Terroir 2020 banner
IVES 9 IVES Conference Series 9 Microbial metagenomics of vineyard soils and wine terroir

Microbial metagenomics of vineyard soils and wine terroir

Abstract

Aims: The aims of this study were to (i) characterize bacterial and fungal communities in selected Australian vineyard soils and (ii) determine if the soil microbiome composition and diversity varied between different zones within a vineyard. 

Rationale: The soil on which vines are grown has been suggested to impart a unique quality to the grapes and wine due to the physiological responses of the vines to soil type, topography and climatic conditions, in addition to their viticultural management. The influence of bacteria and fungi in wine fermentation is well known but little is known about the effect of soil microbes, other than microbial pathogens, on grape composition or their role in vintage or site (terroir) impacts on grape composition. 

Methods and Results: We investigated the potential relationships between soil microbiome composition measured using a metagenomic approach (16S rRNA and ITS region amplicon and metagenomic sequencing) and inherent spatial variation in grape metabolite composition, specifically the concentration of the ‘impact aroma compound’ rotundone in Shiraz grapes (Vitis vinifera L.) grown in vineyards in the Grampians region of Victoria and in the Adelaide Hills in South Australia. Results from the metagenomics analysis of surface soil samples collected from the previously identified ‘rotundone zones’ in a vineyard indicated marked differences in the genetic diversity and composition of the soil bacterial and fungal microbiomes of these zones. Soils from the high rotundone zone exhibited higher diversity of bacteria, but lower diversity of fungi, compared to the soils in the Low rotundone zone. In addition, the network analysis of the microbial community in the High rotundone zone soils appeared well structured, especially with respect to the bacterial community, compared to that in the Low rotundone zone soils. A few specific taxa/groups of microorganisms e.g. Acidobacteria-GP4 and GP7, Rhizobiales, Burkholdiales, Gaiellales, Alphaproteobacteria and the Nectriaceae and Tremellaceae families of fungi, were associated with the rotundone-based variation. Short-term mulching effects did not seem to mask the rotundone zone-based variation. Predictive functional profiling using 16S rRNA marker gene sequences, FAPROTAX-based analysis indicated differences in functional categories such as manganese oxidation, methylotrophy, methanotrophy, oxidation of sulfur compounds. These findings suggest that the observed taxonomic variation needs to be translated into functional aspects of soil microbiome before mechanistic links to rotundone concentrations can be established.

Conclusions:  

Distinct differences in soil bacterial and fungal community composition and structure in different zones within the same vineyard are associated with different propensities for grape berry rotundone concentration. Also, high rotundone zone soil exhibited a well-connected microbial community network by comparison with the Low rotundone zone soil.

Significance and impact of the Study: These findings of a systematic rotundone zone-based variation in soil microbiomes paves the way to bring together understanding of microbial ecology and viticultural management for improved grape composition and wine flavour (terroir).

DOI:

Publication date: March 17, 2021

Issue: Terroir 2020

Type: Video

Authors

Vadakattu Gupta1, Rob Bramley1, Paul Greenfield2, Julian Yu3, Markus Herderich4

1CSIRO Ag & Food, Urrbrae, SA, Australia 
2CSIRO Energy, North Ryde, NSW, Australia 
3Arizona State University, Arizona, USA 
4AWRI, Urrbrae, SA, Australia

Contact the author

Keywords

Rotundone, microbiome diversity, bacteria, fungi, grapes

Tags

IVES Conference Series | Terroir 2020

Citation

Related articles…

Aromatic maturity is a cornerstone of terroir expression in red wine

Harvesting grapes at adequate maturity is key to the production of high-quality red wines. Enologists and wine makers define several types of maturity, including technical maturity, phenolic maturity and aromatic maturity. Technical maturity and phenolic maturity are relatively well documented in the scientific literature, while articles on aromatic maturity are scarcer. This is surprising, because aromatic maturity is, without a doubt, the most important of the three in determining wine quality and typicity (including terroir expression). Optimal terroir expression can be obtained when the different types of maturity are reached at the same time, or within a short time frame. This is more likely to occur when the ripening takes place under mild temperatures, neither too cool, nor too hot. Aromatic expression in wine can be driven, from low to high maturity, by green, herbal, fresh fruit, ripe fruit, jammy fruit, candied fruit or cooked fruit aromas. Green and cooked fruit aromas are not desirable in red wines, while the levels of other aromatic compounds contribute to the typicity of the wine in relation to its origin. Wines produced in cool climates, or on cool soils in temperate climates, are likely to express herbal or fresh fruit aromas; while wines produced under warm climates, or on warm soils in temperate climates, may express ripe fruit, jammy fruit or candied fruit aromas. Growers can optimize terroir expression through their choice of grapevine variety. Early ripening varieties perform better in cool climates and late ripening varieties in warm climates. Additionally, maturity can be advanced or delayed by different canopy management practices or training systems.

