Ph.D.

Plant Science and Biodiversity Centre is an external educational institution for doctoral studies (Ph.D.) and, based on framework agreements with universities, participates in the implementation of the following doctoral study programmes:

• Faculty of Natural Sciences, Comenius University in Bratislava: Botany, Plant Physiology, Genetics, Biotechnology, General Ecology and Ecology of Individuals and Populations
• Slovak University of Agriculture in Nitra: Agrobiotechnologies, Molecular Biology

The study programmes are also offered in English, and we accept international students.

Doctoral studies are also carried out in the form of “cotutelle”, currently in contractual cooperation with Charles University in Prague.

Proposed Topics for Doctoral Studies in the Field of Ecological and Environmental Sciences with the start of studies in the academic year 2026/2027

• The hidden partners of Solenopsora: A Holobiont Perspective

  Supervisor: Mgr. Anna Bérešová, PhD.

  Co-supervisor: Mgr. Zuzana Fačkovcová, PhD.

  Institution: Institute of Botany, CBRB SAS, Bratislava

  Study programme: Ecology and Environmental Protection

  Topic for: Faculty of Natural Sciences, CU

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: yes

  Keywords: symbioses, symbioses, ecological guilds, metabarcoding

  
  

  Abstract (including objectives):

  The traditional view of the lichen thallus as a consortium of a fungus and a photosynthesizing alga or cyanobacterium has changed substantially in recent years. It is now known that the holobiont system of lichen symbiosis is complex. In addition to stable, dominant lichen partners – the mycobiont and photobiont – it includes other associated components. In particular, additional fungi associated with lichen thalli have been shown to be diverse and are represented by both symptomatic and asymptomatic taxa, all of which constitute the lichen mycobiome. European Mediterranean and other regions with a Mediterranean climate are among the most important biodiversity centres in the world. The distribution of Solenopsora A. Massal. (Catillariaceae) species has been intensively studied within their species ranges since 2010, providing a clear overview enabling evaluation of their biogeography and its relationship to the Mediterranean climate type. We identified mycobionts of European taxa, which interestingly indicate polyphyly and unresolved infrageneric taxonomy. Another open question concerns the photosynthesizing partners: the revealed photobiont lineages are so far undescribed, and it remains unclear whether their patterns correlate with ecological guilds. Finally, it is necessary to focus on the overall diversity of bionts of selected species from both macro- and microecological perspectives. The aim of the thesis is therefore to investigate the evolutionary and ecological diversity of Solenopsora holobionts by resolving taxonomic issues related to the polyphyletic nature of their mycobionts, determining whether photobiont lineages correspond to ecological guilds, and characterizing the full spectrum of associated bionts across micro- and macroecological gradients.

  
  

  Proposed methods:

  • Most material has already been collected for previous studies; additional fieldwork may be conducted if necessary
  • Genetic data: Sanger sequencing – DNA isolation (already completed for most samples), PCR amplification of selected regions, purification of products, sequence analysis
  • Metagenomic profiling / metabarcoding – isolation of environmental DNA from lichen thalli (holobiont) ensuring high quality and sufficient concentration (already completed for part of the samples), amplification of target regions (ITS1 and ITS2), library preparation, Illumina MiSeq sequencing by a commercial provider, and processing of amplicon sequences using an appropriate bioinformatic pipeline (e.g. SEED2)

  
  

  International cooperation: Erasmus stay, Lab of Lucia Muggia – Department of Life Sciences, University of Trieste

  Expected publication outputs (WoS journals): High-quality WoS papers (preferably Q1): 3

  Expected funding: VEGA 2/0046/25; APVV 24-0473; DoktoGrant

Proposed doctoral dissertation topics in the field of Biology with the start of studies in the academic year 2026/2027

• Species diversity, phylogeography and biogeographical barriers of ectomycorrhizal fungi of the genus Russula, subgenus Heterophyllidia

  Supervisor: Mgr. Miroslav Caboň, PhD.

  Specialist supervisor: Mgr. Slavomír Adamčík, PhD.

  Institution: Institute of Botany, CBRB SAS

  Study programme: Botany

  Topic for: Faculty of Natural Sciences, CU, Department of Botany

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: yes

  
  

  Abstract (including objectives):

  The genus Russula is among the most species-rich and ecologically most important groups of ectomycorrhizal fungi, occurring from boreal to tropical habitats. The subgenus Heterophyllidia comprises several morphologically similar phylogenetic lineages with a complex evolutionary history and insufficiently explored geographic distribution. Despite their wide distribution and ecological importance, species diversity, phylogeography, and the role of biogeographical barriers in this group remain poorly understood.
  
