11. DNAqua-Net : developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in EuropeFlorian Leese, Tina Eleršek, Cene Fišer, Ana Rotter, Bojana Žegura, Irena Maček, 2016, original scientific article Abstract: The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.
Keywords: aquatic ecosystems, biodiversity, monitoring, genomic tools
Published in DiRROS: 25.07.2024; Views: 140; Downloads: 69
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12. Scaphoideus titanus forecasting and management : quo vadis?Elena Gonella, Giovanni Benelli, Nathalie Arricau-Bouvery, Domenico Bosco, Meta Virant-Doberlet, 2024, review article Abstract: Scaphoideus titanus Ball (Hemiptera: Cicadellidae) is a major pest for European viticulture due to its high efficiency in the transmission of one of the most destructive pathogens for grapevine, namely flavescence dorée phytoplasmas. Although it plays a major role in spreading this disease, S. titanus is part of a complex epidemiological cycle involving several alternative vectors with variable relevance for phytoplasma spread. Here we provide an updated review on S. titanus monitoring and modelling, as well as the available tools for management of this pest and for limiting phytoplasma transmission and, thus, also spread. Insecticide-based control is examined; additional emphasis is placed on innovative and low-impact control approaches, such as vibrational mating disruption, biocontrol, and methods to reduce vector competence. We also discuss the main emerging challenges to the implementation of effective and sustainable control programs against S. titanus.
Keywords: epidemiology, pest monitoring, modelling, Integrated Pest Management, vibrational mating disruption, biological control, plant resistance elicitors, RNA-interference, symbiotic control, entomology, insects, plant protection
Published in DiRROS: 23.07.2024; Views: 122; Downloads: 109
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13. Challenges in harmonized assessment of heavy metals in the Adriatic and Ionian SeasDaniela Berto, Margherita Malgorzata Formalewicz, Giordano Giorgi, Federico Rampazzo, Claudia Gion, Benedetta Trabucco, Michele Giani, Marina Lipizer, Slavica Matijević, Helen Kaberi, Christina Zeri, Oliver Bajt, Nevenka Mikac, Danijela Joksimović, Andriana Aravantinou, Mateja Poje, Magdalena Cara, Loredana Manfra, 2020, original scientific article Abstract: The Adriatic-Ionian region (ADRION Region) shows strong development in terms of urban expansion in coastal and inland areas as well as increasing maritime traffic and offshore hydrocarbon extraction activities. A serious risk of pollution arises from hazardous substances requiring reliable and coherent monitoring and assessment programs. EU Directives (WFD – Water Framework Directive, MSFD – Marine Strategy Framework Directive) and Barcelona Convention protocols, aim to assess the level of pollution with the objective to implement measures to prevent and/or mitigate impacts on the marine environment. This high level integration process has to be based on common and agreed protocols for monitoring of contaminants. Aiming to share best practices to encourage a harmonized implementation of monitoring and assessment of contaminants, an extensive review of monitoring and analytical protocols adopted by six EU and non-EU countries along the Adriatic and Ionian seas was carried out in the framework of the Interreg Adrion project HarmoNIA (Interreg V-B Adriatic-Ionian (ADRION), 2018–2020). This paper presents a methodological proposal to define a common protocol for the evaluation of the metal contamination of seawater, sediment and biota. Contaminants have been chosen following preliminary consultations among countries of the ADRION area, considering objectives of WFD and MSFD, as well as Environmental Impact Assessment (EIA) procedures for offshore platforms. Information was gathered relative to matrix characteristics and quality assurance/quality control of the analytical performance (sample preservation, analytical methodology, reference materials, limit of detection, and limit of quantification, accuracy, reproducibility, etc.). The comparison of information provided by laboratories of nine institutions highlighted the request for harmonization in terms of sampling procedures, matrix characterization, preservation procedures, analytical methods and LOQ values. Although appropriate environmental quality standards for biota and sediment matrices should be established at national level and also through regional and sub-regional cooperation, as required by the WFD and MSFD, the proposed LOQ values, even if challenging, represent a benchmark and a stimulus to optimize analytical performance, to ensure the best level of protection to the coastal and offshore environment in the ADRION Region.
