Studies

Modules

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, 3^rd 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 biodiversity analysis (MBA, 4^th semester module for the B.Sc. in Environmental Engineering)

Molecular biological diagnosis and analysis are increasingly used in the field and 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, 2018](PDF 184,7 KB)

Semester theses

The following semester’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:

• Jonas Iseli (2024): Enterobacter bulb decay of onions: an unknown plant disease?
• Diego Beck (2024): Phages to fight against the emerging multidrug pathogen Phytobacter.
• Jana Jucker (2023): Potenzial von Umwelt-DNA (eDNA) auf Pflanzenblättern.
• Sina Spieser (2023): Detection of crayfish by environmental DNA.
• Lena Schär (2023): Combatting Botrytis cinerea in viticulture: exploring potential microbial antagonists.
• Robin Giacomelli (2023): Ability of bacteria and fungi to degrade polylactic acid (PLA) or polybutylene succinate (PBS) in the environment.
• Larissa Stebler (2022): Ability of bacteria and fungi form cold environment plastispheres to degrade plastics. [Collaboration with WSL]
• Manuel Oberhänsli (2022): Antifungal activity of six representative Erwinia strains with focus on kanosamine production.
• Robin Pfaff (2022): In silico genetic diversity within Aloe.
• Simone Dordoni (2022): Natürliche Bekämpfung von Botrytis cinerea.
• Mirco Pirozzi (2022): The quest for the origin of Phytobacter spp.
• Robin Pfaff (2022): Primer search for the development of a reliable metagenomics method for mycorrhiza.
• Jennifer Miguez Vasquez (2022): Comparative genomics of antibiotics multidrug resistance in Phytobacter spp. and related species.
• Sarah Wirth (2022): DNA ist nicht gleich DNA: spezifische Markersuche für die Umweltgenomik.
• Diego Marzà (2021): Anti-Botrytis Strategie: Bacillus amyloliquefaciens als Nischenbesetzer.
• Sarah Wirth (2021): Population genetics methods for characterizing Brachypodium pinnatum: a literature review.
• Yannick Moos (2021): Diagnostics of the most common fish pathogens in Swiss aquaculture: a literature study.
• 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. [Diagn Microbiol Infect Dis. 2024]
• Simon Carnal (2020): MinION™ Sequenzierung ausgewählter CRISPR Regionen von Erwinia amylovora Isolaten. [J Plant Pathol, 2021]
• 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. [BMC Phytopathol Res, 2021]
• Alexia Roschi (2017): Molekularer Nachweis der Streptomycinresistenz im Feuerbranderreger Erwinia amylovora. [J Plant Pathol, 2021]
• 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, 2016](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.

Bachelor theses

The following bachelor’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:

• Dominic Eichhorn (2024): Comparison of a classic waterbird counting method with eDNA metabarcoding on Lake Zurich. [Collaboration with Horticulture Research Group]
• Debora Lang (2022): Charakterisierung von Mikroorganismen mit Biokontrollpotenzial gegen Botrytis cinerea bei der Erdbeere durch mikrobiologische in vitro Methoden. [Collaboration with HAFL]
• Andrea Usuelli (2022): Isolation and characterization of bacteriophages against the emerging multidrug resistance Phytobacter spp. [Collaboration with ILGI, Food Microbiology Research Group]
• Andrea Michlig (2021): Genetischer Fingerabdruck der in der Schweiz stark bedrohten Orchidee Anacamptis coriophora (Wanzen-Knabenkraut) (L.) mittels DNA-Analyse. [Collaboration with Urban Ecology Research Group]
• Isabelle Rose Michel (2021): Search for Phytobacter spp. in environmental and clinical samples. [Diagn Microbiol Infect Dis. 2024]
• 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] [Aqua und Gas, 2022](PDF 894,5 KB)
• 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 Zürich, Group of Crop Science]
• Fabienne Eppisser (2019): Off-flavour control through UV/ozone in aquaculture: Increasing resource efficiency in aquaculture systems. [Collaboration with Research Group Aquaculture Systems]
• Keerthanah Karuparan (2019): Diversität von Archaeen in Methanisierungsreaktoren. [Collaboration with Section of Environmental Biotechnology and Bioenergy]
• 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, 2019](PDF 272,2 KB)
• Dominik Rutz (2018): Assembly, annotation and comparative genomics of the genomes of Pseudomonas wadenswilerensis CCOS 864^T and Pseudomonas reidholzensis CCOS 865^T.
• Daniela Lüthi (2017): Comparative genomics of Collimonas sp. CCOS 246 to related species.
• Mathieu Robin (2015): Genetischer Verbissnachweis.
• Yvonne Bollinger (2014): Gestaltung von Platzpärken am Beispiel des Vulkanplatzes in Zürich.
• Joël Wieser (2014): Untersuchung des Lebensraumtyps der einheimischen Orchidee Serapias vomeracea (Pflugschar-Zungenstendel).

