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Abstract: Marine ecosystems are constantly influenced by anthropogenic pressures, including inputs of nutrients, pollutants, and allochthonous microorganisms. These inputs can disrupt the dynamics of marine microbiomes, which encompass the majority of biomass and highest diversity of all life forms, controlling most biogeochemical cycles in the ocean realm. Despite their importance for public safety and potential influence on marine ecosystems functioning, knowledge of the impact of these perturbations on coastal microbiome dynamics remains in its infancy. The research objectives of this dissertation were to: (1) characterize the composition of the coastal microbiome in anthropogenically impacted coastal ecosystem; (2) investigate the genetic potential of selected microorganisms for pathogenicity and ecological adaptations; and (3) explore the effects of wastewater on the dynamics and functioning of the coastal microbiome, as well as its implications for the biogeochemical state of the ecosystem. To address the first aim, we conducted a year-round in situ survey of the pelagic microbiome within anthropogenically impacted coastal ecosystem, focusing on the seasonal and spatial dynamics of traditional and alternative faecal bacterial indicators. We used a culture-independent approach combined with 16S rRNA amplicon sequencing, which overcome limitations of culture-based methods. This analysis revealed that the microbiome was primarily structured by seasonal changes, regardless of proximity to pollution sources. The statistical tool and oceanographic model we applied indicated that riverine water serves as a key vector for introducing allochthonous microbes. This study underscores the importance of molecular approaches combined with statistical and oceanographic modelling for advancing environmental health assessments and detecting microbial indicators. To address the second aim, we applied whole-genome sequencing to assess the pathogenic potential and genomic features of selected Vibrio isolates. During the analysis, we identified cross-contamination in one isolate, which presented an opportunity to evaluate the effectiveness of bioinformatics workflows for contaminant removal and genome recovery. We reconstructed high-quality genomes of one Vibrio isolate from both axenic and contaminated cultures. Genomic analyses revealed that this isolate belongs to a sub-lineage of Vibrio campbellii associated with diseases in marine organisms. Moreover, this genome harboured a novel Vibrio plasmid linked to bacterial defense mechanisms and horizontal gene transfer, potentially offering a competitive advantage to this putative pathogen. This study highlights the utility of WGS and advanced bioinformatics in overcoming challenges posed by non-axenic cultures and provides new insights into the genomic characteristics of V. campbellii. To address the third aim, we conducted a short-term microcosm experiment simulating wastewater discharge into coastal seawater, testing two types of wastewaters: (a) unfiltered, containing nutrients, pollutants, and allochthonous microbes, and (b) pre-filtered, retaining only nutrients and pollutants. Our results showed that wastewater, significantly increased nutrient levels (dissolved organic carbon, ammonium, orthophosphate). Using a multi-omics approach with measurements of microbial metabolic activity, we found that nutrient enrichment significantly influenced bacterial metabolism. This was evidenced by enriched protein profiles and increased leucine aminopeptidase and olease activity, indicating bacterial degradation of complex proteins and lipids. At the same time, the phosphate input resulted in a decreased alkaline phosphatase activity, with important implications for phosphorus cycling. Overall, wastewater primarily induced functional shifts in coastal microbiomes, highlighting the resilience and functional redundancy of coastal microbial communities and hence the biogeochemical processes they operate.
Keywords: coastal microbiome, anthropogenic impact, wastewater pollution, bacterial community dynamics, allochthonous microorganisms, potential pathogens, Vibrio campbellii, multi-omics, whole-genome assembly, dissertations
Published in RUNG: 16.04.2025; Views: 351; Downloads: 3
Full text (10,24 MB)

Abstract: Hemicellulose, one of the key components of lignocellulosic biomass, and its sugar monomers offer significant potential as a substrate for producing value-added platform chemicals. With both pentoses (xylose and arabinose) and hexoses (glucose, galactose, and mannose), the conversion of hemicellulose can yield various products including furfural, hydroxymethylfurfural (HMF), and levulinic acid. This doctoral thesis investigates the dehydration of various hemicellulose-derived monosaccharides, utilizing catalyst-free systems, as well as homogeneous and heterogeneous catalysts, in both aqueous and organic solvents. Monosaccharide conversion was evaluated in a catalyst-free aqueous solution at temperatures ranging between 130 – 190 °C. Conducting dehydration reactions under simple, hydrothermal conditions highlighted the differences in the reactivity of individual monosaccharides. Experimental data from extensive activity testing enabled the development of accurate