TY - THES A1 - Erdmann, Eileen A. T1 - Genetic tools for targeted genome editing and random mutagenesis of the rock-inhabiting black fungus Knufia petricola N2 - Rock-inhabiting black fungi are ubiquitously found on sun-exposed natural and human-made surfaces. These stresstolerant biofilm-formers are known to force the deterioration of the colonized surfaces. Black fungi belong to different classes of Ascomycota (Arthoniomycetes, Eurotiomycetes, and Dothideomycetes) but evolved the same morpho-physiological adaptations such as strong melanized multilayered cell walls and slow yeast-like or meristematic growth to resist extreme environmental conditions. The rock-inhabitant Knufia petricola was chosen as representative of the polyphyletic group of black fungi for studying mineral weathering, biofilm formation, and interaction with phototrophic microbes. For understanding the molecular basis of these traits, the genetic information and its regulation must be explored. Thus, the genome was sequenced, first -omics datasets obtained and protocols for the transformation of protoplasts and CRISPR/Cas9-based genome editing were implemented to enable genetic studies. In scope of this work, the transformation protocol was optimized to improve the regeneration of K. petricola protoplasts. The successful implementation of multiplexed CRISPR/Cas9 and three additional selection marker systems (geneticin/nptII, glufosinate/bar, chlorimuron ethyl/sur) extended the existing strategies for targeted genome editing. While in the first promoter studies only constitutive promoters (PoliC, PgpdA) were identified as appropriate for expression of fluorescent reporter genes in K. petricola, the functionality of an inducible promoter (synthetic TET-on promoter system) could later be demonstrated. The identification and validation of defined genomic insertion sites enabled the neutral or color-based selection (igr1-5 or pks1, phs1, ade2) as well as the detection of correctly integrated expression constructs. Using the color-based transformant screening (black – pink/white/rose) accelerated the selection of transformants, especially for localization and protein-protein interaction studies (e.g., by studying bimolecular fluorescence complementation). Additionally, the fusion of two or three genes via the viral P2A motif was shown to allow the expression of multiple genes from a single expression cassette/integration site. Finally, the established tools enabled the implementation of a forward genetics tool (customized Ac/Ds transposon system) for regulatable in-vivo mutagenesis of K. petricola. The isolation and characterization of revertants/Ds reinsertion mutants demonstrated the functionality of the system which marks an important milestone for assigning functions to yet unknown species- and/or trait-specific genes. In sum, the genetic engineering toolbox is now fully equipped which paves the way for exploring the biology of K. petricola and other black fungi. KW - Microcolonial fungi KW - Genetic engineering KW - CRISPR/Cas9-mediated genome editing KW - DHN melanin KW - Transposon mutagenesis PY - 2024 SP - 1 EP - 231 CY - Berlin AN - OPUS4-62364 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - THES A1 - Kittner, Maria T1 - Entwicklung eines Konzeptes zur verbesserten Abbaubarkeit von Polymeren unter realitätsnahen Umweltbedingungen N2 - Das Ziel dieses Grundlagenforschungsprojektes war, die Abbaubarkeit syntheti-scher Polymere unter realitätsnahen Umweltbedingungen durch eine Mischung bzw. Blend eines Hydrolyse- mit einem Oxidations-empfindlichen Polymer zu verbessern, während er unter Nutzungsbedingungen stabil sein sollte. Die Arbeits-hypothese war, dass sich die Polymere gegenseitig in ihrem Abbau beschleunigen, wenn sie der alternierenden Wechselbeanspruchung aus UV-Strahlung und hydrolytischer Beanspruchung ausgesetzt sind. Hierfür wurden vier Blends aus Polylactid (PLA) und Polystyrol (PS) oder Polymethylmethacrylat (PMMA) in unterschiedlichen Mischverhältnissen und Phasenstrukturen mittels additiver Fertigung hergestellt. Die Blends wurden über acht Wochen bei 45 °C mittels alternierender Wechselbeanspruchung aus je fünf Tagen UV-Bestrahlung und zwei Tagen hydrolytischer Beanspruchung beschleunigt gealtert. Für eine Basis-charakterisierung und als Vergleichsgrundlage wurden zusätzlich die Ausgangs-polymere PLA, PS und PMMA jeweils einzeln der hydrolytischen Beanspruchung, UV-Beanspruchung und alternierenden Wechselbeanspruchung unterzogen. Neben der Bestimmung der physiko-chemischen Effekte auf Prüfkörperoberflächen und Bulk wurden erstmalig auch die Wassermedien auf Mikroplastikgehalte und ökotoxikologische Wirkungen analysiert. Die Ergebnisse ergaben, dass reines PLA kaum degradierte, aber der PLA-Abbau sowohl durch Mischung mit PS als auch PMMA verstärkt wurde. Entgegen der Hypothese wurde dadurch allerdings sowohl die Degradation von PS als auch von PMMA gehemmt. Es konnte gezeigt werden, dass sich PS und PMMA im Blend mit PLA durch radikalische Depolymerisation abbauten und die dabei entstehenden Radikale die PLA-Hydrolyse beschleunigten, was wiederum den Abbau der PS- und PMMA-Phasen verlangsamte. Die Ergebnisse zeigten, dass bei dem PLA/PS-Schichtblend (PLA/PS-50) der höchste PS-Gehalt von 50 % den stärksten Effekt auf den PLA-Abbau hatte. Insgesamt war allerdings selbst in diesem Fall die PLA-Degradation nach achtwöchiger