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Structure and function of microbial communities of montane spruce forest
Štursová, Martina ; Baldrian, Petr (advisor) ; Uhlík, Ondřej (referee) ; Slaninová Kyselková, Martina (referee)
Structure and function of soil microbial communities in montane spruce forest Martina Štursová Abstract Coniferous forests are spatially heterogeneous environments and represent an important ecosystem that acts as carbon sink under current climate storing large amounts of carbon in standing biomass or as soil organic matter. The formation of organic matter via decomposition of dead biomass and transformation of rhizodeposited organic compounds is primarily mediated by microbial community of forest topsoil. Despite growing insight into the composition of these soil communities, little is known about the microbes actually responsible for those transformation processes, about the drivers shaping these communities or their response to increasing numbers of severe disturbances. Studies presented in this thesis contribute to filling the information. The studies were carried out in unmanaged spruce forests in the highest elevations of Bohemian Forest, in both, the undisturbed areas as well as those affected by bark beetle outbreaks at different time periods. Combination of methods including culturing of fungi, enzymatic activity measurements or high throughput sequencing were used to describe the microbial communities, their distribution in space and time, and factors involved in shaping these communities in those...
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Actinobacteria communities in natural and anthropogenic environments
Faitová, Andrea ; Marečková, Markéta (advisor) ; Slaninová Kyselková, Martina (referee) ; Yurado Lobo, Valme (referee)
10 Abstract Actinobacteria are important bacterial group participating in various ecosystem processes particularly in the decomposition of complex organic compounds. Their abilities enable them to surviving in harsh conditions of oligotrophic habitats like lakes, deserts, cave walls or recalcitrant and resistant litter in soil, where Actinobacteria often dominate. Although certain biotic and abiotic factors were recognized to modulate Actinobacteria incidence in such habitats, the influence of anthropogenic pressure on their communities is scarcely known. The main objective of this thesis is therefore to determine differences of Actinobacteria communities under the direct (the human visitors changing microenvironment of caves, part 1) and indirect (climate change factors like altered precipitation or plant litter quality, part 2) anthropogenic influence in two habitats, plant litter in soil and cave walls, where Actinobacteria play important roles and dominate. In a first part of the thesis we monitored Actinobacteria communities in French limestone caves walls differently affected by humans (pristine versus anthropized caves). For identification of important species like potential pathogens or pigments producing Actinobacteria using amplicon sequencing of environmental DNA (Illumina MiSeq), we firstly used...
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Structure and function of microbial communities of montane spruce forest
Štursová, Martina ; Baldrian, Petr (advisor) ; Uhlík, Ondřej (referee) ; Slaninová Kyselková, Martina (referee)
Structure and function of soil microbial communities in montane spruce forest Martina Štursová Abstract Coniferous forests are spatially heterogeneous environments and represent an important ecosystem that acts as carbon sink under current climate storing large amounts of carbon in standing biomass or as soil organic matter. The formation of organic matter via decomposition of dead biomass and transformation of rhizodeposited organic compounds is primarily mediated by microbial community of forest topsoil. Despite growing insight into the composition of these soil communities, little is known about the microbes actually responsible for those transformation processes, about the drivers shaping these communities or their response to increasing numbers of severe disturbances. Studies presented in this thesis contribute to filling the information. The studies were carried out in unmanaged spruce forests in the highest elevations of Bohemian Forest, in both, the undisturbed areas as well as those affected by bark beetle outbreaks at different time periods. Combination of methods including culturing of fungi, enzymatic activity measurements or high throughput sequencing were used to describe the microbial communities, their distribution in space and time, and factors involved in shaping these communities in those...
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Combination of biochemical and high-throughput-sequencing approaches to study the role of Antinobacteria and fungi in the decomposition of plant biomass
Větrovský, Tomáš ; Baldrian, Petr (advisor) ; Slaninová Kyselková, Martina (referee) ; Tomšovský, Michal (referee)
Dead plant biomass is a key pool of carbon in terrestrial ecosystems. Its decomposition in soil environments is thus an essential process of the carbon cycle. Fungi are considered to be the primary decomposers in soil ecosystems because of their physiological adaptations and enzymatic apparatus composed from highly effective oxidative and hydrolytic enzymes. Many recent works show that in addition to fungi, bacteria may also play a significant role in lignocellulose decomposition and among bacteria, the members of the phylum Actinobacteria are often regarded to significantly contribute to cellulose and lignocellulose decomposition. This thesis is focused on the evaluation of the role that fungi and Actinobacteria play in dead plant biomass degradation. First, it explored mechanisms involved in degradation, in particular the enzymatic breakdown of major lignocellulose components as cellulose, hemicelluloses and lignin. Enzymatic apparatus of the saprotrophic fungus Fomes fomentarius was explored both in vitro as well as in vivo. Several Actinobacteria were isolated from soil and comparative experiments, investigating production of hydrolytic enzymes, were carried out to track the transformation of polysaccharides and lignin by these strains. To explain the roles of lignocellulose decomposers in...
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Secondary metabolite production in actinomycetes causing and suppressing common scab of potatoes
Komžák, Ondřej ; Bosáková, Zuzana (advisor) ; Slaninová Kyselková, Martina (referee)
This diploma thesis focused on screening for bacterial pathogens and antagonists suppressing common scab mainly caused by Streptomyces scabiei. Common scab affects some agricultural crops causing significant economical losses. Bacterial strains, mostly streptomycetes, were isolated from potato rhizosphere because they belong to most important producents of secondary metabolites and the causative agents of the disease are also members of this genus. The isolated bacteria were characterised by PCR amplification and sequencing of 16S rRNA gene to reveal their phylogenetic relationships. The ability of isolated strains to suppress growth of Streptomyces scabiei was tested by a simple co-cultivation experiment. The strains were tested by PCR for presence of specific genes for biosynthesis of thaxtomin A, a common virulence factor found in all described pathogens causing symptoms of this disease on the surface of affected tubers. Genes for synthesis of thaxtomin belong to pathogenicity island. Standard of phytotoxin thaxtomin A was used to optimize its analysis by mass spectroscopy for further in vivo and in vitro experiments. Phylogenetic analysis of strains harboring one of the genes necessary for thaxtomin A biosynthesis supported the hypothesis of sharing the pathogenicity island by horizontal gene...
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