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Microbiology in environment protection

General data

Course ID: 1400-113MIKwOS Erasmus code / ISCED: 13.4 / (0511) Biology
Course title: Microbiology in environment protection Name in Polish: Mikrobiologia w ochronie środowiska
Department: Faculty of Biology
Course groups: Requisite subjects for second-year students of Environmental Protection
ECTS credit allocation (and other scores): 6.00
Language: Polish
Type of course:

obligatory courses

Prerequisites (description):

Students of the Faculty of Biology of the University of Warsaw must have the first year of the first level programme (Bachelor's) completed. Others are expected to have knowledge of biology on advanced secondary school level.

Short description:


Basic characteristics of microorganisms and viruses in different environments including environments contaminated and degraded. The structure and physiology of prokaryotic cells. Adaptation of microorganisms to the environment. Measurements of microbial activities. Application of unique metabolism and activity of microorganisms for environment protection: in sewage treatment technologies, bioremediation and restoration of degraded environments.


Basic microbiological techniques. Isolation of microorganisms from various environments. Morphology and structure of bacterial cells. Bacterial physiology – metabolic activity influencing environment. Bacterial contamination of water and food. Influence of environmental factors on microflora.

Visualization and identification of microorganisms – epifluorescence microscopy, computer image analysis. Measurements of microbial activities. Monitoring of toxic cyanobacteria by molecular and immunoenzymatic analyses.

Full description:

Lecture – part one:

1. General characteristics of microorganisms: taxonomy, biodiversity, common and unique features, dissemination in the environment, contribution to biosphere transformation. Viruses.

2. The structure of prokaryotic cells and its role in adjustment to environment.

3. Metabolic diversity of microorganisms – part 1

energy and carbon sources, the sources of other biogenic elements, nitrogen fixation, fermentations, aerobic and anaerobic respiration

4. Metabolic diversity of microorganisms – part 2,

chemolithoautotrophy and methylotrophy

5. Influence of physical and chemical environmental factors on microorganisms. Extreme environments.

6. Expansion strategies of microorganisms: bacterial taxes, quorum sensing, biofilms, mats, relations between microorganisms and micro - and macroorganisms.

7. Water and food bacterial contamination. Mechanisms of bacterial pathogenesis. Antibiotic resistance prevalence in bacteria.

Lecture - part two:

1. Methods used in environmental microbiology

2. Basic characteristics of terrestrial, aquatic and degraded ecosystems

3. Relationships between environment and microorganisms; the influence of environmental factors on microorganisms and the modifications of environments by microorganisms

4. Role of microorganisms in nitrogen, phosphorous and carbon cycling (A)

5. Role of microorganisms in nitrogen, phosphorous and carbon cycling (B)

6. The application of unique metabolism and activity of microorganisms for environment protection of and in technologies used to remove nutrients and anthropogenic pollutants (waste water treatments, bioremediation of soils, restoration of degraded ecosystems)

7. Microorganisms as a threat for human health and other organisms in various environments: cyanobacteria and algae as a source of toxins, pathogenic microorganisms.

Laboratory – part one; Bacterial Genetics Department

First four lab classes constitute a logical sequence aimed at comparison of quantitative and qualitative composition of microorganisms in natural environments.


1.1 Basic microbiological techniques - sterilization, microbial media, pure culture isolation, estimation of number of bacteria (viable/total counts).

1.2. Isolation of bacteria and fungi from different environments – water, soil and air, comparison of quantitative and qualitative composition of microorganisms (saprofits, thermophiles, psychrophiles, Actinobacteria, moulds, spore-forming and hemolytic bacteria)


2.1.Isolation of pure cultures of microorganisms from different natural environments.

2.2 Antibiotic production by isolated Actinobacteria.

2.3 Utilization of organic compounds (cellulose, starch, lipids, proteins) and nitrogen sources transformation by microorganisms from water and soil.


3.1 Aerobic and anaerobic metabolism (intensity of respiration – reduction of methylen blue, fermentations, catalase activity, microaerophilic conditions)


4.1 Morphology and structure of bacterial cells (staining procedures, wet mounts of living cells; endospores and capsule).


5.1 Bacteriologic examination of water (coliform test) and food (isolation of Campylobacter from chicken meat).


6.1 Bacterial cultures and factors influencing the growth rate (UV radiation, antibiotic resistance, heavy ion influence and transformation of arsenic).


