Harnessing the potential of oxidative and weakly fermentative yeasts in biocontrol and bioprotection

Abstract

There is increasing demand for sustainable alternatives to chemical fungicides and preservatives due to the negative impact that they have on the environment, human and animal health. This has led to intensified interest in microbial biocontrol and bioprotection strategies. Oxidative and weakly fermentative yeasts represent an underexplored group of microorganisms with considerable potential for managing undesirable microorganisms. These yeasts produce limited amounts of ethanol and carbon dioxide while exhibiting diverse mechanisms of antagonism against spoilage and pathogenic microorganisms. Their biocontrol and bioprotection activity is mediated through nutrient and space competition, antimicrobial metabolites and hydrolytic enzymes production, biofilm formation, induction of host resistance, and modulation of microbial communities. These characteristics make such yeasts particularly attractive for applications in fresh produce, fermented beverages, and agricultural systems where minimal alteration of the final product is desirable. Furthermore, their reduced fermentative activity lowers the risk of undesirable sensory changes while maintaining effective suppression of fruit and beverage spoilage microorganisms. Despite these advantages, their commercial application remains limited. This review examines current knowledge of oxidative and weakly fermentative yeasts as biological control agents, highlights their applications in fruits and beverages, factors affecting their efficacy, and challenges for their integration into sustainable biocontrol and bioprotection strategies.

Oxidative and weakly fermentative yeasts represent a treasure trove of biological alternatives to chemical fungicides and preservatives, offering sustainable protection to fruits and beverages.

Introduction

Fruits constitute a critical component of the human diet, providing various nutrients, including carbohydrates, vitamins, and antioxidants. They may be consumed fresh or dried, and are widely processed into different beverages such as juices, wines, and ciders. Fresh fruits harbour a wide variety of endophytic and epiphytic microbiota. Among the epiphytic microbiota are phytopathogenic fungi that can infect the fruit leading to pre- and post-harvest damage, thereby reducing the quality of the fruit as well as their nutritional value. Common phytopathogens include species of the genera Botrytis, Aspergillus, Alternaria, Penicillium, Colletotrichum, and Rhizopus (Oztekin et al. 2023). In addition, beverages, particularly those involving fruit substrates such as wine, cider, and juices, are often exposed to unwanted microbial growth during critical stages such as harvest, transport, pre-fermentation handling, and during storage. Traditionally, synthetic fungicides are used in conjunction with various agricultural practices to manage phytopathogens in the field, while post-harvest, various antimicrobials, and preservatives are applied to limit spoilage (Burandt et al. 2024, Si et al. 2025). However, growing concerns over the risk of chemical residues and the environmental impact of synthetic fungicides, as well as consumer demand for more natural and sustainable crop production strategies, have spurred interest in biological alternatives (Burandt et al. 2024, Si et al. 2025).

Yeasts, which are common colonizers of fruit surfaces and key drivers of fermentation processes, have emerged as attractive candidates for microbial control of spoilage agents in fruit and beverage production systems. Fruits harbour oligotrophic yeasts that thrive in nutrient-poor environments and have oxidative metabolism, as well as copiotrophic yeasts that thrive in nutrient-rich environments like sugary, ripening or damaged fruits (Costantini et al. 2022). The copiotrophic yeasts play a major role in the fermentation and spoilage of fruit. Among them are strong fermenters like Saccharomyces cerevisiae that dominate alcoholic fermentations, and a diverse community of non-Saccharomyces yeasts that are either weak and/or moderate fermenters (Costantini et al. 2022, Martíns et al. 2024). The oxidative and weakly fermentative yeasts have attracted increasing attention as suitable biological alternatives to synthetic fungicides in the biological control of phytopathogens as well as bioprotection against beverage spoilage microbiota (Cordero-Bueso et al. 2017, Maluleke et al. 2022, Esteves et al. 2023, Öztekin and Karbancioglu-Guler 2023). Some of the traits that make these yeasts desirable include adaptation to the fruit microenvironment, lack of production of anthropotoxic substances, and resistance to most agrochemicals (Agirman et al. 2023).

Oxidative and weakly fermentative yeasts of the genera Metschnikowia, Candida, Kluyveromyces, Pichia, Rhodotorula, and Sporobolomyces have gained research interest due to their ability to inhibit phytopathogens and suppress spoilage microorganisms through a combination of mechanisms, including competition for space and nutrients, production of antimicrobial metabolites, as well as iron sequestration (Maluleke et al. 2022, Esteves et al. 2023). While oxidative yeasts are more suited for applications as biocontrol agents due to their ability to colonize wounds or natural openings of fruit without initiating fermentations, weakly fermentative yeasts are increasingly explored for protecting grape musts, fruit juices and other substrates during cold soak, pre-fermentation maceration, or low-alcohol beverage production where control of undesirable microbial growth is essential but ethanol formation must be minimized (Windholtz et al. 2021a, 2023, Aragno et al. 2024, Ruci et al. 2025). Consequently, weakly fermentative yeasts have some modest contribution to the chemical and sensory properties of the beverages in which they are applied as bioprotectants, in a species- and strain-dependent manner (Nadai et al. 2018, Windholtz et al. 2021a, Simonin et al. 2022, Puyo et al. 2023a). Indeed, in the past decade, a considerable amount of literature has been published on the bioprotection and fermentation capabilities of weakly fermentative yeasts such as Metschnikowia pulcherrima, Pichia kluyveri, and Suhomyces pyralidae (Puyo et al. 2023a, Guan et al. 2025, Guzzon et al. 2025).