  The aim of the doctoral thesis is to comprehensively investigate the species diversity of representatives of the subgenus Heterophyllidia, with a focus on European and North American taxa. The study will help identify the main historical and contemporary biogeographical barriers that have shaped their evolutionary and spatial structure. The research will be based on the integration of molecular phylogenetic analyses, phylogeographic approaches, ecological data, and spatial analyses of species distributions. Particular attention will be paid to the role of geographical barriers, such as mountain systems, climatic transitions, and historical refugia, in shaping the diversity of this subgenus.
  
  The results will contribute to a better understanding of evolutionary processes, the refinement of species concepts within the genus Russula, and the general understanding of biogeographical patterns of ectomycorrhizal fungi. The study will also provide important background data for biodiversity conservation of forest ecosystems and for future macroecological and global evolutionary studies of the genus Russula.

  
  

  Proposed methodological approaches:

  • Combination of routinely used methods for phylogenetic studies (PCR amplification, Sanger sequencing, multilocus analyses)
  • Modern high-throughput sequencing approaches (whole-genome sequencing and data analysis)
  • Light microscopy and preparation of micromorphological profiles of species identified in molecular analyses

  
  

  International cooperation: Acquisition of additional herbarium material from international collaborators

  Expected publication outputs in WoS journals:

  • Phylogenetic and morphological delimitation of representatives of Russula subgenus Heterophyllidia, including reconstruction of ancestral characters – 2 papers (e.g. MycoKeys, Mycological Progress, IMA Fungus)
  • Identification of historical barriers and evolutionary history of representatives of Russula subgenus Heterophyllidia (e.g. Molecular Phylogenetics and Evolution, Fungal Ecology)

  Expected funding: APVV-24-0473 (2025–2029); VEGA 2/0048/26

  Keywords (3–5): evolution, cryptic speciation, mycology, Basidiomycota

• Biodiversity change in a transforming landscape: long-term development of aquatic invertebrate diversity based on historical and contemporary data

  Supervisor: Tomáš Čejka

  Specialist supervisor: —

  Institution: Institute of Botany, CBRB SAS, v. v. i.

  Study programme: Zoology

  Topic for: Faculty of Natural Sciences, CU, Department of Zoology

  Topic unavailable for external study (internal study only): no

  Topic available for international students: no

  
  

  Abstract (including objectives):

  The proposed doctoral dissertation focuses on the analysis of spatio-temporal changes in aquatic invertebrate communities in the context of dynamic landscape transformation and increasing anthropogenic pressure. A key pillar of the research is the comparison of extensive historical datasets with the current state of biota, which allows the identification of long-term biodiversity trends that often remain undetected by short-term monitoring. The study integrates both taxonomic and functional approaches, with an emphasis on the ecological traits and roles of organisms within ecosystems.
  
  Using advanced statistical methods, the research examines key environmental and ecological factors driving transformations in freshwater communities. The results will provide a comprehensive view of the stability and integrity of aquatic ecosystems and establish a scientific basis for predicting their future development.

  Aims of the study:

  • To evaluate long-term changes in the diversity of selected groups of aquatic invertebrates based on historical and contemporary data.
  • To identify key environmental and anthropogenic factors (e.g. land-use change, climate change, pollution) influencing the taxonomic and functional composition of communities.
  • To assess the consequences of taxonomic and functional changes for ecosystem processes and the ecological status of aquatic habitats.
  • To formulate practical recommendations for biodiversity monitoring and conservation in the context of adaptive landscape management.

  
  

  Proposed methodological approaches:

  • Compilation and critical analysis of historical data, including harmonisation of historical nomenclature with current taxonomic systems.
  • Field research and collection of macrozoobenthos samples using standardised methods (e.g. multi-habitat sampling).
  • Laboratory processing, taxonomic identification and functional classification of taxa (biological traits) using European databases.
  • Analysis of environmental variables and landscape changes using GIS tools and measurements of physicochemical water parameters.
  • Statistical analyses including trend models (GLMM/GAMM), multivariate analyses (PCoA, NMDS, PERMANOVA), trait–environment analyses (RLQ, fourth-corner), and visualisation of results.

