Studies and continuing education in environmental genomics and system biology
The Environmental Genomics and Systems Biology Research Group is involved in the development of the following modules, both of which are part of the Minor Field Diagnostics and Analytics, but which can also be attended as stand-alone modules.
Biosynthesis and Analytics (BSA, 3rd semester module for the B.Sc. in Environmental Engineering)
Vitally important processes such as growth, energy generation, reproduction, pathogen defence etc. can only be explained in the context of the underlying biochemical building blocks and processes. A real understanding of the way that living processes operate and are controlled at the cellular and sub-cellular levels is only possible through a combination of biology, chemistry and physics. During theoretical lectures and lab-based practical courses, students will be introduced to the chemical mechanisms operating in organisms and shown how to investigate biochemical processes methodically by means of laboratory experiments.
Molecular biological analysis and application (MBAA, 4th semester module for the B.Sc. in Environmental Engineering)
Molecular biological diagnosis and analysis is increasingly used in the field and is therefore gaining practical significance in several areas of natural resource sciences. The aim of this module is to become acquainted with these methods and procedures as well as to use specific methods and to examine their practical significance and application. The module gives an overview of their application in nature conservation and environmental protection, as well as in agriculture and eco technologies. Methods of analysis and for appraisal of findings are acquired. The module is an emerging project and some changes may be made. [IUNR Magazin] (PDF 184,7 KB)
The following semester’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:
- Nils Etter (2021): Entwicklung einer eDNA-Methode für den Kleinsäuger-Nachweis aus der Mammalia-Box.
- Livia Hess (2021): Evaluation of indigenous plant growth promoting rhizobacteria as means to increase salt tolerance of plants.
- Sarah Helbling (2021): Umwelt-DNA Metabarcoding zum Nachweis von Kleinsäugerarten in Gewässerproben.
- Julian Kreiner (2021): Community analysis of bacterial 16S rRNA gene amplicons with the Flongle flow cell.
- Isabelle Michel (2020): Detection of Phytobacter spp. in environmental samples.
- Simon Carnal (2020): MinION™ Sequenzierung ausgewählter CRISPR Regionen von Erwinia amylovora Isolaten.
- Fabienne Kuhn (2020): Genetic diversity of wild peonies in the peony garden at ZHAW Campus Grüental in Wädenswil.
- Anke Grings (2020): Bacteria and plant communities in saline soils in the region of Charrat-Martigny (Valais, Switzerland).
- Sabrina Lötscher (2020): Vergleich zweier DNA-Extraktionskits und Primersets zur Analyse von Beutetier-DNA in Kotproben des grossen Mausohrs (Myotis myotis). [Collaboration with Wildlife Management Research Group]
- Severin Erb (2019): Frequency of multidrug resistance in ESBL isolates from water samples. [Collaboration with Eawag]
- Filipe de Sa (2019): Verantwortung übernehmen – Zigarettenstummel in der Umwelt.
- Victor Bühlmann (2018): Transport of bacteria through natural soil.
- Philipp von Ow (2018): Biokontrolle mittels Mikroorganismen als Bekämpfungsmassnahme gegen pathogene Organismen in Aquaponik.
- Severin Erb (2018): "The big fight" - Antibiotika-Resistenz im Gewässer.
- Nora Vogel (2018): Gentiana sp. - Genetische und phänotypische Untersuchungen im Jurapark Aargau.
- Mirjam Kurz (2018): Molecular analysis of the distribution of two ancestral populations of Erwinia amylovora in Europe using CRISPR data.
- Alexia Roschi (2017): Molekularer Nachweis der Streptomycinresistenz im Feuerbranderreger Erwinia amylovora. [J Plant Pathol, 2020]
- Mireia Marcé Escursell (2016): Differential fitness of Erwinia amylovora isolates carrying different variants of the rpsL gene leading to high level of streptomycin resistance. [IUNR Intern] (PDF 216,8 KB)
- Priska Stierli (2016): Vergleich und Charakterisierung von Genomsequenzen der neuen Spezies Erwinia gerundensis.
- Nicola Rhyner (2016): Application of MALDI-TOF mass spectrometry profiling for inter- and intrapopulation discrimination of Orchidaceae.
- Sarah Schuhmacher & Dominique Wildi (2015): Quantifizierung der mikrobiellen Populationen in der Rhizosphäre von Weizen.
The following bachelor’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:
- Isabelle Rose Michel (2021): Search for Phytobacter spp. in environmental and clinical samples.
- Fabienne Kuhn (2021): Chloroplast genomic diversity of wild peonies: the search for subspecies-level speciation.
