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Temporal changes in the genetic and morphological diversity of silica-scaled chrysomonads (Stramenopiles, Chrysophyceae)
Tučková, Kateřina ; Škaloud, Pavel (advisor) ; Nedbalová, Linda (referee)
Temporal dynamics on short time scales is a very interesting area of research. Usually, temporal studies are done on a scale of months or years. However, microorganisms have a much shorter generation time and therefore changes can take place on a much smaller time scales. At the same time, almost none of the temporal studies go to the species level and mostly stay at the class level. That species dynamics change within days we know from observation, but this has never been properly verified. The genera Mallomonas and Synura from the class Chrysophyceae were chosen to study short-term temporal changes These two genera are characterized by the formation of siliceous scales on the surface of their cells, by which they are well morphologically identifiable to the species level. However, since species identification by microscopy is an old but traditional method, a new molecular method for species identification at the locality, i.e. metabarcoding, was also used. These two methods have been shown similar results for describing the golden algae community. At the same time, it was confirmed that temporal dynamics occur at the species level, but also at the section level in the genus Synura. Subsequently, it was possible to relate the environmental factors that cause temporal changes in the community to...
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There is something in the air: Diversity of lichen symbionts in the aeroplankton
Veselá, Veronika ; Škaloud, Pavel (advisor) ; Vančurová, Lucie (referee)
Lichens that reproduce primarily sexually rely on the presence of their symbionts in the environment. A new lichen cannot develop without direct contact between the filaments of the germinating spore and a compatible symbiotic alga. However, the results of earlier studies do not provide solid evidence for photobiont presence on lichen-colonized substrates. The objective of this thesis was to assess various environmental types (air, bark, soil, stone, and artificial substrates) as potential sources of symbiotic algae. To achieve in-depth understanding of the diversity of green algae at a long-studied Central Bohemian study-site, Illumina MiSeq metabarcoding of the ITS2 rDNA region was combined with traditional sequencing of lichen algal ITS rDNA and morphological observations. The methods used revealed 283 species-level lineages and 1313 OTUs, many of which belonged to unknown species or higher taxonomic categories. All photobiont species associating solely with sexual lichens at the site could also be found in the vicinity of lichen thalli. As a result, both the substrates and the air, where these symbiotic algae occurred as well, may act as photobiont sources. In contrast, many symbionts that associate only with asexual lichen species, were never found at the site outside of lichen thalli....
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Complexity of lichen symbiosis
Černajová, Ivana ; Škaloud, Pavel (advisor) ; Palice, Zdeněk (referee) ; Spribille, Toby (referee)
Lichens are currently viewed as complex symbiotic systems. In addition to the main mycobiont and photobiont, a variety of associated fungi, bacteria and algae/cyanobacteria (minor/accessory photobionts) have been recognized. Their diversity has been intensively studied, but is still far from being fully apprehended. Likewise, recognition of the significance of the associated organisms to the whole system is still at the beginning but various crucial roles, from constitutive morphogenetic through physiological to various means of increasing the lichen's fitness, have already been suggested. The present thesis attempts to approach lichens in their full complexity. Focusing on two model systems; the Cladonia-Asterochloris association and ecologically delimited communities of Verrucariaceae; it aims: i) to examine patterns in photobiont choice and their relationship to lichen ecology; ii) to set a framework for in-vitro mycobiont-photobiont compatibility testing; iii) to explore the diversity of selected associated fungi and their possible relationships with the lichen host. We have shown that Verrucariaceae in the intertidal zone associate with largely understudied Ulvophycean photobionts. They mainly belong to Kornmanniaceae, Ulvales, and include a variety of novel lineages, one of which was...
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Genome size variation in microalgae and its evolutionary consequences
Čertnerová, Dora ; Škaloud, Pavel (advisor) ; Boenigk, Jens (referee) ; Bureš, Petr (referee)
Eukaryotic organisms exhibit tremendous variability in genome size with no apparent connection to their biological complexity. Although this variation is known to correlate with numerous phenotypic traits, its evolutionary consequences remain widely unknown. This particularly applies to microalgae, where the genome size estimation is often methodologically challenging. Yet, microalgae represent a promising model group to study genome size evolution owing to their lower body complexity, short generation time and large population sizes, the latter two allowing them to quickly respond to environmental challenges. The main aim of this thesis was to enhance our understanding of genome size variation in microalgae and its evolutionary consequences. To do so, together with my co-authors, I summarized the flow cytometry (FCM) protocols used for microalgae and microorganisms possessing small genomes and addressed their limitations resulting mainly from insufficient amounts of biomass, difficulties with nuclei extraction and prominent background noise due to presence of various pigments and secondary metabolites. Further, I provided best practice recommendations that include, among others, analysing young cultures, avoiding long-term cultivation, and testing different isolation buffers and nuclei isolation...
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Let's meet in the littoral: Diversity of symbiosis in the Verrucariaceae lichens
Schmidtová, Jana ; Škaloud, Pavel (advisor) ; Peksa, Ondřej (referee)
Lichens are organisms formed by several symbiotic partners, most importantly a fungus (mycobiont) and an alga or cyanobacteria (photobiont). Although most lichens are terrestrial, some can be found also in aquatic environments. Black crustose lichens from the family Verrucariaceae (Verrucariales, Eurotiomycetes, Ascomycota) were able to adapt to this environment very well and often dominate in the seashore near fluctuating water level. The ability of these lichens to inhabit various environments is associated with their unusually wide range of photobionts. However, this symbiont is not known to most of them. This work investigates the diversity of lichens of the family Verrucariaceae in the littoral zone of the Baltic and the North Sea coasts, the relationships between symbionts and the connection between lichen diversity and the salinity gradient. Using metabarcoding, the diversity of free-living algae in the vicinity of the studied lichens is determined and the symbiotic algae are compared with the photobionts found in the lichens. Mycobionts and photobionts were identified using ITS and 18S rDNA. A total of nine lineages of mycobionts and photobionts were found. The most common lichen turned out to be the species Hydropunctaria maura with its photobiont Pseudendoclonium submarinum. For several...
