Current status and future trends of eco-friendly management of postharvest fungal decays in tomato fruit

Abstract

This article reviews sustainable strategies to control postharvest fungal decay (e.g., Botrytis cinerea, Alternaria spp., and Colletotrichum gloeosporioide) in tomato. Eco-friendly alternatives to synthetic fungicides, focusing on microbial antagonists, and integrated approaches combining biological control with natural compounds, are discussed. Emerging technologies like microbial consortia, nanomaterials, and CRISPR/Cas9 show great potential, though further research and regulatory approval are required. These sustainable methods are crucial for maintaining tomato quality and yield while supporting environmentally responsible production.

Introduction

Tomatoes are widely consumed in China and many other countries. The most recent data show that annual tomato production globally has exceeded 192 million tons in 2023, with that in China being ~70 million tons¹, and plays a major role in the national agricultural economy. Tomato fruits, however, are susceptible to a variety of pathogens, including bacteria, fungi, and viruses that infect tomatoes at different stages of production. With the change in global climate, tomato fruits have become increasingly susceptible to pathogen infection.

Being a soft, fleshy fruit that quickly loses its firm texture during over-ripening, the postharvest loss of tomato could account for up to 50% of the harvest in some extreme cases^2,3. In particular, the infection of tomatoes by postharvest decay fungi, such as Botrytis cinerea, Alternaria alternata, Rhizopus stolonifer, Fusarium oxysporum, Colletotrichum gloeosporioides, Alternaria solani, Colletotrichum acutatum, and Fusarium sp., with B. cinerea being the most prevalent^4,5, causes significant reductions in quality and marketable yield^6,7. In this regard, different disease management methods can be used to mitigate the losses resulting from postharvest decay pathogens effectively. In response to the demand for sustainable agricultural development, environmental pollution, consumer concerns about the harm of fruit drug residues to human health, and regulatory restrictions on the use of synthetic drugs in postharvest chemicals, alternative disease management practices have always been a focus of extensive research. Eco-friendly (low toxicity and environmental impact) management of postharvest diseases, such as biological control^8–11, application of natural compounds¹², and integrated management methods have received a great deal of attention and wider application. Representative studies on eco-friendly methods of postharvest fungal decay management in tomatoes utilizing microbial antagonists are listed in Table 1.

Table 1.

Representative studies on the use of microbial antagonists for the management of postharvest diseases of tomato

Control method	Disease	Pathogen	Host	Reference
Biocontrol yeast Wickerhamomyces anomalus	Gray mold; Black rot; Fusarium wilt	B. cinerea; A. alternata; F. oxysporum	Tomato (S. lycopersicum cv. Zhefen 301)	49,107–109
Biocontrol yeast Candida guilliermondii	Gray mold	B. cinerea	Tomato (S. lycopersicum)	110
Biocontrol yeast Rhodosporidium paludigenum	Black rot	A. alternata	Cherry tomato (L. esculentum)	111
Biocontrol yeast Saccharomyces cerevisiae	Gray mold	B. cinerea	Cherry tomato (L. esculentum)	50
Biocontrol yeast Pichia caribbica	Black rot	A. alternata	Tomato (S. lycopersicum)	51
Biocontrol yeast Pichia guilliermondii	Early blight; Soft rot; Gray mold	A. solani; R.stolonifer; B. cinerea	Tomato (S. lycopersicum)	98
Biocontrol yeast Pichia kudriavzevii	Gray mold; Black rot	B. cinerea; A. alternata	Cherry tomato (L. esculentum cv. Miny Tomato)	105
Biocontrol yeast Bacillus subtilis	Gray mold	B. cinerea	Cherry tomato (L. esculentum)	112
Biocontrol yeast Bacillus mojavensis	Gray mold	B. cinerea	Cherry tomatoes (S. lycopersicum cv. Ailsa Craig)	55
Biocontrol yeast Bacillus cereus	Fusarium wilt	F. oxysporum	Cherry tomato (L. esculentum)	113
Biocontrol fungus Metarhizium anisopliae	Gray mold	B. cinerea	Cherry tomato (L. esculentum)	114
Biocontrol fungus Clonostachys rosea	Gray mold	B. cinerea	Tomato (S. lycopersicum)	10
Chitosan	Gray mold; Early blight	B. cinerea; A. solani	Cherry tomato (L. esculentum)	115,116
Harpin	Gray mold; Black rot	B. cinerea; A. alternata	Tomato (S. lycopersicum)	75
Dextran	Gray mold	B. cinerea	Cherry tomato (L. esculentum)	63
Yeast mannan	Black rot	A. alternata	Tomato (S. lycopersicum cv. Tuofu)	64
Antimicrobial peptide	Gray mold	B. cinerea	Cherry tomato (L. esculentum)	65
Essential oils	Black rot; Gray mold	A. alternata; B. cinerea	Cherry tomato (L. esculentum)	68,117,118
Chlorogenic acid	Fusarium wilt	Fusarium sp.	Cherry tomato (L. esculentum)	71
Gallic Acid	Early blight	A. solani	Tomato (S. lycopersicum)	73
Melatonin	Gray mold	B. cinerea	Cherry tomato (S. lycopersicum cv. No. 3 Zhengyinfen)	72
Methyl Jasmonate	Gray mold	B. cinerea	Tomato (S. lycopersicum)	30
Hot water	Gray mold	B. cinerea	Cherry tomato (L. esculentum cv. Fenhong)	119
Supplemental FR	Gray mold	B. cinerea	Tomato (S. lycopersicum)	89
ozone	Gray mold; Black rot	B. cinerea A. alternata	Cherry tomato (L. esculentum cv. Mareta)	120,121
N-vanillyl-octanamide	Anthracnose; Gray mold; Fusarium wilt; Early blight	C. gloeosporioides; B. cinerea; C. acutatum; Fusarium sp; A. solani	Tomato (S. lycopersicum)	122
Phenolic acids	Gray mold	B. cinerea	Tomato (S. lycopersicum cv. ChangFeng 903)	123
L-glutamate	Gray mold; Black rot	B. cinerea; A. alternata	Tomato (S. lycopersicum cv. Qianxi)	124,125
Selenium	Gray mold	B. cinerea	Cherry tomato (L. esculentum cv. Zhenbao)	126
Nanomaterial	Fusarium wilt	F. oxypsorum	Tomato (S. lycopersicum	127
Biocontrol yeast Candida guilliermondii+ hot water	Gray mold	B. cinerea	Cherry tomato (L. esculentum cv. Fenhong)	119
Biocontrol yeast Cryptococcus laurentii+ hot air	Gray mold	B. cinerea	Tomato (S. lycopersicum vr. Qianxi)	128
Chitosan + Vanillin	Fusarium wilt	F. oxysporum	Cherry tomato (L. esculentum)	102
Chitosan + Bacillomycin D	Soft rot; Gray mold	R. stolonifer; B. cinerea	Tomato (S. lycopersicum cv. Qian xi)	129

The objective of the present review is to provide an overview of the use of microbial antagonists and integrated, eco-friendly management methods to control the major postharvest fungal pathogens of tomatoes and their mechanisms of action. Recent novel, technological advances, such as the use of CRISPR/Cas9 technology, nanomaterials, and microbial consortia, are also discussed.

