751-5127-01L  The Microbiome of the Plant-Soil System: Part II

SemesterSpring Semester 2020
LecturersM. Hartmann
Periodicityyearly recurring course
Language of instructionEnglish
CommentThe course 751-5127-00 The Microbiome of the Plant-Soil System: Part I is a prerequisit of this course (for MSc students).

PhD-students from the Plant Science Centre or from the Life Science Zurich Graduate School should register via the Link (> Select Plant Sciences)


751-5127-01 PThe Microbiome of the Plant-Soil System: Part II
Block course from 22.-25. June 2020.
30s hrs
22.06. - 25.06.09:15-17:00LFW C 11 »
M. Hartmann

Catalogue data

AbstractThis computer block course provides a thorough introduction to the application of next-generation sequencing techniques for analyzing diversity of microbial communities. Using a combination of theoretical lectures and hands-on computer exercises, the participants learn the computational steps from bioinformatic processing of sequencing reads down to the final statistical evaluations.
ObjectiveAfter the course, the participants will be able to
1) understand the concept, potential and limitation of microbial NGS applications
2) know how to process raw metabarcoding data to obtain meaningful information
3) use multivariate statistical methods evaluate and visualize microbial community data
4) make informed decisions on best practices for their own data
Prerequisites / NoticeThe participants should have some background in microbial ecology and understand the basics of next-generation sequencing techniques as a tool to study microbes in the environment. Participants that are not familiar with these topics are encouraged to take the course unit «The Microbiome of the Plant-Soil System: Part I» as preparatory class (mandatory for master students). No programming or scripting expertise is required, but some basic experience with using command line applications is of advantage since not all the basics can be thoroughly covered in that short amount of time. However, some basic introduction to UNIX-based command line applications will be provided on the first day. All hands-on exercises will be run on UNIX-environments (Linux, Mac) and participants are expected to bring their own UNIX-based laptop (please consult your IT representative if necessary). All statistical analyses will be run in R using RStudio (any operating system). Participants should have installed the following software packages on their computers: Miniconda, R and RStudio, all other software tools will be installed on site using the Miniconda package manager.

Performance assessment

Performance assessment information (valid until the course unit is held again)
Performance assessment as a semester course
ECTS credits1 credit
ExaminersM. Hartmann
Typeungraded semester performance
Language of examinationEnglish
RepetitionRepetition only possible after re-enrolling for the course unit.

Learning materials

No public learning materials available.
Only public learning materials are listed.


No information on groups available.


Places5 at the most
Waiting listuntil 05.06.2020

Offered in

Agricultural Sciences MasterAgriculture and EnvironmentW DrInformation
Agricultural Sciences MasterAgriculture and EnvironmentW DrInformation
Agricultural Sciences MasterFunctioning of Soil SystemsWInformation
Doctoral Department of Environmental SciencesGraduate Programme in Plant SciencesWInformation
Environmental Sciences MasterAdditional ElectivesWInformation