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...

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...

This Master's thesis is focused on problems of modern agriculture. Current agriculture is facing many problems that already exceed the production area. Among these belong soil degradation caused by inappropriate agricultural practices, erosion phenomena, etc. Both developed and developing countries have experienced these problems. This soil degradation is mainly caused due to lack of soil organic matter content. Current agriculture therefore faces the issue of how to solve this problem. A simple solution is based on increasing the content of the soil organic matter in arable land. In the first part, this thesis describes various problems of modern agriculture and also suggests possible solutions. Regarding to content of soil organic matter, the thesis proposes solutions in the form of compost application into the soil. Besides compost, thesis presents an alternative organic fertilizer Jatropha seed cake. Jatropha seed cake is produced as waste after oil extraction from seeds of Jatropha curcas L. In the first part both of these substrates are further described, along with characterization of Jatropha curcas L. The aim of this thesis was to compare the fertilizing effects of Jatropha seed cake with compost. For this purpose, a pot experiment was conducted under controlled laboratory conditions. Application effect of Jatropha seed cake and compost on soil and plants was monitored at selected soil indicators. The results describe the impact of Jatropha seed cake and compost application on production of plant biomass, soil hydrophobicity rate, mineral nitrogen mobility and soil microbial activity.

The microbiological quality of raw milk from the perspective of the health of dairy products is one of the most important features. The amount of microorganisms is influenced by storage temperature and time of milk. In the thesis was observed dynamics of total bacteria count (TBC) in raw milk depending on the selected factors (months, seasons, point of collection, the length of storage). To life of microorganisms contributes warm weather. The largest increase in TBC was observed in the months of April and May to 108 thousand /1 Ml. It is necessary to place great emphasis on rapid cooling of milk (max 150 min.) to the desired temperature (8 °C). Increase TBC could be caused by long transportation time of sampling raw milk from a milk vending machine to evaluate the quality and microbiological indicators. In the second part of the thesis are compares the quality and microbiological characteristics of raw milk from selected milk vending machines. When evaluating the samples taken from the farm, average values of TBC were higher (43 thousand/ml) compared to samples collected from the milk vending machines (6 thousand/ml). Reason of higher values from farms could be caused by poor hygiene of the milk and his secondary contaminations. In contrast, the average results from samples taken from the milk vending machines were more than excellent. That´s shows tight control of cooling milk during transportation from the farm to the milk vending machine. Next reason better results is right cooling and to maintain a constant temperature in the grades (from 0.5 to 1 °C). That´s temperature, which prevents the growth of microorganisms.

The aim of the study was to evaluate the total viable count and detects each microorganism by the use of mass spectroscopy. In the period of June to December 2017 35 samples of pasteurized milk from two vending machines (Hodkovice, Suchdol) were tested. For comparison samples were divided to warmer season (June-Septemeber) and colder season (October-December) sampling. The total amount of microorganism was determined in each sample of milk and total viable count was estimated by the use of mass spectroscopy MALDI-TOF. The total viable count in the tested pasteurized milk were from 3,27 log KTJ/ml up to 7,35 log KTJ/ml. The mass spectroscopy detected 210 microorganisms belonging to 20 families of gram-positive and gram-negative bacteria and one species of eukaryot organism. The most often identified species belong the Enterobacteriaceae family.

Graduation theses were inquired into question of presence of total bacteria count (TBC) in four selected cattle-raising. The breeds differ from each other with technology of lairege and milking, predipping, grazing and herd size. The first was lairage in stanction housing and in-stall milking pipeline system and embodied average values TBC from 10 {$\bullet$} 103 {$\bullet$} ml-1 till 179 {$\bullet$} 103 {$\bullet$} ml-1. The second breed was lairaged in loose grate without littered housing and got milking parlour and embodied average values TBC from 5,5 {$\bullet$} 103 {$\bullet$} ml-1 till 68,75 {$\bullet$} 103 {$\bullet$} ml-1.The third and the fourth breeds were lairaged in loose cubicle littered housing and got milking parlour and embodied average values TBC from 5 {$\bullet$} 103 {$\bullet$} ml-1 till 34,33 {$\bullet$} 103 {$\bullet$} ml-1. There was not statically conclusive difference in analysis of total bacteria count on level - significance P < 0,05 between lairage in stanction littered housing and in-stall milking pipeline system and lairage in loose cubicle littered housing and milking parlour and lairage in loose cubicle littered housing and milking parlour, when the Students test was used. The stud with lairage in loose grate without littered housing and milking parlour had the top microbial contaminaton of milk. It had serious defections of hygiene lairage and milking. It succeeded to significant differences in value TBC in bulk milk sample on level - significance P < 0,05.

