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β-tubulin paralogs in Aspergillus: taxonomical importance and molecular tools for distinguishing
Hubka, Vít ; Kolařík, Miroslav (advisor) ; Bunček, Martin (referee)
A beta-tubulin gene (benA) is widely used in taxonomy and identification of Aspergillus spp. and other Fungi.Across Aspergillus spp. There is either one (benA) or two beta-tubulin paralogs (benA and tubC). The risk ofcontemporary use of sequences of paralogous genes with non-homologous function in the same phylogeneticanalysis is well known. It is evident that it had happened repeatedly in Aspergillus section Nigri. It is alarmingthat conventional primers for amplification of partial benA sequence can specifically amplify tubC paralog insome species. In this work, both paralogs were characterised in a set of species. The beta-tubulin primers in usewere revised and new, more benA specific primers were designed. Applicability of some markers such as basecomposition, codon usage and length of introns for distinguishing -tubulin paralogs benA and tubC is tested. Alarge study on molecular diversity of 349 isolates of Aspergillus (PCR-fingerprint, sequence data - ITS, benA,rpb2, caM) originating from Czech culture collections and from clinical material is also included. 82 specieswere identified, togetherwith nine tentative new taxa belonging to sections with high economic impact - Nigri,Fumigati or Aspergillus (Eurotium spp.). Five species from Section Aspergillus could be synonymised withexisting taxa. A study...
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Mycorrhizal and endophytic roots of aquatic plants
Borovec, Ondřej ; Vohník, Martin (advisor) ; Kolařík, Miroslav (referee)
Interactions between fungi and plants can be found all around us. We would hardly find a plant neither containing a single hypha in its rhizosphere nor infested with a fungal pathogen. Whereas interactions of these organisms are well and described in terrestrial ecosystems, situation below the water level is completely different. The status of aquatic fungi and their relation to aquatic plants is to date not clear at all regarding difficulties of reaching them and huge value of terrestric interactions, which occupy most of the experts. All the basic plant-fungus interactions have been detected also underwater. As well as on the land, the most widespread aquatic mycorrhizal association is arbuscular mycorrhiza. On the contrary, the other well known mycorrhiza types such as orchid or ericoid mycorrhiza do not occur in the aquatic environment where their hosts are absent. On the other hand, endophytism is relatively frequent. Ascomycetous fungi with dark septate hyphae, collectively being referred to as "dark septate endophytes" (DSE), seem to be as abundant in the water as on the land. Additionally, aquatic plants are being challenged by numerous fungal parasites. AMF may play an important role in nutrient uptake of some plants from the aquatic environment. However, many species of aquatic plants are...
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Endophytic fungi in above-ground tissues of plants of the family Ericaceae
Koudelková, Barbora ; Koukol, Ondřej (advisor) ; Kolařík, Miroslav (referee)
Many studies focus on endophytic fungi. However, above-ground tissues of plants of the family Ericaceae are not largely examined. Most of the literature concerns the fungi forming ericoid mykorhiza. This bachelor thesis sums up the diversity studies of the endophytic fungi in the family Ericaceae, compares the frequency and the overlap of fungi in different host plants and geographical regions and also the occurence of fungi in living and dead plant tissues. The methods of fungal isolation and identification are accented.
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Diversity and ecology of endophytic fungi in different parts of pants.
Kovaříčková, Adéla ; Prášil, Karel (advisor) ; Kolařík, Miroslav (referee)
Even though endophytic fungi have been studied intensively in the past years, little attention has been payed to endophytic colonisation of a whole plant. The search part of this work is about the differences in diversity and ecology of endophytes within whole plants, whose single parts represent qualitatively different environments for growth of endophytic fungi. The main difference is between the colonisation of systemic endophytes of grasses from family Clavicipitaceae and the colonisation of taxonomically heterogenous group of non-systemic endophytes. A systemic endophyte colonizes all above-ground organs of grass, while a non-systemic endophytes form only local infections, and their species composition in specific plant parts differs. The practical part of this work encompasses the pilot study of species diversity of endophytic fungi from woody parts (branches, stems and roots) of an elm tree (Ulmus laevis). There are differences in the frequency of colonisation among samples cultivated on agar plates, and also in diversity of isolated fungal genera.
