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Taxonomy, diversity and clinical relevance of the genus Aspergillus
Hubka, Vít ; Kolařík, Miroslav (advisor) ; Labuda, Roman (referee) ; de Beer, Wilhelm (referee)
Aspergillus is a speciose genus encompassing nearly 400 species that has significant economic impacts on human health, the food industry, biotechnology and pharmacology. The research included in this thesis focuses on current issues related to the generic concept, subgeneric classification and species delimitation in Aspergillus. It addresses the need for revisions of several sections or species complexes. It provides novel information regarding etiology of aspergillosis as well as the antifungal susceptibilities of several less common opportunistic pathogens. The taxonomic section of the thesis contributes to the taxonomic stability and the new concept of the genus Aspergillus, which changed in response to the discontinuation of dual nomenclature in fungi. Sufficient arguments were collected (e.g., verification of monophyly, unifying phenotypic characters) for maintaining a broad concept of the genus and avoiding splitting it into several genera. All genera typified by sexual morphs and having Aspergillus asexual states were synonymized with Aspergillus and the appropriate names adopted; new combinations were made for teleomorphic species that lacked Aspergillus names. This thesis also contributed to infrageneric taxonomy of the genus via the proposal of four new sections in the subg. Circumdati,...
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The effect of microbiota on pathogenesis of gut diseases
Galanová, Natalie ; Kolařík, Miroslav (advisor) ; Hudcovic, Tomáš (referee)
Gut microbiota is considered an important factor in the development of various diseases including inflammatory bowel disease (IBD, n = 127), Ulcerative colitis, Crohn's disease, and colorectal cancer (CRC, n = 64). A part of this thtesis is to prepare clinical material of different sorts (stool, biopsy) for sequencing on Illumina Miseq platform. This is achieved trough DNA isolation, amplification of 16S and internal transcribed spacer (ITS), normalization and ligation of sequencing adaptors. The aim of this project is to describe the differences between microbiota in healthy and diseased subjects in case of IBD or unimpaired and tumorous tissue for CRC patients. This research is also being based on cultivation, where a fresh stool samples (n = 3) are cultivated in a broad range of conditions, which enables us to obtain ecophysiological and species diversity of these samples by traditional and molecular methods. The cultivable fungi are also assigned reliable taxonomy by amplification of relevant genes (ITS1, β tubulin, second largest subunit of RNA polymerase II, RPB2) followed by both-sided Sanger sequencing. Selected species of fungi are processed into lysates, which are used for stimulation of mice macrofage cell line (RAW). Therefore the impact on immunity response is studied in vitro and...
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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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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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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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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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Interactions of initially mycoheterotrophic plants with environment
Figura, Tomáš ; Ponert, Jan (advisor) ; Kolařík, Miroslav (referee) ; Janoušková, Martina (referee)
Initially mycoheterotrophic plants have recently been declining in the wild, even without apparent causes. They are affected by a number of biotic and abiotic factors. The aim of this work is to investigate how selected factors, such as nitrate or symbiotic fungi, may influence their distribution in nature. In particular, the work applies in vitro experiments, molecular determination of fungal symbionts and stable isotope analyses. It describes both the effects of abiotic factor, specifically nitrate, and biotic interactions of initially mycoheterotrophic plants with fungal symbionts. The inhibition of germination by extremely low concentrations of nitrate in asymbiotic in vitro cultures was observed in several orchid species. The degree of sensitivity of each species to nitrate corresponds with the nitrate content of the soil and the nutrient availability requirements of the species according to Ellenberg indicator values. The inhibitory effect of nitrate on orchid germination was also observed in symbiotic in vitro cultures. Out of five tested fungal strains, only one Ceratobasidium was capable of eliminating the inhibitory effect of nitrate. Furthermore, the work reveals that green mixotrophic orchids use photosynthates to nourish the aboveground parts, whereas the belowground parts are...
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Fungal secondary metabollites with antiviral activity
Besedová, Alena ; Čmoková, Adéla (advisor) ; Kolařík, Miroslav (referee)
The past year 2020 has clearly shown how quickly some viral infections can reach pandemic proportions. Thus, there is still a need to discover new substances with antiviral activity. Such substances (eg. asteltoxin E, cytosporaquinone B) have been discovered in the past in several groups of fungi, however, their potential as a source of virostatic chemotherapeutics has not been much explored. The possible use of fungi as a source of substances with antiviral activity is also indicated by the use of some species (eg. Ganoderma linghzi, Lentinula edoles) in the alleviation or prevention of viral diseases in traditional medicine. In most cases, however, it was not possible to find substances responsible for this effect. Therefore, in my bachelor's thesis I will first analyse kinds of fungi traditionally used as treatment of viral infections in traditional medicine. I will also summarize the most important fungal substances for which antiviral activity has been demonstrated. The bachelor's thesis will provide a comprehensive overview of currently known secondary metabolites of fungi and their virostatic effects. The information summarized in the work may point to possible candidates in the fight against viral infections.
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Fungal metabolism modulation by plant substances
Sedláková, Vendula ; Čmoková, Adéla (advisor) ; Kolařík, Miroslav (referee)
Phytochemicals are bioactive substances by which plants affect organisms in their vicinity. Fungi often respond to their presence by metabolism alternation, which is manifested by the production of secondary metabolites, an increase in biomass or the regulation of virulence. These changes can be caused by phytochemicals (e.g. curcumin, EGCG) with abilities to modulate epigenetic information. The first half of the work is devoted to mechanisms of epigenetic modification (e.g. methylation, histone modification), which were studied in fungi. The second half summarizes studies focused on phytochemicals, in which the ability to modify epigenetic information in eukaryotic organisms was observed. The bachelor's thesis thus brings valuable knowledge about the possibility of modifying fungal metabolism by phytochemicals, which are often waste products of industry. Information summarized in this work can have a significant impact on improving biotechnological processes, where there is an effort to increase biomass yield or induce the production of secondary metabolites in cases where their production is normally suppressed. Key words: secondary metabolites, epigenetics, epigenetic modification, phytochemicals, filamentous fungi
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