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Povzetek: Although geographically well apart, there are interesting similarities between the ecosystems of the Sea of Marmara and the Adriatic Sea. In this study, following an evaluation of the ecological problems as well as oceanography, productivity, plankton biomass of these seas, macro-jellyfish ecology of the two ecosystems were discussed comparatively. The Sea of Marmara and the Adriatic Sea are among the areas where increases in jellyfish and mucilage events have been observed in recent decades. Environmental problems such as global warming, oxygen depletion, eutrophication, overfishing, intense maritime traffic, and habitat destruction are causing opportunistic and alien species to increase in both abundance and number of species. As biodiversity declines due to habitat destruction, so does the ecosystem’s means and ability to combat the invasion of alien species in both ecosystems. Accordingly, disruption of lower food chains can put pressure on the entire ecosystem and affect socio-ecological prospects. The number of species of Scyphozoa and Ctenophora was found to be higher in the Adraitic Sea compared to the Sea of Marmara. Mass occurrences with a clear seasonal pattern and related to the geographical location were observed for Aurelia aurita, Rhizostoma pulmo, Chrysaora hysoscella and non-native Mnemiopsis leidyi in the Marmara Sea. However, although A. aurita and R. pulmo show widespread blooms according to the seasons and regions in the Adriatic Sea, C. hysoscella and M. leidyi produced blooms limited to a few areas. Negative and positive interactions of macrojelyfishes with human were also considered. Semi-enclosed seas such as the Sea of Marmara and the Adriatic Sea are representative of many temperate coastal waters where climate change and anthropogenic stressors are increasing, and the ecosystem has changed from a fish-dominated to a jellyfish-dominated ecosystem.
Ključne besede: jellyfish, eutrophication, diversity, introduce, fisheries
Objavljeno v DiRROS: 07.05.2025; Ogledov: 114; Prenosov: 52
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Povzetek: Pseudo-nitzschia, a globally distributed diatom genus, dominates phytoplankton communities in biomass and abundance, with some species producing domoic acid (DA), the neurotoxin responsible for Amnesic Shellfish Poisoning (ASP). The Adriatic Sea has become a hub of Pseudo-nitzschia research over the past 15 years. This review synthesizes multidisciplinary research across Adriatic sub-basins, integrating morphological, genetic, and ecological data. While ASP has never been documented in the Adriatic, DA was occasionally detected in shellfish. The production was linked to toxic species such as P. multistriata, P. calliantha, and P. galaxiae, which were found to produce DA in cultures from Adriatic isolates. Despite progress, LM-based monitoring remains prevalent, underestimating species complexity and toxigenic potential. Electron microscopy and genetic barcoding have nonetheless revealed new insights into the species composition of this genus in Adriatic. A total of 14 species have been reported so far with prominent regional disparity: the northern and middle Adriatic host higher diversity, contrasting with the southern Adriatic, where only five species were confirmed, and research remains sparse. Seasonal dynamics show summer-autumn peaks in abundance, though interannual and regional variability is notable. We present recent advances from the Adriatic including the discovery of Pseudo-nitzschia-infecting viruses, population genomic insights in P. multistriata, and metabarcoding-driven revelations of cryptic diversity. Finally, we highlight critical knowledge gaps, including the ecological drivers of toxicity and the impacts of oligotrophication on community shifts. Collaborative, high-resolution methodologies (e.g., omics, automated imaging) are urged to address emerging challenges under climate change and anthropogenic pressures.
