Our ongoing projects
2026-2029
Defining biology and adaptive constraints of newly discovered plant viruses through the use of synthetic virology and deep mutational scanning (SNEP-VIMS)
Funding: Slovenian Research and Innovation Agency (ARIS)
Leading organization: NIB, Department of Biotechnology and Systems Biology
Project leader: Denis Kutnjak
Involved researchers from NIB: Maja Ferle, Ion Gutierrez Aguirre, Živa Lengar, Kristina Gruden, Tjaša Lukan, Katja Stare
Discovery of many previously unknown plant viruses in crops, wild plants and environmental samples triggers subsequent concerns about their significance, such as their potential for emergence as disease agents in agriculture. One of the important questions associated with these discoveries is: can viruses discovered in wild plants or weeds infect crop plants or can they obtain this ability through adaptation? To address this question, we would like to reach beyond classical infectivity tests (inoculation of crop plant species with plant sap containing a particular newly discovered virus) and test the adaptation potential of such viruses. In our previous metagenomics studies, we have discovered many new virus species in wild plants and in the environment. Here, we will select candidate model viruses, among those discovered by metagenomcis, for characterisation of possible constraints and trade-offs during adaptation of those viruses to new hosts. We aim to achieve this by combining newest approaches for preparation of infectious viral clones, deep mutational scanning and high-throughput sequencing linked with experimental evolution.
2026-2029
Virome characterization and dynamics in successful crayfish invaders
Funding: Slovenian Research and Innovation Agency (ARIS) (N1-0441)
Leading organization: NIB, Department of Biotechnology and Systems Biology
Project leader: Denis Kutnjak
Involved researchers from NIB-MICRO: Katarina Bačnik, Andrea Belamarić
ViroCray project will explore and characterize viromes of three crayfish invaders using a large-scale approach that accounts for population and species differences in introduction history, population age, size and co-occurrence with other native or invasive congeners. This is a trilateral multigency Weave project, in which we will combine our expertise in high-throughput sequencing (HTS) based approaches to studying viromes (SI) with expertise in crayfish ecology and experimental studies (CZ, group of Antonin Kouba) and crayfish immunology, histopathology and invasion ecology (HR, group of Sandra Hudina). This will allow us to examine the effects of extrinsic and intrinsic factors shaping virome diversity, assess its dynamics in response to interspecies contact and to explore key invasion hypotheses on microbes.
2026-2028
Exploring spider web viromes for surveillance of virus diversity in ecosystems
Funding: Slovenian Research and Innovation Agency (ARIS) postdoctoral project
Leading organization: NIB, Department of Biotechnology and Systems Biology
Project leader: Anja Pecman
Modern molecular biology techniques, particularly environmental DNA (eDNA) analysis, have great potential to revolutionize biodiversity and microbial community monitoring by overcoming the limitations of traditional, invasive approaches. While eDNA has been widely used to assess diverse organisms across multiple matrices, the use of spider webs as passive eDNA samplers, especially for studying viral diversity, remains largely unexplored. Acting as natural air filters, spider webs capture genetic material from their environment, positioning them as a promising tool for ecological surveillance. As key predators, spiders and their webs interact with a diverse array of viruses through their prey and environmental exposure. Few viruses have been detected in some spider species; however, viral diversity present in spider webs remains unexplored.
To fill this gap, Linyphia triangularis was selected as a model species due to its high population density across Slovenia. We hypothesize that spider webs can serve as efficient passive samplers for viral monitoring. Using high-throughput sequencing–based metagenomic approaches, this research will expand knowledge of viral biodiversity, support the development of spider webs as tools for environmental virus monitoring, and improve detection of known and novel viral pathogens, contributing to ecosystem health monitoring and early warning of emerging viral threats.
