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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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Vegetation of post-mining sites determines soil microbial community structure and soil processes
Urbanová, Michaela ; Baldrian, Petr (advisor) ; Chroňáková, Alica (referee) ; Bárta, Jiří (referee)
This thesis consists of three published articles and one submitted article, and is focused on the evaluation of the effects of vegetation on soil microbial communities and processes on brown coal post-mining sites. The research sites served as deposits of infertile waste material, by which the indigenous vegetation has been buried and thus the whole ecosystem was destroyed. The restoration of the ecosystem structure and functions at these areas was based on the improvement of biotic and abiotic properties of excavated soil substrate either using assisted afforestation or using spontaneous plant succession. In this work, biochemical and molecular techniques were employed in order to testify the effect of the vegetation on soil microbial processes, structure of soil microbial communities and to follow the chemical changes in the litter composition during its decomposition. Litter chemistry, enzymatic activities and microbial biomass were followed by standard biochemical procedures including spectrometry and HPLC. Bacterial microarray was used for assessing the composition of bacterial communities in the soil of successional plots. 454-pyrosequencing was employed for detailed identification of fungal and bacterial community composition in the litter layer and the bulk soil under different tree...
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Molecular biology of soil fungi participating in litter decomposition in forest ecosystems
Voříšková, Jana
In forest ecosystems, substantial part of carbon enters soil in the form of plant litter. The decomposition of litter and soil organic matter represents an important process affecting nutrient cycling and carbon balance in soils. Fungi are considered the primary decomposers in terrestrial ecosystems due to the production of wide range of extracellular enzymes that allow them to attack the lignocellulose matrix in litter. Even if fungi represent key players in organic matter decomposition, the information about the structure and diversity of their communities is still limited and the roles of individual fungal taxa in forest soils remain unclear. This Ph.D. thesis focused on the characterization of fungal communities in forest soils and their potential to decompose plant litter. The method for in-depth analysis of complex microbial communities from environmental samples was established and used. In addition, single eukaryotic functional gene was analysed in soil for the first time at a depth that allowed reliable estimation of diversity. It was demonstrated that microbial community composition differs among horizons of forest soil profile. Despite similar diversity, significant differences in microbial community composition were observed between the DNA and RNA. Several microbial groups highly...
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The importance of bacteria for deadwood decomposition in forest ecosystems
Némethová, Ema ; Baldrian, Petr (advisor) ; Bárta, Jiří (referee)
Forest ecosystems represent a huge reservoir of carbon. The volume of deadwood in managed forests is in the tens of m3 h-1, while unmanaged forests have the volume of deadwood in hundreds of m3 ha- 1. Deadwood is a substrate with a high potential for decomposition. However, deadwood is a specific habitat that has a high C/N ratio and changes due to ongoing decomposition. The C/N ratio decreases with increasing decay time. In addition to the C/N ratio, the pH also changes during the wood pulping process, due to the decomposition of plant biomass by fungi. Moreover, deadwood has a high impermeability. The main decomposers of dead wood are fungi. In addition to them, bacteria, which are numerous in deadwood, also contribute to decomposition. Bacterial communities that decompose woody biomass are affected by these factors, and their distribution is also affected by dead tree species. The aim of this study was to describe how bacterial communities associated with deadwood change during decay. The most significant factor in the decomposition by bacterial communities is the time of decay. Bacteria found in short-decaying wood (less than 16 years old) are more diverse than those found in long-decaying wood. Methylotrophic bacteria and N-fixing bacteria are common in short-decaying wood as well. N-fixing...
