Plant–Microbe Interactions for Improving Postharvest Shelf Life and Quality of Fresh Produce Through Protective Mechanisms

Abstract

Postharvest spoilage of horticultural produce is a significant challenge, contributing to substantial food waste and economic losses. Traditional preservation methods, such as chemical preservatives and fungicides, are increasingly being replaced by sustainable, chemical-free alternatives. Microbial interventions using beneficial bacteria, fungi, and yeasts have emerged as effective solutions to enhance the postharvest quality and extend shelf life. Advancements in omics technologies, such as metabolomics, transcriptomics, and microbiomics, have provided deeper insights into plant–microbe interactions, facilitating more targeted and effective microbial treatments. The integration of artificial intelligence (AI) and machine learning further supports the selection of optimal microbial strains tailored to specific crops and storage conditions, further enhancing the treatment efficacy. Additionally, the integration of smart cold storage systems and real-time microbial monitoring through sensor technologies offers innovative approaches to optimize microbial interventions during storage and transport. This review examines the mechanisms through which microbes enhance the postharvest quality, the role of omics technologies in improving microbial treatments, and the challenges associated with variability and regulatory approval. Amid growing consumer demand for organic and sustainable solutions, microbial-based postharvest preservation offers a promising, eco-friendly alternative to conventional chemical treatments, ensuring safer, longer-lasting produce while reducing food waste and environmental impact.

1. Introduction

Postharvest losses in horticulture are a significant global issue, with up to 30% of produce wasted due to spoilage, reduced shelf life, and quality deterioration [1,2]. These losses not only threaten food security, but also contribute to increased economic costs and environmental concerns. In developed countries, postharvest waste is often associated with overproduction, whereas in developing countries, inadequate storage, transportation, and preservation techniques exacerbate the problem. Fruits, vegetables, and flowers are particularly susceptible to rapid deterioration after harvest as they are biologically active and continue to undergo respiration and biochemical transformations [3]. Processes such as ripening and senescence result in a reduction in quality, flavor, texture, and nutritional value, making postharvest preservation a critical concern for the horticultural industry [4,5]. The growing demand for safe, high-quality produce with extended shelf life has driven the development of advanced preservation techniques aimed at mitigating these losses.

Traditional chemical-based preservation methods, such as the use of fungicides, pesticides, and synthetic preservatives, have been widely employed to extend shelf life and prevent microbial spoilage [6,7]. However, these approaches are increasingly under scrutiny due to concerns regarding their potential impacts on human health, environmental sustainability, and the emergence of microbial resistance. The overuse of chemical treatments raises concerns regarding residue accumulation on food products, the development of resistant strains of bacteria and fungi, and detrimental effects on beneficial microorganisms in the environment. Furthermore, growing consumer demand for organic and clean-label produce has accelerated the search for alternative preservation strategies that align with modern trends in sustainable agriculture and food safety [8,9].

The direct application of plant-associated microbes in postharvest preservation, such as endophytes, rhizobacteria, and epiphytes, has shown potential in extending shelf life and improving safety. However, while these microbes are primarily known for their role in promoting plant growth and enhancing stress tolerance, it is important to clarify that their benefits to postharvest quality often stem from their direct antimicrobial activities and ethylene regulation, not solely from their growth-promoting functions [9,10,11,12]. Notably, their beneficial effects can persist after harvest, influencing postharvest processes such as ripening, ethylene production, microbial resistance, and the preservation of nutritional content [13,14]. An enhanced understanding of plant–microbe interactions during postharvest storage has opened new avenues for the development of sustainable, chemical-free preservation methods that enhance both the shelf life and safety of horticultural products.

The potential of plant–microbe interactions in postharvest management extends beyond spoilage reduction; these interactions can also improve the nutritional and bioactive profiles of stored produce [10,15]. Beneficial microbes have been shown to modulate the levels of antioxidants, phenolic compounds, and other secondary metabolites that contribute to the health benefits of fruits and vegetables [16]. Additionally, microbial metabolites, such as volatile organic compounds (VOCs) and enzymes, can delay senescence, suppress the growth of spoilage organisms, and promote resistance to postharvest diseases [17,18]. This natural approach to preservation aligns with consumer preferences for healthier, environmentally friendly food products while also enhancing the economic value of horticultural crops by reducing waste and improving product quality throughout storage and distribution.

The scope of this review was to explore the role of plant–microbe interactions in enhancing the postharvest shelf life and safety of fresh produce. It examines the physiological changes that occur in postharvest produce, with a focus on biochemical transformations, ethylene regulation, and microbial spoilage agents involved in quality deterioration. The review also highlights the mechanisms by which beneficial microbes, such as endophytes, rhizobacteria, and epiphytes, contribute to delaying ripening, preventing microbial growth, and enhancing the nutritional value of stored produce. Additionally, the review covers various applications of microbial interventions including microbial coatings, biocontrol agents, and fermentation-based treatments. It also examines the role of advanced omics technologies, metabolomics, transcriptomics, and microbiomics in deepening our understanding of plant–microbe interactions and in predicting postharvest quality. The review also addresses the challenges and regulatory aspects associated with microbial-based preservation methods, providing a comprehensive understanding of their potential to improve postharvest management practices.

2. Postharvest Spoilage and Physiological Changes in Fresh Produce

Postharvest spoilage in fresh produce is a multifaceted process influenced by both physiological changes and microbial activity [19,20]. Following harvest, produce undergoes a series of natural processes, including ripening, senescence, and biochemical transformations, which significantly impact the quality and shelf life. These changes are further complicated by the presence of microorganisms that cause decay, wilting, and the degradation of essential nutrients. Current conventional preservation methods, such as cold storage, modified atmosphere packaging (MAP), and ethylene inhibitors, while effective to some extent, have limitations. Cold storage, for example, can lead to chilling injuries in certain crops, resulting in discoloration and reduced quality. Studies have shown that cold storage at controlled freezing points (e.g., −1 °C) can reduce chilling injury compared with conventional cold storage at 4 °C, preserving the quality of crops like sweet corn [21]. Modified atmosphere packaging has also been widely used to extend shelf life and preserve the quality of various fruits. It is particularly effective for blueberries, where MAP at 0 °C helped reduce weight loss and maintain the appearance and texture during storage [22]. Similarly, MAP has been proven to extend the shelf life of fruits like passion fruit, reducing ethylene production and slowing down the ripening process. Finally, ethylene inhibitors such as 1-MCP and AVG are widely used to delay fruit ripening. These inhibitors have been shown to reduce fruit softening, maintain firmness, and prevent decay in avocados [23]. However, despite their benefits, these methods cannot completely halt quality deterioration, particularly in highly sensitive fruits. Therefore, while these preservation methods offer some benefits, they each have their limitations, requiring continuous research and improvement. Understanding the interplay between physiological processes and microbial growth is essential for developing strategies to extend the shelf life of perishable crops [24,25]. The processes of spoilage and quality deterioration, including microbial involvement (e.g., fungi and bacteria) and physiological changes such as ethylene production and senescence, are illustrated in Figure 1, which provides a visual representation of these contributing factors.

2.1. Physiological Changes During Storage

Ripening and senescence are the primary physiological changes that occur in harvested produce. Ripening involves a series of coordinated biochemical transformations that alter the texture, color, aroma, and taste of fruits and vegetables, enhancing their palatability for consumption. This process is tightly regulated by plant hormones, with ethylene serving as the key regulator. Ethylene is a gaseous plant hormone that promotes the onset of ripening in many fruits and vegetables [26,27]. It triggers the breakdown of starches into sugars, the softening of cell walls, and the degradation of chlorophyll, all of which are essential for fruit maturation. However, excessive ethylene production can lead to premature ripening, reduced shelf life, and accelerated senescence. Therefore, regulating ethylene production through controlled storage conditions or external interventions is crucial to extending the postharvest lifespan of produce [28].

Temperature and humidity also play pivotal roles in influencing the rates of ripening and senescence. Low temperatures are typically used to slow these processes by reducing the metabolic activity of the produce, thereby extending the shelf life [29]. However, improper temperature management can result in chilling injuries, leading to discoloration, tissue breakdown, and overall quality loss. Similarly, humidity must be carefully controlled, as excessive moisture can promote mold growth and bacterial proliferation, whereas insufficient humidity can lead to dehydration and shriveling. Therefore, maintaining an optimal balance of temperature and humidity is crucial for preserving the quality of produce during storage [30,31].