2026-2029
The role of bacteriophages in the transmission of antibiotic resistance genes in natural recreational water environments from the ”one health” perspective
Funding: Slovenian Research and Innovation Agency (ARIS)
Leading organization: University of Ljubljana, Biotechnical Faculty (Project leader: Jerneja Zupančič Čremožnik)
Leader at NIB: Denis Kutnjak
Involved researchers from NIB: Katarina Bačnik, Ion Gutierrez Aguirre
The aim of this project is to investigate the possible role of bacteriophages in the development and spread of antibiotic resistance in bathing waters. The increasing number of ARB/ARG in natural recreational waters should be considered as microbiological pollution for which regular monitoring should be introduced. Although recent research on ARG in the environment can largely rely on culture-independent metagenomic analyses, a culture-based approach is still required to investigate the actual horizontal transmission, the frequency of transmission and the host and environmental factors influencing the frequency of transmission of ARG via plasmids and/or phages, including their host range, as these data cannot be obtained by bioinformatic analyses alone. In this project, we will combine both culturing and metagenomic approaches, where our group will contribute expertise in the latter.
2026-2029
Viral Infection-Driven Changes in Phytoplankton Aggregates and Their Microbial Processing (VIRAMP)
Funding: Slovenian Research and Innovation Agency (ARIS)
Leading organization: NIB, Marine biology station
Project leader: Timotej Turk Dermastia
Involved researchers from NIB-MICRO: Denis Kutnjak
Marine phytoplankton plays a key role in carbon sequestration, yet the factors controlling carbon export efficiency in coastal seas remain poorly understood. Viral infections can strongly influence these processes by altering phytoplankton aggregation and the microbial processing of particulate organic matter. VIRAMP investigates how viral infections modify the formation, physicochemical properties, and microbial communities of phytoplankton aggregates. Focusing on diatoms and their viruses, the project combines laboratory experiments with field studies in the Northern Adriatic Sea to compare aggregates formed by healthy and virus‑infected phytoplankton populations. Our group contributes in characterisation of environmental viromes associated with diatom bloom dynamics.
2025-2027
Estimating risks associated with the presence and survival of plant viruses and viroids in compost and other organic waste fertilisers
Funding: Slovenian Research and Innovation Agency (ARIS, L4-60158) & Ministry of Agriculture, Forestry and Food & Bia d.o.o. & Kogal d.o.o.
Leading organization: NIB, Department of Biotechnology and Systems Biology
Partners: University of Ljubljana – Biotechnical faculty, Bia d.o.o
Project leader: Nataša Mehle
Involved researchers from NIB: Denis Kutnjak, Ion Gutiérrez-Aguirre, Ana Vučurović, Irena Bajde, Marko Marohnić, Andrea Belamarić, Jakob Brodarič
In the project, we will address important issues related to the risks associated with plant viruses and viroids in the use of fertilisers from organic waste. We will develop efficient methods for the detection of plant pathogenic viruses and viroids in various organic waste fertilisers that can be used to assess the potential risk associated with the use of such products in agriculture and horticulture. Since the composition of the matrix can have a significant impact on the retention of viruses and viroids, the development of suitable virus concentration and enrichment and nucleic acids isolation methods for organic waste fertilisers is the first major aim of our study. In addition to targeted detection methods for monitoring plant pathogenic viruses and viroids, such as PCR-based methods, we will also use a non-targeted high-throughput sequencing approach, which will be particularly valuable for studying the virome of various organic waste fertilisers, including insect frass, which has not been adequately studied so far. Finally, our study will also determine the persistence of selected stable viruses and viroids in organic waste fertilisers and insect frass. We will compare this with the efficiency of degradation during the composting process under strictly controlled conditions with defined substrate and inoculum concentrations and with degradation in the growing substrate alone.
2025-2028
The role of the microbiome in the life and death of bloom-forming jellyfish (JELLY-BIOME)
Funding: Slovenian Research and Innovation Agency (ARIS) (J1-60007)
Leading organization: NIB, Marine biology station
Project leader: Tinkara Tinta
Involved researchers from NIB-MICRO: Denis Kutnjak, Anja Pecman
The overarching ambition of JELLY-BIOME project is to elucidate the role of the microbiome in the life and decay of its bloom-forming gelatinous host. Particularly, we will focus on the composition and functional traits of the jellyfish microbiome at the transition from a healthy to senescent stage of the host’s bloom to elucidate the role of the microbiome in the collapse of jellyfish blooms. To tackle this objective, we will apply an integrated transdisciplinary approach – from single proteins to the complex host-microbiome system. Our group is specifically investigating underexplored viromes of both jellyfish and the environmental waters surrounding them.
