Field of Study – Biology (N 010)

More than 1,000 cases of foodborne parasitic infections are reported in the EU every year. The impact of foodborne parasitic infections on human health varies considerably depending on the species of parasite, ranging from mild illness to severe illness and possibly death. Predatory mammals are widespread in Europe and are hosts to a wide range of parasites. It is estimated that predatory mammals host approximately 43% of human infectious agents and are susceptible to a wide range of pathogenic microparasites. Ecological factors, together with environmental changes, mainly due to human activities, can increase the risk of parasite transmission between wildlife, domestic animals and humans. Control of foodborne parasites is therefore a high priority for quality assessment in slaughterhouses and food companies, and the role of predators as potential hosts of these parasites can help to understand the routes of transmission of infections and the measures to control them.

Due to their dietary habits, predators are hosts to many parasitic groups, including those dangerous to humans. As many wild predators increasingly visit human populated areas and come into contact with domestic animals, the likelihood of outbreaks of various parasites is high.  Domestic cats and wild felids are important hosts of Sarcocystis, Toxoplasma protists and Toxocara nematodes. Toxoplama gondii is a zoonotic pathogen of worldwide importance and has been extensively studied, but recently there has been almost no scientific studies on this pathogen in Lithuania, whose definitive hosts are cats. Globally, there is still a lack of studies assessing the prevalence of T. gondii in samples from wild felid predators. Toxocariasis is a well-known zoonotic disease caused by Toxocara nematodes and is mainly children are infected through dirty hands, unwashed fruit and vegetables. Cats spread Toxocara cati and Toxascaris leonina, while the infection rates of these parasites in urban environments in Lithuania have not been studied in detail.

The role of wild and domestic feline predators in the distribution of Sarcocystis, Toxoplasma and Toxocara parasites

Samples of Eurasian lynx (Lynx lynx), Spanish lynx (Lynx pardinus) and domestic cats are to be tested for these parasites. The diversity of samples planned to be tested is notable, with intestinal and faeces samples from the Eurasian lynx in Lithuania, faeces samples from domestic cats, and environmental samples collected at winter houses set up at stray cat feeding sites in Vilnius, at playgrounds and in sandboxes. DNA samples extracted from excrements of Spanish lynx will also be analysed in collaboration with Iberian scientists. Faecal samples from the Eurasian lynx will be collected in collaboration with scientists from the Nature Research Centre, Laboratory of Mammal Ecology. Intestinal samples and muscles of the Eurasian lynx will be collected in collaboration with the Tado Ivanauskas Zoological Museum, the national institution responsible for the monitoring of dead and injured wild animals. Parasites will be isolated and concentrated using traditional morphological-parasitological methods. Species richness and distribution of the parasites will be revealed using DNA analysis techniques and bioinformatic analysis. The results obtained will be useful for the assessment of the distribution of parasites of importance for humans and domestic animals in natural and urban environments. Based on investigations described, 4-5 scientific papers are planned to be published.

In recent decades, one of the major threats to ecosystems has been the extremely rapid
spread of causal agents of plant diseases (pathogens, insects, etc.) (Santini et al., 2013; Sikes et al., 2018; Caballol et al., 2024; Schertler et al., 2024). It is driven by climate change and intensive international trade (Kutnar et al., 2021), which introduces plant disease-causing organisms into new areas and causes enormous economic and environmental losses (Raum et al., 2023). Current crop protection practises, both in Europe and worldwide, are characterised by a high use of synthetic fertilisers and pesticides (FAO, 2021). For example, chemical pesticides used as traditional control agents, while considered effective, raise a number of environmental and health concerns, including soil degradation, water contamination and the development of resistant strains of pathogens. This has led to an increased search for alternative control measures and a review of disease control strategies. This is particularly important after the European Commission published its Green Deal strategy, which aims to reduce the overall use of chemical pesticides and their risks by 50% by 2030 (European Commission: The European Green Deal, https://commission.europa.eu/ strategy-and-policy/priorities-2019-2024/european-green-deal_en), and presented an action plan to prevent pollution (EC: Zero Pollution Action Plan, https://environment.ec.europa.eu/strategy/zero pollution-action-plan_en#:~:text=On%2012%20May%202021%2C%20the,the%20Zero%20
Pollution%20Stakeholder%20Platform).

