3. Doktoritööd
Selle kollektsiooni püsiv URIhttp://hdl.handle.net/10492/2490
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Kirje Desiccation tolerance of bryophytes and lichens under changing climate conditions(Estonian University of Life Sciences, 2026) Morales Sánchez, José Ángel; Mark, Kristiina (advisor); Niinemets, Ülo (advisor); Perera-Castro, Alicia V. (opponent)ABSTRACT. Intracellular water is essential for the metabolism of all living organisms, including photosynthesis and respiration. Loss of water usually causes severe cellular damage or leads to the death of the organism. Bryophytes and lichens are among the few organisms that can tolerate complete desiccation and resume their biological activity once rehydrated. However, desiccation tolerance varies widely between species, and our understanding of how this trait adapts to different climate conditions remains limited. As a result, bryophytes and lichens are often excluded from climate and vegetation prediction models, which complicates the assessment of environmental changes in areas where bryophytes and lichens dominate the vegetation. The doctoral thesis investigates the physiological responses of bryophytes and lichens to desiccation-rehydration cycles, and how these responses depend on environmental conditions. The work evaluates experimental methodologies and analyses changes in photosynthesis, carbon balance, chlorophyll fluorescence, and emissions of volatile organic compounds. The results show that existing protocols are inconsistent, and that assessing desiccation tolerance requires a broader taxonomic and ecological range of species. Harmonizing methods for measuring molecular, cellular, and physiological traits is important to compare results and predict how communities will respond to environmental change. The study tested a gas exchange system designed and built by the research group, which allows real time monitoring of physiological changes during desiccation and rehydration cycles using a novel in chamber humidification system. The system improved the ability to monitor recovery and allowed physiological measurements to be linked with emissions of volatile compounds. The improved methodology was also used to examine how long term exposure to elevated carbon dioxide (CO₂) affects desiccation tolerance in mosses. Although photosynthesis increased temporarily, the effect did not persist, and by the end of the year desiccation tolerance had declined in all four bryophyte species studied. Overall, the thesis provides an overview of the-state-of-the-art of desiccation tolerance in bryophytes, presents an improved measurement method, and highlights the importance of standardization and multi species studies for understanding the impacts of climate change.Kirje Changes in plant carbon gain and volatile emissions under elevated CO₂ concentration and heat stress(Estonian University of Life Sciences, 2026) Abiola, Yusuph Olawale; Niinemets, Ülo (advisor); Institute of Agriculture and Environmental Sciences; Loreto, Francesco (opponent)ABSTRACT. Climate change is reshaping the growth conditions for cultivated crops. Rising atmospheric carbon dioxide (CO₂) levels and increasing temperatures are two major challenges facing plants. Elevated CO₂ can initially boost plant growth by enhancing photosynthesis, but its benefits are not always sustained over the long term, especially when nutrients become limiting. Meanwhile, warmer temperatures impose heat stress that disrupts the plant’s photosynthetic machinery and overall productivity. In response, plants release natural chemicals called volatile organic compounds (VOCs) that help in stress defense and communication with their environment. This thesis investigated the impacts of increased CO₂ and heat stress, both individually and in combination, on plant carbon gain and VOC emissions in tropical fruit trees, avocado (Persea americana) and soursop (Annona muricata), as well as the Mediterranean herb, oregano (Origanum vulgare). In avocado, elevated CO₂ improved growth and enhanced recovery after heat stress, especially in young leaves. In contrast, soursop responded differently: elevated CO₂ declined photosynthetic performance and growth due to internal limitations that reduced their ability to convert carbon into growth. Heat stress consistently impaired photosynthesis mainly through internal biochemical limitations rather than stomatal closure. In oregano, prior exposure to mild heat (heat priming) improved tolerance to subsequent severe heat. Heat stress also triggered strong emissions of volatile compounds that protect plant cells and signal stress. Overall, this thesis shows that plant resilience to climate change depends on species-specific traits, developmental stage, and prior stress exposure. These findings improve our understanding of how to predict crop performance under changing environmental conditions and support the development of plant varieties better adapted to both current and future climates.Kirje Food web interactions, habitat complexity, and human pressure as key determinants of fish community dynamics in temperate lakes(Estonian University of Life Sciences, 2026) Puncule, Linda; Zingel, Priit (advisor); Zagars, Matiss (advisor); Institute of Agriculture and Environmental Sciences; Lauridsen, Torben Linding (opponent)ABSTRACT. Food web interactions, habitat complexity, and human pressure as key determinants of fish community dynamics in temperate lakes. This doctoral thesis investigates the ecological drivers of fish community dynamics and food web stability in northern temperate lakes across Latvia and Estonia. By synthesizing three research articles, the study examines how the interplay between habitat complexity, food availability, and anthropogenic pressures shapes the growth and recruitment of fish populations. A primary focus is placed on young-of-the-year (YOY) fish, whose physiological vulnerability and reliance on specific nursery habitats make them sensitive early-warning indicators of ecosystem health and shifts in trophic regulation. The research demonstrates that the biomass and composition of zooplankton in littoral zones are fundamental determinants of YOY diet, growth, and condition, establishing a clear bottom-up link between productivity and fish recruitment. Furthermore, the study identifies the structural role of diverse macrophyte assemblages, particularly