- Sabrina Lötscher (2020): Das Beutetierspektrum und der Jagdlebensraum des Grossen Mausohrs Myotis myotis. [Collaboration with Wildlife Management Research Group]
- Severin Erb (2020): Antibiotic resistance in high and low nucleic acid content bacteria. [Collaboration with Eawag Kastanienbaum]
- Fabian Gebhardt (2020): Untersuchungen zur generativen Fortpflanzungsstrategie des gelben Frauenschuhes Cypripedium calceolus. [Collaboration with Urban Ecology Research Group]
- Samuel Wildhaber (2019): Investigating the nitrogen cycle using the amoA gene in aquaponics. [Collaboration with ETH Zurich, Group of Crop Science]
- Fabienne Eppisser (2019): Off-flavour control through UV/ozone in aquaculture: Increasing resource efficiency in aquaculture systems. [Collaboration with Aquaculture Systems Research Group]
- Keerthanah Kuruparan (2019): Diversität von Archaeen in Methanisierungsreaktoren. [Collaboration with ICBT]
- Victor Bühlmann (2019): Extent of gene flow from introduced Oriental beech (Fagus orientalis) to native European beech (Fagus sylvatica): investigation in a 100-year-old Oriental beech plantation. [Collaboration with WSL]
- Mirjam Kurz (2018): Evidence for hybridization between exotic Fagus orientalis and native Fagus sylvatica in a forest stand of Switzerland. [Collaboration with WSL] [IUNR Magazin] (PDF 272,2 KB)
- Dominik Rutz (2018): Assembly, annotation and comparative genomics of the genomes of Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T.
- Daniela Lüthi (2017): Comparative genomics of Collimonas sp. CCOS 246 to related species.
- Mathieu Robin (2015): Genetic evidence of damage caused by wild animals.
- Yvonne Bollinger (2014): Design of open space parks following the example of Zurich’s Vulkanplatz.
- Joël Wieser (2014): Investigation into the habitat type of the native orchid Serapias vomeracea (ploughshare serapias).
The following master’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:
- Tamara Mainetti (2020): Effects of a wastewater treatment plant on the microbial community and its ability to degrade 17ß-estradiol-3-sulfate. [Collaboration with ICBT and Uni Ljubljana]
- Jena Jamšek (2020): Quantitative determination of nitrogen cycling functional genes in an aquaponic system. [Collaboration with Ecological Engineering Research Group and Uni Ljubljana]
- Nicola Rhyner (2019): Using microsatellite markers to assess post-stocking survival and genetic structure of atlantic trout (Salmo trutta L.) in a pre-alpine water system. [Collaboration with Aquaculture Systems Research Group] [IUNR Magazin] (PDF 236,1 KB)
- Andrea Bohny (2019): Microbial and chemical characterization of biofilms in an aquaponic system. [Collaboration with Ecological Engineering Research Group and ETH Zurich]
- Moritz Kaufmann (2019): Evolution of multidrug resistance in pEL60 plasmids. [MS-LS ACLS]
- Jonas Siegrist (2019): Genome mining of polyketide and nonribosomal peptide synthases in actinomycetes. [MS-LS ACLS, Collaboration with Martin Sievers (ICBT)]
- Anuschka Neira (2019): Biodiversity of soil bacteria in greenhouses. [MSc ENR; Collaboration with Soil Ecology Research Group]
- Nadine Antenen (2017): The impact of hydropower on microbial diversity and community structure in floodplains. [Collaboration with Ecohydrology Research Group]
- Julia Eichmann (2016): Expression analyses of selected genes of Vitis vinifera during early infection stages of its major pathogens Plasmopara viticola and Botrytis cinerea. [Collaboration with Viticulture Research Group]
The following Ph.D. theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:
- Zala Schmautz (2020): Characterization of nitrogen dynamics in an aquaponic system. [Collaboration with Ecotechnology Research Group and ETH Zürich]
- Michael Gétaz (2018): Genomic investigations of the strawberry quarantine bacteria pathogen Xanthomonas fragaria for a better integrative pest management.
- Michela Ruinelli (2017): Genomic investigations of members of the Pseudomonas syringae species complex associated with Prunus spp. and kiwifruit.
Within the module Internship in International Cooperation (IZA) the following internship has been completed:
- Simon Carnal (2020): Analysis of CRISPR regions in Erwinia amylovora and possible bacterial biocontrol isolates against fire blight and fungal-induced diseases. [Collaboration with the Kyrgyz-Turkish Manas University, Bishkek (Kyrgyzstan)] (Link to Simon's blog)