analysing the plant microbiome for control of pathogens
TRANSCRIPT
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)
0
10
20
30
40
50
60
70
80
S. magellanicum S. fallax S. fallax
Rel
atie
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