MEM Ongoing projects


Tree and country – influence of trees on diversity of soil microorganisms in agricultural land, Slovak Research and Development Agency project no. APVV-20-0257, years 2021-2025


Fungal hybrid heme peroxidases from primeval forest with application in environmental biotechnologies, Slovak Research and Development Agency project no. APVV-20-0284, years 2021-2025


Hybrid heme peroxidases (EC are newly discovered specific oxidoreductases capable of cleaving reactive peroxide bonds in inorganic as well as organic compounds. Concomitantly to this cleavage they oxidize mainly organic compounds forming radical products that can enter polymerization reactions. Over 260 complete sequences from various regions of whole genome DNA were discovered. After their RNA splicing and translation in corresponding protein sequences they exhibit a high level of conservation. So far they were discovered solely in the kingdom of fungi. According to their typical essential sequence patterns responsible for heme binding they all belong to the large peroxidase-catalase superfamily couting currently over 41000 representatives from prokaryotes and eukaryotes. With their catalytic activity hybrid peroxidases represent efficient extracellular enzymatic antioxidants with broad application in defence against toxic effects of the oxidative stress. Recently, their expression and function was described in phytopathogenic fungi.


The objective of our proposed project is the discovery of complete DNA gene clusters, corresponding mRNA transcripts and translated secreted isozymes of hybrid heme peroxidases among non-pathogenic fungi isolated from unique primeval forest biotopes of Slovakia. Our goal is to obtain a stable level of expression for selected recombinant hybrid peroxidases with highest level of catalytic efficiency typical for this subfamily. We aim to purify sufficient amounts of this unique enzymatic antioxidants to allow the resolution of 3D structure from produced protein crystals. This shall lead to the explanation of their peculiar reactivity on the base of structure-function relationships in the conserved catalytic centre. No such crystal structure for any hybrid peroxidases is known yet so its availability for unique peroxidases from primeval forest biotopes will allow great future applications in green biotechnologies.

Role of the MEM team

The project is coordinated by Marcel Zámocký from Institute of Molecular Biology of the Slovak Academy of Sciences and the research is also performed in collaborations with the team of Stanislav Stuchlík from Comenius University in Bratislava, Faculty of Natural Sciences. MEM team is responsible for collections of fungal material in field, for DNA extractions from environmental and pure culture samples and for identification of fungi.


Aliens among us: Spatio-temporal dynamics of plant invasions and their adverse impact on ecosystems, Slovak Research and Development Agency project no. APVV-19-0134


Plant invasions are an ongoing process threatening biodiversity at the species, habitat and landscape levels. The unique composition of alien flora at a regional level is mainly influenced by climate and cultural factors. The proposed project focuses on the environmental background of plant invasions in Slovakia. Dynamics of plant invasions are studied in riparian vegetation along rivers that play a dominant role in the natural spreading of invasive plants and on semi-natural grasslands which represent the most invaded non-anthropogenic habitats in Slovakia. We will compare non-invaded plots and in plots invaded by F. japonica agg. or S. canadensis agg. An integrative approach will be used to study the impact of plant invasions, combining diversity of plants, bryophytes, fungi – by environmental DNA sequencing, molluscs and soil invertebrates with seed bank and soil properties.

Using time series of vegetation, seed bank, and soil properties, we will reveal spatio-temporal changes in riparian ecosystems which will be further linked with environmental and human factors. Based on field and revised herbarium data, we will reveal the ecological demands of model invasive plant groups (Fallopia japonica agg. and Solidago canadensis agg.) and estimate their potential distribution under current and future climate conditions. We will compare multiple-taxa diversity (plants, bryophytes, fungi – by environmental DNA sequencing, molluscs and soil invertebrates) in non-invaded plots and in plots invaded by F. japonica agg. or S. canadensis agg. Further analyses of soil properties, seed bank, microbial activity, and fungal trophic structure will shed light on changes of belowground ecosystem processes at studied plots.


