We are focused on studies related to marine microbial ecology, physical oceanography, sedimentology and interdisciplinary physical-biological research.

 

We study the interactions between marine organisms and their environment, focusing on how biological processes in the ocean are influenced by physical, chemical, and geological factors. It encompasses the diversity of marine life, from microscopic plankton to gelatinous zooplankton, and investigates their roles in oceanic food webs, nutrient cycling, and ecosystem dynamics. By understanding the relationships between marine life and their surroundings, we aim to uncover how these systems respond to natural and anthropogenic changes, such as climate change and pollution, contributing to our knowledge of ocean health and global biogeochemical cycles.

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Fields of research and expertise

 

 

Research:

 

- Research on the structure and functioning of microbial communities (with emphasis on bacteria) and their changes due to climate change and other anthropogenic pressures

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

- Research on interactions between microbes and other planktonic organisms, with emphasis on microbial interactions with gelatinous zooplankton throughout their life span and their consequences for marine ecosystem functioning and biogeochemical cycles

- Distribution and role of potential pathogens, antimicrobial resistance genes and mobile genetic elements in coastal marine environments

- Biogeochemical cycling of mercury

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

- Geochemical and biological processes in hypersaline environments

- Jellyfish population dynamics modelling using Lagrangian Individual Based Models

- Marine ecosystem interactions research with coupled physical-biogeochemical models

- Research of water mass and sediment dynamics in coastal seas using high resolution numerical models

- Numerical forecasting of water mass and sediment dynamics in coastal seas

- Analysis of measured oceanographic data and results of numerical models using statistical and machine learning methods

- Modelling the dispersal of pollutants in marine environment

 

Expertise:

 

- Determination of the structure and functioning of microbial communities using cultivation-independent methods (multi-omics approaches spanning from metagenomics to metaproteomics), next-generation sequencing, and advanced bioinformatics and computational biology tools

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

- Analysis of microbial activity at the single-cell level using microscopy-based approaches

- Measurement of prokaryotic heterotrophic production using radiolabeled compounds (³H)

- Ultra-clean sampling of trace metals in marine environments (Diffusive Gradients in Thin Films – DGT, and GEOTRACES protocols), analysis and interpretation of metal complexation and bioavailability for phytoplankton and macrophytes

- Mercury speciation (dissolved gaseous mercury, monomethylmercury, total mercury)

- Numerical modelling of water mass and sediment dynamics with high resolution numerical models, applied for planning of mariculture, deposition of dredged sediments in navigable waterways, outfalls and dilution of sewage and storm water runoffs

- Acquisition, quality control and cleaning of oceanographic measurement data

- Application of statistical and machine learning methods to oceanographic measurements and numerical modelling results in forecast of sea-surface elevation

- Analysis of time series of oceanographic data in estimates of climatic trends

- Providing measurement data and metadata to various international infrastructures that allow users to access this data

- Operational oceanography

- Use of machine learning for coastal flooding forecasts

- Modelling the dispersal of pollutants in marine environment

- In situ data acquisition for marine aplications – measurements of currents, temperature, salinity, Ph, oxygen concetration, turbidity, etc.

 

 

Staff members

 

dr. Martin Vodopivec, Scientific Associate, Head of WG Dynamics of ocean and marine microbiomes

https://www.nib.si/mbp/en/cv/martin-vodopivec

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Assist. Prof. dr. Tinkara Tinta, Senior Scientific Associate, Deputy head of WG

https://www.nib.si/mbp/en/cv/tinkara-tinta

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dr. Branko Čermelj, Research Counsellor

https://www.nib.si/mbp/sl/cv/branko-cermelj

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Assist. Prof. dr. Matjaž Ličer, Scientific Associate

https://www.nib.si/mbp/en/cv/matjaz-licer

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dr. Arne Bratkič, Scientific Associate

https://www.nib.si/mbp/sl/cv/arne-bratkic

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dr. Tanja Vojvoda Zeljko, Scientific Associate

