Short overview on microbial ecology of the vineyards Stéphane Compant Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria Stephane.Compant@ait.ac.at
Summary Intro Ecology of bacteria Ecology of fungi Conclusions
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
The Plant as a holobiont plant genomics microbial communities Plant Holobiont environmental conditions stress The plant helpers: oomycetes, fungi, bacteria, archaea
With grapevine? Which taxa? Which niches? Functionalities? Bacteria, fungi?
Illumina sequencing Bacterial vine microbiota Culturable approaches Rhizosphere Endorhiza Environmental Microbiology 2016 Microbial Ecol 2011
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
Leaf microbiota of cv. Zweigelt. Different bacterial communities according to plant parts at berry harvest of cv. Zweigelt
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
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.
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): e73013. doi:10.1371/journal.pone.0073013 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073013 Iratxe Zarraonaindia et al. mbio 2015; doi:10.1128/mbio.02527-14
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
Endophytic bacteria in wood parts (stem) Molecular Biology and Evolution 2014 P. acnes and grapevine
Ways of colonization
Ways of colonization Grapevine and weeds share bacterial taxa Envioronmental Microbiology 2016
Fungi? From Jack A. Gilbert et al. PNAS 2014;111:5-6
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
Fungi? From Emilie Bruez Trunk pathogens and grapevine
Bacteria within trunk (cv. Zweigelt) Symptomatic wood with LTSD Symptomatic wood without LTSD Non Symptomatic wood with LTSD Non Sympt. wood without LTSD Xylem
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): e85622. doi:10.1371/journal.pone.0085622 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085622
Endophytes Epiphytes Bacteria within leaves (cv. Zweigelt) Symptomatic Non Symptomatic Symptomatic Non Symptomatic Systemic impact of fungal trunk diseases on bacterial communities
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
MMBR 2015
Natural protection or not The good microbiota for biocontrol, systemic resistance + nutrient acquisition for the plants
Use of microbes Biocontrol 2010
What is missing? Some future prospects needed for trunk diseases and others
Understanding before efficient biocontrol solutions
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
Take home message
ACKNOWLEDGMENTS Fib. Thank you Xyl.
AIT Austrian Institute of Technology