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After one week of waiting, that morning, I woke up nervous, as always when I had to check the results of my experiments. I’m dedicated to developing innovative biocontrol strategies against Botrytis cinerea, a fungal pathogen that poses a significant risk to grape production across the globe. This focus on practical solutions not only addresses a key challenge but also contributes to more sustainable winemaking practices.

In the lab, I had prepared over 70 Petri dishes – the result of testing several microbial candidates in triplicate, each against two different Botrytis strains. That morning, they were finally ready to be checked. After a quick coffee, I made my way to the University of Milan, where I was the first to arrive at the lab. I put on my lab coat, headed straight to the incubators, and carefully retrieved the Petri dishes – each one holding the potential for an eco-friendly solution to vineyard pathogens.

What makes this experience truly exciting is that every experiment I design and every result I achieve carry real significance, and these results would be the outcome of months of dedicated lab work.

A fulfilling journey never comes without challenges

I’ve always dreamed of pursuing a PhD, but life took me on a different journey, leading me to spend three years working at a pharmaceutical company. I learned so much during that time and had a great experience. While I enjoyed my time in the lab, I missed the academic research setting. Now that I’m back in an academic lab, with petri dishes, microscopes, and the rhythm of daily experiments, I feel reconnected to what I enjoy most about research.

Still, research never follows a straight path; mine is no exception. Every experiment presents unexpected challenges, ideas that seemed simple at first, often turn out to be more complex. Refining protocols, interpreting results, and solving problems have become an integral part of my daily routine, often teaching me more than I expected.

One of the biggest lessons I have learned is the importance of collaboration. While I spend a significant amount of time in the lab working on my experiments, I’ve discovered that sharing ideas and seeking input from colleagues can be incredibly beneficial. Participating in discussions and collaborating with others not only enhances my understanding of the topic but also enriches the overall research process. Science should not be viewed as an individual endeavour, as exchanging insights and viewpoints fosters a collaborative atmosphere that paves the way for enhanced creativity and achievements.

In addition, I have realised how important effective communication is, as sharing our findings and thoughts clearly enhances teamwork and promotes an environment conducive to research. The value of disseminating knowledge is significant as it allows for a deeper understanding of our work. When researchers communicate openly, they create opportunities for constructive feedback and new perspectives that can lead to innovative solutions.

Another key takeaway is that research is all about adaptability. Things rarely go as planned, and adjusting while keeping the bigger picture in mind is essential for success. Sometimes experiments don’t go as expected, but instead of seeing them as setbacks, I now view them as opportunities to learn and improve my approach. Adopting this mindset has helped me develop my ability to think more creatively when faced with unexpected challenges.

Success in a petri dish

This time, we were successful. Looking at my petri dishes through the microscope, I could clearly see how much the mold had been inhibited. We successfully identified promising microorganisms with strong biocontrol potential against Botrytis. We’ve since quantified the results by measuring the inhibition zones and we’ve selected the best candidates based on their efficacy. My focus then shifted to unravelling the mechanisms of action that contribute to their effectiveness, investigating their interactions with Botrytis at the transcriptomic and metabolomic levels to identify the key genes and metabolites involved in the biocontrol process.

Now, I am entering one of the most crucial phases of my project, where I will explore how biocontrol agents interact with Botrytis at a molecular level. This stage is full of challenges, requiring close attention to detail and rigorous analysis. However, it is also one of the most thrilling aspects of my research. Each discovery helps uncover the mechanisms behind their effectiveness, bringing us closer to practical applications in vineyards. Seeing the potential impact of this work motivates me to keep pushing forward.

The next challenge is to take this research beyond the lab and into the vineyards, where we’ll conduct field trials to evaluate its real impact not only on disease control but also on grape and wine quality. Seeing how these microorganisms perform in real vineyard conditions will be a crucial step toward bridging the gap between experimental results and practical applications.

Knowing that my research could contribute to sustainable, eco-friendly solutions, reducing the use of chemical pesticides, and protecting our environment is incredibly fulfilling. I can’t wait to see where this journey takes me, and I’m excited about the potential impact my work can have on the wine industry and beyond.

By Aubrey Lee, Eco2Wine doctoral candidate

I stepped into uncharted territory for my PhD. My master’s research primarily focused on evaluating agronomic performance and nutrients in mushrooms. Diving into wine biotechnology required perseverance and hard work.

However, I learned that, even though I needed advice from experts to guide me, I must take hold of the steering wheel and control the direction I’m heading in. It’s easy to blindly take every suggestion when unsure of your path and allow others to steer the wheel in a direction different from what you originally planned. I remind myself to always filter the suggestions I receive, think critically, and decide what’s best to achieve the objectives of my project.