Major postharvest fungal diseases of tomatoes

Gray mold (Botrytis cinerea)

B. cinerea, the causal agent of gray mold, is a necrotrophic fungal pathogen with a broad host range, capable of infecting more than 500 plant species, and is considered one of the most economically important plant pathogens that cause major losses in fresh fruits and vegetables¹³. Gray mold caused by B. cinerea results in significant reductions in yield during both the preharvest and postharvest production of vegetables, fruits, flowers, and other crops, causing considerable economic losses worldwide. B. cinerea typically infects plants in the field, and after initial colonization, the infection becomes latent until harvest, storage, and postharvest ripening. Fruits lose their innate resistance during postharvest ripening and become susceptible to infection by fungal pathogens, which often transition from a latent stage to an active lesion stage, resulting in decay and contamination of stored fruit¹⁴. Tomato storage conditions are difficult, largely attributed to tomato fruit is highly susceptible to postharvest decay by B. cinerea and is regarded as a good model system to study postharvest diseases in fruit crops.

B. cinerea typically cannot penetrate the outer cuticle and epidermal cell walls of a host plant when attempting to establish an infection. Therefore, B. cinerea secretes a variety of cell wall-degrading enzymes (CWDEs) to degrade the plant cell wall. Several genes encoding plant cell wall modifying enzymes and proteins, such as polygalacturonase (PG) and pectate lyase (PL), have been reported to be involved in resistance to Botrytis spp. in tomato fruits¹⁵. CWDEs comprise different classes of carbohydrate-active enzymes (CAZymes), including carbohydrate esterases (CEs), glycoside hydrolases (GHs), and polysaccharide lyases (PLs). Although, there is a high degree of redundancy among CWDEs, in a few cases, the loss of a single gene has a significant impact on pathogenicity. For example, letion of either bcpg1 or bcpg2, two B. cinerea endopolygalacturonase genes, was reported to reduce fungal virulence^15,16. A reduction in pathogenicity was also observed following the deletion of a cellobiohydrolase gene (bccbh) and an endoglucanase gene (bceg)^17,18 reported that the transcription factor BcXyr1 positively regulates the expression of CAZyme-encoding genes and that the deletion of bcxyr1 significantly reduced the virulence of B. cinerea.

Reactive oxygen species (ROS) are the main products generated by NADPH oxidase (NOX) or as a natural byproduct of metabolic processes and play an important role in the pathogenic process of B. cinerea. The catalytic transmembrane subunits, BcNoxA and BcNoxB, function in the formation of sclerotia, with BcNoxA involved in fostering lesion development and BcNoxB fostering penetration, while BcNoxR functions as a regulator of both subunits. Deletion mutants of different Nox subunits exhibit defective sclerotium formation, mycelial growth, and appressorium formation¹⁹. Virus-induced gene silencing (VIGS) of SlPti5 in tomatoes inhibited early plant growth, increased susceptibility to infection, promoted ROS generation, affected the expression of ROS scavenging genes, and attenuated the expression of defense-related genes and ethylene/jasmonic acid metabolism²⁰. Li et al.²¹ reported that knocking out SlNPR1 (Non-expressor of pathogenesis-related gene 1) in B. cinerea resulted in increased defense enzyme activity in tomato plants, relative to wild-type B. cinerea, altered ROS homeostasis, and generally increased the resistance of tomato to B. cinerea. Zhang et al.²² analyzed the mixed transcriptome derived from B. cinerea- infected tomato leaves at 24 h post-inoculation and identified a new fungal transcription factor BcCGF1 in B. cinerea that plays a pleiotropic role in conidial germination, asexual reproduction, infection structure formation, host penetration, stress adaptation, and virulence. BcCGF1 enhances the virulence of B. cinerea by promoting infection-related development in B. cinerea controlled by BcCGF1-mediated endogenous ROS production.

Studies have also been conducted on the functional role of other B. cinerea genes related to growth, metabolism, and/or virulence, including two DNA methyltransferase genes, BcDIM2 and BcRID2²³, an efflux transporter²⁴, and actin¹⁷. The involvement of several other genes in tomato resistance to B. cinerea has also been documented, including SlSKIP²⁵, SlTCP29²⁶, SlMAPK3²⁷, SlMYC2²⁸, SlARG2²⁹, SlERF2³⁰, SlPti5²⁰, SlNPR1²¹, SlMBF1³¹, SlMYB1³², and SlERF.C1³³. In this regard, SlERF.C1, a member of the Group IX ERFs in tomato, can bind to the kinase MPK8 and enhance its regulation of the downstream target gene PR by phosphorylating SlERF.C1, which in turn improves the postharvest resistance of tomato to gray mold³³.

B. cinerea was shown to uptake small double-stranded RNA (dsRNA) molecules from a host plant. Notably, dsRNA can regulate gene expression through the RNA interference system. Duanis-Assaf et al.³⁴ targeted three essential transcripts active in the fungal ergosterol biosynthesis pathway and synthesized pray formulations of dsERG1, dsERG11, and dsERG13. The synthesized formulations significantly inhibited B. cinerea germination and growth on the surface of fruits and vegetables. RNAs that target pathogen genes represent a new and novel class of environmentally friendly fungicides. Future studies using CRISPR/Cas9-based methodology will provide data on the role of specific functional groups in degradative enzymes involved in disease development and used to generate fungal strains with multiple gene deletions³⁵. With the in-depth analysis of the interaction mechanism between B. cinerea and tomato, more and more genes that promote B. cinerea infection, as well as genes related to resistance or susceptibility to B. cinerea in tomatoes, have been excavated. Genetic engineering methods such as CRISPR/Cas9-based methodology to improve tomato resistance to B. cinerea have become an important development direction.

