in lower plants (selected algae taxons and moss Physcomitrella patens) and to elucidate connection between telomere function and DNA repair processes. ISB is involved in the investigation of the evolutionary divergence of telomere structures and maintenance mechanisms in algae. Specific objectives include: (1) Characterization of telomere structure and telomere maitenance mechanism(s) in chlamydomonadalean Caudivolvoxa clade,and (2) Dynamics of DNA repair in green algae .

Main coordinator of the whole project: Prof. RNDr. Jiří Fajkus, CSc. (Masarykova univerzita Brno)

Financování (roky): 2013 - 2015
Poskytovatel (financování): GA ČR

Soil fungi contributing to nitrous oxide (N2O) emissions from upland pasture soil and their in situ detection

The proposed project is focused on the problems of production of greenhouse gas - nitrous oxide (N2O). N2O emitted by soil microorganisms contributes to the climate changes as very potent greenhouse gas. N2O production has been found not only in bacteria, but also in fungi. The main part of the project is aimed on the key enzyme of fungal denitrifying pathway (unique cytochrome P450nor), which catalyses conversion of NO to N2O. The project is focused on the evaluation of N2O-forming potential of fungi isolated from pasture soil impacted by overwintering cattle. It is suggested, that the ratio of fungal N2O producers will increase along the impact intensity, as a form of adaptation to nitrogen inputs. The substantial aims of the project will be subsequent testing of in situ detection of fungal producers using PCR method focused on P450nor gene, screening of speci c phospholipids of anaerobicaly growing fungi (NEL-PLFA) in soil, and evaluation of fungal contribution to the total N2O emissions under laboratory conditions in the microcosm experiment.

Garant: Jirout Jiří

Improved and justified methodology for greenhouse gas emission measurements under conditions of low-tech agriculture

The present project is designed to improve research on soil nitrogen and carbon cycling, aiming in general to develop, test, and justify robust and simplified analytical protocols for determination of greenhouse gas emissions, namely nitrous oxide emissions, and if applicable, methane and carbon dioxide emissions, under conditions of low-tech agricultural management. The overall aim of the project is thus seen in a better understanding of soil microbial processes producing important greenhouse gases; an improved knowledge on regulatory mechanisms of these processes will be used in a better control of emissions from agricultural soils. In the proposed project, existing field experiments (established by CRP participants), will be used for field measurements and sampling. The experimental plots will be carefully selected to obtain a set of soil and environmental conditions and covering major types of fertilizer and management. Fluxes of gases of interest will be determined using the static chambers of different size and construction. Gas samples will be sampled in the experimental fields and sent to the applicant’s laboratory. Here they will be analyzed for N2O (and CH4 and CO2 if applicable) content on gas chromatographs equipped with the TCD, ECD and FID. Specific objectives of the project include: (i) Development of sampling and analytical protocol(s) for nitrous oxide (and methane and carbon dioxide) flux determinations; simple and robust enough to be performed in low-tech and low-input agro-ecosystems. (ii) Testing the protocols using gas samples from well-defined conditions; further improvement and justification of the protocols if necessary. (iii) Analyses of 650 gas samples sent to the laboratory (sampled in field conditions). (iv) Data and results evaluation, preparation of final report.

Poskytovatel (financování): IAEA Vienna

Spots of methane production and consumption in terrestrial ecosystem: key for understanding methane turnover

Methane is one of the most important trace as well as greenhouse gases. The most of atmospheric methane has been produced by anaerobic Archaea. Global methane sources are dominated by fluxes from natural wetlands and sediments, agroecosystems, and animal digestive tracts. Soil is a significant methane sink. The proposed project is designed to study methane production and consumption in terrestrial ecosystem, with special attention to cattle grazed grassland soil as a potential source and sink of methane and to soil invertebrates as
potential direct and indirect methane producers. In particular the project will focus on processes of establishment, stability and resilience of microbial communities responsible for methane production and consumption, and on interactions between soil invertebrates and methanogenic microorganisms. The project will result in a better understanding of carbon ransformations in grasslands and seminatural ecosystems; the results obtained will improve mitigation strategies for methane emissions from grazed pastures.