This review provides an overview of oxidative and weakly fermentative yeasts as biocontrol and bioprotection agents in fruit and beverage production systems. We first define and contextualize weakly fermentative yeasts within the broader yeast landscape and examine their ecology and target pathogens. The modes of action as well as the practical applications in preharvest and postharvest, and beverage production settings are discussed. Our aim is to highlight the current state of affairs in research and development on oxidative and weakly fermentative yeasts for their potential to support sustainable high-quality beverage production systems. To avoid confusion, currently accepted species names will be used throughout the review, with synonyms and basonyms provided in Supplementary Table S1 for reference.

Weakly fermentative yeasts: definition and ecological context

Yeasts associated with fruits and beverage production display varying energy and metabolic systems. Two groups can be identified: (i) obligate aerobes with no ability to ferment sugars and (ii) facultative anaerobes with varying abilities to ferment sugars. The facultative anaerobes can be further categorized into strong, moderate, and weak fermenters. Strong fermenters are Crabtree-positive with a characteristic ability to ferment under aerobic conditions if sugar is available above a certain threshold (>0.8 mM). These yeasts (e.g. Saccharomyces spp., Vanderwaltozyma polyspora, Schizosaccharomyces pombe) display rapid glucose uptake, an overflow metabolism and high ethanol accumulation and tolerance. They are both short- and long-term Crabtree-positive (Hagman and Piskur 2015). Unlike the archetype Crabtree-positive yeasts, moderate fermenters often ferment under oxygen limitation or very high sugar, and they are both moderately short- and long-term Crabtree-positive like Lachancea kluyveri, Lachancea waltii, and Torulaspora franciscae (Hagman and Piskur 2015). In contrast, weak fermenters are often classified as Crabtree-negative or very weakly positive. Such yeasts may be both short- and long-term Crabtree-negative like Kluyveromyces marxianus or weak short-term Crabtree-positive and long-term Crabtree-negative like Kluyveromyces lactis (Hagman and Piskur 2015). Interestingly, most of the non-Saccharomyces yeasts widely studied for biocontrol and bioprotection in the production of fruit crops and associated beverages are either non-fermentative or display low to moderate fermentation power and are mainly Crabtree-negative (Table 1).

Table 1.

Energy metabolism of non-Saccharomyces yeasts with biocontrol activity.

Species	Fermentative power	Crabtree status	Reference
Candida oleophila	Moderate	Positive	Papanikolaou et al. (2017)
Cryptococcus albidus	Non-fermentative	Negative	Veiga et al. (2000)
Debaryomyces hansenii	Low	Negative	Veiga et al. (2000), Contreras et al. (2014)
Hanseniaspora uvarum	Low	Negative	Venturin et al. (1995)
Hyphopichia burtonii	Low	Unknown	Rollero et al. (2018)
Hyphopichia pseudoburtonii	Low	Unknown	Rollero et al. (2018)
Kazachstania spp.	Moderate	Positive	Hagman et al. (2013)
Kluyveromyces marxianus	Low	Negative	Veiga et al. (2000), Contreras et al. (2015), Tyibilika et al. (2024)
Lachancea thermotolerans	Moderate	Positive	Veiga et al. (2000), Hagman et al. (2013)
Metschnikowia pulcherrima	Low	Negative	Schnierda et al. (2014), Barkhuizen et al. (2021), Carbon et al. (2023)
Meyerozyma caribbica	Moderate	Unknown/not determined	Muynarsk et al. (2026)
Meyerozyma guilliermondii	Low	Negative	Papon et al. (2013), Qi et al. (2014), Carbon et al. (2023)
Pichia kudriavzevii	Low	Negative	Schnierda et al. (2014), Barkhuizen et al. (2021)
Pichia kluyveri	Low	Negative	Rollero et al. (2018)
Rhodotorula glutinis	Non-fermentative	Negative	Veiga et al. (2000), Papanikolaou et al. 2017)
Saturnispora silvae	Low	Positive	Horianopoulos et al. (2026)
Sporobolomyces roseus	Non-fermentative	Negative	Contreras et al. (2015)
Starmerella bacillaris	Low-moderate	Negative	Pontes et al. (2024), Tyibilika et al. (2024)
Torulaspora delbrueckii	Moderate	Positive	Hagman et al. (2013)
Wickerhamomyces anomalus	Low	Negative	Veiga et al. (2000), Passoth et al. (2006), Rollero et al. (2018)
Zygotorulaspora florentina	Moderate	Positive	Hagman et al. (2013)

Biological control vs. bioprotection

The production of good-quality fruit crops for direct consumption, or to produce alcoholic and non-alcoholic beverages, as well as functional beverages, relies on the successful prevention of fruit deterioration due to phytopathogens or beverage spoilage by microbial contaminants. For centuries, chemical fungicides and preservatives were the primary methods used to ensure that fruits are protected from fungal diseases and spoilage microorganisms. However, alternative approaches such as biocontrol and bioprotection have gained traction and are becoming the method of choice to manage crop and beverage quality.

Although closely related, the two approaches are conceptually distinct. As proposed by Stenberg et al. (2021), biocontrol in its strict sense refers to the use of living organisms to suppress target pests through direct or indirect ecological interactions, thereby reducing damage to crops (Fig. 1). In contrast, bioprotection is an umbrella concept encompassing all biologically derived strategies for pest management, including both living and non-living nature-based products. In this context, bioprotection can be achieved with microorganisms, metabolites, plant and animal extracts, and essential oils (Stenberg et al. 2021).

Figure 1.

Examples of yeast genera involved biocontrol (direct suppression of pathogens and pests via competition, antibiosis, and mycoparasitism) and bioprotection (enhancement of plant stress tolerance and growth through induced resistance, nutrient mobilization, and root development) of fruit and beverages against phytopathogens and spoilage microorganisms. Created in BioRender. Setati, E. (2026) https://BioRender.com/rj86kg8.

