Microbial Interactions: Essential Part of Below-Ground Biocontrol

Wietse de Boer

NIOO-KNAW (Microbial Ecology)

WUR (Soil Quality)

Wageningen

Email: w.deboer@nioo.knaw.nl

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