Rootstocks are the link between the soil and scion in grapevines, can provide tolerance to abiotic and biotic stresses, and regulate yield and grape quality. The vascular system of grapevine rootstocks in nurseries is still an underexplored niche for research, despite its potential for hosting beneficial and pathogenic microorganisms. The purpose of this study was to investigate the changes in the composition of fungal communities in 110 Richter and 41 Berlandieri rootstocks at four stages of the grapevine propagation process. Taxonomic analysis revealed that the fungal community predominantly consisted of phylum Ascomycota in all stages of the propagation process. The alpha-diversity of fungal communities differed among sampling times for both rootstocks, with richness and fungal diversity in the vascular system decreasing through the propagation process. The core microbiome was composed of the genera Cadophora, Cladosporium, Penicillium and Alternaria in both rootstocks, while the pathogenic genus Neofusicoccum was identified as a persistent taxon throughout the propagation process. FUNguild analysis showed that the relative abundance of plant pathogens associated with trunk diseases increased towards the last stage in nurseries. Fungal communities in the vascular system of grapevine rootstocks differed between the different stages of the propagation process in nurseries. Numerous genera associated with potential biocontrol activity and grapevine trunk diseases were identified. Understanding the large diversity of fungi in the rootstock vascular tissue and the interactions between fungal microbiota and grapevine will help to develop sustainable strategies for grapevine protection.

Bordeaux Sciences Agro INRAE ISVV SAVE 33140 Villenave d'Ornon France

Departamento de Protección Vegetal Facultad de Agronomía Universidad de la República Montevideo 12900 Uruguay

Faculty of Horticulture Mendeleum Institute of Genetics Mendel University in Brno Valticka 334 69144 Lednice Czech Republic

Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux UMR 5254 Université de Pau et des Pays de l'Adour E2S UPPA CNRS IBEAS Avenue de l'Université 64013 Pau France

Instituto de Ciencias de la Vid y del Vino Consejo Superior de Investigaciones Científicas Universidad de la Rioja Gobierno de La Rioja Ctra LO 20 Salida 13 Finca La Grajera 26071 Logroño Spain

Université de Bordeaux Bordeaux Sciences Agro UMR 1065 SAVE 33175 Gradignan France

Zobrazit více v PubMed

Mudge K., Janick J., Scofield S., Goldschmidt E.E. A history of grafting. Hortic. Rev. 2009;35:437–493. doi: 10.1002/9780470593776.ch9. DOI

Marín D., Armengol J., Carbonell-Bejerano P., Escalona J., Gramaje D., Hernández-Montes E., Intrigliolo D., Martínez-Zapater J., Medrano H., Mirás-Avalos J., et al. Challenges of viticulture adaptation to global change: Tackling the issue from the roots. Aust. J. Grape Wine Res. 2021;27:8–25. doi: 10.1111/ajgw.12463. DOI

Waite H., Whitelaw-Weckert M., Torley P. Grapevine propagation: Principles and methods for the production of high-quality grapevine planting material. N. Z. J. Crop Hortic. Sci. 2015;43:144–161. doi: 10.1080/01140671.2014.978340. DOI

Gramaje D., Armengol J. Fungal trunk pathogens in the grapevine propagation process: Potential inoculum sources, detection, identification, and management strategies. Plant Dis. 2011;95:1040–1055. doi: 10.1094/PDIS-01-11-0025. PubMed DOI

Bokulich N.A., Thorngate J.H., Richardson P.M., Mills D.A. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proc. Natl. Acad. Sci. USA. 2014;111:E139–E148. doi: 10.1073/pnas.1317377110. PubMed DOI PMC

Perazzolli M., Antonielli L., Storari M., Puopolo G., Pancher M., Giovannini O., Pindo M., Pertot I. Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides. Appl. Environ. Microbiol. 2014;80:3585–3596. doi: 10.1128/AEM.00415-14. PubMed DOI PMC

Zarraonaindia I., Owens S.M., Weisenhorn P., West K., Hampton-Marcell J., Lax S., Bokulich N.A., Mills D.A., Martin G., Taghavi S., et al. The soil microbiome influences grapevine-associated microbiota. mBio. 2015;6:e02527-14. doi: 10.1128/mBio.02527-14. PubMed DOI PMC