In fruit production, biocontrol is often integrated into the pre- and postharvest management strategies to prevent rot caused by Botrytis cinerea on a myriad of crops (Supplementary Table S2), Penicillium spp. and Aspergillus spp. on citrus and pome fruit, and Colletotrichum spp., Fusarium spp., Rhizopus spp., and Alternaria alternata on other fruit (e.g. strawberries, blueberries, kiwifruit, jujube, and papaya). Bioprotection, on the other hand, is aimed at increasing the microbial safety and extending the shelf-life of non-alcoholic beverages (Fig. 1). It also encompasses control of spoilage organisms, as well as reducing the use of chemicals such as chlorine to decontaminate fresh fruit (Linares-Morales et al. 2018), and SO₂ as an antiseptic and antioxidant to suppress undesirable microorganisms and prevent juice oxidation (Puyo et al. 2024). For instance, in wine production, bioprotection is typically implemented in pre-fermentation stages to reduce sulfite use (Simonin et al. 2020, 2022, Lebleux et al. 2023, Windholtz et al. 2023, Puyo et al. 2024, Bene et al. 2025), and to suppress spoilage yeasts such as Brettanomyces bruxellensis (Veloso et al. 2024, Guzzon et al. 2025). In addition, yeast-mediated detoxification of fruit juices for complete removal of mycotoxins is emerging as a bioprotective strategy, as recently demonstrated by Zhou et al. (2025) with the removal of patulin from apple juice using a strain of Wickerhamomyces anomalus.

Mechanisms of biocontrol and bioprotection

Biocontrol and bioprotectant agents inhibit phytopathogens and suppress spoilage microorganisms through multiple synergistic mechanisms (Spadaro and Droby 2016, Freimoser et al. 2019). Competition for space and nutrients enables these yeasts to colonize fruit wounds and natural openings, pre-empting pathogen establishment (Spadaro and Droby 2016, Wu et al. 2025). This is particularly critical for oxidative yeasts, which can establish on fruit surfaces without consuming fermentable sugars, making them ideal for fresh fruit biocontrol where fermentation must be avoided (Martín et al. 2024). It is important however to note that this mechanism depends on various factors, including sufficient antagonist cell concentrations, rapid growth and colonization of wound areas, as well as biofilm formation and adhesion to the hyphae of target pathogens as reviewed by Agirman et al. (2023).

Another mechanism is production of antimicrobial metabolites, which encompasses several classes of compounds. For instance, volatile organic compounds (VOCs), including alcohols, esters, and terpenes can diffuse through air spaces and remotely inhibit pathogens (Arrarte et al. 2017, Tilocca et al. 2020). Additionally, other biocontrol and bioprotectant agents employ direct contact in tandem with production of hydrolytic enzymes such as chitinases, β-glucanases, and proteases that degrade fungal cell wall components, killing hyphae and spores (Dmytruk et al. 2026), while others produce antimicrobial peptides and killer toxins (mycocins), which are small proteinaceous compounds that implant into pathogen cell membranes creating pores that disrupt ion homeostasis and induce intracellular reactive oxygen species (ROS) accumulation, leading to cell death (Oufensou et al. 2023, Oztekin et al. 2023, El Dana et al. 2025). Killer toxins produced by non-Saccharomyces yeasts such as P. kluyveri (Pintar and Starmer 2003) and Wickerhamomyces anomalus (Mannazzu et al. 2019), exhibit species-specific fungicidal activity against spoilage fungi including Brettanomyces bruxellensis and Penicillium spp. (Dmytruk et al. 2026).

Iron sequestration represents a sophisticated competitive mechanism. For instance, pulcherrimin (produced by M. pulcherrima) binds Fe(III) with extremely high affinity, precipitating it as insoluble complexes (Wang et al. 2023, 2025). This deprives phytopathogens of essential iron, which is required for respiration, DNA synthesis, and enzymatic reactions. Many fungal pathogens cannot grow under iron-limited conditions, making this mechanism particularly effective against postharvest decay (Pijuan et al. 2023).

Yeasts often rely on multiple mechanisms, which might all not be actively simultaneously. Indeed, Agirman et al. (2023) allude to the fact that the activation of any given mechanism may be influenced by the characteristics of the target pathogen, the host plant as well as environmental factors.

Yeasts as biocontrol agents on fruits

Yeasts have emerged as desirable candidates for pre- and post-harvest management of fruit and beverage spoilage. This is mainly due to their ability to colonize different surfaces, utilize diverse carbon sources as well as their ability to tolerate broad temperature and pH conditions. Over the past decade, many yeasts have been extensively evaluated for their ability to inhibit critical fruit pathogens and to prevent wine spoilage. Mostly oxidative and weakly fermentative yeasts, in the two phyla Ascomycota and Basidiomycota that dominate fruit surfaces, have been screened. Evidently, the biocontrol potential in the Ascomycota is widely distributed within the class Pichiomycetes (Supplementary Table S1), with genera such as Candida, Metschnikowia, Meyerozyma, and Pichia most represented (Supplementary Table S2). Other genera such as Wickerhamomyces and Starmerella in the class Saccharomycetes and Dipodascomycetes, respectively, have also been widely studied. In the Basidiomycota, the biocontrol agents are mainly assigned in the class Microbotryomycetes and Tremellomycetes (Supplementary Table S1; Supplementary Table S2). Among the Pichiomycetes, Metschnikowia pulcherrima, Meyerozyma guilliermondii, Suhomyces pyralidae, Candida oleophila, and Meyerozyma caribbica have been more widely characterized (Fig. 2). Moreover, commercial products have been developed for bioprotection of beverages such as wine and for postharvest biocontrol of fungal pathogens of fruits. These include M. pulcherrima Zymaflore™ KHIO^MP (Laffort), Level² Guardia™ (Lallemand), C. oleophila Nexy® (Agrauxine by Lesaffre), and S. pyralidae Level² SALVA™ (Lallemand).

