The apple skin microbiome implications for postharvest quality. Andreas Bühlmann Agroscope

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1 The apple skin microbiome implications for postharvest quality Andreas Bühlmann Agroscope 1

2 Microbiome of an apple Pathogens are fungi, beneficials are yeast Pre- and post harvest differences New technologies allow to study communities Controlling the microbiome along the value chain There are antagonists, but not widely used formulation, timing mixtures 2

3 Microbiome of an apple Beneficials Yeast Pathogens Fungi Host genotype 3

4 Set up and aim Exististing Low residue trial Characterize microbial load on apples from harvest to retail Can we predict pathogen damage before symptoms appear focus on Neofabraea Can we identify ideal biocontrol mixtures 4

5 Kontrolle Lagerung Shelf Life Methods Low residue trial - orchard

C C C C C C C C C C C C C C C C C C C C C C C C C C Topaz D D D D D D D D D D D D D D D D

6 Methods Microbiology Varieties Okt 15 Nov 15 Dez 15 Jan 16 Feb 16 Mrz 16 Apr 16 Mai 16 SL 7d SL14d Ariane A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A Otava C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C Topaz D D D D D D D D D D D D D D D D D D D D D D D D D D D D D D Counting colonies, species identification, sanger sequencing 6

7 CFU/cm2 Apple Skin CFU/cm 2 apple skin Results Microbiology Microorganisms per month 216 Okt 15 Nov 15Dez 15 Jan 16 Feb 16 Mrz 16 Apr 16 Mai 16 NL7 NL14 Sampling date Microorganisms per month 217 Okt 15 Nov 15 Dez 15 Jan 16 Feb 16 Mrz 16 Apr 16 Mai 16 NL7 NL14 Sampling Date 7

8 CFU/cm 2 apple skin CFU/cm 2 apple skin Results Microbiology Microorganisms per variety/ treatment 216 Microorganisms per variety/ treatment Variety/ treatment Variety/ Treatment 8

9 CFU/cm 2 Apfelschale CFU/cm 2 apple skin Results Microbiology Species composition per variety 216 Species composition per variety other other Alternaria Aspergillus Alternaria Aspergillus 8 6 Penicillium 8 6 Penicillium 4 2 Ariane Otava Topaz Sorte Rhodotorula/Erythrob asidium Metschnikowia Aureobasidium 4 2 Ariane Otava Topaz Variety Rhodotorula/Erythrob asidium Metschnikowia Aureobasidium 9

Methods Metagenomics Agar plates Varieties Okt 15 Nov 15 Dez 15 Jan 16 Feb 16 Mrz 16 Apr 16 Mai 16 SL 7d SL14d Treatment C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP C LR

10 Methods Metagenomics Agar plates Varieties Okt 15 Nov 15 Dez 15 Jan 16 Feb 16 Mrz 16 Apr 16 Mai 16 SL 7d SL14d Treatment C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP C LR IP Ariane A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A Otava B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B Topaz C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C Metagenomics Bacteria/fungi Varieties Okt 15 Jan 16 Mai 16 SL14d Treatment C LR IP C LR IP C LR IP C LR IP Ariane A A A A A A A A A A A A Otava B B B B B B B B B B B B Topaz D D D D D D D D D D D D wash Database comparison >seq1 Aureobasidium >seq2 Penicillium >seq3. 1

11 Results Metagenomics ~ 36Gbp sequence data ~1Mio reads/ sample Bsp. Ariane Control 11

12 Results Metagenomics 12

13 Results Metagenomics 13

14 Kontrolle Low-Residue IP Kontrolle Low-Residue IP Kontrolle Low-Residue % fruit with symptoms IP Kontrolle Low-Residue IP Number of Reads Results Metagenomics Correlate metagenomics and disease scoring Storage Diseases Visual Inpsection Storage Diseases Metagenomics Otava Ariane Otava Ariane Bull's eye rot Calyx rot Grey mould rot Neofabraea Sclerotinia Botrytis 14

15 % fruit with symptoms Changing the microbiome Biocontrol trial with yeasts 6 AL April 4 AL Juni a 4 2 a Kontrolle Captan + Flint a a a 3 x Hefe M 2 x Hefe M 2 ab ab Kontrolle Captan + Flint b 3 x Hefe M 2 x Hefe M 15

16 Conclusions/ Outlook Pathogens can be detected on symptomless apple Narrow down Neofabrea growth in storage January May Apply metagenomics in orchard - identify time of infection Identify key species driving the composition of the apple skin microbiome in order to identify possible antagonists Apply antagonists in the field Reduce postharves losses 16

17 Thanks Agroscope Gruppe Petignat Frey/Ahrens Molecular diagnostics Genomics Bioinformatics Freimoser/Lutz Phytopathology Näf/Perren Fruit extension Gasser/Kellerhals Apple breeding and genetic ressources Drissner/Gafner Food microbiology Christen/ Gabioud - Fruit crops in alpine regions External EUFRUIT/ EU Post- harvest people Fenaco EMPA/ Thijs Defraeye 17

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