This document outlines a 3-credit PhD course on plant-microbe interactions exploring how beneficial microorganisms can improve crop productivity in a sustainable way. The course will be held at Makerere University in Uganda in 2014 and taught by professors from Makerere and the Swedish University of Agricultural Sciences. It involves lectures, seminars, practical laboratory and bioinformatics exercises, field trips, group discussions and a final student project presentation. The goal is for students to learn how microbes support crop production through beneficial interactions and development of stress management techniques as alternatives to agrochemicals.

1. PhD course: Plant-microbe interactions
- exploring microbes to improve crop
productivity. (3 credits) at Makerere
University, Uganda 2014
Makerere Univ: Thomas Odong, Patrick Rubaihayo
SLU: Johan Meijer, Sarosh Bejai, Adnan Niazi

2. Subjects:
Plant-microbe interactions or how can beneficial microorganisms compatible
with crop plants be identified and further developed to support sustainable
crop production by improving stress management & avoiding agrochemicals.
Pathogen
Beneficial microbe
(PGPB/PGPR)
HR-resistant plant
Priming (latent defense)
Growth promotion
(hypersensitive
reaction)
SA
stress
abiotic-biotic
(salicylic acid)
JA (jasmonic acid)
SAR – protection
(PR-proteins)
ISR - protection
(?????????)
Nature Chemical Biology 5, 308 - 316 (2009)

3. Target group:
• Students with an interest in (sustainable) crop production.
• Suitable background agronomy, life sciences,...
• Cross-over microbiology, plant biology, soil science, plant
pathology.
• Some prior lab experience wih steril technique is advantageous.
Learning goals:
• To know the basic concepts of plant-microbe interactions with
emphasis on beneficial interactions and how microbes can
support crop production.
• A survey of state-of-the-art of tools and concepts are presented.
• To develop strategies on how to develop and implement these
techniques into the participants specific projects and problems.

4. Teaching:
Read 9 papers before course with some questions provided -survey of the topic
(1 poor quality)
Seminars (3 papers) - survey of the topic, quality discussion, exp design, knowledge
gaps
Lectures - traditional - questions at coffee brakes
Practical x2 – wetlab + bioinformatics (computer/data bases)
low cost: simple techniques, easy access data bases
Field trip study visit – farming scale - experimental
Group discussions – related to papers and generic potential/problems with
biocontrol (SWAT)
Exam-project presentation - Own pet subject + generic problem
Follow-up - SKYPE disucssion 1/3 months post course

5. Date
Sun
1
Mon
2
Tue
3
Wed
4
Thu
5 Fri
6 Sat
7Sun
8
Mon
9
Tue
10
Wed
11
Thu
Read 9 papers from the literature list.
Arrival - get together in the evening
9-9.30
Introduction. Course outline. JM, PR, SB, TO
9.30-12
Student presentations (10-10.30 Break)
12-13
Lunch
13.00-14.30 Plants and biotic stress.
14.30-15
Break
15.00-16.30 Plants and abiotic stress.
8.30-10
Molecular Plant-Microbe Interactions.
10-10.30
Break
10.30-12
Plant Growth Promoting Bacteria.
12-13
Lunch
13-14.30
Biocontrol agents.
14.30-15
Break
15-17
Paper discussion I. JM, PR, SB, TO
8.30-12
Practical. SB,JM
12-13
Lunch
13-14
Gene expression - techniques . XX
14-17
Practical. SB,JM
8.30-12
Practical. SB,JM
12-13
Lunch
13-14
Cell signaling, damage & death - techniques. XX
14-17
Practical. SB,JM
8.30-18
Excursion – field trip
9.00-16
Practical + Bioinformatics exercise I. AN,SB,JM,
13-15
Paper discussion 2. JM, PR, SB, TO
Not scheduled
8.30-10
Functional genomics.
10-10.30
Break
10.30-12
Bioinformatics.
12-13
Lunch
13-17
Bioinformatics exercise II. AN
8.30-11
Group exercise I. JM, PR, SB, TO
11-12
Group exercise I summary. JM, PR, SB, TO
13-15.30 Group exercise II. JM, PR, SB, TO
15.30-16.30 Group exercise II summary. JM, PR, SB, TO
8.30-10.30 Paper discussion 3. JM, PR, SB, TO
10.30-11
Break
11-12
Lab practical survey. JM, PR, SB, TO
12-13
Lunch
13.30-17
Prepare presentation.
18
Dinner
9 -12
Student presentations. JM, PR, SB, TO
12-13
Lunch
13-16
Student presentations. JM, PR, SB, TO
Course summary, course evaluation. JM, PR, SB, TO
Follow-up meetings: 1 + 3 months later

6. Remaining ?
Harmonize learning objectives?
Teaching resources?
Computer connection (bioinformatics)?
When can the course be given?
Security issues?
Health/disease issues?
Interaction (mix people)?
Follow-up - pressure or inspiration?