Bokulich, N. A. et al. Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. MBio, https://doi.org/10.1128/mBio.00631-16 (2016).
Zohary, D. The Domestication of the Grapevine Vitis Vinifera L. in the Near East (Chapter 2) in The Origins and Ancient History of Wine (eds McGovern, P. E., Katz, S. H. & Fleming, S. J.) 21–28. (Routledge, 2003).
Whalen, P. ‘Insofar as the ruby wine seduces them’: cultural strategies for selling wine in inter-war Burgundy. Contemp. Eur. Hist. 18, 67–98 (2009).
Østerlie, M. & Wicklund, T. In Nutritional and Health Aspects of Food in Nordic Countries (eds Bar, E., Wirtanen, G. & Veslemøy Andersen, V.) Ch. 2 (Elsevier Inc., 2018).
Planète Terroirs. The future needs terroirs. https://planeteterroirs.org/ (2010).
California Wine-Growing Regions, https://discovercaliforniawines.com/wine-map-winery-directory/
Agricultura, M. D. E. & Ambiente. Compendio informativo en relación con las DOPs/IGPs y terminos tradicionales de vino, las indicaciones geograficas de bebidas espirituosas, y las indicaciones geograficas de productos vitivinicolas aromatizados. https://www.mapa.gob.es/es/alimentacion/temas/calidad-diferenciada/relaciondisposicionesdopseigpsdevinosbbeevinosaromatiz_tcm30-432336.pdf (2016).
Ballantyne, D., Terblanche, N. S., Lecat, B. & Chapuis, C. Old world and new world wine concepts of terroir and wine: perspectives of three renowned non-French wine makers. J. Wine Res. 30, 122–143 (2019).
OIV. Resolution OIV/VITI 333/2010, definition of vitivinicultural “terroir”. https://www.oiv.int/public/medias/379/viti-2010-1-en.pdf (2010).
Belda, I., Zarraonaindia, I., Perisin, M., Palacios, A. & Acedo, A. From vineyard soil to wine fermentation: microbiome approximations to explain the ‘terroir’ Concept. Front. Microbiol. 8, 1–12 (2017).
Zarraonaindia, I. et al. The soil microbiome influences grapevine-associated microbiota. MBio 6, 1–10 (2015).
Google Scholar
Burns, K. N. et al. Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: differentiation by vineyard management. Soil Biol. Biochem. 103, 337–348 (2016).
Google Scholar
Bokulich, N. A., Joseph, C. M. L., Allen, G., Benson, A. K. & Mills, D. A. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLoS ONE 7, 3–12 (2012).
Portillo, M., del, C., Franquès, J., Araque, I., Reguant, C. & Bordons, A. Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain). Int. J. Food Microbiol. 219, 56–63 (2016).
Mezzasalma, V. et al. Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production. PLoS ONE 12, 1–20 (2017).
Hermans, S. M. et al. Using soil bacterial communities to predict physico-chemical variables and soil quality. Microbiome 8, 1–13 (2020).
OIV. Functional biodiversity in the vineyard. https://www.oiv.int/public/medias/6367/functional-biodiversity-in-the-vineyard-oiv-expertise-docume.pdf (2018).
Ortiz-Álvarez, R. et al. Network properties of local fungal communities reveal the anthropogenic disturbance consequences of farming practices in vineyard soils. mSystems 6, e00344-21 (2021).
Knight, S., Klaere, S., Fedrizzi, B. & Goddard, M. R. Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir. Sci. Rep. 5, 1–10 (2015).
Belda, I. et al. Unraveling the enzymatic basis of wine ‘flavorome’: a phylo-functional study of wine related yeast species. Front. Microbiol. 7, 1–13 (2016).
Gilbert, J. A., van der Lelie, D. & Zarraonaindia, I. Microbial terroir for wine grapes. Proc. Natl Acad. Sci. USA 111, 5–6 (2014).
Google Scholar
Belda, I. et al. Microbiomics to Define Wine Terroir (Chapter: 3.32) in Comprehensive Foodomics (Ed. Cifuentes, A.) 438–451 (Elsevier, 2021).
Van der Heijden, M. G. A. & Hartmann, M. Networking in the plant microbiome. PLoS Biol. 14, e1002378 (2016).
Altieri, M. A. In Invertebrate Biodiversity as Bioindicators of Sustainable Landscapes (1999).
Brussaard, L., de Ruiter, P. C. & Brown, G. G. Soil biodiversity for agricultural sustainability. Agric. Ecosyst. Environ. 121, 233–244 (2007).
