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Analysis of secondary metabolites from Streptomyces by Raman spectroscopy in vivo
Mikulová, Adéla ; Petříčková, K. ; Bobek, J. ; Chroňáková, Alica ; Samek, Ota ; Pilát, Zdeněk
The work deals with the study of Raman spectra of secondary metabolites of bacteria of the genus Streptomyces, especially polyene antifungal agents. Purified isolates and commercial standards of these compounds were used to obtain reference spectra from which spectral markers characterizing specific details of the chemical structure were derived. Verification of the observed markers was performed using in silico Raman spectra predictions. Subsequently, these findings were used for the spectroscopic characterization of the composition of secondary metabolites in vivo, directly in bacteria growing on a solid medium. The developed methodologies will help to optimize the conditions for the biotechnological production of antibiotics.
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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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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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Diversity of the soil microbial community and its functional aspects in man-influenced environments
CHROŇÁKOVÁ, Alica
Diversity of the soil microbial community and its functional aspects were investigated in man-influenced environments, such as colliery spoil heaps in post mining sites and upland pasture used for outdoor cattle husbandry. The study was based on the cultivation of bacteria and streptomycetes as well as culture-independent approaches. Cultivated bacteria and streptomycetes were characterized by phenotypic and genotypic means. The culture-independent approaches were based on an analysis of environmental DNA in terms of both qualitative and quantitative parameters.
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Culture Collection of Soil Actinomycetes in the Institute of Soil Biology BC ASCR, v.v.i. České Budějovice
Krištůfek, Václav ; Chroňáková, Alica ; Elhottová, Dana ; Petrásek, Jiří ; Němec, Jan
The Culture Collection of Actinomycetes in České Budějovice (CCACB) was established in 2006 that serves as a depository for cultures of soil actinomycetes. The cultures can be used for research, industrial applications, education and general scientific interest. Cultures are preserved mainly in glycerol or freeze-dried conserves. CCACB will offer strains of actinomycetes, namely streptomycetes (more than 900 cultures at the present moment), in catalogue of cultures www.upb.cas.cz, www.actinomycetes.cz.
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Detection of microorganisms in the soil using CARD-FISH (Catalyzed Reporter Deposition - Fluorescence in situ hybridization)
Krištůfek, Václav ; Kasalický, Vojtěch ; Chroňáková, Alica ; Elhottová, Dana ; Němec, Jan
CARD-FISH protocol (Catalyzed Reporter Deposition - Fluorescence in situ Hybridization) for detection of soil microbial community composition was successfully established in the Institute of Soil Biology. CARD-FISH is the relatively new molecular biology tool permitting to quantify distinct groups of microorganisms by hybridization of specific oligonucleotide probes. Compared to classic FISH-protocol the probe-attached enzyme amplifies the fluorescent signal and enables to detect nearly all microorganisms in soil or in organic compounds. As the first, we used this method to determine the bacterial community composition of a dated layer of guano-heap from Domica Cave (Slovak Carst National Park, Slovakia). We quantified the percentuel composition of Archaea, Eubacteria (.i.Planktomycetales, Verrucomicrobiales./i. included) and major bacterial groups (Actinobacteria, proteobacteria, .i.Cytophaga-Flavobacter./i.-Bacteroidetes, Sphingobacteria).
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Soil microorganisms as controllers of methane emission from soils
Elhottová, Dana ; Němcová, Anna ; Chroňáková, Alica ; Šimek, Miloslav
The pilot study on functional microbial groups responsible for methanogenic and methanotrophic processes in soil of specific model ecosystem – the cattle overwintering pasture was given. The enrichment by methanogenic archaea was shown in soils strongly impacted due to cattle pasture. The increased methanogenic abundance was accompanied by increased abundance of methylotrophic bacteria. Nevertheless, the ratio of methylotrophic to methanogenic microorganisms was significantly higher in the control soils without cattle impact in comparison to the cattle-impacted soils.
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Nitrogen and carbon transformation processes in soil in permanent grasslands - research in cattle overwintering area
Šimek, Miloslav ; Hynšt, Jaroslav ; Čuhel, Jiří ; Elhottová, Dana ; Chroňáková, Alica ; Němcová, Anna ; Jirout, Jiří ; Krištůfek, Václav
Agricultural soils represent a significant source of greenhouse gases (carbon dioxide, nitrous oxide and methane). Pasture soils and especially overwintering areas receive large amounts of nutrients as animal excrements. Together with other effects, this creates good conditions for high rates of nitrogen and carbon transformations, and also for substantial losses in the form of gaseous metabolites. This paper informs on research of a specific model ecosystem – the cattle overwintering area. Research is focused either on the structure of soil microbial community and on its activities including the formation of gases in, and their emission from the soil to atmosphere.
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