31
Stéphane Compant Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria [email protected] Short overview on microbial ecology of the vineyards
Stéphane Compant
Center for Health & Bioresources,
AIT Austrian Institute of Technology GmbH,
3430 Tulln, Austria
Short overview on microbial ecology
of the vineyards
Summary
Ecology
of bacteria
ConclusionsEcology
of fungi
Intro
The plant helpers or neutral and detrimental ones
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: oomycetes, fungi, bacteria, archaea
The Plant as a holobiont
environmental conditions
microbial communities
plant genomics
Plant Holobiont
stress
Bacteria, fungi?
With grapevine?
Which taxa?
Which niches?
Functionalities?
Bacterial vine microbiota
Rhizosphere Endorhiza
Illumina sequencingCulturable approaches
Microbial Ecol 2011Environmental
Microbiology 2016
Endophytes in different plant parts at berry harvest of cv.
Zweigelt
Stalk and berries
Microbial Ecol 2011
Different
communities
and composition
in different plant
parts of Zweigelt
cv.
Different bacterial communities according to plant parts at
berry harvest of cv. Zweigelt
Leaf microbiota of cv. Zweigelt.
From the rhizosphere to the plant endosphere compartment
Firmicutes
Bacillus spp.
At berry harvest
Endorhiza Rhizoplane
a
b
c
e f
d
g
Rh
Rh
Co
Co
Co
Xy
Xy
Book microbial ecology, 2013;
Soil Biol Biochem 2010;
Microbial Ecology 2011
Where they are and from where they derive? Niches
and ways of colonization of endophytes
Source(s) of colonization, in particular of Bacillus spp.
All bacteria
Specific taxa
Stomata
(ovary and
pedicel)
Anthosphere
(carposphere? ) and
soil origins
Bacillus spp.
Niches and ways of colonization
Fruits and seeds
Book microbial ecology, 2013;
Microbial Ecology 2011
Bacteria and relation with organs
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
Bipartite network of OTU
sharing between samples.
A specific endosymbiont associated with grapevine
Human transfer of a bacterial endophyte in grapevine stem
How grapevine got pimples:
The interkingdom horizontal
transfer of an unusual
symbiont
Grapevine got pimples since
domestication
Molecular Biology and
Evolution 2014
P. acnes and grapevine
Endophytic bacteria in wood parts (stem)
Molecular Biology and Evolution 2014
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
Trunk pathogens and grapevine
From Emilie Bruez
Fungi?
Bacteria within trunk (cv. Zweigelt)
Xylem
Symptomatic wood with LTSD Symptomatic wood without LTSD
Non Sympt. wood without LTSDNon Symptomatic wood with LTSD
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
Bacteria within leaves (cv. Zweigelt)
Systemic impact of
fungal trunk diseases
on bacterial
communities
Symptomatic Non Symptomatic
Epip
hyt
esEn
do
ph
ytes
Symptomatic Non Symptomatic
Plant growth-promoting microorganisms (epi and endophytes)
can contribute to better plant growth and protection
AEM 2005a SBB 2010
Functions and use of good microbiota ?
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 tohelp vineyards
• And so on…
Take home message
ACKNOWLEDGMENTS
Thank you
Fib.
Xyl.
