Microbial Interactions: Essential Part of Below-Ground Biocontrol Wietse de Boer

Transcription

1 Microbial Interactions: Essential Part of Below-Ground Biocontrol Wietse de Boer NIOO-KNAW (Microbial Ecology) WUR (Soil Quality) Wageningen

2 Rhizosphere: Hotspot of Microbial Activity Dead epidermal & cortical cells Rhizosphere Exudates (sugars, amino acids, organic acids) Rootcap and Mucilage

3 Microbes & Rhizosphere Saprotrophs Root exudates Pathogens

4 Competition for Root Exudates Fungi Bacteria Root Exudates Growth-suppressing compounds (Antagonism)

5 Competition and Disease Suppression Microbial Activity Root Exudates Saprotrophs Pathogens Microbial Antagonism Suppressing Compounds

6 Pairwise Interactions Suppression Fungal Pathogen Biocontrol Product

7 Pairwise Interactions Suppression Fungal Pathogen Detailed Mechanisms Fungus Defense Gene Expression Bacterium Identity inhibitors and genes Regulation inhibitors: Fungal compounds, Medium composition

8 Multiple Interactions - Suppression Bacterial Interactions & Suppressing compounds Silencing

9 Multiple Interactions - Suppression Bacterial Interactions & Suppressing compounds No Change

10 Multiple Interactions - Suppression Bacterial Interactions & Suppressing compounds Triggering

11 Stimulation of Suppressing Activity by Interaction Bacterial Zone Pseudomonas Pseudomonas Zone Pedobacter. Pedobacter Zone Interaction Garbeva et al. (2011) ISME J. 5:973-

12 Antibiotic Production during Bacterial Interactions Fungus as bioindicator Broadspectrum antibiotic: inhibiting both bacteria and fungi Inhibitor Inhibitor B 1 B 2 Nutrient-poor Agar Signal

13 Effect Bacterial Interactions on Suppressing Activity Gain > 2500 pairwise interactions Meaning for Biocontrol Loss No Change Tyc et al Frontiers in Microbiology 5: 567

14 Community Interactions - Suppression Microbial Properties Abundance Activity Diversity Key species Details on Interactions

15 Community versus Pairwise Interactions Communities: Multiple Interactions Functional Redundancy (catabolism, anabolism) Pair-wise: One Interaction One Mechanism

16 Examples Redundancy Rhizoctonia Suppression Bacterial species Inhibiting Mechanism Bacillus subtilis RB14 Burkholderia pyrrocinia BC11 Streptomyces griseoviridis Pseudomonas fluorescens DR54 Serratia plymutica HRO-C48 Many more Iturin A, Surfactin Lipopeptide AFC-BC11 Chitinases, polyenes, macrolactones Vicosinamide Haterumalide, volatiles Many more

17 Community versus Pairwise Interactions Explanation? Communities: Multiple Interactions Functional Redundancy (catabolism, anabolism) Pair-wise: One Interaction One Mechanism

18 Microbial Inoculants & Indigenous Microbial Communities Biocontrol Bacterium? Pathogen suppression Pathogen suppression

19 Expected versus real behavior of biocontrol inoculants Microbial Inoculants Resistance against biocontrol invaders by indigenous rhizosphere bacterial communities

20 Possibilities to Improve Success Biocontrol Bacteria Biocontrol Bacterium Screen for succesful invaders Steering Interactions Addition of compounds that specifically promote the biocontrol strain Pathogen suppression Pathogen suppression Manipulate community (stress) to increase succesful establishment of biocontrol bacteria

21 Example to Improve Success Microbial Inoculants Transient Phase (New colonisation) Microbial Inoculant

22 Steering Indigenous Rhizosphere Microbial Communies Make use of beneficial microbes that are adapted to the local situation!

23 Crop Farming = Microbe Farming Agricultural Management (crop choice, organic amendments, tillage) Increased disease control Shift in microbial community functioning

24 Microbe Farming Which microbial functions should be stimulated? How can these functions be stimulated?

25 Extrapolation of Pairwise Fungal-Bacterial Interactions Quantification Range of compounds (enzymes, inhibitors, signals, etc.) Classification in major functional groups of metabolites Steering, Management De Boer (2017) Curr. Opin. Microbiol. 37, 35-41

26 Competition on a Distance: Suppressing VOCs (Volatile Organic Compounds) Geosmin VOCs: Rapid spreading in airfilled pores

27 Screening for Volatile-Suppression in Soils Pathogenic Fungus Agar Volatiles Soil Weight or Extension sterilized Untreated

28 Hyphal weight (percentage of control) Volatiles & Natural Disease Suppression Pythium ultimum 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% No Suppression Strong Suppression Agricultural Soils in the Netherlands Pythium = Oomycete Maaike Van Agtmaal (2015) Ph.D thesis

29 Link between Pairwise and Community Functioning Quantification Range of VOCs Sulfur containing VOCs (methyl sulfides) S-containing organic material High S Cover Crops

30 SaproFeed: Application of Competition in Agriculture Fungi stimulating soil amendment Saprotrophic fungi Fungal phytopathogens Antifungal bacteria De Boer et al (2015) PlosOne 10:e

31 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