Practical course on analysing the diversity of microbial eukaryotes in environments 1400-ADMEE-en
This intensive week-long practical course focuses on metabarcoding and single-cell approaches for studying eukaryotic diversity in environmental samples from aquatic, soil, and intestinal environments using nanopore sequencing technology. Students will learn the complete workflow from environmental sampling and metadata collection through DNA isolation, sequencing, diversity estimation, and ecological data interpretation.
During the first part of the course, participants will collect and process diverse environmental samples and learn a variety of laboratory techniques, including filtration-based sample preparation, DNA isolation using different extraction protocols, single-cell picking and manipulation, and DNA isolation from individual cells. Students will prepare sequencing libraries and perform in-house sequencing using the Oxford Nanopore MinION platform.
The second part of the course will focus on bioinformatics and ecological data analysis. Students will process molecular sequencing data, estimate and compare diversity across samples and sequencing approaches, and integrate environmental metadata into downstream This intensive week-long practical course focuses on metabarcoding and single-cell approaches for studying eukaryotic diversity in environmental samples from aquatic, soil, and intestinal environments using nanopore sequencing technology. Students will learn the complete workflow from environmental sampling and metadata collection through DNA isolation, sequencing, diversity estimation, and ecological data interpretation.
During the first part of the course, participants will collect and process diverse environmental samples and learn a variety of laboratory techniques, including filtration-based sample preparation, DNA isolation using different extraction protocols, single-cell picking and manipulation, and DNA isolation from individual cells. Students will prepare sequencing libraries and perform in-house sequencing using the Oxford Nanopore MinION platform.
The second part of the course will focus on bioinformatics and ecological data analysis. Students will process molecular sequencing data, estimate and compare diversity across samples and sequencing approaches, and integrate environmental metadata into downstream analyses. Practical exercises will include community composition analyses, diversity estimation, ordination methods, and identification of ecological patterns associated with environmental variables.
The practical training will be accompanied by a series of lectures covering the technical aspects of metabarcoding and nanopore sequencing, the diversity and ecology of microbial eukaryotes in different environments, and statistical and computational approaches to molecular and ecological data analysis.
Course coordinators
Type of course
Mode
Learning outcomes
PRK7
KNOWLEDGE
1. Has the knowledge about structural, genetic, metabolic and functional diversity of eukaryotic microorganisms (K_W03)
2. Understand relations between eukaryotic microorganisms and environment, applying the hypothesis of temporal and spatial determinants of biodiversity (K_W04)
3. Is familiar with up-to-date laboratory techniques of data collection used in eukaryotic microorganisms biology (K_W12)
4. Knows the principles of planning research and performing experiments with the use of specialized methods to study microbial eukaryotes (K_W13)
ABILITIES
1. Is able to choose proper tools and techniques for solving problems of eukaryotic microbiology (K_U01)
2. Under the supervision of a scientific supervisor can plan and perform an experiment using the known methods of studying the diversity of eukaryotic microorganisms (K_U07)
3. Has the ability to prepare and deliver oral presentations in English at the B2+ level (K_U11)
SOCIAL AWARENESS
1. Understands the need to discover new species and identify known species of eukaryotic microorganisms and is able to pass this knowledge on to others (K_K01)
2. Is able to work in a team, carrying out his/her own research and co-organizing the work of the entire team (K_K04)
PRK8 Doctoral School of exact & natural sciences
PRK7
KNOWLEDGE
1. Has the knowledge about structural, genetic, metabolic and functional diversity of eukaryotic microorganisms (K_W03)
2. Understand relations between eukaryotic microorganisms and environment, applying the hypothesis of temporal and spatial determinants of biodiversity (K_W04)
3. Is familiar with up-to-date laboratory techniques of data collection used in eukaryotic microorganisms biology (K_W12)
4. Knows the principles of planning research and performing experiments with the use of specialized methods to study microbial eukaryotes (K_W13)
ABILITIES
1. Is able to choose proper tools and techniques for solving problems of eukaryotic microbiology (K_U01)
2. Under the supervision of a scientific supervisor can plan and perform an experiment using the known methods of studying the diversity of eukaryotic microorganisms (K_U07)
3. Has the ability to prepare and deliver oral presentations in English at the B2+ level (K_U11)
SOCIAL AWARENESS
1. Understands the need to discover new species and identify known species of eukaryotic microorganisms and is able to pass this knowledge on to others (K_K01)
2. Is able to work in a team, carrying out his/her own research and co-organizing the work of the entire team (K_K04)
PRK8 Doctoral School of exact & natural sciences
KNOWLEDGE
1. Has advanced knowledge of modern approaches for studying eukaryotic microbial diversity using molecular and sequencing technologies, including (WG_01, WG_02).
2. Understands the relationships between microbial eukaryotic diversity and environmental conditions, including the role of environmental metadata in ecological analyses (WG_01, WG_03).
3. Knows the methodology of environmental sampling, DNA isolation, library preparation, and molecular data generation and analysis in studies of microbial eukaryotes (WG_03).
4. Is familiar with bioinformatic and statistical approaches used for the analysis of biodiversity and ecological data (WG_03).
SKILLS
1. Is able to design and perform studies of microbial eukaryotic diversity using molecular and metabarcoding approaches (UW_01, UO_01).
2. Is able to apply laboratory techniques related to environmental sampling, filtration, DNA isolation, library preparation, and nanopore sequencing (UW_01).
3. Is able to analyse molecular and environmental datasets, interpret ecological patterns, and apply bioinformatic and statistical methods (UW_02).
4. Is able to present and discuss scientific results in English in an international scientific environment (UK_01, UK_04, UK_05).
SOCIAL COMPETENCES
1. Is ready to critically evaluate molecular and ecological data analyses and their interpretation in the context of biodiversity research (KK_01, KK_02).
2. Is prepared to work collaboratively in laboratory and field-based research projects (KO_01).
3. Understands the importance of microbial diversity research for understanding and protecting natural ecosystems (KK_03, KO_02).
Assessment criteria
Oral presentation of the project conducted during the course (data generation, data analysis, presentation.
Portfolio exam (project and presentation)
Notes
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Term 2026Z:
The course can accommodate in total 20 students (max. 10 students from the University of Warsaw) and will be held at the Field Station of the Faculty of Biology in Urwitałt from October 13th to 22nd (7 days of classes), 2026. The course will be conducted in English and taught by lecturers from the Charles University in Prague and Univerisyt of Warsaw. To register, please sign up in the USOS system and send an e-mail to a.karnkowska@uw.edu.pl. This will enable us to contact you efficiently. If the number of applicants exceeds the number of available places, preference will be given to PhD students and graduates of courses in microbiology (microbiology, but also mycology, field mycology, biology of eukaryotic microorganisms) and in bioinformatics (bioinformatics, practical bioinformatics, phylogenetics and metagenomics). The course is available to Erasmus students only upon prior arrangement with the course coordinator. If you have any further questions, please contact the coordinator by e-mail (a.karnkowska@uw.edu.pl). |