Fungi in Horticultural Crops: Promotion, Pathogenicity and Monitoring

Abstract

In this review, we aim to provide a comprehensive overview of the roles of fungi in horticultural crops. Their beneficial roles and pathogenic effects are investigated. In addition, the recent advancements in fungal detection and management strategies (especially the use of spectral analysis) are summarized. Beneficial fungi, including plant growth-promoting fungi (PGPF), ectomycorrhizal fungi (ECM), and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake, promote root and shoot development, improve photosynthetic efficiency, and support plant resilience against biotic and abiotic stresses. Additionally, beneficial fungi contribute to flowering, seed germination, and disease management through biofertilizers, microbial pesticides, and mycoinsecticides. Conversely, pathogenic fungi cause significant diseases affecting roots, stems, leaves, flowers, and fruits, leading to crop yield losses. Advanced spectral analysis techniques, such as Fourier Transform Infrared Spectroscopy (FTIR), Near-Infrared Spectroscopy (NIR), Raman, and Visible and Near-Infrared Spectroscopy (Vis-NIR), alongside traditional methods like Polymerase Chain Reaction (PCR) and Enzyme-Linked Immunosorbent Assay (ELISA), have shown promise in detecting and managing fungal pathogens. Emerging applications of fungi in sustainable agriculture, including biofertilizers and eco-friendly pest management, are discussed, underscoring their potential to enhance crop productivity and mitigate environmental impacts. This review provides a comprehensive understanding of the complex roles of fungi in horticulture and explores innovative detection and management strategies.

1. Introduction

Fungi play critical roles in many ecosystems [1]. They have significant functions in terrestrial ecosystem functioning, biogeochemical cycling, and plant community dynamics [2]. Beyond their fundamental ecological significance, fungi offer immense potential for addressing critical global challenges, particularly within the agricultural sector. Some fungi are capable of improving plant development through indirect and direct mechanisms. They enhance fertilizer availability and absorption while also improving soil quality. Furthermore, they can boost the resistance of plants to biotic and abiotic stress in many horticultural crops (e.g., vegetables, fruits, and herbs) [3].

Despite their beneficial roles, some are destructive pathogens. Globally, more than 19,000 fungal species have been identified as plant pathogens [4], and fungi account for about 70% of all pathogens causing plant diseases [5]. Unlike bacteria and viruses, fungi have a nucleus and multiple organelles. Many fungi reproduce via spores. The spores are dispersed by wind, soil, water, insects, and other invertebrates, enabling them to infect plant tissues and spread across entire crops [6]. Fungal diseases severely impact horticultural crops. For example, strawberries are commonly infected by Podosphaera aphanis, causing powdery mildew on leaves, fruits, and petioles [7]. Similarly, tomato crops suffer yield loss exceeding 20% due to gray mold caused by Botrytis cinerea [8]. While fungi can colonize and influence multiple plant organs, we focus here on their ecological roles, symbiotic relationships, or pathogenic effects on the most frequently encountered organs.

Early detection of fungal infections is crucial for agricultural productivity. Spectral technology has been extensively employed to identify plant diseases, as it is non-destructive, easy to set up, and highly repeatable [9,10]. This technology measures the fraction of radiation reflected by a subject relative to incoming radiation [11]. Reflectance is related to the absorption and propagation of each frequency; thereby it works as an indicator for plant status under ambient or experimental circumstances [12]. Spectral vegetation indices derived from spectroscopy have been extensively used to monitor plant health and identify diseases like anthracnose and gray mold [13,14]. Significant technological and analytical advancements have dramatically enhanced the capability of spectral methods for early, specific, and large-scale fungal disease detection [15,16]. These converging advancements have transformed spectral technology from a general health indicator into a powerful tool for the pre-symptomatic detection and specific identification of economically critical fungal pathogens.

