Syllabus
1. Microbial ecology - introduction, microorganisms, role in ecosystem. State of ecology of microorganisms in comparison with general ecology. History of microorganism ecology, revolutionary approaches in recent decades. Microorganisms in laboratory and in nature - differences. Small scales and niches, habitats of microorganisms, functional groups, role in ecosystem. Characteristics of ecological importance of main groups of microorganisms, viruses in ecosystem. Difficulties of species definition in bacteria and archea, ecotype, speciation. Problems with cultivation of microorganisms, reasons and possible solutions.
2. Microorganisms and environment. Law of tolerance and law of minimum, effects of physical factors on multicellular organisms and microorganisms, comparison. Extremophiles, environmental factors in nature and laboratory. Temperature - division into groups based on optimal growth temperature, characteristics of cold and high temperature environments, adaptation of cytoplasmic membranes and enzymes. Oxygen, toxic forms of oxygen, the relationship of microorganisms to oxygen and the type of energy metabolism. Redox potential of the environment and metabolism. Water, water activity, osmophilic and halophilic organisms and their environment and adaptation, cell drying, endolithic bacteria. pH environment, acidophilic and alkalifile organisms, problems with preservation of intracellular pH.
3. Ecophysiology of microorganisms. Energy metabolisms and their combinations in microorganisms. Adaptation to starvation to source C, N, S, P. Stringent response, catabolic repression. Long-term adaptations to starvation, surface enlargement, dwarf cells. Types of life strategies in prokaryotes as optimal use of resources. Kinetics of microbial population growth in ecosystem, K and r strategies. Movement: whips, swarming, gliding, gas vacuoles, types of taxis. Growth of microorganisms on surfaces - biofilms, advantages of life in biofilm, adhesion, balance in biofilm.
4. Metabolism of microorganisms Gradient of redox potential of the environment and types of metabolisms. Oxygen and oxygenase reactions, aerobic respiration. Anaerobic respiration of nitrate and denitrification, other electron acceptors for anaerobic respiration (iron and other metal ions, TMAO, DMSO, fumarate). Fermentation as incomplete oxidation of carbon compounds. Ways of further oxidation of fermentation products: reduction of iron and manganese ions, secondary syntrophic fermentation, sulfate respiration and methanogenesis as the completion of mineralization in an anaerobic environment. Chemolithotrophy - oxidation of sulphate and ferrous ions depending on pH and redox potential, nitrification, anammox, hydrogen oxidation as an alternative to chemoorganotrophy. Phototrophy - spectrum of light in different environments, anoxygenic and oxygenic photosynthesis, photopigments and absorption maxima, groups of phototrophic organisms and their environment.
5. Biogeochemical cycles - cycle of carbon, nitrogen, sulfur, iron. Sources of carbon in the environment, animal and plant polymers, reasons for slow degradation, humic acids. Phototrophy of prokaryotes and primary production, carbon dioxide and methane as greenhouse gases, competition for hydrogen in anaerobic environment, metabolisms in rocks far below the earth's surface. Nitrogen: environmental sources, nitrogen fixation, ammonification and assimilation of nitrogen, DNRA, denitrification and nitrification. Sulfur: environmental sources, assimilation and mineralization, importance of chemolithotrophic oxidation of sulphane and respiration of sulphate, possibility of primary production by means of chemolithotrophy on the ocean floor. Iron: sources in the environment, its redox cycles in neutral and acidic pH, mine water acidification.
6. Function of microorganisms in the environment and methods of their study Ecosystem functions: importance of individual species and microbial communities. Methodological approaches in ecology of microorganisms. Cultivation and isolation of pure cultures of microorganisms from nature, enrichment and selection methods, physiological characterization of cultures. Determination of microbial biomass. Respirometry and determination of enzyme activities. Measurement of metabolic activities and metabolic diversity of microorganisms in natural environment.
7. Diversity of microorganisms. Microorganisms in the environment - (in) cultivation; means of description of species and metabolic diversity. Limits of possibilities and accuracy. Genes used for taxonomic and functional description of community composition and dynamics, sequence database. Isolation of environmental DNA, use of molecular methods for analysis of gene diversity. Metagenome sequencing, new methods of next-generation sequencing and their use in microbial ecology.
8. Interactions of microorganisms. Life strategies and their consequences. Reproduction and distribution of K, r. Disturbance and reaction to stress situations. Biorhythms, migration, diversity, distribution and their context in relation to population and community. Basic trophic relations. Intra and interspecific competition, predation, decomposition, parasitism, symbiosis and mutualism, communication between microorganisms. Secondary metabolites and their function, competition or communication?
9. Fungi in ecosystem. Basic physiological characteristics and ecological specifics of fungi and fungal microorganisms. Growth of hyphal microorganisms, nutrient uptake. Saprotophic and fungi, decomposition of organic substances and cellular digestion by enzymes. Symbiosis - mycorrhizal fungi and lichens. Mushroom adaptation to environmental conditions. Interaction of fungi with other organisms in the ecosystem.
10. Microorganisms in soil. Factors influencing and limiting the life of microorganisms in terrestrial ecosystems. Soil structure as an environment for coexistence of microorganisms. niches, redundancy, succession. Soil degradation. Stability. Examples: relationship between diversity and activity - denitrifying bacteria; seasonal changes of the bacterial community; functional redundancy of the bacterial community depending on the degree of soil amelioration.
11. Microorganisms in fresh water. Factors influencing and limiting life of microorganisms in aquatic environment. Processes prevailing at different depths of standing waters and in different phases of flowing water. Microbial trophic loop. Examples: seasonal dynamics of microbial communities in flowing water and sediment; vertical and seasonal variability of bacterioplankton groups in still fresh water; representation, activity and community structure of methane oxidizing bacteria in the water column.
12. Genetic equipment of microorganisms Genetic equipment of microorganisms - genomics; information resulting from the sequencing of bacterial genomes: share of shared genes, environmental specific gene equipment, occurrence and organization of genes spread horizontally. Natural diversity of enzyme equipment and adaptability. Communication, production of biologically active substances. Adaptation to anthropogenic effects, antibiotic resistance. Approaches to the study of horizontally shared genes in the environment: metagenome libraries, enrichment methods and clone selection.
Annotation
The lecture shows the role of microorganisms in ecosystems where these organisms are an essential and irreplaceable component. It discusses physiological and molecular biological methods of microbial communities analysis, role of microorganisms in biogeochemical cycles, concrete examples of environment and role of microorganisms in it.
The lecture is based on basic knowledge of biochemistry, molecular biology, ecology and microbiology. It is intended for students of bachelor study programs in the Biology study program, or for follow-up master students.