Plant pathogenic microorganisms have posed a major threat to ecosystems in recent years, with climate change, global trade and, in particular, intensive monocultures in both agriculture and forestry driving the spread and emergence of new diseases (Fisher et al., 2012; Jeger et al., 2021). It is estimated that up to 40% of economically important crop yields are lost annually due to damage caused by plant pathogens and pests (Savary et al., 2019), which has led to a significant increase in the use of pesticides to protect crops (FAO, 2021). Currently, mainly synthetic pesticides are used to protect crops from pathogens. While effective, they ultimately have a negative impact on the environment and pose health risks to consumers and animals, can harm non-target plants, insects, etc., and contribute to soil, water and air pollution and biodiversity loss. This has led to the search for alternative biopesticides that are safer for nature and humans, and microorganisms have been cited as some of the most important sources of biopesticides, with certain species or consortia showing potential antibacterial and/or antifungal activity (Ab Rahman et al, 2018; Jeger et al., 2021; Lahlali et al., 2022; Pandit et al., 2022). And while research on individual microorganisms has increased in recent years, there is a lack of theoretical and practical knowledge to successfully build and apply consortia of them. It is therefore hoped that once the activities envisaged in the PhD topic are carried out, the research results will provide new scientific information on the changes in microorganism species and populations under biotic stress, which can serve as a basis for improving microorganism selection and research methods that would increase the qualitative value of crops (and thus yields).

The PhD will include the following research work:

– isolation of microorganisms from natural environments or simulated biotic/abiotic

environments (soil, Fabaceae rhizosphere, endosphere);

– metagenomic analysis, phylogenetic analysis, classification, bioinformatic and statistical

analysis of microorganisms;

– identification of selected microorganisms suitable for the control of pathogenic microorganisms

(Fusarium, Alternaria, etc.) by molecular biological techniques;

– functional characterisation of microorganisms by identifying direct and indirect plant growthpromoting properties;

– inoculation of plant cultures with prepared cultures of microorganisms to evaluate their

potential to increase the plant’s tolerance to the biotic agents under investigation in vitro.

In recent decades, one of the major threats to ecosystems has been the extremely rapid
spread of plant-damaging organisms (pathogens, pests, etc.). Driven by climate change and
intensive international trade (Kutnar et al., 2021), plant pathogens are invading new areas and
causing enormous economic and ecological losses (Raum et al., 2023). The relevance of this topic
lies in its far-reaching effects: it is well known that pests are vectors for a wide range of
microorganisms (such as bacteria, fungi, etc.), many of which are pathogenic to plants, animals or
humans. It is therefore crucial to study the biodiversity of insect-borne microorganisms, as they play a crucial role in shaping the behaviour, virulence and adaptability of pests and have important
implications for agriculture, forests, ecological balance and public health (Santini et al., 2013; Sikes
et al., 2018; Caballol et al., 2024; Schertler et al., 2024). Although this area is of great interest for
both research and practical applications, data on pest-associated microbial communities are
unfortunately very scarce (Gurung et al., 2019). Many studies focus on a relatively narrow range of
pathogens without considering the broader complexity of the microbiome. Furthermore, the
dynamic interactions between pests, their microbiota and environmental factors are poorly