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dr. Neža Orel, Assistant with a PhD

https://www.nib.si/mbp/en/cv/neza-orel

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Maja Starovič, PhD student

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Črtomir Ernesto Perharič Bailey, PhD student

https://www.nib.si/mbp/en/cv/crtomir-perharic

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Projects

 

 

(2025-2028)

The role of the microbiome in the life and death of bloom-forming jellyfish (JELLY-BIOME)

PI: WEAVE Austrian-Slovenian joint research project

Leader fo NIB: Tinkara Tinta

Project number: ARIS-FWF, J1-60007, PIN3614124

(2025-2027)

Jellyfish Blooms: An Overlooked Hotspots and Potential Vectors for Antimicrobial Resistance Transmission in the Marine Environment (JELLY-ARM)

PI: Slovenian-German Bilateral project

Leader fo NIB: Tinkara Tinta

Project number: BI-DE/25-27-001

(2023-2026)

Plankton biodivErsity Through Remote sensing and omIcs in the MEDiterranean Sea

BIODIVERSA+ 2021-2022 project: Plankton biodivErsity Through Remote sensing and omIcs in the MEDiterranean Sea ( PETRI-MED)

https://petri-med.icm.csic.es

(2026-2029)

Antibiotic Resistance Genes - Threat to Marine Coastal Ecosystem Services (SEA THREAT)

PI: ARIS

Leader: Tanja Vojvoda Zeljko

 

 

 

 

Publications

 

MARCHESE, Christian, ZOFFOLI, Maria Laura, RAMOND, Pierre, LOGARES, Ramiro, BOUGET, François-Yves, GALAND, Pierre E., TINTA, Tinkara, OREL, Neža, VOLPE, Gianluca, LANDOLFI, Angela, ORGANELLI, Emanuele. Machine learning-driven mapping of prokaryotic community diversity in the Mediterranean Sea using omics, earth observation, and model data. Ecological Informatics. 2026, vol. 95, [article no.] 103747. ISSN 1574-9541.https://doi.org/10.1016/j.ecoinf.2026.103747, DOI: 10.1016/j.ecoinf.2026.103747.

 

PERHARIČ, Črtomir, VODOPIVEC, Martin, HERNDL, Gerhard J., LIČER, Matjaž. Dynamic sinking and surface-area based decay modeling reduce estimates of gelatinous zooplankton-mediated carbon export to the Deep Sea. Global biogeochemical cycles. Mar. 2026, vol. 40, iss. 3, [article no.] e2025gb008937, str. 1-19, ilustr. ISSN 1944-9224. https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2025GB008937, DOI: 10.1029/2025GB008937.

 

HUBOT, Nathan, GIERING, Sarah L.C., OREL, Neža, KLUN, Katja, HERNDL, Gerhard J., HOHAUS, Felix, LUCAS, Cathy H., TINTA, Tinkara. Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community. PeerJ. 2026, vol. 14, [article no.] e20784, str. 1-27, ilustr. ISSN 2167-8359. https://peerj.com/articles/20784/, DOI: 10.7717/peerj.20784.

 

OREL, Neža, FADEEV, Eduard, CELUSSI, Mauro, TURK, Valentina, KLUN, Katja, AFJEHI-SADAT, Leila, HERNDL, Gerhard J., TINTA, Tinkara. Down the drain: exploring wastewater’s role in coastal microbiome transformations. Microbiome. 2026, vol. 14, art. no. 46, str. 1-22, ilustr. ISSN 2049-2618. https://link.springer.com/article/10.1186/s40168-025-02298-1, DOI: 10.1186/s40168-025-02298-1.

 

ZUPANČIČ MUC, Matjaž, ZAVRTANIK, Vitjan, BARTH, Alexander, ALVERA-AZCÁRATE, Aida, LIČER, Matjaž, KRISTAN, Matej. CRITER 1.0 : a coarse reconstruction with iterative refinement network for sparse spatio-temporal satellite data. Geoscientific model development. [Online ed.]. Sept. 2025, vol. 18, iss. 17, str. 5549–5573, ilustr., zvd. ISSN 1991-9603. https://gmd.copernicus.org/articles/18/5549/2025/, DOI: 10.5194/gmd-18-5549-2025.