Master theses

The following master’s theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:

• Gioele Pinana (2023): Population genetic structure of Alpine chamois (Rupicapra rupicapra) in the Ticino alps, Switzerland. [MS-ENR; Collaboration with Wildlife Management Research Group]
• Andrea Michlig (2023): Comparison of eDNA metabarcoding and qPCR for detection of newt communities using surface water. [MS-ENR; Collaboration with Environmental Planning Research Group]
• Mirjam Kurz (2023): Detecting invasive pests using airborne environmental DNA. [MS-ENR]
• Sara Jordan (2022): Community analysis of methanogenic microbiomes in biogas reactors. [MS-LS ACLS]
• Nurdzane Memeti (2022): The CRISPR region analysis program (CRAP). [MS-LS ACLS]
• Valentin Bolt (2022): Genome sequence and antibacterial compounds from Streptomyces sampsonii strain Stup19_F108. [MS-LS PB; Collaboration with ICBT]
• Katjuša Mežek (2022): Microbial community dynamics in green wall systems for greywater treatment. [Collaboration with Ecotechnology Research Group and Uni Ljubljana]
• Cédric von Gunten (2021): Public sequencing data mining and in silico protein masses prediction for improving accurate subspecies determination in Bacillus cereus using MALDI-TOF MS [MS-LS ACLS; Collaboration with Labor Spiez]
• Sebastian von Rotz (2021): Evaluation and development of a bioinformatics workflow for amplicon sequencing with nanopore long read technology [MS-LS ACLS]
• Arburon Sulja (2021): Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734 [MS-LS PB ; Collaboration with ICBT] [BMC Genomics, 2022]
• Christian Sprecher (2021): Comparative genomics provides new insights into host specificity and evolutionary history of Erwinia amylovora [MS-ENR]
• Florentina Gartmann (2021): Bioponics, an organic closed-loop soilless cultivation system: Management, characteristics, and fungal biocontrol compared to hydroponics and soil cultivation [MS-ENR, Collaboration with Ecotechnology Research Group] [Agronomy, 2023]
• 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] [Arch Microbiol, 2021]
• Jena Jamšek (2020): Quantitative determination of nitrogen cycling functional genes in an aquaponic system. [Collaboration with Ecotechnology 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 Research Group Aquaculture Systems] [IUNR Magazin, 2019(PDF 236,1 KB)]
• Andrea Bohny (2019): Microbial and chemical characterization of biofilms in an aquaponic system. [Collaboration with Ecotechnology Research Group and ETH Zürich]
• 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] [Sci Tot Environm, 2021]
• 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]

Ph.D. theses

The following Ph.D. theses have been completed to date in the areas covered by the Environmental Genomics and Systems Biology Research Group:

• Moritz Kaufmann (2024): Unravelling the impact of chitin soil amendment on plant using Omics technologies with lettuce as a model organism.
• Nay Dia (2022): The genomic diversity, taxonomy, and diagnostics of the Xanthomonas hortorum – Xanthomonas hydrangeae complex.
• 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.

IZA Internship

Within the module Internship in International Cooperation (IZA) the following internship has been completed:

• Manuel Oberhänsli (2023): Elaboration of methodology to study the effects of climate change on the behaviour of four large mammal species in the Tien Shan Mountain habitats. [Collaboration with Ilbirs Foundation, Bishkek (Kyrgyzstan)] (Link zum Blog von Manuel Oberhänsli)
• Simon Carnal (2020): Analysis of CRISPR regions in Erwinia amylovora and possible bacterial biocontrol isolates against fire blight and fungal-induced diseases. [Collaboration with Kyrgyz-Turkish Manas University, Bishkek (Kyrgyzstan)] (Link zum Blog von Simon Carnal) [J Plant Pathol, 2021]