Martin Hartmann: Catalogue data in Spring Semester 2020

Name	Dr. Martin Hartmann
Address	Professur Nachhaltige Agrarökosyst ETH Zürich, LFH B 6 Universitätstrasse 2 8092 Zürich SWITZERLAND
Telephone	+41 44 633 88 36
E-mail	martin.hartmann@usys.ethz.ch
URL	http://www.microbiome.ch
Department	Environmental Systems Science
Relationship	Lecturer

Number	Title	ECTS	Hours	Lecturers
751-5000-00L	Sustainable Agroecosystems I	2 credits	2G	J. Six, M. Hartmann, A. Hofmann, C. Schöb
Abstract	This lecture with integrated exercises and farm visit introduces the factors, processes and interactions that control the functioning of temperate and tropical agroecosystems. Students will be guided to critically examine agricultural practices and management strategies to increase resource use efficiency, while minimizing negative impacts on the environment and ensuring socio-economic viability.
Learning objective	Students critically analyze concepts of sustainable agriculture.
Literature	Gliessman, S.R. (2015) Agroecology: The ecology of sustainable food systems, CRC Press, 371 p.
Prerequisites / Notice	The integrated exercises allow students to put their knowledge into practice in a greenhouse experiment, the "Complex vegetable system challenge".
751-5127-00L	The Microbiome of the Plant-Soil System: Part I	2 credits	2G	M. Hartmann
Abstract	This class conveys the current knowledge and state-of-the-art methods for studying the plant-soil microbiome through a combination of theoretical input lectures, selected case studies from ongoing research projects, and flipped classroom assignments.
Learning objective	After the course, the participants will be able to (1) explain how microorganisms influence and respond to changes in the plant-soil system (2) evaluate the strengths and limitations of specific methods used in microbial ecology research (3) critically assess current research findings in this field
Content	The plant-soil microbiome is an essential component of agroecosystems, regulating crop growth, nutrient use efficiency, stress resilience, and disease resistance. In this course, students will develop a fundamental understanding of (i) how microorganisms shape the functioning of the plant-soil system, (ii) how ecosystem management and global changes are influencing diversity and functioning of these microbial systems, and (iii) how the microbiome might be managed to improve sustainable agricultural production. A strong focus will be placed on getting to know the methodological toolbox to study microbes in the environment including different next-generation DNA sequencing applications such as metabarcoding and metagenomics. Theoretical input lectures will be combined with presentations of current research projects. Flipped classroom assignments will be used to critically discuss research findings of specific publications or to evaluate the strength and limitation of the specific methods.
Literature	Madigan MT, Bender KS, Buckley DH, Sattley WM and Stahl DA (2019). Brock Biology of Microorganisms, 15th edition, Pearson Education Limited. Paul E (2014). Soil Microbiology, Ecology and Biochemistry, 4th edition, Academic Press.
Prerequisites / Notice	The participants should have some basic background in biology and a keen interested in learning and discussing how microorganisms shape the functioning of our planet. Whereas this course unit can be taken as standalone class, it also serves as preparatory class for the hands-on block course on microbiome analysis (The Microbiome of the Plant-Soil System: Part II).
751-5127-01L	The Microbiome of the Plant-Soil System: Part II The 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 https://ethz.ch/services/en/service/courses-continuing-education.html (> Select Plant Sciences)	1 credit	2P	M. Hartmann
Abstract	This 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.
Learning objective	After 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 / Notice	The 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.