  
  

  International cooperation: no

  Expected publication outputs in WoS journals: Diversity and Distributions, Oecologia, Journal of Animal Ecology, Basic and Applied Ecology, Contributions to Zoology, Zoological Studies

  Expected funding: VEGA, project No. 2/0087/25

  Keywords (3–5): aquatic invertebrates, biodiversity, functional diversity, long-term changes, landscape change, anthropogenic factors

• Transgenerational effects of chronic ionising radiation on aquatic plants

  Supervisor: Maksym Danchenko

  Specialist supervisor: —

  Institution: Institute of Plant Genetics and Biotechnology, CBRB SAS, Nitra

  Study programme: Plant Physiology

  Topic for: Faculty of Natural Sciences, CU, Department of Plant Physiology

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: yes

  
  

  Abstract (including objectives):

  Ionising radiation affects aquatic ecosystems structured by plants, disrupting biochemical and physiological homeostasis, causing DNA damage and the formation of reactive oxygen species (ROS). Recent studies have demonstrated weakened immunity in chronically irradiated plants. Aquatic plants in the Chernobyl zone have been exposed to radionuclide contamination over long periods and may therefore develop stress memory persisting across generations.
  
  We hypothesise that epigenetically maintained adaptive memory modifies the phenotypes of plant offspring, particularly their radiation tolerance, nuclear proteome and immunity. Seeds of common reed (Phragmites australis) were collected from well characterised relatively clean and radioactively contaminated aquatic reservoirs in the Chernobyl zone. Following exposure to experimental chronic radiation, plants will be cultivated hydroponically.
  
  Nuclear proteome profiling using liquid chromatography coupled with mass spectrometry will allow identification of regulatory and structural proteins involved in stress responses. Inheritance mechanisms, particularly differentially methylated genomic regions, will be investigated using bisulphite sequencing. The intensity of fungal infection will be assessed microscopically and complemented by targeted analysis of the expression of immunity-related genes.
  
  The results will elucidate the mechanisms and consequences of transgenerational plant adaptation to growth in radiologically contaminated environments and contribute to understanding stress memory in aquatic plants.

  
  

  Proposed methodological approaches:

  • Proteome profiling using liquid chromatography coupled with mass spectrometry.
  • Determination of epigenetic regulation using bisulphite sequencing.
  • Gene expression analysis using qPCR.
  • Cellular localisation of biomolecules using fluorescence microscopy.

  
  

  International cooperation: Belgian Nuclear Research Centre

  Expected publication outputs in WoS journals: Journal of Experimental Botany

  Expected funding: VV-MVP-24-0368

  Keywords (3–5): radioactive contamination, common reed, stress memory, proteome

• Identification of the role of the SYT3 gene in plant ontogeny and responses to environmental stresses

  Supervisor: Assoc. Prof. RNDr. Ján Jásik, DrSc.

  Specialist supervisor: —

  Institution: Institute of Botany, CBRB SAS, v. v. i.

  Study programme: Plant Physiology

  Topic for: Faculty of Natural Sciences, CU, Department of Plant Physiology

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: —

  
  

  Abstract (including objectives):

  Synaptotagmins, known as calcium sensors in animal neurons, have been studied in considerable detail; however, their identification in plants was unexpected. In the model organism Arabidopsis thaliana, synaptotagmin SYT1 is involved in responses to various environmental stresses, while the roles of other members of this gene family remain largely unexplored.
  
  This doctoral thesis focuses on the characterisation of the SYT3 gene in the terrestrial plant model organisms Arabidopsis thaliana and Physcomitrium patens. The aim of the study is to elucidate the role of the SYT3 gene in plant ontogeny and in responses to environmental stresses. The gene will be analysed using standard methods of gene expression analysis at multiple levels (GUS, GFP, qPCR), as well as functional analysis of available T-DNA insertion mutants and knock-down/out lines generated by homologous recombination and CRISPR/Cas9-mediated genome editing.

  
  

  Proposed methodological approaches:

  • Recombinant DNA technologies, plant transformation using Agrobacterium and protoplasts.
  • Gene expression analyses: GUS and GFP reporter systems, semi- and qRT-PCR, western blotting, and immunolocalisation techniques.
  • Quantitative confocal microscopy.
  • Genome editing using CRISPR/Cas9, homologous recombination, genotyping (PCR, Southern blotting), and phenotyping of mutant lines.
  • In vitro cultivation of plant material.

  
  

  International cooperation: —

  Expected publication outputs in WoS journals: The results will be published in leading international first-quartile journals focused on experimental plant biology (Plant Physiology, BMC Plant Biology, Plant Science, Plant Stress).

  Expected funding: APVV-23-0463

  Keywords (3–5): Arabidopsis thaliana, Physcomitrium patens, SYNAPTOTAGMIN3, gene expression, genotyping and phenotyping of mutants

• Identification of molecular markers for different stages of adventitious root differentiation

  Supervisor: Assoc. Prof. RNDr. Ján Jásik, DrSc.

