Analysing the plant microbiome for control of pathogens

Advanced Biocontrol Technologies

Gabriele Berg TU Graz AUSTRIA

Gabriele Berg, TU Graz & ACIB, Austria

Start Up Biotenzz GmbH Dr. Henry Müller roombiotic GmBH Dr. Stefan Liebminger

Microbial ecology Plant Microbiome

Biocontrol Biotechnology

INTRODUCTION: Methods and content

New bioinformatoric tools

New techniques for sequencing

New techniques for microscopy

I. Detection of new bio-

resouces and agents

II. New predictable biocontrol strategies

III. Mode of action/

interaction

Optimization of fermentation

and formulation Risk

assessment

Advanced Biocontrol Technologies advanced by new tools

[Berg et al. Microbiol Biotech 2009, Agronomy 2013]

I. Detection of new bio-resources A) Mosses

The Sphagnum moss project (FWF) Anastasia Bragina Lisa Oberrauner-Wappnis Wladimir Chebotar Andrej Sherbakov (St. Petersburg)

The biocontrol project (ACIB) Christin Zachow, Christina Müller Ralf Tilcher, KWS Saat AG (Einbeck) Christina Donat, Bio-Ferm (Tulln) Henry Müller, Biotenzz (Graz)

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S. magellanicum S. fallax S. fallax

Rel

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abu

ndan

ce, %

Other Rhodobacteraceae StappiaMethylocystaceae Methylocystis Sphingomonadaceae SphingomonasBradyrhizobiaceae Rhodoblastus Bradyrhizobiaceae Af ipiaAcetobacteraceae Acidomonas Rhizobiaceae RhizobiumHyphomicrobiaceae Rhodoplanes Acetobacteraceae AcidiphiliumCaulobacteraceae Caulobacter Acetobacteraceae GluconacetobacterCaulobacteraceae Brevundimonas Sphingomonadaceae NovosphingobiumAcetobacteraceae Roseomonas Bradyrhizobiaceae BradyrhizobiumAcetobacteraceae Stella Acetobacteraceae RhodopilaCaulobacteraceae Phenylobacterium Rhodospirillaceae MagnetospirillumAcetobacteraceae Acidocella Acetobacteraceae Acidisphaera

BGametophyte Sporophyte

All stages of mosses contain a core microbiome

Gametophyt Sporophyt 16S rRNA amplicon library

[Bragina et al. ISME J 2012]

Sphagnum mosses as tool for biocontrol:

The species-specific core microbiome can be used for biocontrol.

The Sphagnum metagenome

Specific genetic features: • horizontal gene transfer • stress tolerance • interaction via quorum sensing • nutrient exchange • high number of mobile elements

[Shcherbakov et al. Microbiol. 2012; Bragina et al. Mol. Ecol. 2014]

Detection of new bio-resources B) Lichens

[Zachow et al. Agronomy 2013]

Biosprospecting diversity

II. Predictable strategies by theories A) Lettuce

The Lettuce project (EU) Armin Erlacher, Massimiliano Cardinale Martin Grube (KFU Graz)

Lettuce: specificity and co-occurrence patterns

• significant differences at species and cultivar level • 12.5% cultivar-specific bacteria; 49% core microbiome

Domestication lead to bacterial diversification in lettuce root system.

Lettuce: specificity and co-occurrence patterns

Spearman correlations between OTUs showed that co-occurrence prevailed over co-exclusion • predominant taxa with positive interactions but not involved in • highly correlated modules, low colonization resistance

Streptomyces and Actinobacteria-6

Pseudomonas Xanthomonas Anaerolinae

Sphingomonas Flavobacterium

Chloroflexi

Loose network structure

Susceptibility to pathogens? Good establishment of Biocontrol agents?

Treatment with biologicals: Profile clustering network

Acinetobacter and Alkanindiges were identified as indicators of healthy plants

The Core microbiome

Lettuce: the rhizosphere as functional hotspot

Enterobacteria: yellow

Lettuce leaves: only internal colonization

The seed microbiome project (ACIB) Christin Zachow, Henry Müller Ralf Tilcher (KWS SAAT AG)

II. Predictable strategies by theories B) Seeds

Seeds are an important source for microbes? Cultivar* Properties Production Country Lot.-No.

MATTEA KWS Rhizoctonia-tolerant 2011 Italy 3011-259 C

MATTEA KWS Rhizoctonia-tolerant 2011 France 3011-535 C

LAETITIA KWS Rhizoctonia-tolerant 2008 Italy 308-0041 E

LAETITIA KWS Rhizoctonia-tolerant 2008 France 308-0430 E

BERETTA KWS Rhizoctonia-susceptible 2011 Italy 3011-076 C9

BERETTA KWS Rhizoctonia-susceptible 2011 France 3011-404 C9

BELLADONNA KWS Rhizoctonia-susceptible 2011 Italy 1611-062 M

BELLADONNA KWS Rhizoctonia-susceptible 2011 France 3011-585 C

ISABELLA KWS Rhizoctonia-effective 2011 Italy 3011-221 C9

ISABELLA KWS Rhizoctonia-effective 2011 France 3011-507 C

*KWS SAAT AG provided

Germination

• Unweighted unifrac 2D PCoA plots, total dataset Rhizosphere, soil

Cultivar-specific seed microbiomes

MATTEA

tolerant

LAETITIA

BERETTA

susceptible

BELLADONNA

ISABELLA

effective

Reads representing P. fluorescens SBW25, F113, P. poae RE*1-1-14

explain this phenomenon

III. Mode of action/risk assessments

S. rhizophila DSM14405T

The Stenotrophomonas project (FWF) Peyman Alavi, Henry Müller

Root extracts Verticillium stress

Glucosylglycerol [Alavi et al. Frontiers Microbiol. 2013]

Stress protection: Mode of interaction

A-biotic stress

Suicide at 37°C

OUTLOOK

Advanced Biocontrol Technologies advanced by new tools

VISION: Healthy food for our health

[Berg et al. Agronomy 2013]

Advanced Biocontrol Technologies provide new solutions