1. The ocean sampling day consortiumAnna Kopf, Valentina Turk, Tinkara Tinta, 2015, drugi znanstveni članki Povzetek: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
Objavljeno v DiRROS: 07.08.2024; Ogledov: 87; Prenosov: 89
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2. Jellyfish-associated microbiome in the marine environment : exploring its biotechnological potentialTinkara Tinta, Tjaša Kogovšek, Katja Klun, Alenka Malej, Gerhard J. Herndl, Valentina Turk, 2019, pregledni znanstveni članek Povzetek: Despite accumulating evidence of the importance of the jellyfish-associated microbiome to jellyfish, its potential relevance to blue biotechnology has only recently been recognized. In this review, we emphasize the biotechnological potential of host–microorganism systems and focus on gelatinous zooplankton as a host for the microbiome with biotechnological potential. The basic characteristics of jellyfish-associated microbial communities, the mechanisms underlying the jellyfish-microbe relationship, and the role/function of the jellyfish-associated microbiome and its biotechnological potential are reviewed. It appears that the jellyfish-associated microbiome is discrete from the microbial community in the ambient seawater, exhibiting a certain degree of specialization with some preferences for specific jellyfish taxa and for specific jellyfish populations, life stages, and body parts. In addition, different sampling approaches and methodologies to study the phylogenetic diversity of the jellyfish-associated microbiome are described and discussed. Finally, some general conclusions are drawn from the existing literature and future research directions are highlighted on the jellyfish-associated microbiome. Ključne besede: Cnidaria, Ctenophora, biodiversity, bioactive compounds, microbial communities, blue biotechnology Objavljeno v DiRROS: 06.08.2024; Ogledov: 166; Prenosov: 75
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3. The importance of jellyfish-microbe interactions for biogeochemical cycles in the oceanTinkara Tinta, Katja Klun, Gerhard J. Herndl, 2021, pregledni znanstveni članek Povzetek: Jellyfish blooms can represent a significant but largely overlooked source of organic matter (OM), in particular at the local and regional scale. We provide an overview of the current state of knowledge on the bloom-forming jellyfish as sink and source of OM for microorganisms. In particularly, we compare the composition, concentration, and release rates of the OM excreted by living jellyfish with the OM stored within jellyfish biomass, which becomes available to the ocean's interior only once jellyfish decay. We discuss how these two stoichiometrically different jelly-OM pools might influence the dynamics of microbial community and the surrounding ecosystem. We conceptualize routes of jelly-OM in the ocean, focusing on different envisioned fates of detrital jelly-OM. In this conceptual framework, we revise possible interactions between different jelly-OM pools and microbes and highlight major knowledge gaps to be addressed in the future. Objavljeno v DiRROS: 05.08.2024; Ogledov: 105; Prenosov: 93
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4. The epiplankton community in the southern Adriatic: multiple trophic levels along the south - north and inshore-offshore gradientsValentina Turk, Davor Lučić, Jakica Njire, Senka Terzić, Tinkara Tinta, Adam Benović, Alenka Malej, 2012, izvirni znanstveni članek Povzetek: The epiplankton community was investigated during Meduza cruises along south - north and offshore – inshore transects in the middle and southern Adriatic in spring 2002. The diel and vertical distribution of heterotrophic bacteria, phytoplankton pigment composition, micro- and mesozooplankton were assessed. At most stations we observed a thermocline at approximately 20 m and a prominent chlorophyll a peak at about 70 m depth. The integrated phytoplankton and bacterial biomass were lower at the station in the central part of the southern Adriatic, and increased gradually towards middle Adriatic and towards coastal stations. Vertical profiles of both bacterial abundance and production showed a distinct peak in the surface layer. Bacterial abundance was high also in the layer of the deep chlorophyll a maximum. Higher bacterial production was associated with elevated abundance of pico- and nanoplankton feeding zooplankton indicating that bacterial populations were generally controlled by predation. Ključne besede: Meduza project, heterotrophic bacteria, Adriatic Sea, South Adriatic Sea, phytoplankton pigments, open sea, microzooplankton, mesozooplankton, research cruises Objavljeno v DiRROS: 05.08.2024; Ogledov: 113; Prenosov: 57
