Articles

Katherine Rabik wrote an article about Eco2Wine for the Marie Curie Alumni Association Newsletter special edition about science communication in December 2025. She shared some reflections about the successes and challenges we’ve faced integrating science communication training and practice into a natural sciences project. Eco2Wine can serve as a valuable case study for other MSCA-DN projects looking to adopt a similar model

Winemaking isn’t just a craft; it’s a living process powered by some of nature’s smallest yet most essential workers: yeasts. They work together to shape the final taste and aroma of wine. The most well-known yeast used in fermentation is Saccharomyces cerevisiae, but in recent years, other yeast species such as Torulaspora delbrueckii, Lachancea thermotolerans, Hanseniaspora uvarum, and Metschnikowia pulcherrima have gained interest. But what’s truly fascinating is how these yeasts “talk” to each other during fermentation: sending signals, cooperating, and sometimes even competing^[1]. By understanding this microbial communication, we open doors for new possibilities in winemaking, enhancing flavour complexity and adding a touch of magic to every bottle^[2].

However, there exists one potential yeast communication method that warrants further research to deepen our understanding: tiny structures known as extracellular vesicles (EVs). These vesicles carry proteins, lipids, and genetic materials, allowing cells to transmit signals to one another^[3]. Might they be impacting yeast behaviour during fermentation?

Extracellular Vesicles: A New Way for Yeasts to Talk?

Recent research has shown that several wine yeast species, including S. cerevisiae, T. delbrueckii, and L. thermotolerans, release EVs into their environment when fermenting grape juice. One of the main proteins found in these vesicles is an enzyme called exo-1,3-β-glucanase, which is used for yeast wall metabolism. However, scientists discovered that this enzyme isn’t responsible for the way T. delbrueckii affects other yeasts’growth^[2].

This raises an interesting question: if this enzyme isn’t the key factor, what else in the vesicles could be influencing yeast interactions? One possibility is that EVs carry other molecules that help yeasts compete, cooperate, or adapt to stress during fermentation.

How Do Yeasts Detect and React to EVs?

Yeasts interact in diverse ways: competing for resources or cooperating through nutrient sharing, but recent findings suggest that some species can specifically recognize signals from others. For instance, researchers observed that S. cerevisiae altered its gene expression after exposure to extracellular vesicles (EVs) from M. pulcherrima, even in the absence of living cells, highlighting the signalling potential of EVs. This evidence supports the idea that EVs act as important biochemical messengers that influence yeast metabolism and behaviour^[4].

On the other hand, an example of interactions with an impact on specific metabolites, although the communication signals remain unidentified, is the co-inoculation of S. cerevisiae and Saccharomyces uvarum to explore their molecular interactions during fermentation. Through proteomic and metabolomic analyses, significant changes were observed in key metabolic pathways, such as tryptophan metabolism (Figure 1). Additionally, it has been proposed that interspecies interactions stimulate biosynthetic routes like the shikimate pathway and indole production, which showed a natural enrichment in metabolites of the aromatic amino acid biosynthesis pathway^[5].

Interactions between Saccharomyces and Non-Saccharomyces yeasts: a pathway to wine aroma and quality (Image created with bioRender).

In a quiet industrial park on the outskirts of Florence lies the unassuming headquarters of Parsec, a company that blends engineering with oenology and serves as an Associated Partner of Eco2Wine. Katherine Rabik, one of the Eco2Wine doctoral candidates, recently spent two weeks at Parsec, where she met with their head engineer and consulting oenologists, toured their facilities, and visited wineries using Parsec’s systems in real-world settings. What Parsec does may seem technical at first glance, but the underlying goal is simple: to give winemakers greater precision, more control, and the space to let fermentations and wine aging unfold properly.

Parsec’s central headquarters are located in Florence, Italy.

In recent years, cold temperature technology has gained growing relevance in modern winemaking due to its positive impact on the aromatic profile and sensory attributes of wines – improving the overall wine quality in terms of its colour, aroma and final taste. This technology can be strategically implemented at different stages of the enological process to optimize both chemical and sensory attributes¹. Additionally, cold temperatures in the form of cryopreservation can be used to preserve communities of microorganisms for long periods of time. Within the Eco2Wine project, we aim to preserve the microbial consortia as untouched as possible as a “time-capsule” of biodiversity for future use of winemakers.