2.2. Microbial Spoilage Agents

Microbial spoilage is a major contributor to postharvest losses. Various microorganisms, including fungi and bacteria, are responsible for the decay and deterioration of stored produce [32]. Fungi such as Botrytis and Penicillium are among the most common spoilage agents. These pathogens can rapidly colonize fruits and vegetables, causing soft rot, mold growth, and the production of mycotoxins. Mycotoxins, toxic secondary metabolites produced by certain fungal species, pose a serious food safety risk due to their potential adverse effects on human health [33,34]. Fungal infections often originate in wounds or damaged tissues and can rapidly spread under humid conditions, resulting in significant losses. In addition to fungi, bacteria species such as Pseudomonas and Erwinia also contribute to spoilage. These bacteria are known to cause soft rot and slime formation in fruits and vegetables, particularly in high-humidity environments. Bacterial spoilage typically begins at the tissue level and can lead to tissue breakdown, unpleasant odors, and the loss of structural integrity in the produce [24].

The spoilage process is influenced by several factors including microbial growth, the accumulation of metabolic waste products, and the secretion of enzymes that degrade cell wall components. Metabolic by-products of microbial activity, such as acids, alcohols, and volatile organic compounds, further exacerbate quality deterioration. Additionally, the contamination of produce with mycotoxins poses a significant food safety concern, as these toxins can affect large quantities of produce [13]. Common strategies employed to mitigate microbial spoilage include temperature control, humidity management, and the use of natural or synthetic antimicrobial agents. However, these strategies are often insufficient on their own. Thus, the development of more sustainable and effective microbial control methods is essential for reducing postharvest losses.

3. Microbial Communities and Their Role in Postharvest Quality Enhancement

A potentially sustainable approach to managing postharvest pathogens involves the utilization of beneficial microorganisms that can reside within plant tissues as endophytes, on their surfaces as epiphytes, or in the surrounding soil as rhizospheric microbes [35]. These microorganisms, depending on their characteristics, are classified as plant growth-promoting bacteria, biocontrol or biological control agents, or mycorrhizal fungi. Beneficial microorganisms are typically isolated from plant-associated microbial communities (also referred to as plant microbiota) and are subsequently evaluated for their anticipated advantageous properties [36]. In a pioneering study, Tronsmo and Dennis [37] introduced the concept of utilizing microbial antagonists for postharvest disease management, specifically focusing on the control of Botrytis rot in strawberries (Fragaria × ananassa Duch.). They demonstrated the potential of Trichoderma species as effective biocontrol agents, showing that these microorganisms could inhibit the growth of Botrytis cinerea, the causative agent of the rot, during the postharvest period. This early research laid the foundation for subsequent studies exploring the role of beneficial microbes in protecting crops postharvest, contributing to the development of sustainable and eco-friendly agricultural practices. Similarly, a study on the control of brown rot in stone fruits was conducted by Pusey and Wilson [38], who demonstrated the effectiveness of Bacillus subtilis in managing Monilinia fructicola, the causal agent of the disease. They tested various bacterial strains, including Pseudomonas cepacia, P. fluorescens, Bacillus thuringiensis, and two isolates of B. subtilis (B-3 and B-1849), on wounded peaches, nectarines, apricots, and plums. Among the strains, B. subtilis strain B-3 exhibited the most consistent control of brown rot. This strain significantly inhibited disease progression, and at higher concentrations, prevented infection, although the fruit eventually decayed due to other fungi. Notably, B-3 was effective across a wide range of temperatures and inoculum levels, suggesting its potential for broad postharvest application. The antifungal activity of B-3 was linked to the production of an antifungal substance, as shown by its culture filtrate, which retained activity even after autoclaving. This study laid the foundation for B. subtilis-based biological control strategies in postharvest disease management [38].

There are two basic approaches for using microbial antagonists to control postharvest diseases of fruits and vegetables. The first approach involves microorganisms that naturally exist on the produce, which can be promoted and managed. The second approach involves the artificial introduction of microorganisms to target postharvest pathogens. Postharvest microbial antagonists, naturally present on the surface of fruits and vegetables, are isolated and applied to control diseases. Chalutz and Wilson [39] demonstrated that concentrated washings from citrus fruits contained bacteria and yeast that suppressed fungal growth, suggesting that washed fruits are more susceptible to decay than unwashed ones. In contrast, the artificial introduction of microbial antagonists involves deliberately applying microorganisms to manage postharvest diseases. This method has proven more effective than other biological control strategies for managing diseases in various fruits and vegetables. Microbial communities play a critical role in enhancing the postharvest quality and longevity of horticultural produce through plant–microbe interactions such as ethylene suppression, antimicrobial activity, and microbial treatments aimed at reducing spoilage [10,13]. These communities consist of various plant-associated microorganisms, including endophytes, rhizobacteria, and epiphytes, which not only contribute to plant health, but also play a direct role in postharvest preservation by modulating ripening, suppressing spoilage-causing pathogens, and enhancing the nutritional profile of stored produce [5,40]. These microorganisms reside in various plant niches such as internal tissues, surfaces, and the rhizosphere, and interact with plants in a variety of beneficial ways such as enhancing shelf life and delaying senescence.

The plant microbiome, which encompasses the collective genomes of all microorganisms associated with a plant, has garnered significant attention for its role in postharvest preservation such as extending shelf life, reducing spoilage, and enhancing the nutritional quality of stored produce [5,41]. Understanding the diverse functions of these plant-associated microbes and their direct impact on postharvest quality is essential for developing microbial-based postharvest applications that extend the shelf life and reduce spoilage in stored produce. Bananas (Musa acuminata) are highly susceptible to postharvest diseases such as anthracnose, crown rot, and blossom end rot. The study of De Costa and Erabadupitiya [42] reported an integrated approach that combined hot water treatment with antagonistic bacteria from the banana fructosphere to control these diseases. In this study, Burkholderia cepacia demonstrated an effective control of postharvest pathogens, remaining viable and active even after prolonged storage. When combined with hot water treatment, B. cepacia provided superior control of anthracnose, crown rot, and blossom end rot, surpassing the efficacy of each treatment individually. This integrated approach offers a promising, non-chemical strategy for managing postharvest diseases in bananas [42]. The study of Kefialew and Ayalew [43] revealed the biocontrol potential of fungi and bacteria against Colletotrichum gloeosporioides, the causative agent of mango anthracnose, focusing on postharvest control. They evaluated four bacterial isolates, five yeast strains, and two filamentous fungi. The isolates significantly inhibited spore germination and the hyphal growth of C. gloeosporioides in vitro and reduced the anthracnose severity on artificially inoculated mango fruits. The most effective isolates, including Brevundimonas diminuta and a novel yeast species B-65-23, controlled the anthracnose severity on naturally infected fruits, keeping it below 5% over 12 days compared with 29% in untreated fruit. The findings highlight the potential of these biocontrol agents for managing postharvest mango anthracnose. Thus, beneficial microbes play a vital role in postharvest crop protection and quality enhancement by naturally inhibiting pathogens that cause spoilage and decay. These microbes prevent pathogen colonization through mechanisms like biofilm formation and antimicrobial compound production, reducing the need for chemical preservatives.

Overview of Plant-Associated Microbes

The plant-associated microbiome comprises several distinct groups of microorganisms, each playing a unique role in plant health and postharvest preservation including ethylene regulation, antimicrobial metabolite production, and nutrient modulation. These microorganisms are known to produce antimicrobial secondary metabolites and influence stress responses in postharvest conditions as well as modulate ethylene production, which impacts fruit ripening and longevity [13,44,45]. Endophytes, rhizobacteria, and epiphytes not only promote plant growth, but also enhance the postharvest quality by directly suppressing pathogen growth, modulating ripening, and enhancing the nutritional value of stored produce [46,47]. Endophytes are microorganisms that inhabit internal plant tissues, such as roots, stems, and leaves, without damaging the plant [48,49]. These microbes directly enhance postharvest preservation by reducing microbial spoilage and delaying senescence. Rhizobacteria, which inhabit the rhizosphere, the soil region surrounding plant roots, are well-known for their ability to enhance plant growth and improve the postharvest quality through nutrient cycling, nitrogen fixation, and the production of growth-promoting substances [10,50]. Additionally, they protect plants from pathogens by outcompeting harmful microbes. In contrast, epiphytes inhabit the external surfaces of plants, such as leaves and stems, and help protect plants from pathogen invasion by producing antimicrobial compounds and triggering systemic resistance mechanisms within the plant during the postharvest phase. These microbes significantly contribute to the postharvest quality by enhancing the nutritional value, reducing spoilage, and maintaining the quality of stored produce. The complex interactions between these microorganisms and their host plants during storage play a key role in maintaining produce quality, making them a valuable resource for postharvest management [10,51,52]. The study of Pierce et al. [53] revealed that postharvest loss in climacteric fruits, such as bananas, avocados, and peaches, which continue to ripen after harvest, led to quality degradation, mechanical injury, and increased susceptibility to chill injury during transportation and storage. They applied a novel solution using a catalyst derived from Rhodococcus rhodochrous (DAP 96253), a strain induced to produce high levels of nitrile hydratase. The catalyst, when placed in proximity to the fruit without direct contact, effectively delayed ripening at ambient temperatures, extending the shelf life of the fruits and eliminating the need for refrigeration. Organoleptic evaluations of catalyst-exposed peaches revealed that, despite the delayed ripening, the treated fruits attained full natural ripeness in terms of aroma, flavor, sweetness, and juice content, suggesting that the catalyst preserves fruit quality while extending shelf life. This approach offers a promising, environmentally friendly, and cost-effective strategy for mitigating postharvest fruit degradation, providing an alternative to conventional preservation methods and maintaining fruit quality during storage and transportation [53]. Similarly, in another study, Pierce et al. [54] reported that induced cells of Rhodococcus rhodochrous (DAP 96253) delayed the ripening of fruits when placed in the near vicinity of fruits such as peaches, bananas, and avocados.