2. Benefits of Fungi on Horticultural Crops

2.1. On Nutrient Organs

Plant rhizosphere microorganisms form complex microecosystems where both endophytic and ectomycorrhizal fungi usually coexist at the tips of mycorrhizal roots. Plant Growth Promoting Fungi (PGPF) constitute a significant portion of rhizosphere-resident fungi. They have attracted much attention because of their involvement in promoting plant growth [17]. These fungi are recognized as an essential source of beneficial biotic inducers for their host plants. PGPF produce defense-related proteins, defensive/volatile chemicals, and phytohormones that inhibit pathogens, therefore enabling plants to deal with diverse biological and abiotic challenges [18]. PGPF have demonstrated substantial benefits in many horticultural crops, including Danshen (Salvia miltiorrhiza Bunge), grapevine (Vitis vinifera L.), and lettuce (Lactuca sativa L.) [19,20,21]. The inoculation of plants with certain PGPF results in a remarkable increase in root biomass. Upon root colonization, PGPF form intricate networks with plant roots, enhancing water and nutrient uptake efficiency. Furthermore, the application of PGPF metabolites to plant roots also induces physiological changes that promote root proliferation. Penicillium, Trichoderma, and Phoma are the most important PGPF [22]. For example, in cucumber plants, soil treated with barley grain inoculum of Penicillium simplicissimum greatly boosted root development within three weeks [23]. The PGPF Phoma sp. and P. simplicissimum effectively induce systemic resistance in cucumber against Colletotrichum orbiculare, the causal agent of anthracnose [24]. PGPF also mediate positive effects of fungi on plant stems and leaves. Trichoderma asperellum can induce the production of multiple beneficial enzymes for lettuce roots, including peroxidase, polyphenol oxidase, and the cell wall-degrading enzymes β-1,3-glucanase and chitinase [25].

Ectomycorrhizal (ECM) fungi are another group of widespread symbiotic fungi within plant root systems [26]. ECM fungi are capable of producing extracellular antibiotics that protect roots against infections from pathogenic fungi. ECM fungi can also bind toxic substances, such as aluminum, in the hyphal sheath, thereby reducing harmful component uptake by the roots. Therefore, the root system of horticultural crops will grow robustly with the assistance of ECM fungi [27,28,29]. Fully mycoheterotrophic (FMH) orchids in temperate regions, having completely lost photosynthetic capability, depend exclusively on ECM fungal partnerships to obtain carbon and mineral nutrients—deriving photosynthates from nearby trees via underground mycorrhizal networks [30].

Arbuscular mycorrhizal fungi (AMF) belonging to the phylum Glomeromycota are asexual, obligately symbiotic organisms with distinctive architecture and chromosomal structures [31]. They inhabit dual environments, namely the soil and the host plant roots [32]. About 80% of plants in the terrestrial system have AMF, which live symbiotically as obligate biotrophs in the roots [33]. AMF symbiosis enhances the nutrient cycle by supplying plants with essential nutrients, thereby accelerating rooting, budding, and flowering [33]. AMF are able to boost the process of respiration in horticultural crops [34]. Moreover, the plant-AMF symbiosis has been proven to increase the capacity of plants to tolerate several abiotic challenges, e.g., drought and salt stress [35,36]. For example, mycorrhizal hyphae can take up water, which enhances the water and nutrient contents in crops such as lettuce [37]. This promotes improvements in net transpiration and water usage efficiency. These enzymes help the plants to defend against fungal pathogens, e.g., leaf spot fungus. Micropropagated coconut (Cocos nucifera L.) plantlets infected with AMF show a significant increase in the leaf area and stem diameter, enhancing their adaptability and survival rates [38]. Additionally, AMF enhance leaf photosynthetic pigments via an effective synergism between transpiration and photosynthesis under mycorrhization, such as chlorophyll in mulberry (Morus alba L.) and carotenoids in lettuce, improving their nutritional value and/or photosynthetic efficiency [39]. It was also observed that AMF can enhance the gas exchange capacity of mulberry leaves [40].

AMF also relieves bicarbonate (HCO₃⁻) stress. Irrigation water with high HCO₃⁻ levels can be harmful to plant development. Inoculation with AMF enhances plant resistance to HCO₃⁻, as evidenced by increased leaf area, chemical content, and photosynthetic efficiency of Rosa multiflora cv. Burr [41].