West E.R., Cother E.J., Steel C.C., Ash G.J. The characterization and diversity of bacterial endophytes of grapevine. Can. J. Microbiol. 2010;56:209–216. doi: 10.1139/W10-004. PubMed DOI

Compant S., Mitter B., Colli-Mull J.G., Gangl H., Sessitsch A. Endophytes of grapevine flowers, berries, and seeds: Identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microb. Ecol. 2011;62:188–197. doi: 10.1007/s00248-011-9883-y. PubMed DOI

Baldan E., Nigris S., Populin F., Zottini M., Squartini A., Baldan B. Identification of culturable bacterial endophyte community isolated from tissues of Vitis vinifera “Glera”. Plant Biosyst. 2014;148:508–516. doi: 10.1080/11263504.2014.916364. DOI

Kraus C., Voegele R.T., Fischer M. Temporal development of the culturable, endophytic fungal community in healthy grapevine branches and occurrence of GTD-associated fungi. Microb. Ecol. 2019;77:866–876. doi: 10.1007/s00248-018-1280-3. PubMed DOI

Faist H., Keller A., Hentschel U., Deeken R. Grapevine (Vitis vinifera) crown galls host distinct microbiota. Appl. Environ. Microbiol. 2016;82:5542–5552. doi: 10.1128/AEM.01131-16. PubMed DOI PMC

Deyett E., Roper M.C., Ruegger P., Yang J., Borneman J., Rolshausen P.E. Microbial landscape of the grapevine endosphere in the context of Pierce’s disease. Phytobiomes. 2017;1:138–149. doi: 10.1094/PBIOMES-08-17-0033-R. DOI

Dissanayake A.J., Purahong W., Wubet T., Hyde K.D., Zhang W., Xu H., Zhang G., Fu C., Liu M., Xing Q., et al. Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine (Vitis vinifera) Fungal Divers. 2018;90:85–107. doi: 10.1007/s13225-018-0399-3. DOI

Eichmeier A., Pečenka J., Peňázová E., Baránek M., Català-García S., León M., Armengol J., Gramaje D. High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity. Fungal Ecol. 2018;36:26–38. doi: 10.1016/j.funeco.2018.07.011. DOI

Bruez E., Vallance J., Gautier A., Laval V., Compant S., Maurer W., Sessitsch A., Lebrun M.H., Rey P. Major changes in grapevine wood microbiota are associated with the onset of esca, a devastating trunk disease. Environ. Microbiol. 2020;22:5189–5206. doi: 10.1111/1462-2920.15180. PubMed DOI

Bruez E., Larignon P., Bertsch C., Robert-Siegwald G., Lebrun M.H., Rey P., Fontaine F. Impacts of sodium arsenite on wood microbiota of Esca-diseased grapevines. J. Fungi. 2021;7:498. doi: 10.3390/jof7070498. PubMed DOI PMC

Martínez-Diz M.P., Eichmeier A., Spetik M., Bujanda R., Díaz-Fernández A., Díaz-Losada E., Gramaje D. Grapevine pruning time affects natural wound colonization by wood-invading fungi. Fungal Ecol. 2020;48:1–13. doi: 10.1016/j.funeco.2020.100994. DOI

Waite H., May P. The effects of hot water treatment, hydration and order of nursery operations on cuttings of Vitis vinifera cultivars. Phytopathol. Mediterr. 2005;44:144–152.

Gramaje D., Úrbez-Torres J.R., Sosnowski M.R. Managing grapevine trunk diseases with respect to etiology and epidemiology: Current strategies and future prospects. Plant Dis. 2018;102:12–39. doi: 10.1094/PDIS-04-17-0512-FE. PubMed DOI

Berlanas C., Ojeda S., López-Manzanares B., Andrés-Sodupe M., Bujanda R., Martínez-Diz M.P., Díaz-Losada E., Gramaje D. Occurrence and diversity of black-foot disease fungi in symptomless grapevine nursery stock in Spain. Plant Dis. 2020;104:94–104. doi: 10.1094/PDIS-03-19-0484-RE. PubMed DOI