The role of the plant microbiome in postharvest quality is multifaceted. Beneficial microbes can influence various key factors such as the rate of ripening, susceptibility to pathogens, and the retention of nutritional value. For instance, certain bacteria and fungi can slow ripening by suppressing ethylene production or by producing compounds that inhibit pathogen growth [55]. Additionally, microbial communities can enhance the overall stress resilience of plants, thereby reducing the likelihood of spoilage after harvest [41]. The diversity of microorganisms within the plant microbiome, along with their ability to interact with plant tissues, contributes significantly to maintaining produce quality during storage, making them a valuable resource for postharvest management.

4. Mechanisms Through Which Microbes Enhance Postharvest Traits

Postharvest biocontrol systems involve a complex mechanism of interaction between microbial antagonists, pathogens, and the host plant, all influenced by environmental factors. Microbial antagonists inhibit pathogen growth through competition or the production of antimicrobial compounds, while the host plant’s defense mechanisms and environmental conditions such as temperature and humidity affect the effectiveness of this interaction [35]. The success of biocontrol strategies depends on the balance between these elements and their external conditions. Microbial communities play a crucial role in enhancing the postharvest qualities of horticultural produce through various biochemical and physiological mechanisms (

Table 1. Key microbial species and their roles in postharvest enhancement.

Microbial Species	Key Mechanisms for Postharvest Enhancement	References
Bacillus subtilis	Antimicrobial activity (surfactin, iturin, fengycin) Suppression of ethylene production Induction of systemic resistance (ISR) via volatile organic compounds	[63]
Pseudomonas fluorescens	Antimicrobial activity (produces phenazines, pyoluteorin) Ethylene suppression Induction of systemic resistance (ISR) via jasmonic acid (JA) and ethylene pathways	[64]
Pseudomonas aeruginosa	Antimicrobial activity (produces pyocyanin, phenazines) Suppression of ethylene production Ability to form biofilms contributing to resistance against pathogens	[65,66]
Pseudomonas protegens	Antimicrobial activity (produces 2,4-diacetylphloroglucinol) Induction of systemic resistance (ISR) Rhizosphere colonization and pathogen suppression	[67]
Bacillus amyloliquefaciens	Antimicrobial activity (produces surfactin, bacillomycin) Induction of systemic resistance Plant growth promotion through nutrient competition	[68]
Bacillus cereus	Antimicrobial activity (produces chitinases, lipopeptides) Inhibition of fungal growth Root colonization promoting plant health and disease suppression	[69]
Pseudomonas corrugata	Biocontrol agent against Phytophthora blight of pepper Antimicrobial activity through biofilm formation and motility Root colonization and pathogen suppression	[70]
Pseudomonas pseudoalcaligenes	Antimicrobial activity (produces protease and lecithinase) Enzyme production for pathogen inhibition Biofilm formation contributing to pathogen resistance	[71]
Pseudomonas fluorescens biovar III	Antimicrobial activity against various food spoilage microorganisms Ethylene suppression and pathogen inhibition	[72]
Pseudomonas sp. GOM7	Antimicrobial activity (produces bioactive metabolites against methicillin-resistant Staphylococcus aureus) Potential biocontrol agent for foodborne pathogens	[73]

). These include ethylene suppression, antimicrobial metabolite production, induced systemic resistance (ISR), and the stabilization of nutritional and bioactive compounds [10,56]. These direct microbial applications contribute significantly to improving the postharvest quality and extending shelf life. For example, endophytes and rhizobacteria have been shown to suppress ethylene production and reduce microbial spoilage through the production of volatile organic compounds (VOCs) [57,58,59]. A deeper understanding of these mechanisms enables the strategic use of beneficial microbes in postharvest management, offering a sustainable and effective alternative to traditional chemical-based preservation methods [60]. Additionally, quorum sensing interference, a process where microbes communicate through signaling molecules to regulate gene expression collectively, has emerged as a novel mechanism through which microbes enhance postharvest traits. By interfering with the quorum sensing pathways of spoilage-causing pathogens, beneficial microbes can inhibit the expression of virulence factors, reducing pathogen growth and improving the overall safety and quality of stored produce [10,61,62]. Figure 2 provides an overview of these mechanisms, illustrating how microbial activities, such as ethylene suppression, antimicrobial activity, ISR activation, and nutrient modulation, collectively contribute to improved postharvest quality.

4.1. Ethylene Regulation and Delayed Senescence

Ethylene is a key plant hormone that regulates various aspects of fruit ripening and senescence. Following harvest, elevated ethylene levels can significantly reduce the quality and shelf life of horticultural produce [27,74]. The microbial regulation of ethylene production is a critical mechanism for enhancing postharvest traits. One of the primary ways that beneficial microbes influence ethylene levels is through the activity of ACC deaminase. This enzyme, synthesized by certain microbial genera, such as Pseudomonas and Bacillus, degrades 1-aminocyclopropane-1-carboxylate (ACC), the precursor of ethylene, thereby limiting ethylene production (Figure 3). By lowering the ACC concentrations, these microbes directly delay the ripening and senescence processes, resulting in an extended shelf life and reduced spoilage during storage and transportation [75,76].

In addition to ACC deaminase activity, microbes also suppress ethylene signaling [77]. Certain beneficial microbes such as Pseudomonas produce compounds that interfere with ethylene receptor pathways, reducing the plant’s sensitivity to ethylene [78]. This suppression of ethylene signaling prevents the rapid onset of senescence and allows produce to retain freshness for a longer period. Collectively, these microbial mechanisms contribute to an extended postharvest lifespan for various fruits and vegetables, preserving their freshness and quality during storage and transportation.

4.2. Antimicrobial Metabolites and Biocontrol

One of the key strategies by which microbes enhance postharvest traits is through the production of antimicrobial metabolites. These metabolites are crucial in inhibiting the growth of spoilage-causing pathogens, thereby reducing the risk of the microbial-induced degradation of produce [46,79]. Volatile organic compounds (VOCs) are a class of antimicrobial metabolites produced by microbes such as Bacillus and Pseudomonas. These VOCs can inhibit the growth of fungi and bacteria by disrupting their cellular processes [80]. For instance, certain VOCs interfere with fungal spore germination, preventing the establishment of fungal infections on the surface of fruits and vegetables. By producing these VOCs, beneficial microbes serve as natural fungicide agents, offering a chemical-free alternative for preventing postharvest spoilage (Table 2).

Additionally, microbes produce lytic enzymes, such as chitinases, glucanases, and proteases, which degrade the cell walls of fungal and bacterial pathogens [81]. These enzymes break down the structural components of pathogens, preventing them from infecting or spreading within the plant tissues. Siderophores, another important class of antimicrobial metabolites, are compounds produced by microbes that bind to iron, a critical nutrient for microbial growth [82]. Through ion sequestration, siderophores limit access to this essential resource for pathogenic microbes, thereby inhibiting their growth and spread. The competition for iron between beneficial microbes and spoilage-causing pathogens is a key strategy in enhancing the postharvest quality by reducing microbial contamination and spoilage.

Table 2. Microbial metabolites for postharvest enhancement (VOCs, lipopeptides, enzymes) and their antimicrobial activities.

