Analysing the plant microbiome for pathogen control

Transcription

1 Analysing the plant microbiome for pathogen control Gabriele Berg, TU Graz & ACIB, Austria Gabriele Berg Gabriele Berg TU Graz TU Graz AUSTRIA

2 Microbial ecology Plant Microbiome Biocontrol Biotechnology Start Ups Biotenzz GmbH Dr. Henry Müller roombiotic GmBH Dr. Stefan Liebminger

3 INTRODUCTION: Methods and content Advanced Biocontrol Technologies advanced by new tools New techniques for sequencing New bioinformatoric tools New techniques for microscopy I. Detection of new bioresources and agents II. New predictable biocontrol strategies [Berg et al. Microbiol Biotech 2009, Agronomy 2013] III. Mode of action/ interaction Risk assessment IV. Bioprospecting

4 Detection of new bio-resources Grape

5 The grape microbiome: cultivar specificity Plasmopara viticola downy mildew of grape Endemic on wild Vitisspecies of North America; first observed in Europe in 1878 Plasmoparaviticola and Erysiphenecator account for more than 70 % of fungicides used in viticulture

6 The grape microbiome: cultivar specificity Alphaproteobacteria: cultivar-specific composition 100 % Sphingomonadaceae Rhodobacteraceae Rhizobiaceae Methylocystaceae Methylobacteriaceae 0 % Brucellaceae Bradyrhizobiaceae Relative alphaproteobacterial family abundances within samples

7 The grape microbiome: cultivar specificity Alphaproteobacteria: cultivar-specific diversity lowly resistant (AL/LA) susceptible highly resistant(mt) (RI/AM) moderately resistant (SY) Dissimilarities between alphaproteobacterial communities according to P. viticola resistance levels of their hosts (weighted UniFrac PCoA) Relative abundance of taxa accounting for the differences in beta diversity of bacterial communities (one-way ANOVA, P<0.01).

8 Alphaproteobacteria: colonization pattern

9 Alphaproteobacteria: colonization patterns

10 The grape microbiome: organic vs. conventional x-fold difference in A. pullulans ITS copy number 10000,0 1000,0 100,0 10,0 1,0 0,1 organic conventional Higher proportion of antagonists against Botrytis cinerea in organic viticulture Aureobasidium pullulans was enriched under organic conditions In organic viticulture we found an example for natural biocontrol. [Schmid et al. Appl. Environ. Microbiol. 2011]

11 Detection of new bio-resources The microbiome is plant-specific and adapted to the conditions within the ecosystem.

12 Biosprospecting diversity [Zachow et al. Agronomy 2013]

13 II. Predictable strategies by theories Lettuce The Lettuce project (EU) Armin Erlacher, Massimiliano Cardinale Martin Grube (KFU Graz)

14 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 is characterized by a loose microbial network.

15 Treatment with biologicals: Profile clustering network [Erlacher et al. Front. Microbiol. 2014] The Core microbiome The structure of the microbial network is important for health and disease. Acinetobacter and Alkanindiges were identified as indicators of healthy plants

16 Lettuce leaves: only internal colonization Hypothesis: Natural vaccination by plant-associated bacteria. Enterobacteria: yellow

17 III. Mode of action/risk assessments S. rhizophila DSM14405 T The Stenotrophomonas project (FWF) Peyman Alavi, Henry Müller

18 Stress protection: Mode of interaction Root extracts A-biotic stress Verticillium stress Microbiome shift Suicide at 37 C Glucosylglycerol [Ryan et al. Nat. Microb. Rev. 2009; Schmidt et al. Biol. Fertil. Soils 2010; Alavi et al. Frontiers Microbiol. 2013, BMC Genomics 2014]

19 IV. Bioprospecting 39 VOCs Methanol-oxo-benzoate Paenibacillus Verticillium 15 VOCs 1,2,4-Benzentricarboxylic acid, 1,2-dimethylester N-α, N-ω-Di-cbz-L-arginine Exploiting the intense microbial cross talks on/in plants

20 Bioprospecting Volatiles Enrichment + Bait plants Isolation [Bragina et al. Mol. Ecol. 2014; Müller et al. AEM 2015] Metagenome Mining + Fosmid libraries

21 Use of natural volatiles of bacterial origin Pyrazines are heterocyclic aromatic organic compounds. Derivatives such as phenazine are well known for their antitumor, antibiotic and diuretic activities. Pyrazine is a component in traditional Chinese medicine.

22 OUR VISION: Healthy food for our health CONCLUSIONS 1. Novel techniques allow deep insights into the microbiome networkanda better, knowledge-basedandpredictedcontrol. 2. A stable microbial network can avoid pathogen outbreaks. 3. A stablenetworkcanalso supportplant andhuman health. 4. Direct and indirect microbiome control is possible. 5. Microbial interactions should be exploited: Archaea Bacteria Fungi Protists.