Microbiology and geomicrobiology I

This course is part of the programme
Karstology (Third Cycle)

Objectives and competences

The progress of nature sciences in the last years has shown that many processes in the underground are closely related to microbiota. At the end of the course the student is able to distinguish between different microscopic forms of life, to evaluate the impact and role of microbiota in the underground (e.g. formation of minerals) and their species diversity, to know indicator species, which shows organic load of the underground, and to gain an insight on the microorganisms that represent biohazard for human health during research work in the subsurface.




• Microbial diversity in the underground
• Geomicrobiology and ecological interactions in caves
• Microbes and natural processes in the underground
• Eutrophication of the underground
• Caves as a source of new microbial species
• Microbes in caves related with biohazard

Intended learning outcomes

Cave microbiology has recently been founded as a new interdisciplinary field of microbiology, geology and chemistry that studies the microscopic forms of life in the caves and their impact on natural processes. The student is capable of independent interpretation of (geo)microbiological results, setting up of experiments, he/she learns basic aseptic techniques and sampling on the field – in caves, and learns to use the selected software tools and applications for data analysis.


• Madigan M. T., Martinko J. M., Stahl D., Clark D. P. 2012: Brock biology of microorganisms. Pearson, cop., Boston.
• White W. B., Culver D. C. 2012: Encyclopedia of Caves. Elsevier, Amsterdam.
• Wilkens H., Culver D. C., Humphreys W. 2000: Ecosystems of the World. Subterranean Ecosystems. Elsevier, Amsterdam.
• Selected articles from scientific journals.


The oral exam is designed to assess the knowledge acquired by the student during the lectures and the ability to understand, articulate and express the new acquired skills. The prerequisite for examination is the presence at field work, a short written paper (5-10 pages) by which the student highlights a certain topic which can be linked to his/her PhD thesis. 50/50

Lecturer's references

Associate Professor of Microbiology.



MULEC, Janez, OARGA-MULEC, Andreea, HOLKO, Ladislav, PAŠIĆ, Lejla, KOPITAR, Andreja Nataša, ELERŠEK, Tina, MIHEVC, Andrej. Microbiota entrapped in recently-formed ice : Paradana Ice Cave, Slovenia. Scientific reports. 21 Jan. 2021, vol. 11, art. no. 1993, str. 1-12, ilustr. ISSN 2045-2322. https://www.nature.com/articles/s41598-021-81528-6, DOI: 10.1038/s41598-021-81528-6. [COBISS.SI-ID 48378115]

JOHNSTON, Vanessa E., MARTÍN-PÉREZ, Andrea, SKOK, Sara, MULEC, Janez. Microbially-mediated carbonate dissolution and precipitation : towards a protocol for ex-situ, cave-analogue cultivation experiments. International journal of speleology. May 2021, vol. 50, iss. 2, str. 137-155, [21] str. (appendix), ilustr. ISSN 0392-6672. https://scholarcommons.usf.edu/ijs/vol50/iss2/3/, DOI: 10.5038/1827-806X.50.2.2372. [COBISS.SI-ID 61329667]

MULEC, Janez, SIMČIČ, Saša, KOTAR, Tadeja, KOFOL, Romina, STOPINŠEK, Sanja. Survey of Histoplasma capsulatum in bat guano and status of histoplasmosis in Slovenia, Central Europe. International journal of speleology. Jan. 2020, vol. 49, iss. 1, str. 1-10, [3] str. (appendix), ilustr. ISSN 0392-6672. DOI: 10.5038/1827-806X.49.1.2297. [COBISS.SI-ID 45788461]

MULEC, Janez. Phototrophs in caves. V: MOLDOVAN, Oana Teodora (ur.), KOVÁČ, Ĺubomir (ur.), HALSE, Stuart (ur.). Cave ecology. Cham: Springer, 2019. Str. 91-106, ilustr. Ecological studies, Analysis and Synthesis, 235. ISBN 978-3-319-98850-4, ISBN 978-3-319-98852-8. ISSN 0070-8356. https://link.springer.com/chapter/10.1007/978-3-319-98852-8_6. [COBISS.SI-ID 44146477]

MULEC, Janez, OARGA-MULEC, Andreea, ŠTURM, Samo, TOMAZIN, Rok, MATOS, Tadeja. Spacio-temporal distribution and tourist impact on airborne bacteria in a cave (Škocjan Caves, Slovenia). Diversity. 2017, vol. 9, iss. 3, str. 1-14, ilustr. ISSN 1424-2818. http://www.mdpi.com/1424-2818/9/3/28/html, DOI: 10.3390/d9030028. [COBISS.SI-ID 41852973]