floating-leaved vegetation, in providing essential refugia and modulating planktonic food web interactions. These vegetated habitats enhance ecological resilience by facilitating resource partitioning and buffering against environmental disturbances, thereby maintaining the structural integrity of the aquatic community. Conversely, the thesis highlights the destabilizing effects of human activities, such as overfishing and poaching, which disproportionately target large piscivores. The loss of these keystone predators triggers a trophic cascade, leading to an overabundance of planktivorous fish and a subsequent decline in water quality through increased nutrient resuspension. The findings conclude that ensuring long-term lake sustainability requires an integrated management approach that prioritizes the conservation of complex littoral habitats alongside rigorous fisheries enforcement to safeguard top-down regulatory mechanisms.Kirje Evaluation of nanocarriers and application methods for dsRNA delivery in Brassicogethes aeneus(Estonian University of Life Sciences, 2026) Kallavus, Triin; Veromann, Eve (advisor); Willow, Jonathan (advisor); de Schutter, Kristof (advisor); Taning, Clauvis Nji Tizi (advisor); Estonian University of Life Sciences. Institute of Agriculture and Environmental Sciences; Ghent University; Kiss, Jozsef (opponent)ABSTRACT. The pollen beetle (Brassicogethes aeneus) is a major pest of oilseed rape (Brassica napus), causing substantial yield losses primarily through feeding damage to flower buds before flowering. Increasing resistance to conventional insecticides and their negative effects on non-target organisms highlight the urgent need for sustainable pest control strategies. RNA interference (RNAi) has emerged as a promising alternative due to its high specificity and environmental compatibility. This thesis evaluates the potential of RNAi for controlling B. aeneus by targeting two genes, αCOP and dre4, and by comparing naked dsRNA with nanocarrier-complexed dsRNA delivered via different feeding substrates. Initial plant-based experiments using spray-induced gene silencing (SIGS) demonstrated that even high concentrations of naked dsαCOP applied to B. napus plants did not significantly affect beetle survival, despite moderate transcript suppression. These results indicate that Hypothesis I, predicting effective pollen beetle control via SIGS, was not supported. In contrast, naked dsαCOP delivered in sugar water induced strong, dose-dependent RNAi effects and high mortality, confirming αCOP as a highly effective target. The dre4 gene was less robust, producing significant mortality only under optimized feeding conditions. Nanocarrier-based delivery systems, including polymer-, lipid-, peptide-, and clay-based carriers, successfully protected dsRNA from degradation in gut fluid but did not consistently enhance gene silencing or mortality. Thus, Hypothesis II, which predicted increased RNAi efficacy using nanocarriers, was only partially supported, as improved stability alone was insufficient and some carriers delayed or reduced the RNAi response. Overall, this study demonstrates that RNAi is functional in B. aeneus, with αCOP being a highly effective target when dsRNA is delivered in a bioavailable form. Delivery method strongly determines efficacy: naked dsRNA in sugar water caused high mortality, whereas SIGS via plants was ineffective. Although nanocarriers improved dsRNA stability, their biological effects were variable, and transcript knockdown did not consistently translate into mortality. These findings highlight the need to clarify dsRNA uptake mechanisms, further optimize nanocarriers for controlled dsRNA release, and develop delivery strategies effective under field conditions.Kirje Occurrence and trophic interactions of the potentially toxic bloom-forming cyanobacterial genus Microcystis in shallow temperate lakes(Estonian University of Life Sciences, 2026) Gonzales Ferraz, Margarita Esmeralda; Agasild, Helen (advisor); Panksep, Kristel (advisor); Nõges, Tiina (advisor); Institute of Agriculture and Environmental Sciences; Dimante-Deimantovica, Inta (opponent)ABSTRACT. The increasing frequency and intensity of toxic cyanobacterial blooms pose a serious threat to aquatic ecosystems and the services they provide. Among the dominant bloom-forming genera, Microcystis is commonly observed in highly eutrophic waterbodies and represents a major concern due to its toxin production and potential contamination of food webs. As toxic and non-toxic strains of Microcystis often coexist within the same assemblage, qPCR targeting the genus-specific microcystin synthetase gene mcyE is a valuable tool for determining toxigenic strains in the environment and in the consumer diet. The research focused on bloom-forming and potentially toxic cyanobacteria, Microcystis, by characterizing the dynamics of its toxic strains and environmental drivers, as well as its trophic interactions in the aquatic food webs of lakes Võrtsjärv and Peipsi. The research demonstrated that in temperate, ice-covered lakes, Microcystis's ability to produce toxigenic strains may persist year-round. Application of genus-specific qPCR detection in zooplankton gut contents revealed that in natural waterbodies, various cladoceran and copepod species can consume toxigenic Microcystis strains, potentially posing a risk to higher trophic levels. It also showed that even in lakes with very low levels of toxigenic Microcystis, toxic cell trophic pathways can still occur, as evidenced in Lake Võrtsjärv. The research further emphasizes that, to assess the toxicity risk of Microcystis to the food web, the knowledge of grazer assemblages and their dynamics is essential. Further research on Estonia’s large lakes, Võrtsjärv and Peipsi, should focus on directly measuring cyanotoxin concentrations to better assess the potential risks of microcystin contamination in these ecosystems.Kirje Context- and scale-dependent anatomical constraints on stomatal kinetics across plant lineages(Estonian University of Life Sciences, 2026) Kübarsepp, Liisa; Niinemets, Ülo (advisor); Tosens, Tiina (advisor); Institute of Agricultural and Environmental Sciences; Tolleter, Dimitri (opponent)ABSTRACT. Plants breathe through tiny pores on their leaves called stomata. How fast these pores open and close strongly influences how efficiently plants take up carbon