1. Dispersal similarly shapes both population genetics and community patterns in the marine realmGuillem Chust, Ernesto Villarino, Anne Chenuil, Xabier Irigoien, Nihayet Bizsel, Antonio Bode, Serena Fonda Umani, Patricija Mozetič, Ángel Borja, 2016, original scientific article Abstract: Dispersal plays a key role to connect populations and, if limited, is one of the main processes to maintain and generate regional biodiversity. According to neutral theories of molecular evolution and biodiversity, dispersal limitation of propagules and population stochasticity are integral to shaping both genetic and community structure. We conducted a parallel analysis of biological connectivity at genetic and community levels in marine groups with different dispersal traits. We compiled large data sets of population genetic structure (98 benthic macroinvertebrate and 35 planktonic species) and biogeographic data (2193 benthic macroinvertebrate and 734 planktonic species). We estimated dispersal distances from population genetic data (i.e., FST vs. geographic distance) and from %-diversity at the community level. Dispersal distances ranked the biological groups in the same order at both genetic and community levels, as predicted by organism dispersal ability and seascape connectivity: macrozoobenthic species without dispersing larvae, followed by macrozoobenthic species with dispersing larvae and plankton (phyto- and zooplankton). This ranking order is associated with constraints to the movement of macrozoobenthos within the seabed compared with the pelagic habitat. We showed that dispersal limitation similarly determines the connectivity degree of communities and populations, supporting the predictions of neutral theories in marine biodiversity patterns.
Keywords: sea, phytoplankton, dispersal, distribution, ocean sampling, Atlantic Ocean, Gulf of Trieste
Published in DiRROS: 25.07.2024; Views: 99; Downloads: 96
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2. Phytoplankton across Tropical and Subtropical Regions of the Atlantic, Indian and Pacific oceansMarta Estrada, Maximino Delgado, Dolores Blasco, Mikel Latasa, Ana Maria Cabello, Verónica Benitez-Barrios, Eugenio Fraile-Nuez, Patricija Mozetič, Monteserrat Vidal, 2016, original scientific article Abstract: We examine the large-scale distribution patterns of the nano- and microphytoplankton collected from 145 oceanic stations, at 3 m depth, the 20% light level and the depth of the sub-surface chlorophyll maximum, during the Malaspina-2010 Expedition (December 2010-July 2011), which covered 15 biogeographical provinces across the Atlantic, Indian and Pacific oceans, between 35°N and 40°S. In general, the water column was stratified, the surface layers were nutrient-poor and the nano- and microplankton (hereafter phytoplankton, for simplicity, although it included also heterotrophic protists) community was dominated by dinoflagellates, other flagellates and coccolithophores, while the contribution of diatoms was only important in zones with shallow nutriclines such as the equatorial upwelling regions. We applied a principal component analysis to the correlation matrix among the abundances (after logarithmic transform) of the 76 most frequent taxa to synthesize the information contained in the phytoplankton data set. The main trends of variability identified consisted of: 1) A contrast between the community composition of the upper and the lower parts of the euphotic zone, expressed respectively by positive or negative scores of the first principal component, which was positively correlated with taxa such as the dinoflagellates Oxytoxum minutum and Scrippsiella spp., and the coccolithophores Discosphaera tubifera and Syracosphaera pulchra (HOL and HET), and negatively correlated with taxa like Ophia-ster hydroideus (coccolithophore) and several diatoms, 2) a general abundance gradient between phytoplankton-rich regions with high abundances of dinoflagellate, coccolitho-phore and ciliate taxa, and phytoplankton-poor regions (second principal component), 3) differences in dominant phytoplankton and ciliate taxa among the Atlantic, the Indian and the Pacific oceans (third principal component) and 4) the occurrence of a diatom-dominated assemblage (the fourth principal component assemblage), including several pennate taxa, Planktoniella sol, Hemiaulus hauckii and Pseudo-nitzschia spp., in the divergence regions.