  Specialist supervisor: —

  Institution: Institute of Botany, CBRB SAS, v. v. i.

  Study programme: Plant Physiology

  Topic for: Faculty of Natural Sciences, CU, Department of Plant Physiology

  Topic unavailable for external study (internal study only): —

  Topic available for international students: yes

  
  

  Abstract (including objectives):

  The formation of a high-quality adventitious root system is an essential prerequisite for plant propagation via stem cuttings. Adventitious roots develop de novo from already differentiated cells of various organs, which must be reprogrammed. This process is accompanied by pronounced changes at the molecular, physiological, and morphological levels.
  
  The general aim of this doctoral thesis is to contribute, using modern molecular and cell-biological approaches, to the understanding of factors determining optimal adventitious root formation. Based on proteomic and transcriptomic analyses, key marker genes involved in the regulation of individual stages of adventitious root formation—from the reprogramming of differentiated cells to the outgrowth of root primordia—will be identified.
  
  The validity of the identified markers will be verified in both herbaceous plants and woody species, and the acquired knowledge will be used to propose application procedures in breeding practice, with a focus on optimising rooting of economically important species.

  
  

  Proposed methodological approaches:

  • In vitro cultivation.
  • MALDI-TOF, RNA-Seq, semi-qPCR and qPCR, western blotting.
  • Histochemical and immunolocalisation techniques.
  • Quantitative confocal and electron microscopy.
  • Bioinformatic analyses.

  
  

  International cooperation: —

  Expected publication outputs in WoS journals: The results may be published in leading international first-quartile journals focused on experimental plant biology (Current Plant Biology, Plant Physiology, BMC Plant Biology).

  Expected funding: VEGA 2/0073/26

  Keywords (3–5): Arabidopsis thaliana, Populus alba, gene expression, adventitious roots, markers

• The role of extracellular proteins in the early stages of somatic embryogenesis in selected conifer species

  Supervisor: Katarína Klubicová

  Specialist supervisor: Jozef Mravec

  Institution: Institute of Plant Genetics and Biotechnology, CBRB SAS, v. v. i., Akademická 2, 950 07 Nitra

  Study programme: Genetics

  Topic for: Faculty of Natural Sciences, CU – Department of Genetics

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: no

  
  

  Abstract (including objectives):

  Plants have the ability to form somatic embryos from somatic cells without the need for fusion of gametes; this process is referred to as somatic embryogenesis (SE). It represents an efficient regeneration system for the propagation of coniferous tree species under in vitro conditions and, at the same time, a suitable model for studying fundamental questions of plant development. Despite the fact that somatic embryogenesis has been induced in many conifer species, the mechanisms leading to the reprogramming of somatic cells into embryogenic ones are still not fully understood.
  
  A better understanding of these mechanisms may lead to improvements in existing protocols and to more efficient use of this regeneration system. Extracellular proteins, including cell wall proteins, influence cell wall composition and thereby affect numerous physiological processes, including somatic embryogenesis.
  
  The aim of this doctoral thesis is to systematically study the role of extracellular proteins in the early stages of somatic embryogenesis in selected conifer species. To this end, proteomic approaches will be employed to monitor protein dynamics, their interactions, functions, and post-translational modifications during the transition of somatic cells to embryogenic ones. Based on the obtained results, promising proteins and enzymes will be identified and further analysed using microscopic methods. The results may lead to the identification of SE markers and to the optimisation of existing protocols for selected conifer species.

  
  

  Proposed methodological approaches:

  • Preparation of plant material: induction and maintenance of embryogenic lines and their characterisation (growth, maturation capacity).
  • Proteomic analysis of proteins from embryogenic lines with different embryogenic capacities.
  • Analysis of the activity of selected enzymes as potential markers.
  • Visualisation of changes in cell wall composition using immunofluorescence labelling and scanning confocal microscopy.

  
  

  International cooperation: Collaboration with Teresa Hazubska-Przybył (Institute of Dendrology of the Polish Academy of Sciences); participation in the COST project PLANTWALLK aimed at establishing further international collaborations.

  Expected publication outputs in WoS journals: e.g. Plant Science, Plant Cell Reports, Development

  Expected funding: VEGA 2/0014/26 (rating A); IMPULZ

  Keywords (3–5):

• Unravelling the mystery of intracellular mannan using novel glycobiological research tools

  Supervisor: Mgr. Jozef Mravec, PhD.