Gramaje D., Mostert L., Armengol J. Characterization of Cadophora luteo-olivacea and C. melinii isolates obtained from grapevines and environmental samples from grapevine nurseries in Spain. Phytopathol. Mediterr. 2011;50:112–126. doi: 10.14601/Phytopathol_Mediterr-8723. DOI

Aroca Á., Gramaje D., Armengol J., García-Jiménez J., Raposo R. Evaluation of the grapevine nursery propagation process as a source of Phaeoacremonium spp. and Phaeomoniella chlamydospora and occurrence of trunk disease pathogens in rootstock mother vines in Spain. Eur. J. Plant Pathol. 2010;126:165–174. doi: 10.1007/s10658-009-9530-3. DOI

Berlanas C., Berbegal M., Elena G., Laidani M., Cibriain J.F., Sagües A., Gramaje D. The fungal and bacterial rhizosphere microbiome associated with grapevine rootstock genotypes in mature and young vineyards. Front. Microbiol. 2019;10:1142. doi: 10.3389/fmicb.2019.01142. PubMed DOI PMC

Gramaje D., García-Jiménez J., Armengol J. Field evaluation of grapevine rootstocks inoculated with fungi associated with Petri disease and Esca. Am. J. Enol. Vitic. 2010;61:512–520. doi: 10.5344/ajev.2010.10021. DOI

Alaniz S., García-Jiménez J., Abad-Campos P., Armengol J. Susceptibility of grapevine rootstocks to Cylindrocarpon liriodendri and C. macrodidymum. Sci. Hortic. 2010;125:305–308. doi: 10.1016/j.scienta.2010.04.009. DOI

Eguizábal E. Master’s Thesis. University of La Rioja; La Rioja, Spain: 2018. Development of a Non-Destructive Method to Detected and Identify Fungal Pathogens of Grapevine Planting Material. Publication No. 3382. (In Spanish)

Turenne C.Y., Sanche S.E., Hoban D.J., Karlowsky J.A., Kabani A.M. Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system. J. Clin. Microbiol. 1999;37:1846–1851. doi: 10.1128/JCM.37.6.1846-1851.1999. PubMed DOI PMC

White T.J., Bruns T., Lee S.H., Taylor J.W. Amplification and direct sequencing of fungal ribosomal RNA genes for phy-logenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., White T.J., editors. PCR Protocols: A Guide to Methods and Applications. Academic Press; San Diego, CA, USA: 1990. pp. 315–322. DOI

Chong J., Liu P., Zhou G., Xia J. Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat. Protoc. 2020;15:799–821. doi: 10.1038/s41596-019-0264-1. PubMed DOI

Baksi K.D., Kuntal B.K., Mande S.S. ‘TIME’: A web application for obtaining insights into microbial ecology using longitudinal microbiome data. Front. Microbiol. 2018;9:36. doi: 10.3389/fmicb.2018.00036. PubMed DOI PMC

Caporaso J.C., Lauber C.L., Costello E.K., Berg-Lyons D., Gonzalez A., Stombaugh J., Knights D., Gajer P., Ravel J., Fierer N., et al. Moving pictures of the human microbiome. Genome Biol. 2011;12:R50. doi: 10.1186/gb-2011-12-5-r50. PubMed DOI PMC

Nguyen N.H., Song Z., Bates S.T., Branco S., Tedersoo L., Menke J., Schilling J.S., Kennedy P.G. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 2016;20:241–248. doi: 10.1016/j.funeco.2015.06.006. DOI

Nguyen N.H., Smith D., Peay K., Kennedy P. Parsing ecological signal from noise in next generation amplicon sequencing. New Phytol. 2015;205:1389–1393. doi: 10.1111/nph.12923. PubMed DOI

Ollat N., Peccoux A., Papura D., Esmenjaud D., Marguerit E., Tandonnet J.P., Bordenave L., Cookson S.J., Barrieu F., Rossdeutsch L., et al. Rootstocks as a component of adaptation to environment. In: Gerós H., Chaves M.M., Gil H.M., Delrot S., editors. Grapevine in a Changing Environment. John Wiley; Chichester, UK: 2016. pp. 68–108.