Keywords: sea, phytoplankton, research programmes, ocean expeditions, Malaspina 2010, distribution, ocean sampling, Atlantic Ocean, Pacific, Indian Ocean
Published in DiRROS: 25.07.2024; Views: 203; Downloads: 66
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3. Long term results of follow-up after HPV self-sampling with devices Qvintip and HerSwab in women non-attending cervical screening programmeTeodora Bokan, Urška Ivanuš, Tine Jerman, Iztok Takač, Darja Arko, 2021, original scientific article Abstract: We are presenting the results of the Slovenian human papillomaviruses (HPV) self-sampling pilot study in colposcopy population of National Cervical Cancer Screening Programme ZORA for the first time. One-year and four-year follow-up results are presented for two different self-sampling devices. Participants and methods. A total of 209 women were enrolled in the study at colposcopy clinic. Prior to the gynaecological examination, all women performed self-collected vaginal swab at the clinic; 111 using Qvintip and 98 using HerSwab self-sampling device. After self-sampling, two cervical smears were taken by a clinician; first for conventional cytology and second for HPV test. After that, all women underwent colposcopy and a cervical biopsy if needed. We compared sensitivity, specificity, and predictive values of cytology (at the cut-off atypical squamous cells of undetermined significance or more [ASC-US+]) and HPV test (on self- and clinician-taken samples) for the detection of cervical intraepithelial neoplasia grade 2 or more (CIN2+) after one and four years of follow-up. Hybrid Capture 2 (HC2) assay was used for all HPV testing. Results. The mean age of 209 women was 37.6 years and HPV positivity rate 67.0% (140/209), 36.9 years and 70.3% (78/111) in the Qvintip group and 38.4 years and 63.3% (62/98) in the HerSwab group, respectively. Overall, percent agreement between self and clinician-taken samples was 81.8% (kappa 0.534) in the Qvintip and 77.1% (kappa 0.456) in the HerSwab group. In the Qvintip group, the longitudinal sensitivity, specificity, positive and negative predictive values were 71.8%, 75.0%, 83.6%, 60.0% for cytology; 83.1%, 51.3%, 75.6% and 62.5% for HPV test of self-taken samples and 94.4%, 57.5%, 79.8% and 85.2% for HPV test on clinician-taken samples. In the HerSwab group, the corresponding results were 71.7%, 46.7%, 61.3%, 58.3% for cytology; 75.0%, 47.7%, 62.9% and 61.8% for HPV test on self-taken samples and 94.3%, 44.4%, 66.7% and 87.0% for clinician-taken samples, respectively. Conclusions. The results confirm that HPV self-sampling is not as accurate as clinician sampling when HC2 is used. All HPV tests showed a higher sensitivity in detecting CIN2+ compared to cytology. Due to non-inferior longitudinal sensitivity of HPV self-sampling compared to cytology, HPV self-sampling might be an option for non-attenders to the National Cancer Screening Programme.
Keywords: HPV self-sampling, cytology, high-grade intraepithelial lesion, screening programmes
Published in DiRROS: 19.07.2024; Views: 110; Downloads: 39
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4. 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, original scientific article Abstract: 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.
Keywords: marine microbiome, standardized sampling, inter-comparison, amplicon sequencing, microbial diversity, seawater sampling
Published in DiRROS: 12.07.2024; Views: 89; Downloads: 127
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5. Highly specific qPCR and amplicon sequencing method for detection of quarantine citrus pathogen Phyllosticta citricarpaapplicable for air samplesJanja Zajc, Zala Kogej Zwitter, Sara Fišer, Cene Gostinčar, Antonio Vicent, Anaïs Galvañ Domenech, Luca Riccioni, Neil Boonham, Maja Ravnikar, Polona Kogovšek, 2023, original scientific article Abstract: The fungus Phyllosticta citricarpa is a quarantine pathogen in the EU and is of high economic importance in many parts of the world where favourable climate conditions drive the development of citrus black spot (CBS) disease. Disease symptoms include necrotic lesions on leaves and fruits. Low disease pressure can reduce crop market-ability, while higher disease pressure can cause premature fruit drop, significantly increasing crop losses. The wind-dispersed spores of P. citricarpa are especially prob-lematic for rapid pathogen dispersal, but also provide an opportunity for early detec-tion of the disease spreading into a new area. In this study we have developed and validated a quantitative PCR (qPCR) assay based on the TEF1-α sequence. Specificity testing demonstrated that it is currently the only qPCR assay that does not cross- react with closely related Phyllosticta species. The assay is sensitive and can detect a single copy of the TEF1 gene in a reaction, it is highly repeatable and reproducible and can be used for testing of the sticky tapes from spore traps as well as citrus fruit sam-ples. High-throughput sequencing (HTS) of the DNA barcodes ITS1 and TEF1 was also explored for the detection and discrimination of P. citricarpa. The limit of detection of the HTS was 1000 spores on a daily spore trap tape. This study makes an important improvement to the diagnostics of the CBS and the methods developed can also be applied to improve the surveillance and early detection of the pathogen when linked to spore samplers in the field.
