Auflistung nach Autor:in "Baschien, Christiane"

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Analyse von aquatischen Pilzen mittels TaqMan® Real Time PCR
(2016) Baschien, Christiane; Carl, Steffen C.; Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen
Im Rahmen des Spritzfolgeprojektes 2015 wurden am Umweltbundesamt (UBA) Effekte auf die aquatischePilzgemeinschaft untersucht. Dazu wurden am Leibniz-Institut Deutsche Sammlung von Mikroorganismenund Zellkulturen (DSMZ, Braunschweig) Erlenblattscheiben (Alnus glutinosa) mit demubiquitären Pilz Cladosporium ramotenellum sowie den aquatischen Hyphomyceten Tetracladiummarchalianum und Neonectria lugdunensis beimpft. Beimpfte und unbeimpfte Blattscheiben wurden inden Hallen Fließgewässermesokosmen am UBA-Versuchsfeld in Berlin Marienfelde von April bis Juliexponiert. Während der Exposition wurden die Blattscheiben gegenüber einer realistischen Spritzfolgevon 9 Fungiziden, 4 Insektiziden und 4 Herbiziden in "Regulatorisch akzeptablen Konzentrationen"(RAK) ausgesetzt und zu 7 Terminen beprobt. Parallele Probenahmen beimpfter Blattscheiben an derDSMZ wurden zum Vergleich der nicht exponierten Pilze unter Laborbedingungen mitgeführt. Zieledes Projektes waren a) Blattscheiben mit den drei Arten aquatischer Pilze zu beimpfen b) TaxonspezifischeqPCR Assays für diese drei Arten zu entwickeln und zu evaluieren c) zu testen ob die Anwendungvon taxonspezifischen qPCR Assays sich eignet, um Abundanzen aquatischer Pilze unter realistischenExpositionsbedingungen nachzuweisen.Die Wiederfindung der Zielpilze mit den neu entwickelten taxonspezifischen qPCR Assays war in denLaborproben höher als in den Mesokosmenproben. Die Abundanzen der Zielpilze waren zwischenKontroll-und Pestizid-Behandlungsrinnen nicht signifikant unterschiedlich. Die qPCR Ergebnisseergaben außerdem, dass N. lugdunensis sich vor C. ramotenellum bei der Besiedelung der Blattscheibendurchgesetzt hat. T. marchalianum wurde nur in den Laborkontrollen und frühen Kontrollrinnenproebenwieder gefunden.
Quelle: Forschungsbericht
Analyse von aquatischen Pilzen mittels TaqMan® Real Time PCR
(2016) Baschien, Christiane; Carl, Steffen C.; Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen
Im Rahmen des Spritzfolgeprojektes 2015 wurden am Umweltbundesamt (UBA) Effekte auf die aquatischePilzgemeinschaft untersucht. Dazu wurden am Leibniz-Institut Deutsche Sammlung von Mikroorganismenund Zellkulturen (DSMZ, Braunschweig) Erlenblattscheiben (Alnus glutinosa) mit demubiquitären Pilz Cladosporium ramotenellum sowie den aquatischen Hyphomyceten Tetracladiummarchalianum und Neonectria lugdunensis beimpft. Beimpfte und unbeimpfte Blattscheiben wurden inden Hallen Fließgewässermesokosmen am UBA-Versuchsfeld in Berlin Marienfelde von April bis Juliexponiert. Während der Exposition wurden die Blattscheiben gegenüber einer realistischen Spritzfolgevon 9 Fungiziden, 4 Insektiziden und 4 Herbiziden in "Regulatorisch akzeptablen Konzentrationen"(RAK) ausgesetzt und zu 7 Terminen beprobt. Parallele Probenahmen beimpfter Blattscheiben an derDSMZ wurden zum Vergleich der nicht exponierten Pilze unter Laborbedingungen mitgeführt. Zieledes Projektes waren a) Blattscheiben mit den drei Arten aquatischer Pilze zu beimpfen b) TaxonspezifischeqPCR Assays für diese drei Arten zu entwickeln und zu evaluieren c) zu testen ob die Anwendungvon taxonspezifischen qPCR Assays sich eignet, um Abundanzen aquatischer Pilze unter realistischenExpositionsbedingungen nachzuweisen.Die Wiederfindung der Zielpilze mit den neu entwickelten taxonspezifischen qPCR Assays war in denLaborproben höher als in den Mesokosmenproben. Die Abundanzen der Zielpilze waren zwischenKontroll-und Pestizid-Behandlungsrinnen nicht signifikant unterschiedlich. Die qPCR Ergebnisseergaben außerdem, dass N. lugdunensis sich vor C. ramotenellum bei der Besiedelung der Blattscheibendurchgesetzt hat. T. marchalianum wurde nur in den Laborkontrollen und frühen Kontrollrinnenproebenwieder gefunden.