Beanspruchung als gering einzustufen. Der totale Masseverlust von PLA/PS-50 entsprach nach achtwöchiger Wechselbeanspruchung -2,6 ± 0,2 mg absolut bzw. ca. -1,5 ± 0,1 % der Prüfkörpermasse, wovon 0,001 % in partikuläres Mikroplastik fragmentierte (PLA: 0,2 – 2,7 μg/g; PS: 3,0 – 3,4 μg/g). Folglich war der größte Teil des Masseverlustes der Prüfkörper auf die Bildung gelöster und/oder gasförmiger Degradationsprodukte zurückzuführen. Ferner zeigten ökotoxikologische Untersuchungen der wechselbeanspruchten Wassermedien von PLA/PS-50 eine zunehmende Hemmung des Algenwachstums der Grünalge Desmodesmus subspicatus, die nach sechs Wochen Wechsel-beanspruchung zu 100 % Hemmung und nach acht Wochen zu einem Absterben der eingesetzten Algenzellen führte. Ergänzende Algenwachstumshemmungstests mit 2 Prüfkörpern der Ausgangspolymere PLA und PS zeigten, dass dies nicht auf der Bildung von partikulärem Mikroplastik, sondern gelösten PS-Degradations-produkten basierte, wie z. B. Benzaldehyd oder Benzoesäure. Zusammenfassend lässt sich sagen, dass nur eine geringe Beschleunigung des PLA-Abbaus bei gleichzeitiger Hemmung des PS- bzw. PMMA-Abbaus stattfand - und das auch erst bei hohen PS- bzw. PMMA-Gehalten. Weiterführende Experimente zeigten, dass dies speziell für PS höchst bedenklich und nicht empfehlenswert ist, da es abhängig von der Konzentration der gelösten PS-Degradationsprodukte zu starken ökotoxikologischen Effekten kommen kann, die von der Hemmung des Algen-wachstums bis zum Algenabsterben reichen können. Folglich konnte die Arbeits-hypothese nur sehr eingeschränkt verifiziert werden und ist mit den hier untersuchten Polymeren als nicht zielführend einzuschätzen. KW - Polymer KW - Blend KW - Microplastik KW - Degradation KW - Umweltsimulation PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-609879 DO - https://doi.org/10.14279/depositonce-21006 SP - 1 EP - 109 PB - Depostit Once CY - Berlin AN - OPUS4-60987 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - THES A1 - Usmani, Shirin T1 - Wood treated with nano metal fluorides - relations between composition, size, and durability N2 - In this study, nanoscopic particles of magnesium Fluoride (MgF2) and calcium fluoride (CaF2) also known as nano metal fluorides (NMFs), were evaluated for their potential to improve wood durability. Even though these fluorides are sparingly soluble, their synthesis in the form of nano-sized particles turns them into promising candidates for wood preservation. Their distinct property of low-water solubility is proposed to maintain long-lasting protection of treated wood by reducing the leaching of fluoride. Analytical methods were used to characterize the synthesized NMFs and their distribution in treated wood specimens. Transmission electron microscopy images showed that these fluoride particles are smaller than 10 nm. In nano metal fluoride (NMF) treated specimens, aggregates of these particles are uniformly distributed in the wood matrix as confirmed with scanning electron microscopy images and their corresponding energy-dispersive X-ray spectroscopy maps. The fluoride aggregates form a protective layer around the tracheid walls and block the bordered pits, thus reducing the possible flow path for water absorption into wood. This is reflected in the reduced swelling and increased hydrophobicity of wood treated with NMFs. The biocidal efficacy of NMFs was tested against brown-rot fungi (Coniophora puteanaand Rhodonia placenta), white-rot fungus (Trametes versicolor), and termites (Coptotermes formosanus). The fungal and termite tests were performed in accordance with the EN 113 (1996) and EN 117 (2012) standards, respectively. Prior to fungal tests, the NMF treated wood specimens were leached according to the EN 84 (1997)standard. Compared to untreated specimens, the NMF treated wood specimens have a higher resistance to decay caused by brown-rot fungi, white-rot fungus, and termites. Although all NMF treatments in wood reduce the mass loss caused by fungal decay, only the combined treatment of MgF2 and CaF2 has efficacy against both brown-rot fungi and white-rot fungus. Similarly, wood treated with the combined NMF formulation is the least susceptible to attack by C. formosanus.It is proposed that combining MgF2 and CaF2changes their overall solubility to promote the release of fluoride ions at the optimal concentration needed for biocidal efficacy against fungi and termites. In this thesis, it was proven that even after leaching, sufficient fluoride was present to protect NMF treated wood from fungal decay. This shows that NMFs are robust enough for above ground contact outdoor applications of wood, where permanent wetness cannot be avoided according to Use Class 3.2, as per the EN 335 (2013) standard. Also, they pose a low risk to human health and the environment because they are sparingly soluble. Since NMFs significantly reduce the decay of wood, the CO2 fixed in it will be retained for longer than in unpreserved wood. Overall, the novel results of this study show the potential of NMFs to increase the service life of building materials made from non-durable wood. KW - Termites KW - Nano metal fluorides KW - Solubility KW - Wood protection KW - Fungi PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-525108 DO - https://doi.org/10.18452/22553 SP - i EP - 118 PB - Humboldt-Universität zu Berlin CY - Berlin AN - OPUS4-52510 