Supporting plant health through microbial communities: the apple fruit case
Sébastien Massart Haissam Jijakli – Abdoul Sare Plant Pathology Laboratory – TERRA Gembloux Agro-Bio Tech – University of Liège
Belgium
sebastien.massart@uliege.be
@Be_Phytopath
Introduction
The biocontrol agent
Biocontrol agents & postharvest disease ?
• Losses of 15-25%after harvest • Major fungal diseases :
– Wound parasites • Botrytis cinerea • Penicillium expansum – Latent infections
• Gloeosporides sp.
Pichia anomala (strain K) & Candida oleophila (strain O)
Biocontrol agents & postharvest disease ?
Mode of action
Ecological fitness
Large scale trials and EU registration
Biocontrol agents efficacy ?
Introduction
The Plant
A plant or an ecological niche ?
Source: wikipedia
Nutrient & growth Growth & stress,
Resistance,
Interaction with pathogens,
Interaction with other trophic levels.
Plants & microbial communities?
Environment Soil, climate… Plant Species, genotype, seed/plantlet, stage Microbial communities
Introduction
The Plant,
Its microbiome
&
The BCA
Mutualism +/+ Commensalism +/0 Amenalism 0/- Neutralism 0/0 Parasitism +/-Competition-/-Plant microbiota & biocontrol ?
Biocontrol Agent (BCA) - Yeast Mutualism +/+ Commensalism +/0 Amenalism 0/- Neutralism 0/0 Parasitism +/-Competition
-/-Plant microbiota & biocontrol ?
Biocontrol Agent (BCA) - Yeast Plant pathogen ISR Elicitor BCA Pathogen Molecules
Plant microbiota & biocontrol ?
ISR
Helper strains
Biocontrol prebioitics
Objectives
1. Harvest contrasted microbial communities 2. Characterization of microbe composition 3. Microbiota biocontrol properties 4. New BCA
Identify beneficial plant microbiota
Results
0. Microbiota harvesting ?
0. Microbiota harvesting ?
4 successive washings:
no more differences
30% BufferDiversity &
4 washes
Phytosanitary treatments Cultivars
Conservation orchard
(Never treated, 35 years old) 9
Light organic 3
Organic
3 Conventional
1. Microbiota biobanking
= 15 contrasted microbiota from Belgium
Microbiota
Microbiota Biobank
Taxonomy
Amplification of 16S (bacteria) & ITS (fungi) Illumina Miseq Sequencing (2x250nt)
15 Microbiota
Microbiota Biobank
2. HTS for microbiota characterization
Functional DNA extraction and sequencing Illumina Hiseq Sequencing (2x100nt)
Study of genes and functions
PCoA of Weighted UniFrac (bacteria)
Bacteria
3. Taxonomic characterization
Contrasted microbiota at taxonomic level
+
B. cinerea (106)+
Strain K (105) 4. Biological characterizationEffect on biocontrol agent (Pichia anomala strain K)
Microbiota B. cinerea (106) Microbiota
+
or Biocontrol properties Im pa ct o n ef fic ac y ( % ) -50 -40 -30 -20 -100 10 20 30 40 50 60 70 80 90 100 4. Biological characterization Strain KEffect on biocontrol agent (Pichia anomala strain K) ?
-50 -40 -30 -20 -100 10 20 30 40 50 60 70 80 90 100 5. Biological characterization
Statistical groups (Tukey test)
In cr ea se o f e ff ic ac y ( % )
Effect on biocontrol agent (Pichia anomala strain K) ?
5. Biological characterization
Biocontrol properties of the microbial communities alone ?
0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 0,8 0,9 Ef fic ac y of p ro te ct io n (% ) Microbiota ab b bc bc bc c c a a
6. Innovative biocontrol
Clustering taxonomical
characterization and biocontrol
properties ?
Ef
fic
ac
y
Theorical microbe species
6. Innovative biocontrol
Microbiota Microbiota +BCA (1) Microbiota +BCA (2) Microbiota +BCA (3)
New genus & >90% efficacy
Conclusions
Species pathogen’s friends
Species BCA’s friends Species pathogen’s
enemy
Species as BCA
Opening new research axes to improve disease control
Research perspective
1) Coping diversity = which niche level ? 2) Standardisation / harmonisation ! 3) From catalogue to functional links !
& thank you for your attention
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