In this article, we will explore why cryopreservation is necessary for the preservation of wine microbial consortia, as well as the benefits of using cold temperature technology during maceration and fermentation to improve wine quality.

Cryopreservation 

The use of low-temperature technologies in oenology extends beyond the processing of grapes to cryopreservation, a biological application using ultra-low temperature (below 0℃) for the long-term preservation of microorganisms.

At ultra-low temperatures, microorganisms are mostly inactivated from evolution, hence maintaining their genetic stability. Although sometimes chemical changes within cells could happen due to free radical formation and ionizing radiation¹, cryopreservation is still considered a good option for long term preservation. It does not involve routine manipulation which reduces the risk of contamination and human errors.

Why is cryopreservation necessary in oenology? 

In oenology, the concept of terroir refers to the combination of environmental factors contributing to the wine quality. These environmental factors shape the microbial diversity present in the vineyard². This being said, each vineyard has its own unique microbial consortia that contribute to the unique taste and aroma of wine produced in the region. Thus, cryopreservation becomes necessary with the increasing interest in indigenous yeast strains and their application to small and specific wine production.

Problems in preservation of indigenous strains 

However, the preservation of indigenous yeasts presents some problems. First, only a small percentage of yeasts can be actively dried. In the past, yeasts were preserved with traditional methods, using agar and liquid culture; it only preserved less than 1% of the total microbial population³. Furthermore, some yeasts exist in a viable but non-culturable state (VBNC); a phenomenon where the yeasts are alive but unable to grow and form colonies on media⁴. With the traditional methods, they are unable to be isolated and stored.

Secondly, there is an increasing interest in preserving microbial consortia – a community of two or more microorganisms. The cryopreservation of microbial consortia is not straightforward – it requires time and research for the protocol optimization. Different yeast species will have different biological responses to the cryopreservation condition⁵, making the optimization process complex.

Optimization of cryopreservation protocol

Today, the optimal cryopreservation protocol for winemaking yeasts is still not well-defined yet, especially for microbial consortia. One of the research aims of Eco2Wine is to come up with a protocol that ensures the highest quality of cryopreserved indigenous yeasts. This will support the overall project goal of developing techniques for more natural wine production.

Impact on grape aroma compounds and sensory properties of wine

Cold temperature technology can also be applied during maceration and fermentation to improve the wine quality. ​Studies have shown that the use of cold temperature technology during maceration enhances the aromatic profile of wines^6,7. These methods involve freezing grape berries to facilitate the extraction of aroma compounds, leading to wines with more intense and stable aromas. Freezing grapes before winemaking significantly affects their chemical composition. Research conducted by Carillo et al.⁸ found that phenolic acids (such as gallic and caffeic acid) and polyphenols differ between wines made from fresh and frozen grapes.

Similarly, freezing also impacts acetaldehyde levels and volatile compounds, with frozen grape juice having a different aroma profile compared to fresh juice⁹. The effects of freezing vary depending on the grape variety and the specific freezing method used. While fresh juice is preferable for analyzing volatile compounds, long-term storage at -80°C or in liquid nitrogen is recommended to minimize biochemical changes¹⁰. Additionally, freezing reduces anthocyanins, total phenolics, and terpenic alcohols, which are important for wine color and aroma⁸.

Apart from that, wines made from grapes treated with liquid CO₂ (inertized wine) had better color and phenol concentration compared to untreated wines. Additionally, non-trained judges preferred these wines, suggesting they align with consumer tastes⁸. Cold pre-fermentation maceration also enhances aroma compounds (terpenes, thiols, esters, and phenols) by increasing their extraction from the grape skin. This process can modify the nutrient composition of the grape must, leading to wines with improved aromatic complexity and overall quality¹¹. Overall, research suggests that the application of cold temperature technology enhances aroma intensity, making them a valuable tool for improving wine quality¹².

The journey of winemaking begins in the vineyard.  Behind the vibrant green vine leaves and juicy firm grape berries, hides an unseen ecosystem – a rich and dynamic microbial ecosystem. These microorganisms are an integral part of viticulture and oenology, albeit often unseen. They are sources of biodiversity and play important roles in various functions and balances, including nutrient cycling and maintaining the health of grapevines.¹  In winemaking, a diverse microbial ecosystem enhances fermentation efficiency and stability.² Apart from that, these site-specific microorganisms contribute to the terroir concept in winemaking – where the environment such as soil, topography, climate, and landscape characteristics influence the complexity of wine aromas and flavour profiles.³ They act as silent sculptors, crafting the character in each bottle of wine in a subtle yet distinctive way. These tiny microorganisms work silently, interacting from the vineyard to the winery, to produce a unique wine.