Figure 2.

A treemap showing the frequency of occurrence (i.e. the number of articles in which the species was reported) in bioprospecting campaigns for biological control agents against various fungal pathogens of fruit crops and beverages spoilage yeasts represented in Supplementary Table S2. Species with one or two citations were either grouped under their respective genus or grouped into ‘Others’.

Pichiomycetes

Candida oleophila

Amongst the yeasts found in the class Pichiomycetes, Candida oleophila showed biocontrol activity against Penicillium digitatum and P. italicum on citrus fruits (Bar-Shimon et al. 2004, Liu et al. 2019 ). Competition for nutrients and space is believed to be the major mode of action (Liu et al. 2019), but C. oleophila is capable of producing and secreting various cell wall-degrading enzymes, including exo-β-1,3-glucanase, chitinase, and protease (Bar-Shimon et al. 2004, Freimoser et al. 2019, Comitini et al. 2023), and has also been reported to induce host resistance (Liu et al. 2019).

In addition to direct competition, C. oleophila relies on its own genetic adaptation to survive wound-induced stress and its ability to act as a bio-elicitor that primes the host plant’s immune response. This is characterized by a burst of ROS particularly on fruit wounds (Nie et al. 2019, Li et al. 2023). Regarding elicitation of the host defence, C. oleophila up-regulates genes encoding pathogenesis-related proteins in the host plant, including β-1,3-glucanases that degrade the fungal cell wall of invading pathogens (Rovetto et al. 2024) as well as genes encoding defensive enzymes like peroxidase (POD), which helps detoxify harmful ROS and phenylalanine ammonia-lyase (PAL), which is involved in defence responses against infections (Gao et al. 2021, Rovetto et al. 2024). At the genetic level, the biocontrol capabilities of C. oleophila are regulated by the MADS-box transcriptional factor Rlm1, critical for maintaining cell wall integrity, endoplasmic reticulum function, and overall tolerance to abiotic stresses, including heat, salt, and oxidative stress (Sui et al. 2020).

Studies have shown that enhancing the tolerance of C. oleophila to oxidative stress typical in fruit wounds significantly boosts its biocontrol efficacy. For instance, pre-treatment of the yeast with caffeic acid prior to application was shown to up-regulate yeast antioxidant genes such as catalase (CAT), tioredoxin reductase (TrxR), and glutathione peroxidase (GPX), thereby enabling the yeast to efficiently detoxify ROS (Li et al. 2023). Similarly, culturing the yeast with trehalose promoted intracellular accumulation, and triggered upregulation of CAT and TrxR (Nie et al. 2019). Alternatively, C. oleophila can be combined with oligogalacturonide, a pectin-derived bio-elicitor resulting in increased POD and PAL enzyme activity in host fruit (Gao et al. 2021).

The C. oleophila strains I-182 and O have been developed into the biocontrol products Aspire® and Nexy®, respectively. The latter was the first biocontrol yeast to be registered against a post-harvest disease (Wisniewski et al. 2007), while C. oleophila strain O has been approved as a plant protection agent in Europe since 2015 (European Food Safety Authority, EFSA 2015).

Metschnikowia pulcherrima

The pulcherriminic acid-secreting yeast M. pulcherrima was shown to control P. digitatum and P. expansum on lemons (Oztekin and Karbancioglu-Guler (2021), strawberries and mandarins (Parafati et al. 2017), as well as Botrytis cinerea on grapes (Parafati et al. 2015, Agarbati et al. 2022), strawberries, and mandarins (Parafati et al. 2017, Öztekin and Karbancioglu-Guler 2023). Strains of M. pulcherrima may also exhibit both intra- and interspecific antagonistic activity and have been shown to inhibit P. membranifaciens, H. uvarum, and T. delbrueckii strains (Vepštaitė-Monstavičė et al. 2025). The biocontrol ability of M. pulcherrima may be attributed to the production of killer toxins (Puyo et al. 2023a) or the activity of pulcherrimin, a well-known compound for antimicrobial properties (Sipiczki 2006, 2020, Gore-Lloyd et al. 2019). Several authors reported multiple mechanisms of action, such as production of lytic enzymes and VOCs, biofilm formation, and iron depletion (Parafati et al. 2015, Oztekin and Karbancioglu-Guler 2021). In addition to antifungal activity, several M. pulcherrima isolates also showed antibacterial activity against Staphylococcus aureus, Salmonella enterica, and Escherichia coli (Hicks et al. 2021), which increases their potential for application in the food industry. Mechanisms of antimicrobial activity included the production of pulcherrimin, and other proteins that are produced specifically in response to the presence of some bacteria (Hicks et al. 2021).

Meyerozyma spp.

Meyerozyma species, particularly Meyerozyma guilliermondii and Meyerozyma caribbica, have been studied for many years to unravel their biocontrol potential. Strains of these species display biocontrol activity and capability to suppress a wide array of postharvest phytopathogenic fungi across diverse fruit hosts.