dioxide while avoiding water loss—an ability that will be crucial under future climate change. This PhD thesis explores how the shape, size, and arrangement of stomata determine how quickly they respond to changes in light, carbon dioxide, and humidity. By comparing ancient plant groups such as ferns with modern flowering plants and crops, the work shows that stomatal speed is not controlled by size alone. Instead, plants rely on coordinated combinations of anatomical traits, shaped by their evolutionary history. The thesis also demonstrates how new modelling approaches and artificial intelligence can dramatically speed up stomatal analysis, making it more practical for plant breeding. Together, these findings open new pathways for developing climate resilient crops.Kirje Leaf internal anatomy as a key to photosynthetic performance and stress resilience across plant lineages(Estonian University of Life Sciences, 2025) Rikisahedew, Jesamine Jöneva; Tosens, Tiina (advisor); Niinemets, Ülo (advisor); Institute of Agricultural and Environmental Sciences; Centritto, Mauro (opponent)ABSTRACT. Plants capture carbon from the air and transform it into life-sustaining sugars through photosynthesis. But leaves do far more than just absorb sunlight — they must also defend themselves from herbivores, survive drought and heat, and communicate with their environment. This creates a constant balancing act: carbon invested in protection cannot be used for growth, and structural toughness can make it harder for carbon dioxide to reach the photosynthetic machinery inside the leaf. This thesis explores how different plants solve that challenge by examining the link between leaf anatomy, photosynthesis, and chemical defence. Three very different plant groups were studied to understand this balance across evolution and environments. First, lemongrass — a fragrant grass known for its essential oils — was used to discover how specialised defence cells called idioblasts release stored aromatic compounds when the plant is stressed. The work reveals how leaf structure protects these valuable chemicals until a threat triggers their rapid release. Second, maize and wheat were examined to improve simple and reliable methods for preparing leaf tissues for microscopy. Understanding tiny structural details is essential for breeding crops with more efficient photosynthesis, especially those using the advanced C₄ pathway that helps plants thrive in hot and dry climates. Finally, ancient plants were studied to determine why their leaves have unusually strong walls and tough tissues. These structures help them survive extreme environments, but also restrict the flow of carbon dioxide inside the leaf — limiting photosynthesis. The research identified which microscopic features most strongly regulate this internal carbon transfer. By combining insights from chemical defence, crop efficiency, and plant evolution, this thesis shows that leaf anatomy is a key driver of plant performance. Understanding these internal structures helps explain how plants manage their carbon economy — and offers new ideas for improving resilience and productivity in a changing world.Kirje Effects of light availability on moss canopy structural, chemical and physiological traits(Estonian University of Life Sciences, 2025) Tobias, Mari; Niinemets, Ülo (advisor); Institute of Agricultural and Environmental Sciences; Zotz, Gerhard (opponent)ABSTRACT. Light is essential to all green plants for photosynthesis, but it is highly variable environmental factor. It varies at temporal and spatial scales, both across the habitats and within the plant canopies. The plant canopy is adapted to light harvesting, interception and photosynthetic production, but it can only acclimate to changing light conditions within certain limits. The overall objective of this thesis was to gain insight into how the moss canopy as a whole responses to variations in light availability. Leaf area index (LAI) is one of the most widely used measurements for describing vascular plant canopy structure, and it characterizes the capacity of canopies to exchange energy and matter with the environment. The LAI and its underlying structural canopy traits were investigated in eleven moss species, eight acrocarpous species (Aulacomnium palustre, Ceratodon purpureus, Dicranum polysetum, D. scoparium, Hedwigia ciliata, Polytrichum commune, Racomitrium canescens and Syntrichia ruralis) and three pleurocarpous species (Hypnum cupressiforme, Pleurozium schreberi and Pseudoscleropodium purum). We found that structural traits were highly variable while LAI variability was low due to the underlying trait trade-offs (leaf size vs. leaf number and total shoot leaf area vs. shoot number) as in vascular plants. Despite this, moss LAI values were higher than typical vascular plants. The great structural variability found in every level (leaf, shoot and canopy) indicate that the structural differentiation serves multiple roles: maintenance of moss hydration, avoidance of photoinhibition and efficient light harvesting for photosynthesis. Using P. schreberi as an example we demonstrate how further there are major variations in moss chemical and physiological traits across the habitats and from top to bottom of the moss canopies. At the same time across-habitat variation in photosynthesis was low as is characteristic to shade plants and within-canopy trait acclimation to reduction in light availability was strongly curbed by an interacting age gradient. Overall, the data shown in this thesis collectively highlight that moss canopy functioning profoundly differs from vascular plant canopies.Kirje Uncovering the patterns of woody plants’ adaptations to tolerate multiple abiotic stresses(Estonian University of Life Sciences, 2025) Pavanetto, Nicola; Laanisto, Lauri (advisor); Puglielli, Giacomo (advisor); Institute of Agricultural and Environmental Sciences; Pugnaire, Francisco (opponent); Davison, John (pre-opponent)ABSTRACT. Identifying the ecological constraints on plants' adaptive strategies to tolerate multiple abiotic stresses is fundamental to plant ecology. Recently, a stress tolerance trade-off space (STS) was formalized, defining the limits of abiotic stress tolerance strategies of woody plants of the Northern Hemisphere. This thesis aimed to establish the STS as both a conceptual and practical tool for characterising woody plant