CREPIDOTUS
What we (do not) know about the genus Crepidotus (Agaricomycotina, fungi), 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
Background
Fungi of the genus Crepidotus (Agaricomycotina) have pileate fruiting bodies with a lamellate hymenophore and a typically reduced stipe. They grow on various dead plant substrates, especially wood. They are circumpolarly widespread and relatively common from tropical to hemiboreal regions. The genus Crepidotus has been monographically studied several times, but the individual species were defined only on the basis of morphological features. Phylogenetic studies have confirmed the genus Crepidotus as a separate lineage within Agaricomycotina, but species delimitations and phylogenetic relationships are not sufficiently known and supported.
Hypotheses
- (I) Crepidotus is a monophyletic genus with several well-defined lineages;
- (II) current infrageneric classification based on morphology does not correspond to phylogenetic grouping.
Aims
- (I) to revise the taxonomic, systematic, and phylogenetic status of species within the genus;
- (II) to identify host and substrate ranges of the Crepidotus species;
- (III) to infer phylogenetic relations within the genus.
The project is performed only by MEM members; the principal investigator is Soňa Jančovičová.
STRAKA
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
https://ibot.sav.sk/mem-straka
FunPoxHyb
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
Background
Hybrid heme peroxidases (EC 1.11.1.7) 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.
Aims
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.
Clavariaceae
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
Background
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.
Aims
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.
Návratová projektová schéma SAV pre rodičov po návrate z materskej a/alebo rodičovskej dovolenky
Optimization of PCR protocols for better interpretation of historical herbarium specimens in the genus Russula
Michaela Caboňová
The project deals with improving the current methodological procedures routinely used for studying historical herbarium specimens in the genus Russula. The study of the diversity of this genus is significantly limited by the necessity to interpret older species names due to nomenclatural priority according to the rules of the International Code of the Nomenclature. Type specimens corresponding to individual species names often have highly degraded DNA, which significantly reduces the success of molecular analyses using traditional methods. The aim of the project is to design new primers specifically tailored for individual subgenera within the genus Russula to increase the success rate of PCR reactions and subsequent sequencing outputs. Improved procedures will enable better molecular analysis not only of historical herbarium specimens but also of recent collections with degraded DNA often due to collection in inaccessible areas and areas with poorly developed infrastructure. Indirectly, the results of the project will contribute to the global study of this significant ectomycorrhizal genus in hard-to-reach areas.
Doktogrant
Soil microbial community changes along an elevational gradient in beech forests of central Slovakia (2025)
Shanza Zaib
Supervisor: Miroslav Caboň
The project aims to build upon our comprehensive research on fungal diversity changes along an altitudinal gradient in a beech forest in central Slovakia, specifically in the Javorie Mountains. Based on previous soil sample collection at different elevations, followed by analyses of soil physico-chemical properties, enzymatic activity assessments, and fungal metabarcoding, we have gained valuable insights into the fungal component of these ecosystems. The project suggests a comprehensive metabarcoding analysis of bacterial communities as a complementary component of the soil microbiome. By examining the presence and functional dynamics of bacterial communities in connection with our existing fungal data, we aim to clarify the complex interactions between fungal and bacterial components within this ecosystem. This holistic approach will contribute to a more comprehensive understanding of the forest microbiome along the altitudinal gradient and enhance our knowledge of its ecological intricacies and the potential impacts of environmental changes.