We want to understand ecological demands of model invasive plants (Fallopia japonica agg. and Solidago canadensis agg.) and to estimate their potential distribution under current and future climate conditions. Temporal changes in riparian ecosystems will be further linked with environmental and human factors. The aim is to recognise the impact of invasive plants on the ecological processes in soil and biological diversity of invaded areas. In addition to general trends, we also study species or group-specific patterns.

Role of the MEM team

Soil, rhizosphere and fine roots of selected invasive plants and native control plants will be samples from invaded, contact and natural plots. The sampling is repeated on ten such triple plots for Solidago gigantea agg. and Solidago canadensis agg. As control plants are selected Dactylis glomerata and Galium verum. Our aim is to compare how much are natural fungal microbial communities altered by the invasion.


Market-demanded research for sustainable and inovative food, funded by Operational Program Integrated Infrastructure within the project: Demand-driven Research for the Sustainable and Innovative Food, Drive4SIFood 313011V336, co-financed by the European Regional Development Fund



Sustainable agricultural production requires a synergy, interdisciplinary and progressive approach to produce healthy, functional and safe food under current climate changes. The project is oriented to research and development of innovative food supporting sustainable health, especially for vulnerable groups of the human population. The tools to implement these requirements are 15 activities using circular approach to achieve the goals. The project is coordinated by Slovak Agricultural University Nitra, has seven more partners including Plant Science and Biodiversity Centre SAS. Our institute deals with Amaranthus seeds as an alternative source of food.


The general goal of the project is to develop knowledge for production of quality, safe and innovative food, to implement it to environment-friendly production and to achieve energy efficient production. The object of the project at our institute is to understand efficient production of Amaranthus seed, and to produce safe food avoiding contamination.

Role of the MEM team

Our objective is to assess fungal endophyte diversity of Amaranthus seeds. These fungi can be food contaminants and potentially toxic for human. We want to understand which environmental factors during the plant production and seed storage influence the fungal endophyte community to avoid potential seed contamination.


Unraveling of functional diversity and ecological role of fungi of the family Clavariaceae, Scientific Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic and Slovak Academy of Sciences project no. VEGA 2/0050/22, years 2022-2025


Clavariaceae are terrestrial fungi (Basidiomacetes, Agaricomycotina) with club or corral shaped fruiting bodies known as indicators of natural value of grasslands. Several studies demonstrated that Clavariaceae are root endophytes and may form an unspecified symbiosis with vascular plants. Diversity, habitat specificity and trophic interaction of the group are not well understood. This project aims to explore Clavariaceae diversity both by Sanger sequencing of targeted DNA regions using samples from fruiting bodies and by metabarcoding using high throughput sequencing of soil and plant root samples. Phylogenetic studies based on multi-loci data from Sanger sequences and morphology will be used to distinguish species diversity of the group. Our aim is to asses overall local Clavariaceae diversity in grasslands and to distinguish Clavariaceae endophyte diversity and plant specifity. We will use data from amplicon sequencing of bulk soil, rhizosphere and plant roots. This project have ambition to test possible in vitro cultivation of Clavariaceae with partner plants that may facilitate further studies of trophic style of these fungi.


Clavariaceae is well known and species rich family of clavaroid fungi but species circumscriptions and phylogeny of the family lack relevant studies using comprehensive molecular data. The most recent metabarcoding studies assign Clavariaceae in the trophic guild CHEGD (the group named by acronym of Clavariaceae, Hygrophoraceae, Entolomataceae, Geoglossaceae and Dermoloma), but it is not proved if they are symbiotic with vascular plants.

The project has three main aims:

· to revise taxonomic, systematic and phylogenetic status of clavaroid members of the family Clavariaceae

· to trace of ecological role, niche preferences and conservation status of Clavariaceae

· to analyse life style and trophic interactions of Clavariaceae

To achieve these aims we will use following major approaches: a) Sanger sequencing of fruiting bodies and molecular phylogenetic analyses, b) Illumina high throughput sequencing of environmental samples and c) in vitro cultivations of Clavariaceae strains with partner plants.

The project is performed only by MEM members; the principal investigator is Miroslav Caboň.