Microbiological monitoring of Natura 2000 Biotop - Inaccessible cave formations

Slovak caves for the uniqueness belongs to the UNESCO World Natural Heritage. Cave organisms in Slovakia are still insufficiently explored. Thanks to the increased and systematic bio-speleology research in the last decade, the situation begins to change. Currently (2010-2012) an intensive microbiological monitoring is carried out in selected inaccessible karst caves: Ardovská jaskyňa, Drienovská jaskyňa, Stará brzotínská jaskyňa, Bobačka, Jaskyňa mŕtvych netopierov, Demänovská jaskyňa mieru, Suchá jaskyňa, Harmanecká jaskyňa, Perlová jaskyňa a Modrovská jaskyňa. The aim is to contribute to a comprehensive image of the state of Biotop 8310 (Inaccessible cave formations, Natura 2000) and lay the foundation for monitoring the trend of this biotop in Slovakia including the design of monitoring methodology. Monitored habitats illustrated a scale of a natural variability of selected caves; the main studied habitats are speleoaerosol, wide range of cave sediments, parietal and soil above the caves. The methodology includes a set of isolation, cultivation and identification procedures describing the quantity and species composition of cultivable heterotrophic forms of bacteria, microscopic fungi, algae and cyanobacteria, as well as quantitative and qualitative analysis of complex microbial communities in natural conditions, including the domain Archaea. The results constitute a unique set of data on microbial species diversity of all major taxa, size and richness of communities colonizing cave habitats, the occurrence of typical, rare or bio-hazardous species. The obtained results not only enrich the knowledge of the biology and ecology of cave organisms, but also provide valuable information about possible health risks for visitors to the caves, and vice versa on the possible introduction of microorganisms from the surface environment. Microbiological monitoring in form of research task is handled by contract between BC AS CR (ISB) and Administration of Slovak Caves SR.

Characterization and risk assessment of the antibiotic resistance-reservoirs in soil

The massive application of antibiotics (ATB) over 50 years for therapeutic and sub-therapeutic purpose resulted in the widespread occurrence of ATB-resistant bacteria. Prevention of the ATB-resistance dissemination through the environmental food chains is a current issue that needs intensive ecological investigation. The proposed project has an ambition to improve the understanding of the secondary and primary ATB-resistance pattern in soils. The project is predicated on the need to bring more information about the natural soil microflora in role of ATB resistence dissemination. The primary and secondary resistance to the tetracycline (TET), the product of soil bacteria and the ATB with very long and massive application history will be investigated in two independent ecosystem models: (1) in agricultural soils under long-term cyclic fertilization by manure containing TET residues and (2) in the undisturbed pristine soil beyond civilization reach. More information about TET-resistance ecology associated with the natural and human-affected soil and identification the soil microflora potential as the invasive elements responsible for the ATB-resistance dissemination in environment should be acquired.

Spontaneous succession in damaged sites

Primary succession at post mining sites is strongly affected by changes in soil microstructure which is driven by interactions between soil environment, plant community and soil biota, both soil fauna and microorganisms. Presented papers demonstrated the importance of interactions between individual trophic levels for the ecosystem development.

Garant: Frouz Jan

The effect of natural dieback of mountain spruce forest on microclomate. chemistry, and biodiversity of terrestrial and aquatic ecosystems - Part Effect on soil fauna

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 Plesne Lake catchment. Windthrows occurred also in catchments of Certovo 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 e ffects of natural forest dieback on the individual ecosystem parts. We propose (1) mass budget study on changes in element uxes and pools on a whole-catchment scale (forest, soil, waters); (2) evaluation of e ffects on microclimate, hydrology, and soil and aquatic chemistry and biodiversity; and (3) projection of the net eff ects to other mountain areas, for di erent forestry practices, and along the anticipated trends in climate and atmospheric pollution.

Main coordinator of the whole project: J. Kopáček (Biology Centre AS CR)

Poskytovatel (financování): Czech Science Foundation (GA ČR)


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

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