Microbial Metabolite	Source Microbe	Key Activity/Mechanism	Examples/Applications	References
Lipopeptides (surfactin, iturin, fengycin)	Bacillus subtilis, Bacillus pumilus	Antimicrobial activity against fungi and bacteria Disrupt cell membranes Induce systemic resistance (ISR) in plants	Used to control fungal infections in fruits like apples, tomatoes, and strawberries.	[36,83,84]
Volatile organic compounds (VOCs)	Bacillus siamensis, Pseudomonas sp. AN3A02	Inhibit fungal growth Broad-spectrum antimicrobial properties Reduce postharvest disease incidence and maintain fruit quality	Reduces fungal growth on blueberries, extending shelf life.	[10,85]
Volatile organic compounds (VOCs)	Pseudomonas sp. AN3A02	Antifungal activity against Botrytis cinerea Inhibit hyphal growth and spore germination Reduce fungal infection in blueberries	Prevents fungal infection on blueberries during storage.	[35,83]
Gliotoxin (lipopeptide)	Aspergillus fumigatus	Antimicrobial activity through zinc chelation Inhibit metallo-β-lactamases and bacterial growth	Inhibits fungal growth and provides a biocontrol agent in citrus fruits.	[10,86]
Cyclic lipopeptides (alterochromides)	Pseudoalteromonas sp. strain T1lg65	Antimicrobial activity against bacteria and fungi Antimicrobial peptides with potential for biocontrol applications Antifungal and antibacterial properties	Used for biocontrol of postharvest fruit pathogens.	[83,87]
Antifungal enzymes (e.g., chitinase, β-1,3-glucanase)	Bacillus spp., Pseudomonas spp.	Breakdown of fungal cell walls Inhibit fungal growth, particularly Botrytis cinerea Induce of systemic resistance	Reduces fungal infections in apples and tomatoes during storage.	[88,89]
Antimicrobial polyketides (e.g., difficidin)	Bacillus spp.	Antifungal and antibacterial properties Biocontrol agent for a wide range of plant pathogens	Used in postharvest management of fruits to control fungal and bacterial pathogens.	[35,90]
Lipopeptides (surfactins, plipastatins)	Bacillus subtilis	Antifungal activity against Fusarium species Biocontrol activity in postharvest fruits	Effective in controlling Fusarium and preventing spoilage in postharvest fruits.	[91,92]
Volatile organic compounds (VOCs)	Clavispora lusitaniae	Fungistatic and fungicidal effects against citrus postharvest pathogens Reduce mycelial growth of Penicillium digitatum and Geotrichum citri-aurantii	Reduces spoilage and enhances the quality of citrus fruits during postharvest.	[10,86]
Volatile organic compounds (VOCs)	Bacillus siamensis	Inhibit Botrytis cinerea and Rhizopus stolonifer Reduce postharvest disease and extends fruit shelf life	Reduces postharvest diseases in strawberries and extends shelf life.	[40,93]

Table 2. Microbial metabolites for postharvest enhancement (VOCs, lipopeptides, enzymes) and their antimicrobial activities.

Microbial Metabolite	Source Microbe	Key Activity/Mechanism	Examples/Applications	References
Lipopeptides (surfactin, iturin, fengycin)	Bacillus subtilis, Bacillus pumilus	Antimicrobial activity against fungi and bacteria Disrupt cell membranes Induce systemic resistance (ISR) in plants	Used to control fungal infections in fruits like apples, tomatoes, and strawberries.	[36,83,84]
Volatile organic compounds (VOCs)	Bacillus siamensis, Pseudomonas sp. AN3A02	Inhibit fungal growth Broad-spectrum antimicrobial properties Reduce postharvest disease incidence and maintain fruit quality	Reduces fungal growth on blueberries, extending shelf life.	[10,85]
Volatile organic compounds (VOCs)	Pseudomonas sp. AN3A02	Antifungal activity against Botrytis cinerea Inhibit hyphal growth and spore germination Reduce fungal infection in blueberries	Prevents fungal infection on blueberries during storage.	[35,83]
Gliotoxin (lipopeptide)	Aspergillus fumigatus	Antimicrobial activity through zinc chelation Inhibit metallo-β-lactamases and bacterial growth	Inhibits fungal growth and provides a biocontrol agent in citrus fruits.	[10,86]
Cyclic lipopeptides (alterochromides)	Pseudoalteromonas sp. strain T1lg65	Antimicrobial activity against bacteria and fungi Antimicrobial peptides with potential for biocontrol applications Antifungal and antibacterial properties	Used for biocontrol of postharvest fruit pathogens.	[83,87]
Antifungal enzymes (e.g., chitinase, β-1,3-glucanase)	Bacillus spp., Pseudomonas spp.	Breakdown of fungal cell walls Inhibit fungal growth, particularly Botrytis cinerea Induce of systemic resistance	Reduces fungal infections in apples and tomatoes during storage.	[88,89]
Antimicrobial polyketides (e.g., difficidin)	Bacillus spp.	Antifungal and antibacterial properties Biocontrol agent for a wide range of plant pathogens	Used in postharvest management of fruits to control fungal and bacterial pathogens.	[35,90]
Lipopeptides (surfactins, plipastatins)	Bacillus subtilis	Antifungal activity against Fusarium species Biocontrol activity in postharvest fruits	Effective in controlling Fusarium and preventing spoilage in postharvest fruits.	[91,92]
Volatile organic compounds (VOCs)	Clavispora lusitaniae	Fungistatic and fungicidal effects against citrus postharvest pathogens Reduce mycelial growth of Penicillium digitatum and Geotrichum citri-aurantii	Reduces spoilage and enhances the quality of citrus fruits during postharvest.	[10,86]
Volatile organic compounds (VOCs)	Bacillus siamensis	Inhibit Botrytis cinerea and Rhizopus stolonifer Reduce postharvest disease and extends fruit shelf life	Reduces postharvest diseases in strawberries and extends shelf life.	[40,93]

4.3. Induced Systemic Resistance (ISR)

The activation of induced systemic resistance (ISR) is an essential mechanism through which microbes enhance postharvest traits [94]. ISR is a defense response triggered when plants are exposed to beneficial microbes, which stimulate the plant’s immune system to protect against subsequent pathogen attacks. Microbial elicitors, such as flavonoids, polysaccharides, and other signaling molecules, play a key role in inducing ISR in plants [95]. These elicitors activate a cascade of defense responses, including the production of pathogenesis-related (PR) proteins, which are crucial for plant defense against pathogens. By enhancing the plant’s immune response, ISR provides long-lasting protection against microbial pathogens during the postharvest phase, thus reducing spoilage and maintaining produce quality [96,97].

Furthermore, the induction of ISR also promotes resistance to oxidative stress, a common cause of quality deterioration in stored produce. The activation of stress-related genes and pathways helps mitigate the effects of environmental stresses such as high humidity, temperature fluctuations, and pathogen invasion. By strengthening the plant’s immune system, beneficial microbes ensure that produce remains fresh and disease-free during storage, which is particularly important for fruits and vegetables that are highly susceptible to microbial infections during the postharvest phase [98].

4.4. Enhancement of Nutritional and Bioactive Compounds

Beneficial microbes also play a significant role in enhancing the nutritional and bioactive content of postharvest produce [55]. During storage, many fruits and vegetables undergo biochemical transformations that can lead to the loss of essential nutrients and bioactive compounds. However, certain microbes can stabilize these compounds, preserving their levels and thereby enhancing the nutritional value of the produce [13,40]. For instance, microbes such as Lactobacillus species have been shown to produce metabolites that help maintain the quality and stability of stored produce, reducing degradation during postharvest storage [99,100,101,102].

In addition to stabilizing vitamins and minerals, beneficial microbes can also enhance the levels of phenolic compounds, antioxidants, and flavonoids, which are associated with the health benefits of fruits and vegetables [103]. These compounds contribute significantly to the nutritional value of produce and provide protective effects against oxidative damage. By promoting the synthesis or preservation of these bioactive compounds, beneficial microbes help maintain both the overall quality and health benefits of stored produce, making them a valuable tool in postharvest management.

Through various mechanisms, such as ethylene regulation, antimicrobial metabolite production, induced systemic resistance, and the enhancement of nutritional compounds, microbes play a pivotal role in improving postharvest quality, extending shelf life, and reducing spoilage. These strategies provide an eco-friendly and sustainable alternative to traditional chemical preservation methods, presenting new opportunities for the improved postharvest management of horticultural crops [98,104,105,106,107,108].