2024-2027
Development and implementation of methods for monitoring the occurrence and spread of African swine fever and highly pathogenic avian influenza viruses
Funding: Slovenian Research and Innovation Agency (ARIS), Ministry of Agriculture, Forestry and Food (V4-2416)
Leading organization: University of Ljubljana, Veterinary Faculty
Leader at NIB: Ion Gutiérrez-Aguirre
Involved researchers from NIB: Maja Ferle, Nina Prezelj, Neža Praček
In this project we are leading the Work package 2. Our role is to assess whether a wastewater-based epidemiology strategy is useful for monitoring the occurrence of influenza and African swine fever. The basis will be an already validated methodology for monitoring SARS-CoV-2 in wastewater that we implemented during the COVID 19 pandemics, which we will adapt and validate for ASFV and AIV. The validated protocol will be applied in the form of a pilot monitoring to wastewater samples from a Slovenian wastewater treatment plant.
2024-2027
Investigating the epidemiology and control of citrus black spot, caused by the plant pathogenic fungus Phyllosticta citricarpa, in Mediterranean citrus growing areas in Tunisia
Funding: European Food Safety Authority (GP/EFSA/PLANTS/2023/06)
Leading organization: NIB, Department of Biotechnology and Systems Biology
Project leader: Polona Kogovšek
Involved researchers from NIB: Zala Kogej Zwitter, Maja Ferle, Sara Fišer
Infection of citrus by the ascomycete fungus Phyllosticta citricarpa causes citrus black spot disease (CBS), resulting in major economic losses. The disease is most widespread in humid regions of Australia, Brazil, China, and southern Africa, but in 2019 P. citricarpa presence was confirmed in Tunisia, which is highly concerning for Mediterranean EU countries. Main objectives of the project ETHICS are to investigate the epidemiology of the P. citricarpa in Tunisia; and to develop strategies for control of P. citricarpa in citrus orchards. To generate more data infection model, we continue monitoring of CBS epidemiology in Tunisian citrus orchards for additional two years (continuation of the project CBS – Epidemiology). Phyllosticta isolates are collected at different locations for mating type and population genetics analysis; air and rain dispersed spores are collected and analysed with qPCR for evaluation of the time/weather related spore dispersion; disease curve is monitored, and meteorological data collected. Different CBS control strategies will be evaluated, such as chemical, microbial antagonists based and plant-derived compounds. Most promising control strategy will be employed in infected citrus orchard. The project aim is to reduce the knowledge gaps that will support risk assessment and modelling and support development of integrated pest and disease management (IPM) strategies, applicable for EU citrus growing regions.
2024-2026
Influenza A Viruses Surveillance in Birds, Mammals, and Environment
Funding: European Health and Digital Executive Agency (HaDEA), European Food Safety Authority (EFSA) (101132734)
Leading organization: Administration for Food Safety, Veterinary Sector and Plant Protection, Ministry of Agriculture, Forestry and Food
Leader at NIB: Ion Gutiérrez-Aguirre
Involved researchers from NIB: Neža Praček, Anja Pecman, Maja Ferle, Živa Lengar, Denis Kutnjak
The project will contribute to the setting and scaling up of animal health and environmental surveillance system, including the systematic ongoing collection of data by EFSA. It will focus on surveillance for Influenza A Viruses in Birds, Mammals, and Environment. The project IAVSur – BMI is based on the four crucial segments of IAV ecology: 1. Wild birds, 2. Wild mammals, 3. Domestic mammals and 4. Environment. By bridging veterinary science, biology and environmental science we aim at providing the missing link to achieve a better understanding of the whole range of IAV ecology and better apprehend the risk and impact on the animal and human health. Ultimately, this project will lead to improved collaboration at multiple organization levels and harmonized approach to the complex ecology of IAVs and will enable prioritization of future surveillance and research agendas. This will provide evidence and methods to support decision-making and prioritize actions at the national and EU level.
