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…

Diagnosis of soil quality and evaluation of the impact of viticultural practices on soil biodiversity in a vineyard in southwestern France

Viticulture is facing two major changes – climate change and agroecological transition. In both cases, soil quality is seen as a lever to move towards a more sustainable viticulture. However, soil biological quality is little considered in the implementation of viticultural practices. Gascogn’Innov (2017-2022) is an Operational Group funded by the European Innovation Partnership for Agriculture. As such, it brings together winegrowers from the south-west of France, scientists, advisors and technicians, around a project focused on viticultural soil biological functioning and the design of technical routes more respectful toward soil heritage. To achieve this, the project aims to acquire references on the impact of viticultural practices on soil biology from a dynamic way, and to test a methodology to integrate information provided by the soil bioindicators to manage farming systems. A set of indicators of soil biological quality are evaluated in the project: microorganisms (bacteria and fungi abundance and diversity), fauna (abundance and diversity of nematodes and earthworms), physico-chemical characteristics, soil structure assessment and degradation rate of organic matter. Based on a network of 13 plots that have been subject to an initial diagnosis in 2017, several agronomical practices to restore soil fertility are experimented to redesign the cropping system (for instance plant cover, organic matter inputs, reduction of herbicides, mineral fertilizers). System redesign was made in collaboration by winegrowers and an interdisciplinary group of experts (agronomists, biologists). Several indicators are measured on vine and soil at each vintage to assess vine health and productivity. At the end of the project (2021), a final diagnosis was carried out. Gascogn’Innov allowed to create a regional database on the quality of wine-growing soils, which permitted to evaluate the effect of practices according to soil types. Especially, decreasing the intensity of tillage and increasing the duration and diversity of grass coverage tends to increase the abundance of all the organisms studied. This project confirmed the value of soil biological quality indicators to drive the sustainability of practices, but also highlighted the key-role of expertise, in both agronomy and soil biology, to help winegrowers understand and appropriate their soil quality diagnoses.

Influence of weather and climatic conditions on the viticultural production in Croatia

The research includes an analysis of the impact of weather conditions on phenological development of the vine and grape quality, through monitoring of four experimental cultivars (Chardonnay, Graševina, Merlot and Plavac mali) over two production years. In each experimental vineyard, which were evenly distributed throughout the regions of Slavonia and The Croatian Danube, Croatian Uplands,

Delaying irrigation initiation linearly reduces yield with little impact on maturity in Pinot noir

When to initiate irrigation is a critical annual management decision that has cascading effects on grapevine productivity and wine quality in the context of climate change. A multi-site trial was begun in 2021 to optimize irrigation initiation timing using midday stem water potential (ψstem) thresholds characterized as departures from non-stressed baseline ψstemvalues (Δψstem). Plant material, vine and row spacing, and trellising systems were concomitant among sites, while vine age, soil type, and pruning systems varied. Five target Δψstem thresholds were arranged in an RCBD and replicated eight times at each site: 0.2, 0.4, 0.6, 0.8, and 1.0 MPa (T1, T2, T3, T4, and T5, respectively). When thresholds were reached, plots were irrigated weekly at 70% ETc. Yield components and berry composition were quantified at harvest. To better generalize inferences across sites, data were analyzed by ANOVA using a mixed model including site as a random factor. Across sites, irrigation was initiated at Δψstem = 0.24, 0.50, 0.65, 0.93, and 0.98 MPa for T1, T2, T3, T4, and T5, respectively. Consistent significant negative linear trends were found for several key yield and berry composition variables. Yield decreased by 12.9, 15.9, 19.5, and 27.4% for T2, T3, T4, and T5, respectively, compared to T1 (p < 0.0001) across sites that were driven by similarly linear reductions in berry weight (p < 0.0001). Comparatively, berry composition varied little among treatments. Juice total soluble solids decreased linearly from T1 to T5 – though only ranged 0.9 Brix (p = 0.012). Because producers are paid by the ton, and contracts simply stipulate a target maturity level, first-year results suggest that there is no economic incentive to induce moderate water deficits before irrigation initiation, regardless of vineyard site. Subsequent years will further elucidate the carryover effects of delaying irrigation initiation on productivity over the long term.

Grapevine yield-gap: identification of environmental limitations by soil and climate zoning in Languedoc-Roussillon region (south of France)

Grapevine yield has been historically overlooked, assuming a strong trade-off between grape yield and wine quality. At present, menaced by climate change, many vineyards in Southern France are far from the quality label threshold, becoming grapevine yield-gaps a major subject of concern. Although yield-gaps are well studied in arable crops, we know very little about grapevine yield-gaps. In the present study, we analysed the environmental component of grapevine yield-gaps linked to climate and soil resources in the Languedoc Roussillon. We used SAFRAN data and IGP Pays d’Oc wine yields from 2010 to 2018. We selected climate and soil indicators proving to have a significant effect on average wine yield-gaps at the municipality scale. The most significant factors of grapevine yield were the Soil Available Water Capacity; followed by the Huglin Index and the Climatic Dryness Index. The Days of Frost; the Soil pH; and the Very Hot Days were also significant. Then, we clustered geographical zones presenting similar indicators, facilitating the identification of resources yield-gaps. We discussed the number of zones with the experts of IGP Pays d’Oc label, obtaining 7 zones with similar limitations for grapevine yield. Finally, we analysed the main resources causing yield-gaps and the grapevine varieties planted on each zone. Mapping grapevine resource yield-gaps are the first stage for understanding grapevine yield-gaps at the regional scale.

Climate change impacts: a multi-stress issue

With the aim of producing premium wines, it is admitted that moderate environmental stresses may contribute to the accumulation of compounds of interest in grapes. However the ongoing climate change, with the appearance of more limiting conditions of production is a major concern for the wine industry economic. Will it be possible to maintain the vineyards in place, to preserve the current grape varieties and how should we anticipate the adaptation measures to ensure the sustainability of vineyards? In this context, the question of the responses and adaptation of grapevine to abiotic stresses becomes a major scientific issue to tackle. An abiotic stress can be defined as the effect of a specific factor of the physico-chemical environment of the plants (temperature, availability of water and minerals, light, etc.) which reduces growth, and for a crop such as the vine, the yield, the composition of the fruits and the sustainability of the plants. Water stress is in many minds, but a systemic vision is essential for at least two reasons. The first reason is that in natural environments, a single factor is rarely limiting, and plants have to deal with a combination of constraints, as for example heat and drought, both in time and at a given time. The second reason is that plants, including grapevine, have central mechanisms of stress responses, as redox regulatory pathways, that play an important role in adaptation and survival. Here we will review the most recent studies dealing with this issue to provide a better understanding of the grapevine responses to a combination of environmental constraints and of the underlying regulatory pathways, which may be very helpful to design more adapted solutions to cope with climate change.