Soil quality in Beaujolais vineyard. Importance of pedology and cultural practices

A pedological study was carried out from 2009 to 2017 in Beaujolais vineyard, to improve physical and chemical knowledge of soils. It was completed in 2016 and 2017 by the current study, dealing with microbial aspects, in order to build a reference frame for improved advice in soil management. Microbial biomass was measured on representative plots of the six most common soil types identified in Beaujolais and, for each soil type, on plots with different levels of the main impacting parameters: total organic carbon, pH, cation exchange capacity, extractable copper. A total of 59 soil samples were collected. Confirming the results of various trials carried out in Beaujolais over the past 20 years, the results of the present study showed that the soils were still alive, but exhibited a large variability of biological parameters, which appeared dependant on both pedological and anthropic factors. Therefore, a good interpretation of biological parameters and advice for vine growers must rely on a pedologically-based referential with differentiated main driving factors. For example, the control of pH is of primary importance in granitic soils and in no way organic matter addition can improve soil quality if pH is too low. Conversely, in calcareous soils, biological parameters are more directly affected by direct or indirect (cover crops for example) inputs of organic matter. The use of biological parameters, such as microbial biomass, is of great potential value to improve advice on agro-viticultural practices (soil management, fertilization, liming, etc.), basis of a sustainable wine production on fragile soils.

Copper contamination in vineyard soils of Bordeaux: spatial risk assessment for the replanting of vines and crops

Copper (Cu) is widely and historically used in viticulture as a fungicide against mildew. Cu has a strong affinity for soil organic matter and accumulates in topsoil horizons. Thus, Cu may negatively affect soil organisms and plants, consequently reducing soil fertility and productivity. The Bordeaux vineyards have the largest vineyard surfaces (26%) within French controlled appellation and a great proportion of French wine production (around 5 million hl per year). Considering the local context of vineyard surfaces decreasing (vine uprooting) and possible new crop plantation, the issue of Cu potential toxicity rises. Therefore, the aims of this work are firstly to evaluate the Cu contamination in vineyard soils of Bordeaux, secondly to produce a risk assessment map for new vine or crop plantation. We used soil analyses from several local studies to build a database with 4496 soil horizon samples. The database was enhanced by means of pedotransfer functions in order to estimate the bioaccessible (EDTA-extractable) Cu in soils of samples without measurements. From this database, 1797 georeferenced samples with CuEDTA concentrations in the topsoil (0-50 cm depth) were used for kriging interpolation in order to produce the spatial distribution map of CuEDTA in vineyard soils. Then, the spatial distribution of Cu was crossed with vine uprooting surfaces and municipality boundaries. CuEDTAconcentrations ranged from 0.52 to 459 mg/kg and showed clear anomalies. Our results from spatial analysis showed that almost 50% of vineyard soil surfaces have CuEDTA concentrations higher than 30 mg/kg (moderate risk for new plantation) and 20% with concentrations higher than 50 mg/kg (high risk for new plantation). A decision-support map based on municipalities was realised to provide a simple tool to stakeholders concerned by land use management.

Extreme canopy management for vineyard adaptation to climate change: is it a good idea?

Climate change constitutes an enormous challenge for humankind and for all human activities, viticulture not being an exception. Long-term strategic changes are probably needed the most, but growers also need to deal with short-term changes: summers that are getting progressively warmer, earlier harvest dates and higher pH in musts and wines. In the last 10-15 years, a relevant corpus of research is being developed worldwide in order to evaluate to which extent extreme canopy management operations, aimed at reducing leaf area and, thus, limiting the source to sink ratio, could be useful to delay ripening. Although extreme canopy management can result in relevant delays in harvest dates, longer term studies, as well as detailed analysis of their implications on carbohydrate reserves, bud fertility and future yield are desirable before these practices can be recommended.

Impact of climate variability and change on grape yield in Italy

Viticulture is entangled with weather and climate. Therefore, areas currently suitable for grape production can be challenged by climate change. Winegrowers in Italy already experiences the effect of climate change, especially in the form of warmer growing season, more frequent drought periods, and increased frequency of weather extremes.
The aim of this study is to investigate the impact of climate variability and change on grape yield in Italy to provide winegrowers the information needed to make their business more sustainable and resilient to climate change. We computed a specific range of bioclimatic indices, selected by the International Organisation of Vine and Wine (OIV), and correlated them to grape yield data. We have worked in collaboration with some wine consortiums in northern and central Italy, which provided grape yield data for our analysis.
Using climate variables from the E-OBS dataset we investigate how the bioclimatic indices changed in the past, and the impact of this change on grape productivity in the study areas. The climate impact on productivity is also investigated by using high-resolution convection-permitting models (CPMs – 2.2 horizontal resolution), with the purpose of estimating productivity in future emission scenarios. The CPMs are likely the best available option for this kind of impact studies since they allow a better representation of small-scale processes and features, explicitly resolve deep convection, and show an improved representation of extremes. In our study, we also compare CPMs with regional climate models (RCMs – 12 km horizontal resolution) to assess the added value of high-resolution models for impact studies. Further development of our study will lead to assessing the future suitability for vine cultivation and could lead to the construction of a statistical model for future projection of grape yield.