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - THES A1 - Schmidt, Selina T1 - Effects of biocides on processes underlying resistance evolution N2 - Antimicrobial resistance (AMR) is a global health problem. It is well known that antibiotics can drive evolutionary processes that underlie antimicrobial resistance (AMR) evolution and spread in clinical and environmental settings. In contrast, less is known about the effects of antimicrobial substances that are used as biocides (i.e. disinfectants and preservatives) on AMR evolution and spread. Biocides are present in various settings, interacting with diverse microbial communities. Therefore, it is crucial to evaluate their role in the evolution and dissemination of antimicrobial resistance. Biocides occur in a wide range of concentrations in various environmental settings. By examining how the various concentrations affect selection mechanisms, we gain insights into potential developments related to antimicrobial resistance. The aim of this PhD thesis is to investigate the effects of biocides on processes underlying resistance evolution. Specifically, the work focused on key mechanisms for resistance spread, resistance evolution, and the effect of selection pressures on evolved resistance mechanisms. The thesis is structured around three major objectives: (i) to determine the effect of biocides on the evolution of resistance by affecting the rate of occurrence of de novo mutations, (ii) to determine the effect of biocides on the spread of resistance genes by modifying the rate of horizontal gene transfer (HGT) processes, and (iii) to investigate the selective drivers of the emergence of antimicrobial resistance in adaptive laboratory evolution (ALE) experiments. De-novo mutations are spontaneous mutations that occur at a certain rate in microorganisms. The effect of biocides at subinhibitory environmentally relevant concentrations on the mutation rate in Acinetobacer baylyi, Bacillus subtilis and Escherichia coli was assessed with the fluctuation assay. The results showed that biocides affected mutation rates in a species and substance dependent matter. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in E. coli, whereas no increases were identified for B. subtilis and A. baylyi. Horizontal gene transfer refers to diverse mechanisms that mediate the transfer of mobile genetic elements between microorganisms. This work focused on conjugation and transformation. Conjugation is a process whereby a conjugative plasmid is transferred from a donor cell to a recipient cell. Transformation is a process whereby exogenous donor DNA is taken up into a recipient cell and integrated into the recipient’s’ genome. The effects of subinhibitory environmentally relevant biocide concentrations on the conjugation rate of E. coli and the transformation rate of the naturally competent organisms A. baylyi in were assessed. The results showed that benzalkonium chloride (BAC), chlorhexidine and permethrin increased conjugation in E. coli, while none of the biocides increased transformation rates in A. baylyi. To further understand the molecular mechanisms underlying the effects on mutation and conjugation rates, I investigated the induction of the RpoS-mediated general stress and the RecA-linked SOS response upon biocide exposure. The results show a link between the general stress and the SOS response with increased rates of mutation and conjugation, but not for all biocides. One major approach to study the evolutionary response of bacteria to antimicrobials are ALE experiments with growth at subinhibitory concentrations linked to serial subculturing over many generations. Such experiments have been used to study resistance evolution to antibiotics and biocides. However, previous work showed that adaptation to biocide stress may be mediated by different evolutionary drivers. Here, I investigated the contributions of evolution for increased survival as opposed to improved growth in ALE experiments with E. coli exposed to subinhibitory BAC concentrations. Two distinct evolutionary treatments selecting for survival only or survival and growth led to specific evolutionary adaptations apparent in the phenotypes and genotypes of the evolved populations. Populations growing in the presence of BAC evolved increased fitness in the presence of BAC associated with higher resistance to BAC and cross-resistance to antibiotics, while this was not the case for populations evolving for increased survival only. Genotypic characterization by whole genome sequencing of the evolved populations revealed parallelism in mutated genes among replicate populations and distinct differences across treatments. Treatments selecting for survival and growth showed mutations in stress response related genes (hslO and tufA), while selection for survival led to mutations in genes for metabolic regulation (cyaA) and cellular structure (flagella fliJ). In summary, this thesis shows that biocides affect AMR evolution and emphasizes the importance of understanding of how biocides impact the molecular and evolutionary process that underlie AMR evolution. KW - Biocides KW - Antimicrobial resistances KW - Microbial survival mechanisms PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:188-refubium-43383-9 SP - 1 EP - 101 PB - Freie Universität CY - Berlin AN - OPUS4-60678 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -