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Biodiverzita myxozoí v přehradní nádrži Římov zjištěná analýzou environmentální DNA
BÜRGEROVÁ, Monika
Myxozoans represent a diverse group of microscopic endoparasites primarily infecting fish, including over 2,600 nominal species. Despite the extensive number of described species, their diversity remains still unexplored and underestimated. The detection and surveillance of myxozoan parasites in previously unexamined areas can reveal crucial pathogens linked to fish mortality and discover myxozoans biodiversity. This thesis investigates the parasite diversity in the Římov Reservoir, focusing on myxozoan detection through environmental DNA (eDNA). A comparison of detected diversity at various sites and in different environmental samples across the Římov Reservoir unveiled interesting patterns of read abundance and number of OTUs within each myxozoan clade. This study underscores the importance of eDNA analysis in detecting pathogens and assessing biodiversity in myxozoan parasites.
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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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Metabarcoding and environmental sequencing projects
Kandaurova, Ekaterina ; Hampl, Vladimír (advisor) ; Poláková, Kateřina (referee)
The thesis explores the use of metabarcoding in projects uncovering biological diversity and its applications in various fields of biology. The thesis provides an overview of the principles and workflow of metabarcoding, including the choice of specific molecular markers for various groups of organisms and the bioinformatics aspect of data analysis. Limitations of metabarcoding, such as lack of standardization, primer bias and targeting metabolically inactive organisms are discussed along with potential strategies for overcoming these obstacles. The practical application of metabarcoding is demonstrated on examples of its use in sequencing projects, such as Human Microbiome Project or TARA Oceans expedition. The potential of using metabarcoding for research purposes is discussed from the perspective of paleontology, diet analysis, and conservation biology. Overall, this work aims to assess the potential of metabarcoding as a powerful tool and could serve as an initial guidance for researchers interested in utilizing metabarcoding for their scientific investigations. Keywords: metabarcoding, eDNA, molecular markers, NGS, bioinformatics, biodiversity.
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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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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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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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Ecological aspects affecting microbiota in the digestive tracts of birds
Schmiedová, Lucie ; Kreisinger, Jakub (advisor) ; Mrázek, Jakub (referee) ; Gvoždíková Javůrková, Veronika (referee)
The results indicate that songbird GM is dominated by the bacterial phyla Proteobacteria, Firmicutes, Actinobacteria, Tenericutes, Bacteroidetes and Chlamydia, a community that differs from that of mammals. A t the interspecies l evel, GM composition is mainly influenced by phylogeny and less so by sampling site. While ecological factors , and especially diet , are important GM predictors in mammals, the effect of ecological factors , including diet , have a much smaller effect on inte r - and intraspecific variability in songbird GM composition . Our data from barn swallows ( Hirundo rustica ) suggest an effect of social GM transmission among adults forming social pair s, as well as trans - generational transmission from a social mother to her own nestlings. At the same time, we observed differ ing GM in adults and nestlings, with no dramatic change in GM with nestling age, a process previously recognised in mammals. Part of the GM detected appears to remain stable over time , and is therefore su itable for further detailed study. To conclude, our studies demonstrate that s ongbird GM differs from that of mammals and that the factors influencing GM composition appear to differ from those in mammals , thereby highlighting the importance of study ing mu ltiple vertebrate groups (not just mammals ) when...
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A comparison of metabarcoding and morphology-based identification of protist communities
Tučková, Kateřina ; Škaloud, Pavel (advisor) ; Steinová, Jana (referee)
This thesis is focusing on metabarcoding; its history, principles and current use in science. Metabarcoding brings us a new way to observe a diversity of protists. Although the protists are ubiquitous on the Earth and play a key role in the majority of biological processes, our knowledge of their diversity is still very poor. Traditional microscopy techniques are mostly based on morphology-based identification of taxa. However, they are not so suitable for investigating protist diversity due to their small size, low concentration in the environment, and the convergent morphological evolution of many groups. Similarly, the metabarcoding has its pros and cons, as well. This thesis summarizes pros and cons of both techniques, trying to emphasize the need to both of them to gain a more complete insight into the diversity of protists on the Earth.
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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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