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Research PhD courses

Frontiers in Microbial Ecology: Eco-Evolutionary Dynamics of Microbial-Host Interactions

A Postgraduate course on the Isle of Schiermonnikoog, the Netherlands, 8-13 April 2018


Under the auspices of the Research Schools RSEE, PE&RC & SENSE:
Prof.dr Joana Falcao Salles (Microbial Community Ecology, University of Groningen)
Prof.dr Wietse de Boer (Microbial Ecology, NIOO-KNAW)
Prof.dr Toby Kiers (Evolutionary Biology, Free University of Amsterdam)
Dr Alexandre Jousset (Environmental Biology, Utrecht University)
Dr Corine Eising (Coordinator Research School Ecology & Evolution)

Guest lecturers

Dr John McCutcheon (Microbial Genomics and Symbyosis, University of Montana, USA)
Dr Fabrice Roux (Plant-Microbe Interactions, INRA, France) Cancelled
Prof.dr Jos Raaijmakers (Microbial Ecology, NIOO-KNAW)
Prof.dr Jennifer Lau (Community and Evolutionary Ecology, Michigan State University, USA)

Scope of the course

Microbes colonize each inch of our planet and play key roles in biogeochemical processes of all of Earth’s ecosystems. Microbes also colonize every single living creature on earth, be they plants, coral reefs, insects or humans, playing a vital role in host homeostasis. In addition to being omnipresent, microbial-host interactions vary both in the strength –from tight host-symbiont coevolution to non-specific association – and in the type of ecological interaction, ranging from mutualistic – for instance, through the provision of essential nutrients, development of host immune defence and host behaviour – to negative associations. The microbiome can also influence host mating choice, success and directly impact host fitness and survival, being thus a key component of host evolution. Although the microbiome has been accepted as a host trait, we still lack knowledge on how the microbiome is transmitted from one generation to another, the mechanisms driving the natural microbiome fluctuation, and their consequences for host fitness.

This course will examine our current understanding of the eco-evolutionary dynamics controlling host-microbiome interactions, by focusing on questions such as how and why microbial-host associations are formed, how they are maintained, and what the relevance is of these associations for host survival and adaptation to a changing world. These questions will be addressed using two main hosts – plants and insects – allowing us (i) to provide an overview of the current ecological and evolutionary overarching knowledge underlying host microbiome associations, (ii) to identify key aspects as well as the gap of knowledge inherent to each host and (iii) to use the knowledge built on each system to move towards a unified view of microbial-host interactions.

Aims of the course

To provide students with an appreciation of the most important current developments in the field of microbial-host interactions. The main goal of the course will be achieved if the participants acquire novel ideas and techniques for their own research. The course is primarily aimed at PhD level students, but is also open to advanced Master level students with interest in microbial ecology.

Contents and structure

This course is a combination of lectures on the above topics, given by a limited number of expert teachers, and discussion of key aspects of host microbiome interactions, to be raised by students and lecturers. During the period of the course the students will develop these concepts further, in groups and with the help of lecturers, which can potentially result in a publication in the form of a review or opinion paper (see Adam et al, 2016. Frontiers in Microbiology, doi: 10.3389/fmicb.2016.01079, which was developed during the third Frontiers in Microbial Ecology course, in 2015).


1. Doing simple experiments can still lead to discoveries

2. Good symbionts sometimes go bad

3. Stable endosymbionts are sometimes not stable

4. Plant microbiomes: diversity, assembly, engineering

5. Metagenomics of rhizosphere and endosphere (suppressive soils as model)

6. Impact of microorganisms on plant growth and health

7. Rapid evolution of resource mutualisms: when is rapid evolution most likely?

8. Plant-microbe mediated eco-evolutionary feedbacks

9. Plant-microbe interactions in a changing world

10. Applied plant-microbe interactions: applying basic science to agriculture and conservation

Provisional Programme

Day 1 (Sunday 8 April 2018): Arrival, Registration and Dinner at the course venue, Field station the Herdershut, Schiermonnikoog, the Netherlands
17.00 - 19.00 Welcome, sleeping arrangements, drinks & dinner
19.30 - 20.00 Introduction to the course (Joana Falcao Salles)
20.00 - 22.00 Pitch talks by course participants

Day 2 (Monday 9 April):