 

VODOPIVEC, Martin, MALEJ, Alenka. Spatially explicit individual-based model reveals the mauve stinger jellyfish distribution in the Mediterranean Sea. Ecological modelling. [Print ed.]. Jun. 2025, vol. 505, [article no.] 111109, str. 1-13, ilustr. ISSN 0304-3800. https://www.sciencedirect.com/science/article/pii/S030438002500095X, DOI: 10.1016/j.ecolmodel.2025.111109.

 

OREL, Neža, LOKOVŠEK, Ana, ORLANDO-BONACA, Martina, TINTA, Tinkara. Diversity of the surface microbiome of canopy-forming brown macroalgae (Fucales) in the northern Adriatic. Microbiology spectrum. [Spletna izd.]. Apr. 2025, [art. no.] e02204-24, ilustr., zvd. ISSN 2165-0497.https://journals.asm.org/doi/10.1128/spectrum.02204-24, DOI:10.1128/spectrum.02204-24.

 

RUS, Marko, MIHANOVIĆ, Hrvoje, LIČER, Matjaž (vodilni avtor), KRISTAN, Matej (vodilni avtor). HIDRA3 : a deep-learning model for multipoint ensemble sea level forecasting in the presence of tide gauge sensor failures. Geoscientific model development. Feb. 2025, vol. 18, iss. 3, str. 605-620, ilustr. ISSN 1991-9603.https://gmd.copernicus.org/articles/18/605/2025/, DOI:10.5194/gmd-18-605-2025.

 

ELENA, Alan X., OREL, Neža, FANG, Peiju, HERNDL, Gerhard J., BERENDONK, Thomas U., TINTA, Tinkara, KLÜMPER, Uli. Jellyfish blooms : an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments. mSystems. ilustr. ISSN 2379-5077. https://journals.asm.org/doi/10.1128/msystems.01012-24, DOI: 10.1128/msystems.01012-24.

 

BRATKIC, Arne, JAZBEC, Anze, TOPLAK, Natasa, KOREN, Simon, LOJEN, Sonja, TINTA, Tinkara, KOSTANJSEK, Rok, SNOJ, Luka. The colonization of an irradiated environment: the case of microbial biofilm in a nuclear reactor. International Journal of Radiation Biology. 2024, vol. 100, iss. 1, str. 108–121. ISSN 0955-3002. https://doi.org/10.1080/09553002.2023.2258206, DOI: 10.1080/09553002.2023.2258206.

 

OREL, Neža, FADEEV, Eduard, HERNDL, Gerhard J., TURK, Valentina, TINTA, Tinkara. Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii. BMC Genomics. 2024, vol. 25, iss. 1, [article no.] 146. ISSN 1471-2164. https://doi.org/10.1186/s12864-024-10062-2, DOI: 10.1186/s12864-024-10062-2.

 

FADEEV, E., HENNENFEIND, J. H., AMANO, C., ZHAO, Z., KLUN, K., HERNDL, G. J., TINTA, T. Bacterial degradation of ctenophore Mnemiopsis leidyi organic matter. mSystems. 2024, vol. 9, [article no.] e01264-23. ISSN 2379-5077. https://doi.org/10.1128/msystems.01264-23, DOI: 10.1128/msystems.01264-23.

 

CELUSSI, M., MANNA, V., BANCHI, E., FONTI, V., BAZZARO, M., FLANDER-PUTRLE, V. et al. Annual recurrence of prokaryotic climax communities in shallow waters of the North Mediterranean. Environmental Microbiology. 2024, vol. 26, iss. 3, [article no.] e16595. https://doi.org/10.1111/1462-2920.16595, DOI: 10.1111/1462-2920.16595.

 

TINTA, Tinkara, ZHAO, Zihao, BAYER, Barbara, HERNDL, Gerhard J. Jellyfish detritus supports niche partitioning and metabolic interactions among pelagic marine bacteria. Microbiome. 2023, vol. 11, iss. 1, [article no.] 156. ISSN 2049-2618. https://doi.org/10.1186/s40168-023-01598-8, DOI: 10.1186/s40168-023-01598-8.