2.2. On Reproductive Organs

Fungi play a significant role in promoting flowering and seed germination in horticultural crops, which are essential biological processes for plant reproduction and productivity. The application of fungi appears to influence the genetic flexibility of blooming, an essential factor for plants [42]. The process of blooming begins when nutrients and phytohormones are present in the shoot apex at the appropriate concentration. Root inoculation with PGPF can affect hormone production and photosynthate availability to indirectly stimulate flowering time, quantity, and size in host plants [43]. For example, when Trichoderma spp. was applied to soil as a peat-bran formulation for floricultural crops, there was an increase in the number of flower buds in chrysanthemums and petunias. Under similar conditions, periwinkles, asters, and marigolds also bloomed earlier [44]. Additionally, addition of Trichoderma as a dry fermenter to the growth media increased the quantity and weight of blossoms in verbena and petunias [45]. Similarly, Trichoderma harzianum and Penicillium chrysogenum can induce early flowering for tomatoes [20]. The nematophagous fungus Pochonia chlamydosporia is able to accelerate blooming in tomatoes by root colonization as well [46].

Fungi have been shown to have a positive impact on fertilization and the early growth of seedlings. Cucumber seeds showed a 30% increase in seedling emergence after being amended with T. harzianum propagules [47]. Seed priming with T. harzianum, Phoma multirostrata, and P. chrysogenum resulted in improved seedling growth and strength in tomatoes [48]. Presoaking seeds in the microbial filtrates of Penicillium strains was particularly effective in enhancing the development of tomato seeds [49]. Additionally, similar improvement in seed germination and seedling vigor in different plants has been observed after application of other PGPF [50]. PGPF colonization during the seed stage has been proven to promote fast establishment of seedlings and enhance plant longevity [51]. Clonostachys rosea isolates, for instance, inhibited pre- and post-emergence mortality induced by Alternaria dauci and A. radicina, resulting in more viable seedlings in carrots [52]. Similarly, C. rosea isolates also enhanced the rate of seedling development in carrots and onions [53]. These findings address the capacity of PGPF to promote seed germination by mitigating the harmful impacts of seed-borne infections [54].

Some fungi may also be functional in overcoming seed dormancy. The synthesis of chemicals, including gibberellins and cytokinin, by fungi may induce seed germination by enhancing the embryo’s development potential and triggering hydrolytic enzymes [55]. In the wild, seeds from certain plants, like orchids, rely on nutrients provided by specific fungi for germination due to their lack of endosperm. Rhizoctonia is a common fungal genus that accelerates orchid seed germination and seedling development [56]. Additionally, other fungi such as Penicillium, Chaetomium, and Choanephora have been reported to enhance seed hatching and germination in orchids [51].

Many fungi can emit volatile organic compounds (VOCs), which have a profound impact on plant physiology [57]. For instance, 6-pentyl-2H-pyran-2-one (6-PP), a major VOC biosynthesized by Trichoderma spp., promotes plant growth [58]. It affects the root structure by limiting main root development and promoting peripheral root production. Plants cultivated in the presence of VOCs produced by several fungi have demonstrated increased vigor and early blooming characteristics.

Many fungi, including T. viride, P. chrysogenum, Saccharomyces cerevisiae, and P. aurantiogriseum, emit VOCs. VOCs are regarded as potential and ecologically friendly fumigant agents for influencing fruit postharvest diseases. The antagonist yeast S. cerevisiae produces VOCs that can suppress the growth of plant diseases, such as the filamentous fungus (Phyllosticta citricarpa, inducing black spot in citrus). Fumigating citrus fruits with S. cerevisiae VOCs is one potential eco-friendly method to reduce citrus black spot disease during transportation [59].

3. Hazardous Fungi on Horticultural Crops

3.1. On Nutrient Organs

Many phytopathogenic fungi invade plant tissues via specialized hyphae. The pathways include adhesion to the plant cuticle, germ tube growth, appressorium formation with high turgor pressure, and secretion of cell wall-degrading enzymes to penetrate the cuticle and cell wall [60]. Many fungi, such as Podosphaera, Penicillium, Alicorhagia, Rhizoctonia, Fusarium, and Mucor, can induce root diseases. Among these, Fusarium are predominant pathogens [61].