kinetic models. Aiming at the optimization of reaction parameters relevant to the post-Organosolv production of furanics and levulinic acid, sulfuric and formic acid were introduced into the reaction system as homogeneous acid catalysts. Reaction kinetics of acid catalysed conversion using sulfuric and formic acid indicated a significant reduction in the activation energy of ketose dehydration. In addition, the addition of both acids enhanced the dehydration rates and promoted the conversion of HMF towards levulinic acid due to its low activation energies 86 – 91 kJ mol−1 and high reaction rate constants. The established kinetic model for individual saccharides was proven to be robust and able to accurately predict optimal reaction conditions for two distinct industrially relevant hemicellulose streams. In pursuit of a more sustainable and recyclable catalyst, various zeolites, specifically H-BEA, were tested. Although H-BEA exhibited excellent catalytic activity, its selectivity towards furanics remained limited in aqueous media. The low activation energy for HMF rehydration facilitated the formation of levulinic acid even at a moderate reaction temperature of 165 °C. Notably, the addition of THF as an organic solvent in combination with H-BEA, drastically improved the product selectivity towards furanics, particularly furfural. In addition to H-BEA zeolite, various types of zeolites with different Si/Al ratios were studied. Catalyst characterization revealed a strong correlation between catalytic activity and acidity. The addition of THF resulted in 90 mol % of furfural after only 30 min, demonstrating an exponential increase in dehydration rates and a decrease in activation energies. This zeolite-THF system was therefore applied for tandem reactions involving both xylose dehydration and furfural hydrogenation. The addition of metallic active sites via a Ni/H-BEA catalyst, and a hydrogen atmosphere, resulted in the catalytic hydrogenation of xylose to tetrahydrofurfuryl alcohol. Adjusting reaction temperatures allowed the production of secondary hydrogenated (2-methylfuran and 2-methyltetrahydrofuran) and dehydration products (tetrahydropyran), while the addition of water as a co-solvent with THF resulted in the complete inhibition of dehydration reactions and the selective formation of xylitol. Through a systematic study of reaction conditions and the development of comprehensive kinetic models, this work provides an in-depth investigation of monosaccharide dehydration. This doctoral thesis represents a comprehensive study to systematically investigate both catalytic and non-catalytic dehydration of five relevant monosaccharides, providing a methodical kinetic modelling approach that addresses the challenges associated with the complexity related to hemicellulose conversion.
Keywords: hemicellulose, monosaccharides, kinetic modelling, furanics, catalysis, dissertations
Published in RUNG: 19.02.2025; Views: 784; Downloads: 18
Full text (11,80 MB)

Abstract: The Zimm-Bragg (ZB) model serves as a fundamental framework for elucidating conformational transitions in biopolymers, offering simplicity and efficacy in processing experimental data. This study provides a comprehensive review of the Zimm-Bragg model and its Hamiltonian formulation, with particular emphasis on incorporating water interactions and chain size effects into the computational framework. We propose a modified ZB model that accounts for water-polypeptide interactions, demonstrating its ability to describe phenomena such as cold denaturation and helix-coil transitions. In the realm of NanoBioTechnologies, the manipulation of short polypeptide chains is commonplace. Experimental investigation of these chains in vitro often relies on techniques like Circular Dichroism (CD) and timeresolved infrared spectroscopy. Determining interaction parameters necessitates processing the temperature dependence of the normalized degree of helicity through model fitting. Leveraging recent advancements in the Hamiltonian formulation of the Zimm and Bragg model, we explicitly incorporate chain length and solvent effects into the theoretical description. The resulting expression for helicity degree adeptly fits experimental data, yielding hydrogen bonding energies and nucleation parameter values consistent with field standards. Differential Scanning Calorimetry (DSC) stands as a potent tool for measuring the specific heat profile of materials, including proteins. However, relating the measured profile to microscopic properties requires a suitable model for fitting. We propose a novel algorithm for processing DSC experimental data based on the ZB theory of protein folding in water. This approach complements the classical two-state paradigm and provides insights into protein-water and intraprotein hydrogen bonding energies. An analytical expression for heat capacity, considering water interaction, is derived and successfully applied to fit numerous DSC experimental datasets reported in the literature. Additionally, we compare this approach with the classical two-state model, demonstrating its efficacy in fitting DSC data. Furthermore, we have developed and launched a free online tool for processing CD and DSC experimental data related to protein folding, aiming to support scientific research.