Keywords: hazardous substances, harmonized protocols, integrated approach, monitoring, assessment of contaminants, heavy metals, Adriatic-Ionian Sea region
Published in DiRROS: 22.07.2024; Views: 215; Downloads: 133
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14. Challenges in harmonized environmental impact assessment (EIA), monitoring and decommissioning procedures of offshore platforms in Adriatic-Ionian (ADRION) regionLoredana Manfra, Claudia Virno Lamberti, Silvia Ceracchi, Giordano Giorgi, Daniela Berto, Marina Lipizer, Michele Giani, Oliver Bajt, Maja Fafanđel, Magdalena Cara, Slavica Matijević, Milena Mitrić, Stefanos Papazisimou, Mateja Poje, Christina Zeri, Benedetta Trabucco, 2020, original scientific article Abstract: A harmonized and integrated approach for monitoring and assessment of contamination, including hydrocarbon exploitation one, is required both by Marine Strategy Framework Directive (MSFD) at EU level and by the Ecosystem Approach (EcAp) program of the Barcelona Convention at Mediterranean level. A broad review of protocols of environmental impact assessment (EIA) procedures, monitoring and decommissioning of offshore platforms adopted by EU and non-EU countries along the Adriatic-Ionian seas was carried out in the framework of the Interreg offshore platforms in Adriatic-Ionian (ADRION) project HarmoNIA (Harmonization and networking for contaminant assessment in the Ionian and Adriatic Seas). The comparison of information provided by six ADRION countries and the application of a harmonized and integrated approach has highlighted specific challenges for managing offshore platform impacts emerged at ADRION level: (i) need of the same legislative level (the Offshore Protocol of Barcelona Convention is not ratified by all countries); (ii) set up of a task force of ADRION experts for discussing critical issues related to impacts of offshore platforms; (iii) harmonization, at the regional level, of EIA procedures, monitoring and decommissioning; (iv) need of an agreed and common list of recommended parameters to monitor in water, sediment and biota for the assessment of impacts due to platform installations and PFW discharges.
Keywords: harmonized protocols, environmental impact assessment, monitoring, decommissioning, offshore platforms, Adriatic-Ionian Sea region, MSFD, Barcelona Convention
Published in DiRROS: 22.07.2024; Views: 239; Downloads: 68
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15. Feasibility of droplet digital PCR analysis of plasma cell-free DNA from kidney transplant patientsBarbara Jerič Kokelj, Maja Štalekar, Sebastian Vencken, David Dobnik, Polona Kogovšek, Matjaž Stanonik, Miha Arnol, Maja Ravnikar, 2021, original scientific article Abstract: Increasing research demonstrates the potential of donor-derived cell-free DNA (dd-cfDNA) as a biomarker for monitoring the health of various solid organ transplants. Several methods have been proposed for cfDNA analysis, including real-time PCR, digital PCR, and next generation sequencing-based approaches. We sought to revise the droplet digital PCR (ddPCR)-based approach to quantify relative dd-cfDNA in plasma from kidney transplant (KTx) patients using a novel pilot set of assays targeting single nucleotide polymorphisms that have a very high potential to distinguish cfDNA from two individuals. The assays are capable of accurate quantification of down to 0.1% minor allele content when analyzing 165 ng of human DNA. We found no significant differences in the yield of extracted cfDNA using the three different commercial kits tested. More cfDNA was extracted from the plasma of KTx patients than from healthy volunteers, especially early after transplantation. The median level of donor-derived minor alleles in KTx samples was 0.35%. We found that ddPCR using the evaluated assays within specific range is suitable for analysis of KTx patientsʼ plasma but recommend prior genotyping of donor DNA and performing reliable preamplification of cfDNA.
Keywords: kidney transplantation, droplet digital PCR, plasma cell-free DNA, minor allele quantification, assay evaluation, graft health monitoring
Published in DiRROS: 19.07.2024; Views: 130; Downloads: 66
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16. Is it time for ecotremology?Rok Šturm, Juan José López Díez, Jernej Polajnar, Jérôme Sueur, Meta Virant-Doberlet, 2022, original scientific article Abstract: Our awareness of air-borne sounds in natural and urban habitats has led to the recent recognition of soundscape ecology and ecoacoustics as interdisciplinary fields of research that can help us better understand ecological processes and ecosystem dynamics. Because the vibroscape (i.e., the substrate-borne vibrations occurring in a given environment) is hidden to the human senses, we have largely overlooked its ecological significance. Substrate vibrations provide information crucial to the reproduction and survival of most animals, especially arthropods, which are essential to ecosystem functioning. Thus, vibroscape is an important component of the environment perceived by the majority of animals. Nowadays, when the environment is rapidly changing due to human activities, climate change, and invasive species, this hidden vibratory world is also likely to change without our notice, with potentially crucial effects on arthropod communities. Here, we introduce ecotremology, a discipline that mainly aims at studying substrate-borne vibrations for unraveling ecological processes and biological conservation. As biotremology follows the main research concepts of bioacoustics, ecotremology is consistent with the paradigms of ecoacoustics. We argue that information extracted from substrate vibrations present in the environment can be used to comprehensively assess and reliably predict ecosystem changes. We identify key research questions and discuss the technical challenges associated with ecotremology studies.