Fusarium, especially F. oxysporum, has caused two widespread diseases in the roots of horticultural crops, i.e., wilt disease and root rot. Pathogenic and non-pathogenic strains of F. oxysporum are difficult to distinguish based on morphology alone [62,63]. Plant roots emit peroxidases, which F. oxysporum detects chemotropically. It primarily enters roots through gaps in the epidermal cell layer [64,65]. The hyphae move intercellularly toward the vascular parenchyma cells, then infiltrate the xylem vessels, and eventually colonize the cortical cells [66]. This can cause progressive wilting or even death of horticultural plants [62,67,68]. The pathogenic strains cause vascular wilt disease in many horticultural crops, including bananas, melons, cruciferous and solanaceous vegetables [69,70]. It has also been widely documented that F. oxysporum is a fungal pathogen that causes root rot. This root and crown rot disease has been reported on horticultural crops including pea (Pisum sativum), sugar beet (Beta vulgaris), and sweet potato (Ipomoea batatas) [71,72,73]. Typically, an infected plant will show signs of retarded growth and browning rot inside the crown and root. On the other hand, peach root rot, attributed to Armillaria tabescens (Desarmillaria tabescens), initiates as brown spots on fibrous roots, progressing to lateral/main root decay and vascular necrosis, ultimately triggering shoot dieback and tree mortality [74]. Phytophytora spp. cause citrus root rot and gummosis, leading to root decay and gum oozing from the trunk base near the soil line [75].

Many fungal pathogens can cause rot or wilt in plant stems. It has been demonstrated that F. oxysporum is responsible for stem rot on a variety of plants, such as Cymbidium ensifolium (L.) Sw. (Orchidaceae) [76,77]. The stem rot disease triggered by F. oxysporum was initially reported in cucumbers and results in substantial yield reductions for greenhouse-grown plants [78]. Delphinium plants (Delphinium elatum L.) show signs of stem canker and serious wilt [79]. Based on morphological traits, nucleotide sequences, and host range, the fungus isolated from the infected crown was identified as F. oxysporum f. sp. Delphinii. The fungus generated similar stem canker and wilt symptoms in delphinium plants that were inoculated. Sclerotinia stem and leaf rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) [80] is a destructive soilborne disease affecting many vegetables worldwide, such as Brassicaceae species [81]. In Indian mustard (Brassica juncea L.), stem blight was observed with lesions spreading from the stems to the petioles and midribs of leaves. Symptoms of the disease included the formation of small (2–7 mm), circular to irregular, dark gray to black lesions with a slight bluish cast. The isolated pathogen was confirmed as Nigrospora oryzae [82]. In addition, the fungus also causes leaf spot disease on a large scale in blueberries [83]. Gummy stem blight, caused by the fungus Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), is a devastating disease of cucurbits such as cucumber, pumpkin, and melon [84]. In seedlings, initial angular, water-soaked lesions develop on cotyledons and leaves, advancing into petioles. Critically, this progresses to stem necrosis and wilting. In mature plants, symptoms include crown blight, basal leaf desiccation, and severe defoliation. Stem manifestations are particularly evident as dark, necrotic cankers. Additionally, fruit rot may occur [85]. Botryosphaeria dothidea and B. obtuse cause peach gummosis, which primarily affects trunks and main branches. Initial pale-yellow gum exudates darken to reddish-brown upon air exposure, eventually hardening into amber resin. This infection often leads to wood decay, leaf yellowing, and shoot dieback [86].