Other decay fungi

Although not as harmful as gray mold, several other fungal pathogens can also reduce the marketable yield and quality of tomatoes. A. alternata enters tomato fruit tissues during the harvest or preharvest period through wounds or natural openings, remains dormant for several days, and then becomes active, producing black spots designated as Alternaria rot. The spots appear as sunken lesions and are mainly found near the blossom or peduncle end of the fruit. The infection deteriorates fruit quality and hence its commodity value, resulting in significant economic losses³⁶. Previous studies by Yang et al.³⁷ reported that the application of glutamate could enhance the resistance of tomato fruit to A. alternata through glutamate-related metabolic pathways, including the γ-aminobutyric acid shunt, the tricarboxylic acid cycle, and proline biosynthesis from glutamate. More recently, Yang et al.³⁸ reported that exogenous treatment of tomato fruit with ethylene after inoculation with A. alternata accelerated disease development, where the application of ethephon (0.1 g/L) increased susceptibility to A. alternata infection in both untreated and glutamate-treated tomato fruit. Moghaddam et al.³⁹ conducted RT-qPCR and spectrophotometry analysis of 35 tomato genotypes and found that the expression level of antifungal genes in the fruit of 14 of the genotypes was enhanced one- to fifty-fold in response to inoculation with A. alternata. Additionally, in a comparison of susceptible and resistant tomato varieties, WRKY and PR genes were upregulated in the disease-resistant varieties, indicating that WRKYs induced by A. alternata may be involved in the increased expression of PR genes.

Colletotrichum species are characterized by a semi-biotrophic lifestyle. Fungal species in this genus initially infect their host through a short biotrophic phase, associated with large intracellular primary hyphae. The fungus later switches to a necrotrophic phase, associated with narrower secondary hyphae that spread throughout the host tissue⁴⁰. Anthracnose, caused by Colletotrichum sp., is a major plant pathogen worldwide, causing rot in many different fruits, including tomato, mango, and apple, resulting in significant global economic losses⁴¹. Mahto et al. ⁴² constructed transgenic lines of chili and tomato expressing CgCOM1-RNAi, which inhibited the germination, germ tube development, mycelial formation, and the growth of anthracnose conidia, and enhanced resistance to anthracnose in tomato-related crops. Spore germination and the development of an infection structure in C. gloeosporioides are highly sensitive to ethylene levels, and C. gloeosporioides may recognize the maturation of fruits by sensing ethylene. Ethylene significantly promotes the expression of genes related to melanin synthesis, chitin deacetylation, hydrophobic surface binding proteins, and appressorium-associated structure proteins in C. gloeosporioides⁴³.

Postharvest diseases of tomatoes not only cause significant economic losses but can also directly impact food safety and human health through the production of mycotoxins. Fortunately, eco-friendly management methods have been developed that reduce the economic losses caused by postharvest diseases and also address the food safety problems related to mycotoxins.

Eco-friendly management of postharvest fungal decays

Biological control

The biological control ability of many microorganisms is reportedly able to antagonize pathogens, expected to replace chemical fungicides attributed to their safety, economy, and effectiveness. Extensive research has been conducted on the use of antagonistic microorganisms to control postharvest diseases in horticultural crops, including tomatoes. Numerous studies have shown that antagonistic strains of yeast, bacteria, fungi, and actinomycetes can effectively control postharvest diseases in horticultural products under laboratory conditions⁴⁴.

Most studies on managing postharvest diseases of tomatoes have focused on the use of antagonistic yeasts. Many yeast species and strains of yeast species exhibiting biocontrol properties have been isolated over the past several decades, and some yeast-based products have been commercialized, such as Aspire^® and Nexy^® (Candida oleophila), CandifruitTM^® (Candida sake), Yieldplus^® (Cryptococcus albidus), Shemer^® (Metschnikowia fructicola), and BoniProtect^® (Aureobasidium pullulans), registered for use against several postharvest pathogens on many different fruit crops^45,46. Competition for nutrients and space is considered to be the main method by which antagonistic yeasts inhibit the establishment and growth of postharvest fungal pathogens. Antagonistic bacteria have also been used to compete with fungal pathogens for nutrients and space, thus preventing the establishment of fungal pathogens. Shi⁴⁷ et al. reported that A. pullulans S-2 exhibited excellent survival and colonization ability and competed with pathogenic fungi, such as Cladosporium, Mycosphaerella, Alternaria, and Penicillium, for nutrients and space, thus inhibiting the growth of pathogenic fungi and effectively controlling disease development. Shi et al.⁴⁷ also demonstrated that living yeast cells could inhibit B. cinerea. The authors indicated that environmental adaptability, induction of host resistance, biofilm formation, and production of antimicrobial volatile organic compounds (VOCs) also represent important mechanisms of action displayed by A. pullulans S2. The antagonistic yeast A. pullulans S2 could reduce postharvest disease incidence of tomato fruit, significantly change fungal and bacterial communities, and increase the beneficial taxa of fungi and bacteria on the surface of tomato fruits⁴⁸. Recent studies have shown that W. anomalus reduces the disease severity index in tomatoes and also increases the population of some plant growth promotion bacteria, such as Pantoea sp. and Pseudomonas sp., as well as biocontrol agents such as Golubevia sp. and Papiliotrema sp., and decreases the abundance of potential pathogens⁴⁹. Notably, the addition of exogenous nutrients significantly reduced biocontrol activity, indicating that nutrient competition may represent a major mechanism of action.

The induction of a ROS burst in plants by antagonistic yeast is thought to be one of its mechanisms of action and may lead to the activation of signaling pathways to initiate an induced resistance response. Zhao et al.⁵⁰ reported that the S. cerevisiae EBY100 strain significantly upregulated genes involved in salicylic acid and jasmonic acid biosynthesis and plant defense in tomato wounds and also induced ROS production in tomato fruits, all of which resulted in enhanced resistance to B. cinerea. The use of the antagonistic yeast P. caribbica has been reported to increase the expression of ROS scavenging and PR genes, as well as enhance the activity of defense-related enzymes, and promote the production of total phenols, lignin, and flavonoids, in cherry tomatoes, all of which contribute to the inhibition of black spot caused by A. alternata⁵¹. The investigation of ref.⁵² shows that Wickerhamomyces anomalus can effectively reduce germ tube elongation, inhibit spore germination of A. alternata, and then control black spot disease in cherry tomatoes. W. anomalus reduces the content of malondialdehyde, increases the ascorbate peroxidase and chitinase, and upregulates the expression of genes related to the enhancement of protecting enzyme activity, defense, and antioxidant capacity of fruits and triggers ROS-induced disease response in tomatoes.

