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….

Thank you !

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%