1. Viral lysis accelerates microbial succession patterns resembling diatom senescenceTimotej Turk Dermastia, Ion Gutiérrez-Aguirre, Tinkara Rupnik, Tinkara Tinta, 2026, original scientific article Abstract: Diatom blooms influence carbon cycling through organic matter production and its deposition or remineralization – processes mediated by the microbial community. Viruses can influence diatom bloom dynamics and even terminate blooms, yet interactions between diatoms, their viruses, and associated bacteria remain poorly resolved. Here, we examined how infection of the toxigenic diatom Pseudo-nitzschia galaxiae by its ssRNA virus PnGalRNAV reshapes host physiology, microbiome structure, and organic-matter processing in non-axenic batch cultures. Using epi-fluorescence microscopy, 16S rRNA amplicon sequencing, and metatranscriptomics, we linked microbial composition, localisation, and functional activity during viral lysis. Infection rapidly collapsed diatom growth and induced a senescence-like host state, with broad repression of photosynthesis, silicon metabolism, and core biosynthetic pathways, alongside induction of heat-shock and other stress-related genes. Concurrently, phycosphere-associated bacteria declined, detritosphere-associated bacteria increased, and community composition shifted from Marinobacter (Gammaproteobacteria) dominated, towards Flavobacteriaceae (Bacteroidetes) dominated, especially by Polaribacter. In non-infected controls Alphaproteobacteria proved to benefit from the stable healthy phycospheres with a distinct DOM pool. Bacterial metatranscriptomes showed significant upregulation of polysaccharide-degradation-associated genes in infected cultures, indicating active utilisation of lysis-derived diatom glycans. Similar compositional and metabolic profiles in infected cultures and later-stage senescent controls suggest infection accelerated senescence-associated microbial processes. Overall, viral lysis converted a productive diatom culture into a detrital, DOM-rich environment that selects for specialised polysaccharide degraders, redirects carbon through the viral shunt and may accelerate nutrient recycling in coastal systems. Extending this approach to natural microbial communities and diverse diatom–virus systems will help determine whether these mechanisms are broadly conserved.
Keywords: diatoms, virus, bacteria, Pseudo-nitzschia, shunt, senescence, microbiome, phycosphere
Published in DiRROS: 10.08.2026; Views: 73; Downloads: 36
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2. Machine learning predictions for microbial eukaryotic plankton: implications from unevenly structured dataChristian Marchese, Maria Laura Zoffoli, Pierre Ramond, Timotej Turk Dermastia, Tinkara Tinta, Ramiro Logares, Pierre E. Galand, Emanuele Organelli, 2026, original scientific article Abstract: Machine learning models provide a scalable approach for predicting the diversity of eukaryotic microbial plankton from environmental predictors. However, the extent to which these models generalize to data outside the training set remains poorly quantified. In this study, XGBoost was used to predict the 18S rRNA gene Shannon Diversity Index (SDI) from seven environmental predictors derived from satellite and model data. Surface samples were collected between 2001 and 2025 at two fixed stations in the northwestern Mediterranean (BBMO and SOLA), one fixed station in the northern Adriatic Sea (VIDA), and during the HOTMIX expedition, which sampled an east-west open-sea transect across the Mediterranean Sea. Model performance was assessed using standard repeated K-fold cross-validation (CV), Leave-One-Dataset-Out CV (LODO-CV), and a blocked spatiotemporal CV that combined LODO with temporal forward chaining. Under standard K-fold CV, the model showed moderate performance (R² = 0.44, RMSE = 0.59). In contrast, performance declined substantially under LODO-CV (R² = 0.09, RMSE = 0.73), with uniformly low per-dataset generalization, a pattern also observed with blocked spatiotemporal CV. VIDA and HOTMIX sampled environmental regimes distinct from those at BBMO and SOLA, which may partly explain their poor transferability. Additionally, BBMO and SOLA, despite similar environmental conditions, exhibited poor transferability, indicating that technical differences among independently collected 18S rRNA datasets likely constrain transferability, although their effects cannot be disentangled from environmental variation. Overall, these results highlight the limitations of imbalanced training data and underscore the importance of spatially explicit evaluation, protocol standardization, and environmentally representative coverage.