understood, limiting our ability to predict disease outbreaks or develop effective control measures (Holt et al., 2024). Another pressing issue is the rapid evolution of interactions between pests and pathogens caused by anthropogenic activities such as overuse of pesticides and drastic habitat changes. This leads to the emergence of new strains or species that can overcome existing disease control strategies (Lange et al., 2023). These challenges require advanced tools for analysing microorganisms, integrative ecological studies and targeted interventions to interrupt the spread of pathogens. To develop sustainable solutions for pathogen control, it is therefore essential to gather as much information as possible about microbial biodiversity and the interactions between pests and microbiota.
Research into the microbiota of pests has expanded considerably in recent years due to the
need to understand their ecological role, their interactions with pathogenic microorganisms and
their impact on agriculture, forestry and public health. Research on pest-related microbiota focuses on their diversity, functions and potential use in pest and pathogen control (Lange et al., 2023; Coolen et al., 2022). One of the most important areas of research is the study of the diversity of microbial communities in pests. Studies using high-throughput sequencing techniques have shown that pests have complex microbiome communities consisting of bacteria, fungi and other organisms. This microbiota plays an important role in influencing the physiology, reproduction and adaptability of pests. Studies on the microbiota of aphids, for example, have emphasised their symbiotic relationship with bacteria such as Buchnera aphidicola, which provide the host with important nutrients (Coolen et al., 2022). Another important topic is the role of the microbiota in interactions between pests and pathogens. Studies have shown that pest-associated microorganisms can modulate the transmission of plant, animal and human pathogens. For example, pests (such as bark beetles) have fungi that contribute to their ability to infect and destroy host trees, with significant ecological and economic consequences (Chakraborty et al., 2023).
Research into the microbiota of pests is a relatively new field with a very practical focus –
research into manipulating the microbiota of pests to reduce the potential for pathogen transmission is becoming increasingly popular. However, there are still research gaps, particularly in understanding the dynamic interactions between pests, their microbiota and environmental factors. Therefore, it is expected that the research results from the PhD activities will provide new scientific information on the pest-associated microbiota, with the aim of translating this knowledge into practical and sustainable strategies for pest and pathogen control. Further interdisciplinary research will help to better anticipate and mitigate the pest-related problems that have emerged in recent decades, not only in Europe but worldwide.

The PhD will include the following research:
– inventory and taxonomic classification of pest microbiomes (inventory of microbial taxa
associated with a pest species (as Ips typographus or other(s)) using sequencing techniques
such as 16S rRNA, ITS, metagenomics, etc.);
– functional characterisation of the influence of microorganisms on the virulence of pests;
– development of approaches/solutions for biological pest control using selected microorganism
strains;
– optimisation of feeding techniques for pest larvae with microorganism cultures (development
of in vivo protocols).

Climate change and the intensification of environmental conditions pose challenges to plant productivity and survival. Due to unusual temperature fluctuations (including sudden frost episodes), drought, soil salinity, and heavy metal pollution, plants experience abiotic stress, which reduces yield and threatens food security. Therefore, it is essential to deepen knowledge on plant resistance mechanisms and develop innovative plant protection strategies.

Plants adapt to unfavorable environmental conditions through physiological, biochemical, and genetic mechanisms. In recent decades, there has been a growing number of studies aimed at understanding the mechanisms of plant responses to abiotic stress (Rouphael & Colla, 2020). Significant attention is given to the functioning of the antioxidant system, signaling pathways (including phytohormones), gene expression, and metabolite analysis (Mittler, 2017; Verma et al., 2020). Alongside fundamental research on plant stress mechanisms, intensive studies are being conducted to explore genetic, physiological, biochemical, and agronomic modifications of these mechanisms. It is now crucial that these approaches are not only innovative but also sustainable (Zhao et al., 2021; Borrelli et al., 2018).The aim of this study is to analyze the physiological and biochemical responses of plants to abiotic stress and explore ways to enhance their tolerance. Molecular, cellular, and ecophysiological adaptations will be investigated during the doctoral studies, with particular attention to the activity of antioxidant systems, regulation of signaling pathways, and the search for innovative plant protection measures. It is expected that the research results will contribute to the expansion of fundamental knowledge and the development of practically applicable methods that will help ensure sustainable agriculture, higher yields, and plant adaptation to changing environmental conditions.

The planned research will be conducted under controlled laboratory conditions. The effects of model unfavorable environmental conditions and growth regulators on the functioning and productivity of economically valuable plants will be assessed using physiological-biochemical and morphometric methods.

The doctoral candidate is expected to participate in international events and training. The research findings will be disseminated at international scientific conferences and published in international scientific journals indexed in Clarivate Analytics Web of Science (CA WoS).