  Specialist supervisor: Mgr. Veronika Mistríková, PhD.

  Institution: Institute of Plant Genetics and Biotechnology, CBRB SAS, Nitra

  Study programme: Plant Physiology

  Topic for: Faculty of Natural Sciences, CU, Department of Plant Physiology

  Topic unavailable for external study (internal study only): yes (internal study only)

  Topic available for international students: yes

  
  

  Abstract (including objectives):

  Plant polysaccharides are traditionally divided into storage polysaccharides (e.g. starch) and polysaccharides with a structural function in the cell wall (cellulose, hemicelluloses, pectins). However, recent experimental data suggest that this classification may be overly simplistic. One such example is mannan – a polymer of mannose linked by β-1,4 bonds – which accumulates in intracellular structures in some plant species. These structures may serve a storage function similar to starch granules, or may fulfil another, as yet unknown, biological role.
  
  Accumulation of intracellular mannan appears to be characteristic mainly of monocotyledonous plants. The aim of this doctoral thesis is to apply advanced glycobiological and imaging methods to elucidate the function of intracellular mannan and to compare its occurrence and role in monocotyledonous and dicotyledonous plants.
  
  The main objectives of the project are: (i) detailed characterisation of mannan-containing subcellular structures using modern microscopic techniques; (ii) isolation of intracellular mannan and its profiling using monoclonal antibodies and newly developed probes such as DNA aptamers; (iii) isolation and phenotypic characterisation of a mutant of the grass model organism Brachypodium distachyon with a disrupted mannan synthase (CSLA) gene. The results are expected to contribute to a better understanding of the biological function of mannan in plants and to broaden its potential use as a nutritionally valuable dietary fibre.

  
  

  Proposed methodological approaches:

  • Cultivation of plants under controlled conditions and sample preparation for microscopic analyses, including fixation, embedding, and sectioning of plant material using an ultramicrotome.
  • Visualisation of mannan localisation using immunolabelling for scanning confocal and electron microscopy.
  • Development, characterisation, and application of probes (aptamers) through in vitro selection.
  • Identification of a mutant in the mannan synthase gene in Brachypodium distachyon and its phenotypic analysis.
  • Isolation of intracellular mannan and its analysis using comprehensive microarray polymer profiling (CoMPP); the PhD student will complete a short-term research stay at the University of Copenhagen.

  
  

  International cooperation: Short-term research stay at the University of Copenhagen in connection with training in the CoMPP method.

  Expected publication outputs in WoS journals: Plant Journal, Plant Cell, Plant Physiology, New Phytologist

  Expected funding: IMPULZ grant – CARBODNA project (SAS, 1 September 2022 – 31 August 2027); planned VEGA and APVV applications.

  Keywords (3–5): mannan, cell wall, organelle, scanning confocal and electron microscopy, probe, Brachypodium distachyon

• Spatial modelling of plant species distributions and landscape ecological connectivity in the context of climate change and biological invasions

  Supervisor: RNDr. Dušan Senko, PhD.

  Specialist supervisor: —

  Institution: Institute of Botany, CBRB SAS

  Study programme: Botany

  Topic for: Faculty of Natural Sciences, CU, Department of Botany

  Topic unavailable for external study (internal study only): no

  Topic available for international students: no

  
  

  Abstract (including objectives):

  The spatial distribution of plant species directly reflects their ecological requirements, historical factors, and their ability to respond to changing environmental conditions. In recent years, there has been a substantial increase in the availability of occurrence data and geospatial resources, including aerial and satellite imagery, digital elevation models, soil and climate maps, and Earth observation products. These data enable the application of modern Species Distribution Models (SDMs, using multiple algorithms) to predict both current and future species distributions.

  The doctoral project will focus on the development and comparison of SDMs for selected (primarily invasive or potentially invasive) plant species in Central Europe and the Carpathian region. Trained models will be used to identify potential new occurrence sites and to predict distributional changes by the years 2050 and 2070 under different climate scenarios.

  Special attention will be paid to the assessment of landscape ecological connectivity, its changes as a result of fragmentation and human activities (urbanisation, infrastructure development, agricultural intensification, forestry), and its importance for species spread. The project will integrate environmental data, Earth observation data, and potentially genetic or population-level information to produce a spatially explicit assessment of future biological invasion risk.

  The topic addresses current challenges in biodiversity conservation and is aligned with international research initiatives focused on anticipating and assessing the risks of biological invasions under climate change, with practical outputs for nature conservation and landscape management.