07.30 - 09.00 Breakfast + cleaning up
09.00 - 10.00 Lecture Jos Raaijmakers + discussion
10.00 - 10.30 Coffee break
10.30 - 11.30 Lecture Jennifer Lau + discussion
11.30 - 12.30 Debating session, led by course participants
12.30 - 14:00 Lunch + cleaning up
14.00 - 15.30 Introduction of course coordinators Alexandre Jousset & Toby Kiers
15.30 - 16.00 Tea break
16.00 - 16.30 Introduction to group activity, group formation
16.30 - 18.30 Group activity
18.30 - 19.00 Free time
19.00 - 20.30 Dinner
20.30 - 21.30 Group activity

Day 3 (Tuesday 10 April):

07.30 - 09.00 Breakfast + cleaning up
09.00 - 10.00 Lecture John McCutcheon+ discussion
10.00 - 10.30 Coffee break
10.30 - 11.30 Lecture Jos Raaijmakers+ discussion
11.30 - 12.30 Debating session, led by course participants
12.30 - 14.00 Lunch + cleaning up
14.00 - 15.30 Group activity
15.30 - 16.00 Tea break
16.00 - 18.30 Group activity
18.30 - 19.00 Free time
19.00 - 20.30 Dinner
20.30 - 21.30 Leisure discussion, free time

Day 4 (Wednesday 11 April, Fieldtrip):

07.30 - 09.00 Breakfast + cleaning up
09.00 - 10.00 Lecture Joana Falcao Salles
10.00 - 10.30 Short lecture on excursion (Joana Falcao Salles)
10.30 - 11.00 Coffee break
11.15 - 16.00 Excursion to the chronosequence (low tide 13.30)
16.00 - 18.00 Free time, leisure discussion
18.00 - 19.30 Dinner
19.30 - 21.00 Favorite Microbial Ecology internet movies

Day 5 (Thursday 12 April):

07.30 - 09.00 Breakfast + cleaning up
09.00 - 10.00 Lecture Wietse de Boer
10.00 - 10.30 Coffee break
10.30 - 11.30 Lecture Jennifer Lau
11.30 - 12.30 Debating session led by participants
12.30 - 13.00 Lunch + cleaning up
13.00 - 15.00 Group activity
15.00 - 15.30 Tea break
15.30 - 18.30 Group activity
18.30 - 19.00 Free time
19.00 - 20.30 Dinner
20.30 - 21.30 Prepare presentations

Day 6 (Friday 13 April):

07.30 - 09.00 Breakfast + cleaning up
09.00 - 10.00 Group presentations
10.00 - 10.30 Coffee break
10.30 - 12.30 Group presentations
12.30 - 13.30 Lunch + cleaning up
13.30 - 14.30 Course closure and evaluation
14.30 - 15.00 Tea break
15.00 - 16.00 Packing & cleaning
16.30 Ferry to the main land
General Information

Required knowledge & preparation

* Students should work / have a strong interest in the field of Evolutionary Biology and/or Microbial Ecology
* Poster: You have to prepare a poster on your own work to be discussed at the course. Send in your A4 poster as pdf before March 15th  at the very latest and prepare a short 5-minute powerpoint presentation (3 slides maximum) to start the discussion on your poster. We will print the posters in a booklet so you can read them before the discussion.
* A number of relevant publications will be made available for you to read in preparation for the course.

Course material PDF copies of relevant papers will be provided. Please bring your own computer to the course.
Course credits 2 ECTS
Location The course will be held at the University of Groningen's fieldstation on Schiermonnikoog, 'the Herdershut' Heereweg 10, 9166 SE, Schiermonnikoog, phone 0519-531363. Transportation to and from the venue will be coordinated at a set time.
Duration & date 5 days. The course will kick off on Sunday night 8 April and finishes at 16.00 on Friday 13 April 2018
Costs * Registration fee is € 350,- for PhD students with an approved TSP participating in RSEE, SENSE or PE&RC. Other PhD participants pay € 500,- and non-PhD participants pay € 725,-
Participants The minimum number of participants is 12, the maximum 20. If space allows for it, highly qualified Master students may be admitted. Master student participants: please contact C.M. Eising

Please note the course is now fully booked! Unfortunately our venue is unable to accommodate more people. if you would like to be put on the waiting list, please fill out the registration form, but please note that access to the course is certainly not guaranteed. Registration

Please note that for the course to continue, the minimum number of participants is 12, so please register at your earliest convenience. The maximum number of participants is 20. PhD student applications will be handled on a first come, first serve basis. However, master student applications will be reviewed and prioritized.
Please take note of our cancellation policy.

Last modified:17 June 2019 5.07 p.m.