The potential of biocontrol bacteria, such as Pseudomonas spp. and Bacillus spp., as biological control agents against postharvest decay have been reported extensively. Panebianco et al.⁵³ investigated beneficial epiphytic and endophytic microbial populations of seven cultivars of tomato fruit from the Pachino district labeled as “protected geographical indication” by the European Community, and about 240 tomato fruit-associated bacteria were isolated with antagonistic activity against tomato postharvest pathogens, such as B. cinerea and A. alternata. Among them, eight representative strains showed significant antagonistic activity against B. cinerea and A. alternata on tomato fruit belonging to Pseudomonas, Bacillus, and Enterobacter genera, considered the main genera against tomato postharvest decay. Several studies were conducted on the ability of biocontrol bacteria, especially Bacillus, to control postharvest diseases in tomatoes. The bacterial agent prepared with Bacillus amyloliquefaciens can significantly inhibit fungal activity, such as B. cinerea, A. alternata, and F. oxysporum. The spores of Bacillus amyloliquefaciens colonized the surface of tomatoes, competing with pathogenic fungi for space and parasitism and reducing the rotting rate of tomatoes⁵⁴. Bacillus mojavensis D50 strain isolated by ref.⁵⁵ (from tomato rhizosphere soil was reported to inhibit gray mold infections by 69.88%. The application of D50 fermentation broth in tomato wounds significantly enhanced antioxidant and defense-related enzyme activity in tomato tissues, including peroxidase (POD), catalase (CAT), polyphenol oxidase (PPO), superoxide dismutase (SOD), and phenylalanine lyase (PAL) and gray mold prevention was associated with enhanced transcript levels of systemic acquired resistance-related marker genes⁵⁵. Pseudomonas koreensis B17-12 isolated Fraxinus hupehensis effectively against A. solani, B. cinerea, and P. infestans by producing VOCs may be an excellent candidate for reduced postharvest tomato blight and gray mold⁵⁶. Similarly, by releasing VOCs, Burkholderia cenocepacia ETR-B22 inhibits B. cinerea’s mycelial growth and spore germination. VOCs produced by Burkholderia cenocepacia ETR-B22 fumigation significantly reduced the disease incidence, disease index, and weight loss of postharvest tomato fruits⁴.

In addition, the fungal and actinomycete biocontrol agents, Metarhizium anisopliae, Clonostachys rosea, Streptomyces sp., and others have been reported to control postharvest gray mold in tomatoes effectively. In this regard, cp ATPase subunit CFl is a key protein involved in Clonostachys rosea-induced resistance to B. cinerea in tomatoes, where it functions as a key regulator of signaling associated with cellular redox homeostasis, ATP biosynthesis, and the expression of resistant genes that modulate immunity to B. cinerea^10,57. Hajji-Hedfi et al.⁵⁸ showed that Trichoderma longibrachiatum can produce hydrolytic enzymes such as chitinase (CHI), protease, and glucanase inhibit the hyphae growth of B. cinerea, and significantly reduce the disease severity in tomato fruit and the seedlings. The combination of salicylic acid and culture filtrates of T. longibrachiatum significantly induces ROS enzyme activity and biochemical and physiological changes in tomato fruit. Khairy et al.¹³ (suggested that Trichoderma culture filtrate significantly reduced B. cinerea growth, among them, culture solution of T. reesei significantly reduced the incidence rate and severity of the disease in tomato fruit by 80.5 and 90.5%, respectively, at 70% concentration. Moreover, the secondary metabolites of several Trichoderma have strong antifungal activity against B. cinerea.

The phosphopantetheinyl transferase (PPtase) genes, overexpressed in the Streptomyces albiflaviniger (S. albiflaviniger) strain, show 4.7 times higher antagonistic activity than the wild-type strain against P. citrinum. The fermented extracts of the PPtase-overexpressed S. albiflaviniger strain significantly reduce postharvest tomato fruit decay by 89.71,% attributed to activated secondary metabolites PPtase-overexpressed strain⁵⁹. Streptomyces rectiviolaceus DY46 has antagonistic activity against B. cinerea, significantly decreasing the incidence of gray mold by 80.0% in tomato fruits. The 32, 33-didehydroroflamycoin (DDHR) was identified as the main active ingredient from the cell extract of Streptomyces rectiviolaceus DY46 inhibiting the mycelial growth of various plant pathogenic fungi, such as B. cinerea, R. stolonifer var. stolonifer, and F. oxysporum f. sp. lycopersici at concentrations of 8–64 mg L⁻¹. Moreover, DDHR (100 mg L⁻¹) significantly reduced the incidence of tomato fruit gray mold by 88.9%⁶⁰.

In addition to traditional microbial antagonists, the use of probiotics and their postbiotics has emerged as a promising strategy for controlling postharvest decay and extending the shelf life of tomato fruit. Probiotics, such as lactic acid bacteria (LAB), can colonize the surface of tomato fruit, competing with pathogenic fungi for nutrients and space. For instance, LAB strains such as Lactiplantibacillus plantarum have been shown to produce postbiotics, including lactic acid, acetic acid, phenyllactic acid and pyrazine derivatives, that suppress fungal growth of Penicillium expansum and Aspergillus flavus on tomato fruit. Bio-preservation of tomato with the cell-free supernatants fermented by L. plantarum TR7 and L. plantarum TR71 decreased the microbial count by 1.98–3.89 log₁₀ spores per gram in comparison to the treatment with medium non-fermented⁶¹. Furthermore, L. plantarum can be applied as part of edible coatings with exopolysaccharide, providing a dual function of pathogen inhibition and preservation of tomato fruit⁶². The integration of probiotics and postbiotics into postharvest management strategies offers a sustainable and eco-friendly approach to reducing decay and spoilage, while also improving the overall shelf life and marketability of tomato fruit.