Deyett E., Rolshausen P.E. temporal dynamics of the sap microbiome of grapevine under high Pierce’s disease pressure. Front. Plant Sci. 2019;10:1246. doi: 10.3389/fpls.2019.01246. PubMed DOI PMC

Deyett E., Rolshausen P.E. Endophytic microbial assemblage in grapevine. FEMS Microbiol. Ecol. 2020;96:fiaa053. doi: 10.1093/femsec/fiaa053. PubMed DOI

Martínez-Diz M.P., Andrés-Sodupe M., Bujanda R., Díaz-Losada E., Eichmeier A., Gramaje D. Soil-plant compartments affect fungal microbiome diversity and composition in grapevine. Fungal Ecol. 2019;41:234–244. doi: 10.1016/j.funeco.2019.07.003. DOI

Fan Y., Gao L., Chang P., Li Z. Endophytic fungal community in grape is correlated to foliar age and domestication. Ann. Microbiol. 2020;70:1–8. doi: 10.1186/s13213-020-01574-9. DOI

Knapp D.G., Lázár A., Molnár A., Vajna B., Karácsony Z., Váczy K.Z., Kovács G.M. Above-ground parts of white grapevine Vitis vinifera cv. Furmint share core members of the fungal microbiome. Environ. Microbiol. Rep. 2021;13:509–520. doi: 10.1111/1758-2229.12950. PubMed DOI

Liu D., Howell K. Community succession of the grapevine fungal microbiome in the annual growth cycle. Environ. Microbiol. 2021;23:1842–1857. doi: 10.1111/1462-2920.15172. PubMed DOI

Radić T., Likar M., Hančević K., Regvar M., Čarija M., Zdunić G. Root-associated community composition and co-occurrence patterns of fungi in wild grapevine. Fungal Ecol. 2021;50:101034. doi: 10.1016/j.funeco.2020.101034. DOI

Carbone M.J., Alaniz S., Mondino P., Gelabert M., Eichmeier A., Tekielska D., Bujanda R., Gramaje D. Drought influences fungal community dynamics in the grapevine rhizosphere and root microbiome. J. Fungi. 2021;7:686. doi: 10.3390/jof7090686. PubMed DOI PMC

Casieri L., Hofstetter V., Viret O., Gindro K. Fungal communities living in the wood of different cultivars of young Vitis vinifera plants. Phytopathol. Mediterr. 2009;48:73–83.

Hofstetter V., Buyck B., Croll D., Viret O., Couloux A., Gindro K. What if esca disease of grapevine were not a fungal disease? Fungal Divers. 2012;54:51–67. doi: 10.1007/s13225-012-0171-z. DOI

Bruez E., Vallance J., Gerbore J., Lecomte P., Da Costa J.-P., Guérin-Dubrana L., Rey P. Analyses of the temporal dynamics of fungal communities colonizing the healthy wood tissues of esca leaf-symptomatic and asymptomatic vines. PLoS ONE. 2014;9:e95928. doi: 10.1371/journal.pone.0095928. PubMed DOI PMC

Fischer M., Schneider P., Kraus C., Molnar M., Dubois C., d’Aguiar D., Haag N. Grapevine trunk disease in German viticulture: Occurrence of lesser known fungi and first report of Phaeoacremonium viticola and P. fraxinopennsylvanicum. Vitis. 2016;55:145–156. doi: 10.5073/vitis.2016.55.145-156. DOI

Gomzhina M.M., Gasich E.L., Khlopunova L.B., Gannibal P.B. Paraphoma species associated with Convolvulaceae. Mycol. Prog. 2020;19:185–194. doi: 10.1007/s11557-020-01558-8. DOI

Pinto C., dos Santos Custodio V., Nunes M., Songy A., Rabenoelina F., Courteaux B., Clement C., Catarina-Gomes A., Fontaine F. Understand the potential role of Aureobasidium pullulans, a resident microorganism from grapevine, to prevent the infection caused by Diplodia seriata. Front. Microbiol. 2018;9:3047. doi: 10.3389/fmicb.2018.03047. PubMed DOI PMC