5. Microbial Interventions for Postharvest Disease Control and Quality Enhancement

The molecular mechanisms of biocontrol agents are integral to their effectiveness in controlling postharvest pathogens, extending shelf life and quality, while mediating interactions between pathogens and biocontrol agents [109]. Common mechanisms include competition for nutrients and space, where biocontrol agents outcompete pathogens for essential resources, thus preventing pathogen growth; mycoparasitism, in which biocontrol agents, particularly fungi, parasitize and degrade the pathogen; and the production of volatile organic compounds (VOCs), which inhibit pathogen growth and disrupt pathogen communication. Additionally, biocontrol agents can form biofilms on plant surfaces, creating protective barriers that hinder pathogen attachment and growth. They also induce systemic resistance in plants, activating defense pathways that enhance the plant’s ability to resist pathogen invasion [110]. Beyond these, quorum sensing allows biocontrol agents to coordinate the expression of antimicrobial compounds, and oxidative bursts—the rapid production of reactive oxygen species (ROS)—serve as a direct defense mechanism, damaging pathogens and triggering plant immune responses. Together, these diverse mechanisms enable biocontrol agents to efficiently manage postharvest pathogens, offering a sustainable and eco-friendly alternative to chemical treatments while also improving the quality and shelf life of harvested fruits and vegetables.

Shelf-life extension of harvested fruits is a key focus in postharvest management. Wisniewski and Droby [109] reported the functional role of the fruit-associated microbiome within biocontrol systems, highlighting its potential for improving fruit preservation. They proposed that the microbial strains or consortia naturally inhabiting the fruit surface could be harnessed to extend shelf life and mitigate the growth of phytopathogens during postharvest storage. By leveraging the diverse and synergistic interactions within these microbial communities, they suggested that these microorganisms could offer a sustainable and eco-friendly alternative to other treatments, contributing to the control of fruit decay and enhancing overall fruit quality throughout storage periods.

Microbial interventions have gained recognition as a sustainable and effective strategy for controlling postharvest diseases and enhancing the quality of horticultural produce. These interventions leverage the natural capabilities of beneficial microbes to prevent spoilage, suppress pathogens, and preserve the freshness and nutritional value of fruits and vegetables [35]. The use of microbial-based technologies offers an eco-friendly alternative to traditional chemical preservatives, which are increasingly scrutinized for their potential environmental impact and concerns regarding consumer health. Microbial interventions not only control pathogens, but also enhance the postharvest shelf life by exploiting the interaction between microorganisms and plants. Methods such as microbial coatings and biofilms, spray treatments, biological control agents (BCAs), microbial washes, and fermentation treatments directly influence plant physiology. These interventions activate plant defense mechanisms and promote the establishment of beneficial microbial communities at the plant surface, which are crucial for extending shelf life. These microbial-based treatments have demonstrated the ability to improve the produce quality by reducing spoilage and enhancing pathogen resistance. While microbial interventions help mitigate spoilage by controlling pathogens, they also enhance the plant’s natural resistance mechanisms. The interaction between beneficial microbes and the plant surface can activate systemic plant responses, strengthening the plant’s innate ability to resist environmental stress and microbial invasion. This dynamic interaction is crucial for prolonging the postharvest shelf life of produce. However, the effectiveness of microbial interventions can vary significantly depending on factors like crop variety, environmental conditions, and storage parameters. When combined with other postharvest technologies like modified atmosphere packaging (MAP) and edible coatings, microbial treatments can offer synergistic benefits, improving the overall preservation effectiveness. Although microbial-based treatments offer great potential, the inconsistency of their success across different settings needs to be addressed. The stability of these treatments in response to environmental stressors also remains a challenge, requiring further research into improving their long-term effectiveness. Moreover, while omics technologies are being applied to enhance microbial treatments, they have revealed that the complexity of plant–microbe interactions remains poorly understood, and crop-specific microbial consortia are still not fully optimized.

The promising results of certain microbial antagonists in laboratory studies conducted in packing houses have sparked significant interest among agrochemical companies for the development and commercialization of bioproducts aimed at controlling postharvest diseases in fruits and vegetables. These biocontrol agents, typically derived from naturally occurring microorganisms, provide an environmentally friendly alternative to chemical fungicides. As concerns over pesticide residues and environmental sustainability grow, microbial antagonists offer a viable solution for reducing the reliance on synthetic chemicals in postharvest management [111]. The success of these agents in controlled environments has led to their incorporation into commercial products, with notable examples including YieldPlus (USA), BIOSAVE-110 (The Netherlands), SMARTBLOCK (USA), T-22 (USA), BioProtect (USA), and BioTelo (Spain). These bioproducts have been successfully employed worldwide to manage a wide range of postharvest pathogens such as Botrytis cinerea, Penicillium spp., and Rhizopus spp. By effectively controlling these pathogens, they help extend the shelf life and improve the quality of fresh produce. Moreover, these microbial agents contribute to integrated pest management strategies, promoting sustainable agricultural practices. The widespread adoption of bioproducts like ASPIRE and BIOSAVE-110 highlights the growing recognition of microbial antagonists as a key element in postharvest disease control. This shift toward natural solutions not only reduces spoilage, but also offers a basis for microbial interventions as a sustainable and effective strategy for controlling postharvest diseases and is recognized as a more eco-friendly and sustainable approach to managing postharvest diseases, aligning with the global trend toward greener agricultural practices (Figure 4).

5.1. Microbial Coatings and Biofilms

The use of microbial coatings and biofilms is a promising microbial intervention for postharvest disease control. Edible coatings are thin layers of material applied to the surface of fruits and vegetables, serving as protective barriers that reduce moisture loss, delay ripening, and inhibit pathogen entry [112,113]. These coatings are typically composed of natural polymers, such as chitosan, alginate, and cellulose, which can be combined with beneficial microbes to enhance their effectiveness. The inclusion of microbes in these coatings provides protection from physical damage as well as microbial spoilage [114]. For instance, the inclusion of Pseudomonas or Bacillus strains in edible coatings has been shown to reduce fungal infections and extend the shelf life of fruits such as apples, tomatoes, and strawberries. These microbes release antimicrobial compounds, such as volatile organic compounds (VOCs) and enzymes, that target spoilage-causing pathogens, while the coating itself serves as a physical barrier [36].

Additionally, biofilms, dense layers of microbial communities attached to surfaces, have been utilized as protective agents in postharvest preservation. Biofilms form on the surfaces of produce and create a stable environment for beneficial microbes, allowing them to exert their antimicrobial effects over an extended period [115]. The microbial consortia within biofilms often act synergistically, with different species targeting a variety of spoilage agents. Moreover, biofilms can serve as controlled-release systems for protective agents, ensuring a steady release of antimicrobial metabolites, thereby enhancing the shelf life of produce without the need for frequent reapplication [116]. This controlled-release system is particularly beneficial in reducing postharvest spoilage and maintaining produce quality throughout storage and transport, particularly in highly perishable crops [117].

5.2. Spray Treatments and Biological Control Agents (BCAs)

Another widely adopted microbial intervention for postharvest disease control is the use of spray treatments using biological control agents (BCAs). BCAs comprise a variety of beneficial microorganisms, such as bacteria, fungi, and yeasts, that can be sprayed onto harvested produce to protect it from pathogen infection. These microbes function by outcompeting harmful pathogens for resources, producing antimicrobial substances, or directly inhibiting the growth of spoilage organisms [111,118]. For instance, bacterial suspensions of Bacillus subtilis and Pseudomonas fluorescens have been shown to effectively reduce the incidence of Penicillium and Botrytis infections in fruits such as apples and berries [119,120]. Similarly, fungal antagonists such as Trichoderma spp. are applied to suppress postharvest fungal diseases including molds affecting vegetables such as cucumbers and tomatoes [121,122].

Several commercial microbial-based products, such as Serenade^® and Aspire^®, have been developed and are now widely used in postharvest disease management. These products contain active biological agents and are applied to crops during or shortly after harvest [123,124]. For instance, Serenade^® contains the bacterium Bacillus subtilis, which has demonstrated efficacy in suppressing a broad range of fungal and bacterial pathogens on postharvest fruits and vegetables. Aspire^®, which contains a mix of beneficial fungi, is used to control pathogens such as Fusarium and Rhizopus on stored produce [125]. These microbial-based products have gained popularity due to their effectiveness in reducing spoilage while leaving no harmful residues on the produce, making them a suitable alternative to chemical fungicides [126].

Table 3. Active ingredients in commercial microbial-based postharvest products, their applications, and effectiveness against specific pathogens.