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Induction of sporulation and sexual state formation in Ascomycota (Fungi)
Dudová, Zuzana ; Kolařík, Miroslav (advisor) ; Novotný, David (referee)
The aim of this study was to summarize factors that induce sporulation of anamorph and fruiting body formation in ascomycetous fungi. These factors are, depending on a species, light, water, air and nutrients availability, presence of various chemical compounds and osmolarity. Specific media and cultivation conditions used for sporulation induction are reviewed. I concentrated on mating type (MAT) genes and genes involved in the process of conidiation in the chapter about genetic background of fructification and sporulation. Key words: sporulation, fruiting body formation, MAT genes, mating factors, anamorph, teleomorph, Ascomycota, homothallism, heterothallism.
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Fungal genetics, genome evolution and use of flow cytometry in study of DNA
Würtherlová, Tereza ; Kostovčík, Martin (referee) ; Kolařík, Miroslav (advisor)
The fungal genome is a dynamically changing structure. By its remodelling, the organism can respond to the environmental changes and develop itself. The genome expansion is often accompanied by transition to parasitic or mutualistic way of life. The genome expansion can be caused by the multiplication of some chromosomes (aneuploidisation), the whole genome duplication (polyploidisation) or the spreading of repetitive sequences. The impact of genome size to the ecology and life strategy of the organisms is more and more studied in recent years. In mycology, nevertheless, it escapes sufficient attention. The flow cytometry (FCM) is a modern and progressively developing method that enables to determine the genome size and estimate CG/AT base ratio. The combination of FCM with knowledge of the fungal ecology and forces that form the genome enable to discover a general trends of the evolutionary processes. My study summarises knowledge about the processes leading to changes in the size/structure of the fungal genome, the correlations with genome size and presents the principle of flow cytometry and its application in mycology.
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Comparison of ITS nrDNA and alternative markers for fungal metabarcoding in environmental samples
Zelenka, Tomáš ; Kolařík, Miroslav (advisor) ; Mašek, Tomáš (referee)
The study of fungal diversity may lead to many fundamental discoveries and conclusions. Molecular genetics, and particularly high throughput sequencing methods using short DNA fragments as barcodes, has recently experienced a boom. The most frequently used marker for fungal research is the partial region of nuclear ribosomal DNA called ITS (Internal Transcribed Spacer). It occurs in the form of tandem repetitions of up to 200 copies. This fact greatly simplifies its amplification from the environment but also introduces some negatives. One of them can be an existence of intragenomic and intraspecific variability which confounds diversity estimates by exaggerating the real number of species. Using alternative low-copy markers can easily prevent these problems. In this study EF-1α and RPB2 protein- coding genes were compared with traditionally used ITS1 and ITS2 markers. An artificial mock community was created by blending genomic DNA of different fungal lineages. The community was sequenced for all markers and the data were processed according to guidelines commonly used in environmental studies. The results show that ITS2 is unequivocally a more suitable marker for environmental studies than other compared markers. The average coefficient of overestimation was deemed to be approximately two for ITS1, ITS2,...
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Testing of the interactions of Pythium oligandrum with patoghenic and non-pathogenic fungi
Kolařík, Miroslav
The final report summarizes results of five main objectives defined by the contract. 1. Characterization of the bacterial and fungal contamination of various samples, quantification of the active compound. 2. Utilization of the nutrient sources by Pythium oligandrum. 3. Molecular genetics characterization of P. oligandrum. 4. Interaction of P. oligandrum with selected yeasts and moulds. 5. Testing of the preparation Biorepel in the real conditions.
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