Meyerozyma guilliermondii is a highly versatile, broad-spectrum antagonistic yeast. Indeed, strains of this species have been shown to significantly reduce the incidence and severity of blue mould (Penicillium expansum, P. italicum, P. crustosum) on oranges, apples, and pears (Lopez-Cruz et al. 2023), and Orah (a citrus hybrid; Ye et al. 2024), grey mould (B. cinerea) on apples and pears, table grapes, and blueberries (Lopez-Cruz et al. 2023, Sepúlveda et al. 2023, Covarrubias-Rivera et al. 2025), green mould (Penicillium digitatum) on oranges, soft rot (Rhizopus stolonifer, Cladosporium cladosporioides) on apples and pears (Lopez-Cruz et al. 2023) and blueberries (Covarrubias-Rivera et al. 2025), as well as Colletotrichum gloeosporioides infection of papaya fruit (López-Cruz et al. 2025). Application by spraying was reported to result in better fruit surface colonization and disease suppression than dipping (Lopez-Cruz et al. 2023). Similarly, M. caribbica displays considerable biocontrol properties against P. expansum and Botryosphaeria spp. on kiwifruit (Pan et al. 2022, Qiu et al. 2022), P. expansum on apples (Yang et al. 2020) and pears (Zhang et al. 2026) as well as Alternaria alternata in jujube fruits (Deng et al. 2022).

Biocontrol by M. guilliermondii and M. caribbica is attributed to a complex mechanism of action encompassing different strategies. Both can grow rapidly to colonize fruit wounds and surfaces, and outcompete the pathogens for simple sugars, amino acids and space (Deng et al. 2022, Pan et al. 2022, Qiu et al. 2022, Ayon-Macias et al. 2025). On Orah fruits, M. guilliermondii was also shown to increase the diversity and interaction density of the native fungal microbiome, thus creating a competitive ecological network that crowds out the pathogen while simultaneously, inducing the downregulation of host metabolites associated with pathogen growth (Ye et al. 2024). In addition, the production of VOCs, with phenyl ethanol as the hallmark VOC, as well as the secretion of chitinases, β-1,3-glucanases, and proteases that facilitate hyperparasitism, have been highlighted as part of the important arsenal of M. guilliermondii and M. caribbica, when confronting various pathogens (Sepúlveda et al. 2023, Ayon-Macias et al. 2025, Zhang et al. 2026). Biofilm formation and production of siderophores to sequester iron have been highlighted in M. caribbica (Qiu et al. 2022, Sepúlveda et al. 2023).

Recently, M. caribbica and M. guilliermondii used in co-cultures in a 1:1 ratio were shown to result in an additive synergistic effect, with significant reduction in severity of disease caused by R. stolonifer and Lasiodiplodia theobromae in jackfruit (Ayon-Macias et al. 2025). Moreover, the biocontrol efficacy of Meyerozyma species can be improved by using specific biochemical supplements and physical treatments. For instance, xylitol was shown to protect M. guilliermondii against abiotic oxidative stress, by reducing intracellular accumulation of ROS. Furthermore, this sugar alcohol prevented mitochondrial membrane dysfunction and preserved ATP production (Zhang et al. 2025). Similarly, calcium ascorbate enhanced oxidative stress tolerance by upregulating antioxidant genes and increasing the activities of superoxide dismutase and catalase and promoted environmental adaptability and metabolic capacity by upregulating genes linked to ribosome synthesis, accelerating cell division, and increasing succinate dehydrogenase activity to boost ATP production (Guo et al. 2023). In contrast, supplementation with phytic acid was shown to enhance the ability of M. caribbica to regulate ROS metabolism and defence mechanisms with the host fruit unlike xylitol and calcium carbonate that protect the yeast cells (Foku et al. 2024). Finally, the amino acid phenylalanine was shown to promote the formation of dense biofilms by M. caribbica and secretion of extracellular matrix that allow the yeast to adhere tightly to fruit wounds and outcompete pathogens (Deng et al. 2022).

Pichia kluyveri

Several Pichia species, such as Pichia manshurica (synonym: Pichia galeiformis, Chen et al. 2020), and Pichia membranifaciens (Lutz et al. 2013) have been evaluated as biocontrol agents against various postharvest pathogens. Pichia manshurica showed potential to control postharvest green mould (P. digitatum) on citrus, and the mechanisms of action included competition for space and nutrients, as well as production of VOCs (Chen et al. 2020).

Pichia kluyveri inhibited the growth of Alternaria alstroemeriae (Mewa-Ngongang et al. 2019b), B. cinerea (Mewa-Ngongang et al. 2019b, Gomomo et al. 2025a), Colletotrichum acutatum (Mewa-Ngongang et al. 2019b), R. stolonifer (Mewa-Ngongang et al. 2019b), P. digitatum, P. expansum, and P. italicum (Gomomo et al. 2025b) during in vitro and in vivo trials on apples, grapes, and citrus. Mechanisms of action were competition for nutrients and space, production of lytic enzymes and VOCs, or the synergistic interaction of these modes (Mewa-Ngongang et al. 2019b, Gomomo et al. 2022, 2025a, 2025b). Pichia kluyveri also inhibited the growth of Brettanomyces anomalus, B. bruxellensis, and Zygosaccharomyces cidri in vitro through the production of antimicrobial compounds (Mewa-Ngongang et al. 2019a).

Suhomyces pyralidae

Suhomyces pyralidae (formerly: Candida pyralidae) showed effective inhibition of A. alstroemeriae (Gomomo et al. 2022), B. cinerea (Mewa-Ngongang et al. 2019b, Gomomo et al. 2025a, Nkomonde et al. 2025), Colletotrichum acutatum (Mewa-Ngongang et al. 2019b), Fusarium fujikuroi (Nkomonde et al. 2025), P. digitatum, P. expansum, P. italicum (Gomomo et al. 2025b), and R. stolonifer (Mewa-Ngongang et al. 2019b) during in vitro and in vivo trials on apple, pear, strawberry, tomato, grapes, and citrus. Mechanisms of action were competition for nutrients and space, production of lytic enzymes, as well as VOCs, or the synergistic interaction of these modes (Mewa-Ngongang et al. 2019b, Gomomo et al. 2025a, 2025b, Nkomonde et al. 2025). Mehlomakulu et al. (2014, 2017) demonstrated inhibition of B. bruxellensis, through the production of killer toxins, during in vitro studies. In addition, S. pyralidae was reported to suppress the growth of other yeasts such as M. guilliermondii (previously: Candida guilliermondii), B. anomalus, and Zygosaccharomyces bailii in vitro through the production of antimicrobial compounds (Mewa-Ngongang et al. 2019a).