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Phytomyxid infection of the seagrass Halophila stipulacea: phylogeny, distribution and new insights into its life cycle
Kolátková, Viktorie ; Vohník, Martin (advisor) ; Škaloud, Pavel (referee)
Marine phytomyxids (Cercozoa: Phytomyxea) represent a group of obligate biotrophic eukaryotes known for infecting several algae and oomycetes and counted among three taxa generally reported to behave as seagrass-pathogens. Due to their low-key nature, they are observed only sporadically and very limited information about their diversity, life cycles or distribution is available. In order to extend the knowledge of this enigmatic group of marine protists, an extensive research on a phytomyxid found in the invasive seagrass Halophila stipulacea was carried out. In situ observations, light and scanning electron microscopy and molecular methods were used to approach the species' ecology, geographical range and phylogenetic placement within the class Phytomyxea. The organism was confirmed to be present in the Red, the Mediterreanean and the Caribbean Sea, suggesting a potential case of a host-parasite comigration on a global scale. Phylogenetically it represents the first and so far the only described member of the "TAGIRI-5 environmental clade" - possibly a whole new order within the Phytomyxea, outside the already established Plasmodiophorida and Phagomyxida. The infection rates and times of occurrence are specified for all the finding-sites, indicating an interesting seasonal pattern in the...
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Diversity and function of pattern structures in the microworld
Hirnerová, Anna ; Škaloud, Pavel (advisor) ; Němcová, Yvonne (referee)
This thesis summarizes current knowledge of patterns and structures at various scales, with an emphasis on the use of these patterns in the microworld and also on the materials that are most often used. Patterns are applied in all areas of natural processes and human activity. There are many analogous models at different scales, but we do not know if they have the same self-organizing mechanisms. Many patterns formed by microorganisms can be prepared without their presence, on the basis of physical and chemical methods, so they are probably created under certain parameters that can be influenced by a given protist. These patterns are evolutionarily advantageous for microorganisms, because they provide them with a number of functional adaptations, mainly in connection with defense against predators and movement in the water column, which is based on the organism's life strategy. The mathematical description of the pattern is extremely important for its further research and for determining the laws that have allowed the organism to benefit from its parameters. Keywords: pattern, structure, convection, reaction - diffusion model, geometry, protist, microorganism, skeletons, shells, scales
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Photobiont dynamics of Stereocaulon lichens
Vančurová, Lucie ; Škaloud, Pavel (advisor) ; Bérešová, Anna (referee) ; Dal Grande, Francesco (referee)
7 Abstract Lichens are an iconic example of symbiosis. They are widespread throughout the world. In some ecosystems, lichens are dominant autotrophs, sometimes one of the few living organisms capable of surviving local conditions. They grow on a variety of substrata, including artificial surfaces. Great diversity of their life strategies is related to the diversity of symbiotic partners forming the lichen thalli, which remains largely unresearched. Lichens as sessile organisms often have to face a changing environment or adapt to conditions at new localities where their propagules can spread. We have chosen the widespread genus Stereocaulon as a model system for studying symbiotic relationships in lichens and the connection of this relationships with environmental conditions. The main goals of this thesis were (1) to uncover the diversity of phycobionts (i.e., green algal photobionts) associated with Stereocaulon within the whole genus and particular species-level lineages; (2) to identify environmental factors affecting the distribution of phycobionts and their relationships with mycobionts on a global and local scale; and (3) to inspect the possibility of sharing phycobiont pool with other lichens and soil. For this purpose, we used phylogenetic analyses (ITS rDNA, 18S rDNA, rbcL, and actin type I gene),...
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Autotrophic microbial communities on needles of gymnosperms
Nováková, Radka ; Neustupa, Jiří (advisor) ; Škaloud, Pavel (referee)
This bachelor thesis summarizes available data on autotrophic microbial communities on needles of gymnosperms. This new phenomenon has been observed since 1980'. In my thesis the composition of these communities is described. In addition, their seasonal development, the correlation of species and abundance data with air pollution (mostly nitrogen and sulphur concentrations) are also referred. Except bioindication studies that used these epiphytic communities, similar papers using lichens were also included. The thesis also contains a chapter with detailed description of three most frequent green algae species occurring on needles. In my own work, relationship between epiphytic quantitave parameters of needle-inhabiting communities (thickness, cover, algae amount) of English Yew (Taxus baccata L.) were analyzed in relation to the air pollution data in Prague.
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Red algae (Rhodophyta) in freshwater ecosystems
Štifterová, Anna ; Neustupa, Jiří (advisor) ; Škaloud, Pavel (referee)
This bachelor thesis is focused on an interesting group freshwater red algae (Rhodophyta). This group comprises organisms from quite distant evolutionary clades, nevertheless sharing similar ecological requirements. They mostly occur in unpolluted lotic ecosystems. In the theoretical part, I summarized publications dealing with the general and ecological aspects of distribution of these algae (mainly of the genus Batrachospermum). For example, the issue of seasonal populational dynamics, or their role in succession of benthic algal communities. The practical part includes floristic data on findings of various species of freshwater red algae, predominantly from the Czech Republic. Furhermore, it includes observation on seasonality of a single population of Batrachospermum gelatinosum.
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