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Variety features differentiate microbiota in the grape leaves

Publication: Canadian Journal of Microbiology
8 June 2020


The dependence of plant health and crop quality on the epiphytic microbial community has been extensively addressed, but little is known about plant-associated microbial communities under natural conditions. In this study, the bacterial and fungal communities on grape leaves were analyzed by 16S rRNA gene and internal transcribed spacer high-throughput sequencing, respectively. The results showed differences in the composition of the microbial communities on leaf samples of nine wine grape varieties. The most abundant bacterial genus was Pseudomonas, and the top three varieties with Pseudomonas were Zinfandel (22.6%), Syrah (21.6%), and Merlot (13.5%). The most abundant fungal genus was Alternaria, and the cultivar with the lowest abundance of Alternaria was Zinfandel (33.6%), indicating that these communities had different habitat preferences. The linear discriminant analysis effect size of all species showed that the bacteria Enterococcus, Massilia, and Kocuria were significantly enriched on the leaves of Merlot, Syrah, Cabernet Sauvignon, respectively; Pseudomonadales and Pantoea on Zinfandel; and Bacillus, Turicibacter, and Romboutsia on Pinot Noir. Similarly, the fungi Cladosporium, Phoma, and Sporormiella were significantly enriched on Zinfandel, Lon, and Gem, respectively. Both Bray–Curtis and unweighted UniFrac revealed that bacteria and fungi have a significant impact (P < 0.01), and the results further proved that variety is the most important factor affecting the microbial community. The findings indicate that some beneficial or harmful microorganisms existing on the wine grape leaves might affect the health of the grape plants and the wine-making process.


La dépendance de la santé des végétaux et de la qualité des cultures à l’égard de la communauté microbienne épiphyte a été largement abordée, mais on sait peu de choses sur les communautés microbiennes associées aux végétaux dans des conditions naturelles. Dans cette étude, les communautés bactériennes et fongiques présentes sur les feuilles de vigne ont été analysées par séquençage à haut débit du gène de l’ARNr 16S bactérien et de l’espaceur interne transcrit fongique. Les résultats ont montré des différences dans la composition des communautés microbiennes d’échantillons de feuilles de neuf variétés de raisin de cuve. Le genre bactérien le plus abondant était Pseudomonas et les trois principales variétés abritant Pseudomonas étaient le zinfandel (22,6 %), la syrah (21,6 %) et le merlot (13,5 %). Le genre fongique le plus abondant était Alternaria et le cultivar montrant la plus faible abondance d’Alternaria était le zinfandel (33,6 %), indiquant que ces communautés avaient des préférences d’habitat différentes. La taille de l’effet de l’analyse discriminante linéaire de toutes les espèces a montré que les bactéries Enterococcus, Massilia, Kocuria, Pseudomonadales et Pantoea étaient significativement enrichies sur le merlot, la syrah, le cabernet sauvignon et le zinfandel, respectivement, alors que Bacillus, Turicibacter et Romboutsia étaient significativement enrichies sur le pinot noir. De même, les champignons Cladosporium, Phoma et Sporormiella étaient significativement enrichis sur le zinfandel, le longane et le gem, respectivement. La distance de Bray–Curtis et la distance de l’UniFrac non pondérée ont toutes deux révélé que les bactéries et les champignons ont un impact significatif (P < 0,01) et les résultats ont prouvé que la variété constitue le facteur le plus important qui affecte la communauté microbienne. Les résultats indiquent que certains microorganismes bénéfiques ou nuisibles présents sur les feuilles de vigne pourraient affecter la santé des plants de vigne et le processus de vinification. [Traduit par la Rédaction]