Saccharomycetes

Kluyveromyces marxianus

Kluyveromyces marxianus was able to protect strawberries against B. cinerea (Dos Santos et al. 2023), apples against P. expansum (Huang et al. 2024), as well as tomatoes and grapes against Aspergillus carbonarius and F. oxysporum (Alasmar et al. 2020). Furthermore, mycocin extracts from K. marxianus showed stable and effective antibacterial properties against pathogenic E. coli both in vivo and in vitro (Chen et al. 2015). Mechanisms of action include the production of lytic enzymes (Dos Santos et al. 2023), VOCs (Alasmar et al. 2020), competition for resources and space, as well as activation of genes involved in the transduction of plant hormone signals (Huang et al. 2024).

Wickerhamomyces anomalus

Wickerhamomyces anomalus (formerly Pichia anomala) has attracted attention as a potential biocontrol agent against blue and grey mould on various fruit including strawberries and mandarins (Parafati et al. 2017, Zhao et al. 2026), apple (Kwasiborski et al. 2014, Zhao et al. 2021), grapes (Maluleke et al. 2022), oranges (Aloui et al. 2015 ), kiwifruit (Zhao et al. 2023a), and peaches (Zhou et al. 2024). Although there are intraspecific variations in antifungal activity and the expressed mechanisms of action, strains of W. anomalus have been reported to inhibit pathogen mycelial growth by competitive colonization of fruit surfaces, natural or mechanical wounds (Kwasiborski et al. 2014, Zhao et al. 2021, 2023a). Along with this, the production of cell wall-degrading enzymes, particularly glucanases and chitinases, has been implicated in the mycelial growth-inhibiting capacity of W. anomalus strains (Muhammed et al. 2019, Maluleke et al. 2022).

Recently, strains of W. anomalus were shown to form robust biofilms and adhere tightly to the hyphae of B. cinerea and P. expansum on kiwifruit, thereby creating a mechanical barrier that restricts pathogen spread and alter hyphal structure (Zhao et al. 2023b, Zhou et al. 2024), while also producing potent antifungal VOCs such as 2-phenylethyl acetate, 1-butanol, and phenylethyl alcohol (Zhao et al. 2023b), which can suppress mycelial growth and spore germination. Beyond direct antagonism against target pathogens, some strains of W. anomalus modulate the fruit’s microbiota, decreasing the abundance of pathogenic fungi while promoting beneficial bacteria (Zhao et al. 2023a). Such a shift in community structure enhances the disease-suppressive microbiome on the host fruit.

Although it is a potent biocontrol agent, the efficacy of W. anomalus is dose-dependent, with optimal or complete suppression of target pathogens achieved at 1 × 10⁸–1 × 10⁹ cells/ml in vitro but not always in vivo (Zhao et al. 2021, 2023a, 2026, Zhou et al. 2024). Nonetheless, the biocontrol potential can be enhanced by combining W. anomalus with natural elicitors like 1% chitosan, which boosts the production of antifungal VOCs and enhances the defence enzyme activities and ROS scavenging capacity within the fruit host (Guo et al. 2025).

Tremellomycetes

Naganishia albida

Naganishia albida (synonym: Cryptococcus albidus) controlled the growth of B. cinerea on strawberry fruit and plants in field trials (Kowalska et al. 2012), inhibited B. cinerea and P. expansum on apples (Fan and Tian 2001) and pears (Lutz et al. 2013), P. digitatum on citrus (Oro et al. 2016), as well as Monilinia fructicola, P. expansum, and Rhizopus stolonifer on apples (Chan and Tian 2005). Similarly, Papiliotrema laurentii (synonym: Cryptococcus laurentii) was found to inhibit postharvest decay of peaches by various phytopathogens without causing any negative impact on fruit quality (Zhang et al. 2007). Importantly, the depence of efficacy on the cell contration of the yeast was emphasized. Mechanisms of action include attachment to fungal hyphae, along with the secretion of extracellular lytic enzymes (Chan and Tian 2005, Lutz et al. 2013), wound colonization, germination inhibition, biofilm formation, secretion of killer toxins, and competition for nutrients (Lutz et al. 2013, Freimoser et al. 2019).

Microbotryomycetes

Rhodotorula dairenensis demonstrated effective inhibition against B. cinerea and F. fujikuroi in vitro, as well as in vivo on pears and tomatoes (Gomomo et al. 2022, Nkomonde et al. 2025). Mechanisms of action were competition for nutrients and space, as well as production of lytic enzymes and VOCs (Gomomo et al. 2022, Nkomonde et al. 2025). In contrast, Rhodotorula mucilaginosa was found to inhibit postharvest grey mould, blue mould and antural decay of apples through competition for space and nutrients, as well as induction of host defence enzymes such as peroxidase and polyphenoloxidase (Li et al. 2011).

Sporidiobolus pararoseus suppressed Aspergillus niger on grapes (Li et al. 2017), Monilinia fructicola on nectarines (Janisiewicz et al. 2010), and B. cinerea on strawberries (Huang et al. 2012, Li et al. 2024) and peaches (Shen et al. 2019). The modes of action include enhanced competitiveness for nutrients and space, as well as an induction of host defence enzymes thereby enhancing the disease resistance of the fruits (Li et al. 2017).