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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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Effects of plants on the structure, function and diversity of bacterial communities
Havlíčková, Petra ; Baldrian, Petr (advisor) ; Kopecký, Jan (referee)
Vegetation is known to influence the composition of microbial communities. Bacteria can act as roots symbionts or be involved in the decomposition of plant biomass. They can be influenced by soil chemistry but also by plant exudates. Some plants produce targeted exudates to attract specific bacteria to their roots. Bacteria associate with plants frequently but the effect of plant diversity on bacterial communities on their roots and in the surrounding soil remains unclear. The aim of this work was to describe the relationship between the diversity and community composition of bacteria and the diversity of vegetation in forest and grassland ecosystems. The study areas were selected to represent a gradient of vegetation in Bohemian Forest NP and in White Carpathian flowery grasslands. I hypothesized that the diversity and evenness of bacterial community increase with increasing plant diversity. The composition of bacterial community was characterized by 16S rRNA sequencing. The composition of vegetation was determined by phytocenological relevées and by molecular markers trnL. In grassland ecosystem, there was a positive relationship between plant and bacterial diversity only in shoots. The space and vegetation were identified as an important drivers of bacterial community composition in shoots. The...
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Vegetation of post-mining sites determines soil microbial community structure and soil processes
Urbanová, Michaela ; Baldrian, Petr (advisor) ; Bárta, Jiří (referee) ; Chroňáková, Alica (referee)
Vegetation of post-mining sites determines soil microbial community structure and soil processes Mgr. Michaela Urbanová Abstract The aim of this thesis, which consists of four published articles, was to investigate the effect of vegetation on soil microbial communities and processes in de novo developing soil substrate on the brown-coal spoil heaps in the surrounding of city Sokolov. Spoil material - soil clayey substrate, which had been gradually mined from the opencast brown coal mine, stratified onto spoil heaps and reclaimed by assisted afforestation with selected tree species or left for spontaneous plant succession, changes its biotic and abiotic characteristic in the course of time and particularly under the influence of plants. Changes of spoil substrate characteristics are related to the growth of plant roots and particularly also to the production of plant biomass, which is decomposed gradually and takes part of soil, where participates to soil organic matter. The process of plant dead materials decomposition and transformation is the function of the activity of soil organisms and among them notably soil microorganisms. Moreover, the presence of many of them is closely related to the presence of vegetation, whose symbionts or pathogens are. The exact mechanisms of the plant-microbes interactions...
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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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Molecular biology of soil fungi participating in litter decomposition in forest ecosystems
Voříšková, Jana ; Baldrian, Petr (advisor) ; Gryndler, Milan (referee) ; Koukol, Ondřej (referee)
In forest ecosystems, substantial part of carbon enters soil in the form of plant litter. The decomposition of litter and soil organic matter represents an important process affecting nutrient cycling and carbon balance in soils. Fungi are considered the primary decomposers in terrestrial ecosystems due to the production of wide range of extracellular enzymes that allow them to attack the lignocellulose matrix in litter. Even if fungi represent key players in organic matter decomposition, the information about the structure and diversity of their communities is still limited and the roles of individual fungal taxa in forest soils remain unclear. This Ph.D. thesis focused on the characterization of fungal communities in forest soils and their potential to decompose plant litter. The method for in-depth analysis of complex microbial communities from environmental samples was established and used. In addition, single eukaryotic functional gene was analysed in soil for the first time at a depth that allowed reliable estimation of diversity. It was demonstrated that microbial community composition differs among horizons of forest soil profile. Despite similar diversity, significant differences in microbial community composition were observed between the DNA and RNA. Several microbial groups highly...
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Molecular biology of soil fungi participating in litter decomposition in forest ecosystems
Voříšková, Jana
In forest ecosystems, substantial part of carbon enters soil in the form of plant litter. The decomposition of litter and soil organic matter represents an important process affecting nutrient cycling and carbon balance in soils. Fungi are considered the primary decomposers in terrestrial ecosystems due to the production of wide range of extracellular enzymes that allow them to attack the lignocellulose matrix in litter. Even if fungi represent key players in organic matter decomposition, the information about the structure and diversity of their communities is still limited and the roles of individual fungal taxa in forest soils remain unclear. This Ph.D. thesis focused on the characterization of fungal communities in forest soils and their potential to decompose plant litter. The method for in-depth analysis of complex microbial communities from environmental samples was established and used. In addition, single eukaryotic functional gene was analysed in soil for the first time at a depth that allowed reliable estimation of diversity. It was demonstrated that microbial community composition differs among horizons of forest soil profile. Despite similar diversity, significant differences in microbial community composition were observed between the DNA and RNA. Several microbial groups highly...
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