adaptations to abiotic stress through the integration of multiple ecological dimensions, including functional traits and environmental conditions at species' habitats. To support the analysis, a new R package, funspace, was developed for multivariate trait-space analysis and visualisation. Species positions within the STS were linked to six key plant traits - plant size, wood density, seed mass, and leaf-economic traits - as well as species occurrence records with associated climatic and soil variables. Generalised additive models and clustering analyses were used to identify trait–tolerance relationships and reveal global geographic patterns of stress tolerance strategies. Distinct stress-tolerance strategies were related to contrasting plant functional trait syndromes that depended on plant functional type considered. Macroecological analyses showed that size-related traits and soil fertility were the primary determinants of drought and waterlogging/cold tolerance strategies, whereas climatic factors primarily shaped shade tolerance. These findings led to the identification of "stress tolerance biomes"—geographic regions characterised by specialized stress tolerance syndromes—and "polytolerance hotspots," regions with frequent coexistence of multiple tolerance strategies. Collectively, this thesis provides a comprehensive synthesis of woody plant adaptations to multiple abiotic stresses, offering a robust conceptual framework and practical tools for understanding and exploring the multidimensional nature of plant stress tolerance strategies.Kirje Multi-scale modelling and upscaling ecosystem function dynamics in Boreal Baltic coastal meadows using remote sensing platforms(Estonian University of Life Sciences, 2025) Martínez Prentice, Ricardo; Sepp, Kalev (advisor); Villoslada Peciña, Miguel (advisor); Ward, Raymond David (advisor); Institute of Agricultural and Environmental Sciences; Muro, Javier (opponent); Kmoch, Alexander (pre-opponent)ABSTRACT. Boreal Baltic Coastal Meadows face degradation caused by agricultural intensification and the abandonment of traditional management practices. In Estonia, they have been in decline over the past century, with 82% of managed coastal meadow areas lost by the year 2000. Since Estonia’s accession to the European Union, restoration efforts supported by EU agricultural funding have led to a noticeable recovery. By the end of 2019, 10700 hectares were restored. However, these coastal meadows remain under pressure from both abandonment and intensive grazing. Previous studies aimed at assessing the current state of preservation and restoration efforts for coastal meadows have accounted for their multi-faceted dynamics. High-precision Remote Sensing (RS) technologies detect those dynamics by capturing the variety of features in multispectral wavelengths, being able to retrieve key parameters such as plant community distribution and biophysical variables—supported by UAVs and field sampling. In this way, monitoring coastal meadows has evolved from static, site-limited surveys to spatially continuous approaches that reflect ecological variability across scales. The integration of UAV data with satellite imagery allows for both fine-scale resolution and landscape-scale coverage. The information retrieved by these platforms support evidence-based decision-making for restoration planning, agri-environmental policy implementation, and adaptive management, particularly in regions facing pressures from climate change and land-use transitions. The present thesis contributes to the monitoring of coastal meadows by extending high-precision mapping approaches to satellite-based imagery at coarser spatial resolutions. It tests the correspondence between UAV-mounted cameras and the sensors on board two well-known, medium-resolution, and publicly available satellite platforms: the European Space Agency's Sentinel-2 (S2) and the NASA–U.S. Geological Survey Landsat 8 (L8), both of which provide continuous Earth Observation (EO) data. The goal is to leverage UAV-based studies and make it feasible to expand monitoring efforts across larger areas of coastal meadows, particularly those protected under the EU Habitats Directive, Annex I (92/43/EEC). The use of publicly available satellite data also will facilitate the rapid automating and integration of UAV data with satellite data provided from Estonia’s national EO platforms. This can offer rapid decision-support tools for farmers receiving national subsidies to preserve the ecological state of coastal meadows. This work states three hypothesis. The first posits that pixel-based classification of very high-resolution UAV imagery yields more accurate maps of plant community distribution in coastal meadows than object-based methods. The second and third hypotheses propose that very high-resolution UAV data can be effectively upscaled to estimate Plant Fractional Cover (PFC) and Surface Soil Moisture (SSM) at the spatial resolutions of Sentinel-2 (10 m) and Landsat 8 (30 m), respectively, based on the spectral compatibility between sensors and calibration procedures. To enhance predictive performance, the study employs Random Forest (RF) and XGBoost algorithms, both of which demonstrate strong capabilities in handling complex, non-linear relationships. Their non-parametric and ensemble-based nature makes them particularly effective in modeling the spatial heterogeneity typical of coastal meadow ecosystems. Pixel-based classification proved more accurate than object-based methods for mapping Plant Communities, as it better captured the heterogeneous spectral variation typical of coastal meadows. On the other hand, upscaled UAV-derived Plant Community classification values were used both to assess the spectral correspondence between S2 and Parrot Sequoia (PS) images and to train S2-based RF models for estimating PFC. SSM was estimated at L8 scale using calibrated Temperature Vegetation Dryness Index (TVDI) values derived from UAV imagery and ground-based volumetric water content (VWC) measurements, resulting in very high-resolution SSM maps that were upscaled to L8 scale to train XGBoost models in three different months. The resulting predictions outperformed existing medium-resolution SSM estimation methods reported in the literature. The models yielded moderate to high performance, underscoring the importance of integrating vegetation indices (VIs) with auxiliary variables such as Digital Elevation Models (DEMs) and Land Surface Temperature (LST). Collectively, these results demonstrate the potential for scalable and automated monitoring frameworks that can inform both ecological research and the implementation of policy instruments—including agri-environmental subsidies and restoration programs—aimed at supporting the sustainable management of coastal meadows.Kirje Non-native species invasion strategies and effects on freshwater native communities(Estonian University of Life Sciences, 2025) Teesalu, Paul; Ercoli, Fabio (advisor); Tuvikene, Arvo (advisor); Institute of Agricultural and Environmental Sciences; Tricarico, Elena (opponent)ABSTRACT. The spread of invasive species has been forecasted to increase, particularly in freshwater ecosystems due to anthropogenic and environmental changes taking place at increasing rates. Invasive species generally adapt quickly to new environments, have high reproductive rates and can tolerate a wide range of conditions. This thesis studied three invasive species in the Narva reservoir area and found that their success is linked to dietary flexibility, behaviour, and tolerance to temperature changes. The Amur sleeper fish (Percottus glenii) can inhabit various waterbodies, for example, we found it in a warm-water channel, a large reservoir and a small pond. The Amur sleeper demonstrated great dietary plasticity, or the ability to consume a wide range of prey items. As Amur sleeper individuals grew, their diet shifted from a benthivorous diet to a piscivorous diet. The small amphipod Gmelinoides fasciatus, which has outcompeted and displaced native gammarid Gammarus lacustris in Lake Peipsi, exhibits superior predator avoidance and shows a more pronounced behavioural response to predators than its native counterpart, increasing its survivability. Marbled crayfish (Procambarus fallax virginalis) can shift from a protein rich macroinvertebrate based diet to a macrophyte based diet, indicating great dietary plasticity. Additionally, marbled crayfish, despite being considered a warm-water species, could withstand a wide range of water temperatures ranging from 0-30 °C over an extended period at our study site. During the implementation of invasive species management programs, it is important to consider their environmental tolerance, dietary adaptability and behavioural traits. As conditions change in our freshwater lakes and reservoirs, it is likely that invasive species will continue to be a problem, highlighting the need to understand and manage their spread to protect native freshwater ecosystems.Kirje Weeds in different cropping systems(Estonian University of Life Sciences, 2025) Madsen, Helena; Talgre, Liina (advisor); Luik, Anne (advisor); Institute of Agricultural and Environmental Sciences; Romaneckas, Kęstutis (opponent)ABSTRACT. Weeds play multiple roles in an agroecosystem. On the one hand they compete with crops for water and nutrients and on the other hand they enhance biodiversity within the field community, thereby providing environmental benefits. The aim of this study was to investigate weed occurrence in a long-term crop rotation experiment. The five-field rotation (barley undersown with clover, clover, winter wheat, pea, potato) was conducted under five different cropping systems. In two conventional systems herbicides were used for weed control, one of them also used mineral fertilizers. One organic system followed the crop rotation as a control variant. The remaining two systems used winter cover crops; composted manure was additionally applied to one of the systems. Weed occurrence and species composition depended on both the cropping system and the crop. In the first rotation the study of weed seedbank in the soil revealed that the number of weed seeds in organic cropping remained at a similar level compared to conventional systems, but species diversity was higher in organic systems. The highest number of weed seeds was found in the soil of pea fields across all systems except in organic system with winter cover crops. The lowest seed count was found in the soil of barley undersown with clover fields in conventional system with mineral fertilizers and in organic system with manure. In the second rotation, studies showed that weed biomass and density of occurrence was increased in all cropping systems, but significantly more in organic systems than in conventional ones. Also, weed diversity increased more in organic systems, being highest in the organic system with winter cover crops. Among the crops, weed biomass and density were high in pea and low in barley. Among the winter cover crops winter rye suppressed weeds most. However, likely due to their low biomass, winter cover crops did not achieve weed suppression comparable to herbicides. Nevertheless, winter cover crops improved soil properties and had a yield-enhancing effect.Kirje The effect of land use and agricultural management systems on earthworm communities and soil quality(Estonian University of Life Sciences, 2025) Sutri, Merit; Reintam, Endla (advisor); Shanskiy, Merrit (advisor); Ivask, Mari (advisor); Institute of Agricultural and Environmental Sciences; Garré, Sarah (opponent)ABSTRACT. The loss of soil biodiversity is considered one of the greatest threats to soil functioning in Europe. Due to their significant role in the soil, their abundance is considered one of the most suitable indicators of soil quality. To prevent the loss of soil quality and the decline of biological diversity, several sustainable agricultural practices have been proposed. However, it is still unclear whether these practices help maintain soil quality and earthworm communities in Estonia. The aim of this doctoral thesis was to investigate how land use and agricultural practices affect earthworm communities and soil quality in Estonia under field conditions. To assess soil quality, eight farm fields were selected, differing in tillage and land use, including grassland, no-tillage, minimum and conventional tillage fields. To determine how land use and agricultural practices affect earthworm communities, data on earthworm species abundance from research projects conducted in Estonia were compiled. The results showed that soil quality was better in fields with minimum tillage. The latter had lower penetration resistance, and higher porosity, water holding