Munkvold G.P., Marois J.J. Efficacy of natural epiphytes and colonisers of grapevine pruning wounds for biological control of Eutypa dieback. Phytopathology. 1993;83:624–629. doi: 10.1094/Phyto-83-624. DOI

Maldonado-González M.M., Martínez-Diz M.P., Andrés-Sodupe M., Bujanda R., Díaz-Losada E., Gramaje D. Quantification of Cadophora luteo-olivacea from grapevine nursery stock and vineyard soil using droplet digital PCR. Plant Dis. 2020;104:2269–2274. doi: 10.1094/PDIS-09-19-2035-RE. PubMed DOI

Halleen F., Mostert L., Crous P.W. Pathogenicity testing of lesser-known vascular fungi of grapevines. Australas. Plant Pathol. 2007;36:277–285. doi: 10.1071/AP07019. DOI

Úrbez-Torres J.R., Leavitt G.M., Guerrero J.C., Guevara J., Gubler W.D. Identification and pathogenicity of Lasiodiplodia theobromae and Diplodia seriata, the causal agents of Bot canker diseases of grapevines in Mexico. Plant Dis. 2008;92:519–529. doi: 10.1094/PDIS-92-4-0519. PubMed DOI

Úrbez-Torres J.R., Gubler W.D. Pathogenicity and epidemiology of Botryosphaeriaceae from grapevines in California. Plant Dis. 2009;93:584–592. doi: 10.1094/PDIS-93-6-0584. PubMed DOI

Spagnolo A., Marchi G., Peduto F., Phillips A., Surico G. Detection of Botryosphaeriaceae species within grapevine woody tissues by nested PCR, with particular emphasis on the Neofusicoccum parvum/N. ribis complex. Eur. J. Plant Pathol. 2011;129:485–500. doi: 10.1007/s10658-010-9715-9. DOI

Aroca A., García-Figueres F., Bracamonte L., Luque J., Raposo R. A survey of trunk disease pathogens within rootstocks of grapevines in Spain. Eur. J. Plant Pathol. 2006;115:195–202. doi: 10.1007/s10658-006-9008-5. DOI

Waite H., Gramaje D., Whitelaw-Weckert M., Torley P., Hardie J. Soaking grapevine cuttings in water: A potential source of cross contamination by micro-organisms. Phytopathol. Mediterr. 2013;52:359–368.

Agustí-Brisach C., Armengol J. Black-foot disease of grapevine: An update on taxonomy, epidemiology and management strategies. Phytopathol. Mediterr. 2013;52:245–261.

Halleen F., Crous P.W., Petrini O. Fungi associated with healthy grapevine cuttings in nurseries, with special reference to pathogens involved in the decline of young vines. Australas. Plant Pathol. 2003;32:47–52. doi: 10.1071/AP02062. DOI

Agustí-Brisach C., Gramaje D., García-Jiménez J., Armengol J. Detection of black-foot disease pathogens in the grapevine nursery propagation process in Spain. Eur. J. Plant Pathol. 2013;137:103–112. doi: 10.1007/s10658-013-0221-8. DOI

Armengol J., Gramaje D. Soilborne fungal pathogens affecting grapevine rootstocks: Current status and future prospects. Acta Hortic. 2016;1136:235–238. doi: 10.17660/ActaHortic.2016.1136.32. DOI

Billones-Baaijens R., Jaspers M., Allard A., Hong Y., Ridgway H., Jones E. Management of Botryosphaeriaceae species infection in grapevine propagation materials. Phytopathol. Mediterr. 2015;54:355–367.

Probst C., Jones E.E., Ridgway H.J., Jaspers M.V. Cylindrocarpon black foot in nurseries-two factors that can increase infection. Australas. Plant Pathol. 2012;41:157–163. doi: 10.1007/s13313-011-0103-5. DOI

Whitelaw-Weckert M., Rahman L., Appleby L.M., Hall A., Clark A.C., Waite H., Hardie W.J. Co-infection by Botryosphaeriaceae and Ilyonectria spp. fungi during propagation causes decline of young grafted grapevines. Plant Pathol. 2013;62:1226–1237. doi: 10.1111/ppa.12059. DOI

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