Commercial Product	Active Ingredient(s)	Application Area	Pathogens Controlled	Effectiveness	References
Bio-save 10LP	Pseudomonas syringae	Postharvest fruit and vegetable treatments	Botrytis cinerea, Penicillium spp. Fusarium spp.	Effective in reducing postharvest rots, particularly on potatoes, cherries, and pome fruits.	[127]
Bio-save	Pseudomonas syringae	Postharvest fruit treatments, especially for citrus and apples	Botrytis cinerea, Penicillium expansum	Demonstrates substantial effectiveness against Botrytis and Penicillium in apples and citrus, reducing disease incidence.	[128,129,130,131]
Aspire	Candida sake and Candida oleophila	Postharvest fruit treatment	Penicillium spp. Botrytis cinerea, Monilinia spp.	High efficacy in reducing rots in stored fruits such as apples and pears. Results show disease reduction of up to 50–70%.	[132,133,134,135]
Kodiak	Bacillus subtilis	Postharvest fruit and vegetable treatment	Botrytis cinerea, Alternaria spp. Rhizopus stolonifer	Strong inhibitory effects on Botrytis and Alternaria, effective in preventing spoilage and improving shelf life by 30–40%.	[136]
Serenade	Bacillus subtilis	Postharvest fruit and vegetable treatment	Botrytis cinerea, Rhizopus spp. Fusarium spp.	Shows broad-spectrum biocontrol activity, particularly in reducing Botrytis on grapes, with efficacy rates of over 60% under controlled conditions.	[136]
Soilguard	Trichoderma harzianum	Soil and postharvest fruit treatment	Fusarium oxysporum, Rhizoctonia solani, Alternaria spp.	Effective at controlling soilborne pathogens and postharvest pathogens such as Fusarium. Reduces spoilage by up to 45%.	[136]
Trichojet	Trichoderma spp.	Postharvest fruit and vegetable treatment	Botrytis cinerea, Penicillium expansum, Alternaria spp.	Controls major postharvest pathogens such as Penicillium and Alternaria with significant reductions in rotting and increased shelf life of treated produce.	[136]
Prev-Am Plus	Citrus essential oils	Citrus postharvest treatment	Penicillium spp., Alternaria spp., Geotrichum candidum	Controls Penicillium and Alternaria in citrus with significant reductions in decay and fungal growth, ensuring longer shelf life.	[137]
Biorend	Chitosan	Postharvest treatment for pears and apples	Botrytis cinerea, Penicillium expansum, Alternaria spp.	High efficacy in controlling Botrytis and Penicillium, with a reduction in disease incidence by up to 71% compared with copper-based treatments.	[137]
Kiram	Mineral fertilizers	Postharvest control of citrus anthracnose	Colletotrichum gloeosporioides	Demonstrates effectiveness in reducing disease incidence and severity in citrus fruits in field trials, significantly better than chemical treatments.	[137]

presents a detailed overview of the active ingredients in these commercial microbial products, their specific applications, and their effectiveness against various pathogens.

5.3. Microbial Washes and Fermentation Treatments

Microbial washes and fermentation treatments are emerging as innovative approaches for reducing spoilage and enhancing the quality of postharvest produce. Microbial washes involve the application of water or solutions containing beneficial microbes, such as lactic acid bacteria (LAB) or Bacillus species, to the surface of harvested crops [138,139]. These washes help lower the microbial load on produce by either outcompeting spoilage-causing pathogens or producing antimicrobial substances that inhibit pathogen growth. For instance, Lactobacillus species have been effectively used in microbial washes to reduce the presence of E. coli and other harmful bacteria on leafy greens and tomatoes. These treatments are particularly beneficial for fresh-cut produce, which is highly susceptible to contamination during handling and processing [60].

Fermentation by-products, such as organic acids, antimicrobial peptides, and other metabolites, can also be used in postharvest treatments to control microbial growth and enhance the quality of stored produce. Fermented plant extracts and biological preservatives derived from fermentation processes have demonstrated efficacy in inhibiting the growth of a variety of pathogens, including Botrytis cinerea and Fusarium spp., which contribute significantly to postharvest losses [56,140]. A case study involving the use of fermented rice bran extracts demonstrated its effectiveness in controlling Penicillium rot in citrus fruits [141]. Similarly, fermented citrus extracts have been used to reduce spoilage and extend shelf life in strawberries and grapes. These treatments provide an added layer of protection by delivering natural antimicrobial agents that can be applied directly to produce, thereby enhancing the shelf life and preserving safety and quality [142].

Postharvest quality can be significantly improved through various microbial interventions such as coatings and biofilms, spray treatments and BCAs, and microbial washes and fermentation treatments [10,143]. These methods not only provide effective protection against spoilage and pathogens, but also contribute to the sustainability of agricultural practices by reducing the dependence on chemical pesticides and preservatives. The continued development and adoption of microbial technologies will be instrumental in enhancing food safety, extending shelf life, and minimizing food waste, making them an integral part of modern postharvest management systems [36,56,104].

6. Integration of Omics Approaches to Decoding Plant–Microbe Interactions in Postharvest Systems

The integration of metabolomics, transcriptomics, and microbiomics, along with AI technologies, has provided powerful tools for enhancing the application of microbial treatments in postharvest management [144,145]. For instance, metabolomics is being used to identify metabolic shifts in response to microbial interactions, providing insights into spoilage resistance and quality retention during storage [144,146]. Recent studies have also demonstrated how these technologies can reveal specific metabolic pathways that are activated in response to beneficial microbes, enabling more targeted interventions. These technologies enable the comprehensive analysis of the biochemical, genetic, and microbial dynamics that influence the quality, safety, and shelf life of stored products [147,148]. Omics-based approaches have revolutionized postharvest biology by facilitating the identification of molecular markers associated with spoilage resistance, optimizing microbial treatments, and guiding the development of sustainable strategies to enhance postharvest quality [145]. The integration of these high-throughput technologies offers a holistic approach, enabling a better understanding of the plant–microbe interactions for improved postharvest preservation and extended shelf life, driving innovation in microbial treatments (

Table 4. Omics tools used in plant–microbe postharvest research and their applications in quality prediction.

Omics Tool	Technology/Approach	Application in Plant–Microbe Postharvest Research	Role in Quality Prediction	References
Metabolomics	Mass spectrometry, NMR, GC-MS	Detects and quantifies metabolites at the plant–microbe interface	Used for detecting metabolic changes that reflect plant stress or microbial interaction, predicting spoilage or ripeness.	[144,151]
Transcriptomics	RNA-Seq, microarray	Analyzes gene expression in response to microbial interactions	Assesses plant’s genetic response to microbial activity, predicting quality traits such as pathogen resistance and ripening.	[148,152]
Microbiomics	Metagenomics, 16S rRNA sequencing	Studies microbial community composition on plant surfaces	Determines microbial community impact on postharvest quality and pathogen control.	[40,153]
Proteomics	LC-MS/MS, 2D gel electrophoresis	Identifies proteins involved in plant–microbe interactions	Identifies key proteins that influence plant resistance, shelf life, and quality	[154]
Fluxomics	Stable isotope labeling, GC-MS	Studies metabolic flux changes in response to microbial interaction	Determines changes in metabolic pathways that impact plant quality attributes such as nutrient content and storage capacity.	[155,156]
Integrated Omics	Multi-omics data integration	Combines genomics, proteomics, metabolomics, and transcriptomics to assess microbial interactions	Predicts quality outcomes by integrating diverse omics data to understand holistic changes in plant metabolism and microbial influence.	[144,145]

). The study by Santin et al. [149] utilized a metabolomics-based approach to elucidate the biochemical mechanisms associated with key processes such as ripening, senescence, and the responses of peaches to various postharvest treatments and storage conditions. Their study provided a valuable framework for understanding how these factors influence the quality and shelf-life of peaches. However, a single-omics approach, such as metabolomics, while informative, is often insufficient for capturing the full complexity of postharvest fruit physiology. A more comprehensive and detailed mechanistic understanding of how postharvest treatments and storage conditions affect fruit would benefit from the integration of multi-omics strategies, which combine data from genomics, transcriptomics, proteomics, and metabolomics. This integrated approach enables a more holistic view of the underlying biological networks and molecular pathways. In this regard, Yan et al. [150] demonstrated the potential of a multi-omics approach for apples, providing an in-depth analysis of how various postharvest interventions influence apple fruit quality at the molecular level, thus offering a more complete understanding of the mechanisms governing fruit preservation and aging processes. Postharvest management can be greatly enhanced through the integration of multi-omics analyses, which provide a comprehensive understanding of the complex metabolic and biological processes. By elucidating these mechanisms, we can gain deeper insights into the physiological and biological processes of fruits and vegetables, ultimately leading to more effective and targeted postharvest management strategies.