2025-2026
A closer look at viruses and viroids: Together for safer use of fertilizers from organic waste
Funding: Slovenian Research and Innovation Agency (ARIS) (O4-60158)
Leading organization: NIB, Department of Biotechnology and Systems Biology
Partner: University of Ljubljana – Biotechnical faculty
Project leader: Nataša Mehle
Involved researcher from NIB: Ana Vučurović
The proposed project involves engaging the public in scientific research, making science more accessible to the broader community, and enhancing understanding of its importance for society and the environment. The primary goal is to promote collaboration between researchers and citizen scientists. The project’s activities are aligned with the scientific work conducted within project L4_60158, titled Estimating Risks Associated with the Presence and Survival of Plant Viruses and Viroids in Compost and Other Organic Waste Fertilizers.
In the initial phase, a citizen science plan will be developed, including methodologies for public engagement, communication, and data collection and processing. Online surveys will enable the public to report the types and origins of fertilizers used and their application practices. This approach will complement the list of fertilizers created within WP2 of project L4_60158 with data on practices from amateur gardeners and professional growers. Survey results will be presented as general findings and statistical summaries. Based on the data collected, selected participants will be invited to submit samples of fertilizers, for which they will receive clear instructions on proper sampling and labeling. Laboratory analyses of these samples, conducted within WP2 of L4_60158, will provide insights into the presence of viruses and viroids and contribute to a better understanding of the sustainable use of organic waste fertilizers.
Additionally, the proposed project will develop an online manual for safe handling of infected plants and raise public awareness about the importance of certified fertilizers and proper handling of organic waste. Key project results will be disseminated to the wider public and decision-makers via social media, popular publications, and other communication channels, contributing to reducing the risks of spreading plant pathogens.
2023-2026
Dynamics of virome composition across the expanding invasion range: a comparative study of invasive and native crayfish
Funding: Slovenian Research and Innovation Agency (ARIS) (Z1-50017) postdoctoral project
Leading organization: NIB, Department of Biotechnology and Systems Biology
Leader at NIB: Katarina Bačnik
In this project we aim to study the impact of invasion on the virome of most successful invasive species of freshwater invertebrates in Europe, the signal crayfish Pacifastacus leniusculus. In our recent study, we have identified novel and divergent signal crayfish associated RNA viruses. We now aim to elucidate the potential differences in viral diversity and prevalence along signal crayfish invasion range in Korana River, Croatia, where the signal crayfish is spreading successfully in both upstream and downstream directions. Recently established populations at invasion fronts co-occur with native congener (narrow-clawed crayfish, Pontastacus leptodactylus), which has been gradually displaced at invasion core sites. Therefore, we further aim to compare the viromes of co-occurring and phylogenetically related crayfish: the invasive signal crayfish and the native narrow-clawed crayfish Pontastacus leptodactylus. To address the dynamics of viromes` compositions and interconnectedness of native and invasive host viromes, an innovative and interdisciplinary approach is required. Therefore, we will combine the extensive sampling of mixed- and single-species population and control crayfish population, optimized sample preparation for non-targeted high-throughput sequencing followed by state-of-the-art bioinformatics analysis to explore the viral sequences detected in hepatopancreas tissue. Using statistical analysis, we will investigate the correlations and possible influence of measured intrinsic (condition index, histopathological scores,) and extrinsic (mixed- and single-species population density) factors on the viral diversity and prevalence detected across the expanding invasion range. We will discover novel viruses, observe their morphology, analyze their phylogenetic relationships with known viruses and elucidate the within-host patterns of virus nucleotide diversity potentially revealing the adaptations that occur with inter-species transmission of viruses.