Leaf spots on many horticultural crops are usually caused by fungi. Fungal pathogens are transmitted to plant leaves by external vectors or internally from roots. The symptoms of leaf spot appeared predominantly on the leaf margin and main veins [87]. Leaf spot is recognized as one of the most devastating diseases in pineapples, caused by several pathogens, including Colletotrichum ananas, Chalara paradoxa, and Curvularia clavata [87,88,89]. These appeared as irregular grayish-brown lesions with yellow, chlorotic, or necrotic areas that were water-soaked. Over recent years, apple leaf blotch has been observed as well, in which fungal species from the genus Alternaria were isolated from symptomatic leaf tissues. Biological analyses confirmed that these isolates belong to the A. arborescens complex [90]. The fungal genus Alternaria is also a significant pathogen causing leaf spot diseases in roses, strawberries, and cruciferous vegetables (e.g., cabbage, broccoli) [91,92,93]. Key species include A. alternata (affecting roses and strawberries) and A. brassicicola/brassicae (targeting crucifers). Symptoms typically manifest as dark brown to black, circular or irregular lesions on leaves, often surrounded by yellow halos. Crucifers frequently exhibit distinctive concentric rings within the spots. Severe infections cause lesions to coalesce, leading to leaf yellowing, withering, and premature defoliation. Strawberries may also show purple-edged spots on leaves and black, sunken lesions on fruit, while crucifers can develop infections on flower heads (e.g., cauliflower curds) and seed pods. The most devastating foliar pathogen in sugar beet worldwide is Cercospora leaf spot, which is caused by Cercospora beticola [94]. The edges and main veins of sugar beet leaves are the most infected areas. Additionally, it has been demonstrated that leaf spots in peppers are induced by C. oxysporum. This results in irregular brown spots ranging from 1 to 4 mm in diameter [95].

Rust disease of pears and apples, caused by Gymnosporangium spp., primarily infects leaves, forming yellow to bright orange spots on the upper surface where the internal pycnial stage develops, while the lower surface produces distinctive aecia appearing as fibrous, milky-white clusters [96,97]. Downy mildew is the most serious fungal disease of grapes. It is caused by Plasmopara viticola. At the initial stage of the infection, pale yellow oil spots appear on the front of the leaves. When the environment is wet, dense white patches appear on the back of the leaves. In severe cases, the leaves become necrotic and fall early [98].

Leaf blight in many horticultural crops is also commonly caused by fungi. Leaves severely affected by blight turn brown, curl, wither, and may even die. Camellia oleifera, a widely cultivated woody shrub in China, frequently suffers from leaf blight [99]. Morphological characteristics of the isolates (collected from the symptomatic leaves) matched the description of Nigrospora chinensis [100]. Several pathogenic fungi cause leaf blight diseases in oil palm as well [101,102]. For instance, Curvularia leaf blight (caused by Curvularia eragrostidis) has been identified as a prevalent disease affecting oil palms [103]. This condition initially shows up as dark spots encircled by a yellow to rust-brown area. Over time, the lesions on the leaves expand from 5 to 10 mm in diameter, shifting from a circular to an elliptical form. As the lesions enlarge and coalesce, the affected leaves become blighted [104]. Peach leaf curl, induced by Taphrina deformans [105], distorts young leaves into reddish, hypertrophied, brittle structures with grayish-white fungal coating, severely reducing photosynthesis and causing flower/fruit drop or mummified cracked fruits.

Powdery mildew, caused by various host-specific obligate fungal pathogens, consistently manifests as a conspicuous white to grayish-white, powdery or felt-like fungal coating on the surfaces of leaves, stems, and fruits. This dense layer of mycelium and spores severely inhibits photosynthesis, leading to chlorosis, yellowing, curling, distortion, and premature senescence of foliage, often culminating in premature leaf drop. Infected fruits develop surface blemishes, distortion, cracking, premature drop, or mummification. While these core symptoms are similar, the disease is caused by distinct pathogens depending on the host: Erysiphe neolycopersici on tomato [106], Leveillula taurica on pepper [107], Podosphaera xanthii on cucurbits [108], Erysiphe necator on grape [109], Podosphaera leucotricha on apple and pear [110,111], and P. aphanis on strawberry [112].