6.1. Metabolomics

Metabolomics, the large-scale study of metabolites in biological systems, has become an indispensable tool in postharvest research [88]. Profiling the metabolite shifts that occur during microbial interactions under postharvest conditions provides crucial insights into the effects of beneficial microbes on plant biochemistry [157,158]. During storage, horticultural produce undergoes a range of metabolic changes, such as sugar degradation, organic acid production, and the accumulation of secondary metabolites such as phenolics and flavonoids [159,160]. For instance, the application of beneficial microbes has been shown to stabilize the levels of antioxidants, vitamins, and phenolic compounds, all of which are essential to the health benefits and commercial value of produce. Utilizing advanced techniques such as liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS), researchers can evaluate the effects of microbial treatments on these metabolites and monitor the preservation of key compounds that impact the flavor, texture, and nutritional value [161]. For instance, the application of beneficial microbes has been shown to stabilize the levels of antioxidants, vitamins, and phenolic compounds, all of which are essential to the health benefits and commercial value of produce [162]. Additionally, the profiling of volatile organic compounds (VOCs) produced by both plants and microbes during storage can provide valuable insights into the biochemical processes associated with ripening, senescence, and microbial growth. This information can be used to optimize storage conditions and microbial treatments to ensure an extended shelf life [163].

The use of LC-MS and GC-MS technologies in postharvest metabolomics not only facilitates the identification of individual metabolites, but also reveals broader metabolic patterns and pathways influenced by plant–microbe interactions [151]. Such insights are crucial for understanding how microbes modulate plant metabolism during the postharvest phase. For instance, specific microbial strains may stimulate the synthesis of bioactive compounds, such as flavonoids, which contribute to the overall quality and health benefits of fruits and vegetables [164,165]. Additionally, metabolomic analyses can help identify biomarkers associated with the onset of spoilage, enabling the development of predictive models for postharvest disease management. This information can be used to optimize the storage conditions and microbial treatments to ensure an extended shelf life and improved postharvest quality [166].

6.2. Transcriptomics

Transcriptomics, the study of gene expression in response to environmental factors, is a vital omics approach used for understanding plant–microbe interactions during the postharvest phase [148]. Gene expression studies provide insights into plant responses to microbial treatments, particularly in terms of stress response and defense mechanisms [167]. For instance, the application of Bacillus or Pseudomonas species can trigger the expression of genes encoding pathogenesis-related (PR) proteins, which play a crucial role in plant immunity by inhibiting pathogen growth and enhancing disease resistance.

Moreover, transcriptomic analyses enable the identification of plant genes that are involved in the regulation of ripening and senescence processes, both of which significantly impact the postharvest quality [168]. The modulation of these genes through microbial treatments can delay ripening, reduce spoilage, and enhance the nutritional quality of stored produce. For example, microbes that produce ACC deaminase can downregulate the ethylene biosynthesis pathway, thereby lowering ethylene production and delaying fruit ripening [169]. By analyzing the expression of ethylene-responsive genes and other plant hormones, transcriptomic approaches provide a deeper understanding of the potential of microbial treatments for regulating plant growth and development during storage [170]. This knowledge is vital for the development of strategies that not only extend shelf life, but also preserve the nutritional and sensory quality of postharvest produce.

6.3. Microbiomics

The microbiome, which refers to the community of microorganisms associated with plants, plays a crucial role in determining the postharvest quality of produce. Microbiomics refers to the study of microbial communities, their composition, diversity, and functional potential, particularly in relation to postharvest storage [40,171]. For example, 16S rRNA sequencing is used to identify bacterial communities on plant surfaces such as the fruit skins, leaves, and stems. This approach helps researchers understand how the microbial community evolves during storage and interacts with plant tissues [11].

In addition to bacteria, microbiomic studies also examine fungi, yeasts, and other microbes that colonize plant tissues during storage [13]. Shifts in these microbial communities can promote the growth of beneficial microbes while suppressing harmful pathogens, thus enhancing the postharvest shelf life of produce [172,173]. These dynamics allow for the identification of microbial biomarkers associated with healthy, long-lasting produce. Furthermore, the application of beneficial microbes, such as lactic acid bacteria (LAB) or Bacillus species, can alter the composition of the plant microbiome, promoting the dominance of beneficial microorganisms while suppressing harmful pathogens [174,175]. This shift in the microbial community can enhance the postharvest shelf life of produce by reducing spoilage and improving the overall safety and quality of stored produce.

The integration of microbiomic approaches with other omics technologies, such as metabolomics and transcriptomics, provides a comprehensive understanding of plant–microbe interactions during the postharvest phase [144,176]. By examining the microbiome in conjunction with plant biochemical and genetic responses, researchers can gain deeper insights into how microbial communities influence the postharvest quality, allowing for the optimization of microbial treatments for various storage conditions. This holistic approach to understanding plant–microbe interactions in postharvest systems will enable the development of more effective, sustainable methods for preserving horticultural produce and reducing postharvest losses.

Fluxomics, in conjunction with metabolomics, is crucial for understanding the metabolic pathways in plants during microbial interactions. Using stable isotope labeling and GC-MS, fluxomics traces metabolic fluxes, revealing how microbes influence plant processes such as nutrient flow, shelf life, and quality attributes like flavor, texture, and nutritional content. It decodes metabolic exchanges between the plants and microbes, enhancing agricultural productivity and ecosystem sustainability [156,177]. Fluxomics also connects cellular processes to whole-plant traits, highlighting its role in plant phenotyping and improving the plant quality influenced by microbial activity [155]. As the technology advances, it offers deeper insights into optimizing plant growth and quality [178].

7. Challenges and Regulatory Considerations

Although microbial treatments offer promising solutions for enhancing the postharvest quality and controlling spoilage, several challenges hinder their consistent and effective application. These challenges include not only scientific and technical limitations, but also regulatory and consumer acceptance issues [24,35]. The variability in microbial treatment effectiveness across different storage conditions, combined with regulatory hurdles and consumer perceptions, hinders the widespread adoption of these techniques [126,179]. Addressing these challenges is essential for unlocking the full potential of microbial-based approaches in postharvest management and ensuring their long-term benefits to the food industry.

7.1. Consistency and Efficacy of Microbial Treatments

Fruits and vegetables naturally host distinct microbial communities that contribute to their flavor, aroma, and other sensory characteristics [180]. The introduction of external microbiomes has the potential to disrupt the native microbial equilibrium. The introduction of foreign microbiomes may interfere with these communities, potentially resulting in unanticipated alterations to the sensory properties of the fruit. Therefore, it is imperative to carefully select microbiome strains to mitigate any disruption to the indigenous microbiota and preserve the fruit’s intrinsic qualities [181,182]. Similarly, one of the primary challenges in the application of microbial treatments for postharvest disease control and quality enhancement is the variability in microbial effectiveness across different storage conditions. The efficacy of microbial agents can be influenced by various environmental factors such as the storage temperature, humidity, and specific crop variety being treated [183,184]. For instance, the effectiveness of Bacillus subtilis in controlling fungal growth on apples is significantly higher under cold storage conditions but may decrease in high humidity environments. Similarly, Pseudomonas fluorescens has been found to be more effective in inhibiting Penicillium growth in tomatoes when stored at lower temperatures [185].

Storage temperature plays a pivotal role in determining microbial activity. Although microbial growth typically slows at lower temperatures, cold storage can also adversely affect the survival of beneficial microbes, particularly those sensitive to cold stress [33]. For example, lactic acid bacteria (LAB) strains used in microbial washes are less effective in colder conditions because their metabolic processes are slower at low temperatures. In contrast, high humidity may promote the growth of both spoilage-causing pathogens and the beneficial microbes applied to produce. The key challenge lies in creating a balance that maintains the optimal storage conditions for both the produce and the microbial agents [186]. Furthermore, crop variety plays a crucial role, as different cultivars of the same fruit or vegetable may exhibit varying levels of resistance to microbial treatments. For instance, certain tomato cultivars, such as ‘Roma’, may exhibit greater resistance to Botrytis cinerea than others, influencing the overall success of microbial treatments [187]. This variability in microbial effectiveness across storage conditions highlights the need for the careful optimization of microbial treatment protocols tailored to each specific crop type and storage condition, a process that can be both complex and resource-intensive. Moreover, understanding the complex interactions between antagonistic microorganisms and the fruit microbiome is crucial for developing novel strategies to reduce postharvest waste. By gaining insights into how beneficial and harmful microbes interact within the fruit’s native microbiota, researchers can identify ways to enhance the natural defense mechanisms of fruits against pathogens [12]. This knowledge could lead to the discovery of innovative biocontrol methods or microbiome management techniques that help preserve fruit quality and extend shelf life. Ultimately, such advancements could contribute to more sustainable agricultural practices by minimizing the loss of fruit due to microbial spoilage and improving postharvest management.