2023-2026
Early detection and management of important grapevine diseases (RESENS-VITIS)
Funding: Slovenian Research and Innovation Agency (ARIS) & Ministry of Agriculture, Forestry and Food (L7-50153)
Leading organization: Agricultural Institute of Slovenia (Saša Širca)
Leader at NIB: Nataša Mehle
Involved researchers from NIB: Ana Vučurović, Zala Kogej Zwitter, Irena Bajde, Jakob Brodarič, Tjaša Jakomin
Grapevine diseases caused by phytoplasmas, viruses, and fungi severely reduce yield and can kill plants. Among the most damaging are Flavescence dorée phytoplasma, grapevine fanleaf virus, and ESCA. At NIB we participate in the project in the Flavescence dorée phytoplasma work package. Flavescence dorée phytoplasma spreads via the leafhopper Scaphoideus titanus. Current control measures, such as insecticides, are only partly effective, and disease outbreaks persist. Since infected plants cannot be cured, early detection and removal are essential. However, assessing vineyard health is costly and time-consuming, and visual symptoms are often misleading, requiring molecular tests. The project aims to overcome these limitations by using hyperspectral imaging for early disease detection. Within the project, time-series data will be collected from drones and aircraft in vineyards across Primorska and Štajerska to develop reliable remote sensing models.
2023-2026
Coronaviral therapeutic target mutagenesis platform for communal treatment evaluation and the development of pan-coronavirus inhibitors
Funding: Slovenian Research and Innovation Agency (ARIS) (J7-50043)
Leading organization: Faculty of Chemistry and Chemical Technology (Marko Jukič)
Leader at NIB: Polona Kogovšek
Involved researchers from NIB: Arijana Filipić, Nina Kobe, Tjaša Jakomin
With onset of COVID -19 disease, researchers have been studying not only SARS-CoV-2, but also outbreaks of highly pathogenic beta and alpha coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), that have occurred before, and similar viruses widespread in animal host pools and cause high morbidity in livestock (Swine Acute Diarrhea Syndrome Coronavirus or SADS-CoV). Our main concern is ‘host jumping’, where coronaviruses ‘jump’ from animal pools to the human host and potentially infect humans, as well as evolutionary selection, which produces mutations and new viral variants with higher virulence and/or transmissibility. Examination of the coronaviral proteome reveals structurally related potential therapeutic targets common to several viral strains. With the emergence of new viral variants, it is evident that a variant-agnostic and, moreover, a pan-coronaviral approach to small molecule drug development for similar situations in the future will be very valuable. Moreover, a quick and informative approach to study prospective viral mutations before they occur in the population, would be of immense value. The proposed project therefore invests heavily in developing experimentally supported in silico viral mutagenesis platform. The goal is to highlight the current viral mutation impact on the action of antiviral compounds and study the effect of future yet-to-be seen viral mutations on potential viral therapeutic targets and consequently on antiviral drugs. Using all the conglomerated and systematized data, the project proceeds to antiviral medicinal chemistry, focusing on three prominent therapeutic targets. The project will develop novel coronaviral main- as well as papain-like protease inhibitors, with a focus on the activity against multiple coronaviruses. Last but not least, the proposed research project will investigate spike protein binding of SARS-CoV-2 variants from a human host cell perspective, looking at the neuropilin-1 coreceptor as a potential target for inhibitor and molecular probe design. The developed compounds will be biologically evaluated in vitro on isolated proteins as well as studied on infected cell lines.
2000-ongoing
National expert program in the field of plant health – Section: viruses, viroids and phytoplasmas
Funding: Ministry of Agriculture, Forestry and Food; Administration of the Republic of Slovenia for Food Safety, Veterinary Sector and Plant Protection (UVHVVR)
Leading organization: NIB, Department of Biotechnology and Systems Biology
Project leader: Nataša Mehle
Involved researchers from NIB: Ana Vučurović, Irena Bajde, Jakob Brodarič, Tjaša Jakomin, Denis Kutnjak, Anja Pecman
The programme provides national expert support in plant health for the domains of plant viruses, viroids and phytoplasmas. Activities include accredited molecular diagnostics, method development and optimisation, expert interpretation of findings from official surveillance, and preparation of technical recommendations for the plant‑health authority. The work also comprises maintenance of validated diagnostic procedures, reference materials and quality assurances needed for reliable detection and identification of regulated and emerging harmful organisms within these pathogen groups.