capacity, and water permeability compared to no-tillage and conventional tillage fields. The no-tillage system created the most favourable habitat conditions for earthworms compared to minimum and conventional tillage systems. Although the fields under organic farming had a higher Shannon diversity index, no significant effect of farming system on earthworm abundance was found. Natural and semi-natural grasslands had higher earthworm abundance and diversity compared to arable land. Overall, the natural variation in soils can have a greater impact on earthworm species diversity than the agricultural management used in the field. Therefore, the effect of the environmentally friendly practices can be modest, although these practices can still improve other parameters of soil quality.Kirje Dietary fiber content of cereal grains influenced by weather, fertilization and cropping system(Estonian University of Life Sciences, 2025) Khaleghdoust, Banafsheh; Loit-Harro, Evelin (advisor); Korge, Mailiis (advisor); Värnik, Rando (advisor); Institute of Agricultural and Environmental Sciences; Stoddard, Frederick (opponent)ABSTRACT. Cereal grains like wheat, barley, and oats are crucial for global nutrition, providing essential dietary fibers such as arabinoxylans (AX) and beta-glucans (BG). This thesis examines how weather conditions, nitrogen fertilization, and intercropping affect AX and BG content in cereal grains grown in Estonia. It aims to identify best practices for enhancing nutritional value and sustainability in cereal production, supporting global health and environmental resilience. The thesis is based on three field experiments in Estonia: two at the Estonian University of Life Sciences in Tartu County and one at the METK in Jõgeva County. The first experiment (2014-2021) analyzed winter wheat and spring barley grains under various fertilization regimes and weather conditions and the second (2021) evaluated the genotype effect on AX and BG content in different wheat and barley varieties. The third experiment (2022-2023) compared barley and oat grains dietary fiber content in mono-cropping and intercropping systems. AX and BG contents were determined enzymatically and statistical analyses were performed to assess treatment effects. The study found that weather conditions significantly influenced dietary fiber content in cereal grains. Higher temperatures during the grain-filling period increased AX and BG content in winter wheat and spring barley. Moreover, nitrogen fertilization effect on AX and BG content in cereal grains was limited. Winter wheat AX content in organic system was higher only at lower grain filling temperatures when compared to conventional systems. Intercropping had mixed effects on dietary fiber content, with decreasing BG content in intercropped barley and unaffected content of AX in barley and oats. Genotypic variation in both fiber content was less when compared to the impact of species. In conclusion findings of this thesis demonstrate the possibility to enhance the dietary fiber content of cereal grains while promoting sustainable agriculture.Kirje Phenotypic traits influencing changes in potato late blight pathogen Phytophthora infestans populations in Europe(Estonian University of Life Sciences, 2025) Puidet, Britt; Mänd, Marika (advisor); Koppel, Mati (advisor); Kiiker, Riinu (advisor); Institute of Agricultural and Environmental Sciences; Andersson, Björn (opponent)ABSTRACT. Potato late blight, caused by Phytophthora infestans, remains a substantial threat to global food security. European P. infestans populations are generally divided into Northern (genetically diverse) and Western (mainly clonal) populations. However, new genotypes have recently emerged and successfully established themselves in Northern Europe. Additionally, new strains that are more aggressive and more virulent or exhibit fungicide sensitivity to widely used active ingredients emerge frequently. The main objectives of this thesis were to study the drivers of new invasive lineages of P. infestans in Europe and the reason behind the shift in Northern European populations. Samples were collected from potato plants from conventional production fields, organic fields and trap nurseries in Estonia, Denmark, Norway, the UK, and France in ten growing seasons (between 2005-¬2022). DNA acquired from all the samples was genotyped through simple sequence repeat analysis. Phenotypic experiments were performed for samples collected in 2016 and 2017 and involved testing the isolates’ fungicide sensitivity to active ingredients widely used in Europe and evaluating their virulence to assess the ability of P. infestans to damage potato plants. Various population genetic indices were calculated to characterise the genetic diversity and dynamics of the pathogen in Estonia. Results showed that the Western European genotype EU_37_A2 exhibits fluazinam resistance, likely aiding its invasiveness. Genotype EU_41_A2 has successfully been established in Northern Europe, possibly due to higher virulence combined with other fitness traits or changes in environmental conditions not examined in this study. Substantial genetic and genotypic diversity persists in Estonia, suggesting a high likelihood of random mating. Still, monitoring results showed introductions of clonal lineages to the country, which creates a potential risk for future establishment. Our findings underscore the importance of continuous pathogen population monitoring to enable timely adjustments in control strategies.Kirje Factors affecting beekeeping sustainability: pathogen spread, diagnostics and queen breeding(Estonian University of Life Sciences, 2025) Naudi, Sigmar; Mänd, Marika (advisor); Karise, Reet (advisor); van der Steen, Jozef (opponent)ABSTRACT. The decline of pollinators is a global issue caused by diseases, parasites, poor nutrition, pesticides, habitat loss, and climate change. The honeybee (Apis mellifera Linnaeus) is a vital pollinator that helps maintain ecosystem balance and ensure food security. Although the number of managed bee colonies has increased in recent decades, beekeepers continue to face various challenges, including the spread of diseases, the impact of pesticides, and bee health issues. This doctoral theses focuses on identifying several of these threats, investigating major bee diseases, the effects of pollutants, their interactions, and developing