The long-term cattle impact on soil methanotrophs was investigated at cattle overwintering area located at the ecofarm in the South Bohemia. Four sets of soil samples were sampled in spring and fall of 2009 and 2010. Differences in methanotrophic community structure among experimental sites and were investigated by DGGE and MISA. Real-Time PCR was used for estimation of quantity of Type I methanotrophs. The CARD-FISH method was used to estimate the percentage shared and cell counts of Type I and Type II methanotrophs among all prokaryotic cells. Substantial part of the thesis was focused on optimization of methods used.

During this PhD. thesis, the importance of methane-oxidizing bacteria (methanotrophs) and their ecological demands were studied on the longitudinal transect along an important European river - the River Elbe. However, it was necessary to adjust methodologies for precise measurements of methane oxidation in such a variable aquatic environment. Based on laboratory experiments and field measurements, several key methodological recommendations for future planning of methane oxidation rate estimations in an unknown environment have been identified or specified. In line with the variability of the river habitats, considerable heterogeneity was also found in the obtained data on methane concentration and methanotrophical activity. Probably, some of the most important information gathered during many field sampling campaigns is that sites with the highest methane concentration usually showed a very low activity of methanotrophic bacteria (resulting in higher methane emissions). These sites are predominantly human modified sections of the river, such as locks, weirs, harbors and canals. On the contrary, the free-flowing parts of the river, modified only by groynes, showed low level of methane concentration. And so groynes could represent a more effective solution and "natural-close" habitats of navigability of rivers.