Other species

Yeast species from the genus Candida, other than C. oleophila have been applied as biocontrol agents to various crops and showed a broad spectrum of activity. Candida intermedia inhibited Colletotrichum gloeosporioides in avocado (Campos‐Martínez et al. 2016), Candida membranifaciens suppressed B. cinerea in grapes (Kasfi et al. 2018) and controlled Botryosphaeria dothidea in mango (Terao et al. 2017). Candida tropicalis reduced decay in litchi (Zhimo et al. 2018) and Colletotrichum musae in bananas (Zhimo et al. 2017). It also worked synergistically with plant extracts to control P. digitatum in citrus (Sukorini et al. 2013). Candida tropicalis also showed inhibition against Alt. alternata, B. cinerea, Aspergillus spp., Curvularia spp., R. stolonifer, and Colletotrichum gloeosporioides in vitro (Baral et al. 2025). Mechanisms such as rapid colonization, competition for nutrients and space, production of hydrolytic enzymes, induction of host defences, and antifungal compound production contribute to its antagonistic action (Terao et al. 2017, Zhimo et al. 2018, Baral et al. 2025).

Yeasts as bioprotectants in beverages

Bioprotection is positioned as an alternative to chemical preservatives in the production of beverages. It relies on the use of beneficial microorganisms (currently mainly yeasts) to control undesirable microbes or toxins in food systems through natural ecological interactions (Chacon-Rodriguez et al. 2020). Bioprotection of beverages is in infancy and has mainly been investigated in winemaking where grape musts are inoculated with selected antagonistic yeasts during pre-fermentative stages (Windholtz et al. 2021a, 2021b, Puyo et al. 2024, Veloso et al. 2024). Weakly fermentative yeasts such as M. pulcherrima and M. fructicola demonstrate strong antagonistic activity against spoilage yeasts such as B. bruxellensis, Hanseniaspora spp., and acetic acid bacteria (Aragno et al. 2024). However, efficacy is strain and context dependent. For instance, in their study Simonin et al. (2020) observed no influence of M. pulcherrima MCR24 strain on B. bruxellensis and acetic acid bacteria population on Pinot Noir in three wineries. Similarly, Candida spp. have been investigated for their ability to suppress the growth of spoilage microorganisms, with C. oleophila displaying significant efficacy against lactic acid bacteria, while C. boidinii was effective against acetic acid bacteria and B. bruxellensis (Veloso et al. 2024). In contrast, Zhang et al. (2025) used K. marxianus XZ1 to degrade patulin, and this strain removed 100% of the patulin in raw apple juice and commercial apple juice after 60 h. Patulin is a prevalent mycotoxin synthesized by various fungi of the genera Aspergillus, Byssochlamys, Paecilomyces, and Penicillium (Ioi et al. 2017, Agriopoulou et al. 2020). Bioprotective yeasts can also modulate the fermentation microbiome. For instance, a strain of P. kluyveri decreased the relative abundance of acetic acid bacteria and increased lactic acid bacteria, while an H. uvarum strain reduced the diversity and richness of the fungal community (Guan et al. 2025).

Similar mechanisms of action, such as nutrient competition, oxygen depletion, production of antimicrobial compounds, niche exclusion, and cell-to-cell contact, employed by various biocontrol yeasts are also used in bioprotection (Puyo et al. 2023a, 2024, Windholtz et al. 2023, Barbato et al. 2025, Guan et al. 2025). The bioprotective effect of various yeasts is dependent on the ratio of the inoculated strain to the native spoilage microbiota (Puyo et al. 2023a, Guan et al. 2025), grape maturity (Windholtz et al. 2021b) as well as temperature and settling time (Simonin et al. 2022). While bioprotection is effective in preventing microbial spoilage, its efficacy regarding protection against oxidation is not yet comparable to that of SO₂ (Lebleux et al. 2023). To overcome this limitation, recent strategies have evaluated the combination of bioprotective yeasts with oenological tannins such as quebracho or gall nut tannins and found such additions to provide the necessary antioxidant power in rosé and white wines to a degree comparable to SO₂ (Puyo et al. 2023b).

Factors affecting the efficacy of biocontrol and bioprotectant agents

While microbial biocontrol agents and bioprotectants offer promising alternatives to chemical pesticides, their efficacy is highly variable and influenced by multiple interacting factors. Environmental conditions critically determine the performance of biocontrol agents. Temperature, pH, humidity, UV exposure, rainfall, and substrate characteristics all influence activity (Carbó et al. 2019). Most yeasts exhibit optimal antagonistic activity within the 15–30°C range, with reduced efficacy at extremes. UV radiation compromises epiphytic survival on plant surfaces, limiting field applications unless protective formulations are employed. In fermentation substrates, high SO₂ and sugar levels can inhibit yeast growth (Sui et al. 2015). In contrast, pre-adaptation of the biocontrol agents may enhance biocontrol efficacy. Indeed, Sui et al. (2021) demostrated that exposure of Debaryomyces hansenii to sublethal doses of H₂O₂ improved the tolerance of the yeast to accummulation of ROS at wound sites on the fruit and enhanced its biocontrol efficacy against B. cinerea and A. alternata.

Application timing substantially affects outcomes. Pre-inoculation applying biocontrol agents before pathogen introduction consistently outperforms post-inoculation by allowing protective microbiota to establish on plant surfaces or wounds prior to pathogen challenge (Fenta et al. 2023). There appears to be a critical application window, particularly for fruit wound colonization (Ramudingana et al. 2025).

Strain-specific variation is a major determinant of efficacy. Within the same species, individual strains exhibit markedly different antagonistic potencies based on killer toxin, siderophore, and VOC production (Legein et al. 2020, Roca-Couso et al. 2021). Some strains show strong activity, while others are negligible. Industrial applications require substantially higher concentrations of biological agents than ambient background levels, raising questions about environmental persistence (Roca-Couso et al. 2021, Fenta et al. 2023).

