WG Microorganisms and biogeochemical cycles

WG Microorganisms and biogeochemical cycles


We study the structure and function of marine micro-organisms in the cycling of matter and in interactions with other organisms, both in natural environments and under controlled conditions.



Research and expertise



-  Investigating the structure and function of microbial communities (microalgae, bacteria, archaea, viruses) and their changes in the context of climate change and other anthropogenic impacts

-  The role of microbial communities in nutrient cycling in coastal marine ecosystems

Ecology of Harmful Algal Blooms

-  Development of diversity indices for assessing the ecological status of the sea

-  Understanding the functional ecology of phytoplankton species based on their functional traits

-  Maintaining a long-term series of biological and chemical data to study changes and trends through statistical analysis and modelling

-  Investigate genetic traits of ecologically important species (including HAB) and introduce new methods for environmental diagnostics

Investigate interaction of microbes with planktonic organisms with emphasis on microbe-gelatinous plankton interactions and consequences

-   Distribution and role of potential pathogens in coastal marine environments and development of new detection methods

-  Response of microbes to anthropogenic impacts and various organic pollutants

- Geochemical and biological processes in hypersaline environments



-  Integrative taxonomy of microalgae (light and electron microscopy, phylogenetic barcoding of individual strains, metabarcoding of phytoplankton communities)

-  Determination of structure and function of microbial communities using NGS  and state-of-the-art tools of bioinformatics and computational biology

Cultivation, taxonomic identification and investigation of physiology and biochemistry of selected bacterial and microalgal strains from the culture collection at the MBP

-  Microscopy-based analysis of microbial metabolic activities at the single cell level

-  Measurement of primary and bacterial production using radiolabeled isotopes (14C, 3H)

-  Chemotaxonomy (HPLC pigment analyses)

-  Toxicity of phytoplankton


Staff members



Assoc. Prof. Dr. Patricija Mozetič, Scientific Counsellor, Head of WG Microorganisms and biogeochemical cycles


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Dr. Vesna Flander-Putrle, Senior Research Associate


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Dr Janja Francé, Senior Research Associate


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Dr Katja Klun, Scientific Associate


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Assoc. Prof. Dr. Nives Kovač, Senior Scientific Associate


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Neža Orel, Young Researcher


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Dr Tinkara Tinta, Scientific Associate


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Dr. Timotej Turk Dermastia, Research Assistant


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Coastal Sea Research – ARRS Research Programme P1-0237




DE-COMB - Decay of an invasive ctenophore blooms as a perturbation to the coastal marine microbial community - from molecules to ecosystem - an integrated interdisciplinary approach – Slovenian (ARRS) – Austrian Research Project J7-2599

1.11.2020 - 31.10.2023



Drivers that structure coastal marine microbiome with emphasis on pathogens – an integrated approach - ARRS Research Project J1-9157

1.7.2018 - 30.06.2021



GoJelly - A gelatinous solution to plastic pollution (H2020-BG)

2018 - 2021



SMS - Sensing toxicants in Marine waters makes Sense using biosensors (FP7-OCEAN)

1.8.2013 - 31.8.2017



INTERFACES - Ecohydrological interfaces as critical hotspots for transformations of ecosystem exchange fluxes (FP7-ITN)

2013 - 2017



OceanGov - Ocean Governance for Sustainability - challenges, options and the role of science (COST Action CA15217)

28.9.2016 - 31.12.2020



BALMAS - Ballast water management system for Adriatic Sea protection (Adriatic IPA CBC)

2013 - 2016


NC IOC - National Committee of the Intergovernmental Oceanographic Commission (operating under the premises of the Slovenian National Commission for UNESCO)

Recurring annual programme since 1994



MEDREGION - Support Mediterranean Member States towards the implementation of the Marine Strategy Framework Directive new GES Decision and programmes of measures and contribute to regional/subregional cooperation




ABIOMMED - Support Coherent and Coordinated Assessment of Biodiversity and Measures Across Mediterranean for the Next 6-year Cycle of MSFD Implementation



National monitoring of biological quality elements for ecological quality of marine waters - Slovenian Environment Agency (ARSO)




