Environmental Microbiology and Bioremediation

This course is part of the programme
Bachelor's programme in Environment (first cycle)

Objectives and competences

The main goal is to know and understand the role of microbes in biogeochemical processes in different ecosystems. The students will learn the basic microbiological principles, the methods in microbial ecology and their theoretical and practical use.
The knowledge can give the base for understanding processes and changes in the environment.
The students can get some skills to recognise the ecological problems and critical evaluation of the human impacts on pollution, climate changes and as well as environmental protection.
The lectures will be implemented with individual practical work in the laboratory and presentations of the seminars.
The students can get general competences in microbial ecology.


Knowledge of basic biology


• Basic principles in microbiology and microbial ecology
• Basic in cell structure and function
• Newest methods in microbial ecology
• Microbial biodiversity
• Metabolisms, growth and regulation
• Water quality and common sources of infections
• Aquatic ecology
• Microbes in soil and sediments
• Basics of underground microbiology
• Aero-microbiology
• Microenvironments and biofilms
• Microbiology and extreme environments
• Biogeochemistry and nutrient cycles
• Biotransformations and biodegradations

Intended learning outcomes

Students will get the basic knowledge how to prepare and perform sampling and microbial analyses to determine the abundance, growth rate and microbial community composition together with the basic environmental paramethers.
The knowledge can be used to prevent infections and to protect human and environmental health.
Students will get basic knowledge to determine the role of microbes:

  • in different habitates,
  • in different biogeochemical cycles,
  • to determine their role in nutrient cycling
  • to determine water quality,
  • in degradation of natural organic compounds and selected pollutants in the environment.


• M. T. Madigan, J. M. Martinko, D. A. Stahl, D. P. Clark: Brock Biology of microorganisms – 13. izdaja (2012), Pearson Education, Inc., publishing as Benjamin Cummings, San Francisco Catalogue E-version
• L. Pepper, C. P. Gerba, T. J. Gentry: Environmental Microbiology – 3. izdaja (2015), Academic Press, Elsevier E-version


• Presentation of the seminar paper (15 %) • Intermediate practice test (25 %) • Written or oral examination (60 %)

Lecturer's references

Assistant Professor in the field of Microbiology.

I do the research in the field of ecology and biodiversity of yeasts and filamentous fungi, mainly of those associated with grape, and I study yeast biodiversity potential for possible biotechnological applications. In the Center of Wine Research group I am involved in numerous research and applicative projects in Slovenia and abroad. I act as a mentor to PhD students, undergraduate and Master’s students.

DASHKO, Sofia, LIU, Ping, VOLK, Helena, BUTINAR, Lorena, PIŠKUR, Jure, FAY, Justin. Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations. Frontiers in microbiology, ISSN 1664-302X, Feb. 2016, vol. 7, str. 1-24. http://dx.doi.org/10.3389/fmicb.2016.00215, doi: 10.3389/fmicb.2016.00215. [COBISS.SI-ID 4142075]

STERNAD LEMUT, Melita, SIVILOTTI, Paolo, BUTINAR, Lorena, LAGANIS, Jana, VRHOVŠEK, Urška. Pre-flowering leaf removal alters grape microbial population and offers good potential for a more sustainable and cost-effective management of a Pinot Noir vineyard. Australian journal of grape and wine research, ISSN 1322-7130, 2015, vol. 21, no. 3, str. 439-450, ilustr., doi: 10.1111/ajgw.12148. [COBISS.SI-ID 3908091]

DASHKO, Sofia, ZHOU, Nerve, TINTA, Tinkara, SIVILOTTI, Paolo, STERNAD LEMUT, Melita, TROŠT, Kajetan, GAMERO, Amparo, BOEKHOUT, Teun, BUTINAR, Lorena, VRHOVŠEK, Urška, PIŠKUR, Jure. Use of non-conventional yeast improves the wine aroma profile of Ribolla Gialla. Journal of industrial microbiology & biotechnology, ISSN 1367-5435, 2015, vol. 42, issue 7, str. 997-1010. http://link.springer.com/article/10.1007%2Fs10295-015-1620-y, doi: 10.1007/s10295-015-1620-y. [COBISS.SI-ID 3433807]

BUTINAR, Lorena, MOHORČIČ, Martina, DEYRIS, Valérie, DUQUESNE, Katia, IACAZIO, Gilles, CLAEYS-BRUNO, Magalie, FRIEDRICH, Josepha, ALPHAND, Veronique. Prevalence and specificity of Baeyer-Villiger monooxygenases in fungi. Phytochemistry, ISSN 0031-9422. [Print ed.], 2015, vol. 117, str. 144-153, ilustr., doi: 10.1016/j.phytochem.2015.06.009. [COBISS.SI-ID 3958267]

BUTINAR, Lorena, FRISVAD, Jens Christian, GUNDE-CIMERMAN, Nina. Hypersaline waters : a potential source of foodborne toxigenic aspergilli and penicillia. FEMS microbiology, ecology, ISSN 0168-6496, 2011, vol. 77, no. 1, str. 186-199, doi: 10.1111/j.1574-6941.2011.01108.x. [COBISS.SI-ID 1882107]

BUTINAR, Lorena, STRMOLE, Tadeja, GUNDE-CIMERMAN, Nina. Relative incidence of ascomycetous yeasts in Arctic coastal environments. Microbial ecology, ISSN 0095-3628, 2011, vol. 61, no. 4, str. 832-843, doi: 10.1007/s00248-010-9794-3. [COBISS.SI-ID 1780731]