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Barata A., Malfeito-Ferreira M., and Loureiro V. 2012. The microbial ecology of wine grape berries. Int. J. Food Microbiol. 153(3): 243–259.
Berg J., Tom-Petersen A., and Nybroe O. 2005. Copper amendment of agricultural soil selects for bacterial antibiotic resistance in the field. Lett. Appl. Microbiol. 40(2): 146–151.
Biasolo G.A.D., Kucmanski D.A., Salamoni S.P., Gardin J.P., Minotto E.B., and Baratto C.M. 2016. Isolation, characterization and selection of bacteria that promote plant growth in grapevines (Vitis sp.). J. Agri. Sci. 9(1): 184–194.
Bodenhausen N., Horton M.W., and Bergelson J. 2013. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS ONE, 8(2): e56329.
Bokulich N.A., Joseph C.M., Allen G., Benson A.K., and Mills D.A. 2012. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLoS ONE, 7(5): e36357.
Bokulich N.A., Torngate J.H., Richardson P.M., and Mills D.A. 2014. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proc. Natl. Acad. Sci. USA, 111: E139–E148.
Bokulich N.A., Collins T.S., Masarweh C., Allen G., Heymann H., Ebeler S.E., and Mills D.A. 2016. Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. MBio, 7(3): e00631–00616.
Bulgari D., Casati P., Brusetti L., Quaglino F., Brasca M., Daffonchio D., and Bianco A. 2009. Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR. J. Microbiol. 47(4): 393–401.
Chelius M. and Triplett E.W. 2001. The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb. Ecol. 41: 252–263.
Compant S., Mitter B., Colli-Mull J.G., Gangl H., and Sessitsch A. 2011. Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microb. Ecol. 62: 188–197.
Coombe B.G. 1995. Growth stages of the grapevine: adoption of a system for identifying grapevine growth stages. Aust. J. Grape Wine Res. 1: 104–110.
Faust K., Sathirapongsasuti J.F., Izard J., Segata N., Gevers D., Raes J., and Huttenhower C. 2012. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8(7): e1002606.
Gardes M. and Bruns T.D. 1993. ITS primers with enhanced specificity for basidiomycetes — application to the identification of mycorrhizae and rusts. Mol. Ecol. 2: 113–118.
Godálová Z., Kraková L., Puškárová A., Bučková M., Kuchta T., Piknová L., and Pangallo D. 2016. Bacterial consortia at different wine fermentation phases of two typical Central European grape varieties: Blaufränkisch (Frankovka modrá) and Grüner Veltliner (Veltlínske zelené). Int. J. Food Microbiol. 217: 110–116.
Grangeteau C., Gerhards D., Rousseaux S., Von Wallbrunn C., Alexandre H., and Guilloux-Benatier M. 2015. Diversity of yeast strains of the genus Hanseniaspora in the winery environment: What is their involvement in grape must fermentation? Food Microbiol. 50: 70–77.
Holt H.E., Francis I.L., Field J., Herderich M.J., and Iland P.G. 2008. Relationships between berry size, berry phenolic composition and wine quality scores for Cabernet Sauvignon (Vitis vinifera L.) from different pruning treatments and different vintages. Aust. J. Grape Wine Res. 14(3): 191–202.
Knight S., Klaere S., Fedrizzi B., and Goddard M.R. 2015. Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir. Sci. Rep. 5: 14233.
Leveau J.H.J. and Tech J.J. 2011. Grapevine microbiomics: bacterial diversity on grape leaves and berries revealed by high-throughput sequence analysis of 16S rRNA Amplicons. Acta Hortic. 905: 31–42.
Li S.S., Cheng C., Li Z., Chen J.Y., and Yan B. 2010. Yeast species associated with wine grapes in China. Int. J. Food Microbiol. 138(1): 85–90.
Lindow S.E. and Leveau J.H.J. 2002. Phyllosphere microbiology. Curr. Opin. Biotechnol. 13(3): 238–243.
Lonvaud-funel, A. 1999. Lactic acid bacteria in the quality improvement and depreciation of wine. In Lactic acid bacteria: genetics, metabolism and applications. Edited by W. Konings, O.P. Kuipers, and J.H.J. Huis in ’t Veld. Kluwer Academic Publishers, the Netherlands. pp. 317–331.
Martins G., Lauga B., Miot-Sertier A., Lonvaud A., Soulas M.L., Soulas G., and Isabelle M.P. 2013. Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations. PLoS ONE, 8(8): e73013.
Marzano M., Fosso B., Manzaric C., Grieco F., Intranuovo M., Cozzi G., et al. 2016. Complexity and dynamics of the winemaking bacterial communities in berries, musts, and wines from Apulian grape cultivars through time and space. PLoS ONE, 11(6): e0157383.
Motta S.D. and Valente Soares L.M. 2001. Survey of Brazilian tomato products for alternariol, alternariol monomethyl ether, tenuazonic acid and cyclopiazonic acid. Food Addit. Contam. 18(7): 630–634.
