COMMENTARY COMMENTARY Microbial terroir for wine grapes Jack A. Gilberta,b,1, Daniel van der Leliec, and Iratxe Zarraonaindiaa,d presence of phytotoxic contaminants), to pre- aInstitute for Genomic and Systems Biology, Argonne National Laboratory, Argonne, IL 60439; b c venting the growth or activity of plant patho- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637; Center of gens through competition for space and Excellence for Agricultural Biosolutions, FMC Corporation, Research Triangle Park, NC 27703; nutrients, antibiosis, production of hydrolytic and dIkerbasque, Basque Foundation for Science, 48011 Bilbao, Spain enzymes, inhibition of pathogen-produced enzymes or toxins, and through systemic in- duction of plant defense mechanisms (3, 4). The viticulture industry has been selectively and fungi, respectively, from grape must The most widely studied group of plant- growing vine cultivars with different traits (freshly pressed grape juice, containing the associated microorganisms live in the soil (grape size, shape, color, flavor, yield of fruit, skins and seeds) from plants in eight vine- surroundingtherootsorinsidetherootsthem- and so forth) for millennia, and small varia- yards representing four of the major wine selves (endophytes); the interface between tions in soil composition, water management, growing regions in California. The authors roots and soil is often considered the key climate, and the aspect of vineyards have show that the microbiomes (bacterial and point of interaction between a plant and its long been associated with shifts in these traits. fungal taxonomic structure) associated with environment. However, microbes colonizing As such, many different clonal varieties of this early fermentation stage show defined at the root can also migrate through the plant vines exist, even within given grape varieties, biogeography, illustrating that different wine- to colonize aerial tissues, either internally or such as merlot, pinot noir, and chardonnay. growing regions maintain different microbial externally (epiphytes). However, the exact The commensal microbial flora that coexists communities, with some influences from the way in which microbes make this journey is with the plant may be one of the key factors grape variety and the year of production. poorly understood (3). Many microorgan- that influence these traits. To date, the role of Bacteria and fungi live in complex coasso- isms that actively colonize these tissues have microbes has been largely ignored, outside of ciations with plants and have important roles multiple metabolic activities that support plant health, either by promoting growth or microbial pathogens, mainly because the in shaping the quality of the soil and in suppressing disease-causing pathogens; how- technologies did not exist to allow us to look promoting the productivity and health of the ever, disassociating these two traits and in any real depth or breadth at the commu- plant itself. As with the human microbiome assigning activities to specifictaxaisoften nity structure of the multitudes of bacterial (2), the plant microbiome has both direct and problematic because of the numerous code- and fungal species associated with each plant. indirect relationships with its host, from trans- pendent interactions between the many dif- In PNAS, Bokulich et al. (1) used next-gen- forming the availability of organic matter and ferent species. These beneficial organisms eration sequencing of 16S rRNA and internal essential nutrients in the soil, including nitro- have a very broad phylogeny, but several of fi transcribed spacer ribosomal sequence to de- gen xation, mitigating the impact of envi- them have been well studied, including bac- termine the relative abundances of bacteria ronmental stresses (such as drought or the terial genera, such as Azospirillum, Bacillus, etc. (5). In Fig. 1 we highlight some micro- organisms that have shown association with the different tissues. Traditionally, to overcome reduced eco- nomic yields caused by disease, viticulturists inoculate the plants with potential antago- nists as a biological control for grapevine pathogens (3). However, as our understand- ing of bacterial and fungal influence on plant characteristics improves, it is possible that microbes could be added to affect other traits. It is possible that different bacteria associated with different tissues could influence the fla- vor and productivity of grapes, which could impact the organoleptic characteristics of wine. The well-known influence of bacteria and fungi in the wine fermentation, particu- larly lactic acid bacteria and yeasts, has led to the development of commercial products, including specificfungaltaxatoimprovewine fermentation processes and flavor. However,

Author contributions: J.A.G., D.v.d.L., and I.Z. wrote the paper.

The authors declare no conflict of interest. See companion article on page E139. Fig. 1. Diagrammatic representation of some of characteristic bacteria and fungi known to show associations with 1To whom correspondence should be addressed. E-mail: the different tissues of Vitis vinifera. [email protected].