Selected publications


Tinta T., Klun K., Herndl G.J. The importance of jellyfish-microbe interactions for biogeochemical cycles in the ocean. Limnology and Oceanography 2021. DOI: 10.1002/LNO.11741

Turk, V., Malkin, S., Celussi, M., Tinta, T., Ceam, J., Malfatti, F., Chen, F. Ecological role of microbes : current knowledge and future prospects. Ed.: V: Malone, T. C., Malej, A., Faganeli, J.. Coastal ecosystems in transition : a comparative analysis of the northern Adriatic and Chesapeake Bay, (Geophysical monograph series). 1st ed. Hoboken: American Geophysical Union: Wiley. 2021, str. 129-145. doi: 10.1002/9781119543626.ch7

Brush, M.J., Mozetič, P., Francé, J., Bernardi Aubry, F., Djakovac, T., Faganeli, J., Harris, L.A., Niesen, M. 2021. Phytoplankton dynamics in a changing environment. In: Malone, T.C., Malej, A., Faganeli, J. (eds.). Coastal ecosystems in transition: a comparative analysis of the northern Adriatic and Chesapeake Bay, (Geophysical monograph series). AGU: Wiley. DOI: 10.1002/9781119543626.ch4.

Francé, J., Varkitzi, I., Stanca, E., Cozzoli, F., Skejić, S., Ungaro, N., Vascotto, I., Mozetič, P., Ninčević Gladan, Ž., Assimakopoulou, G., Pavlidou, A., Zervoudaki, S., Pagou, K., Basset, A., 2021. Large-scale testing of phytoplankton diversity indices for environmental assessment in Mediterranean sub-regions (Adriatic, Ionian and Aegean Seas). Ecological Indicators 126, 107630. https://doi.org/10.1016/j.ecolind.2021.107630.

Turk Dermastia, T., Cerino, F., Stanković, D., Francé, J., Ramšak, A., Tušek-Žnidarič, M., Beran, A., Natali, V., Cabrini, M., Mozetič, P. 2020. Ecological time series and integrative taxonomy unveil seasonality and diversity of the toxic diatom Pseudo-nitzschia H. Peragallo in the northern Adriatic Sea. Harmful algae. DOI: 10.1016/j.hal.2020.101773.

Tinta, T., Zhao, Z., Escobar, A., Klun, K., Bayer, B., Amano, C., Bamonti, L., Herndl, G.J. Microbial processing of jellyfish detritus in the ocean. Frontiers in microbiology 2020, DOI: 10.3389/fmicb.2020.590995.

Mozetič, P., Cangini, M., Francé, J., Bastianini, M., Bernardi Aubry, F., Bužančić, M., Cabrini, M., Cerino, F., Čalić, M., D'Adamo, R., et al. 2019. Phytoplankton diversity in Adriatic ports: Lessons from the port baseline survey for the management of harmful algal species. Marine pollution bulletin. DOI: 10.1016/j.marpolbul.2017.12.029.

Giovanardi, F., Francé, J., Mozetič, P., Precali, R., 2018. Development of ecological classification criteria for the Biological Quality Element phytoplankton for Adriatic and Tyrrhenian coastal waters by means of chlorophyll a (2000/60/EC WFD). Ecol. Indic. 93, 316-332. https://doi.org/10.1016/j.ecolind.2018.05.015.

Varkitzi, I., Francé, J., Basset, A., Cozzoli, F., Stanca, E., Zervoudaki, S., Giannakourou, A., Assimakopoulou, G., Venetsanopoulou, A., Mozetič, P., Tinta, T., Skejic, S., Vidjak, O., Cadiou, J.F., Pagou, K., 2018. Pelagic habitats in the Mediterranean Sea: A review of Good Environmental Status (GES) determination for plankton components and identification of gaps and priority needs to improve coherence for the MSFD implementation. Ecol. Indic. 95, 203-218. https://doi.org/10.1016/j.ecolind.2018.07.036.

