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Taxonomic overview of the genus Arthroderma with focus on species associated with reptiles and bats
Kolarczyková, Daniela ; Hubka, Vít (advisor) ; Dobiáš, Radim (referee)
The genus Arthroderma belongs to a group of geophilic dermatophytes that primarily degrade keratin in soil and occasionally cause infections in humans and animals. This species-rich genus has received particular attention in recent years in terms of species occurring in human clinical material or clinical samples isolated from rodents and other mammals, which has been associated with a significant increase in the number of its species. In this thesis, the species diversity of the genus Arthroderma was investigated in material isolated from snakes, bats and cave sediment, a substrate that has been almost unexplored in terms of the occurrence of this genus. The strains studied were isolated during research on bats diseased by "white nose syndrome" and snakes by "snake fungal disease". In the past, the genus Arthroderma has been studied either on the basis of morphology or, after the advent of molecular methods, in terms of multigene phylogeny. However, no monographs have simultaneously combined phenotypic and molecular genetic criteria to assess species boundaries across the genus or a significant part of it. This is one of the reasons why species boundaries are often unclearly defined. Thus, another aim of this work was to improve the multigene phylogeny of the genus by incorporating new strains,...
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Elucidating the evolution and diversity of colonial chrysophytes
Pusztai, Martin ; Škaloud, Pavel (advisor) ; Siver, Peter (referee) ; Gusev, Evgeniy S. (referee)
Our current knowledge of chrysophyte diversity is still generally based on traditional morphospecies descriptions. Accordingly, sequence data exist for the minority of all described species. Consequently, several common morphotypes (e.g. Ochromonas-like flagellate) are scattered across the phylogenetic tree of Chrysophytes. It is evident that the postulated taxonomic diversity certainly does not reflect the real species richness in Chrysophytes. Moreover, recent studies on silica scaled chrysophytes (Mallomonas, Paraphysomonas, Synura) clearly demasked common problematics of (pseudo)cryptic species even within this group possessing relatively good species concept based on the ultrastructure of silica scales and bristles. Contrary, most of chrysophytes are naked flagellates forming stomatocysts as the only solid structure in their life cycles. While single-celled Ochromonas and Spumella were recently revisited using molecular genetic techniques, Uroglena-like colonials remained untreated. Therefore, the main objective of this thesis was to provide a modern taxonomic revision of the widespread colonial chrysophytes causing conspicuous seasonal massive population booms, Synura s.l. and Uroglena s.l., by a polyphasic approach encompassing molecular phylogeny, morphology/ultrastructure and ecology....
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Polyphasic analysis and secondary metabolite patterns in nostocacean cyanobacteria with different life strategies
KUST, Andreja
Unbranched heterocytous cyanobacteria exhibit complex filament and colony architectures and variable life strategies from symbionts to free living planktic and non-planktic species. They are counted among microbial groups showing an extensive production of secondary metabolites, resulting in both pharmaceutically important and toxic compounds. The main focus of this thesis is to broaden our knowledge on bioactive secondary metabolite potential in this widespread group of cyanobacteria. An effective combination of methods including whole genome sequencing, bioinformatic analysis, and analytical chemistry techniques are applied to accomplish this task. The discrepancies in distribution of various classes of compounds among ecological groups defined by different life strategies are discussed. Additionally, the thesis endeavours to test multidisciplinary approaches to tackle taxonomic assignments of unresolved unbranched heterocytous cyanobacteria using morphological, phylogenetic and ecophysiological methods, including a meta-analysis of morphological traits.
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Unveiling hidden species diversity in desmids (Desmidiales, Viridiplantae)
Šťastný, Jan ; Neustupa, Jiří (advisor) ; F.M. Coesel, Peter (referee) ; Kaštovský, Jan (referee)
The delineation of desmid species was traditionally based on purely morphological features. However, a frequent misinterpretation of morphological variability in desmids has led in the past to extensive taxonomical confusion within this important group of green algae which complicates the interpretation of their biodiversity in freshwater ecology, biogeography and biomonitoring. Consequently, I focused in this thesis predominantly on a previously neglected issue, the application of polyphasic approaches in the species-level taxonomy of desmids. In the most studies, a combination of both traditional morphological and modern molecular phylogenetic and geometric morphometric methods has been used to evaluate the taxonomy of selected desmid species, particularly representatives of the morphologically complex genera Micrasterias and Xanthidium. In two papers, I used the combination of traditional morphological and autecological data to clear up the taxonomy of several morphologically less prominent desmid taxa. Generally, the results of the thesis demonstrated that the way we recently see the diversity and distribution of desmids should be thoroughly changed. The real species diversity is mostly distinctly finer than that estimated by classical morphological taxonomy, often corresponds to varieties of...
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Towards a modern revision of the cyanobacteria, a critically important prokaryotic phylum
BOHUNICKÁ, Markéta
With an adoption of modern methods of polyphasic approach to the study of cyanobacteria, an increased demand for the revision of the traditional taxonomy has emerged. This thesis is devoted to the systematic revisions of selected terrestrial cyanobacteria at several taxonomic levels. The methodology included thorough morphological characterization of cultured cyanobacterial strains using light and electron microscopy complemented with analyses of the molecular data: DNA sequencing, phylogenetic analyses based on 16S rRNA gene and the adjacent 16S-23S ITS region, and comparison of the predicted secondary structures of this region. Descriptions of new species, genera, families and an in-depth characterization of a previously poorly known family were achieved.
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Polyphasic approach to the taxonomy of selected cyanobacteria
MAREŠ, Jan
The modern taxonomic revision of cyanobacteria is a work in progress, with both theoretical and practical challenges to be addressed. This thesis investigated selected terrestrial cyanobacterial taxa using a polyphasic approach, based on molecular phylogenetic analysis and accompanied by phenotypic characterization and nomenclatural treatment. Diverse methodological approaches were used including optical and transmission electron microscopy, molecular analysis (DNA sequencing) of cyanobacterial strains, single cells and filaments, and phylogenetic analysis of multiple genomic loci. This study provided systematic revisions of individual cyanobacterial genera and the entire phylum, and suggestions for future study projects.
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Polyphasic approach to the taxonomy of the selected oscillatorian strains (Cyanobacteria)
LOKMER, Ana
Morphology and ultrastructure of 25 oscillatorian strains was examined and phylogenetic analysis of 16S rDNA oscillatorian sequences was conducted. Genera Phormidium and Oscillatoria were shown to be polyphyletic. Although morphologically similar strains are found in different branches of the phylogenetic tree, considerable correlation between molecular, ultrastructural and some morphological and ecological traits was detected in several lineages.
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