The aim of this thesis is to monitor how the amount of water (water activity) affects the amount of microorganisms is selected packaged meat products from the point of view standards, which specify their specific requirements for the health safety of these products. The first part of this work describes various types of packaging materials of meat products, the microorganisms that occur in them and the definition of water activity. The second part describes the actual measurement of water activity and the measurement of the occurrence of microorganisms and coliforms, from selection of suitable meat products, their types of packaging, sample preparation and evaluation of measured methods. The results showed, that the activity of water affects the occurrence of microorganisms and coliforms, in that the higher the activity of water, the higher microorganisms presence.

Raw milk is one of the most monitored product not only in terms of microbial, but also in terms of technology, chemistry and sensory. The aim of the thesis was the examination of the influence of cold chain interruptions on dynamic of total bacteria count (TBC) in raw cow milk. The results show that the temperature and time have a significant impact on TBC. The samples stored during the first three hours of experiment at 15 °C showed (in time 0 - 27 hours) a continuous growth with changing dynamic (5.13, 6.66, resp. log CFU/ml). The samples stored at 30 °C showed a significant increase, however there was a decrease between an hour of 25th and 26th (6.88, 6.69, resp. log CFU/ml). An hour later another increase was found (to 7.37 log CFU/ml). The samples stored at 6 °C showed the lowest values of TBC, although an increase was found after 24 hours (5.87 log CFU/ml). The second part of the thesis was an evaluation of the questionnaire survey among people consuming raw cow milk from a vending machine. The survey showed that more than a half of respondents (88%) interrupt the cold chain for no more than an hour. Then it was found that 75% of respondents do not overcook raw milk. The consumers appreciate the taste of raw milk (35%), freshness (19%), quality (16%), and a nutritional value (12%).

Charles University Faculty of Pharmacy in Hradec Králové Study program: Pharmacy Candidate: Jana Roubalová Consultant: RNDr. Klára Konečná, Ph.D. Title of thesis: Optimization of methods for sensitivity evaluation of biofilm-forming microbial agents towards substances with antimicrobial potential Background: The aim of this diploma thesis was to optimize the methodical approach to the production of yeast biofilms in vitro on the so-called pegs and the walls of the wells of the 96-well panel. This biofilm formation system should be an analogous approach to the commercially available Calgary Biofilm Device. 10 strains of Candida yeast and 4 different culture media (nutritionally poor / rich) were used to optimize the methodology. Both the reference strains and the clinical isolates were among the yeast strains tested. Methods: The ability to form yeast biofilms by different strains in different culture media was evaluated by the approach of fixation, staining of the formed biofilms by crystal violet and extraction and spectrophotometric measurement of the intensity of the extracted color. Results: Individual strains, after cultivation in different media, were categorized according to their ability to form biofilm. Larger yeast adherence occurs in the wells than on pegs where the yeast adhered very...

The goal of the graduation theses was a comparison of the hygenic quality of raw cows milk, it was expressed by the value of total bacterial count (TBC) and somatic cells count (SCC) in four breeds of milking cows using only postdipping (3 breeds) in comparison with breed using predipping and postdipping. The breeds differed in technology of lairage and milking procedures, grazing and the size the herd. During two seasons 2006 till 2007 was discovered that the breeds using predipping and postdipping had significantly less average values of TBC (9,46.103.ml-1) in comparison with the breeds using only postdipping (15,97.103.ml-1), the difference was statistically significant (P = 0,007) on the level of significance P < 0,05. Also it was shown that SCC were below averages levels with using predipping and postdipping (293,47.103.ml-1) in comparison to breeds using only postdipping (312,06.103.ml-1), the difference was also statistically significant (P = 0,01) on the level of significance P < 0,05.