Keywords: detection, fungal spore sampling, internal transcribed region (ITS), translation elongation factor 1-α (TEF1)
Published in DiRROS: 12.07.2024; Views: 118; Downloads: 139
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6. Microplastics in groundwater: pathways, occurrence, and monitoring challengesElvira Colmenarejo Calero, Manca Kovač Viršek, Nina Mali, 2024, original scientific article Abstract: Microplastics (MPs), defined as plastic particles measuring less than 5 mm, are considered an emerging pollutant. Their presence in the water cycle and their interaction with ecological processes pose a significant environmental threat. As groundwater (GW) represents the primary source of drinking water, monitoring MPs in GW and investigating their potential sources and pathways is of urgent importance. This article offers a comprehensive overview of the primary contamination pathways of MPs from surface water, seawater, and soil into the GW. Moreover, it presents an examination of the occurrence of MPs in GW and identifies the challenges associated with their monitoring in GW. This study also discusses the difficulties associated with comparing research results related to MPs in GW, as well as indicating the need for implementing standardised techniques for their sampling and detection. On the basis of our experience and the literature review, we highlight the importance of understanding the specific hydrogeological and hydrogeographic conditions, collecting representative samples, using sampling devices with comparable specifications and comparable laboratory techniques for MP identification, and preventing contamination at all stages of the monitoring process. This review offers valuable insights and practical guidelines on how to improve the reliability and comparability of results between studies monitoring MPs in GW.
Keywords: microplastics, groundwater, sampling, monitoring, aquifer, borehole
Published in DiRROS: 15.05.2024; Views: 228; Downloads: 181
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7. Future possibilities for long-term business cooperation between private forest owners and forest service providers in SloveniaZala Uhan, Nike Krajnc, Špela Pezdevšek Malovrh, 2023, review article Abstract: Private forest ownership, with small and fragmented forest properties prevailing in Europe, is affected by demographic, economic and social changes as well as by forest-related policy goals. This is reflected in the lack of knowledge about forest management, insufficient forest management and underutilization of forest resources. Considering that, business coop- eration between private forest owners and with forest service providers or managers is recog- nized as one of the key instruments to increase the efficiency of private forest management. The aim of this study is to investigate whether there is a potential for further development of forest lease as form of long-term business cooperation. In this research, interviews (n=8) were conducted with tenants who have signed long-term forest lease contracts with private forest owners in Slovenia. The results show that there are limited possibilities for further develop- ment of long-term business cooperation between private forest owners and forest service pro- viders/managers (e.g. forest lease). The results indicate that there are many benefits of long- term business cooperation for both sides, but private forest owners’ interest is questionable. If we want long-term business cooperation (forest lease) to succeed, forest lease should be rec- ognized in legislation, education about business cooperation (forest lease) should be given to public forest service employees, so they could promote forest lease and provide information to private forest owners. In addition, a connection between potential business partners should be established and examples of good practice should be promoted to gain trust between busi- ness partners, which could increase private forest owners’ interest and consequently improve private forest management and utilization of forest resources from private forests.
Keywords: small-scaled private forest owners, business contract, forest lease agreement, snowball sampling
Published in DiRROS: 24.04.2024; Views: 298; Downloads: 112
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8. Control of organic contaminants in groundwater by passive sampling and multivariate statistical analysisAnja Koroša, Nina Mali, 2022, original scientific article Abstract: Organic contaminants in groundwater are among the most challenging chemical compound contaminants today, particularly when it comes to understanding their occurrence, origin, and relations in groundwater, as well as the transport processes, fate, and environmental impacts involved. This paper presents the use of active carbon fibre (AFC) passive sampling and multivariate statistical processing of the results to predict the possible occurrence of organic compounds (OCs) in groundwater and to determine the origin of various anthropogenic activity. This study aims to deepen our knowledge on the control of OCs in groundwater by introducing a multi-analytical and multielemental holistic approach, using the Dravsko polje aquifer, the largest intergranular aquifer in Slovenia, as an example.
