mar452 - Ecology of Marine Microorganisms 2 (Complete module description)

Module label	Ecology of Marine Microorganisms 2
Modulkürzel	mar452
Credit points	6.0 KP
Workload	180 h
Institute directory	Institute for Chemistry and Biology of the Marine Environment
Verwendbarkeit des Moduls	Master's Programme Marine Environmental Sciences (Master) > Mastermodule
Zuständige Personen	Garcia, Sarahi Lorena (module responsibility)
Prerequisites	The modules mar451 Ecology of Marine Microorganisms 1 and mar452 Ecology of Marine Microorganisms 2 can only be taken together.
Skills to be acquired in this module	The learning objectives of the course includes the following: - To apply state-of-the-art ‘omics approaches to various data types to make sense of complex datasets. - To engage with research questions and learn about designing strategies to answer the research questions. - To practice a different set of analytical or computational methods to answer research questions regarding microbial ecology. - To improve discussion, analytical, presentation and writing skills.
Module contents	The oceans are home to many microorganisms. In fact, the number of microbial cells in the oceans rivals that of stars in the known Universe. These countless microorganisms constitute slightly over half of the total biomass in the oceans, playing a crucial role in maintaining the delicate balance of biogeochemical cycles on Earth. In our course, we delve into the fundamentals of computational approaches that now grant unprecedented access to these communities through innovative 'omics strategies. Acquiring a comprehensive understanding of these strategies, including their appropriate applications and limitations, has become an essential skill for any aspiring life scientist. The primary objective of this course is to empower participants to explore the ecology, evolution, and functionality of naturally occurring microbial populations, while grasping the current conceptual framework that aids our comprehension of the most diverse life forms on our planet. Over the span of a week, our course unfolds with a series of lectures and practical exercises, acquainting participants with the foundational concepts of omics strategies. They will delve into the theoretical foundations of prominent 'omics data types and their contemporary uses, encompassing genomics, metagenomics, metatranscriptomics, and various 'omics data analysis methodologies such as metabolic reconstruction in genomes and metagenomes, metagenomic read recruitment, pangenomics, phylogenomics, and microbial population genetics. Moving into the second week, students will embark on small-scale research projects conducted in groups of up to three students. Each group will be presented with research inquiries concerning the ecology of marine microorganisms. Collaboratively, students, alongside instructors and supervisors, will strategize and devise methodologies to address these research questions. Following the designed strategies, students will then execute their plans to find answers to the research inquiries. Finally, they will present their findings to the other groups, fostering a dynamic exchange of insights and perspectives.
Literaturempfehlungen	Will be announced in the course.
Links	Central dogma of molecular biology UNIX shell Beginner's Guide to the Bash Terminal Learning the Shell
Language of instruction	English
Duration (semesters)	1 Semester
Module frequency	annually
Module capacity	20 ( Division between Master Marine Environmental Sciences and Master Microbiology. The final list will be oragnized at the preliminary meeting. )
Type of module	Wahlpflicht / Elective
Module level	MM (Mastermodul / Master module)
Teaching/Learning method	Ü Ecology of marine microbes II SE Ecology of marine microbes II
Previous knowledge	1. To maximize benefit, the participants of this course are expected to be familiar with the central dogma of molecular biology, and able to answer what is a gene, a genome, a transcript, or a protein, and have at least a preliminary understanding of the principles in ecology and evolution, such as the basics of taxonomy and broad ecological principles that maintain complex ecosystems. 2. Throughout the course we will use anvi’o for 'omics analyses. Anvi’o is an open-source software platform that brings together many aspects of today’s cutting-edge computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities. Anvi’o is cited over 1,000 times in the literature, and is actively maintained. It will be most beneficial if the participants have access to personal computers, preferably laptops, that they can bring to the classroom. 3. The participants of this course are also expected to be familiar with the UNIX shell (also known as the ‘terminal environment’, or ‘command line interface’). If you have no prior experience with the command line interface, that is OK, as you will generate those skills throughout the course as the vast majority of data analyses we will do will take place in the command line interface. Arguably, the exposure to the command line environment and developing a level of mastery of it will be one of the most impactful gains you will have from this course that will help you throughout your professional journey almost regardless of which career path you choose that involves data; so if you are not familiar with the command line environment, see this as an opportunity to invest time into developing some skills in it. You can use some of the following material to familiarize yourself with the command line interface. a. Beginner’s Guide to the Bash Terminal (a video introduction to the Linux command line environment – although Joe Collins is talking about Linux, the topics are relevant to anyone who uses a command line environment and Meren strongly recommends everyone to watch this in its entirety, and try to replicate commands). b. Learning the Shell (a chapter from the open book “The Linux Command Line” by William Shotts – Meren highly recommends). 4. The course will require its participants to read and understand contemporary literature written in English.

Form of instruction	SWS	Frequency	Workload of compulsory attendance
Exercises (Praktikum)	4	SoSe	56
Seminar	2	SoSe	28
Präsenzzeit Modul insgesamt			84 h

Examination	Prüfungszeiten	Type of examination
Final exam of module		1 graded examination Portfolio or protocol Active participation Active participation includes regular participation in the internship and accompanying seminar and the creation of a portfolio (report) during or after the end of the internship. This is determined by the lecturer at the beginning of the semester or at the beginning of the course.