Ključne besede: Adriatic, Pseudo-nitzschia, diversity, ecology
Objavljeno v DiRROS: 14.04.2025; Ogledov: 190; Prenosov: 76
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Povzetek: Background Phages are critical components of the gut microbiome, influencing bacterial composition and function as predators, parasites, and modulators of bacterial phenotypes. Prophages, integrated forms of these phages, are prevalent in many bacterial genomes and play a role in bacterial adaptation and evolution. However, the diversity and stability of prophages within gut commensals, particularly in the genera Bacteroides and Phocaeicola, remain underexplored. This study aims to screen and characterize prophages in these genera, providing insights into their diversity, host range, and temporal dynamics in the human gut. Results Using a combination of three bioinformatic tools—Cenote-Taker 3, Vibrant, and PHASTER—we conducted a comprehensive analysis of prophages in Bacteroides and Phocaeicola. Cenote-Taker 3 identified the most diverse set of prophages, with significant overlaps observed between the tools. After clustering high-quality prophages, we identified 22 unique viral operational taxonomic units (vOTUs). Notably, comparisons between prophages identified in isolated bacterial genomes, metaviromes, and large public gut virome databases revealed a broader host range than initially observed in single isolates. Certain prophages were consistent across time points and individuals, suggesting temporal stability. All identified prophages belonged to the Caudoviricetes class and contained genes related to antibiotic resistance, toxin production, and metabolic processes. Conclusions The combined use of multiple prophage detection tools allowed for a more comprehensive assessment of prophage diversity in Bacteroides and Phocaeicola. The identified prophages were not only prevalent but also exhibited broad host ranges and temporal stability. The presence of antibiotic resistance and toxin genes suggests that these prophages may significantly influence bacterial community structure and function in the gut, with potential implications for human health. These findings highlight the importance of using diverse detection tools to accurately assess prophage diversity and dynamics.
Ključne besede: prophage detection, Bacteroides, Phocaeicola, gut microbiome, prophage diversity, Caudoviricetes, antibiotic resistance, phage-bacteria interactions, temporal stability
Objavljeno v DiRROS: 06.03.2025; Ogledov: 224; Prenosov: 188
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Povzetek: Self-organizing maps (SOMs) are a class of neural network algorithms able to visually describe a high-dimensional dataset onto a two-dimensional grid. SOMs were explored to classify soils based on an array of physical, chemical, and biological parameters. Methods: The SOM analysis was performed considering soil physical, chemical, and microbial data gathered from an array of apple orchards and strawberry plantations managed by organic or conventional methods and located in different European climatic zones. Results: The SOM analysis considering the “climatic zone” categorical variables was able to discriminate the samples from the three zones for both crops. The zones were associated with different soil textures and chemical characteristics, and for both crops, the Continental zone was associated with microbial parameters—including biodiversity indices derived from the NGS data analysis. However, the SOM analysis based on the “management method” categorical variables was not able to discriminate the soils between organic and integrated management. Conclusions: This study allowed for the Soil Syst. 2025, 9, 10 https://doi.org/10.3390/soilsystems9010010 Soil Syst. 2025, 9, 10 2 of 14 discrimination of soils of medium- and long-term fruit crops based on their pedo-climatic characteristics and associating these characteristics to some indicators of the soil biome, pointing to the possibility of better understanding the interactions among diverse variables, which could support unraveling the intricate web of relationships that define soil quality.
Ključne besede: apple, neural networks, soil microbiome diversity, strawberry
Objavljeno v DiRROS: 03.02.2025; Ogledov: 252; Prenosov: 74
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Povzetek: The ectomycorrhizal symbionts of silver fir have rarely been analyzed and identified, so little is known about their diversity and distribution. The aim of this study was (1) to analyze the diversity of ectomycorrhizal fungal species in three geographically distinct forest stands of Abies alba and (2) to demonstrate the high temporal variability of the ectomycorrhizal community over two consecutive growing seasons using repeated monthly sampling. Root samples were taken every month during two growing seasons in three silver fir-dominated forest stands. The ectomycorrhizal root tips were first assigned to a morphotype based on morphological characteristics and then identified by sequencing the internal transcribed spacer region. Alpha and beta diversity differed significantly between all three study sites, with the most diverse and even ectomycorrhizal community described in plot Jelovški boršt. The diversity indices over the growing season were different at two of the three study sites, supporting the idea of a fluctuation of ectomycorrhizal taxa during the growing seasons of the two consecutive years. While significant temporal variability was only confirmed for certain ectomycorrhizal taxa, there were no significant changes in the ectomycorrhizal community in general. Thus, we confirmed the high spatial but low temporal variability of the ectomycorrhizal community associated with silver fir.
Ključne besede: ectomycorrhizal community, spatiotemporal variation, silver fir, fungal diversity, forest, root-associated fungi
Objavljeno v DiRROS: 31.01.2025; Ogledov: 220; Prenosov: 132
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