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




- Research into the structure and functioning of microbial communities (phytoplankton, bacteria, archaea, viruses) and their changes due to climate change and other anthropogenic stressors

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

- Ecology of Harmful Algal Blooms

- Development of methods to assess the environmental status of marine waters based on phytoplankton

- Research on genetic traits of ecologically important species (including HAB) and development of new methods in environmental diagnostics

- Research on microbial interactions with other planktonic organisms, with a focus on the interactions between microorganisms and gelatinous plankton and the effects of these interactions on the functioning of marine ecosystems

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

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

- Investigate the diversity of phytoplankton viruses, particularly diatom viruses, and how viral infections affect nutrient cycling.

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

- Focus on jellyfish-microbes' interactions, distribution and the role of potential pathogens in coastal marine environments, and the impact of microbial communities on the functioning and biogeochemical status of the ecosystems.

- Biogeochemical cycling of dissolved and bioavailable metal species in marine environments (open and coastal seas, hydrothermal vents, lagoons)

- Biogeochemistry of mercury and its species

- Geochemical and biological processes in hypersaline environments




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

- Determining the structure and function of microbial communities using cultivation-independent and next-generation sequencing methods as well as state-of-the-art bioinformatics and computational biology tools

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

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

- Classical virology and metagenomic analysis of viral communities

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

- Chemotaxonomy (HPLC pigment analyses)

- Scanning electron microscopy – SEM (biological samples)

- Determination of phytoplankton toxins by enzyme-linked immunosorbent assay (ELISA)

- Ultra-clean trace metal sampling procedures (Diffusive Gradients in Thin-film and Geotraces methodologies), analysis and interpretation of metal complexation and bioavailability for phytoplankton and macrophytes.

- Mercury speciation techniques (dissolved gaseous Hg, monomethylmercury and total mercury)

- Time series analysis


Staff members



Assoc. Prof Dr Patricija Mozetič, scientific counsellor, head of the unit


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Assist. Prof. Dr Tinkara Tinta, scientific associate



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Dr Arne Bratkič, scientific associate



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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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Neža Orel, PhD student


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Petra Slavinec, PhD student



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Timotej Turk Dermastia, postdoc


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Former members:


Prof Dr Jadran Faganeli

Assoc. Prof. Dr Nives Kovač

Assoc. Prof. Dr Valentina Turk

Ivano Vascotto, PhD student






Coastal Sea Research – ARRS Research Programme P1-0237


PI: Patricija Mozetič



Impact of climate change on the onset of phytoplankton blooms and consequences for food web dynamics: comparison between northern and southern Adriatic Bilateral collaboration between Slovenia and Croatia 2023-2024


Leader: Patricija Mozetič



PETRI-MED - Plankton biodivErsity Through Remote sensing and omIcs in the MEDiterranean Sea (Biodiversa+ 2021-2022 Joint Call ‘Supporting the protection of biodiversity and ecosystem across land and sea)


Leader for NIB: Tinkara Tinta



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

Leader: Tinkara Tinta

1.11.2020 – 31.10.2023



Diatom viruses and their role in organic matter cycling in the coastal seas – postoctoral project ARIS 01Z14396

Leader: Timotej Turk Dermastia



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



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


WP leader: Janja Francé



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




Monitoring of biological quality elements for the ecological quality status

Slovenian Environment Agency (ARSO)



Monitoring of toxic phytoplankton in mussel farming areas in Slovenian Sea

Administration for Food Safety, Veterinary Sector and Plant Protection

Leader: Patricija Mozetič


National Committee of the Intergovernmental Oceanographic Commission (under the auspices of the Slovenian National Commission for UNESCO)

Since 1994 continuous activity

Leader: Patricija Mozetič



Selected publications


Tinta, T., Zhao, Z., Bayer, B., Herndl, G.J. Jellyfish detritus supports niche partitioning and metabolic interactions among pelagic marine bacteria. Microbiome. 2023, https://doi.org/10.1186/s40168-023-01598-8


Kovač, N., Hauptman, Ž., Dolenec, M., Škornik, I., Rogan Šmuc, N. 2023. Translocation signatures of major elements in halophytes from hypersaline environments: the case study from Sečovlje Salina (Republic of Slovenia). Journal of soils and sediments. DOI: 10.1007/s11368-023-03654-0


Faganeli, J., Falnoga, I., Klun, K., Mazej, D., Mozetič, P., Zuliani, T., Kovač, N. 2023. Metal(loid)s in suspended particulate matter and plankton from coastal waters (Gulf of Trieste, northern Adriatic Sea). Journal of soils and sediments. DOI: 10.1007/s11368-023-03519-6


Kovač, N., Viers, J., Faganeli, J., Bajt, O., Pokrovsky, O.S. 2023. Elemental composition of plankton exometabolites (mucous macroaggregates): control by biogenic and lithogenic components. Metabolites. DOI: 10.3390/metabo13060726