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5. Bacteria associated with moon jellyfish during bloom and post-bloom periods in the Gulf of Trieste (northern Adriatic)Maja Kos Kramar, Tinkara Tinta, Davor Lučić, Alenka Malej, Valentina Turk, 2019, izvirni znanstveni članek Povzetek: Jellyfish are a prominent component of the plankton community. They frequently form conspicuous blooms which may interfere with different human enterprises. Among the aspects that remain understudied are jellyfish associations with microorganisms having potentially important implications for organic matter cycling. To the best of our knowledge, this study is the first to investigate the bacterial community associated with live moon jellyfish (Aurelia solida, Scyohozoa) in the Adriatic Sea. Using 16S rRNA clone libraries and culture-based methods, we have analyzed the bacterial community composition of different body parts: the exumbrella surface, oral arms, and gastric cavity, and investigated possible differences in medusa-associated bacterial community structure at the time of the jellyfish population peak, and during the senescent phase at the end of bloom. Microbiota associated with moon jellyfish was different from ambient seawater bacterial assemblage and varied between different body parts. Betaproteobacteria (Burkholderia, Cupriavidus and Achromobacter) dominated community in the gastral cavity of medusa, while Alphaproteobacteria (Phaeobacter, Ruegeria) and Gammaproteobacteria (Stenotrophomonas, Alteromonas, Pseudoalteromonas and Vibrio) prevailed on ‘outer’ body parts. Bacterial community structure changed during senescent phase, at the end of the jellyfish bloom, showing an increased abundance of Gammaproteobacteria, exclusively Vibrio. The results of cultured bacterial isolates showed the dominance of Gammaproeteobacteria, especially Vibrio and Pseudoalteromonas in all body parts. Our results suggest that jellyfish associated bacterial community might have an important role for the host, and that anthropogenic pollution in the Gulf of Trieste might affect their community structure. Ključne besede: bacteria, moon jellyfish, Gulf of Trieste, Adriatic sea Objavljeno v DiRROS: 23.07.2024; Ogledov: 127; Prenosov: 116
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6. Microbial processing of jellyfish detritus in the oceanTinkara Tinta, Zihao Zhao, Alvaro Escobar, Katja Klun, Barbara Bayer, Chie Amano, Luca Bamonti, Gerhard J. Herndl, 2020, izvirni znanstveni članek Povzetek: When jellyfish blooms decay, sinking jellyfish detrital organic matter (jelly-OM), rich in proteins and characterized by a low C:N ratio, becomes a significant source of OM for marine microorganisms. Yet, the key players and the process of microbial jelly-OM degradation and the consequences for marine ecosystems remain unclear. We simulated the scenario potentially experienced by the coastal pelagic microbiome after the decay of a bloom of the cosmopolitan Aurelia aurita s.l. We show that about half of the jelly-OM is instantly available as dissolved organic matter and thus, exclusively and readily accessible to microbes. During a typical decay of an A. aurita bloom in the northern Adriatic Sea about 100 mg of jelly-OM L–1 becomes available, about 44 μmol L–1 as dissolved organic carbon (DOC), 13 μmol L–1 as total dissolved nitrogen, 11 μmol L–1 of total hydrolyzable dissolved amino acids (THDAA) and 0.6 μmol L–1 PO43–. The labile jelly-OM was degraded within 1.5 days (>98% of proteins, ∼70% of THDAA, 97% of dissolved free amino acids and the entire jelly-DOC pool) by a consortium of Pseudoalteromonas, Alteromonas, and Vibrio. These bacteria accounted for >90% of all metabolically active jelly-OM degraders, exhibiting high bacterial growth efficiencies. This implies that a major fraction of the detrital jelly-OM is rapidly incorporated into biomass by opportunistic bacteria. Microbial processing of jelly-OM resulted in the accumulation of tryptophan, dissolved combined amino acids and inorganic nutrients, with possible implications for biogeochemical cycles. Objavljeno v DiRROS: 22.07.2024; Ogledov: 136; Prenosov: 127