The first aim of my research is to map the microbial communities in conventional and organic vineyards across some EU regions and South Africa. Once the microbial diversity has been mapped and found, then it is time to maintain it as untouched as possible. For this reason, the second aim of my project is to find the best solution to preserve these microbial communities in and outside their natural habitat.

A first harvest in South Africa

So far, the highlight of my research has been harvesting grapes from the field and transferring them to the laboratory to be further processed for molecular work. I’ve always enjoyed working in the field. I love getting my hands dirty, being surrounded by nature, and feeling the warm sun on my face. Coming from an agricultural science background, I’ve worked in a mushroom cultivation room and small-scale vegetable farm before, but working in the vineyard is a totally new experience.

For the first Chenin Blanc harvest at Stellenbosch University’s vineyard, I felt a mixture of nervousness and excitement – nervous because I had to brief volunteering students on the harvesting process, despite it being my first time as well; excited because I never thought I’d be in sunny South Africa working in a vineyard. I am incredibly grateful for the opportunity.

It went well, and the process became easier over the next harvests. It was fun! While I enjoy working in the lab with pipettes in a sterile environment, a change of scenery refreshes the mind. I feel recharged after outdoor work, and the hands-on experience in the vineyard makes the molecular lab work much more interesting. The experience also helps shape me into a better scientist by giving me a deeper appreciation for the hard work behind viticulture and winemaking.

From the vineyard to the laboratory

I can see the difference in the grape samples between those grown on a conventional vineyard and those in biodynamic conditions, because the former has fewer insects. Now, I look forward to obtaining data to see the difference in microbial communities in those vineyards and how they vary across vineyards with different management practices. The microbes present on the grape surface significantly influence the overall wine quality – its aroma, colour, and taste. This mapping exercise is an important first step to their preservation.

Regardless of the challenges, I have learned much about this new field. For one, even though I am steering the ship, grapes cannot be manipulated to fit our exact schedules. They must be harvested at the right time, at the right maturity, and with the right sugar content. A little rain could cause a delay in harvest, as it dilutes the sugar concentration and causes splitting. Harvest timing is one of the first steps that requires careful attention for a good glass of wine.

Overall, I think my research is progressing well, and I am grateful that the post-doc researchers and lab members have been so generous with their time and knowledge in helping to ensure the success of my experiment. I am certain that I will have to face more challenges in my PhD journey, but I feel relieved knowing that I can always count on my supervisors and lab members for support and guidance.

I started this PhD with very little knowledge of wine science. Navigating through an ocean of advice and making informed decisions has been a crucial part of my growth as a researcher. By the end of my PhD journey, I hope my research will contribute to winemakers having better control and consistency in crafting their wine.

I wish everyone could understand the true meaning of every sip of wine they drink. Each glass represents the dedication of countless individuals—from the farmers tending the vineyards to the winemakers overseeing production, to the oenologists perfecting the flavors, and the scientists striving to enhance aroma profiles while making wine production more sustainable.

The chance to contribute to this intricate process and make a positive impact – even on a small scale – inspired me to join the ambitious Eco2Wine project. My work is not only helping the wine industry combat microorganisms that spoil wine but also enhancing the consumer experience. My research might introduce groundbreaking flavors, allowing people to rediscover wines in a whole new way, which is incredibly rewarding.

A rewarding but challenging journey

My research focuses on how microorganisms influence each other without exchanging nutrients—an area that remains at the core of my work, but it has not been without its challenges. Currently, my research focuses on two main areas. The first involves analyzing transcriptomic data to study how Saccharomyces, a well-known yeast, interacts with other yeasts that could serve as potential fermentation starters alongside S. cerevisiae in wine must. The second area explores the interactions of the spoilage yeast, Brettanomyces bruxellensis, with other yeast species that may act as biocontrol agents.

However, this second yeast can also introduce off-flavors, complicating the process. One of the biggest hurdles has been managing the vast amount of data and understanding the dynamic interactions between these microorganisms over time. To overcome this, I am refining my analytical methods and exploring computational tools that can help extract more meaningful insights from the data.

Instead of changing course, I am adapting, refining my protocols, and exploring alternative approaches to ensure I meet my research objectives.

Progress that came with support

A key to progress has been learning how to collaborate effectively. I’ve had to develop these skills both within my lab and with international project partners. Perhaps most importantly, I’ve learned the value of patience and resilience. After several failed attempts, I’ve learned to step back, reassess, and refine my approach to improve my results.

