Homepage » Courses Offered » Undergraduate Studies » 7th 13B046 Applied & Environmental Microbiology


Compulsory/Elective Code Semester Lectures Practicals Credits ECTS
Elective 13B046 7th  2 Hrs/Wk 3 Hrs/Wk 3 4

The course addresses concepts related to the applications of microorganisms - either as pure cultures or as microbial communities - in the environment and the economy.


Knowledge: Students are expected to acquire knowledge related to: a) the way micro-organisms participate and interact with abiotic and biotic factors in different ecosystems, b) the methodology applied to the microbial analysis of environmental samples, c) the uses and applications of microorganisms in the production of chemicals and biofuels, d) the applications of microorganisms to waste treatment and degradation of organic pollutants, e) the uses of microorganisms in food and beverage production, f) the mathematical models applied in microbial bioreactors

Skills: Students will be able to: a) explain how microorganisms are involved in shaping the different ecosystems, b) apply the appropriate methodology for the analysis of environmental samples, c) analyze and design processes related to the use of microorganisms as biocatalysts in industry and environmental protection


Methods in Microbial Ecology (2 hrs): Culture-Dependent Analyses of Microbial Communities. Enrichment. Isolation. Culture-Independent Microscopic Analyses of Microbial Communities. General Staining Methods. Fluorescence In-Situ Hybridization (FISH). Culture-Independent Genetic Analyses of Microbial Communities. CR Methods of Microbial Community Analysis. Microarrays for Analysis of Microbial Phylogenetic and Functional Diversity. Environmental Genomics and Related Methods. Measuring Microbial Activities in Nature. Chemical Assays, Radioisotopic Methods, and Microsensors. Stable Isotopes. Linking Genes and Functions to Specific Organisms: SIMS, Flow Cytometry, and MAR-FISH, Stable Isotope Probing and Single-Cell Genomics.

Microbial Ecosystems (2 hrs): Microbial Ecology. General Ecological Concepts. Ecosystem Service: Biogeochemistry and Nutrient Cycles. The Microbial Environment. Environments and Microenvironments. Surfaces and Biofilms. Microbial Mats. Terrestrial Environments. Soils. The Subsurface. Aquatic Environments. Freshwaters. The Marine Environment: Phototrophs and Oxygen Relationships. Major Marine Phototrophs. Pelagic Bacteria, Archaea, and Viruses. The Deep Sea and Deep-Sea Sediments. Hydrothermal Vents.

Microbial Symbioses (2 hrs): Symbioses between Microorganisms. Lichens. “Chlorochromatium aggregatum”. Plants as Microbial Habitats. The Legume–Root Nodule Symbiosis. Agrobacterium and Crown Gall Disease. Mycorrhizae. Mammals as Microbial Habitats. The Mammalian Gut. The Rumen and Ruminant Animals. The Human Microbiome. Insects as Microbial Habitats. Heritable Symbionts of Insects. Termites. Aquatic Invertebrates as Microbial Habitats. Hawaiian Bobtail Squid. Marine Invertebrates at Hydrothermal Vents and Gas Seeps. Leeches. Reef-Building Corals.

Continuous growth cultures (8 hrs): Microbial growth parameters. Continuous cultivation system. Estimation of the microbial growth. Production of ethanol and other biotechnological products. Pilot cultivation systems. Parameters of microbial growth in continuous flow cultures and scale up to an industrial scale cultures. Productivity. Yield. Estimation of microbial growth parameters.

Microbiology of Built Environment (4 hrs): Mineral recovery and drainage of acidic mine water. Microbial leaching. Drainage of acidic mine waters. Bioremediation of uranium-contaminated environments. Bioremediation of organic pollutants: hydrocarbons, pesticides and plastics. Wastewater and drinking water treatment. Primary and secondary wastewater treatment. Drinking water purification systems. Water distribution systems in Municipalities and facilities. Microbial corrosion of metals. Biological destruction of rocks and concrete.

Food and waterborne bacterial diseases (4 hrs): Waterborne pathogens. Sources of contamination of water. Public health and water quality. Waterborne diseases. Vibrio cholerae and cholera. The legionellosis. Typhoid fever and Norovirus infections. Foodborne pathogens. Food spoilage and preservation. Foodborne diseases and their epidemiology. Food poisoning. Food poisoning by strains of the genera Staphylococcus and Clostridium. Pathogenicity and infectivity. Adhesion. Exotoxins and endotoxins. Food infections. Salmonellosis, pathogenic strains of E. coli. Campylobacter. Listeria. Other foodborne infectious diseases; Shiga toxin. Proteins with inheritable self-perpetuating change in protein structure (Prions). Scrapie. Bovine spongiform encephalopathy (BSE). Kuru disease.

Eukaryotic pathogens: fungal and parasitic diseases (4 hrs): Fungal infections. Clinically important fungi and mechanisms of the disease. Visceral parasitic infections. Amoebae and other Protozoa: Entamoeba, Naegleria, Balantidium. Giardia intestinalis, Cryptosporidium parvum, Toxoplasma gondii.


1. Isolation of bacteria in pure culture from environmental samples – 2. Monitoring the production of antimicrobials, molecular identification of bacterial producers – 3. Determination of biomass, ethanol and carbon source concentration in a continuous culture – 4. Determination of biomass and protein yield coefficients in a continuous culture – 5. Microbiological analysis of water, determination of suitability for human use – 6. Comparative study of yogurt production by endogenous strains of the genus Lactobacillus

  Lectures: Dimitris HatzinikolaouAssociate Professor of Microbial Biotechnology (Coordinator) - Dr. Efstathios Katsifas (Laboratory Teaching Staff) - Dr. Alexander Savvides (Laboratory Teaching Staff)
  Practicals: Dr. Efstathios Katsifas (Laboratory Teaching Staff) - Dr. Alexander Savvides (Laboratory Teaching Staff)

There are no prerequisites for the student to choose and attend the course. However, in order to achieve better understanding of the course, good knowledge of students in General Microbiology, Biochemistry, Molecular Biology and Plat Physiology is rather appreciated.

The course is offered to Erasmus students: Teaching in Greek language - Exams in English language.

The evaluation process is carried out in the Greek language (English language for Erasmus students) via a written examination covering the whole of the syllabus. Only students who have attended all the laboratory sessions and submitted all the assignments required may participate at be exams. The assignments are graded with a quota of 1/3 of the grade of the laboratory grade. The final exam includes: A. Written exam of the laboratory sessions B. Written exam of the syllabus of the course. The total score is the sum of the two above individual assessments, with quota A: (1/3) x100% - B: (2/3) x100%, respectively. Grate ≥5 at both examinations is required.

  If you require more information, please contact the Course Coordinator, Assoc. Prof Dimitris Hatzinikolaou, at: Tel: [30] 210 727 4140; e-mail: dhatzini[at]biol.uoa[dot]gr