Several strategies have been proposed to enhance the efficacy of biological control agents. For instance, microencapsulation and use of nanocarriers have been suggested as methods to consider for improving stability of biological control agents, enhancing their environmental tolerance, and promoting colonization of fruit surfaces (Liu et al. 2026, López-Cruz et al. 2025). Dry powder, encapsulation, and active dry yeast preparations improve viability, protect against UV and desiccation, and extend field activity explaining why commercial products often outperform raw culture applications (Carbó et al. 2017). This is illustrated by Candida sake CPA-1, which is effective against several postharvest diseases; in one study, the microorganism was optimized in a dry formulation using a fluidized bed drying system to improve shelf life and manipulability for future commercial use. The same study then evaluated the shelf life of the optimized formulation and its efficacy against P. expansum on apples, showing that formulation is essential not only for maintaining viability during storage but also for preserving biocontrol performance in practice (Carbó et al. 2017). Combining biological agents with compounds such as carboxymethyl cellulose, which are generally regarded as safe and other additives such as trehalose has also been proposed as ways to enhance effectivity (Liu et al. 2026). N-acetylglucosamine supplementation of K. marxianus was reported to enhance the production of several biocontrol related enzymes and stress resistance metabolites and utlimately its antagonistic activity against P. expansum (Wu et al. 2023). Recently, pectin-based edible coating embedded with M. guilliermondii was also shown to effectively inhibit spore germination of Colletotrichum gloeosporioides and prevent postharvest spoilage of papaya fruit (López-Cruz et al. 2025).

Environmental implications and challenges in using biocontrol and bioprotectant microorganisms

Chemical pesticides and fungicides have been used efficiently to control pests and diseases, but their long-term use has been linked to detrimental effects on the environment and human health, including biodiversity loss, soil and water contamination, and risks to non-target organisms (Tilocca et al. 2020, Zhang et al. 2020). Similarly, the environmental impact of indiscriminate or prolonged applications of biocontrol agents will need careful evaluation, even though many of these microbes occur naturally in the environment and agricultural ecosystems (van Lenteren et al. 2018). Under industrial-scale agriculture, introduced biocontrol agent populations are typically much higher than ambient background levels, which raises questions about their persistence, interactions with indigenous microbiota, and potential off-target effects (van Lenteren et al. 2018, Hauschild et al. 2025). The use of biocontrol agents in other sectors, such as beverage production and similar industrial processes, introduces additional downstream challenges related to the removal or disposal of live microbial cultures from wastewater and fermentation residues. If not properly managed, these releases could alter local microbial communities or interact unexpectedly with aquatic or terrestrial biota, underscoring the need for robust environmental risk assessments and monitoring protocols for both agricultural and industrial applications of microbial biocontrol and bioprotectant products (Amichot et al. 2025).

A further challenge in the application of biocontrol agents is the cultivation of sufficient biomass (Bejarano and Puopolo 2020). For laboratory-scale evaluations, this is usually not a problem, and the microorganisms can be grown in nutrient-rich laboratory media. However, each species will have their own nutrient requirements, and there is no universal protocol that biocontrol agent manufacturers can follow. Furthermore, laboratory media for large-scale biomass production is unsuitable and uneconomical. Consequently, low-cost substrates have to be considered, and the formulation will most likely require supplementation of essential nutrients. Industrial bio-products and waste material such as molasses, cheese whey, various cereal brans and fibres, and wastewater sludges can serve as alternative carbon and nitrogen sources. Growth parameters such as pH, temperature, and agitation speed need to be specified. Dependent on the industrial process, thermo- and osmotolerant protectants may need to be incorporated to ensure cell survival. The final formulation will also need to adhere to food safety laws. Safety consideration for personnel using or applying the biocontrol will also be required. The fitness and viability of the resultant biomass is also important. Storage and shelf life of the products also needs to be considered, whether it be powder, granules, or emulsions (Bejarano and Puopolo 2020). Additional criteria recently proposed by Agirman et al. (2023) and Liu et al. (2026) for selection of biological control agents include (i) minimum effective dose, (ii) colonization capacity at wound sites and fruit surfaces, (iii) performance stability under fluctuating environmental conditions (e.g. temperature, humidity, modified atmosphere), (iv) presence of defense-priming markers, and (v) organoleptic neutrality as well as absence of toxicological and allergenicity. These criteria expand evaluation procedures for isolation and identification of yeasts with biocontrol potential beyond the typical demonstration of antimicrobial activity and would help address most of the challenges encountered especially when biological control agents are tested in field studies.

Concluding remarks

The use of yeasts as biological control and bioprotection agents shows great potential to be integrated into a sustained agricultural ecosystem. However, further research is needed to optimize and build on the initial promising results published thus far. Evidently, while a large number of yeasts have been characterized, only a few have been developed into commercial products. More research into formulation and storage methods is needed to advance the knowledge beyond just screening and phenotypic characterization, to understanding the genetic and phenotypic mechanisms underpinning the niche construction capabilities and long-term consequences of persistence of biocontrol agents on fruit crops. A positive aspect is that lessons learnt from the use of synthetic pesticides over many years can guide this new technology thereby preventing a repeat of mistakes made. Based on the available literature, it is evident that oxidative and weakly fermentative yeasts will continue to be the focus of research and, despite numerous challenges, will fulfil the needs of commercial agriculture and beverage production facilities in an integrated manner.

Author contributions

E.M., H.W.D., N.P.J., and M.E.S. collected data, analysed data, edited and approved the final version of the manuscript.

Conflicts of interest

The authors declare no competing interests.

Funding

None declared.