Biocontrol in viticulture


José L. Padilla Agudelo and Elena Palencia Mulero


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. 

Fig 1. Flow diagram describing the activities necessary to characterise microbial interactions and produce bioproducts of high biotechnological interest.


1. Stenberg JA, Sundh I, Becher PG, et al. When is it biological control? A framework of definitions, mechanisms, and classifications. J Pest Sci (2004). 2021;94(3):665-676. doi:10.1007/s10340-021-01354-7

2. Zhang H, Godana EA, Sui Y, Yang Q, Zhang X, Zhao L. Biological control as an alternative to synthetic fungicides for the management of grey and blue mould diseases of table grapes: a review. Crit Rev Microbiol. 2020;46(4):450-462. doi:10.1080/1040841X.2020.1794793

3. United Nations. The Sustainable Development Goals.; 2015.

4. Cordero-Bueso G, Mangieri N, Maghradze D, et al. Wild grape-associated yeasts as promising biocontrol agents against Vitis vinifera fungal pathogens. Front Microbiol. 2017;8(NOV). doi:10.3389/fmicb.2017.02025

5. Palmieri D, Ianiri G, Del Grosso C, et al. Advances and Perspectives in the Use of Biocontrol Agents against Fungal Plant Diseases. Horticulturae. 2022;8(7). doi:10.3390/horticulturae8070577

6. Lahlali R, Ezrari S, Radouane N, et al. Biological Control of Plant Pathogens: A Global Perspective. Microorganisms. 2022;10(3). doi:10.3390/microorganisms10030596

7. Ayaz M, Li CH, Ali Q, et al. Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives. Molecules. 2023;28(18). doi:10.3390/molecules28186735

About the authors:

José L. Padilla Agudelo, with a Master’s in Microbiology, and Elena Palencia Mulero, with a Master’s in Microbiology & Health, are both Doctoral Candidates in the prestigious Marie Skłodowska-Curie Action, part of the Horizon Europe Doctoral Network. Their work is funded by the European Union under Grant Agreement 101119480, within the project: “NATURAL MICROBIAL INTERACTIONS IN WINEMAKING-ASSOCIATED ECOSYSTEMS AS A TOOL TO FOSTER WINE INNOVATION (Eco2Wine).”

José is part of Prof. Gustavo A. Cordero Bueso’s team at the University of Cádiz in Spain, while Elena works with Prof. Ileana Vigentini at the University of Milan in Italy, who also coordinates the Eco2Wine Project. Together, they are diving into the “Grapevine and Grape Biocontrol” Work Package, aiming to uncover and explain the molecular mechanisms behind new biocontrol agents that combat the harmful fungus Botrytis cinerea, a major threat to vineyards.

Main Contacts: 

What is a ‘microbiome’, and how does it relate to wine?

What is a ‘microbiome’, and how does it relate to wine?

Karien O’Kennedy

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.


[1] Kumar PS. Microbiomics: Were we all wrong before? Periodontol 2000. 2021;85(1). doi:10.1111/prd.12373

[2] Tronchoni J, Setati ME, Fracassetti D, Valdetara F, Maghradze D, Foschino R, et al. Identifying the Main Drivers in Microbial Diversity for Cabernet Sauvignon Cultivars from Europe to South Africa: Evidence for a Cultivar-Specific Microbial Fingerprint. Journal of Fungi. 2022;8(10). doi:10.3390/jof8101034

[3] Gupta VVSR, Bramley RGV, Greenfield P, Yu J, Herderich MJ. Vineyard soil microbiome composition related to rotundone concentration in Australian cool climate “peppery” Shiraz grapes. Front Microbiol. 2019;10(JULY). doi:10.3389/fmicb.2019.01607

[4] Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560(7717). doi:10.1038/s41586-018-0386-6

[5] Cobos R, Ibañez A, Diez-Galán A, Calvo-Peña C, Ghoreshizadeh S, Coque JJR. The Grapevine Microbiome to the Rescue: Implications for the Biocontrol of Trunk Diseases. Plants. 2022;11(7). doi:10.3390/plants11070840

[6] Bagheri B, Bauer FF, Cardinali G, Setati ME. Ecological interactions are a primary driver of population dynamics in wine yeast microbiota during fermentation. Sci Rep. 2020;10(1). doi:10.1038/s41598-020-61690-z

[7] García-Izquierdo I, Colino-Rabanal VJ, Tamame M, Rodríguez-López F. Microbiota Ecosystem Services in Vineyards and Wine: A Review. Agronomy 2024, Vol 14, Page 131. 2024;14(1):131. doi:10.3390/AGRONOMY14010131

About the author:

Dr Karien O’Kennedy is the Knowledge Transfer Manager for South Africa Wine, an Associated Partner of the Eco2Wine project ( She holds an MSc in Microbiology and a PhD in Science and Technology Studies from Stellenbosch University, South Africa. Her areas of expertise include wine microbiology and academic knowledge production, transfer, and uptake.