The National Reference Laboratory (NRL) for viruses, viroids and phytoplasmas operates as a consortium composed of the National Institute of Biology (leading organisation), the Agricultural Institute of Slovenia and the Slovenian Institute of Hop Research and Brewing. Within this consortium, our group is responsible for viruses and viroids on vegetable and ornamental crops and for all phytoplasmas, while the partner institutions cover the remaining defined areas of their specialisation. Together, the consortium ensures coordinated national diagnostic capacity and harmonised procedures.
In addition, the programme involves active participation in European and Mediterranean Plant Protection Organization (EPPO) expert panel related to diagnostics in virology and phytoplasmology and engagement in several Euphresco research projects that address diagnostic validation, epidemiology and challenges posed by newly emerging pathogens.
Through these activities, the programme supports the UVHVVR in surveillance planning, outbreak response and decision‑making, ensuring a scientifically robust and nationally coordinated diagnostic framework for viruses, viroids and phytoplasmas.
2019-ongoing
European Union Reference Laboratory for Viruses, Viroids and Phytoplasmas
Funding: European Commission under the EU Plant Health Work Programme (DG SANTE)
Consortium:
Netherlands Food and Consumer Product Safety Authority (NVWA), The Netherlands – lead organisation
Centro di Ricerca Difesa e Certificazione (CREA), Italy
National Institute of Biology (NIB), Slovenia
Leader at NIB: Nataša Mehle
Involved researchers from NIB: Ana Vučurović, Irena Bajde, Jakob Brodarič, Anja Pecman, Denis Kutnjak, Tjaša Jakomin, Zala Kogej Zwitter, Veronika Bukvič
The European Union Reference Laboratory (EURL) for viruses, viroids and phytoplasmas provides EU‑wide scientific and technical support to ensure accurate, harmonised and high‑quality diagnostics for these pathogen groups across Member States. Our work includes the development, optimisation and validation of diagnostic methods, preparation of technical guidance and support documents, and the coordination of interlaboratory comparison studies that verify the performance, comparability and robustness of diagnostic procedures used throughout the EU.
The EURL also facilitates structured knowledge exchange through workshops, expert consultations, collaborative studies and direct support to national reference laboratories. This coordinated framework enables the adoption of harmonised diagnostic methods, early identification of methodological challenges and continuous improvement of diagnostic preparedness for regulated and emerging harmful organisms. As a consortium, the EURL strengthens the scientific foundation of the EU plant‑health system and supports Member States in implementing reliable, evidence‑based diagnostics for viruses, viroids and phytoplasmas.
Recently concluded projects
2022-2025
Plant viromes’ fluxes: interconnectedness of urban environment, wild and cultivated plants
Funding: Slovenian Research and Innovation Agency (ARIS) (J4-4553)
Leading organization: NIB, Department of Biotechnology and Systems Biology
Project leader: Denis Kutnjak
Involved researchers from NIB: Lana Vogrinec, Maja Ferle, Živa Lengar, Katarina Bačnik, Ion Gutierrez-Aguirre, Veronika Bukvič
The majority of the plant pathogenic viruses so far recovered from environmental waters are very stable and their dissemination in streams and rivers can enable their long-distance spread. The release of infective plant virions from urban environment (human) to the wider environment has also been proposed and demonstrated recently for environmentally persistent viruses. This could be especially problematic in light of increased irrigation and the use of hydroponic systems in agriculture. Very little is known about virus infections in aquatic plants and even less about the possible water-mediated transmission of plant viruses to aquatic plants.
The aim of this project is to address and answer some of the most pressing questions regarding the gaps in knowledge described above. Can plant viruses released from wastewater persist in the river and possibly infect aquatic plants and river bank vegetation? Is the virome observed in river water influenced by the virome of plants growing in or near the water? Is there any exchange of (or overlap in) plant virus species between river water, proximal aquatic and terrestrial wild plants, and crops?
The outcomes of this project will help to elucidate the flux of plant viruses between different parts of a fragmented anthropogenic ecosystem. Analysis of samples from different constituent parts of the ecosystem, including urban wastewater, recipient river, submerged, bank and surrounding wild vegetation, and selected crops, will give an overview of the viromes present in the environment. Very likely new virus species or new associations of known virus species with different hosts will be revealed. Network inference and network analyses will expose possible overlapping virus species in viromes from different environments. Finally, the experimental system for viral infections of crop and aquatic plants will give insights into the biological relevance of the plant viruses found in the environment.
