Department of Biodiversity and Ecology

The main research focus of the department is the study of biodiversity at different levels and the interactions of its components with the environment. We aim at a wide range of organisms and their assemblages, from plant communities, algae, cyanobacteria and fungi to invertebrates and fish. We study both native and non-native or invasive species in terrestrial and aquatic ecosystems. Geographically, our research is primarily situated in the Carpathian and Pannonian region, but is not exclusively limited to this area; we also work on several more global topics.

Currently, we are studying the structure, evolution and history of communities and populations, we deal with classification, autecological characteristics, systematics and phylogeny. From an evolutionary point of view, we examine trends in population development, environmental adaptations or functional diversity.

The main goal of our research is to better understand the composition, evolution and changes of biodiversity in space and time and to contribute to its conservation.

Our current research groups and their activities

  • Vegetation ecology
    • Study of natural and semi-natural grasslands mainly in the Palaearctic biogeographic realm with the following main aims: i) to evaluate impacts of environmental factors, land use and grassland management regimes on grassland species composition and diversity; ii) to contribute to the development of the international database of multi-scale plant diversity in Palaearctic grasslands; iii) to study ecology and population biology of rare and endangered grassland species; iv) to promote the development of comprehensive and efficient tools for conservation of grassland biodiversity and ecosystem services.
    • Study of vegetation-environment relationships in temperate forests, specifically in various types of mesic forests but also in floodplain and swamp forests within the main biogeographic regions of Central and Southern Europe. The main research topics includes: i) impacts of environmental factors, land use and forest management on plant species composition and species richness of forest understorey; ii) diversity patterns of forests in various biogeographic regions; and iii) mechanisms and processes of plant invasions in forest ecosystems.
    • Study of spatio-temporal changes that translate to changes in diversity and distribution of populations and communities across all organizational levels in the alpine and arctic zones. We focus on the variability of plant communities; land use and management; impact of climate change in this fragile and harsh environment together with other natural and/or human-based disturbances.
    • Study of vegetation changes in various habitats, currently focused mainly on halophytic plant communities, which are on the edge of extinction in Slovakia due to the altered water regime and abandonment. Study of the possibilities of habitat restoration on permanent plots. The use of controlled field experiments to determine the regeneration potential of habitats and the impact of various management methods.
    • Vegetation survey and classification in Europe and beyond with the following main aims: i) to describe the variability of vegetation in various plant communities and habitats; ii) to elucidate the role of habitat conditions and environmental factors on this variability; iii) to delimit vegetation units based on formalized phytosociological methods; iv) to produce vegetation overviews for scientific and nature conservation purposes. Since 1995, we have built the Central Database of Phytosociological Relevés of Slovakia (CDF,, which ranks among the leading ones in Europe and worldwide thanks to its quality and size.
  • Synanthropisation of ecosystems is a long-term global process of interaction between human and other ecosystem parts. Its extent and rate are increasing in direct proportion to the acceleration of human civilization evolution. Its impacts, mainly on biota, are usually negative: fragmentation of ecosystems and habitats is underway, native species retreat or extinct, the effect of natural geographical barriers decreases, many alien organisms become invasive. All these processes result in the homogenisation of biological communities and a dramatic decrease in their resistance and resilience. The loss of autoregulation abilities can result in the destruction or extinction of native, but also man-made ecosystems.
    We focus on:
    - Research of space and time dynamics of synanthropic communities;
    - Investigation of penetration of alien organisms into the native biocenoses;
    - Investigation of linear anthropogenous corridors (e.g. rivers, railways, roads) with regard to distribution of non-native or native rare or halophilous species;
    - Study of alien species and community ecology;
    - Research of species diversity/variability of synanthropic communities and their classification;
