Studies and continuing education in environmental genomics and system biology

Studies

Modules

The Environmental Genomics and Systems Biology Research Group is involved in the development of the following modules.

Molecular biodiversity analysis (MBA, 3^rd 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 part of the Minor Environmental Analysis, but can also be attended as a stand-alone module. [IUNR Magazin, 2018] (PDF 185 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:

• Michèle Pfister (2025): Polymyxin resistance in members of the emerging human pathogen Phytobacter: finding the origin of resistance and its spread [PA BMLD]
• Rinesa Shabija (2025): Isolierung und Identifizierung von Enterobacter-Stämmen aus Zwiebeln [PA BMLD]
• Mariia Gurova (2025): Designing CRAP – The CRISPR Repeat Analysis Program [PA2 ADLS]
• 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. [Zusammenarbeit mit 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). [Zusammenarbeit mit Forschungsgruppe Wildtiermanagement]
• Severin Erb (2019): Frequency of multidrug resistance in ESBL isolates from water samples. [Zusammenarbeit mit 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 217 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:

• Jana Jucker (2025): Plexiglass and eDNA: method validation for biodiversity assessment.
• Sina Spieser (2025): Detection of native and invasive crayfish using environmental DNA.
• Dominic Eichhorn (2024): Comparison of a classic waterbird counting method with eDNA metabarcoding on Lake Zurich. [Zusammenarbeit mit Forschungsgruppe Hortikultur]
• Debora Lang (2022): Charakterisierung von Mikroorganismen mit Biokontrollpotenzial gegen Botrytis cinerea bei der Erdbeere durch mikrobiologische in vitro Methoden. [Zusammenarbeit mit HAFL]
• Andrea Usuelli (2022): Isolation and characterization of bacteriophages against the emerging multidrug resistance Phytobacter spp. [Zusammenarbeit mit ILGI, FG Lebensmittelmikrobiologie]
• Andrea Michlig (2021): Genetischer Fingerabdruck der in der Schweiz stark bedrohten Orchidee Anacamptis coriophora (Wanzen-Knabenkraut) (L.) mittels DNA-Analyse. [Zusammenarbeit mit Forschungsgruppe Stadtökologie]
• 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. [Zusammenarbeit mit Forschungsgruppe Wildtiermanagement]
• Severin Erb (2020): Antibiotic resistance in high and low nucleic acid content bacteria. [Zusammenarbeit mit Eawag Kastanienbaum] [Aqua und Gas, 2022 (PDF 894 kB)]
• Fabian Gebhardt (2020): Untersuchungen zur generativen Fortpflanzungsstrategie des gelben Frauenschuhes Cypripedium calceolus. [Zusammenarbeit mit Forschungsgruppe Stadtökologie]
• Samuel Wildhaber (2019): Investigating the nitrogen cycle using the amoA gene in aquaponics. [Zusammenarbeit mit ETH Zürich, Group of Crop Science]
• Fabienne Eppisser (2019): Off-flavour control through UV/ozone in aquaculture: increasing resource efficiency in aquaculture systems. [Zusammenarbeit mit Forschungsgruppe Aquakultursysteme]
• Keerthanah Karuparan (2019): Diversität von Archaeen in Methanisierungsreaktoren. [Zusammenarbeit mit Fachstelle Umweltbiotechnologie]
• 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. [Zusammenarbeit mit WSL]
• Mirjam Kurz (2018): Evidence for hybridization between exotic Fagus orientalis and native Fagus sylvatica in a forest stand of Switzerland. [Zusammenarbeit mit WSL] [IUNR Magazin, 2019] (PDF 272 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:

• Lia Baumann (2025): Genetic structure and long-term genetic diversity assessment of Burgundy truffle populations in central Europe [MS-ENR; Zusammenarbeit mit WSL]
• Gioele Pinana (2023): Population genetic structure of Alpine chamois (Rupicapra rupicapra) in the Ticino alps, Switzerland. [MS-ENR; Zusammenarbeit mit Forschungsgruppe Wildtiermanagement]
• Andrea Michlig (2023): Comparison of eDNA metabarcoding and qPCR for detection of newt communities using surface water. [MS-ENR; Zusammenarbeit mit Forschungsgruppe Umweltplanung]
• 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; Zusammenarbeit mit ICBT]
• Katjuša Mežek (2022): Microbial community dynamics in green wall systems for greywater treatment. [Zusammenarbeit mit Forschungsgruppe Ökotechnologie und 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; Zusammenarbeit mit 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 ; Zusammenarbeit mit 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, Zusammenarbeit mit Forschungsgruppe Ökotechnologie] [Agronomy, 2023]
• Tamara Mainetti (2020): Effects of a wastewater treatment plant on the microbial community and its ability to degrade 17ß-estradiol-3-sulfate. [Zusammenarbeit mit ICBT und Uni Ljubljana] [Arch Microbiol, 2021]
• Jena Jamšek (2020): Quantitative determination of nitrogen cycling functional genes in an aquaponic system. [Zusammenarbeit mit Forschungsgruppe Ökotechnologie und 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. [Zusammenarbeit mit Forschungsgruppe Aquakultursysteme] [IUNR Magazin, 2019 (PDF 236 kB)]
• Andrea Bohny (2019): Microbial and chemical characterization of biofilms in an aquaponic system. [Zusammenarbeit mit Forschungsgruppe Ökotechnologie und 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, Zusammenarbeit mit Martin Sievers (ICBT)]
• Anuschka Neira (2019): Biodiversity of soil bacteria in greenhouses. [MSc ENR; Zusammenarbeit mit Forschungsgruppe Bodenökologie]
• Nadine Antenen (2017): The impact of hydropower on microbial diversity and community structure in floodplains. [Zusammenarbeit mit Forschungsgruppe Ökohydrologie] [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. [Zusammenarbeit mit Forschungsgruppe Weinbau]

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 Internships

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]