7.1 Discussion about results from previous lab class.

7.2 Summary and consultations.

Laboratory – part two; Microbial Ecology Department

1. Microorganisms from various environments: identification in light and epifluorescence microscope with image analysis system

2. i 3. Microbial processes and environmental biotechnology: respiration and utilization of organic compounds in relation to changes of number, biomass and morphology of heterotrophic bacteria: BZT7, DOC and microscopic analyses

4. i 5. The application in environmental biotechnology of assimilation and transformation of various organic and mineral C, N and P compounds by microorganisms – monitoring of microbial metabolic processes using chemical and biological analyses (spectrocolorymetry, fluorymetry, and microscopic techniques)

6) Activated sludge – use of microbial processes in wastewater treatment plants; the model system of wastewater treatment, efficiency of the model system in removal of C, N and P from sewage

7) Detection and monitoring of toxic cyanobacteria by means of microscopic and molecular analyses, detection of cyanotoxins in aquatic environments (ELISA)

8) Summary


1) Madigan M.T., J.M. Martinko „Brock Biology of Microorganisms”, XI wydanie, Prentice Hall, 2006 and all next editions.

2) Wetzel R. Limnology. Lake and river ecosystems. Academic Press, 2001.

Learning outcomes:


Knows basic terminology of microbial ecology and basic ecological processes. K_W02 Os1

Knows basic laboratory methods, visual and measurement techniques applied in the analysis of natural phenomena. K_W03 Os1

Knows the most important problems of nature conservation and knows their relationships with other disciplines. K_W04 Os1

Knows the global environmental problems and the use of ecology in the practice of conservation and development of the environment. K_W05 Os1

Describes actual problems of civilization associated with the necessity of reconcile economic development with environmental protection requirements and identifies key threats of the state of atmosphere and aquatic and land environments. K_W06 Os1


Is able to conduct microbiological observations and the experiments independently as well as in a group. Knows how to interpret the results applying current knowledge. K_U01 Os1

Appplies basic statistical and bioinformatic methods to describe the results of the experiments. K_U02 Os1

Applies basic analytical techniques used to estimate the condition of the environment. K_U03 Os1

Is able to interpret the appropriate indexes describing the condition of the environment. K_U04 Os1

Evaluates causes of the endangerment of natural environment and diversity of microorganisms and is able to indicate the appropriate scientific methods and techniques, which ensure restoration of the microbial communities in the environment. K_U06 Os1, K_U10 Os1

Applies basic methods of collecting microbial samples from a different environments for microbiological and biochemical analyses allowing the estimation of condition microbial communities. K_U07 Os1

Is able to recognize and explain, using different scientific publications, basic problems in a natural resources management. K_U08 Os1


Feels responsibility for the safety during experiments in microbiological laboratory. K_K01 Os1

Feels the need of constant education and updating the knowledge concerning environmental microbiology necessary in the realization of professional projects in nature preservation. K_K02 Os1

Recognizes the necessity and feels the need of applying and respecting the rules of sustainable development in the everyday life and economy. K_K04 Os1

Exhibits the ability to work in a group as well as independently during experimental tasks and properly solves the work-related problems. K_K05 Os1

Assessment methods and assessment criteria:

The student will receive laboratory credits if he/she:

1) attended at least 85% of the classes (acceptable no more than one absence during each part of laboratory);

2) was working during the classes in the way enabling positive evaluation of his knowledge, skills and social awareness gained during the classes (as described in learning outcomes).

Detailed conditions:

To receive lab credit the student should receive a minimum of 55% of the highest score of the two written tests (each contains open questions).

The course will be evaluated based on a written examination composed of open and closed questions. A score of 55% is required to pass the examination. A student must receive lab credit before he/she can take the exam

Classes in period "Winter semester 2020/21" (past)

Time span: 2020-10-01 - 2021-01-31
Choosen plan division:

see course schedule
Type of class: Class, 60 hours more information
Lecture, 30 hours more information
Coordinators: Bartosz Kiersztyn, Anna Łasica
Group instructors: Iwona Jasser, Bartosz Kiersztyn, Anna Łasica, Waldemar Siuda
Students list: (inaccessible to you)
Examination: Course - Examination
Class - Grading
Lecture - Examination

Blended learning

Classes in period "Winter semester 2021/22" (future)

Time span: 2021-10-01 - 2022-02-20
Choosen plan division:

see course schedule
Type of class: Class, 60 hours more information
Lecture, 30 hours more information
Coordinators: Bartosz Kiersztyn, Anna Łasica
Group instructors: Iwona Jasser, Bartosz Kiersztyn, Anna Łasica, Waldemar Siuda
Students list: (inaccessible to you)
Examination: Course - Examination
Class - Grading
Lecture - Examination
Course descriptions are protected by copyright.
Copyright by University of Warsaw.