Keywords: Zimm-Bragg model, conformational transitions, helix-coil transitions, cold denaturation, circular dichroism, differential scanning calorimetry, protein folding, water-protein interaction, hydrogen bonding energy, degree of helicity, short polypeptide chains, protein heat capacity, protein data analysis, dissertations
Published in RUNG: 27.01.2025; Views: 834; Downloads: 13
Full text (5,12 MB)

Abstract: In recent decades, there has been a growing interest in producing biofuels and biochemicals from renewable sources. Furfural stands as one of the ligno(hemi)cellulosic biomass derived platform chemical, which can be transformed into numerous value-added products. The goal of this PhD was to systematically study hydrotreatment reactions of furfural under varying operating conditions and to gain insights into the reaction mechanism and kinetics. An extensive experimental and computational study of hydrogenation, hydrodeoxygenation, oligomerisation and etherification of furfural in a three-phase batch reactor was performed. The goals were divided into three consecutive objectives. In the first part, hydrotreatment of furfural over Pd/C catalyst under various reaction conditions, including the solvent selection (solventless conditions, tetrahydrofuran, isopropanol), atmosphere (nitrogen, hydrogen), temperature (100–200 °C), pressure (25–75 bar) and stirring speed, was studied. A reaction pathway network and a micro-kinetic model were developed, incorporating thermodynamics (hydrogen solubility), mass transfer, adsorption, desorption, and surface reactions. These phenomena and their contribution to the surface coverages, TOF’s and global reaction rates were studied. The hydrogen presence on the catalyst surface was found to influence the main reaction pathway, leading to ring, aldehyde group or full hydrogenation. In the second part, various monometallic catalysts (Pd/C, Pt/C, Re/C, Ru/C, Rh/C, Ni/C, Cu/C) were tested at 100 -200 °C with 60 bar of hydrogen and tetrahydrofuran as solvent. A generalized reaction pathway network was developed. H2 temperature-programmed reduction (H2-TPR) and CO temperature-programmed desorption (CO-TPD) were conducted, and a regression analysis of the results was subsequently performed by numerical modelling and optimisation. The obtained adsorption and desorption kinetic parameters for active metallic sites were further used in a generalized micro-kinetic model, applicable to all tested catalysts. Pd/C exhibited high activity and non-selective hydrogenation of furfural, while other catalysts showed selective aldehyde group hydrogenation followed by deoxygenation, consistent with density functional theory (DFT) calculations. Ru/C uniquely produced 2 methyltetrahydrofuran and ring-opening products at 200 °C. In silico optimization of reaction conditions for promising catalysts ((Pd/C, Pt/C, Re/C, Ni/C) aimed to maximize the yield of the target product. In the third part, the influence of support on catalytic activity was studied. Hydrotreatment of furfural over Pd/Al2O3, Pd/SiO2, Ru/Al2O3, Ru/SiO2, Ni/Al2O3, and Ni/SiO2 was performed between 150 - 200 °C, using 60 bar of hydrogen and tetrahydrofuran as solvent. The strength and rate of adsorption and desorption to/from acidic, metallic and interface site structures were determined, using H2-TPR, CO-TPD and NH3-TPD and subsequent regression analysis of the results by numerical modelling and optimisation. The resulting parameters were sequentially used in the generalized micro-kinetic model to quantify the contribution of the active metal (Ni, Pd, or Ru), support (Al2O3 or SiO2), interphase sites and their relationship on catalyst activity and selectivity. Evaluation of morphological and structural characteristics, adsorption/desorption and intrinsic reaction kinetics has indicated that the coverage of acidic sites (on alumina or silica) facilitated yielding ring hydrogenation and inhibited deoxygenation, decarbonylation and cyclic compound opening. The rates for aromatics or aldehyde functional groups were, nonetheless, affected in a different order. The used and developed methods and findings of this PhD offer useful guidelines for transforming furfural into high-value chemicals through catalytic hydrotreatment, with significant implications for future research and industrial applications.
Keywords: lignocellulosic biomass, furfural, catalytic hydrogenation, micro-kinetic mass transfer model, reaction kinetics, first-principle methods, furfuryl alcohol, tetrahydrofurfuryl alcoholv, dissertations
Published in RUNG: 08.11.2024; Views: 1241; Downloads: 23
Full text (9,22 MB)

Abstract: Microcystis aeruginosa accumulation in freshwater poses a significant threat to aquatic organisms and human health. The toxicity of Cyanobacteria metabolites urges for the development of methods for their rapid and efficient detection but what is still almost completely missing is the availability of reagents for the quantification of M. aeruginosa cells in water to monitor the fluctuations of its population. In this study, nanobodies against cell surface antigens of the toxic Cyanobacteria M. aeruginosa were recovered bywhole-cell panning of a naive phage display library. Six unique sequences were identified and three of them sub-cloned and purified as fusion immunoreagents together with either green fluorescent protein or Avi-Tag to be used for diagnostics. Theirspecificity and sensitivity were evaluated by immunofluorescence, by fluorescent and colorimetric cell ELISA and by thermal lens spectrometry (TLS). No cross-reactivity with unrelated microalgae was detected, and both ELISA and TLS methods provided a linear range of detection of several logs. The limit-of-detection of TLS was as low as 1 cell/ml.
Keywords: cyanobacteria, nanobodies, phage display, thermal lens spectrometry, dissertations
Published in RUNG: 10.09.2024; Views: 1358; Downloads: 23
Full text (3,80 MB)