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SUMMARY:Assembly and functioning of crop microbiomes
DESCRIPTION:Objectives of the course: Over the past decades\, rapid advances in methods for analysing microbial communities based on high through-put sequencing technologies have revolutionized the way we observe\, quantify\, and understand plant-microbe interactions. This intensive 5-days PhD course provides an in-depth overview of modern sequencing technologies and their applications in understanding microbial–crop interactions. Students will explore how advanced genomic and metagenomic approaches can be used to characterize plant-associated microbiomes\, identify functional traits of beneficial and pathogenic microbes\, and elucidate the molecular mechanisms underpinning plant–microbe relationships. \nThrough a combination of lectures\, wet-lab exercises\, hands-on bioinformatics sessions\, and case study discussions\, participants will gain both theoretical knowledge and practical skills. The course will begin with an introduction to crop-microbiome interactions and to the various sequencing approaches and data types relevant to microbiome and crop–microbe research. It will then cover experimental design considerations\, sampling strategies\, sample preparation\, and data analysis pipelines for amplicon datasets. \nSpecial emphasis will be placed on integrating sequencing data with ecological and physiological information to interpret microbial community functions in the context of crop health\, productivity\, and resilience. Students will also explore stable isotope probing\, long-read metagenomics\, and multi-omics integration. \nLearning outcomes and competencies: \nAt the end of the course\, the student should be able to: \n\nDesign experiments employing sequencing-based methods to investigate microbial–crop interactions.\nProcess and analyze microbial community sequencing data using bioinformatics tools.\nInterpret sequencing results in relation to plant biology and environmental variables.\nCritically assess recent literature and technological advances in microbial genomics and plant–microbe research.\n\nCourse parameters: \nLanguage: English \nLevel of course: PhD course \nTime of year: Q4 2026 \nNo. of contact hours/hours in total incl. preparation\, assignment(s) or the like: 125 \nCapacity limits: 20 \nCompulsory program: \nLectures\, exercises\, student presentations and field and laboratory measurements. Active participation in both lectures\, practical work and student presentations is expected. \nCourse contents: \nThe course provides formal lectures and exercises covering: \n\nOverview of plant–microbe interactions and the role of microbiomes in crop productivity and health\nIntroduction to sequencing platforms\nExperimental design and best practices for sample collection and DNA/RNA extraction\nAmplicon sequencing (16S/ITS) workflows for community profiling\nShotgun metagenomics for functional and taxonomic analysis\nBioinformatics pipelines for sequence data processing and interpretation\nIntegrating multi-omics data with plant physiological and environmental information\nCase studies on beneficial microbes\, plant pathogens\, and rhizosphere ecology\nPhage sequencing\, stable isotope probing\n\nPrerequisites: PhD students with a background in microbiology\, plant sciences\, genomics\, or bioinformatics. \nName of lecturer[s]: Mette Vestergård\, Mogens Nicolaisen\, Chris Barnes\, Henry Janse C. van Rensburg\, Enoch Narh Kudjordjie\, Lisa Martinez\, Remi Moerenhout\, Karl Ludwig Körber\, Tarquin Netherway\, Ella Tali Sieradzki\, Menghui Dong\, Nathan Roussel and others \nType of course/teaching methods: The course will last for five days. Each day begins with a lecture session. The second half of the day will mainly involve hands-on lab or data analysis activities\, and student presentations/discussions of their own projects. \nLiterature: Obligatory reading before the start of the course. The material will be distributed to participants after signing up. \nPreparation: Each student must prepare and submit a short synopsis of their individual presentation of their own project before the course starts. Students should present their own project at the course. \nCourse assessment: Individual student evaluation (pass/not pass) will be based on contribution to class discussions\, group work\, and presentations. \nSpecial comments on this course: The course fee is 1075 Euros (incl. accommodation and meals). Participants are responsible for arranging their own transportation to the campus. \nTime: October 26-30\, 2026 \nPlace: Aarhus University Flakkebjerg\, Forsøgsvej 1\, Slagelse\, Denmark \nRegistration: The deadline for registration is 1st of September 2026. Admission information will be sent out no later than 10th of September. Please note the capacity limit (20 participants). \nFor registration: https://event.au.dk/events/assembly-and-functioning-of-crop-microbiomes \nIf you have any questions regarding registration\, please contact Charlotte Hamann Knudsen\, e-mail: charlotte.knudsen@agro.au.dk; or regarding the course content Mogens Nicolaisen\, e-mail: mn@agro.au.dk \nDisclaimer:\nDDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.
URL:https://ddsa.dk/event/assembly-and-functioning-of-crop-microbiomes/
CATEGORIES:PhD Course
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