Wine, to me, is not just a drink—it’s a fusion of tradition, science, and craftsmanship. And I am excited to be a part, however small, of this journey.”

“I never lose. I either win or learn”

There is something almost poetic about standing in a vineyard, surrounded by rows of vines that stretch toward the horizon, their leaves rustling in the breeze. I have always appreciated the controlled precision of lab work—where bacteria and yeast grow in sterile Petri dishes, their interactions studied under microscopes. But it wasn’t until I walked through the vineyards of La Rioja, Spain, and later among the sunlit fields of Reinecke Wines in South Africa, that I truly understood the impact of my research. Seeing how these microorganisms interact with grapevines in real-world conditions made me realize that biocontrol – introducing natural enemies to control disease – isn’t just a scientific pursuit, it is a bridge between nature and sustainable winemaking.

From discovery to focus

At the beginning of this project, my focus was broad. I aimed to identify and characterise microorganisms that I could isolate from different vine tissues across vineyards in Spain and Italy. I wanted to explore their diversity, to map out their potential as biocontrol agents, and understand how they interact with pathogens. However, as I analyzed their antagonistic activity in both lab and greenhouse conditions, my supervisors encouraged me to refine my approach. Instead of casting a wide net, I began concentrating only on the most promising bacterial and yeast strains—those that showed the strongest potential for controlling fungal diseases. This shift allowed me to go deeper, to move beyond identification and toward uncovering the specific mechanisms driving their biocontrol properties.

Unraveling the mystery of biocontrol

Understanding how these microorganisms suppress phytopathogenic fungi (Botrytis cinerea) has been one of my greatest challenges. The interactions are complex, involving biochemical signals, metabolic exchanges, and intricate molecular processes that I am still working to piece together. Identifying the specific molecules responsible for these effects has proven difficult, requiring specialized techniques and advanced equipment. The process has been far from straightforward, but the challenge itself has been a source of motivation. Each new piece of data, each promising candidate molecule, brings me closer to uncovering the mechanisms that could one day reduce reliance on chemical fungicides in vineyards.

Learning through people

This journey has taken me far beyond microbiology. Delving into biocontrol mechanisms has introduced me to techniques from molecular biology, analytical chemistry, and plant pathology—fields I had never imagined myself working in before. More importantly, it has introduced me to incredible people. Science is often thought of as a solitary pursuit, but I have come to realize that progress depends on collaboration. I have met researchers who have generously shared their expertise, technicians who have guided me through complex methodologies, and mentors who have challenged me to think more critically. These human connections have shaped my experience as much as the research itself.

The complexity of sustainable winemaking

If only more people knew how intricate and ever-changing the process of winemaking truly is. It isn’t just about harvesting grapes and fermenting juice—it is a delicate balance of environmental conditions, vineyard management, and microbial interactions. Finding sustainable alternatives to fungicides isn’t a simple task; each vineyard presents its own unique challenges, and no single biocontrol solution works for all. My work with bacteria and yeast has taught me that nature operates in layers of complexity, and harnessing these microorganisms for sustainable viticulture requires patience, adaptability, and an open mind.

I still find comfort in the lab—the quiet hum of equipment, the precision of pipettes, the satisfaction of a well-designed experiment. But I also know that the true impact of my work lies in the vineyards, where farmers face real challenges every day. Biocontrol isn’t just about scientific discovery; it is about providing real solutions for a more sustainable future. And that is what keeps me moving forward.

I’ve always been captivated by the wide range of scents and flavours in wine, from the sweetness of my grandmother’s strawberry marmalade to the fresh scent of newly cut grass. This ability of each grape variety to ‘speak’ for itself, reflecting the characteristics of the vineyard and winemaker, has always fascinated me, especially when little other intervention was involved.

However, when I started experimenting with fermentations, I quickly realised that “minimal intervention” isn’t as simple as it sounds—ironically, the less you intervene, the more work is required. Native yeasts in the grape juice interact with each other in complicated ways, dictating the fermentation process. Understanding this process is like trying to peek into a closed box to discover what is inside. These tiny interactions have a considerable impact on wine, but how is the big secret that I am trying to uncover.

For my PhD research for the Eco2Wine project, I am studying how different types of yeast interact during fermentation. I use a combination of five yeast species (called a consortium) to understand how they work together to create the flavours we taste in wine. This is the magic of wine, but I want to make sure that the only surprises you get are good ones.

However, the closed box is not giving up its secrets easily.