What shapes the microbial diversity in vineyards?

Microbiomes of vineyards – those on soil and directly associated with grapevines- are shaped by many factors including climate, topography, and viticultural practices.³ Climate, strongly influenced by topography, is a key factor shaping microbial diversity in vineyards.⁴ Studies have shown that vineyards that practice organic and biodynamic management have higher microbial diversity present, including during spontaneous fermentation where the must was found to have higher yeast species richness and diversity.⁴

From lab to vineyard: how biocontrol agents are transforming sustainable winemaking

Synthetic chemicals can be used to suppress harmful pathogens in the vineyard. However, upon application, some beneficial microorganisms are also harmed due to the toxicity of chemical compounds found in synthetic pesticides⁵. Therefore, research into biocontrol agents – a natural alternative – is on the rise to limit or replace synthetic chemicals to combat diseases in the vineyard. Biocontrol agents (BCAs), which include beneficial fungi, bacteria, and yeasts, are playing an increasingly important role in transforming viticulture. By offering natural protection against diseases such as Botrytis cinerea (grey mold), Plasmopara viticola (downy mildew), and Erysiphe necator (powdery mildew), these microbial allies are steering winemaking toward a more sustainable future. ⁶ Their use aims not only to reduce the dependence on synthetic chemicals but also to protect and enhance the natural microbial diversity vital for healthy vine ecosystems.

The power of microorganisms

Specific microorganisms have shown remarkable effectiveness in vineyard protection. Species like Aureobasidium pullulans, Bacillus spp., and Trichoderma spp. suppress pathogenic fungi by competing for nutrients and space, producing antimicrobial compounds, and stimulating the vine’s natural defenses. ^6,7 For instance, A. pullulans, has demonstrated efficacy against B. cinerea by occupying ecological niches that would otherwise be exploited by the pathogen. Similarly, Bacillus subtilis and Bacillus amyloliquefaciens produce a range of bioactive molecules that inhibit pathogen development and enhance plant immunity. Fungal agents like Trichoderma atroviride are particularly valuable for controlling grapevine trunk diseases, contributing to long-term vineyard health and resilience.

The biocontrol sector is experiencing rapid growth. The global market for biological control products exceeded USD 6.6 billion in 2022 and is projected to reach USD 13.7 billion by 2027, reflecting increasing demand for sustainable alternatives, particularly in the European viticulture sector. ⁸

A symbiotic relationship: biocontrol and biodiversity

By choosing beneficial microorganisms instead of chemical pesticides, winegrowers are not just safeguarding their vines, they’re potentially nurturing and boosting the microbial communities in their vineyards. This shift toward biocontrol plays a critical role in preserving biodiversity, promoting healthier soils, and enhancing vineyard resilience against future disease outbreaks and climate challenges. ^1,6,9

A greener path for winemaking

The future of winemaking is turning greener, with biocontrol agents as part of this transformation. By working with nature instead of against it, winegrowers protect their vines, preserve terroir, and maintain the natural balance of their vineyards. This approach helps safeguard the richness of the soils, the resilience of the plants, and the unique character of the grapes. Each harvest reflects the quiet work of the invisible life that supports healthy vines and contributes to the authentic expression of the land. ^{3,4, 9}

Introduction

Various strategies have been and are still being explored to manage diseases in viticulture effectively. These include cultural practices, selection of resistant cultivars, chemical control (fungicides and bactericides), and biocontrol. But what do we know about this last strategy, and why is it important for viticulture?

Biocontrol refers to using living organisms, mainly microorganisms called biocontrol agents (BCAs), to manage and reduce pests, diseases, and invasive species. This environmentally friendly approach is an integral part of control strategies and offers an alternative to chemical pesticides, which can negatively affect the environment and human health.1 Different countries’ and regions’ policies aim to reduce synthetic pesticide use and ensure responsible consumption and production, life on land, and clean water.2,3 However, implementing BCAs requires in-depth studies on the complex interactions in plant-microbe-environment interplay. 