Tinta, T., Vojvoda, J., Mozetič, P., Talaber, I., Vodopivec, M., Malfatti, F., Turk, V. Bacterial community shift is induced by dynamic environmental parameters in a changing coastal ecosystem (northern Adriatic, northeastern Mediterranean Sea) - a 2-year time-series study. Environmental microbiology 2015, DOI: 10.1111/1462-2920.12519.

Mozetič, P., Solidoro, C., Cossarini, G., Socal, G., Precali, R., Francé, J., Bianchi, F., De Vittor, C., Smodlaka, N., Fonda Umani, S. 2010. Recent trends towards oligotrophication of the Northern Adriatic: Evidence from chlorophyll a time series. Estuaries and Coasts, 33, 362-375. https://doi.org/10.1007/s12237-009-9191-7





University of Ljubljana, Biotechnical Faculty https://www.uni-lj.si/university/

Institute “Jožef Stefan” https://www.ijs.si/ijsw/JSI

University of Trieste https://www.units.it/

OGS https://www.ogs.trieste.it/

ISMAR http://www.ismar.cnr.it/

CMR Rovinj https://www.irb.hr/eng/Divisions/Center-for-Marine-Research

University of Zagreb http://www.unizg.hr/homepage/

University of Vienna https://www.univie.ac.at/en/

IOR Split www.izor.hr

Institute for Marine and Coastal Research, University of Dubrovnik, Croatia

Fondazione Centro Ricerche Marine - Laboratoro Nazionale di riferimento per le Biotossine Marine, Cesanatico

Microbia Environnement https://www.microbia-environnement.com/

HCMR https://www.hcmr.gr/

University of Salento https://www.unisalento.it/

Nacionalni veterinarski inštitut UL https://www.vf.uni-lj.si/nvi

Soline, Proizvodnja soli d.o.o.

National Institute of Chemistry (https://www.ki.si/en/)

UN Environmental Programme, Mediterranean Action Plan Coordinating Unit (UNEP/MAP), Athens, Greece

Christian Albrechts University Kiel (CAU), Germany

The National Research Council (CNR), Italy

University of Southern Denmark (SDU), Denmark



Other activities


Education and Outreach:

Members of the group hold teaching positions at the:

-       University of Ljubljana (Biotechnical Faculty, Faculty of Maritime Studies and Transport)

-       University of Primorska (Faculty of Mathematics, Natural Sciences and Information Technologies, Faculty of Education)

-       University of Nova Gorica

-       Jožef Stefan International Postgraduate School


We are dedicated to the development of human resources, not only through the national program for young researchers, but also as supervisors of domestic and foreign students (e.g. students of the laboratory technology program of Berufskolleg Hilden School, Germany) in compulsory internships and supervisors of bachelor, master and doctoral theses.

Through regular outreach activities (e.g. open door events, researcher nights, guided tours) and other dissemination strategies, we contribute to the marine literacy of the society.


National appointments and expert group memberships:

-       National Representative of UNESCO-IOC Intergovernmental Panel on Harmful Algal Blooms (IPHAB) (P. Mozetič)

-       Chair of National Committee of Intergovernmental Oceanographic Commission (NO IOC) of Slovenian National Commission for UNESCO (P. Mozetič)

-       National Focal Point for MED POL (Mediterranean Pollution Monitoring and Research Programme) of UNEP Mediterranean Action Plan (V. Turk)

-       Members of expert groups in support of EU directives (MSFD, WFD)


Awards and recognitions:

-       Slovenian “Prometheus of Science for Excellence in Science Communication Award 2019” to the editorial board of the publication Half a Century Long Path of the Marine Biology Station Piran 1969-2019 of the National Institute of Biology (J. Francé, N. Kovač, P. Mozetič)

-       ARRS scientific achievement “Excellent in Science 2018” in the field of interdisciplinary research for the study of the microbial layer of petola and salt mud in the Sečovlje salt pans

-       Slovenian “Prometheus of Science for Excellence in Science Communication Award 2018” to young researcher T. Turk Dermastia

-       ARRS scientific achievement “Excellent in Science 2015” in the field of natural sciences for describing the impact of environmental parameters on the microbial community dynamics.