Plant pathogens are among the most important components of the microbiome and have a major impact on both ecological and evolutionary processes in host plants. Phytopathogenic micro-organisms (bacteria, fungi) also cause significant economic losses in many parts of the world, with plant diseases accounting for up to 30% of the world’s crop yields, resulting in billions of dollars of losses each year. This has led to a particular focus on the interaction of pathogenic microorganisms with vulnerable plants. Recent research worldwide, including in Europe, is now mainly focused on the specific virulence factors that affect plant health. A better knowledge of the characteristics of pathogenic microorganisms, and an understanding of population structure and dynamics, may lead to the development of more effective control measures and more advanced and specific diagnostic protocols.
Research on plant pathogens causing plant diseases in Lithuania has been fragmented in recent years, with too few studies being conducted. However, they are important in epidemiological terms, as research would provide new information on the distribution of pathogens in Lithuania and, more broadly, in Europe. A better understanding of the structure and dynamics of pathogenic microorganism populations could lead to the development of more effective control measures and more advanced and specific diagnostic protocols. The aim of the research to be carried out is to use molecular biology techniques to identify and genetically characterise the pathogen(s) in host plants and to assess their virulence factors.
This work would contribute to the 2022–2026 scientific research and experimental development programme of the Nature Research Centre “Dispersion of harmful substances, pathogens and other stressors in a changing environment in the context of risk assessment and remediation (POLLUTION)”.

The impact of factors caused by climate change on the functioning of Earth’s organisms and the state of ecosystems is currently a globally relevant topic. Climate change is believed to cause more frequent extreme events, including heavy rainfall, strong winds, heat waves and droughts, which can disrupt plant growth and make plants more vulnerable. Climate change studies show that many plants will be more stressed and less productive in the future. It is predicted that the yield of agricultural crops may decrease by several tens of percent during hot growing seasons. Therefore, studying the reaction of plants to changing conditions is important not only in a fundamental, but also in a practical sense.

Studies have shown that higher than normal temperatures lead to physiological and morphological changes in the plant. They accelerate the life cycle of plants, plants mature faster, so the intensity of photosynthesis changes and the yield decreases. As the competitive conditions of plants change under the influence of climate change, there is a need to strengthen the vital powers of agricultural plants. There is a lack of information on how stressful conditions will affect the physiological responses of plants and what environmentally friendly measures can be useful to reduce the harmful effects on the formation of reproductive organs.

Research will be conducted under natural field conditions and model conditions in the laboratory. Biostimulants will be used to search for means of controlling the processes that determine the productivity of agricultural plants. The effects of model climate change conditions and biostimulants on the functioning and productivity of economically useful plants will be assessed using physiological-biochemical and morphometric methods. Modeling the forecasted climate conditions will allow to study the possible impact on the sustainability of the resource and to search for measures to protect it.

Participation of the doctoral student in international scientific events, courses, and trainings is expected. The results of the work will be published at international scientific conferences and published in Clarivate Analytics Web of Science (CA WoS) referenced scientific journals.

Herbicides are used both worldwide and in Lithuania to accelerate plant growth and increase competition with weeds. Weed competition is one of the most important biotic stress factors leading to a reduction in crop production. Herbicides have been found to cause abiotic stress to plants. Abiotic and biotic stresses of varying severity affect plant development, growth and ultimately productivity. Crop competition with unwanted plant species leads to lower yields, yet herbicides are considered to be the main effective tool for the control of unwanted weeds in modern crop production, helping to protect crop yields, economic profits and reducing competition between plants. The overall use of herbicides continues unabated worldwide, including in Lithuania. Thus, in order to avoid excessive use of herbicides, it is crucial to analyse the potential of using bioactive, environmentally friendly products to accelerate plant growth, to eliminate the adverse effects of herbicides on plants and, ultimately, to reduce the use of herbicides in agriculture. Plant probiotics may serve this purpose, but their potential for use has not yet been fully explored. The potential for their inclusion in plant biotechnology packages for crop production needs to be explored as part of the European Green Deal strategy, incorporating new technologies in the development of sustainable farming policies. In order to clarify the potential of probiotic preparations in eliminating herbicide-induced damage to plants, an analysis of biometric and biochemical parameters (stress level markers, enzymatic and non-enzymatic defence system and hormonal system) will be performed.