potential protection methods. The study assessed the prevalence of the pathogenic microsporidians Nosema apis and N. ceranae in Estonian and Latvian apiaries. The results revealed that in cooler climates, the recently discovered N. ceranae is beginning to replace N. apis, which may lead to differences in the nature, spread, and control of the disease. Additionally, it was found that the simultaneous presence of both pathogens in bees increases infection levels, indicating a synergistic interaction. Research on Paenibacillus larvae, the pathogen responsible for American foulbrood, highlighted the hidden nature of the disease and its spread's dependence on bee density and climatic conditions. The use of qPCR technology proved effective for early disease detection, helping to reduce the severity and extent of infections. To ensure the sustainability of beekeeping, it is crucial that queen bees are healthy and their development is not disrupted. Studies on the fungicide active ingredient tebuconazole showed that, while the substance accumulates in beeswax, its transfer to other hive matrices, including royal jelly and developing bees, is minimal. This suggests the presence of a so-called barrier system within the colony that limits potential exposure to contaminants. However, further research is needed to understand the internal movement of pollutants within the hive and their long-term effects. Additionally, the impact of Nosema species on queen bees was investigated, revealing that infected royal jelly caused only minimal developmental disturbances in queens. Future studies should further analyze the effects of pathogens on different members of the bee colony.Kirje Assessing behavioural traits and ecological impacts of invasive crayfish species in freshwater ecosystem(Estonian University of Life Sciences, 2024) Ghia, Daniela; Sacchi, Roberto (advisor); Ercoli, Fabio (advisor); Institute of Agricultural and Environmental Sciences; Department of Earth and Environmental Sciences, University of Pavia; Maguire, Ivana (opponent); Kozák, Pavel (opponent)ABSTRACT. Biological invasions occur when species spread to new areas, causing ecological, economic, and social problems. Invasive species can be found in various ecosystems, but freshwater ecosystems are particularly vulnerable due to human activities and environmental changes. It has been forecasted that the invasion of alien species will increase by up to 36% by 2050, particularly in Europe. Among these invaders, crayfish are expected to see significant increases globally, representing major threats. These large freshwater invertebrates have attracted the attention of freshwater biologists and ecologists because of their ability to travel long distances, high reproductive rates, and adaptability. To better manage invasive species and conserve native ones, it's crucial to understand their behaviour and impacts on ecosystems. This research study has focused on understanding the behaviour of invasive crayfish and their impacts on freshwater ecosystems. Results highlighted the high adaptability of signal crayfish, which can vary their diet by season and age and, when coexist with native crayfish, they adjust their feeding habits, likely to reduce competition. The study also revealed that signal crayfish individuals coexisting with native crayfish at the invasion front are stronger than those living alone, suggesting a more successful invasion. It has also been found that invasive crayfish have a remarkable ability to disperse over land during droughts, showing their resilience and potential to spread. Additionally, experiments on their reproductive behaviour and the effects of removing female reproductive parts showed that this method could effectively reduce their reproductive capacity. These findings show the importance of considering behavioural traits in managing invasive species. Implementing control programs for invasive crayfish is crucial to preserving biodiversity and maintaining healthy freshwater ecosystems worldwide.Kirje Role of leaf anatomy in photosynthetic modifications during plant ontogeny and upon environmental acclimation(Estonian University of Life Sciences, 2024) Kuusk, Vivian; Niinemets, Ülo (advisor); Institute of Agricultural and Environmental Sciences; Fernández-Marín, Beatriz (opponent)ABSTRACT. To cultivate plant species and varieties best suited to our future environment, it is essential to gain a deep understanding of how plants acclimate to their surrounding conditions and which changes do they undergo during their life. The internal structure of plants, plant anatomy, plays a crucial role in this acclimation. This study focuses on investigating the anatomical and physiological changes that occur during plant aging and in response to high growth temperatures. Plants are the most important component of Earth's ecosystem, as the existence of all other living organisms depends on them. Since plants cannot change their location, they have evolved the ability to adapt to environmental conditions and modify themselves as needed. For young plants, survival and sufficiently rapid growth, including the development of a strong root system and foliage, are of utmost importance. Using three Mediterranean pine species (Pinus halepensis, P. pinea, P. nigra) as examples, we demonstrate how their photosynthetic capacity changes over time depending on the anatomy of their needles and what causes these changes. What makes this study unique is the precise mapping of the changes occurring in the needles as they age and their correlation with photosynthetic capacity. The second aim of this study is to investigate the effects of elevated growth temperatures on plant anatomy and isoprene emission. Almost all plant leaves emit isoprene, the most abundant volatile compound globally, whose emission is strongly influenced by the plant's growth environment. Isoprene is highly chemically reactive and significantly impacts atmospheric chemistry. Given its widespread importance, a detailed understanding of all aspects of its emission is essential to ensure more accurate models and future predictions related to isoprene. This study demonstrates that elevated growth temperatures substantially alter leaf anatomy, which in turn affects photosynthesis and isoprene emission per leaf area. The research aims and succeeds to gain a better understanding of the anatomical changes