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Microbial Interactions: Essential Part of Below-Ground Biocontrol
Wietse de Boer
NIOO-KNAW (Microbial Ecology)
WUR (Soil Quality)
Wageningen
Email: [email protected]
Rhizosphere: Hotspot of Microbial Activity
Rhizosphere
Dead epidermal
& cortical cells
Exudates
(sugars, amino
acids, organic
acids)
Rootcap and Mucilage
Microbes & Rhizosphere
Root exudates
Saprotrophs
Pathogens
Competition for Root Exudates
Growth-suppressing compounds
(Antagonism)
Root Exudates
Bacteria
Fungi
Competition and Disease Suppression
Saprotrophs Pathogens
Root Exudates
Suppressing
Compounds
Microbial Activity
Microbial
Antagonism
Pairwise Interactions – Suppression
Fungal Pathogen
Biocontrol Product
Pairwise Interactions – Suppression
Fungal Pathogen Detailed Mechanisms
Defense Fungus
Bacterium
Regulation inhibitors: Fungal compounds,
Medium composition
Identity inhibitors and genes
Gene Expression
Multiple Interactions - Suppression
Bacterial Interactions &
Suppressing compounds
Silencing
Multiple Interactions - Suppression
Bacterial Interactions &
Suppressing compounds
No Change
Multiple Interactions - Suppression
Bacterial Interactions &
Suppressing compounds
Triggering
Pseudomonas Pedobacter.
Interaction
Stimulation of Suppressing Activity by Interaction
Bacterial Zone
Pseudomonas Zone
Pedobacter Zone
Garbeva et al. (2011) ISME J. 5:973-
B 1
B 2
Nutrient-poor Agar
Antibiotic Production during Bacterial Interactions
• Fungus as bioindicator
Signal
Inhibitor
Inhibitor
Broad-
spectrum
antibiotic:
inhibiting both
bacteria and
fungi
Tyc et al. 2014 Frontiers in Microbiology 5: 567
Effect Bacterial Interactions on Suppressing Activity
> 2500 pairwise interactions
Loss
No Change
Gain
Meaning for Biocontrol
Community Interactions - Suppression
Microbial Properties
Diversity
Key species
Abundance
Activity
Details on Interactions
Communities: Multiple Interactions Functional Redundancy (catabolism, anabolism)
Pair-wise: One Interaction One Mechanism
Community versus Pairwise Interactions
Examples Redundancy Rhizoctonia Suppression
Bacterial species
Bacillus subtilis RB14
Burkholderia pyrrocinia BC11
Streptomyces griseoviridis
Pseudomonas fluorescens DR54
Serratia plymutica HRO-C48
Many more
Inhibiting Mechanism
Iturin A, Surfactin
Lipopeptide AFC-BC11
Chitinases, polyenes,
macrolactones
Vicosinamide
Haterumalide, volatiles
Many more
Communities: Multiple Interactions Functional Redundancy (catabolism, anabolism)
Pair-wise: One Interaction One Mechanism
Community versus Pairwise Interactions
Explanation
?
Biocontrol Bacterium
Pathogen suppression Pathogen suppression
?
Microbial Inoculants & Indigenous Microbial Communities
Expected versus real behavior of biocontrol inoculants
Microbial Inoculants
Resistance against biocontrol “invaders”
by indigenous rhizosphere bacterial communities
Biocontrol Bacterium
Pathogen suppression
Pathogen suppression
Manipulate community (stress)
to increase succesful
establishment of biocontrol bacteria
Screen for succesful invaders
Possibilities to Improve Success Biocontrol Bacteria
Addition of compounds that
specifically promote the
biocontrol strain
Steering Interactions
Example to Improve Success Microbial Inoculants
Transient Phase (New colonisation)
Microbial Inoculant
Steering Indigenous Rhizosphere Microbial Communies
Make use of beneficial microbes that are adapted to the local situation !
Agricultural Management
(crop choice, organic
amendments, tillage)
Shift in microbial
community functioning
Increased
disease control
Crop Farming = Microbe Farming
Microbe Farming
Which microbial functions should be stimulated ?
How can these functions be stimulated ?
Range of compounds (enzymes, inhibitors, signals, etc.)
Classification in major functional groups of metabolites
Quantification
Steering, Management
Extrapolation of Pairwise Fungal-Bacterial Interactions
De Boer (2017) Curr. Opin. Microbiol. 37, 35-41
VOCs: Rapid spreading in air-filled pores
Competition on a Distance: Suppressing VOCs (Volatile Organic Compounds)
Geosmin
Soil
Agar
Pathogenic Fungus
Volatiles
Weight or
Extension sterilized Untreated
Screening for Volatile-Suppression in Soils
Volatiles & Natural Disease Suppression
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 Hyp
hal w
eig
ht
(p
ercen
tag
e o
f co
ntr
ol)
Pythium = Oomycete
Maaike Van Agtmaal (2015) Ph.D thesis
Pythium ultimum
No Suppression
Strong Suppression
Agricultural Soils in the Netherlands
Range of VOCs
Sulfur containing VOCs (methyl sulfides)
Quantification
S-containing organic material
Link between Pairwise and Community Functioning
High S Cover Crops
Fungi
stimulating soil
amendment
↗ Saprotrophic
fungi
↗ Antifungal
bacteria
↘ Fungal
phytopathogens
SaproFeed: Application of Competition in Agriculture
De Boer et al (2015) PlosOne 10:e0137988
Conclusion
Microbial interactions lay at the basis of success and failure of microbe-based biocontrol
Microbial interactions do form the basis for developing strategies to improve biocontrol