In the past several decades, there has been increased research on the biological control of postharvest diseases. Research aimed at the development of commercial products needs to conduct large-scale studies on efficacy and address large-scale production methods, biosafety, formulation, shelf life, and consistent performance. All these needs must be addressed for the commercial development and utilization of biocontrol products for the control of postharvest diseases in tomatoes and other horticultural crops.

Natural compounds

Natural compounds, such as biopolymers, volatiles, extracts, phenolic compounds, hormones, and oxidants, have been used to control tomato postharvest diseases. Among the biopolymers, chitosan has received the most attention. Chitosan (β-(1,4)-2-amino-2-deoxy-d-glucose) is a natural biopolymer, obtained by the deacetylation of chitin. Commercially, chitosan is mainly obtained from crustacean shells, and its application to harvested fruits and vegetables has been shown to induce antioxidant and defense responses, making them more resistant to postharvest pathogens and extending their shelf life¹⁴. Treated plants exhibited elevated levels of defense enzyme activity and enhanced expression of the PIN II gene, which serves as a marker for the defense signaling pathway. Furthermore, the activity of PPO decreased, and total protein and phenolic compounds increased in B. cinerea-infected wounded tomato fruit with chitosan treatment, indicating that chitosan has direct fungal toxicity to B. cinerea and triggers the defensive response of fruits. Lu et al.⁶³ reported that tomato fruit perceives dextrans as a kind of pathogen-associated molecular pattern (PAMP). Dextran treatments induced callose deposition and phenylpropanoid and flavonoid biosynthesis to a greater extent than α-glucanase activity in surface wounds, relative to untreated (control) surface wounds. Enzymatic hydrolysis of dextrans improves host disease resistance against B. cinerea. Yeast mannan (YM) are structurally important polymers present in the outermost layer of the yeast cell wall, accounting for 35–40% of the dry mass of the cell wall. Both vacuum infiltration and coating of tomatoes with 1.0 g/L YM inhibited postharvest black mold rot caused by A. alternata, delayed color development, and inhibited ethylene biosynthesis during storage⁶⁴. Antimicrobial peptides (AMPs) are naturally occurring molecules produced by microbes that provide defense against other microorganisms. Notably, AMPs have also been used to control diseases in fruits and vegetables. Treatment of tomatoes with the antimicrobial peptide CB-M disrupted the cell membrane integrity of B. cinerea and significantly reduced lesion diameter and disease incidence in tomato fruits during storage. The effect was concentration dependent, being more evident with increasing concentrations of CB-M. CB-M may also bind to DNA and degrade/inhibit protein synthesis in B. cinerea⁶⁵. Javed et al.⁶⁶ developed a novel vanillin-deep eutectic agent (V-DEA) from natural compounds with higher antioxidant and antifungal activity to B. cinerea and Fusarium oxysporum than vanillin, suppressing their mycelium growth and spore germination. Successful application of 8-mM V-DEA to prevent postharvest decay of cherry tomatoes, and extend the shelf life of the fruit. In addition to biopolymers, 3-methylbutan-1-ol obtained from the TR1VOC strain of Enterobacter and dimethyl trisulfide obtained from Burkholderia cenocepacia ETR-B22VOC have been shown to inhibit the growth and infection of B. cinerea and F. oxysporum in tomato fruits^4,8.

Higher plants are rich in various bioactive secondary metabolites, including terpenes, alkaloids, and phenols, which have been reported to possess antifungal properties in vitro. For example, phenolic, terpenoid compounds, and aromatic compounds present in Annona muricata fruit extracts significantly reduced the infection rate of A. alternata in tomatoes³⁶. The phytoalexin scopoletin, extracted from Sinomonium acutum, inhibited mycelial growth and conidial germination of B. cinerea and disrupted the cell wall, cell membrane, and infection structure formation. Scopoletin also significantly increased the control efficiency of triadimefon, which is a promising treatment for gray mold⁶⁷. Essential oils are aromatic, volatile secondary metabolites produced by plants. In this regard, several essential oils containing bioactive components are effective fungistatic agents. For example, essential oils extracted from Tetraclinis articulata, Syzygium aromaticum, Origanum vulgare, and have been reported to inhibit the growth of F. oxysporum, and B. cinerea^68–70.

Phenolic compounds constitute the largest class of plant secondary metabolites, with more than 8000 identified phenolic compounds. Chlorogenic acid (CGA) is the most abundant phenolic compound in tomatoes and possesses antioxidant and antibacterial properties. The high level of ROS induced by 2–3 g/L CGA in cherry tomatoes significantly reduced the incidence and severity of fruit rot caused by Fusarium sp., as well as increased defense-related enzyme activity in tomatoes, including catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD)⁷¹. Melatonin is a hormone molecule commonly found in nature and plays an important role in plant biological functions. A preharvest spray application of 0.1 mM melatonin on cherry tomatoes was reported to reduce gray mold caused by B. cinerea and other rots during fruit storage⁷². The increased resistance in cherry tomatoes induced by melatonin is mainly attributed to the regulation of Ca²⁺ signal transduction, ROS burst, and activation of the SA signaling pathway²¹. Zhang et al.²³ found that, in vitro, melatonin has no antifungal activity against B. cinerea, while Selenium can significantly inhibit tomato fruit gray mold caused by B. cinerea. Moreover, the synergistic of melatonin and Selenium improve the activities of SOD, POD, and CAT, and promote the expression of pathogenesis-related (PR) genes, activating the resistance of tomato fruit to B. cinerea.

Gallic acid, a natural polyphenol compound, is a trihydroxy benzoic acid that is found in several plant species. Extracts rich in gallic acid and two of its derivatives (syringic and pyrogallic acids) exhibited significant antifungal activity against A. solani⁷³. Exogenous treatment of tomatoes with gallic acid and its derivatives enhanced several biochemical traits, including chlorophyll content, and improved several yield components⁷³. Foliar application of four cinnamate derivatives (cinnamic acid, ρ-coumaric acid, caffeic acid, and ferulic acid) on greenhouse-grown tomato plants improved plant growth, total chlorophyll content, and yield components, and significantly reduced the severity of early blight (A. alternata) without any evidence of phytotoxicity⁷⁴.