in plants under challenging conditions: when a young plant establishes itself in its habitat and when it grows under temperatures higher than normal for the species.Kirje Suitability of cruciferous oilseeds as cover crops, their disease resistance and optimized cultivation technologies for improved overwintering and yield(Estonian University of Life Sciences, 2024) Lääniste, Peeter; Runno-Paurson, Eve (advisor); Niinemets, Ülo (advisor); Institute of Agricultural and Environmental Sciences; Kadžienė, Gražina (opponent)ABSTRACT. Cruciferous field crops are important as oil crops and inhibitors of some soil pathogens. At the same time they can be susceptible to various other diseases, as they have been intensively cultivated in short rotations. There are lot of problems with the cultivation of the main oil crop - winter rapeseed in Estonia, mostly evident through instability of seed yields. Previous studies have indicated that the cultivation of winter rapeseed as a cover crop reduces the presence of pathogen, that is causing the potato late blight; different cruciferous species have large variation in resistance to crop diseases; and the successful overwintering of winter rapeseed is related to weather conditions, sowing time and seed rates. Therefore, following hypotheses were set at the start of present research: 1) The cultivation of winter rapeseed as a cover crop has positive effect on controlling the abundance of pathogen that is causing late blight in potato, resulting in higher tuber yield; 2) The alternative cruciferous oil crops are more resistant to powdery mildew than spring rapeseed; 3) The spring rapeseed is more susceptible to Alternaria black spot disease than alternative cruciferous species; 4) The growth and development as well as the yield of winter rapeseed is dependent on the sowing time, seed rate and the sum of active temperatures during autumn growth; 5) Successful overwintering and yield potential are directly related to certain crop parameters measured in autumn. Based on the results of present thesis it was found that when cultivating winter rapeseed as a cover crop, the late blight infection emerged slightly later and there was a decrease in damaged area, but the effects on disease suppression and tuber yield were not significant. The alternative cruciferous oil crops like white mustard, ruccola/arugula and oilseed radish were not infected with powdery mildew and black spot disease, even during favourable conditions for the pathogens. Hence, these species could be used as cruciferous crops in rotations without the use of pesticides. The most suitable period for sowing winter rapeseed was in the middle of August, allowing plants to optimize their parameters for winter survival. Good indicator was the time when 7-8 true leaves had been formed, resulting in 70% survival rate and also providing higher seed yield potential.Kirje An integrated evaluation of blue space design interventions for health and well-being(Estonian University of Life Sciences, 2024) Mishra, Himansu Sekhar; Bell, Simon (advisor); Külvik, Mart (advisor); Institute of Agricultural and Environmental Sciences; Ward Thompson, Catharine (opponent); Gidlow, Christopher (pre-opponent)ABSTRACT. This PhD, conducted under the BlueHealth project (Horizon 2020), enhanced public health and urban planning research by focusing on 'blue' spaces—water-based environments beneficial for well-being and healthy behaviour. Despite offering unique recreational and sensory experiences, blue spaces are often underutilised and understudied compared to 'green' spaces. The PhD stands out for its multidisciplinary approach, extensive literature review, and the development of the BlueHealth Environmental Assessment Tool (BEAT), and pre-post physical intervention- assisted approach, which assessed blue spaces for health antecedents and provided evidence for planning and design. In this research, BEAT and other tools from the BlueHealth Project were adapted to support evidence-based co-creation of urban blue space interventions. These interventions engaged various stakeholders and community members, significantly advancing methodologies in environmental assessments and pre-post evaluations. The PhD evaluated the impact of blue space interventions on user frequency, accessibility, inclusivity, diversity, and the local community’s general health and well-being. A key aspect was the implementation of 'urban acupuncture' at Teat’s Hill, Plymouth, UK, involving the community actively in the project lifecycle. The pre-post (2017-2018) place assessment and intervention strategy provided evidence for co-designing a small-scale, impactful intervention for the local community and later assessing its impact. This approach highlighted the effectiveness of small-scale interventions and the need for comprehensive evaluation techniques. The PhD introduced methodological advancements by applying tools like BEAT, BlueHealth Behaviour Assessment Tools (BBAT), and the BlueHealth Community Level Survey (BCLS). These tools demonstrated how evidence-based design of blue space interventions could surpass traditional practices, making them versatile for various urban blue space evaluation, design, and management needs. Community and stakeholder engagement was crucial, with Teat’s Hill showing the benefits of involving local residents in blue space interventions through social events. This participatory approach ensured alignment with community needs and environmental values, fostering ownership and relevance among stakeholders. Additionally, BEAT addressed gaps in current assessment tools by focusing on health and well-being within blue spaces, incorporating sensory and functional affordances. It was designed to balance comprehensiveness and practicality, facilitating pilot testing and validation across awide range of European blue space settings. This thesis argues for the importance of small-scale interventions and community involvement in achieving significant public health benefits. It underscores the complexities of environmental assessments and the need for robust, reliable tools to evaluate diverse impacts of blue spaces, presenting a toolkit for planners. This research contributed methodologically and empirically to the BlueHealth project by enhancing understanding of blue spaces and advocating for their integration into urban planning and public health strategies.