2023-2025
Development of a warning system for detecting the impact of military activities on groundwater
Funding: Slovenian Research and Innovation Agency (ARIS) (V1-2367)
Leading organization: Geological Survey of Slovenia (Anja Koroša)
Leader at NIB: Denis Kutnjak
Involved researchers from NIB: Nina Prezelj, Ion Gutierrez-Aguirre, Maja Ferle
The main objective of the project is to establish a warning system to monitor and control potential impacts of military training sites on groundwater or drinking water sources. The warning system will include the monitoring of relevant chemical, bacteriological and isotopic parameters to a real-time assessment of the potential impact of military training sites on the groundwater system and thus on drinking water sources. The monitoring will consist of two components: continuous monitoring of selected physico-chemical parameters and detailed monitoring of parameters that could be affected by military activities in the area of the aquifer. Detailed monitoring involves monitoring a wider range of parameters that could be characteristic of emissions from military activities or facilities. Indicator parameters that are primarily characteristic of military activities are identified. Based on the experience gained, the warning system for detecting the impact of military activities on groundwater will be optimised.
2023-2025
Validation of molecular diagnostic methods for the detection and identification of tomato mottle mosaic virus (ToMMV-detect)
Funding: Euphresco 2022-A-394 (The Slovenian contribution was funded by the Ministry of Agriculture, Forestry and Food of the Republic of Slovenia)
Leading organization: NIB, Department of Biotechnology and Systems Biology
Partners: AGES (AT), GEVES (FR), JKI (DE), Fera Science Ltd (UK), PPIS (IL), IPSP‑CNR (IT), Naktuinbouw (NL), MPI (NZ), VNIIKR (RU), BIOREBA (CH), ISF, Agdia (FR), USDA‑APHIS‑PPQ (USA), CREA‑DC (IT), DAFF/DEECA (AU), DAFM (IE)
Project leader: Nataša Mehle
Involved researchers from NIB: Ana Vučurović, Irena Bajde, Jakob Brodarič
The ToMMV‑detect project addressed a critical phytosanitary need arising from the emergence of tomato mottle mosaic virus (ToMMV), a tobamovirus with increasing relevance for international seed trade and plant health protection. Before the project, diagnostic laboratories and regulatory authorities faced a fragmented landscape of molecular tests with no coordinated validation, making it difficult to ensure reliable detection, comparable results, and science‑based decision‑making. By bringing together 15 laboratories from 13 countries, the project established an unprecedented international framework for the harmonisation of diagnostic practices. It provided standardised protocols, and a coordinated environment for evaluating molecular assays under comparable conditions. This strengthened diagnostic preparedness, improved the consistency of ToMMV testing globally, and supported the development of unified approaches aligned with EPPO standards. Beyond its technical contributions, ToMMV‑detect significantly enhanced cooperation across the global plant health community. It promoted capacity building, fostered knowledge exchange, and created a shared foundation for future work on emerging viral threats. The availability of harmonised methods and transparent validation data directly supports regulatory processes, strengthens seed trade biosecurity, and increases resilience of diagnostic networks.
In essence, the project filled a major gap in plant virus diagnostics by ensuring that laboratories worldwide can rely on robust, harmonised and internationally recognised tools for the detection of ToMMV.