Quelle: Forschungsbericht
Can the fungicide penconazole alter the community composition of the aquatic mycobiome on Alnus glutinosa leaf litter?
(2023) Carl, Steffen C.; Baschien, Christiane; Mohr, Silvia; Kusebauch, Björn; Sahm, René
Excerpt of an upcoming publication. Abstract: Aquatic fungi (AF) play a key role in the turnover of organic matter in freshwater ecosystems, such as leaf litter in streams. Fungicides that reach streams via spray drift or surface runoff from agricultural activities may endanger the diversity of AF. In the present proof-of-principle study, we used high throughput sequencing (HTS) of total DNA to investigate composition changes of a natural leaf litter associated aquatic mycobiome in stream channels and in flask microcosms that were treated with 250 (micro)g/L of the azole fungicide penconazole. Treated samples were compared with control samples from untreated systems and samples from the reference stream over a period of three weeks. The community composition (in terms of presence/absence) in fungicide treated and control samples was comparable on leaves, which were conditioned for two weeks in the reference stream prior to fungicide exposure. Here, only the read numbers of two key taxa indicated an abundance shift that was most likely related to the fungicide effect. However, strong diversity effects were observed during the following long-term recolonization (85d) of sterilized leaves under penconazole influence (starting with 160 (micro)g/L a. s.), in which key taxa were significantly reduced in their presence or even absent in fungicide treated stream channels. Results imply, that HTS of total DNA seems to be particularly effective to detect changes in AF communities during the colonization of leaf litter. Future effect studies could consider recolonization under different conditions and RNA sequencing of preconditioned leaves to corroborate the findings of the present study. Quelle: https://www.researchgate.net/
Can the fungicide penconazole alter the community composition of the aquatic mycobiome on Alnus glutinosa leaf litter?
(2023) Carl, Steffen C.; Baschien, Christiane; Mohr, Silvia; Kusebauch, Björn; Sahm, René
Excerpt of an upcoming publication. Abstract: Aquatic fungi (AF) play a key role in the turnover of organic matter in freshwater ecosystems, such as leaf litter in streams. Fungicides that reach streams via spray drift or surface runoff from agricultural activities may endanger the diversity of AF. In the present proof-of-principle study, we used high throughput sequencing (HTS) of total DNA to investigate composition changes of a natural leaf litter associated aquatic mycobiome in stream channels and in flask microcosms that were treated with 250 (micro)g/L of the azole fungicide penconazole. Treated samples were compared with control samples from untreated systems and samples from the reference stream over a period of three weeks. The community composition (in terms of presence/absence) in fungicide treated and control samples was comparable on leaves, which were conditioned for two weeks in the reference stream prior to fungicide exposure. Here, only the read numbers of two key taxa indicated an abundance shift that was most likely related to the fungicide effect. However, strong diversity effects were observed during the following long-term recolonization (85d) of sterilized leaves under penconazole influence (starting with 160 (micro)g/L a. s.), in which key taxa were significantly reduced in their presence or even absent in fungicide treated stream channels. Results imply, that HTS of total DNA seems to be particularly effective to detect changes in AF communities during the colonization of leaf litter. Future effect studies could consider recolonization under different conditions and RNA sequencing of preconditioned leaves to corroborate the findings of the present study. Quelle: https://www.researchgate.net/
Effects of laboratory conditions on the composition of leaf detached fungal communities on Alnus glutinosa leaf litter
(2021) Carl, Steffen C.; Mohr, Silvia; Sahm, René; Baschien, Christiane
Mould Specific Quantitative PCR
(2015) Valtanen, Kerttu; Baschien, Christiane; Jacobs, K.L.; Szwezyk, Regine
Spores and conidia of various filamentous fungi are a potential health risk in indoor environments. Currently, convenient, rapid and specific PCR methods for detection of spores and conidia are missing. The MSQPCR assay offers a putative solution allowing the detection of 36 different mould fungi. However, it is not known whether the species selectivity of MSQPCR is sufficient for German indoor environments and how high the ability of the assay is to discriminate between the target species.
We evaluated 108 MSQPCR primers for their specificity, binding affinity, genome locality, oligo quality and PCR product size with NCBI-Genbank Primer BLAST (National Centre of Biotechnology Information, Bethesda), Primer 3 (Untergrasser et al. 2007) and Oligocalc (Kibbe, 2007).. Fungal species frequently detected in water and mould damaged buildings in Germany were compared with the species selection of MSQPCR system to evaluate its applicability for German indoor environments.