 

RUS, Marko, FETTICH, Anja, KRISTAN, Matej, LIČER, Matjaž. HIDRA2 : deep-learning ensemble sea level and storm tide forecasting in the presence of seiches – the case of the northern Adriatic. Geoscientific model development. Jan. 2023, vol. 16, iss. 1, str. 271-288, ilustr. ISSN 1991-959X. https://gmd.copernicus.org/articles/16/271/2023/, https://repozitorij.uni-lj.si/IzpisGradiva.php?id=152345, DOI: 10.5194/gmd-16-271-2023.

 

ĆOSOVIĆ, Vlasta, ŠANJEK, Rahela, HADŽIĆ, Eric, RAKARIĆ, Mihovil, IŠTUK, Željko, ŠUŠMELJ, Kaja, ČERMELJ, Branko, ŽVAB ROŽIČ, Petra. Impact of submarine karst sulfur springs on benthic foraminiferal assemblage in sediment of northern Adriatic Sea. Journal of soils and sediments : protection, risk assessment and remediation. 2023, str. 1-17. ISSN 1439-0108. https://repozitorij.uni-lj.si/IzpisGradiva.php?id=152573, DOI: 10.1007/s11368-023-03614-8.

 

VODOPIVEC, Martin, ZAIMI, Klodian, PELIZ, Álvaro Judice. The freshwater balance of the Adriatic Seastudy : a sensitivity study. Journal of geophysical research. Oceans. 2022, vol. 127, iss. 11, 1-23 str., ilustr., zvd. ISSN 2169-9275. https://doi.org/10.1029/2022JC018870, DOI: 10.1029/2022JC018870.

 

LIPIZER, Marina, ČERMELJ, Branko, et al. Trace metals and polycyclic aromatic hydrocarbons in the Eastern Mediterranean sediments : concentration ranges as a tool for quality control of large data collections. Marine pollution bulletin. Dec. 2022, [vol.] 185, str. [1]-19, ilustr., zvd. ISSN 0025-326X. https://doi.org/10.1016/j.marpolbul.2022.114181, DOI: 10.1016/j.marpolbul.2022.114181.

 

OREL, Neža, FADEEV, Eduard, KLUN, Katja, LIČER, Matjaž, TINTA, Tinkara, TURK, Valentina. Bacterial indicators are ubiquitous members of pelagic microbiome in anthropogenically impacted coastal ecosystem. Frontiers in microbiology. 2022, vol. 12, str. 1-21, ilustr. ISSN 1664-302X. https://www.frontiersin.org/articles/10.3389/fmicb.2021.765091/full, DOI: 10.3389/fmicb.2021.765091.

 

KOTNIK, Jože, ŽAGAR, Dušan, NOVAK, Gorazd, LIČER, Matjaž, HORVAT, Milena. Dissolved gaseous mercury (DGM) in the gulf of Trieste, Northern Adriatic Sea. Journal of marine science and engineering. 2022, vol. 10, no. 5, str. 587-1-587-18, ilustr. ISSN 2077-1312. DOI: 10.3390/jmse10050587.

 

REYES SUÁREZ, Nydia Catalina, TIRELLI, Valentina, URSELLA, Laura, LIČER, Matjaž, CELIO, Massimo, CARDIN, Vanessa. Multi-platform study of the extreme bloom of the barrel jellyfish Rhizostoma pulmo (Cnidaria: Scyphozoa) in the northernmost gulf of the Mediterranean Sea (Gulf of Trieste) in April 2021. Ocean Science. 2022, vol. 18, iss. 5, str. 1321-1337, ilustr. ISSN 1812-0784. https://doi.org/10.5194/os-18-1321-2022, DOI: 10.5194/os-18-1321-2022.

 

BERGAMASCO, Andrea, CUCCO, Andrea, GUGLIELMO, Letterio, MINUTOLI, R., QUATTROCCHI, G., GUGLIELMO, R., PALUMBO, Franca, PANSERA, Marco, ZAGAMI, Giacomo, VODOPIVEC, Martin, MALEJ, Alenka, GRANATA, A. Observing and modeling long-term persistence of P. noctiluca in coupled complementary marine systems (Southern Tyrrhenian Sea and Messina Strait). Scientific reports. 2022, vol. 12, str. 1-20, ilustr. ISSN 2045-2322. https://www.nature.com/articles/s41598-022-18832-2, DOI: 10.1038/s41598-022-18832-2.