www.pnas.org/cgi/doi/10.1073/pnas.1320471110 PNAS | January 7, 2014 | vol. 111 | no. 1 | 5–6 Downloaded by guest on September 26, 2021 the role of prokaryotes was considered to be how sites for agriculture are chosen, or indeed impact which taxa are found in which regions limited to the malolactic fermentation processes, how they could be manipulated by pro- (6). Although it is expected that climatic factors or even to be only detrimental to fermentation biotics designed to establish the “right” could constrain the biogeographic distribution (6). However, metagenomic studies are reveal- bacterial species that can improve soil qual- of grape microbiome, the soil characteristics ing that grapes can harbor a more diverse mi- ity and, hence, crop productivity. This (e.g., availability of nutrients for the plant) crobial community than previously anticipated, practice can also be used to help improve and soil structure still has a great impact on for example in botrytized wine ferments (7). the wine terroir or even reproduce those constraining the microbiota that could colo- Bokulich et al. (1) focus on the bacteria terroirs in sites a priori not suitable for nize the remaining plant niches (11–14). associated with grapes by directly sampling generating a wine with such characteristics. The differences in soil microbiota could the initial stage of fermentation, the wine However, to be able to exploit the vine also generate differential responses in the must. Although not previously determined, microbiome we need to make considerable plant itself, by triggering the expression of i it stands to reason that the same physical and advances, including: ( ) a more comprehen- different compounds or activating defense chemical parameters that determine which sive characterization of the vine-associated mechanisms that could eventually modulate ii plants can grow where (e.g., temperature, hu- microbiota, ( ) an elucidation of the func- the activity and abundances of other microbes midity, precipitation, soil nutrient concentra- tional potential of these communities, and associated with the plant. Elucidating these tions, solar radiation, and so forth) would (iii) a comprehensive analysis of the genomes fi characteristics is essential to enable more also have a signi cant impact on the bioge- and regulatory elements associated with each directed vineyard establishment; this is pred- ography of the bacteria and fungi in the eco- microbe in the context of its interacting role icated on a better understanding of the mecha- systems. The biogeographic regionalization of with the plant and in the fermentation stages nismsthatselectwhichorganismsassociate microbial taxa associated with the grapes begs of wine production. To make these feasible with plant tissues and the environmental thequestion:Wheredothetaxacomefrom? it is necessary to focus both amplicon and factors shaping their complex community For example, is this biogeography based on metagenomic sequencing on a comprehensive composition. Although the biogeography of the native microbial biogeography of the soils assessment of the microbiota of the epiphytes grape-associated taxa is potentially impor- or water in the different regions (8), or do the and endophytes on the grapevine as a whole, tant (1), the factors that shape endophyte plants themselves select for a different micro- including leaves, flowers, roots, stems, and in- biota based on their physiological response to deed the very soil in which the plants are populations in other tissues may be more important, in that these taxa are likely to play different climatic and soil edaphic variables? growing. The microbes associated with grapes fi Up to now, studies of grape microbiota bio- are not isolated from the rest of the grapevine ahighlysigni cant role in changing the pro- geography have mostly focused on the distri- niche, and indeed the roots may be the pri- ductivity, chemical properties, and pathogen bution of yeast, where Saccharomyces cerevi- mary source of colonization, and the transmis- defensefortheplant.Althoughmicroorgan- siae populations have been shown to exhibit sion of these bacteria through the host may be isms associated with grapes are undoubtedly periodic fluctuation in their presence or ab- necessary to elicit the favorable wine character- included in the initial fermentation steps, the sence across different regions, influenced by istics that are sought after. Alternatively, it is bacteria or fungi associated with other plant — — climatic factors and vineyard age and size (9). feasible that the bacteria and fungi only play tissues and indeed the soil may play a fi fl fl Setati et al. (10) studied the spatial distribution a role in the fermentate through release of highly signi cant role in