Keywords: ecotremology, monitoring, hidden biodiversity, vibroscape, vibrational communication
Published in DiRROS: 16.07.2024; Views: 136; Downloads: 121
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17. Validated inventories of non-indigenous species (NIS) for the Mediterranean Sea as tools for regional policy and patterns of NIS spreadMarika Galanidi, Mehdi Aissi, Malek Ali, Ali Bakalem, Michel Bariche, Angela G. Bartolo, Borut Mavrič, Martina Orlando-Bonaca, 2023, original scientific article Abstract: This work presents refined, updated subregional and regional non-indigenous species (NIS) inventories for the Mediterranean Sea, validated by national and taxonomic experts, with species records observed until December 2020. These datasets will be used as the baselines for the implementation of the Integrated Monitoring and Assessment Programme for the Mediterranean (IMAP) and the Mediterranean Quality Status Report 2023. In total, 1006 non-indigenous species have been found in Mediterranean marine and brackish waters. The highest numbers of NIS were observed in Israel, Türkiye, Lebanon and Italy. Approximately 45 species were categorized as data deficient, either due to lack of consensus on their alien status or the validity of their identification. Polychaeta, Foraminifera and macroalgae were the groups with the highest numbers of controversial species. There was a general increase in the yearly rate of new NIS introductions after the late 1990s, which appears to be slowing down in the last decade, but this may be confounded by reporting lags and differential research efforts. Between 1970 and 2020 there has been a steep increase in the proportion of shared species present throughout all four Mediterranean subregions, which are predominantly transported via shipping and recreational boating. While Lessepsian species are gradually spreading westwards and northwards, there is still a considerable invasion debt accumulating in the eastern and central Mediterranean.
Keywords: non-indigenous species, Mediterranean Sea, validation, non-indigenous species inventories, NIS, Integrated Monitoring and Assessment Programme for the Mediterranean, IMAP
Published in DiRROS: 12.07.2024; Views: 154; Downloads: 144
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18. Evaluation of the rbcL marker for metabarcoding of marine diatoms and inference of population structure of selected generaTimotej Turk Dermastia, Ivano Vascotto, Janja Francé, David Stanković, Patricija Mozetič, 2023, original scientific article Abstract: Diatoms are one of the most important phytoplankton groups in the world’s oceans. There are responsible for up to 40% of the photosynthetic activity in the Ocean, and they play an important role in the silicon and carbon cycles by decoupling carbon from atmospheric interactions through sinking and export. These processes are strongly influenced by the taxonomic composition of diatom assemblages. Traditionally, these have been assessed using microscopy, which in some cases is not reliable or reproducible. Next-generation sequencing enabled us to study diversity in a high-throughput manner and uncover new distribution patterns and diversity. However, phylogenetic markers used for this purpose, such as various 18S rDNA regions, are often insufficient because they cannot distinguish between some taxa. In this work, we demonstrate the performance of the chloroplast-encoded rbcL marker for metabarcoding marine diatoms compared to microscopy and 18S-V9 metabarcoding using a series of monthly samples from the Gulf of Trieste (GoT), northern Adriatic Sea. We demonstrate that rbcL is able to detect more taxa compared to 18S-V9 metabarcoding or microscopy, while the overall structure of the diatom assemblage was comparable to the other two methods with some variations, that were taxon dependent. In total, 6 new genera and 22 new diatom species for the study region were identified. We were able to spot misidentification of genera obtained with microscopy such as Pseudo-nitzschia galaxiae, which was mistaken for Cylindrotheca closterium, as well as genera that were completely overlooked, such as Minidiscus and several genera from the Cymatosiraceae family. Furthermore, on the example of two well-studied genera in the region, namely Chaetoceros and particularly Pseudo-nitzschia, we show how the rbcL method can be used to infer even deeper phylogenetic and ecologically significant differences at the species population level. Despite a very thorough community analysis obtained by rbcL the incompleteness of reference databases was still evident, and we shed light on possible improvements. Our work has further implications for studies dealing with taxa distribution and population structure, as well as carbon and silica flux models and networks.