Stachybotrys chartarum, Aspergillus versicolor and Penicillum chrysogenum were used for practical testing of MSQPCR assay. For this purpose, the three reference strains, 5 to 10 additional isolates of the target species and 20 non target species were tested. DNA was extracted from a filtered spore dilution and subjected to the MSQPCR assay. From 108 primers tested, 13% and 24% had no homologies to other than target species on genus level and beyond genus level, respectively. This result was confirmed by the conducted spore experiment with spores of multiple strains.
This work demonstrates that most of the fungal species detected with MSQPCR assay are relevant for European indoor water and mould damages. However, the species spectra should be enlarged and adapted to European conditions. The MSQPCR qPCR primers were not considered specific enough for the detection of target species. We suggest to modify the test system by improved specific primers.
© Valtanen K, Baschien C., Jacobs K., Szwezyk, R.
New qPCR assays for detection of mould fungi in indoor air
(2015) Valtanen, Kerttu; Baschien, Christiane; Jacobs, Kordula; Szwezyk, Regine
An increased spore concentration in indoor air is often the only indication for mould damages in building structures. Rapid detection and identification enables a short-term renovation and reduces exposure times of inhabitants. However, a rapid and specific methods for the practical use to detect spores and conidia in indoor air, is missing. The current PCR based assays are not developed for the identification and quantification of filamentous fungi from spores. Moreover, the number of specific assays is low and many gene regions used to identify fungi do not differentiate the highly diverse filamentous fungi.
In this study, we aimed at developing and validate new qPCR assays for detection of spores and conidia from indoor air samples. We developed specific primers for nested PCR targeting ITS rDNA, betatubuline gene (benA), calmoduline gene (caM) and Translogation Elongation Factor 1á(Tef1) for three fungal species (Stachybotrys chartarum, Aspergillus versicolor and Penicillum chrysogenum) associated with indoor water damages and mould. Primers were designed with the software programs MEGA 5 (Tamura et al. 2011) and Primer 3 (Untergrasser et al. 2007). Primer quality and PCR product size were tested with Primer 3 (Untergrasser et al. 2007) and Oligocalc (Kibbe, 2007). All qPCR assays were validated using spore dilutions of the three reference species with defined DNA concentrations. As internal amplification standard, we used artificial amplicons of the target PCR region.
The specific qPCR assays of the three target species had a high determination coefficient (< 0.995). The detection limit for all assays was 0.1 pg genomic DNA and all tested strains of the three target species (S. chartarum and P. chrysogenum n = 6, A.versicolor n = 10) were detected. The PCR efficiency varied between 65% and 105%.
This study demonstrates that despite improved primers, ITS rDNA did not discriminate all filamentous fungi to species level. The next step will be to optimize the qPCR assays for quantification of spores, and to further develop qPCR assays targeting caM or benA genes.
© Valtanen K, Baschien C., Jacobs K., Szwezyk, R.
Pizza Funghi im Bach!?
(2022) Carl, Steffen C.; Baschien, Christiane
Quantitative real-time PCR (qPCR) to estimate molecular fungal abundance
(2020) Baschien, Christiane; Carl, Steffen C.
Fungi are key players in the decomposition of leaves in freshwaters. This functional role is maintained by a specifically adapted fungal community. To assess the quantitative contribution of single fungal species to the process, it is essential to determine their abundance. Quantitative real-time PCR (qPCR) is the prevalent method for this purpose, because it detects individual species of aquatic fungi in samples composed of multiple species. Quantitative PCR reactions are an extension of the traditional PCR method, which facilitates measuring the exponential amplification of a specific gene region via the emission of fluorescence signals in real time. This chapter describes how to design and validate a qPCR assay for fungal litter decomposers. The method uses a taxon-specific Taqman® probe labelled with a fluorescent reporter which hybridizes between two PCR primers. Due to the 5'-3'-exonuclease activity of DNA polymerase during PCR, the reporter dye is released and the emitted fluorescence is measured at 465-510 nm. Monitoring fungal taxa by qPCR assays opens excellent opportunities to gain new insights in microbial community ecology and ecosystem processes such as litter decomposition that are driven by fungi. © Springer Nature Switzerland AG 2020
UBA-Handlungsempfehlungen zur Beurteilung von Feuchteschäden in Fußböden
(2014) Baschien, Christiane; Szewzyk, Regine