Keywords: cross-validation, data leakage, eukaryotic plankton, machine learning, marine biodiversity, Mediterranean Sea, omics, shannon diversity index
Published in DiRROS: 29.07.2026; Views: 173; Downloads: 98
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3. Bacterial extracellular vesicles exhibit distinct functional potential across biogeographic provinces of the South Pacific OceanEduard Fadeev, Neža Orel, Tinkara Tinta, Leila Afjehi-Sadat, Haoran Liu, 2026, original scientific article Abstract: Bacterial extracellular vesicles (BEVs) are nanoscale membranous structures released by diverse types of bacteria, and are capable of transporting and delivering biological compounds between cells. Experimental investigation of BEVs in laboratory model systems indicates that these nanoparticles may play a number of roles in the ecophysiology of marine bacterial communities, but their functional potential in the environment remains unclear. Here we describe the proteomic composition of BEV populations over more than 5,000 nautical miles of surface waters in the South Pacific, linking BEV cargoes to the bacterial communities producing them. The presence of marine BEVs was consistently observed across a range of biogeochemical conditions, with an overall abundance comparable to that of bacterial cells (up to 108 BEVs L-1). The protein cargo of marine BEVs, however, differed significantly among ocean regions. The BEV populations were enriched in carbohydrate transporters under phytoplankton bloom conditions, and contained iron uptake-related proteins in nutrient-limited waters. These data suggest that BEVs could enable cells to perform key extracellular functions in the marine environment. Our observations highlight the ubiquity of marine BEVs and biogeographic patterns in their ecological potential across oceanic scales.
Keywords: bacterioplankton, membrane vesicles, TonB-dependent receptors, siderophores, saccharide uptake system
Published in DiRROS: 22.07.2026; Views: 137; Downloads: 123
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4. Microbial degradation of jellyfish detritus promotes phytoplankton growth in coastal marine ecosystemsTinkara Tinta, Eduard Fadeev, Mauro Celussi, Cecilia Balestra, Katja Klun, Patricija Mozetič, Gerhard J. Herndl, 2026, original scientific article Abstract: Gelatinous zooplankton (hereinafter cnidarian Medusozoa and ctenophores or “jellyfish”) are widespread in marine ecosystems and can form massive blooms, releasing large amounts of labile, protein-rich organic matter (jelly-OM) upon decay. This material fuels intense bacterial activity, yet its ecological consequences remain poorly understood. We conducted a two-stage microcosm experiment simulating a bloom decay of the invasive ctenophore Mnemiopsis leidyi to examine microbial processing of jelly-OM and its effect on primary production. In the first stage, over the course of three days, we observed jelly-OM stimulating rapid growth of opportunistic bacterial community. The community was dominated by Pseudoalteromonadaceae – key degraders of diverse jellyfish, which exhibited enhanced metabolism of amino acids, lipids, and carbohydrates and elevated extracellular enzymatic activities, including leucine aminopeptidase, lipase, chitinase, and alkaline phosphatase. These processes led to marked ammonium accumulation. In the second stage, exposure of a fresh microbial assemblage to residues from jelly-OM degradation resulted in a significant increase of primary production and phytoplankton biomass over a period of five days. This was dominated by diatoms and was likely fueled by accumulated ammonium. Concurrently, the bacterial community shifted toward taxa typically associated with phytoplankton blooms. Together, these results, further supported by in situ observations, reveal a likely coupling between jellyfish decay and phytoplankton growth, suggesting that jellyfish blooms act as transient but powerful nutrient sources capable of triggering ecosystem shifts. As jellyfish are projected to thrive under future ocean conditions, our findings underscore the need to re-evaluate their role in biogeochemical cycles—particularly as overlooked drivers of phytoplankton dynamics.
Keywords: jellyfish blooms, organic matter degradation, microbial remineralization, phytoplankton dynamics, primary production, biogeochemical cycling, microscopy-based approach, metagenomics
Published in DiRROS: 22.07.2026; Views: 188; Downloads: 151
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5. Machine learning-driven mapping of prokaryotic community diversity in the Mediterranean Sea using omics, earth observation, and model dataChristian Marchese, Maria Laura Zoffoli, Pierre Ramond, Tinkara Tinta, Neža Orel, 2026, original scientific article Abstract: Marine prokaryotic communities are major contributors to oceanic food webs and global biogeochemical cycles. However, basin-scale diversity patterns and environmental drivers remain poorly understood. In this study, we applied a machine-learning framework to model the diversity of marine prokaryotic communities across the Mediterranean Sea. Diversity was quantified using the Shannon Diversity Index (SDI) derived from 16S rRNA gene sequencing. The in situ dataset included ~600 samples collected year-round from 2001 to 2023 at coastal and open-water sites, providing broad temporal coverage and multisite spatial sampling. We trained an XGBoost model using satellite-derived and modeled oceanographic variables matched to the SDI observations. The model achieved robust predictive performance (R2 = 0.78 for training and 0.70 for testing, with RMSE = 0.31 and MAPE = 0.05 across both) and captured broad basin spatial and seasonal patterns in prokaryotic community diversity, with greater uncertainty in less-represented regions. Diversity was highest in nutrient-rich coastal areas and during winter mixing, and lowest in summer-stratified or oligotrophic waters. SHAP analysis identified photoperiod as the most significant predictor, underscoring the central role of seasonal light cycles in shaping prokaryotic community diversity. Other predictors exhibited significant season- and region-dependent effects, each contributing positively within specific environmental thresholds. Climatological diversity maps revealed consistent spatiotemporal patterns, highlighting a notable west-to-east decrease in diversity and coastal hotspots. These results demonstrate that machine learning can identify major environmental drivers of prokaryotic diversity and upscale discrete observations to basin-wide predictions. This approach is transferable to other planktonic groups and supports scalable ecosystem monitoring across environmental gradients.
Keywords: prokaryotic community diversity, machine learning, Mediterranean Sea, omics, Shannon diversity index, remote sensing
Published in DiRROS: 04.05.2026; Views: 324; Downloads: 357
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6. Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial communityNathan Hubot, Sarah L.C. Giering, Neža Orel, Katja Klun, Gerhard J. Herndl, Felix Hohaus, Cathy H. Lucas, Tinkara Tinta, 2026, original scientific article Abstract: Jellyfish are increasingly recognized as a significant contributor to marine organic matter (OM) on a global scale, with implications for ecosystem dynamics. While the role of jellyfish detritus in microbial nutrient cycling has been explored, the contribution of OM released by live jellyfish—primarily as mucus (hereinafter referred to as mucusassociated OM, or MAOM)—remains understudied. This study investigates the release of organic and inorganic nutrients through MAOM from live jellyfish and their effects on ambient microbial communities in the northern Adriatic Sea using a series of leaching and short-term microcosm experiments. Our results show that per gram of MAOM dry weight from the jellyfish Aurelia spp, approximatively 2 µmol of phosphate, 4 µmol of dissolved inorganic nitrogen, 18 µmol dissolved organic nitrogen, 134 µmol of dissolved organic carbon and 15 µmol of dissolved free amino acids can be released in the ambient seawater in 24 h. Almost half of the OM is released as dissolved OM (DOM), of which a substantial part is low molecular weight (<1 kDa) molecules. During the first 20 h, the DOM fraction of MAOM was rapidly consumed by the ambient microbial community without a corresponding increase in biomass, likely due to nitrogen limitation. In the subsequent 22 h, microbial growth accelerated to 0.19 ± 0.03 h−1 until phosphate became limiting, leading to a sharp decline in microbial production. Our metagenomics analysis revealed that the MAOM-degrading microbial community, dominated by Gammaproteobacteria opportunistic copiotrophs, exhibited increased functional capacity for nutrient assimilation and OM degradation, particularly in the transport and metabolism of amino acids (particularly glycine and taurine) and phosphorus. These traits mirror those found in detritus-degrading microbial communities, suggesting that jellyfish blooms promote the emergence of specialized microbial consortia with shared metabolic capabilities. Taken together, our findings highlight that live jellyfish, through the release of OM, play an active and previously underappreciated role in shaping ambient microbial community dynamics and nutrient fluxes in marine systems affected by jellyfish blooms.