Keywords: rbcL, metabarcoding, monitoring, diatoms, population genetics, Pseudo-nitzschia, Adriatic
Published in DiRROS: 12.07.2024; Views: 130; Downloads: 96
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19. Impact of deoxynivalenol and zearalenone as single and combined treatment on DNA, cell cycle and cell proliferation in HepG2 cellsAna-Marija Domijan, Klara Hercog, Martina Štampar, Goran Gajski, Marko Gerić, Marijana Sokolović, Bojana Žegura, 2023, original scientific article Abstract: The study aimed to investigate toxicity and the mechanism of toxicity of two Fusarium mycotoxins, deoxynivalenol (DON) and zearalenone (ZEA). DON and ZEA were applied to HepG2 cells as single compounds and in combination at low environmentally relevant concentrations. HepG2 cells were exposed to DON (0.5, 1, and 2 µM), ZEA (5, 10, and 20 µM) or their combinations (1 µM DON + 5 µM ZEA, 1 µM DON + 10 µM ZEA and 1 µM DON + 20 µM ZEA) for 24 h and cell viability, DNA damage, cell cycle and proliferation were assessed. Both mycotoxins reduced cell viability, however, combined treatment with DON and ZEA resulted in higher reduction of cell viability. DON (1 µM) induced primary DNA damage, while DON (1 µM) in combination with higher ZEA concentrations showed antagonistic effects compared to DON alone at 1 µM. DON arrested HepG2 cells in G2 phase and significantly inhibited cell proliferation, while ZEA had no significant effect on cell cycle. The combined treatment with DON and ZEA arrested cells in G2 phase to a higher extend compared to treatment with single mycotoxins. Potentiating effect observed after DON and ZEA co-exposure at environmentally relevant concentrations indicates that in risk assessment and setting governments’ regulations, mixtures of mycotoxins should be considered.
Keywords: mycotoxins, comet assay, flow cytometry, co-exposure, food monitoring
Published in DiRROS: 12.07.2024; Views: 273; Downloads: 147
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20. Vsebnosti potencialno strupenih elementov v sedimentih in vodah reke Meže in njenih pritokov, ki odvodnjavajo odlagališča rudarskih odpadkovMateja Gosar, Špela Bavec, Miloš Miler, Martin Gaberšek, 2024, original scientific article Abstract: Predstavljeni so rezultati spremljanja vsebnosti potencialno strupenih elementov (PSE) v sedimentih (v letih 2013, 2017, 2020) in vodah (v letih 2017, 2020) reke Meže ter njenih pritokov, ki odvodnjavajo odlagališča rudarskih odpadkov. Skupno 13 vzorčnih mest je vzpostavljenih v vzorčni shemi, ki omogoča dolgoročno opazovanje vpliva odlagališč rudarskih odpadkov. V sedimentih so zaradi vplivov več kot 300-letnega delovanja rudarsko-predelovalne industrije močno povečane vsebnosti PSE, predvsem Pb, Zn, Cd, Mo in As, ki s časom precej nihajo. Razlike v vsebnostih na istih lokacijah v različnih letih so najbolj izrazite v pritokih reke Meže, ki drenirajo odlagališča rudarskih odpadkov. Na vsebnosti imajo pomemben vpliv hidrološki pogoji, saj so ob višjem vodostaju in višjem pretoku vsebnosti PSE večje. Vodna erozija odlagališč ima pomemben vpliv na dotok onesnaženega materiala v vodotoke. V nasprotju s pritoki, v zgornjem toku reke Meže nismo opazili večjega vpliva višjega vodostaja in pretoka na vsebnosti PSE v sedimentih. Dolvodno od Žerjava so nihanja vsebnosti med posameznimi leti oz. različnimi hidrološkimi pogoji tudi v Meži večja. Predstavljeni rezultati kažejo, da so v sedimentih reke Meže in njenih pritokov vsebnosti Pb, Zn, Cd, Mo in As zelo velike ter krepko presegajo zakonsko določeno kritično vrednost za tla. V površinski vodi so vsebnosti PSE lokalno povečane in se s časom bistveno ne spreminjajo. Glede na primerjavo z zakonodajnimi smernicami, so v obravnavanih vodah lokalno presežene koncentracije Pb, Cd in Zn. Ocenjujemo, da je dinamika obremenjenosti sedimentov reke Meže s PSE vzdolž krajev Črna na Koroškem, Žerjav in Mežica zelo kompleksna. Poleg odlagališč rudarskih odpadkov na vsebnosti PSE v sedimentih in vodah vplivajo tudi razpršeni viri v okolju, kot so onesnažena tla in poplavne ravnice ter njihova različna stopnja onesnaženosti, saj je okolje obremenjeno zaradi dolgoletnih rudarskih in talilniških dejavnosti. Dodaten okoljski vpliv ima morda tudi sedanja industrijska dejavnost v dolini reke Meže.
Keywords: rudarjenje, rudarski odpadki, odlagališča odpadkov, potencialno strupeni elementi, rečni sedimenti, monitoring, onesnaženje okolja
Published in DiRROS: 09.07.2024; Views: 135; Downloads: 80
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