Keywords: compounds of concern, groundwater contaminants, organic compounds, passive sampling
Published in DiRROS: 22.06.2022; Views: 771; Downloads: 284
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9. Passive sampling with active carbon fibres in the determination of organic pollutants in groundwaterPrimož Auersperger, Anja Koroša, Nina Mali, Brigita Jamnik, 2022, original scientific article Abstract: Legislation addressing the quality of groundwater and increasing concerns over public health calls for the development of analytical methods that can produce accurate and precise results at the ppt level. Passive sampling has been recognised as a helpful tool in identifying various organic pollutants in groundwater, even when their presence had not yet been identified through conventional groundwater quality monitoring. The article presents an analytical method involving a simple and cost-effective passive sampling device using Zorflex® activated carbon fibres (ACFs) for the qualitative monitoring of a broad range of organic pollutants in water in a single run. The applicability of the method developed was tested in three hydrogeological studies. In the first case, we present a non-targeted qualitative screening and a list of 892 different contaminants detected in the groundwater in Slovenia. In the second case, we discuss the presence and origin of organic compounds in the groundwater from a pilot area of the urban aquifer, Ljubljansko polje. The third case presents a comparison of results between passive and grab sampling. Passive sampling with ACFs confirmed the presence of a pollutant, even when it had not been previously detected through a quantitative method.
Keywords: GC-MS, organic pollutants, qualitative analysis, passive sampling, groundwater
Published in DiRROS: 03.03.2022; Views: 853; Downloads: 348
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10. Growing stock monitoring by European National Forest Inventories : historical origins, current methods and harmonisationThomas Gschwantner, Iciar Alberdi, Sébastien Bauwens, Susann Bender, Dragan Borota, Michal Bošela, Olivier Bouriaud, Johannes Breidenbach, Janis Donis, Christoph Fischer, Mitja Skudnik, 2022, original scientific article Abstract: Wood resources have been essential for human welfare throughout history. Also nowadays, the volume of growing stock (GS) is considered one of the most important forest attributes monitored by National Forest Inventories (NFIs) to inform policy decisions and forest management planning. The origins of forest inventories closely relate to times of early wood shortage in Europe causing the need to explore and plan the utilisation of GS in the catchment areas of mines, saltworks and settlements. Over time, forest surveys became more detailed and their scope turned to larger areas, although they were still conceived as stand-wise inventories. In the 1920s, the first sample-based NFIs were introduced in the northern European countries. Since the earliest beginnings, GS monitoring approaches have considerably evolved. Current NFI methods differ due to country-specific conditions, inventory traditions, and information needs. Consequently, GS estimates were lacking international comparability and were therefore subject to recent harmonisation efforts to meet the increasing demand for consistent forest resource information at European level. As primary large-area monitoring programmes in most European countries, NFIs assess a multitude of variables, describing various aspects of sustainable forest management, including for example wood supply, carbon sequestration, and biodiversity. Many of these contemporary subject matters involve considerations about GS and its changes, at different geographic levels and time frames from past to future developments according to scenario simulations. Due to its historical, continued and currently increasing importance, we provide an up-to-date review focussing on large-area GS monitoring where we i) describe the origins and historical development of European NFIs, ii) address the terminology and present GS definitions of NFIs, iii) summarise the current methods of 23 European NFIs including sampling methods, tree measurements, volume models, estimators, uncertainty components, and the use of air- and space-borne data sources, iv) present the recent progress in NFI harmonisation in Europe, and v) provide an outlook under changing climate and forest-based bioeconomy objectives.
Keywords: forest history, natural resources, sustainability, timber volume, sampling, remote sensing, bioeconomy, climate change
Published in DiRROS: 14.12.2021; Views: 937; Downloads: 678
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