Oliveira M., Arenas M., Lage O., Cunha M., and Amorim M.I. 2018. Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions. Lett. Appl. Microbiol. 66(1): 93–102.
Perazzolli M., Antonielli L., Storari M., Puopolo G., Pancher M., Giovannini O., et al. 2014. Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides. Appl. Environ. Microbiol. 80(12): 3585–3596.
Pereira G.E., Gaudillere J.P., Pieri P., Maucourt M., Deborde C., Moing A., and Rolin D. 2006. Microclimate influence on mineral and metabolic profiles of grape berries. J. Agric. Food Chem. 54(18): 6765–6775.
Portillo M.D.C. and Mas A. 2016. Analysis of microbial diversity and dynamics during wine fermentation of Grenache grape variety by high-throughput barcoding sequencing. LWT - Food Sci. Technol. 72: 317–321.
Portillo M.C., Franquès J., Araque I., Reguant C., and Bordons A. 2016. Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain). Int. J. Food Microbiol. 219: 56–63.
Renouf V., Claisse O., and Lonvaud-Funel A. 2005. Understanding the microbial ecosystem on the grape berry surface through numeration and identification of yeast and bacteria. Aust. J. Grape Wine Res. 11(3): 316–327.
Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75(23): 7537–7541.
Segata N., Izard J., Waldron L., Gevers D., Miropolsky L., Garrett W.S., and Huttenhower C. 2011. Metagenomic biomarker discovery and explanation. Genome Biol. 12: R60.
Singh P., Gobbi A., Santoni S., Hansen L.H., This P., and Péros J.P. 2018. Assessing the impact of plant genetic diversity in shaping the microbial community structure of Vitis vinifera phyllosphere in the Mediterranean. Front. Life Sci. 11(1): 35–46.
Singh P., Santoni S., Weber A., This P., and Péros J.P. 2019. Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures. Sci. Rep. UK, 9.
Stander M.A. and Steyn P.S. 2017. Survey of ochratoxin A in South African wines. S. Afr. J. Enol. Vitic. 23(1): 9–13.
Weiss S., Van Treuren W., Lozupone C., Faust K., Friedman J., Deng Y., et al. 2016. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 10(7): 1669–1681.
West E.R., Cother E.J., Steel C.C., and Ash G.J. 2010. The characterization and diversity of bacterial endophytes of grapevine. Can. J. Microbiol. 56(3): 209–216.
Whipps J.M., Hand P., Pink D., and Bending G.D. 2008. Phyllosphere microbiology with special reference to diversity and plant genotype. J. Appl. Microbiol. 105(6): 1744–1755.
Zhang B.G., Bai Z.H., Hoefel D., Tang L., Wang X.Y., Li B.J., and Li Z.M. 2009. The impacts of cypermethrin pesticide application on the non-target microbial community of the pepper plant phyllosphere. Sci. Total Environ. 407: 1915–1922.
Zhang J., Wang E.T., Singh R.P., Guo C., Shang Y., Chen J., and Liu C. 2019. Grape berry surface bacterial microbiome: impact from the varieties and clones in the same vineyard from central China. J. Appl. Microbiol. 126(1): 204–214.
Zhang S.W., Chen X., Zhong Q.D., Huang Z.B., and Bai Z.H. 2017. Relations among epiphytic microbial communities from soil, leaves and grapes of the grapevine. Front. Life Sci. 10(1): 73–83.

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cover image Canadian Journal of Microbiology
Canadian Journal of Microbiology
Volume 66Number 11November 2020
Pages: 653 - 663


Received: 28 October 2019
Revision received: 27 January 2020
Accepted: 14 February 2020
Accepted manuscript online: 8 June 2020
Version of record online: 8 June 2020


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Key Words

  1. grape leaves
  2. bacterial 16S rRNA gene
  3. fungal internal transcribed spacer (ITS)
  4. high-throughput sequencing


  1. feuilles de vigne
  2. gène de l’ARNr 16S bactérien
  3. espaceur interne transcrit (ITS) fongique
  4. séquençage à haut débit



Shiwei Zhang*
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China.
Yuan Wang*
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China.
Xi Chen
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China.
Bingjian Cui
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China.
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China.
College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
Guoqiang Zhuang [email protected]
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China.
College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.


These authors contributed equally to this work.
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