in uencing the a- of fungal microbial communities within and secondary metabolites, and that they have little vor, color, and quality of the final product; between vineyards from the same terroir, find- direct influence on the grape chemistry. however, this still remains to be shown. ing higher yeast heterogeneity on grape sam- Therefore, as well as soil-derived microbial There is a long way to go, but such work ples collected at different points inside individ- colonization through root endophytes, there provides us tantalizing evidence that the bio- ual vineyards than between vineyards with are additional routes for colonization, including geographic characteristics of terrestrial micro- very contrasting farming strategies, which they soil dust contamination by rain splash, or from organisms may indeed lead to regionalized attribute to myriad microclimates within a vine- people during harvesting, or other agricultural properties associated with valuable crops. yard created by differential shading of grapes practices; indeed, even the phyllosphere (leaf Future work will build on this ecological by leaves, and the aspect of each grape cluster. zone) of nearby plants may transfer microbial observation to change the face of agriculture, Bokulich et al. (1) surveyed 273 grape taxa through aerial or insect transportation, much as the human microbiome is changing musts from two vintages of Chardonnay, which suggests even the local biodiversity may thefaceofmedicine. Zinfandel, and Cabernet Sauvignon, dem- onstrating categorically that these grape- surface microbial communities were signif- 1 Bokulich NA, Thorngate JH, Richardson PM, Mills DA (2014) Microbial 8 Martiny JB, et al. (2006) Microbial biogeography: Putting icantly, albeit rather weakly, different be- biogeography of wine grapes is conditioned by cultivar, vintage, and microorganisms on the map. Nat Rev Microbiol 4(2):102–112. tween regions. However, the authors also climate. Proc Natl Acad Sci USA 111:E139–E148. 9 Barata A, Malfeito-Ferreira M, Loureiro V (2012) The microbial show that the degree of significant differenti- 2 Human Microbiome Project Consortium (2012) Structure, function and ecology of wine grape berries. Int J Food Microbiol 153(3): – diversity of the healthy human microbiome. Nature 486(7402):207 214. 243–259. ation between regions is increased dramati- 3 Compant S, Mitter B, Colli-Mull JG, Gangl H, Sessitsch A (2011) 10 Setati ME, Jacobson D, Andong UC, Bauer F (2012) The fl fi cally when they look at the biogeography Endophytes of grapevine owers, berries, and seeds: identi cation of vineyard yeast microbiome, a mixed model microbial map. PLoS fi cultivable bacteria, comparison with other plant parts, and within a grape variety of vintage. This nding ONE 7(12):e52609. visualization of niches of colonization. Microb Ecol 62(1):188–197. suggests that other factors also play a signifi- 11 Lundberg DS, et al. (2012) Defining the core Arabidopsis 4 Mastretta C, et al. (2006) Endophytic bacteria and their potential thaliana root microbiome. Nature 488(7409):86–90. cant role, including host genotype, and there- application to improve the phytoremediation of contaminated 12 Martins G, et al. (2013) Characterization of epiphytic bacterial fore phenotype (grape variety), and local and environments. Biotechnol Genet Eng Rev 23:175–207. communities from grapes, leaves, bark and soil of grapevine plants 5 Berg G (2009) Plant-microbe interactions promoting plant growth interannual climate variation (vintage). grown, and their relations. PLoS ONE 8(8):e73013. and health: Perspectives for controlled use of microorganisms in 13 Sabate J, Cano J, Esteve-Zarzoso B, Guillamón JM (2002) Isolation Bringing microbial ecology into agriculture agriculture. Appl Microbiol Biotechnol 84(1):11–8. fi presents a golden opportunity to provide 6 Leveau JHJ, Tech JJ (2011) Grapevine microbiomics: Bacterial and identi cation of yeasts associated with vineyard and winery by mechanistic understanding for observations diversity on grape leaves and berries revealed by high-throughput RFLP analysis of ribosomal genes and mitochondrial DNA. – that farmers and viticulturists have been sequence analysis of 16S rRNA amplicons. Acta Hortic 905(2):31–42. Microbiol Res 157(4):267 274. 7 Bokulich NA, Joseph CM, Allen G, Benson AK, Mills DA (2012) 14 Bulgarelli D, Schlaeppi K, Spaepen S, Ver Loren van Themaat E, making for millennia. This is an essential step Next-generation sequencing reveals significant bacterial diversity of Schulze-Lefert P (2013) Structure and functions of the bacterial forward in that it can help to revolutionize botrytized wine. PLoS ONE 7(5):e36357. microbiota of plants. Annu Rev Plant Biol 64:807–838.

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