Nielsen, U. N., Wall, D. H. & Six, J. Soil biodiversity and the environment. Annu. Rev. Environ. Resour. 40, 63–90 (2015).
Wei, Y. J. et al. High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China. PLoS ONE 13, 1–17 (2018).
Liao, J., Xu, Q., Xu, H. & Huang, D. Natural farming improves soil quality and alters microbial diversity in a cabbage field in Japan. Sustain 11, 1–16 (2019).
Yan, J. et al. Plant litter composition selects different soil microbial structures and in turn drives different litter decomposition pattern and soil carbon sequestration capability. Geoderma 319, 194–203 (2018).
Google Scholar
Qiao, Q. et al. The variation in the rhizosphere microbiome of cotton with soil type, genotype and developmental stage. Sci. Rep. 7, 1–10 (2017).
Pacchioni, R. G. et al. Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil. Microbiologyopen 3, 299–315 (2014).
Google Scholar
Ishaq, S. L. et al. Impact of cropping systems, soil inoculum, and plant species identity on soil bacterial community structure. Microb. Ecol. 73, 417–434 (2017).
Google Scholar
Verkley, G. J. M., Da Silva, M., Wicklow, D. T. & Crous, P. W. Paraconiothyrium, a new genus to accommodate the mycoparasite Coniothyrium minitans, anamorphs of Paraphaeosphaeria, and four new species. Stud. Mycol. 50, 323–335 (2004).
Thomma, B. P. H. J. Alternaria spp.: from general saprophyte to specific parasite. Mol. Plant Pathol. 4, 225–236 (2003).
Google Scholar
Mašínová, T. et al. Drivers of yeast community composition in the litter and soil of a temperate forest. FEMS Microbiol. Ecol. 93, 1–10 (2017).
Chen, J., Xu, L., Liu, B. & Liu, X. Taxonomy of Dactylella complex and Vermispora. III. A new genus Brachyphoris and revision of Vermispora. Fungal Divers. 26, 127–142 (2014).
Burns, K. N. et al. Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: differentiation by geographic features. Soil Biol. Biochem. 91, 232–247 (2015).
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 111, 139–148 (2014).
Castañeda, L. E. & Barbosa, O. Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests. PeerJ 5, e3098 (2017).
Google Scholar
Coller, E. et al. Microbiome of vineyard soils is shaped by geography and management. Microbiome 7, 1–15 (2019).
Zhou, J. et al. Wine terroir and the soil bacteria: an amplicon sequencing–based assessment of the Barossa Valley and its sub-regions. Front. Microbiol. 11, 1–15 (2021).
Price, C. A. et al. Testing the metabolic theory of ecology. Ecol. Lett. 15, 1465–1474 (2012).
Google Scholar
Jenerette, G. D., Scott, R. L. & Huxman, T. E. Whole ecosystem metabolic pulses following precipitation events. Funct. Ecol. 22, 924–930 (2008).
Větrovský, T. et al. A meta-analysis of global fungal distribution reveals climate-driven patterns. Nat. Commun. 10, 1–9 (2019).
Arnold, A. E., Maynard, Z., Gilbert, G. S., Coley, P. D. & Kursar, T. A. Are tropical fungal endophytes hyperdiverse? Ecol. Lett. 3, 267–274 (2000).
Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1052–1053 (2014).
Janssen, P. H. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72, 1719–1728 (2006).
Google Scholar
Bintrim, S. B., Donohue, T. J., Handelsman, J., Roberts, G. P. & Goodman, R. M. Molecular phylogeny of Archaea from soil. Proc. Natl Acad. Sci. USA 94, 277–282 (1997).
Google Scholar
Simon, H. M., Dodsworth, J. A. & Goodman, R. M. Crenarchaeota colonize terrestrial plant roots. Environ. Microbiol. 2, 495–505 (2000).
Google Scholar
Buckley, D. H., Graber, J. R. & Schmidt, T. M. Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Appl. Environ. Microbiol. 64, 4333–4339 (1998).
Google Scholar
Ochsenreiter, T., Selezi, D., Quaiser, A., Bonch-Osmolovskaya, L. & Schleper, C. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ. Microbiol. 5, 787–797 (2003).
Google Scholar
Kemnitz, D., Kolb, S. & Conrad, R. High abundance of Crenarchaeota in a temperate acidic forest soil. FEMS Microbiol. Ecol. 60, 442–448 (2007).
Google Scholar
Zhalnina, K. et al. Ca. nitrososphaera and bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Front. Microbiol. 4, 1–13 (2013).