The challenges of a complex process

Since grape harvests only come around once a year, I am conducting fermentations in synthetic grape must, but I quickly learned that it doesn’t always replicate the nuances of real grape must. The first question to investigate is therefore how closely the results from synthetic must translate to the real thing. Building the five-species yeast consortium and optimising the fermentation process has also proven more complicated than I anticipated. Another hurdle I encountered was biomass production. To overcome this, I scaled back to small-scale fermentations for the 2025 harvest, but the challenge will arise again when I transition to larger-scale experiments. I’m optimistic that I will have found a solution by the next harvest.

Adapting and changing plans is just part of the game, and the challenges have also led to opportunities and benefits.

The power of collaboration

With my background in chemicals, working in a microbiology laboratory has been challenging, but it has also opened exciting opportunities to explore this new world and expand my knowledge.

Furthermore, collaborating with my incredible colleagues has become one of my greatest strengths. We regularly discuss our findings, troubleshoot problems, and share insights to improve our methods. These conversations have taught me an important lesson: do not be afraid to admit when things go wrong. Chances are, someone else has faced a similar issue and can offer valuable advice. Working together creates an essential synergy that helps us all progress more efficiently.

So, though the journey has many challenges, I am confident that I will be able to uncover what is hidden in that closed box and share the secrets of fermentation to the benefit of the wine industry at large.

By: Katherine Rabik, Eco2Wine doctoral candidate (Stellenbosch University, South Africa) and science communicator, studying methods for communicating the science of microbiomics to winemakers and growers

It started with an international phone call. Even before my PhD studies with the Eco2Wine project officially got underway, I found myself rushing to make a flight from a cold Calgary airport while straining to hear a German doctoral candidate over the crackling line. We were to meet in a few weeks in South Africa but already had a joint article due. Whether I was ready or not, my global journey into the world of wine had started. 

The chance to work with a global network of researchers was a key motivation for me to join the Eco2Wine project. I grew up travelling, and it’s still one of my largest passions. When I saw “must be willing to travel for extended periods of time” in the list of requirements, it sealed the deal for me.

The decision has paid off. I have five months of research travel planned for 2025 across four different European countries. My first research secondment in April will take me to the University of Perugia in Italy, followed by a visit to our project partner Parsec in Florence and a quick trip to Scotland to attend PCST 2025, the annual global conference of the Public Communication of Science and Technology network. Beyond my own travel, I have had plenty of opportunities to work with people from around the world. From helping a doctoral candidate from Malaysia harvest grapes at a biodynamic vineyard here in South Africa, to writing articles with colleagues from India and France, these collaborations have reinforced the value of diverse perspectives in research. 

Not only am I grateful for these opportunities, but only four months into my project, I am committed to using my work to support an ongoing and proactive dialogue between wine scientists and winemakers. 

However, though my project is faring well, my choice has also resulted in serious challenges. For one, I am only now beginning to learn how complex it is to conduct social science research in seven different countries. By the end of my degree, I think I will be an expert in filling out ethical clearance forms!

In addition to the logistical challenges of a PhD that spans the globe, I have learned the importance of effectively managing my time. Many different tasks, activities, training, and courses call for attention, but I now set boundaries to spend time on my research. 

This has been important because the world of wine science is relatively new to me.

Exploring new territories

I do not have a background in winemaking or microbiology, so it has been vital for me to develop my understanding of these topics before I begin speaking to industry members for my research. 

What has surprised me is just how complex the winemaking process is. I assumed that winemakers had a formula that they would follow every year for their different grape varieties, but this is far from the truth, especially for natural wines. Changes in weather and climate impact each harvest differently, and it’s up to the winemaker to manage the fermentation process to ensure high-quality wines every time. 

Winemakers using indigenous yeasts in their fermentation process face additional complexity. These yeasts introduce more uncertainty compared to standard commercial yeasts. Winemakers who choose this approach are dedicated to adopting eco-friendly and sustainable approaches. 

Back to work 

Defining my research question has been a balancing act of what I’d like to achieve within the feasible time. My original topic has become more focused, while there have also been some exciting additions. I have chosen to concentrate on fewer audiences in my interviews but to add an analysis of media on the wine microbiome in major global wine-producing regions. This will give me an idea of what is being communicated to the public about this science. It will also be interesting to compare this to the dialogue in the industry and academia.

I am currently reviewing literature about wine science communication, which will inform my interview questions. I look forward to being out in the field and talking to winemakers and farmers. I’m excited to learn more about their views on wine microbiomics and how they use wine science research in their practice.

In this way, I hope to broaden my horizons and, importantly, that the results of my work will help communicate the benefits of working with, instead of against, the natural wine microbiome and ultimately contribute to a more sustainable wine industry worldwide. 

Interested in knowing more about my research? Please email me a krabik@sun.ac.za