Zhu and Zhang⁷⁵ reported that harpin (a bacterial hypersensitive response elicitor) effectively controlled gray mold and black rot on inoculated tomato fruit, as well as natural infections on non-inoculated tomatoes. An application of 90 mg/L harpin on tomatoes not only induced the transcriptional expression of defense-related genes, such as chitinase, β-1,3-glucanase, and phenylalanine ammonia-lyase, but also increased the content of total phenolic compounds and lignin in tomato fruits. Notably, harpin did not inhibit the growth of B. cinerea or A. alternata in vitro⁷⁵. The application of methyl jasmonate (MeJA), a natural plant growth regulator, on harvested products, represents a potential method for improving disease resistance. The application of 10 mM MeJA on tomato fruits effectively inhibited the lesion diameter of gray mold. The MeJA application increased ethylene production, enhanced chitinase, β-1,3-glucanase, phenylalanine ammonia-lyase (PAL), and POD activity, and increased the level of pathogenesis-related proteins and the total phenolic content of tomatoes³⁰.

Bio-nanocomposite active packaging films and coatings

Bio-nanocomposites offer a sustainable alternative to plastic usage, and they are considered to be innovative solutions for addressing issues in health, agriculture, energy and environmental domains⁷⁶. The development of bio-nanocomposite active packaging films and coatings has emerged as a promising eco-friendly strategy for preserving tomato fruits (Table 2). These innovative materials combine biodegradable polymers with nanomaterials to create functional packaging that not only extends the shelf life of tomatoes but also actively inhibits the growth of molds and yeasts^77,78, as well as foodborne bacteria^79–81. The integration of nanotechnology with biodegradable materials addresses both environmental concerns and consumer demand for safer food products.

Table 2.

A representative list of bio-nanocomposite active packaging films and coatings applied in tomato preservation

Tomato cultivar	Bio-nanocomposite	Preservation effect	References
Solanum lycopersicum L. cv. Zheza 205	Nano-SiOx/chitosan complex coating	Slowing down moisture loss, gas exchange, respiration rates, and limiting foodborne pathogenic bacterial growth	81
S. lycopersicum L. cv. not specified	Biogenic silver nanoparticles mediated by marine algae	Inhibiting Penicillium italicum blue mold	78
S. lycopersicum L. cv. not specified	Alginate/chitosan nanomultilayer containing Aloe vera	Reducing weight loss, molds and yeasts, and inhibiting ethylene synthesis	77
S. lycopersicum L. cv. Debora	Carnauba wax nanoemulsion	Increasing fruit gloss, improving tomato appearance, and reducing decay	130
S. lycopersicum var. cerasiforme	Edible coatings, based on alginate cross-linked with calcium chloride, and containing an oregano essential oil (OEO) nanoemulsion	Prolonging the tomato shelf life by reducing the growth of the endogenous microbial flora (total microbial load, yeasts, and molds)	131
S. lycopersicum L. cv. not specified	Edible coatings based on Hydroxypropyl methylcellulose containing Piper betel leaf essential oil nanoemulsion	Reducing weight loss, color changes, and decay, and delaying fruit softening	132
S. lycopersicum L. cv. not specified	Chitosan–Nano-ZnO composite film	Maintaining soluble solid content, inhibiting respiration, and exhibiting antibacterial properties	79
L. esculentum cv. Newton	TiO2/clay-nanocomposite film	Decreasing ethylene production, mitigating weight loss, and maintaining pH, titratable acidity, total soluble solids, and firmness	133

Bio-nanocomposite materials are typically composed of biopolymers such as chitosan, starch, cellulose, and polylactic acid, which are reinforced with nanoparticles like silver, zinc oxide, copper oxide, or titanium dioxide. These materials exhibit enhanced mechanical, barrier, and antimicrobial properties, making them ideal for postharvest applications. Chitosan, a natural biopolymer derived from chitin, is one of the most widely studied materials for bio-nanocomposite films and coatings due to its biodegradability, biocompatibility, and inherent antimicrobial properties. When combined with nanoparticles, chitosan-based films can significantly inhibit the foodborne bacterial growth. For instance, ref. ⁷⁹ (2021) prepared a chitosan–Nano-ZnO composite film that did not only effectively inhibit respiration and maintained soluble solid content of cherry tomato, but also exhibit good antibacterial properties against Alicyclobacillus acidoterrestris, Staphylococcus aureus, Escherichia coli, and Salmonella. Moreover, bio-nanocomposite films could be incorporated with natural compounds. Tang et al.⁸² prepared a konjac glucomannan-based tea polyphenols in fucoidan-chitosan nanoparticle film, and found that it could significantly extend the shelf life of cherry tomato.

Despite the promising potential of bio-nanocomposite films and coatings, several challenges need to be addressed for their widespread adoption. These include the high production costs of nanomaterials, potential toxicity concerns, and regulatory hurdles related to the use of nanoparticles in food packaging^83,84. Additionally, further research is needed to optimize the formulation of these materials for large-scale application and to ensure their safety and efficacy under practical storage conditions. Future studies should focus on the development of multifunctional bio-nanocomposite films that combine antimicrobial properties with other beneficial features, such as moisture regulation, ethylene scavenging, and UV protection. The integration of probiotics and postbiotics into bio-nanocomposite coatings also represents a promising avenue for enhancing their antifungal activity and improving the overall quality of tomato during storage⁶². However, further research and development are needed to overcome existing challenges and fully realize the potential of this technology in postharvest preservation.

Modern green technologies

Modern green technologies are revolutionizing the management of postharvest fungal decays in tomatoes. These technologies offer sustainable and eco-friendly alternatives to traditional chemical fungicides, addressing both environmental concerns and consumer demand for safer food products.

