S. E. Lindow and M. T. Brandl, Microbiology of the phyllosphere, Appl. Environ. Microbiol, vol.69, issue.4, pp.1875-1883, 2003.

I. Couée, C. Sulmon, G. Gouesbet, and A. El-amrani, Involvement of soluble sugars in reactive oxygen species and responses to oxidative stress in plants, J. Exp. Bot, vol.57, pp.449-459, 2006.

S. Trouvelot, Carbohydrates in plant immunity and plant protection: roles and potential application as foliar sprays, Front. Plant Sci, vol.5, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02461057

N. A. Bokulich, J. H. Thorngate, P. M. Richardson, and D. A. Mills, Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate, vol.111, pp.139-148, 2014.

K. N. Burns, Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features, Soil Bio, vol.91, pp.232-247, 2015.

M. E. Setati, D. Jacobson, U. C. Andong, and F. F. Bauer, The vineyard yeast microbiome, a mixed model microbial map, PLoS One, vol.7, 2012.

P. E. Corneo, Microbial community structure in vineyard soils across altitudinal gradients and in different seasons, FEMS Microbiol Ecol, vol.84, pp.588-602, 2013.

C. Pinto, Unravelling the Diversity of Grapevine Microbiome, e85622, vol.9, 2014.

I. Zarraonaindia, The soil microbiome influences grapevine-associated microbiota, mBio, vol.6, issue.2, pp.2527-2541, 2015.

P. Singh, S. Santoni, P. This, and J. P. Péros, Genotype-Environment interaction shapes the microbial assemblage in grapevine phyllosphere, An NGS Approach. Microorganisms, vol.6, issue.4, 2018.

M. Perazzolli, Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides, Appl. Environ. Microbiol, vol.80, pp.3585-3596, 2014.

P. Singh, Assessing the impact of plant genetic diversity in shaping the microbial community structure of Vitis vinifera phyllosphere in the Mediterranean, Front. Life Sci, vol.11, pp.35-46, 2018.

M. Gopal and A. Gupta, Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies, Front. Microbiol, vol.7, 1971.

, Scientific RepoRtS |, vol.9, 2019.

G. Cordero-bueso, Wild Grape-Associated Yeasts as Promising Biocontrol Agents against Vitis vinifera Fungal Pathogens, Front. Microbiol, vol.8, 2017.

J. Wen, Transcriptome Sequences Resolve Deep Relationships of the Grape Family, PloS ONE, vol.8, issue.9, 2013.

N. Zhang, J. Wen, and E. A. Zimmer, Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming, PLoS ONE, vol.10, issue.12, p.144701, 2015.

J. Wen, A new phylogenetic tribal classification of the grape family (Vitaceae), J. Syst. Evol, vol.56, pp.262-272, 2018.

J. Péros, Genetic variation and biogeography of the disjunct Vitis subg, J. Biogeogr, vol.38, pp.471-486, 2011.

Y. Wan, A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change, BMC Evol. Biol, vol.13, 2013.

S. Shi, Successional trajectories of rhizosphere bacterial communities over consecutive seasons, vol.6, pp.746-761, 2015.

P. J. Mcmurdie and S. Holmes, Waste not, want not: why rarefying microbiome data is inadmissible, PLoS Comput Biol, vol.10, issue.4, 2014.

J. Aitchison, The statistical analysis of compositional data (with discussion), J R Stat Soc Ser B Stat Methodol, vol.44, issue.2, pp.139-177, 1982.

V. Pawlowsky-glahn, J. J. Egozcue, and R. Tolosana-delgado, Modeling and Analysis of Compositional Data, 2015.

J. N. Paulson, O. C. Stine, H. C. Bravo, and M. Pop, Robust methods for differential abundance analysis in marker gene surveys, Nat Methods, vol.10, issue.12, pp.1200-1202, 2013.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, issue.12, 2014.

S. W. Kembel, T. K. Connor, H. K. Arnold, S. P. Hubbell, and S. J. Wright, Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest, PNAS, vol.111, pp.13715-13735, 2014.

N. Delmotte, Community proteogenomics reveals insights into the physiology of phyllosphere bacteria, PNAS, vol.106, issue.38, pp.16428-16461, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01518391

A. Coince, Leaf and root-associated fungal assemblages do not follow similar elevational diversity patterns, PLOS ONE, vol.9, issue.6, p.100668, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01143027

D. Abanda-nkpwatt, M. Musch, J. Tschiersch, M. Boettner, and W. Schwab, Molecular interaction between Methylobacterium extorquens and seedlings: growth promotion, methanol consumption, and localization of the methanol emission site, J. Exp. Bot, vol.57, issue.15, pp.4025-4057, 2006.