  
  

  Proposed methodological approaches:

  • Collection and processing of occurrence data (databases, literature, field surveys)
  • Environmental and climate data (WorldClim, CMIP6, digital elevation models, soil maps)
  • Earth observation and remote sensing data (satellite and aerial imagery)
  • SDM modelling (MaxEnt, Random Forest, BRT)
  • Model performance evaluation (AUC, TSS, k-fold cross-validation)
  • Ecological connectivity analysis (cost-distance analyses, corridor modelling)
  • Field validation of model predictions

  
  

  International collaboration: —

  Expected publication outputs in WoS journals: High-quality WoS papers (preferably Q1/Q2): 3

  Expected funding: Erasmus; DoktoGrant

  Keywords: spatial modelling, plant species distributions, ecological connectivity, biological invasions, climate change

• Study of evolutionary processes responsible for species diversity in the tribe Alysseae (Brassicaceae)

  Supervisor: RNDr. Stanislav Španiel, PhD.

  Specialist supervisor: Mgr. Judita Zozomová, PhD.

  Institution: Centre of Plant Biology and Biodiversity, SAS, p.r.i., organisational unit Institute of Botany

  Study programme: Botany

  Topic for: Faculty of Natural Sciences, CU, Department of Botany

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: yes

  
  

  Abstract (including objectives):

  Effective conservation and potential economic use of wild-growing plants require a thorough understanding of their actual (often cryptic) species diversity and the evolutionary mechanisms responsible for it. This doctoral project will focus primarily on wild species of the genera Alyssum and Odontarrhena (tribe Alysseae), which represent suitable model systems for studying speciation processes while also having considerable potential for practical applications.

  Representatives of both genera are able to thrive on ultramafic substrates, which are unsuitable for most other plant species. The genus Odontarrhena comprises the highest number of currently known plant species capable of hyperaccumulating heavy metals and is therefore an important research subject in phytoremediation and phytomining (the extraction of heavy metals, especially nickel, using plants).

  Previous studies have shown that the traditionally accepted taxonomic delimitation of species in both genera is largely artificial and inaccurate. These groups are characterised by pronounced ploidy variation (from diploid to octoploid cytotypes), high morphological variability, a broad range of ecological requirements, and wide geographic distribution (Eurasia, North Africa). The centre of their species diversity is located in topographically complex regions of the (sub-)Mediterranean.

  The main objective of the project is to clarify phylogenetic and taxonomic relationships and to identify the evolutionary processes that have shaped this diversity, particularly polyploidisation, hybridisation, allopatric speciation, and ecological diversification. The results will contribute to a better understanding of plant speciation mechanisms and may lead to taxonomic revisions or the description of new taxa.

  An integrative methodological approach will be applied, combining phylogenomic methods, flow cytometry, chromosome counting, multivariate morphometrics, and ecological niche analyses.

  
  

  Proposed methodological approaches:

  • Collection of plant material, mainly in southern Europe (a large part of the material is already available)
  • Flow cytometry (determination of ploidy levels and nuclear genome size)
  • Chromosome number determination
  • Multivariate morphometric analysis
  • Ecological niche analysis and modelling
  • Next-generation sequencing (Illumina): Hyb-Seq and RADseq

  
  

  International collaboration: —

  Expected publication outputs in WoS journals:

  Molecular Phylogenetics and Evolution; Annals of Botany; American Journal of Botany; Botanical Journal of the Linnean Society; Taxon; Plant Systematics and Evolution; Phytotaxa

  (Impact factors according to 2025 Current Contents; journal decile/quartile rankings in the Plant Science category according to the 2025 Scimago Journal Rank)

  Expected funding:

  VEGA 2/0010/25 (2025–2028); bilateral project SAS – TÜBİTAK (2026–2029, under evaluation); APVV (2026–2030, in preparation)

  Keywords: Alysseae, phylogenomics, polyploidy, evolution, taxonomy

• Stability of Aquatic Macrophyte Communities under Changing Climate

  Supervisor: RNDr. Ivana Svitková, PhD.

  Specialist supervisor: Ing. Richard Hrivnák, DrSc.

  Institution: Institute of Botany, CBRB SAS

  Study programme: Botany

  Topic for: Faculty of Natural Sciences, CU, Department of Botany

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: no

  
  

  Abstract (including objectives):

  Shallow standing waters (ponds) are considered hotspots of freshwater biodiversity and serve as refugia for many rare species, several of which occur exclusively in these habitats. Despite their high ecological value, these habitats have historically been overlooked and still receive low priority in both national and international conservation strategies. Ponds are highly sensitive to anthropogenic impacts, which can negatively affect their biodiversity and ecological functioning.

