1. Unearthing the soil-borne microbiome of land plantsRaúl Ochoa-Hueso, David J. Eldridge, Miguel Berdugo, Pankaj Trivedi, Blessing Sokoya, Concha Cano-Díaz, Sebastian Abades, Fernando D. Alfaro, Adebola R. Bamigboye, Felipe Bastida, Tine Grebenc, Tina Unuk Nahberger, 2024, original scientific article Abstract: Plant–soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.
Keywords: belowground networks, environmental thresholds, moss microbiome, plant microbiome, plant–soil interactions
Published in DiRROS: 31.05.2024; Views: 36; Downloads: 32
 Full text (17,56 MB)
This document has many files! More... |
2. Cancer burden in Slovenia with the time trends analysisVesna Zadnik, Maja Primic-Žakelj, Katarina Lokar, Katja Jarm, Urška Ivanuš, Tina Žagar, 2017, original scientific article Abstract: Background The aim of our study was to describe cancer burden and time trends of all cancers combined, the most frequent as well as the rare cancers in Slovenia. Patients and methods The principal data source was the population-based Cancer Registry of Republic of Slovenia. The cancer burden is presented by incidence and prevalence for the period 1950%2013 and by mortality for years 1985%2013. The time trends were characterized in terms of an average annual percent change estimated by the log-linear joinpoint regression. The Dyba-Hakulinen method was used for estimation of incidence in 2016 and the projections of cancer incidence for the year 2025 were calculated applying the Globocan projection software. Results In recent years, near 14,000 Slovenes were diagnosed with cancer per year and just over 6,000 died; more than 94,000 people who were ever diagnosed with cancer are currently living among us. The total burden of cancer is dominated by five most common cancer sites: skin (non-melanoma), colon and rectum, lung, breast and prostate, together representing almost 60% of all new cancer cases. On average the incidence of common cancers in Slovenia is increasing for 3.0% per year in last decade, but the incidence of rare cancers is stable. Conclusions Because cancer occurs more among the elderly, and additionally more numerous post-war generation is entering this age group, it is expected that the burden of this disease will be growing further, even if the level of risk factors remains the same as today.
Keywords: cancer burden, cancer registry, incidence, prevalence
Published in DiRROS: 24.05.2024; Views: 94; Downloads: 75
Full text (557,44 KB)
This document has many files! More... |
3. |
4. Towards the development of a landslide activity map in SloveniaMateja Jemec Auflič, Krištof Oštir, Tanja Grabrijan, Matjaž Ivačič, Tina Peternel, Ela Šegina, 2024, original scientific article Abstract: To create the landslide activity map, we implemented and tested the procedure to fully utilise the 6-day repeatability of the Sentinel-1 constellation in three pilot areas in Slovenia for the observation period from 2017 to 2021. The interferometric processing of the Sentinel-1 images was carried out with ENVI SARScape, while the interpretation of the persistent scatterers InSAR data was done in three steps. In the first step, a preliminary interpretation of the landslide areas was performed by integrating the PS InSAR data into a GIS environment with information that could be relevant to explain the movement patterns of the PS InSAR points. In the second step, a field validation was performed to check the PS InSAR in the field and record the potential damage to the objects indicating the slope mass movements. In the third step, the deformations were identified, and areas of significant movement were determined, consisting of clusters of at least 3 persistent scatterers (PS) with a maximum spacing of 10 m. The landslide activity map was created based on the landslide areas categorised into four classes based on the geotechnical analyses, yearly velocity data obtained by PS InSAR, and validation of annual velocity data obtained by in-situ and GNSS monitoring and field observation. A total of 21 polygons with different landslide activities were identified in three study areas. The overall methodology will help stakeholders in the early mapping and monitoring of landslides to increase the urban resilience.
Keywords: landslides, EO data, sentinel, time series, methodology, Slovenia
Published in DiRROS: 30.04.2024; Views: 150; Downloads: 69
Full text (73,45 MB) |
5. Towards improved online dissolution evaluation of Pt-alloy PEMFC electrocatalysts via electrochemical flow cell - ICP-MS setup upgradesLeonard Moriau, Tina Đukić, Vojtech Domin, Roman Kodym, Martin Prokop, Karel Bouzek, Matija Gatalo, Martin Šala, Nejc Hodnik, 2024, original scientific article Published in DiRROS: 29.04.2024; Views: 138; Downloads: 121
Full text (5,39 MB)
This document has many files! More... |
6. |
7. How beech provenance affects the structure of secondary xylem, leaf traits, and the ectomycorrhizal community under optimal growth conditionsTanja Mrak, Jožica Gričar, Tina Unuk Nahberger, Gregor Božič, Luka Krajnc, Peter Prislan, Domen Arnič, Tom Levanič, Hojka Kraigher, 2024, original scientific article Abstract: Beyond growth parameters and drought tolerance, comparatively little is known about the functioning of different beech (Fagus sylvatica L.) provenances. We investigated properties of leaves, stem secondary xylem, and ectomycorrhiza (ECM), and explored their interdependencies to identify the best performing beech provenance in optimal growth conditions. The study was conducted on 23-year-old trees in a provenance trial. The investigated provenances originated from Atlantic (Belgium—BE), Alpine (Italy—IT, Slovenia—SI), and continental climates (the Czech Republic—CZ). A significant effect of provenance was observed for stem vessel diameters and conductive area, as well as for foliar %C, δ13C, δ15N, and δ18O. δ13C as a proxy of intrinsic water use efficiency (iWUE) showed that the highest iWUE was achieved in BE provenance. Individuals with a better iWUE had wider growth rings regardless of provenance. Better iWUE was associated with lower specific leaf area (SLA). ECM community composition and diversity indices did not differ significantly among the provenances. Specific ECM taxa were associated with individuals with high SLA, δ13C, δ15N, and δ18O. In optimal growth conditions with no stress events, BE is a promising provenance due to an efficient water conducting system with high vessel diameters and conductive area, and high iWUE, while Alpine provenances showed an adaptation of their water conducting system to freezing conditions at their original locations. Integrating findings from different compartments improves our understanding of functioning of different beech provenances.