Keywords: jellyfish, bacteria, biogeochemistry, metagenome
Published in DiRROS: 02.03.2026; Views: 774; Downloads: 278
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7. Down the drain: exploring wastewater’s role in coastal microbiome transformationsNeža Orel, Eduard Fadeev, Mauro Celussi, Valentina Turk, Katja Klun, Leila Afjehi-Sadat, Gerhard J. Herndl, Tinkara Tinta, 2025, original scientific article Abstract: Background Many coastal ecosystems worldwide are impacted by wastewater discharges, which introduce nutrients, pollutants, and allochthonous microbes that can alter microbiome composition and function. Although the severity and distribution of these impacts vary across regions, their potential consequences for key ecological processes remain a concern. The resilience and functional adaptability of native coastal microbiomes are still poorly understood. To study the immediate ecological impact of wastewater discharge on a coastal seawater microbiome, we conducted short-term microcosm experiments, exposing a coastal microbiome to two types of treated wastewater: (i) unfiltered wastewater containing nutrients, pollutants, and allochthonous microbes; and (ii) filtered wastewater containing only nutrients and pollutants. Results By integrating multi-omics and metabolic assays, we show that wastewater-derived organic matter and nutrients (mostly ammonia and phosphate) did not alter the taxonomic composition of the coastal microbiota, but triggered reorganization of metabolic pathways in them. We observed enhanced metabolism of proteins, amino acids, lipids, and carbohydrates, particularly of the lineages Alteromonadales, Rhodobacterales, and Flavobacteriales. Glaciecola (Alteromonadales), a copiotroph with antagonistic traits, significantly contributed to these shifts. Conversely, allochthonous taxa like Legionellales and Pseudomonadales had minimal impact. Elevated phosphorus concentrations resulting from wastewater input reduced the synthesis of proteins linked to scavenging phosphorus from organic phosphorus compounds, including alkaline phosphatase activity in native Rhodobacterales and Flavobacteriales, with important ecological implications for phosphorus-depleted coastal ecosystems. Furthermore, the presence of wastewater caused a decline in relative abundance and metabolic activity of Synechococcus, potentially affecting carbon cycling. Yet, the coastal microbiome rapidly respired wastewater-derived dissolved organic carbon, resulting in bacterial growth efficiencies consistent with global coastal averages. Conclusions Our findings highlight the capacity of coastal microbiomes to withstand wastewater discharge, with critical implications for assessment of anthropogenic perturbations in coastal ecosystems. However, wastewater-driven changes in metabolic functions and niche utilization within the autochthonous microbial community, impacting phosphorus cycling and potentially affecting carbon cycling, may have long-term consequences for ecosystem functioning.