  In recent decades, significant climate change has been observed, accompanied by alterations in hydrological regimes and trophic conditions of aquatic ecosystems. However, the consequences of these changes for the stability of aquatic macrophyte communities remain poorly understood.

  The aim of this doctoral project is (1) to evaluate the temporal dynamics of aquatic macrophyte communities over the past decade and (2) to assess the importance of biotic and environmental factors for the stability of these communities.

  
  

  Proposed methodological approaches:

  The study will build on previous research on pond vegetation conducted between 2012–2014, during which a monitoring network of approximately 100 ponds was established. After more than 10 years, a repeated collection of phytosociological records and environmental assessment of this network will be carried out.

  By repeating the vegetation surveys, the temporal changes in macrophyte diversity can be assessed (objective 1). Simultaneously, physicochemical parameters of the water (nutrient concentrations, chlorophyll a, major ions, electrical conductivity, pH) will be recorded, and water temperature will be continuously monitored using temperature data loggers.

  The functional and taxonomic structure of communities, together with environmental quality data, will serve as the basis for evaluating the influence of biotic and environmental factors on community stability (objective 2). Special attention will be given to the effects of eutrophication and water temperature, which are among the most significant stressors of aquatic ecosystems.

  In a subset of 20 ponds selected to cover a broad gradient of trophic conditions and temperature, temporal dynamics of macrophyte vegetation will be monitored in permanent plots. Standard univariate and multivariate statistical methods will be applied to analyse the data.

  
  

  International collaboration: —

  Expected publication outputs in WoS journals: —

  Expected funding: The research will be conducted within the framework of the STRESSPOND project (APVV-24-0463: “Biodiversity, functioning, and cross-ecosystem relationships of small water bodies under multiple stressors”).

  Keywords: biodiversity, macrophytes, small water bodies, eutrophication

• Mechanisms of Toxic Metalloid Effects on Fast-Growing Woody Plants and Their Potential in Phytoremediation

  Supervisor: doc. RNDr. Marek Vaculík, PhD.

  Specialist supervisor: Mgr. Miroslava Vaculíková, PhD.

  Institution: Department of Experimental Plant Biology, Institute of Botany SAS, CBRB

  Study programme: Plant Physiology

  Topic for: Faculty of Natural Sciences, CU, Department of Plant Physiology

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: yes

  
  

  Abstract (including objectives):

  Metalloids with toxic effects on living organisms, particularly arsenic (As) and antimony (Sb), represent a serious global environmental problem. The main sources of contamination with these elements are mining activities and their subsequent use in various industrial sectors, with additional contributions from military activities and transportation.

  The aim of this doctoral project is to study the mechanisms of uptake, accumulation, and tissue distribution of these elements, combined with a detailed understanding of the anatomical, biochemical, and physiological responses of fast-growing woody plants from the family Salicaceae. The research will utilize a wide range of modern experimental plant biology methods.

  A comprehensive understanding of the response mechanisms of fast-growing woody plants to As and Sb may significantly contribute to more effective planning and practical application of phytoremediation approaches and the restoration of metalloid-contaminated landscapes.

  
  

  Proposed methodological approaches:

  • Growing experimental plants in hydroponics and contaminated soil substrates
  • Measurement of growth parameters and gravimetric determination of plant productivity traits
  • Structural analysis of plant tissues using light and fluorescence microscopy
  • Analysis of elemental composition of plant organs using AAS or ICP-MS
  • Assessment of oxidative damage through reactive oxygen and/or nitrogen species production (spectrophotometric methods)
  • In vivo and in vitro analysis of oxidative stress by measuring enzymatic and non-enzymatic antioxidant activity
  • Analysis of selected secondary metabolites induced by metalloid exposure
  • Proteomic analysis of plant tissues and identification of metalloid-induced proteins
  • Identification and characterization of expression of genes responsible for metalloid uptake and transport (RT-PCR, real-time PCR)

  
  

  International collaboration: Institute of Experimental Plant Biology, CAS (Czech Republic); National Taiwan University (Taiwan); Scuola Superiore Sant’Anna, Pisa (Italy)

  Expected publication outputs in WoS journals: Planta; Plant Physiology and Biochemistry; Environmental and Experimental Botany

  Expected funding: VEGA 2/0047/25; APVV 23-0318

  Keywords: abiotic stress, phytoremediation, oxidative damage, metalloid uptake and accumulation, fast-growing woody plants

Proposed Topics for Doctoral Studies in the Field of Biotechnology Starting in the Academic Year 2026/2027

• Enzymes of Carnivorous Plants from the Genus Drosera with Biotechnological Potential

  Supervisor: Ing. Martin Jopčík, PhD.