In addition to bio-nanocomposite coatings, other nano-technologies have also been actively studied to develop eco-friendly fungicides. For instance, chitosan-decorated copper oxide nanocomposite (CH@CuO NPs) has been shown to suppress the development of B. cinerea by inhibiting hyphal growth, spore germination, and sclerotia formation. This nanocomposite effectively controlled gray mold in both tomato plants and fruits under greenhouse conditions, demonstrating the potential of nanotechnology in postharvest disease management⁸⁵. Imran et al.⁸⁶ isolated indigenous Trichoderma harzianum Tr‑3 and zinc nanoparticles (ZnO-NPs) significantly suppressed the mycelial growth of Botrytis cinerea in vitro. Applications of T. harzianum and ZnO-NPs significantly reduced disease severity and improved catalase and peroxidase activity in ZnO-NP-treated plants, followed by T. harzianum-treated plants in the greenhouse. In addition, zinc oxide nanoparticles (ZnNPs), copper nanoparticles (Cu NPs), and copper nanocomposites (CS–Zn-Cu NCs) significantly inhibited the growth of R. solani, A. alternate, and B. cinerea at 90 μg ml^−1 87. Selenium nanoparticles (SeNPs) synthesized from the water extract of fenugreek seeds exhibit excellent bactericidal activity against Fusarium oxysporum and SeNPs hydrolyze F. oxysporum mycelia within 18 h after treatment. A minimum inhibitory concentration (0.25 mg/mL) of SeNPs treatment can reduce the signs of infection in infected fruits by 100%. SeNP prevents and destroys potential fungal infections after harvesting, and maintains the quality of tomatoes⁸⁸. These results suggested that nanomaterials could suppress postharvest fungal pathogens of tomatoes, either directly or indirectly, as resistance inducers. They are promising for preventing and inhibiting postharvest fungal disease in tomatoes. However, further research is needed on the application of nano-fungicides in postharvest diseases on tomato fruits, and the mechanism involved has not been explored. Nano-fertilizers, nano-fungicides, and nano-biosensors have the potential to enhance plant growth, monitor plant health, and control disease in tomatoes and other horticultural crops. Further studies are needed on the formulation of nanomaterials and to determine if they activate an induced resistance response in tomatoes. In addition to nanotechnology, the use of far-red light has also been explored for their potential in postharvest disease management. While FR light has been shown to enhance tomato growth and fruit set, it may also increase susceptibility to B. cinerea, highlighting the need for careful optimization of light treatments⁸⁹.

CRISPR/Cas9 technology has also emerged as a powerful tool for enhancing the resistance of tomatoes to fungal pathogens. By targeting specific genes involved in disease susceptibility, researchers can develop tomato varieties with improved resistance to postharvest decay. For example, utilizing CRISPR/Cas9 to knock out SlPLC2 (phospholipase C2) in tomato resulted in a phenotype with reduced ROS production, attenuated SA response, and intensified JA response, resulting in enhanced resistance to B. cinerea⁹⁰. Wang et al.⁹¹ utilized CRISPR/Cas9-mediated gene editing to knock out SlDQD/SDH2 in tomatoes, resulting in a phenotype with a significantly lower content of shikimate and flavonoids and increased susceptibility to B. cinerea. Further research should be conducted on tomatoes utilizing CRISPR/Cas9 to identify genes involved in enhancing pre- and postharvest disease resistance. This knowledge can then be used to produce tomato lines with superior disease resistance and reduce the need for other methods of intervention, such as the use of biocontrol agents and/or natural compounds. For example, CRISPR/Cas9-mediated modification of SlATG5 in tomato resulted in a phenotype with decreased resistance to B. cinerea, more severe disease symptoms, and lower defense-related enzyme activity, compared to wild-type plants⁹². This research highlights the importance of SlATG5 in the disease-resistance response of tomatoes. In addition, it was reported that CRISPR/Cas9-mediated mutation of SlMYC2 reduced disease resistance to gray mold in the gene-edited tomato fruits, as well as antioxidant enzyme activity, indicating that SlMYC2 plays a positive regulatory role in MeJA-induced disease resistance in tomato fruits⁹³.

Despite the promising results, the adoption of modern green technologies in postharvest management of tomatoes faces several challenges, including regulatory hurdles, high production costs, and limited consumer awareness. Further research is needed to optimize these technologies for large-scale applications and to ensure their safety and efficacy in practical conditions.

Other methods

Other eco-friendly methods for the management of postharvest diseases in tomatoes have been explored. Physical treatments, such as hot air and hot water, have been reported to effectively control postharvest diseases in cherry tomatoes by altering the wax structure in the cuticle layer. In another study, Wei et al.⁹⁴ treated green-ripe tomato fruits with hot air and stored them at 20 °C for 15 days. Results indicated that the hot air treatment inhibited postharvest disease development and delayed tomato softening by regulating the activity of cell wall-degrading enzymes and the expression of their corresponding genes. The above studies indicate that hot air or water treatments represent an effective, non-chemical method for managing postharvest diseases in horticultural products, including tomatoes.

Notably, supplemental far-red (FR) light treatments of tomato plants have been shown to enhance growth, fruit set, and dry mass partitioning, and increase soluble sugar content in tomatoes but make them more susceptible to B. cinerea^89,95 conducted a transcriptomic analysis of the response of tomato plants to supplemental FR light about disease resistance. Results indicated that supplemental FR light increased the susceptibility of tomatoes to B. cinerea by inhibiting the induction of the PI gene and JA-mediated immune response.

Integrated management

Although several different eco-friendly methods have been used for postharvest disease management, no one method has provided the consistent level of efficacy level required for commercial success. Therefore, integrated management approaches have been proposed to meet the level of consistency and efficacy provided by the use of synthetic chemical products. A diagram of potential integrated management methods that can be used is presented in Fig. 1. Various combinations of biocontrol agents (e.g., antagonistic yeast, bacteria, fungi) and natural compounds (e.g., chitosan, oligochitosan, and sodium alginate) have been used to manage postharvest diseases, such as gray mold, and other naturally occurring rots^96,97. The antagonistic yeasts C. guilliermondii, P. guilliermondii, C. laurentii have been investigated in several studies for the postharvest control of B. cinerea, and R. stolonifera. Heat treatments have also been one of the most promising non-chemical technologies explored for postharvest decay control. Combining Application P. guilliermondii (1 × 10⁸ CFU mL⁻¹) and heat treatment (38 °C for 24 h) can more effectively reduce postharvest fungal (Botrytis cinerea, Alternaria alternata and Rhizopus nigricans) infection in wounds than P. guilliermondii alone, and increase H₂O₂ and lignin deposition of cherry tomato fruit. Association application of P. guilliermondii and heat treatment reduces the tomato fruit’s susceptibility to pathogens attributed to higher activities of PAL and β-1,3-glucanase⁹⁸. Yeast isolates Saccaromyces cerevisiae and Candida tennis, organic salts calcium chloride, sodium benzoate, and potassium sorbate significantly inhibit the mycelia growth of the A. alternate and R. stolonifer. The synergistic of yeast, either S. cerevisiae or C. tenuis and potassium sorbate displayed the highest significant effect in inhibiting postharvest fungal growth, and after them, the synergistic of yeast and sodium benzoate and calcium chloride successively.