    - Study of consequences of fragmentation and homogenisation on native biota, especially its biodiversity on species and genetic level;
    - Utilization of multispectral Earth observation data for study of distribution, direction and rate of spreading of alien organisms and their communities (but also decline of native - Natura 2000 biotopes);
    - Preparation and actualization of comprehensive overall works (Synanthropic vegetation of Slovakia, Inventory of the alien flora of Slovakia) and databases related to them (;
    - Implementation of the principles of the Citizen Science for the data collection on the distribution of the alien organisms and utilisation of the Citizen Science to increase public awareness on the topic of biological invasions (smartphone app VISITOR,
  • Remote sensing represents an efficient tool for collecting data and monitoring landscape variability and vegetation dynamics without making physical contact with the object. Remote sensing scientists and nature monitoring experts must consider mutual cooperation to determine and evaluate the validation of method development while considering a large number of various factors. We concentrated on the development and implementation of novel mathematical methods, computational algorithms and software solutions for satellite data nonlinear diffusion filtering, automated satellite image segmentation and dynamic tracking of objects and regions of interest in satellite images. We focus on the exact localization and classification of NATURA 2000 habitats and dynamic monitoring of qualitative changes by dedicated image segmentation software. The localization, classification and dynamic space-time segmentation and tracking are based on processing and analysis of Sentinel-1 synthetic aperture radar data (SAR), Sentinel-2 multispectral imaging data and its combination; and by using aerial photographs.
  • Biodiversity and ecology of aquatic ecosystems
    • Study of the diversity of the aquatic ecosystems includes: i) description of new taxa, phylogenetic relationships, systematics of selected taxa; ii) biodiversity state research (research on the feasibility and application of innovative methods – DNA barcoding, metabarcoding, environmental DNA); iii) building a national database of DNA barcodes of aquatic biota of Slovakia; iv) analysing relationships between taxonomic and functional diversity of aquatic organisms and the environment, including human impacts; v) identification of indicator groups of aquatic organisms with potential to represent the overall biodiversity of habitats, vi) study of aquatic alien organisms and their effect on native biota of lotic and lentic ecosystems.
    • Research on the ecology of aquatic organisms and their communities is primarily focused on the study of spatio-temporal changes in aquatic biota and environmental conditions.
    • We study the genetic structure of populations mainly in animal species inhabiting specific aquatic habitats (e.g. alpine lakes, karst springs). We study genetic diversity, evolution and changes of populations (dispersal sources, isolation, barriers) in habitats that are highly sensitive to environmental changes and can serve as early warning (sentinel) systems.
    • In this area, our research activities are focused on habitat requirements and migrations of rheophilic fish species in large rivers, analysis of migration barriers and preparation of measures intended to improve them, we are also testing innovative molecular techniques and their effective application in monitoring the ecological state of ecosystems.
  • Laboratory of Molecular ecology and mycology (MEM) deals with functional diversity and interaction of fungi with other components of the environment. Fundamental requirement to understand processes in biological ecosystems is the knowledge of species evolution, phylogeny and adaptations. The laboratory has a tradition in taxonomic and phylogenetic research of fungi. Bioclimatic data are used to link fungal phylogeny with spatial distribution and ecological requirements of pathogenic and mycorrhizal fungal species. Taxonomic knowledge is implemented in metabarcoding studies of fungal communities using environmental DNA. Functional traits of individual fungal species are used to study responses of fungal communities to various ecological factors. The laboratory combines methods of advanced light microscopy, DNA extractions from single organism tissues and environmental DNA, phylogenetic analyses, metabarcoding bioinformatics, cultivations of pure fungal cultures and tracing of microbial enzymatic activities.

Laboratory of Molecular Ecology and Mycology (MEM)

Pedological laboratory

  • sušička laboratórneho skla KBC G – 100/250
    sušička rastlinného materiálu HS 402
    predvážky MP – 30
    predvážky Chirana P3/300
    analytické váhy Radwag AS 310/C/2
    trepačka Chirana
    Eutech PC 650 pH meter, konduktometer
    susička PREMED KBC G - 100/250