Among the characteristics of BCAs is their ability to compete effectively for nutrients and space, which are involved in suppressing pathogen growth. They also produce volatile and non-volatile compounds in a process called antibiosis. Finally, BCAs can directly parasitise pathogens. Nowadays, using BCAs with combined approaches (especially those that operate by different mechanisms of action) is useful because it forces a pathogen to overcome several hurdles instead of just one to establish and develop an infection. Additionally, combinations of approaches may have additive or synergic effects.

How can BCAs be useful?

Using BCAs as a preharvest and postharvest treatment to control diseases caused by pathogens has many advantages:

• They can persist on the fruit surface for an extended period.
• They are generally safer for human health than many chemical agents.
• They are eco-friendly.
• They maintain ecological balance and promote biodiversity.
• They can protect the product from reinfection due to their persistent viability.
• They have a lower potential for pathogens to develop resistance.
• Products treated with BCAs potentially open more export opportunities.2

Finding effective BCAs

In the fight for sustainable disease management, finding effective biological control agents within a diverse microbial landscape – bacteria, yeasts and filamentous fungi – is essential but challenging. Vineyards, which host a remarkable diversity of microbial communities, serve as a natural reservoir of potential BCAs. In vitro assays and in vivo studies are crucial in evaluating their inhibitory activity against target pathogens.4 

However, this search goes beyond finding a single effective agent. The possibility of combining several BCAs should be explored not only to achieve a greater impact but also to reduce the emergence of new resistances. This raises some interesting questions.

Friends or foes?

How do these BCAs interact with each other and with the target pathogen? Will they work together as a team or hinder? If the target pathogen is successfully eliminated, could others take advantage?

Researchers are figuring this out by studying how BCAs interact with each other, with the target pathogen, the host plant and other microorganisms. By unravelling these complex microbial relationships, they are paving the way for a future where we can assemble the ultimate BCA consortium: a powerful, well-coordinated force for sustainable fungal disease control in the vineyard.

How do you unlock the secrets of BCAs?

The widespread adoption of next-generation sequencing (NGS) techniques has revolutionised the field of biocontrol. These techniques, which include whole genome sequencing, transcriptomics, proteomics and metabolomics, allow the identification of the molecular pathways and essential genes that play key roles in biocontrol.5 

Have any BCAs been approved?

Yes, but despite their growing potential, BCAs currently represent a small fraction (1%) of the agricultural control market compared to the dominance of synthetic pesticides (15%) 6. This limited adoption can be attributed to several factors: 

• Efficacy: Sometimes, BCAs may not provide the same level of immediate and predictable disease control as synthetic fungicides. 
• Knowledge gap: Commercialising biopesticides often involves proprietary formulations, limiting publicly available information on successful production and application methods. 
• Registration and patenting: This can be complex and time-consuming, particularly in certain regions (e.g., Europe).  
• Farmer adoption: Financial incentives for farmers to switch from conventional fungicides to BCAs might be limited, especially if they are unaware of and have no experience with this approach. 7  

Challenges aside, there is a strong trend to use microbial biocontrol agents for plant disease management. Therefore, research in this field is expected to continue to attract increasing attention, opening new highways toward an environmentally sustainable future. 

Have you ever wondered what gives your favorite bottle of wine its distinct character? Part of the answer lies in a world invisible to the naked eye but crucially helping to shape the taste and quality of wines: the microbiome.

But hold on, what exactly is a microbiome?

The terms ‘microbiome’ and ‘microbiota’ are often used interchangeably, but they actually refer to different aspects of microbial communities within a particular environment, such as the human body or vineyard soil. Microbiota refers to the collection of microorganisms, including bacteria, fungi, yeasts and viruses inhabiting a specific ecological niche. It focuses on the organisms themselves rather than their genetic material.

On the other hand, microbiome refers to the collective genetic material of all microorganisms present in a particular environment. It encompasses not only the microorganisms themselves but also their genes and their interactions with each other in their host environment. The microbiome provides a more holistic view of microbial communities, incorporating their genetic diversity and ecological functions. 