 

VODOPIVEC, Martin, KONEČNIK RUZZIER, Maja. Opportunities in identifying and marketing windsport tourism destinations : high-resolution wind analysis. Sustainability. 2022, vol. 14, iss. 24, article no. 142416589, str. 1-23. ISSN 2071-1050. https://doi.org/10.3390/su142416589, https://repozitorij.uni-lj.si/IzpisGradiva.php?id=146705, DOI: 10.3390/su142416589.

 

ŽUST, Lojze, FETTICH, Anja, KRISTAN, Matej, LIČER, Matjaž. HIDRA 1.0 : deep-learning-based ensemble sea level forecasting in the northern Adriatic. Geoscientific model development. Apr. 2021, ISSN 1991-959X, vol. 14, no. 4, str. 2057-2074. https://gmd.copernicus.org/articles/14/2057/2021/, DOI: 10.5194/gmd-14-2057-2021.

 

QUERIN, Stefano, COSOLI, Simone, GERIN, Riccardo, LAURENT, Célia, MALAČIČ, Vlado, PRISTOV, Neva, POULAIN, Pierre-Marie. Multi-platform, high-resolution study of a complex coastal system : the TOSCA experiment in the Gulf of Trieste. Journal of marine science and engineering, April 2021, ISSN 2077-1312, 2021, vol. 9, no. 5, str. 1-28. https://www.mdpi.com/2077-1312/9/5/469, DOI: 10.3390/jmse9050469.

 

CHERIF, El Khalil, MOZETIČ, Patricija, FRANCÉ, Janja, FLANDER-PUTRLE, Vesna, FAGANELI PUCER, Jana, VODOPIVEC, Martin. Comparison of in-situ chlorophyll-a time series and sentinel-3 ocean and land color instrument data in Slovenian national waters (Gulf of Trieste, Adriatic Sea). Water. July 2021, vol. 13, iss. 14, str. 1-22, ilustr. ISSN 2073-4441. https://www.mdpi.com/2073-4441/13/14/1903, https://repozitorij.uni-lj.si/IzpisGradiva.php?id=135611, DOI: 10.3390/w13141903.

 

ROVAN, Leja, ZULIANI, Tea, HORVAT, Barbara, KANDUČ, Tjaša, VREČA, Polona, JAMIL, Qasim, ČERMELJ, Branko, BURA-NAKIĆ, Elvira, CUKROV, Neven, ŠTROK, Marko, LOJEN, Sonja. Uranium isotopes as a possible tracer of terrestrial authigenic carbonate. Science of the total environment. 2021, vol. 797, str. 149103-1- 149103-12. ISSN 0048-9697. DOI: 10.1016/j.scitotenv.2021.149103.

 

RUBINO, Angelo, GAČIĆ, Miroslav, BENSI, Manuel, KOVACEVIC, Vedrana, MALAČIČ, Vlado, MENNA, Milena, NEGRETTI, Maria Eletta, SOMMERIA, Joel, ZANCHETTIN, Davide, BARRETO, Ricardo V., URSELLA, Laura, CARDIN, Vanessa, CIVITARESE, Giuseppe, ORLIĆ, Mirko, PETELIN, Boris, SIENA, Giuseppe. Experimental evidence of long-term oceanic circulation reversals without wind influence in the North Ionian Sea. Scientific reports. 2020, vol. 10, str. 1-9. ISSN 2045-2322. https://www.nature.com/articles/s41598-020-57862-6, DOI: 10.1038/s41598-020-57862-6. 5309519

 

BARTH, Alexander, ALVERA-AZCÁRATE, Aida, LIČER, Matjaž, BECKERS, Jean-Marie. DINCAE 1.0 : a convolutional neural network with error estimates to reconstruct sea surface temperature satellite observations. Geoscientific model development. 2020, vol. 13, iss. 3, str. 1609-1622, ilustr. ISSN 1991-959X. DOI: 10.5194/gmd-13-1609-2020.