Fig. 1.

Potential combinations of different eco-friendly methods of postharvest disease control that could be used in an integrated management strategy for decay control in tomatoes.

Cheng et al.⁹⁹ isolated and evaluated three bacterial strains (B. velezebsis (WZ-37), B. subtilis subsp. subtilis (WXCDD105), and B. amyloliquefaciens (SS)) for their biocontrol potential. Each strain exhibited a good inhibitory effect, however, the combined use of SS + WZ-37 possessed the highest level of biocontrol activity, significantly reducing the incidence of gray mold on harvested tomatoes, while improving quality and freshness. The combination of 200 mg/L ε-PL + 400 mg/L chitooligosaccharide, 1500 mg/L ε-PL + 60 mg/L wuyiencin, a secondary metabolite of Streptomyces albulus CK-15 significantly inhibited the infection of B. cinerea on tomato more than any one compound applied alone and the combination of compounds increased POD, SOD, CAT, and PAL activity^12,100. The lactic acid bacteria (LAB) strain Lactiplantibacillus plantarum A6 with edible coatings (ECs) based on exopolysaccharide from Weissella confusa JCA4 as a coating prevents Fusarium sp. and R. stolonifera infection of cherry tomato fruits⁶².

The combination of chitosan and other natural compounds (e.g., bacillomycin D, vanillin, gallic acid, and sodium tripolyphosphate) has been used to manage postharvest fungal rots in tomatoes caused by B. cinerea, and F. oxysporum, and also shown to extend the shelf life of tomatoes^101,102. The L-arginine (Arg, 1 mM) and/or methyl salicylate (MeSA, 0.05 mM) inhibited B. cinerea in tomato fruit. The combination of Arg or MeSA further inhibited the development of postharvest decay in tomato fruits, with the efficacy of B. cinerea better than each individual component. The combination of Arg and MeSA treatment showed enhanced activities of SOD, POD, CAT, and defense-related enzymes, such as chitinase, PPO, PAL, and β-1,3-glucanase, increasing the expression levels of pathogenesis-related genes¹⁰³. The combination of MeSA and 1-MCP enhanced the efficacy of fungal decay inhibition of tomato fruits more than MeSA treatment alone. Moreover, the simultaneous application of MeSA and 1-MCP increases the expression level of the pathogenesis-related protein 1 (PR1) gene, inhibits the increase in conductivity and malondialdehyde content, and improves defense enzyme activity and total phenolic content.

Potential use of the fruit microbiome to manage postharvest decay

Research on the biological control of postharvest fungal rots has mainly focused on the microbial use of single microbial antagonists and identifying their mechanism of action. Recently, comprehensive microbial profiling of the different organs of plants and rhizosphere has become possible due to advances in high-throughput sequencing and the use of universal primer sets that generate amplicon sequences that can be taxonomically identified. This approach overcomes the limitations of culture-based assessments of the microbial community. Results have demonstrated that the endophytic and epiphytic microbiome of plants is rich, diverse, and spatio/temporally highly dynamic. The collective studies thus far conducted have indicated a potential connection between the composition of the microbiome and postharvest disease development.

The combined application of the biocontrol antagonists Metschnikowia fructicola, Bacillus amyloliquefaciens, Trichoderma harzianum, and Beauveria bassiana changed the composition and structure of the microbial community on the fruit surface of strawberries and reduced the incidence of postharvest diseases^104. Liu et al.¹⁰⁵ used amplicon sequencing technology to characterize the effect of the antagonistic yeast P. kudriavzevii on the fungal community of tomato fruit throughout cold storage. Results indicated that 28 days after the P. kudriavzevii treatment, the abundance of Botrytis and Alternaria on tomato fruit decreased, resulting in a compositional change in the structure of the epiphytic microbial community of tomato. Xu et al.¹⁰⁶ conducted a global study of the citrus rhizosphere microbiome and found that the core rhizosphere bacterial species comprised Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax, and Paraburkholderia, some of which represent beneficial plant microbes. These studies have provided valuable data for identifying and utilizing beneficial microorganisms, as well as on the potential use of microbial consortia to improve the disease resistance and quality of horticultural crops.

Conclusions and prospects

Postharvest diseases of fruits and vegetables are estimated to reduce marketable yields by more than 40% globally³⁴. Pathogenic fungi are the main cause of this loss. Therefore, research on technologies to prevent postharvest fungal diseases in fruits and vegetables has become increasingly crucial. Currently, several antagonistic fungi (mainly yeast) and bacteria (mainly Bacillus sp.) have been identified and demonstrated to effectively control postharvest diseases of tomatoes and other horticultural crops. However, achieving the same level of effectiveness and consistent performance as synthetic chemical fungicides has proven to be problematic. Future research on the use of biocontrol agents for the prevention of postharvest decays of tomatoes needs to consider the following two points: (1) Antagonistic microbes should be obtained from unique environments, such as glaciers, deserts, ancient forests, etc. Microbes living in these unique and often stressful environments may produce metabolites that enhance their efficacy in disease control. They may also significantly increase efficacy when used in combination with other biocontrol agents or alternative disease control methods. (2) Biocontrol agents can be used along with other eco-friendly methods in a temporal manner, where one method may be better suited for a particular stage of processing and marketing. For example, natural compounds or physical treatments could be applied before cold storage, and biocontrol agents could be applied during shipping and distribution. Such an approach may prevent interference between methods.

Further in-depth studies also needed to be conducted on the mechanisms involved in postharvest disease control at the molecular level. Future studies will need to take full advantage of -omic technologies (transcriptomics, metabolomics, proteomics, phenomics, etc.) to better understand disease resistance and susceptibility in tomatoes, as well as the role of the microbiome in the health and quality of tomatoes. In addition to traditional disease management methods, efforts should be made to utilize CRISPR/Cas9 technology, nanomaterials, and beneficial microbial consortia to address the demand for eco-friendly methods of postharvest disease control.

Author contributions

All authors read and approved this manuscript. Zhenshuo Wang and Mumian Wu: Writing—original draft. Yawen wang and Qinhong Liao: Writing—review and editing. Yuan Sui: Supervision and funding acquisition. Chao Gong: Conceptualization, project administration and funding acquisition.

Data availability

No datasets were generated or analysed during the current study.

Competing interests

The authors declare no competing interests.