G. Innerebner, C. Knief, and J. A. Vorholt, Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system, Appl. Environ. Microbiol, vol.77, pp.3202-3210, 2011.

M. Grube, F. Schmid, and G. Berg, Black fungi and associated bacterial communities in the phyllosphere of grapevine, Fun. Biol, vol.115, pp.978-986, 2011.

P. Garijo, Presence of enological microorganisms in the grapes and the air of a vineyard during the ripening period, Eur Food Res Technol, vol.233, pp.359-365, 2011.

W. L. Araújo, Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants, Appl. Environ. Microbiol, vol.68, issue.10, pp.4906-4914, 2002.

P. T. Lacava, W. L. Araújo, J. Marcon, W. Maccheroni, and J. L. Azevedo, Interaction between endophytic bacteria from citrus plants and the phytopathogenic bacteria Xylella fastidiosa, causal agent of citrus-variegated chlorosis, Lett Appl Microbiol, vol.39, issue.1, pp.55-64, 2004.

U. Ritpitakphong, The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen, New Phytol, vol.210, pp.1033-1076, 2016.

G. Lopez-velasco, G. E. Welbaum, R. R. Boyer, S. P. Mane, and M. A. Ponder, Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rRNA amplicons, J. Appl. Microbiol, vol.110, pp.1203-1214, 2011.

G. Rastogi, Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce, ISME J, vol.6, pp.1812-1822, 2012.

S. G. Dastager, J. C. Lee, Y. J. Ju, D. J. Park, and C. J. Kim, Rubellimicrobium mesophilum sp. nov., a mesophilic, pigmented bacterium isolated from soil, Int. J. Syst. Evol. Microbiol, vol.58, pp.1797-1800, 2008.

M. Balint, Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera), PLOS ONE, vol.8, issue.1, 2013.

N. Bodenhausen, M. Bortfeld-miller, M. Ackermann, and J. A. Vorholt, A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota, PLoS Genet, vol.10, issue.4, 2014.

I. Alkorta, L. Epelde, and C. Garbisu, Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation, FEMS Microbiol. Lett, vol.364, 2017.

A. K. Fahimipour, Daylight exposure modulates bacterial communities associated with household dust, vol.6, 2018.

A. V. Alekseyenko, Community differentiation of the cutaneous microbiota in psoriasis, vol.1, p.31, 2013.

J. R. White, N. Nagarajan, and M. Pop, Statistical methods for detecting differentially abundant features in clinical metagenomic samples, PLoS Comput Biol, vol.5, issue.4, 2009.

G. Falkenhorst, Serological cross sectional studies on salmonella incidence in eight European countries: no correlation with incidence of reported cases, BMC Public Health, vol.12, 2012.

X. Yin, Structural changes of gut microbiota in a rat non-alcoholic fatty liver disease model treated with a Chinese herbal formula, Syst. Appl. Microbiol, vol.36, issue.3, pp.188-196, 2013.

V. J. Stull, Impact of Edible Cricket Consumption on Gut Microbiota in Healthy Adults, a Double-blind, Randomized Crossover Trial. Sci. Rep, vol.8, 2018.

M. D. Robinson, D. J. Mccarthy, and G. K. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, issue.1, pp.139-140, 2010.

R. S. Souza, Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome, Sci. Rep, vol.6, 2016.

B. J. Callahan, DADA2: High-resolution sample inference from Illumina amplicon data, Nat. Methods, vol.13, pp.581-583, 2016.

, Scientific RepoRtS |, vol.9, 2019.

Q. Wang, G. M. Garrity, J. M. Tiedje, and J. R. Cole, Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol, vol.73, pp.5261-5267, 2007.

K. Abarenkov, The UNITE database for molecular identification of fungi -recent updates and future perspectives, New Phytol, vol.186, pp.281-285, 2010.

P. J. Mcmurdie and S. Holmes, phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data, PLoS ONE, vol.8, 2013.

H. Wickham, Elegant Graphics for Data Analysis, 2009.

Y. Benjamini and Y. Hochberg, Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, J. Royal Stat. Soc, vol.57, pp.289-300, 1995.

J. M. Chambers, A. E. Freeny, and R. M. Heiberger, Analysis of variance, 1992.

J. F. Oksanen, vegan: community Ecology Package, 2017.