 

ZAVRTANIK, Vitjan, VODOPIVEC, Martin, KRISTAN, Matej. A segmentation-based approach for polyp counting in the wild. Engineering applications of artificial intelligence. [Print ed.]. 2020, vol. 88, str. 1-9, ilustr. ISSN 0952-1976. DOI: 10.1016/j.engappai.2019.103399.

 

MOLINA JACK, Maria-Eugenia, BAKIU, Rigers, CASTELLI, Ana, ČERMELJ, Branko, FAFANĐEL, Maja, GEORGOPOULOU, Christina, GIORGI, Giordano, IONA, Athanassia, IVANKOVIC, Damir, KRALJ, Martina, PARTESCANO, Elena, ROTINI, Alice, VELIKONJA, Melita, LIPIZER, Marina. Heavy metals in the Adriatic-Ionian Seas : a case study to illustrate the challenges in data management when dealing with regional datasets. Frontiers in marine science. Sep. 2020, vol. 7, article 571365, str. 1-9, ilustr. ISSN 2296-7745. https://www.frontiersin.org/articles/10.3389/fmars.2020.571365/full, DOI: 10.3389/fmars.2020.571365.

 

LIČER, Matjaž, ESTIVAL, Solène, REYES-SUAREZ, Catalina, DEPONTE, Davide, FETTICH, Anja. Lagrangian modelling of a person lost at sea during the Adriatic scirocco storm of 29 October 2018. Natural hazards and earth system sciences. 2020, vol. 20, iss. 8, str. 2335-2349, ilustr. ISSN 1561-8633. DOI: 10.5194/nhess-20-2335-2020.

 

MALAČIČ, Vlado, ŽAGAR, Nedjeljka. Seawater icicles of the Adriatic Sea. Bulletin of the American Meteorological Society, vol. 100, no. 6, str. 987-994, ISSN 0003-0007, 2019. http://dx.doi.org/10.1175/BAMS-D-18-0118.1, DOI: 10.1175/BAMS-D-18-0118.1.

 

PETELIN, Boris, KONONENKO, Igor, MALAČIČ, Vlado, KUKAR, Matjaž. Frequent subgraph mining in oceanographic multi-level directed graphs. International journal of geographical information science. 2019, vol. 33, no. 10, str. 1936-1959. ISSN 1365-8816. DOI: 10.1080/13658816.2019.1599124.

 

KRALJ, Martina, LIPIZER, Marina, ČERMELJ, Branko, CELIO, Massimo, FABBRO, Cinzia, BRUNETTI, Fabio, FRANCÉ, Janja, MOZETIČ, Patricija, GIANI, Michele. Hypoxia and dissolved oxygen trends in the northeastern Adriatic Sea (Gulf of Trieste). Deep-sea research : topical studies in oceanography. part 2. 2019, vol. 164, str. 74-88. ISSN 0967-0645. DOI: 10.1016/j.dsr2.2019.06.002.

 

MALAČIČ, Vlado. Wind direction measurements on moored coastal buoys. Journal of atmospheric and oceanic technology, vol. 36, no. 7, str. 1401-1418, ISSN 0739-0572, 2019. https://journals.ametsoc.org/doi/10.1175/JTECH-D-18-0171.1, DOI: 10.1175/JTECH-D-18-0171.1.

 

GENOV, Tilen, ANGELINI, Valeria, HACE, Ana, PALMISANO, Giuseppe, PETELIN, Boris, MALAČIČ, Vlado, PARI, Sauro, MAZZARIOL, Sandro. Mid-distance re-sighting of a common bottlenose dolphin in the northern Adriatic Sea: insight into regional movement patterns. Journal of the Marine Biological Association of the United Kingdom. 2016, letn. 96, št. 4, str. 909-914, ilustr. ISSN 0025-3154. http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=10308967&fulltextType=RA&fileId=S0025315415001241, DOI: 10.1017/S0025315415001241.