7.2. Regulatory Approval and Consumer Acceptance

In addition to the technical challenges, regulatory approval and consumer acceptance remain significant barriers to the widespread adoption of microbial treatments in the food industry [188]. Biosafety concerns and food safety regulations must be thoroughly addressed to ensure that microbial treatments are safe for human consumption and do not pose long-term health risks. Regulatory authorities, such as the U.S. Food and Drug Administration (FDA), the European Food Safety Authority (EFSA), and other national and international agencies, require that novel microbial-based products undergo rigorous testing to verify their safety and efficacy before they can be approved for use in food preservation [189,190]. This includes assessing the potential risks such as unintended microbial interactions, allergenicity, and the development of resistance to microbial treatments. For instance, before a microbial-based product like Serenade^®, containing Bacillus subtilis, can be marketed for postharvest use, it must undergo rigorous safety evaluations including tests for allergenicity and resistance development [136]. Ensuring the safety of these treatments typically involves extensive research, clinical trials, and documentation, which can be a lengthy and costly process. Furthermore, specific regional frameworks, such as EFSA’s Qualified Presumption of Safety (QPS) list and FDA’s GRAS (Generally Recognized as Safe) status, provide pathways for regulatory approval but still require a careful evaluation of microbial species to ensure that they are safe for use in postharvest treatments. Organic agriculture also has strict guidelines regarding the use of microbial-based products, where only those approved by certifying bodies like the USDA National Organic Program (NOP) can be used in organic farming practices. Therefore, microbial-based products need to meet these rigorous standards for both conventional and organic markets.

Moreover, consumer perceptions of biological treatments play a significant role in their acceptance. Despite the growing interest in organic and natural food products, some consumers remain skeptical about the safety of biological treatments due to a limited understanding or negative associations with microorganisms [191,192]. This highlights the need for public education and transparent communication regarding the benefits and safety of microbial interventions. Public perception can be influenced by demonstrating the effectiveness of microbial treatments in controlling postharvest diseases without leaving harmful residues as well as the establishment and implementation of safety standards by regulatory agencies. For example, consumer trust in microbial treatments could be bolstered by certifications such as USDA Organic or EFSA-approved safety claims, which assure that microbial agents used in postharvest management do not leave harmful residues or pose health risks [193].

The challenges of regulatory approval and consumer acceptance are closely intertwined, as public trust in microbial treatments often depends on the evidence provided by regulatory agencies. As research continues to demonstrate the efficacy and safety of microbial treatments in postharvest management, and as success case studies emerge from industry trials, the regulatory landscape may evolve to accommodate the use of these biological products [126]. In the long-term, overcoming these challenges will require collaboration between researchers, regulatory bodies, industry stakeholders, and consumers to ensure that microbial interventions are not only effective, but are also safe and widely accepted as viable alternatives to traditional chemical treatments.

8. Future Perspectives

The future of microbial interventions in postharvest management presents promising opportunities, driven by the integration of emerging technologies such as artificial intelligence (AI), machine learning, synthetic microbial consortia, and advanced cold chain logistics [194]. These innovations are expected to significantly enhance the precision, efficiency, and adaptability of microbial treatments, allowing for the optimization of specific crops, storage conditions, and pathogen targets. Continued advancements in these technologies will create new opportunities for improving food quality, extending shelf life, and reducing food waste on a global scale.

Artificial intelligence, in combination with machine learning, holds immense potential for selecting the optimal microbial strains for specific crops [195]. For instance, AI-driven algorithms can predict the most effective microbial strains based on environmental variables, pathogen susceptibility, and plant responses [146,194,196]. Traditionally, identifying the most effective microbial treatment for postharvest preservation has been a complex and time-consuming process, often involving extensive trial and error. The integration of machine learning algorithms will enable the prediction of microbial strains that are most likely to succeed based on factors such as crop variety, environmental conditions, and pathogen susceptibility [196]. For example, a predictive model using deep learning has been employed to assess the effectiveness of biocontrol agents for controlling fungal pathogens like Botrytis cinerea in strawberries, streamlining the process of selecting suitable microbial strains [197,198]. AI can analyze vast datasets containing microbial characteristics, environmental factors, and plant responses, allowing for a more targeted approach to microbial selection [196,199]. This application of AI will not only optimize microbial treatments, but also enable the fine-tuning of application protocols, ensuring consistent performance across a wide range of postharvest conditions.

Another promising development is the creation of synthetic microbial consortia. Unlike single-strain microbial treatments, these consortia consist of multiple, carefully selected microorganisms that work synergistically to protect crops from spoilage and pathogens [200]. The design of synthetic consortia can include specific microbes that target spoilage agents while enhancing shelf life and postharvest quality, thereby providing a more holistic solution to crop preservation [201]. Furthermore, microbial consortia can be designed to provide a controlled release of protective agents, ensuring consistent efficacy throughout the entire postharvest storage period. For instance, a synthetic consortium composed of Bacillus spp. and Pseudomonas spp. has been shown to significantly reduce postharvest fungal infections and extend the shelf life of tomatoes and citrus fruits [202,203]. This tailored approach to microbial treatment holds significant promise for minimizing spoilage and extending the shelf life of perishable produce.

The integration of cold chain logistics with sensor technologies represents another key advancement in microbial postharvest management [204]. Smart cold storage systems, equipped with real-time monitoring capabilities, allow for the continuous tracking of environmental conditions and microbial activity during storage. Monitoring key variables such as temperature, humidity, and the metabolic activity of beneficial microbes can ensure the sustained effectiveness of microbial treatments across the supply chain. This dynamic feedback system will allow for the real-time adjustment of storage conditions, optimizing the effectiveness of microbial interventions. For example, real-time monitoring systems that track the temperature and ethylene levels are being integrated into smart cold storage, enhancing the efficacy of microbial biocontrol agents during storage [204,205,206]. Sensors could monitor the ethylene production and microbial metabolite levels, providing valuable insights into the real-time effectiveness of microbial treatments and ensuring that the produce is maintained under the optimal storage conditions.

Omics data related to postharvest pathology have expanded rapidly in recent years, highlighting the need for focused bioinformatic analysis. Future research should prioritize mining these datasets, leveraging advancements in bioinformatics, new algorithm development, and artificial intelligence. These innovations will facilitate the identification of interactions within complex datasets, enabling a network-based approach to understand plant–microbe interactions more comprehensively, rather than focusing on individual components. This holistic perspective can enhance strategies for managing postharvest diseases, improving crop quality, and reducing food waste [145]. The integration of IoT (Internet of Things) technologies will further enhance this process by enabling data sharing across the supply chain, thereby improving transparency and enhancing the overall management of postharvest produce.

Incorporating these advanced technologies into postharvest management can facilitate a more efficient and responsive food supply chain, minimizing spoilage and waste while maximizing the quality of stored produce. Combining artificial intelligence, synthetic microbial consortia, and smart cold storage systems will enable greater precision in the management of microbial treatments, ensuring that the produce remains safe, fresh, and of high quality throughout the postharvest process. This integrated approach not only enhances the sustainability of the food supply chain, but also contributes to a significant reduction in food waste, providing a more sustainable solution to global food security challenges.

9. Conclusions

Microbial interventions provide a sustainable and effective approach to postharvest management by reducing spoilage, extending shelf life, and preserving the quality of horticultural produce. Beneficial microorganisms, such as bacteria, fungi, and yeasts, play crucial roles in suppressing pathogenic microbes, regulating ripening through ethylene modulation, and enhancing the nutritional value of stored produce. Techniques such as microbial coatings, biofilms, and biological control agents provide effective, chemical-free alternatives to traditional preservatives, minimizing environmental impact while ensuring food safety. The integration of omics technologies, such as metabolomics, transcriptomics, and microbiomics, enhances our understanding of plant–microbe interactions and allows for more precise microbial treatments. These technologies, combined with AI and machine learning for microbial strain selection, provide opportunities to tailor interventions to specific crop types and storage conditions. Moreover, the application of smart cold storage and sensor technologies will further refine microbial treatments, ensuring their continued effectiveness during storage. Microbial-based postharvest strategies align with growing consumer demand for organic and sustainable food preservation methods, providing a promising solution to food waste and postharvest quality loss. The continued development of microbial technologies, supported by ongoing research, will play a vital role in influencing future postharvest management, thereby fostering more resilient and sustainable food systems.