Microbiology

obligatory courses

(in Polish) Dla studentów kierunku Bioinformatyki i Biologii Systemów

Classroom

The aim of the course is the presentation of basic information on prokaryotic microorganisms (bacteria and archaea), as well as on viruses and on methods of their investigation. The course includes: the structure and cell cycles of prokaryotes; their diverse metabolism (with emphasis on unique metabolic features); the reasons for their wide spread and their effect on other organisms and the abiotic environment. Basics of prokaryotic genetics and taxonomy, examples of the industrial use of microorganisms are also discussed as are viruses and their replication strategies. In the laboratory, they also learn basic microbiological techniques.

Course

General characteristics of the domains of Archaea and Bacteria. Basics of prokaryotic taxonomy. Characteristics of the main taxonomic phyla of bacteria (Proteobacteria, Firmicutes, Tenericutes, Actinobacteria, Cyanobacteria, Spirochaetes, Chlorobi, Chloroflexi) and archaea (Euryarchaeota, Crenarchaeota, Thaumarchaeota). Methods used in microbiological research. Structure of prokaryotic cells; differences between bacteria and archaea, gram-negative and gram-positive bacteria and bacteria belonging to various taxonomic phyla. Structure and functions of various cellular organelles. Bacterial genetics: the structure of bacterial genomes, the role of mobile genetic elements (plasmids, transposable elements, gene cassettes of integrons and bacteriophages) and horizontal gene transfer (conjugation, transformation, transduction; transfer of DNA by nanotubes, GTA and membrane vesicles) in variability of prokaryotes. Cell cycles of prokaryotes and the dormant forms of bacteria (endospores, cysts, mixospores, akinetes). Effect of pH, temperature and osmotic pressure on the growth of microorganisms. Extremophilic prokaryotes. Microbial forms in the natural environment - prokaryotic communities: consortia, biofilms, microbial mats. Quorum sensing. Metabolic diversity of prokaryotes – sources of energy, carbon, nitrogen, sulfur, phosphate and other biogenic elements, electron donors and acceptors. Growth factors. Trophic types of prokaryotes. Unique metabolic features of prokaryotes and archaea: chemolithotrophy (nitrifying bacteria and archaea, anammox bacteria, colorless sulfur bacteria, Fe(II) hydrogen and carbon oxide oxidizing bacteria), methanotrophy, nitrogen fixation, anaerobic respiration (nitrate respiration, sulfate and Fe(III) reducing bacteria and archaea, methanogenic archaea), the use of light by prokaryotes (including oxygenic and anoxygenic photosynthesis).

Effect of microorganisms on the abiotic environment (their role in the element cycling) and on other organisms (symbioses). Mutual relations between microorganisms; relations between microorganisms and macroorganisms. Human microbiome. Pathogenic bacteria - virulence factors (including bacterial toxins) and diseases. Prokaryotic and eukaryotic viruses - their structure, life cycles, classification; viral diseases. Infectious diseases - prevention and treatment. Mechanisms of bacterial resistance to antibiotics. The use of microorganisms in food and pharmaceutical industries, waste water treatment and bioremediation.

Laboratory

In the lab students work in small groups. The lab topics are partly connected with the course. They include the following subjects: aseptic technique and sterilization. Microbial media: characteristics, classification, preparation and selection for various purposes. Methods of inoculation of media and culturing methods. Isolation of microorganisms from different environments. Counting methods – direct microscopic count and viable count. Pure culture isolation with the use of direct and indirect methods. Characteristics of microbial cultures. Influence of environmental factors on bacterial growth. Morphology and structure of bacterial cells. Microscopic methods - preparation of smears and staining (simple and differential stains, including Gram stain); the hanging drop method. Bacterial metabolism – the source of carbon (carbon dioxide, high and low molecular weight organic compounds), nitrogen (including nitrogen gas); sources of energy (organic and inorganic compounds); trophic types of bacteria. Bacterial metabolism under aerobic and anaerobic conditions (fermentation and anaerobic respiration). Microbial water contamination - coliform test. Elements of bacterial genetics – conjugation. Basic techniques used in bacteriophage research.

Madigan M.T., J.M. Martinko „Brock Biology of Microorganisms”, XI ed., Prentice Hall, 2006 (and all subsequent editions of this book ).

Having completed the course and the lab the student:

Knowledge

• Knows the structure of prokaryotic microorganisms, as well as their dormant forms, and understands the cellular, biochemical, and genetic bases of their functioning (K_W05 Bl1)

• Knows the structural and metabolic diversity of prokaryotes and the unique features of this group of microorganisms (K_W10 Bl1)

• Knows the bases of structure, genetics and function of viruses, their role in nature and interactions between viruses and live organisms (K_W08 BI1)

• Knows the forms in which microorganisms are present in the environment as well as the causes of their wide spread presence in nature, and understands their influence on other organisms and the abiotic environment (K_W09 Bl1)

• Understands basic terminology categories of: biochemistry, microbiology, microbial genetics and environmental biology of microorganisms (K_W13 BI1, K_W02 Bt1)

• Knows general environmental determinants of life and the influence of environmental factors on the function of prokaryotic microorganisms and viruses (K_W14 BI1)

• Understands the importance of experimental work and knows basic laboratory techniques used in microbiological and genetic research, and is knowledgeable in occupational health and safety (K_W15 BI1, K_W16 Bl1, K_W21 Bl1, K_W04 Bt1, K_W09 Bt1)

• Is acquainted with the bases of prokaryotic taxonomy and basic applications of microbiology in social-economic life (K_W11 Bl1, K_W19 BI1, K_W01 Bt1, K_W05 Bt1)

Skills

• Uses basic microbiological techniques, and is able to explain them (K_U01 BI1, K_U01 Bt1, K_U08 Bt1)

• Is able to analyze the results of the experiments and discuss them (K_U04 BI1)

• Under the supervision of a scientific supervisor, is able to design and perform a simple experiment using the methods acquired; is able to propose methods for performing measurements (K_U06 Bl1, K_U04 Bt1, K_U05 Bt1)

• Is able to use available information sources, including electronic media (K_U03 Bt1, K_U06 Bt1)

• Is able to learn on his/her own microbiological topics indicated by the instructors teaching the course (K_U10 Bl1)

Social awareness

• Can work as part of a team and is open to new ideas (K_K01 Bl1, K_K04 BI1)

• Understands the need for educating the public about the latest achievements in microbiology and biotechnology and is able to pass this knowledge in an intelligible manner (K_K06 Bt1)

• Is careful and critical about mass-media information concerning microbiology and biotechnological achievements (K_K08 Bl1)

• Is responsible for the safety of his/her work and for the equipment used; respects his/her work and the work of others (K_K05 Bl1, K_K03 Bt1)

• Understands the principles of ethical conduct at work and in general (K_K05 Bt1)

• Is willing to engage in continued education and acquire up-to-date scientific knowledge (K_K07 BI1, K_K04 Bt1)

To pass the course (exercises plus lecture) it is necessary to pass the exam.

Detailed conditions for passing the classes:

Laboratory classes (exercises) are classified as students:

1. Availability at the price of 85 percent of classes;

2. Worked in the classroom in social methods that had skills, skills and social skills throughout the social activities.

The exam will include practice and lecture material, it will consist of test questions and semi-open and open questions. To complete the course, it is necessary to obtain 51% of the points

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