2022-2025
Parasitic-like modulation of Bacillus thuringiensis development and larvicidal activity by a bacteriophage
Funding: Slovenian Research and Innovation Agency (ARIS) (J1-4394)
Leading organization: University of Ljubljana, Biotechnical faculty (Matej Butala)
Leader at NIB: Ion Gutiérrez-Aguirre
Involved researchers from NIB: Živa Lengar
Bacteria are preyed upon by bacteriophages (phages), which, like other viruses, hijack the host`s cellular machinery to replicate. It is becoming increasingly clear that phages can have a significant impact not only on bacteria, but also on eukaryotes. In this project, we will determine the physiological changes in the bacterium Bacillus thuringiensis serovar israelensis (including sporulation rate and production of crystal toxins) and insect host enforced by phage-encoded proteins. It is worth noting that majority of biolarvicidal products are based on entomopathogenic B. thuringiensis serovar israelensis. In addition, we will test whether the phage genome (prophage) is packaged in endospores that can allow safe entry of prophage into the insect body. In addition, we will investigate whether phage regulators that affect processes in bacteria, also affect insect larvae. We will also investigate whether similar regulators that modulate phage-baterium-larvae interaction, exist also in other phage or bacteria. We believe that the findings from this project will provide new fundamental knowledge to understand how phage and bacterial transmission is facilitated to other trophic levels. Mosquitoes are one of the most recognized diseasse carrying vectors. The results of this project could pave the way for the development of improved biopesticides.
2022-2025
On-demand Contact Based Antimicrobial Surfaces: Human and Environmental Safe Infection Control Strategy
Funding: Slovenian Research and Innovation Agency (ARIS) (J3-4531)
Leading organization: Jožef Stefan Institute (Marija Vukomanović)
Leader at NIB: Polona Kogovšek
Involved researchers from NIB: Arijana Filipić, Tjaša Jakomin
The project aims engineering the chemistry at the surface of poly-l-lactide (PLLA) organic piezoelectrics, by grafting adhesion molecules with cationic functional groups, to enhance their contact with pathogens for more efficient antimicrobial effect. Different active compounds (Zn ions) are bound to golden nanoparticles to achieve stable antimicrobial activity. The design will enable novel generation of contact-based antimicrobials which use piezo-signal to disintegrate envelope in pathogens leading to their permanent inactivation. We test the effect on a series of clinically relevant pathogens isolated from infected skin and implants, including antibiotic multi-resistant strains and different virus models with and without envelope. Important part of the study is evaluation of compatibility with mammalian cells focused on toxicity in human skin and blood cells. The core benefit of new technology is antibiotic-free and nanoparticle-free approach, based on its ability to use only the chemistry at the surface to enable action against pathogens without direct release or indirect formation of any active substances. Consequently, the technology offers long-term effective infection control with higher level of safety for human and environment in comparison to currently used leaching technologies. (photo author IJS, K9)
2022-2025
Measures to prevent further spread of Grapevine flavescence doree phytoplasma
Funding: Slovenian Research and Innovation Agency (ARIS) & Ministry of Agriculture, Forestry and Food
Leading organization: NIB, Department of Biotechnology and Systems Biology
Partners: Institute of Agriculture and Forestry Maribor, Institute of Agriculture and Forestry Nova Gorica, Slovenian Institute of Hop Research and Brewing, Agricultural Institute of Slovenia
Project leader: Nataša Mehle
Involved researchers from NIB: Zala Kogej Zwitter, Ana Vučurović, Irena Bajde, Jakob Brodarič, Tjaša Jakomin
In the FD-GamePlan project, we investigated the epidemiology of Flavescence dorée (FD) in Slovenia, focusing on vectors, infection reservoirs, and possibilities for early disease detection. We examined the potential for detecting FD phytoplasma in pre-imaginal stages of Scaphoideus titanus and found that the presence of phytoplasma in nymphs is very low, making this approach unsuitable for early infection detection. In vineyards, Scaphoideus titanus was the most common species, while Orientus ishidae was by far the most abundant in hazelnut orchards and their surroundings, with a significant proportion of individuals infected with FD phytoplasma. In other leafhopper species, FD phytoplasma was detected only sporadically. Analyses conducted on hazelnuts showed that, based on this project’s results, hazelnuts are not a key source of Flavescence dorée problems in Slovenian vineyards, but they may represent an important reservoir of genetic diversity of FD-associated phytoplasmas. The project also focused on developing an aerial hyperspectral imaging method to enable spatially precise and earlier detection of FD infections across larger vineyard areas. The project results contribute to a better understanding of FD spread in Slovenia and provide a basis for further improvements in grapevine phytosanitary protection.