Short overview on microbial ecology of the vineyards

Transcription

1 Short overview on microbial ecology of the vineyards Stéphane Compant Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria

2 Summary Intro Ecology of bacteria Ecology of fungi Conclusions

3 The plant free of microbes? The plant microbiota Partida-Martinez LPP, Heil M (2011) The microbe-free plant: fact or artefact? Frontiers in Plant Science 2 The plant helpers or neutral and detrimental ones

4 The Plant as a holobiont plant genomics microbial communities Plant Holobiont environmental conditions stress The plant helpers: oomycetes, fungi, bacteria, archaea

5 With grapevine? Which taxa? Which niches? Functionalities? Bacteria, fungi?

6 Illumina sequencing Bacterial vine microbiota Culturable approaches Rhizosphere Endorhiza Environmental Microbiology 2016 Microbial Ecol 2011

7 Stalk and berries Different communities and composition in different plant parts of Zweigelt cv. Microbial Ecol 2011 Endophytes in different plant parts at berry harvest of cv. Zweigelt

8 Leaf microbiota of cv. Zweigelt. Different bacterial communities according to plant parts at berry harvest of cv. Zweigelt

9 Where they are and from where they derive? Niches and ways of colonization of endophytes At berry harvest Rhizoplane Endorhiza Firmicutes Rh b Co Xy Co a c d Rh Co Bacillus spp. Xy e f g Book microbial ecology, 2013; Soil Biol Biochem 2010; Microbial Ecology 2011 From the rhizosphere to the plant endosphere compartment

10 Niches and ways of colonization Anthosphere (carposphere? ) and soil origins Bacillus spp. Stomata (ovary and pedicel) All bacteria Specific taxa Fruits and seeds Book microbial ecology, 2013; Microbial Ecology 2011 Source(s) of colonization, in particular of Bacillus spp.

11 Bacteria and relation with organs Bipartite network of OTU sharing between samples. Martins G, Lauga B, Miot-Sertier C, Mercier A, Lonvaud A, et al. (2013) Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations. PLOS ONE 8(8): e doi: /journal.pone Iratxe Zarraonaindia et al. mbio 2015; doi: /mbio

12 Human transfer of a bacterial endophyte in grapevine stem Grapevine got pimples since domestication How grapevine got pimples: The interkingdom horizontal transfer of an unusual symbiont Molecular Biology and Evolution 2014 A specific endosymbiont associated with grapevine

13 Endophytic bacteria in wood parts (stem) Molecular Biology and Evolution 2014 P. acnes and grapevine

14 Ways of colonization

15 Ways of colonization Grapevine and weeds share bacterial taxa Envioronmental Microbiology 2016

16 Fungi? From Jack A. Gilbert et al. PNAS 2014;111:5-6

17 Fungi? Distribution of the fungal isolates in the different orders. Plant types: 1. asymptomatic, 2. esca-symptomatic, 3. nursery. from Hofstetter et al., 2012 Fungal Diversity

18 Fungi? From Emilie Bruez Trunk pathogens and grapevine

19 Bacteria within trunk (cv. Zweigelt) Symptomatic wood with LTSD Symptomatic wood without LTSD Non Symptomatic wood with LTSD Non Sympt. wood without LTSD Xylem

20 Fungi associated with leaves Pinto C, Pinho D, Sousa S, Pinheiro M, Egas C, et al. (2014) Unravelling the Diversity of Grapevine Microbiome. PLOS ONE 9(1): e doi: /journal.pone

21 Endophytes Epiphytes Bacteria within leaves (cv. Zweigelt) Symptomatic Non Symptomatic Symptomatic Non Symptomatic Systemic impact of fungal trunk diseases on bacterial communities

22 Functions and use of good microbiota? AEM 2005a SBB 2010 Plant growth-promoting microorganisms (epi and endophytes) can contribute to better plant growth and protection

23 MMBR 2015

24 Natural protection or not The good microbiota for biocontrol, systemic resistance + nutrient acquisition for the plants

25 Use of microbes Biocontrol 2010

26 What is missing? Some future prospects needed for trunk diseases and others

27 Understanding before efficient biocontrol solutions

28 Prospects? Relation of fungi in the different plant parts? Large studies on vine microbiota? Diseases impact on microbiota? Berries, roots, etc Pathobiome for some diseases? Environmental driving forces influencing on vine microbiota? Cultural practices on vine microbiota? Functionality of the vine microbiome in planta? Archaea? What about oomycetes? Linking the vine microbiota to farmer practices should be done to help vineyards And so on

29 Take home message

30 ACKNOWLEDGMENTS Fib. Thank you Xyl.

31 AIT Austrian Institute of Technology