Keywords: wastewater, microorganisms, metagenomics, metaproteomics
Published in DiRROS: 27.01.2026; Views: 534; Downloads: 557
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8. Diversity of the surface microbiome of canopy-forming brown macroalgae (Fucales) in the northern AdriaticNeža Orel, Ana Lokovšek, Martina Orlando-Bonaca, Tinkara Tinta, 2025, original scientific article Abstract: Canopy-forming brown macroalgae (Fucales) offer numerous key ecosystem services in Mediterranean coastal areas. However, anthropogenic pressures and climate change have significantly impacted their habitats, leading to an extensive population decline. Interactions between algae and microbiota are a major ecological aspect, yet they represent a significant knowledge gap. In our baseline study, we describe the diversity and host specificity of the microbiome of two genetically identical but morphologically distinct populations of Gongolaria barbata from anthropogenically impacted northern Adriatic Sea. Our preliminary results showed that the microbiomes of G. barbata exhibited low host specificity, with 75% of the algae-associated amplicon sequence variants (ASVs) being part of the core coastal ecosystem microbiome. However, microbiomes of specific algal parts, ambient seawater, and sediment differed significantly in terms of alpha diversity and composition. In contrast, the holdfast and axis show higher similarity with sediment microbiomes, indicating potential horizontal transmission pathways. Microbiomes associated with deciduous parts of morphologically distinct G. barbata populations showed no difference in alpha diversity and composition. In contrast, higher variation in alpha diversity and lower sequence proportion of shared ASVs were observed in the holdfast and axis of the two distinct populations. Our observational study provides valuable new insights and baseline for future hypothesis-driven research on the interactions between algae and associated microbiota—a knowledge gap that needs to be addressed in the future for better understanding of the ecological and evolutionary dynamics of coastal ecosystems.
Keywords: ecosystem services, anthropogenic pressures, microbiome, host specificity, alpha diversity, marine biology, ecology
Published in DiRROS: 18.04.2025; Views: 1070; Downloads: 965
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9. Jellyfish modulate bacterial dynamic and community structureTinkara Tinta, Tjaša Kogovšek, Alenka Malej, Valentina Turk, 2012, original scientific article Abstract: Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom - forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish - enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to ‘jellyfish - associated’ and ‘free - living’ bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.
Keywords: sea, medusae, research programmes, DGGE, Pelagia noctiluca, gel electrophoresis, oligotrophic waters, Adriatic Sea, jellyfish, gelatinous zooplankton, bacteria, flavobacteria
Published in DiRROS: 26.03.2025; Views: 3555; Downloads: 995
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10. Short-term changes in microbial communities in the water column around the fish farm in the Bay of PiranValentina Turk, Tinkara Tinta, 2021, original scientific article Abstract: A multidisciplinary approach was used to study the impact of fish farming on coastal bacterial communities in the inner part of the Bay of Piran (northern Adriatic). Differences in bacterial abundance, production and the occurrence of selected bacterial groups were studied in the water column around the cage and at different distances from the centre of the fish cage towards the open water, i.e., reference marine station. We also examined the effect of fish feeding on the surrounding system in a short-term in situ experiment based on the simultaneous collection of seawater samples from different locations around the fish cage before and after feeding of fish. Our study suggests that fish feeding has a moderate short-term effect on water column parameters, including bacterial abundance and production, only at a limited distance from the fish cages. The nitrifying, ammonia-oxidizing bacterial groups, as determined by the fluorescent in situ hybridization method, were represented at a higher percentage in the seawater samples in the middle and around the fish cages. β- Proteobacteria, γ-Proteobacteria and the Cytophaga-Flavobacterium group were represented to a higher percentage at sampling sites in the middle of the Bay of Piran and at the reference marine station. The Vibrio group was detected at all sampling sites. The accumulation of organically enriched fish food and waste products released into the seawater during the short-term experiment resulted in a significant increase in particulate matter, orthophosphate and ammonium. In response to the increase in inorganic nutrients, we observed a significant increase in bacterial production, while no significant differences were observed in bacterial abundance in such short time.
Keywords: aquaculture, bacterial abundance, bacterial community composition, bacterial production, fluorescent in situ hybridisation, pollution
Published in DiRROS: 19.03.2025; Views: 953; Downloads: 965
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