Microbiomics, the newest kid on the microbiology block, is the science of collectively characterising and quantifying molecules responsible for a microbial community’s structure, function, and dynamics.¹ Microbiomics employs multiple techniques, including high-throughput sequencing, bioinformatics, and systems biology approaches, to investigate microbial communities and their interactions with their hosts and environments. The field has broad applications in human health, agriculture, environmental science, biotechnology, and beyond, with implications for understanding disease mechanisms and ecosystem dynamics and developing novel therapies and interventions.

Now, how does this relate to wine?

The vineyard microbiome plays a crucial role in shaping the unique characteristics of wines.² The microbiome of the vineyard soil, grapevine, and grapes influences the health and growth of the grapevine and the composition of the grapes. The grape microbiome determines the fermentation microbiome (if no commercial yeast inoculation occurs) and the character of what finally ends up in your glass. 

Vineyard soils, the foundation of wine character

Soils harbour some of the most diverse microbiomes on earth. Observations from studies suggest that different vineyard soil microbiomes can contribute to variations in grape and wine composition and the wine’s terroir. This happens through the vines’ response to the soil microbiome or through the soil microbiome affecting the grape microbiome and, thus, fermentation.³ An example is an Australian study that demonstrated that distinct differences in the bacterial and fungal communities in different zones within the same vineyard are associated with high and low rotundone concentrations in grape berries. Rotundone is an impact aroma compound with a ‘peppery character’ commonly found in cool climate Shiraz from Australia. 

Various abiotic factors, such as geographical origin, climatic conditions, soil composition, and cultivation, can influence the vineyard soil microbiome. Interestingly, biotic factors can also play a significant role, with certain soil fungi that can impose a strong selection on bacteria by producing antimicrobial (antibiotic) compounds.⁴

Soil health is of utmost importance, not only for viticulture but for all agricultural systems. The soil microbiome forms a critical component of soil health. Understanding how agricultural systems, including viticulture, impact the soil microbiome is crucial to ensuring more sustainable agriculture and food for future generations. 

Grapevines, the guardians of wine character

Various factors can influence the microbiome of vines. Vineyard location, farming systems (conventional, organic, biodynamic), viticultural practices and even grape variety are among these factors. A study on Cabernet Sauvignon grapes in four countries with different climates and viticultural traditions using the same experimental layout suggested that grape varieties can have unique microbial fingerprints.²

The different parts of the vine can host various pathogenic and beneficial microorganisms. Beneficial microorganisms can help promote vine health by suppressing the growth of pathogenic organisms and enhancing the plant’s resistance to diseases.⁵ Studying these interactions can pave the way for eco-friendly biological control of grapevine diseases instead of chemical control. Studying the microbiome in vineyards also holds the potential to improve grapevine adaptation to climate change and boost overall sustainability. 

Fermentation, where the magic happens

Microorganisms present on grape surfaces can contribute to the initial stages of fermentation by inoculating grape must with indigenous yeast and bacteria. These native microorganisms initiate spontaneous fermentation, which can influence the chemical composition of the wine, such as its acidity, alcohol content and phenolic profile. Additionally, the microbial communities present during fermentation can lead to the development of complex flavours, aromas and textures in the resulting wine. 

Any given species’ contribution to the wine’s final character depends on its numbers and persistence during fermentation. Many factors can influence these two aspects, including interspecies ecological interactions, as shown by South African and Italian researchers.⁶ Studying the grape juice and fermentation microbiome and the factors that influence it can give winemakers the tools to steer the fermentation in a positive direction for wine quality. It can also help prevent fermentation problems such as stuck fermentations and the formation of off-odours.

Biodiversity for a sustainable future

In the coming decades, the agricultural sector will face major challenges in providing food for a growing world population, but intensive cropping, based on mineral fertilisers and agrochemicals, will continue to impact biodiversity and ecosystems negatively.7 Wine production is no exception to these environmental problems. The study of microorganisms in vineyards and wine production reveals the essential contribution of these invisible communities to the functioning and sustainability of viticultural systems. Microorganisms are vital players in achieving optimal outcomes with diverse influences, from soil health and vine vitality to fermentation and the sensorial profile of a wine. Their complex and symbiotic interaction with the viticultural environment triggers a range of benefits, including the enhancement of final product quality and vineyard resilience against adverse factors.  Understanding the factors that impact microbiome distribution and microbial diversity is essential to better harness natural ecosystems for quality wine production.