Keywords: Fagus sylvatica, provenance trial, stable isotopes, specific leaf area, xylem vessels, ectomycorrhizal fungi
Published in DiRROS: 19.04.2024; Views: 169; Downloads: 665
Full text (2,11 MB)
This document has many files! More... |
8. Urban greenspaces and nearby natural areas support similar levels of soil ecosystem servicesDavid J. Eldridge, Haiying Cui, Jingyi Ding, Miguel Berdugo, Tadeo Sáez-Sandino, Jorge Duran, Juan J. Gaitan, José L. Blanco-Pastor, Alexandra Rodríguez, César Plaza, Tine Grebenc, Tina Unuk Nahberger, 2024, original scientific article Abstract: Greenspaces are important for sustaining healthy urban environments and their human populations. Yet their capacity to support multiple ecosystem services simultaneously (multiservices) compared with nearby natural ecosystems remains virtually unknown. We conducted a global field survey in 56 urban areas to investigate the influence of urban greenspaces on 23 soil and plant attributes and compared them with nearby natural environments. We show that, in general, urban greenspaces and nearby natural areas support similar levels of soil multiservices, with only six of 23 attributes (available phosphorus, water holding capacity, water respiration, plant cover, arbuscular mycorrhizal fungi (AMF), and arachnid richness) significantly greater in greenspaces, and one (available ammonium) greater in natural areas. Further analyses showed that, although natural areas and urban greenspaces delivered a similar number of services at low (>25% threshold) and moderate (>50%) levels of functioning, natural systems supported significantly more functions at high (>75%) levels of functioning. Management practices (mowing) played an important role in explaining urban ecosystem services, but there were no effects of fertilisation or irrigation. Some services declined with increasing site size, for both greenspaces and natural areas. Our work highlights the fact that urban greenspaces are more similar to natural environments than previously reported and underscores the importance of managing urban greenspaces not only for their social and recreational values, but for supporting multiple ecosystem services on which soils and human well-being depends.
Keywords: soil, ecosystem services, urban forests
Published in DiRROS: 17.04.2024; Views: 183; Downloads: 86
Full text (1,91 MB)
This document has many files! More... |
9. Recovering high-quality bacterial genomes from cross-contaminated cultures : a case study of marine Vibrio campbelliiNeža Orel, Eduard Fadeev, Gerhard J. Herndl, Valentina Turk, Tinkara Tinta, 2024, original scientific article Abstract: Background: Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. Results: We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. Conclusions: Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
Keywords: whole-genome assembly, non-axenic culture, plasmid, marine bacteria, marine biology
Published in DiRROS: 28.03.2024; Views: 220; Downloads: 100
Full text (5,87 MB)
This document has many files! More... |
10. Recombinant human erythropoietin alters gene expression and stimulates proliferation of MCF-7 breast cancer cellsNina Trošt, Tina Stepišnik, Sabina Berne, Anja Pucer Janež, Toni Petan, Radovan Komel, Nataša Debeljak, 2013, published scientific conference contribution Abstract: Background. Functional erythropoietin (EPO) signaling is not specific only to erythroid lineages and has been confirmed in several solid tumors, including breast. Three different isoforms of erythropoietin receptor (EPOR) have been reported, the soluble (EPOR-S) and truncated (EPOR-T) forms acting antagonistically to the functional EPOR. In this study, we investigated the effect of human recombinant erythropoietin (rHuEPO) on cell proliferation, early gene response and the expression of EPOR isoforms in the MCF-7 breast cancer cell line.Materials and methods. The MCF-7 cells were cultured with or without rHuEPO for 72 h or 10 weeks and assessed for their growth characteristics, expression of early response genes and different EPOR isoforms. The expression profile of EPOR and EPOR-T was determined in a range of breast cancer cell lines and compared with their invasive properties.Results. MCF-7 cell proliferation after rHuEPO treatment was dependent on the time of treatment and the concentration used. High rHuEPO concentrations (40 U/ml) stimulated cell proliferation independently of a preceding long-term exposure of MCF-7 cells to rHuEPO, while lower concentrations increased MCF-7 proliferation only after 10 weeks of treatment. Gene expression analysis showed activation of EGR1 and FOS, confirming the functionality of EPOR. rHuEPO treatment also slightly increased the expression of the functional EPOR isoform, which, however, persisted throughout the 10 weeks of treatment. The expression levels of EPOR-T were not influenced. There were no correlations between EPOR expression and the invasiveness of MCF-7, MDA-MB-231, Hs578T, Hs578Bst, SKBR3, T-47D and MCF-10A cell lines.Conclusions. rHuEPO modulates MCF-7 cell proliferation in time- and concentration-dependent manner. We confirmed EGR1, FOS and EPOR as transcription targets of the EPO-EPOR signaling loop, but could not correlate the expression of different EPOR isoforms with the invasiveness of breast cancer cell lines.
Keywords: breast cancer, erythropoietin, gene expression
Published in DiRROS: 22.03.2024; Views: 293; Downloads: 73
Full text (850,15 KB)
This document has many files! More... |