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7. Bacterial indicators are ubiquitous members of pelagic microbiome in anthropogenically impacted coastal ecosystemNeža Orel, Eduard Fadeev, Katja Klun, Matjaž Ličer, Tinkara Tinta, Valentina Turk, 2022, izvirni znanstveni članek Povzetek: Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach. Objavljeno v DiRROS: 16.07.2024; Ogledov: 131; Prenosov: 100
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8. Inter-comparison of marine microbiome sampling protocolsFrancisco Pascoal, Maria Paola Tomasino, Roberta Piredda, Grazia Marina Quero, Luís Torgo, Julie Poulain, Tinkara Tinta, Timotej Turk Dermastia, 2023, izvirni znanstveni članek Povzetek: Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22–3 µm, 3–20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and “whole water” (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume. Ključne besede: marine microbiome, standardized sampling, inter-comparison, amplicon sequencing, microbial diversity, seawater sampling Objavljeno v DiRROS: 12.07.2024; Ogledov: 105; Prenosov: 151
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9. PETRI-MED: Advancing satellite-based monitoring for microbial plankton biodiversity in the Mediterranean SeaTinkara Tinta, Janja Francé, Katja Klun, Martin Vodopivec, Neža Orel, Patricija Mozetič, Vesna Flander-Putrle, 2024, objavljeni povzetek znanstvenega prispevka na konferenci Ključne besede: biodiversity, remote sensing, oceanography Objavljeno v DiRROS: 09.07.2024; Ogledov: 144; Prenosov: 75
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10. A global database of dissolved organic matter (DOM) concentration measurements in coastal waters (CoastDOM v1)Christian Lønborg, Cátia Carreira, Gwenaël Abril, Katja Klun, Tinkara Tinta, 2024, izvirni znanstveni članek Povzetek: Measurements of dissolved organic carbon (DOC), nitrogen (DON), and phosphorus (DOP) concentrations are used to characterize the dissolved organic matter (DOM) pool and are important components of biogeochemical cycling in the coastal ocean. Here, we present the first edition of a global database (CoastDOM v1; available at https://doi.org/10.1594/PANGAEA.964012, Lønborg et al., 2023) compiling previously published and unpublished measurements of DOC, DON, and DOP in coastal waters. These data are complemented by hydrographic data such as temperature and salinity and, to the extent possible, other biogeochemical variables (e.g. chlorophyll a, inorganic nutrients) and the inorganic carbon system (e.g. dissolved inorganic carbon and total alkalinity). Overall, CoastDOM v1 includes observations of concentrations from all continents. However, most data were collected in the Northern Hemisphere, with a clear gap in DOM measurements from the Southern Hemisphere. The data included were collected from 1978 to 2022 and consist of 62 338 data points for DOC, 20 356 for DON, and 13 533 for DOP. The number of measurements decreases progressively in the sequence DOC > DON > DOP, reflecting both differences in the maturity of the analytical methods and the greater focus on carbon cycling by the aquatic science community. The global database shows that the average DOC concentration in coastal waters (average ± standard deviation (SD): 182±314 µmolC L−1; median: 103 µmolC L−1) is 13-fold higher than the average coastal DON concentration (13.6 ± 30.4 µmol N L−1; median: 8.0 µmol N L−1), which is itself 39-fold higher than the average coastal DOP concentration (0.34 ± 1.11 µmol P L−1; median: 0.18 µmol P L−1). This dataset will be useful for identifying global spatial and temporal patterns in DOM and will help facilitate the reuse of DOC, DON, and DOP data in studies aimed at better characterizing local biogeochemical processes; closing nutrient budgets; estimating carbon, nitrogen, and phosphorous pools; and establishing a baseline for modelling future changes in coastal waters. Ključne besede: global database, dissolved organic matter, coastal waters, marine biology Objavljeno v DiRROS: 17.05.2024; Ogledov: 255; Prenosov: 390
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