  Specialist Supervisor: Ing. Jana Libantová, CSc.

  Institution: Institute of Plant Genetics and Biotechnology, CBRB SAS, Nitra

  Study Program: Agrobiotechnology

  Topic for: FBP SPU

  Topic unavailable for external study (internal study only): yes (internal study only)

  Topic available for international students: yes

  
  

  Abstract (including objectives):

  This topic builds upon the practical experience of the research group and insights gained during previous studies. The research focuses on carnivorous plants of the genus Drosera, which includes approximately 200 species inhabiting diverse habitats worldwide.
  
  The primary research focus is the characterization of enzymes involved in prey digestion, particularly hydrolytic enzymes of various classes (chitinases, glucanases, proteases, and others). Given the species and ecological diversity within the genus Drosera, and based on recent findings, it is expected that biological analogs of these enzymes exhibit species-specific properties.
  
  The objective of the doctoral project is to identify the sequences of hydrolytic enzymes in multiple Drosera species, determine their gene sequences and expression profiles, and prepare selected candidates as recombinant proteins for subsequent biochemical characterization. The minimal goal of the project is the analysis of at least one enzyme from one previously uncharacterized species.

  
  

  Proposed Methodological Approaches:

  • Isolation of gene sequences using degenerate primers and genome walking techniques.
  • Analysis of gene expression using RT-qPCR.
  • Preparation of recombinant proteins followed by biochemical characterization.

  
  

  International Collaboration: not planned

  Expected Publication Outputs in WoS Journals:

  • Biological characterization of isolated genes with regard to their function in plants (Planta, Physiologia Plantarum).
  • Biochemical characterization of isolated enzymes (Molecular Biotechnology, International Journal of Biological Macromolecules).

  Expected Funding: APVV-20-0545

  Keywords (3–5): Drosera, gene expression analysis, recombinant proteins

• The Role of Extracellular Proteins in Early Stages of Somatic Embryogenesis in Selected Conifer Species

  Supervisor: Katarína Klubicová

  Specialist Supervisor: Jozef Mravec

  Institution: Institute of Plant Genetics and Biotechnology, CBRB SAS, Nitra

  Study Program: Agrobiotechnology

  Topic for: SPU

  Topic unavailable for external study (internal study only): yes

  Topic available for international students: no

  
  

  Abstract (including objectives):

  Plants are capable of forming somatic embryos from somatic cells without the need for gamete fusion; this process is called somatic embryogenesis (SE). It represents an effective regeneration system for propagating coniferous trees in in vitro conditions and is a suitable model for studying fundamental questions of plant development. Although somatic embryogenesis has been induced in many conifer species, the mechanisms leading to the reprogramming of somatic cells into embryogenic cells are not yet fully understood.
  
  A better understanding of these mechanisms could improve existing protocols and enhance the efficiency of the regeneration system. Extracellular proteins, including cell wall proteins, influence cell wall composition and many physiological processes, including somatic embryogenesis.
  
  The objective of the doctoral project is to systematically study the role of extracellular proteins in the early stages of somatic embryogenesis in selected conifer species. Proteomic approaches will be used to monitor protein dynamics, interactions, function, and post-translational modifications during the transformation of somatic cells into embryogenic cells. Based on the results, promising proteins and enzymes will be identified and further analyzed using microscopic methods. The outcomes may lead to the identification of SE markers and the optimization of existing protocols for selected conifer species.

  
  

  Proposed Methodological Approaches:

  • Preparation of plant material: induction and maintenance of embryogenic lines and their characterization (growth, maturation capacity).
  • Proteomic analysis of proteins from embryogenic lines with varying embryogenic potential.
  • Analysis of selected enzyme activities as potential markers.
  • Visualization of changes in cell wall composition using immunofluorescence labeling and confocal laser scanning microscopy.

  
  

  International Collaboration: Collaboration with Teresa Hazubska-Przybył (Institute of Dendrology, Polish Academy of Sciences); involvement in the COST project PLANTWALLK to establish further international collaborations.

  Expected Publication Outputs in WoS Journals: e.g., Plant Science, Plant Cell Reports, Development

  Expected Funding: VEGA 2/0014/26 (evaluation A); IMPULZ

  Keywords (3–5): somatic embryo, cell wall, proteomics, Pinus nigra

More useful information on doctoral studies.