Turk Dermastia, T., Vascotto, I., Francé, J., Stanković, D., Mozetič, P., 2023. Evaluation of the rbcL marker for metabarcoding of marine diatoms and inference of population structure of selected genera. Front. Microbiol. 14.  https://doi.org/10.3389/fmicb.2023.1071379


Bratkič, A., Jazbec, A., Toplak, N., Koren, S., Lojen, S., Tinta, T., Kostanjšek, R., Snoj, L. 2023. The colonization of an irradiated environment: The case of microbial biofilm in a nuclear reactor. International Journal of Radiatioan Biologydoi.org/10.1080/09553002.2023.2258206


Sagarminaga, Y., Garcés, E., Francé, J., Stern, R., Revilla, M., Magaletti, E., Bresnan, E., Tsirtsis, G., Jakobsen, H.H., Sampedro, N., Reñé, A., Camp, J., Borja, Á., Rodríguez, J.G., Spada, E., Pagou, K., De Angelis, R., Lanzén, A., Ferrer, L., Borrello, P., Boicenco, L., Kobos, J., Mazaris, A., Katsanevakis, S., 2023. New tools and recommendations for a better management of harmful algal blooms under the European Marine Strategy Framework Directive. Frontiers in Ocean Sustainability10.3389/focsu.2023.1298800.


Turk, V., Malkin, S., Celussi, M., Tinta, T., Ceam, J., Malfatti, F., Chen, F. 2021. Ecological role of microbes : current knowledge and future prospects. 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.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 Indicatorshttps://doi.org/10.1016/j.ecolind.2021.107630.


Orel, N., Fadeev, E., Klun, K., Ličer, M., Tinta, T, Turk, V. 2022. Bacterial indicators are ubiquitous members of pelagic microbiome in anthropogenically impacted coastal ecosystem. Frontiers in microbiology. DOI: 10.3389/fmicb.2021.765091


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.


Flander-Putrle, V., Francé, J., Mozetič, P., 2022. Phytoplankton Pigments Reveal Size Structure and Interannual Variability of the Coastal Phytoplankton Community (Adriatic Sea). Waterhttps://doi.org/10.3390/w14010023.


Zingone, A., Escalera, L., Aligizaki, K., Fernandez-Tejedor, M., Ismael, A., Montresor, M., Mozetič, P., Taş, S., Totti, C. 2021. Toxic marine microalgae and noxious blooms in the Mediterranean Sea: a contribution to the Global HAB status report. Harmful algae. DOI: 10.1016/j.hal.2020.101843.


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 Coastshttps://doi.org/10.1007/s12237-009-9191-7


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


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.




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

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

National Veterinary Institute https://www.vf.uni-lj.si/en/nvi

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

Soline, Pridelava soli d.o.o. https://www.soline.si/en/

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/

Institute of Oceanography and Fisheries (IOR), Split, Croatia https://galijula.izor.hr/en/

Institute for Marine and Coastal Research, University of Dubrovnik, Croatia https://www.imp-du.com/en

Fondazione Centro Ricerche Marine – Laboratoro Nazionale di riferimento per le Biotossine Marine, Cesenatico, Italy https://www.centroricerchemarine.it/it-IT/index-index/

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

Hellenic Centre for Marine Research (HCMR), Greece, https://www.hcmr.gr/

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

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

Università Politecnica delle Marche, Italy https://www.univpm.it/Entra/

Agenzia regionale per la protezione dell'ambiente del Friuli Venezia Giulia (ARPA FVG), Italy, https://www.arpa.fvg.it/



Other activities


Education and Outreach:


Members of the group have 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 Nova Gorica

- Jožef Stefan International Postgraduate School


We are dedicated to human resources development, not only through the national program for young researchers, but also as tutors of domestic and foreign students in compulsory internships and supervisors of bachelor's, master's, and doctoral theses.

Through regular outreach activities (e.g. open-door events, researcher nights, thematic days) and other dissemination strategies, we contribute to the ocean literacy of the society.


National appointments:


- 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)

- Boards of experts in support of EU directives (MSFD, WFD)[1] [JF2] 

- Scientific board of Faculty for postgraduate studies at University of Nova Gorica (T. Tinta)


Awards, Recognition, Fellowships:


- 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 (N. Kovač, N. Glavaš et al.)

- 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 (T. Tinta et al.)

- FEMS scholarship, University of Vienna, 2021, N. Orel

- Marie Skłodowska Curie (MSCA-IF-EF-ST) fellowship for project 'Microbial degradation of jellyfish-derived substrates', University of Vienna, Austria (2018-2020), T. Tinta

- PostDoctoral Fulbright fellowship for project 'Marine bacteria and aggregates interactions at microscale', Scripps SIO, UCSD, USA (2013-2014), T. Tinta