harnessing the microbiome for organic crop …
TRANSCRIPT
Birgit WassermannGabriele BergHenry MüllerPeter Kusstatscher
HARNESSING THE MICROBIOME FOR ORGANIC CROP MANAGEMENT
MICROBIOME
+
ENVIRONMENTAL CONDITIONS
MICROBIOTA
Bacteria
Fungi
Archaea
Protists
Algae
“THEATRE OF ACTIVITY”MICROBIAL STRUCTURAL ELEMENTS
MICROBIAL METABOLITES
Signallingmolecules
Toxins(An)organicmolecules
Proteins/peptides
LipidsPoly-
saccharides
HOLOBIONT: the eukaryotic host and it´s associated microbiome.
Berg et al. 2019 (under submission)
✓ Emerging pathogens
✓ Increasing resistance against pesticides
✓ Pesticide residues
✓ Non-target effects and environmental problems
MISSION: ENVIRONMENTALLY FRIENDLY BIOCONTROL
SOLUTIONS: MICROBIOME-BASED & INSPIRED BY NATURE
INCREASING PROBLEMS TO CONTROL PLANT PATHOGENS
BIODIVERSITY LOSS WORLD-WIDE
EXPLOITING THE MICROBIOME FOR ONE HEALTH
‚Back to the roots‘ Exploring undisturbedenvironments
Applications in the fieldProtection/promotion in thefield
Applications postharvestProtection during storage
The edible microbiomeand human health
THE EDIBLE MICROBIOME
Wassermann, Müller, Berg. An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? (2019) Front. Microbiol.
AN APPLE A DAY: WHICH BACTERIA DO WE EAT WITH ORGANIC AND CONVENTIONAL APPLES?
The microbial diversity within each apple tissue: Differences in the microbial composition:
THE EDIBLE MICROBIOME
Wassermann, Müller, Berg. An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? (2019) Front. Microbiol.
AN APPLE A DAY: WHICH BACTERIA DO WE EAT WITH ORGANIC AND CONVENTIONAL APPLES?
organic conventional
The apple microbiome is tissue specific.
Significant management effect on the apple microbiome
• Organic apples are significantly more diverse
• Distinct composition (almost 40% of bacteria are different)
• Putative health-beneficial effects of organic apple microbiome
No difference in microbial abundance: 108 bacterial genes / apple.
APPLICATIONS POSTHARVEST
THE POSTHARVEST APPLE MICROBIOME
• The impact of Hot Water Treatment (HWT) on the postharvest microbiome• Increased disease resistance by combined approach using BCA
Wassermann, Kusstatscher, Berg. (2019) Front. Microbiol., Maxin et al. (2014) Erwerbs-Obstbau.
HWT
untreated
Stored for 6 month
healthy
affected
0%
20%
40%
60%
80%
100%
HWT ut.
HWT
HWT induces plant response killing fungal spores.
APPLICATIONS POSTHARVEST
THE POSTHARVEST APPLE MICROBIOME
• The impact of Hot Water Treatment (HWT) on the postharvest microbiome• Increased disease resistance by combined approach using BCA
Wassermann, Kusstatscher, Berg. Microbiome Response to Hot Water Treatment and Potential Synergy With Biological Control on Stored Apples (2019) Front. Microbiol.
Pathogen infection significantly decreases diversity. • 90% of the fungal community was composed by co-
occurring Neofabraea alba and Penicillium expansum.
No significant difference between HWT and untreated healthy• mutual dependency of host and natural microbiome.
Before storageHWT
Untreated healthyUntreated diseased
APPLICATIONS POSTHARVEST
THE POSTHARVEST APPLE MICROBIOME
• The impact of Hot Water Treatment (HWT) on the postharvest microbiome• Increased disease resistence by combined approach using BCA
Wassermann, Kusstatscher, Berg. Microbiome Response to Hot Water Treatment and Potential Synergy With Biological Control on Stored Apples (2019) Front. Microbiol.
Combined approach of HWT and a biological control consortium is efficient in reducing both postharvest pathogens and promote disease resistance.
THE PLANT MICROBIOME IS
o plant genotype-specifico highly diversified and abundanto changed during plants life cycleo vertically transmitted by seedso essential for plant development, resilience and healtho affected by environmental conditions (including management practices)
WHAT CAN WE DO
o consider the natural plant microbiome and its functionality for host and environmental health
o interdisciplinary approaches for microbiome engeneeringo combined breeding and plant protection strategieso support beneficial microbeso rethink sterility in our life
o eat fresh fruits, vegetables & herbs….
Positive bacteria - archaea interactionsNegative fungal interaction
1. ‚BACK TO THE ROOTS‘
THE SEED MICROBIOTA OF ALPINE PLANTS
Wassermann et al. (2019) Microbiome
- High abundances- Consistent ratio
• annual vs. perennial→ the life cycle• capsule vs. achaene→ the fruit morphology
Life cycle: NOFruit morphology: NO
Plant species: EXCEPTIONALLY UNIQUE• 11 out of 11,810 bacteria• 5 out of 3,945 fungi• 0 out of 32 archaea
1. ‚BACK TO THE ROOTS‘
GERMINATION ASSAY OF GENTIANA ASCLEPIADEA
- Different composition- Consistent abundance
healthy healthyaffected affected
Phosphate solubilization 60 %
Protease activity 85.6 %
AHL production 51.2 %
Siderophore production 49.6 %
Auxin production 9.6 %
Nitrogen fixation 4 %
No difference in germination capacity.
Seed microbiota areTRUE ENDOPHYTES.
Plant growth promotingtraits of seed isolates.
2. APPLICATIONS IN THE FIELD
THE MICROBIAL DIVERSITY OF PUMPKIN
Adam et al. (2016) Plant and Soil
The microbiome was shaped by breedingThe microbiome correlated with resistance against• Erwinia carotovora, Enterobacteriaceae
2. APPLICATIONS IN THE FIELD
THE WINE MICROBIOME
Schmid et al. Appl and Environ Microbiol (2011)
Differences between organic and conventional grapes.
Organic farmingbenefits natural biological control agents.
Promising biocontrol agents against Botrytis cinerea isolatedfromorganicgrapes.
Microbiome composition correlates with susceptibilitytowards Plasmopara viticola
2. APPLICATIONS IN THE FIELD
IS IT POSSIBLE TO MANAGE MICROBIAL DIVERSITY?
Berg and Raaijmakers (2018) The ISME J
4. THE EDIBLE MICROBIOME
THE BRASSICA MICROBIOME
Wassermann et al. (2017) Scientific reports.
• Broccoli• White cabbage• Arugula• Horseradish• Cauliflower• Radish• Turnip cabbage
Plant genotype-specific microbiome.
Myrosinase-active endophytes enriched in GLS-secreting, edible plant tissues.
Putative biological control agents within all plants.
Verticillium-antagonistic bacteria represent up to 16% of the vegetable microbiome.
G lucoseMyrosinase
Glucosinolate
Isothiocyanate
HUMAN HEALTH: Myrosinase-active bacteria?
PLANT HEALTH: Biological control and plant growth promotion ability?
APPLICATIONS POSTHARVEST
0% 20% 40% 60% 80% 100%
North America and Oceania
Europe
Japan, Korea, China
North Africa, West and…
Latin America
South and Southeast Asia
Subsaharan Africa
Agriculture Postharvest Processing
Retail Consumption
©FAO 2011
GLOBAL FOOD LOSS
Fruit andvegetables
Meat
DairyFish
Roots andtubers
Cereals
Total
wasted
20%
20% 35%
30%
45%
%
33%
45%