Barata, A., Malfeito-Ferreira, M. & Loureiro, V. The microbial ecology of wine grape berries. Int. J. Food Microbiol. 153, 243–259 (2012).
Google Scholar
Yurkov, A. M. Yeasts of the soil—obscure but precious. Yeast 35, 369–378 (2018).
Google Scholar
Kachalkin, A. V., Abdullabekova, D. A., Magomedova, E. S., Magomedov, G. G. & Chernov, I. Y. Yeasts of the vineyards in Dagestan and other regions. Microbiology 84, 425–432 (2015).
Google Scholar
Čadež, N., Zupan, J. & Raspor, P. The effect of fungicides on yeast communities associated with grape berries. FEMS Yeast Res. 10, 619–630 (2010).
Google Scholar
Comitini, F. & Ciani, M. Influence of fungicide treatments on the occurrence of yeast flora associated with wine grapes. Ann. Microbiol. 58, 489–493 (2008).
Kepler, R. M., Maul, J. E. & Rehner, S. A. Managing the plant microbiome for biocontrol fungi: examples from Hypocreales. Curr. Opin. Microbiol. 37, 48–53 (2017).
Google Scholar
Berendsen, R. L., Pieterse, C. M. J. & Bakker, P. A. H. M. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (2012).
Google Scholar
Liu, D. & Howell, K. Community succession of the grapevine fungal microbiome in the annual growth cycle. Environ. Microbiol. 23, 1842–1857 (2021).
Google Scholar
Delgado-Baquerizo, M. et al. Bacteria found in soil. Science 325, 320–325 (2018).
Egidi, E. et al. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat. Commun. 10, 2369 (2019).
Alonso, A. et al. Looking at the origin: Some insights into the general and fermentative microbiota of vineyard soils. Fermentation 5, 1–15 (2019).
OIV. Resolution OIV-VITI 655-2021. OIV recommendations about valuation and importance of microbial biodiversity in a sustainable vitiviniculture context. https://www.oiv.int/public/medias/8097/en-oiv-viti-655-2021.pdf (2021).
Vishnivetskaya, T. A. et al. Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiol. Ecol. 87, 217–230 (2014).
Google Scholar
Gobbi, A. et al. Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR. PLoS One 14, e0200979 (2019).
Bolyen, E. et al. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ 37, 852–857 (2018).
Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).
Google Scholar
Janssen, S. et al. Phylogenetic placement of exact amplicon sequences improves associations with clinical information. mSystems 3, e00021-18 (2018).
Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 1–17 (2018).
DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).
Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Google Scholar
Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).
Google Scholar
Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005).
Chen, H. VennDiagram: generate high-resolution Venn and Euler plots. R. Packag. Version 1, 1 (2018).
Salonen, A., Salojärvi, J., Lahti, L. & de Vos, W. M. The adult intestinal core microbiota is determined by analysis depth and health status. Clin. Microbiol. Infect. 18, 16–20 (2012).
Google Scholar
Martín-Fernández, J. A., Hron, K., Templ, M., Filzmoser, P. & Palarea-Albaladejo, J. Bayesian-multiplicative treatment of count zeros in compositional data sets. Stat. Model. 15, 134–158 (2015).
Oksanen, J. et al. vegan: community ecology package. R package version 2.4-3. Vienna R Found. Stat. Comput. Sch. (2016).
Wright, M. N. & Ziegler, A. Ranger: a fast implementation of random forests for high dimensional data in C++ and R. J. Stat. Softw. 77, 1–17 (2017).
Team, R. C. R: a language and environment for statistical computing. (2019).
Henschel, A., Anwar, M. Z. & Manohar, V. Comprehensive meta-analysis of ontology annotated 16S rRNA profiles identifies beta diversity clusters of environmental bacterial communities. PLoS Comput. Biol. 11, 1–24 (2015).
Lozupone, C. A. et al. Meta-analyses of studies of the human microbiota. Genome Res. 23, 1704–1714 (2013).
Google Scholar
Lozupone, C. A. & Knight, R. Global patterns in bacterial diversity. Proc. Natl Acad. Sci. USA 104, 11436–11440 (2007).
Google Scholar
Pauvert, C. et al. Bioinformatics matters: the accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline. Fungal Ecol. 41, 23–33 (2019).
Gobbi, A., Kyrkou, I., Filippi, E., Ellegaard-Jensen, L. & Hansen, L. H. Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments. Sci. Rep. 10, 681 (2020).
Engelbrektson, A. et al. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 4, 642–647 (2010).
Google Scholar
Willis, A. D. Rarefaction, alpha diversity, and statistics. Front. Microbiol. 10, 2407 (2019).
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