1. The response of microbes to anthropogenically induced perturbations in the Gulf of Trieste (northern Adriatic Sea) : dissertationNeža Orel, Tinkara Tinta, 2025, doktorska disertacija Opis: 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.
Ključne besede: coastal microbiome, anthropogenic impact, wastewater pollution, bacterial community dynamics, allochthonous microorganisms, potential pathogens, Vibrio campbellii, multi-omics, whole-genome assembly, dissertations
Objavljeno v RUNG: 16.04.2025; Ogledov: 307; Prenosov: 2
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3. Morphological dependencies : a dissertationGuy Tabachnick, 2023, doktorska disertacija Opis: This dissertation investigates morphological dependencies: correlations between two lexically specific patterns, such as selection of inflectional affixes. Previous work has established that such correlations exist in the lexicon of morphologically rich languages (Ackerman et al., 2009; Wurzel, 1989), but has not systematically tested whether speakers productively extend these patterns to novel words. I present a series of corpus and nonce word studies—in Hungarian, Czech, and Russian—testing whether speakers vary their selection of suffixed forms of novel words based on the forms of that word that are presented to them. In all three cases, speakers vary their responses in accordance with the provided stimuli, demonstrating that they have learned and productively apply morphological dependencies from the lexicon.
I present a theoretical account of morphological dependencies that can account for my experimental results, based on the sublexicon model of phonological learning (Allen & Becker, 2015; Becker & Gouskova, 2016; Gouskova et al., 2015). In this model, speakers index lexically specific behavior with diacritic features attached to underlying forms in lexical entries, and learn generalizations over sublexicons defined as words that share a feature. These generalizations are stored as constraints in phonotactic grammars for each sublexicon, enabling speakers to learn phonological and morphological dependencies predicting words that pattern together. This model provides a unified treatment of morphological dependencies and generalizations that are phonological in nature. My studies show a wide range of learned effects, not limited to those that follow an organizational principle like paradigm uniformity. The sublexicon model assumes that speakers can learn arbitrary generalizations without restrictions, giving it needed flexibility over more restrictive models which rely on notions of morphophonological naturalness.
Ključne besede: inflectional affixes, nonce word study, lexical productivity, morphological dependencies, diacritic features, dissertations
Objavljeno v RUNG: 04.03.2024; Ogledov: 2297; Prenosov: 12
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9. Unravelling the molecular basis of hydroxyapatite weathering driven by the ectomycorrhizal fungus Paxillus involutusChristina Paparokidou, 2018, doktorska disertacija Opis: Ectomycorrhizal fungi (EMF) form symbiotic partnerships with tree roots and are able to chemically weather inorganic phosphorus (Pi)-rich minerals, supplying Pi to their host in return for photosynthates. The fungal-driven nutrient cycling from mineral weathering plays a pivotal role in ecosystems and crops productivity, as well as geochemical cycles. The aim of the study presented in this thesis is to unravel the molecular mechanisms by which the EM fungus Paxillus involutus weathers the Pi-rich mineral hydroxyapatite (HAP), either non-symbiotically or in symbiosis with its host tree Pinus sylvestris. Development of an artificial system to study P. involutus responses to varying concentration of Pi led to the identification of five high-affinity Pi transporter genes, of which the expression varies in an inversely proportional manner to Pi availability. Using the same system, whole-transcriptomic data from fungal hyphae unravelled the molecular basis of the EMF ability in Pi uptake at the global gene scale, revealing that EM symbiosis can directly affect Pi-responsive fungal genes such as the Pi transporter PiPT4. A second artificial system was used to study HAP solubilisation driven by P. involutus, which was confirmed by EDX spectroscopy data showing depletion of Pi from the HAP crystals, along with secondary minerals formation. Whole-transcriptomic analysis revealed that EM symbiosis induces a different set of HAP weathering genes in P. involutus hyphae, compared to the fungus growing non-symbiotically, including the specific expression of organic acid metabolic genes, which resulted in enhanced HAP solubilisation. Metabolomic analysis led to the identification of multiple secreted metabolites enriched in the presence of HAP in P. involutus systems grown non-symbiotically or in symbiosis with P. sylvestris seedlings. The analysis also led to the identification of putative novel fungal weathering agents. Results from transcriptomic and metabolomic analyses were ultimately combined in a model of HAP weathering by P. involutus.
Ključne besede: Paxillus involutus, Pinus sylvestris, ectomycorrhizal symbiosis, hydroxyapatite, SEM-EDX, fungal mineral weathering, fungal weathering metabolites, RNA-seq, UPLC-Q-TOF-MS
Objavljeno v RUNG: 03.05.2022; Ogledov: 2926; Prenosov: 0
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