3.2. On Reproductive Organs

Fungal infections are also observed on the flowers of horticultural crops, manifesting as wilting or rotting. In Geraldton waxflower, postharvest flower and bud abscission is a severe issue linked to B. cinerea infection [113]. A. altemata can also cause flower abscission [114]. In Brazil, characteristic and extremely severe signs of Phomopsis rot have been observed in the blooms and unripe fruits of Passiflora edulis [115]. The pathogen was identified as Diaporthe infecunda and was re-isolated from those lesions. D. infecunda can produce specific enzymes or toxins to degrade the tissue surface. Grapevine downy mildew of grapes, caused by Plasmopara viticola, will reduce the frost resistance of buds. Inflorescences and young berries are also susceptible to infection, showing dry brown rot, which eventually leads to falling [98]. The inflorescence and berries are most susceptible to influence when young. They will be covered by white mold. The infected inflorescence is curled and necrotic. The growth of the skin tissue of infected berries is hindered, causing young fruits to swell and split [109].

Stem-end rot (SER) is regarded as the second most serious disease globally, following anthracnose, which is caused by Colletotrichum gloeosporioides. Fruit is vulnerable to a variety of postharvest diseases as it ripens, particularly susceptible to SER [116]. SER is the common post-harvest pathogen in arid regions. At the inflorescence and flowering stages, SER-causing pathogens predominantly enter the stem through wounds and natural openings [117]. These fungi are endophytes, primarily observed in the xylem as well as in the phloem. They remain asymptomatically in the stem tissue until the fruit ripens [118,119]. The primary source of SER is found in tropical and subtropical fruits, such as avocado, carambola, citrus, mangosteen, and mangos [120]. After harvest, there are notable fruit losses as the fruit ripens and SER develops. It is estimated that 30–40% of harvested mango fruits may be lost due to SER. SER symptoms manifest as small, dark brown to black spots at the stem end during the early stages of fruit ripening. As ripening proceeds, SER leads to fruit softening, discoloration, and dark flesh [118]. Botrytis phaeriaceae, a family of pathogenic fungi, can infiltrate mango fruit stems during blooming and colonize them endophytically without exhibiting any outward signs. When fruit ripens or when there is an abiotic stress, those fungi become extremely active. It subsequently results in fruit SER that causes stem and inflorescence dieback [121].

The fruits of horticultural crops can also be affected by fungal infections that alter their appearance. Many spores of pathogenic fungi initiate entry into host tissues via invading existing wounds, thrusting penetration hyphae between epidermal cell interfaces via an appressorium, or directly penetrating the epidermis using cell wall-degrading enzymes (CWDEs). The successful colonization results in the formation of necrotic lesions [122]. For instance, shipping satsuma mandarin fruits develops a huge number of tiny black spots with a branching structure of black hyphae, which significantly reduces their economic value. Cladosporium cladosporioides was commonly isolated from the infected fruits [123]. Green mold is an influential postharvest disease in citrus, caused by Penicillium expansum. Pathogens are prone to infect wounds, and in the early stages, water-stained lesions appear, with a soft and damp surrounding area. White mycelium is produced in the center of the wound and spreads outward. Subsequently, green or dark green powdery mold appeared and rapidly spread, eventually causing the entire fruit to rot [124]. P. aphanis frequently causes powdery mildew in strawberries. After infection, a thin layer of white mycelium initially appears on the abaxial surface of the leaves [112]. At the late stage of infection, the fruit surface is covered with white powder [125], which has been observed in grapes and cucumbers as well [126,127]. B. cinerea can cause various fruit diseases [128]. In grapes, it can lead to gray mold. In the early stages of infection, the color of the berries darkens. Light gray mycelium appears on the surface of the berry. The berries eventually turn brown and rot [129]. In Pisum sativum var. saccharatum, fruits changed to gray-white and progressively became soft-rotted [130]. The pathogen also induces gray mold in strawberries and tomatoes [131,132].

Anthracnose, caused by Colletotrichum spp., severely impacts numerous horticultural crops, including solanaceous vegetables, legumes, and various fruits [133,134]. It is particularly devastating to strawberries, where the fungus causes fruit necrosis and spreads rapidly to healthy plants [135]. In citrus, Colletotrichum infection manifests as brown to black spots on fruit, characterized by small, irregular, sunken lesions [136]. Peach anthracnose manifests as dark brown discoloration, shrinkage, and hardening on young fruits, while young shoots develop dark green, water-soaked lesions that evolve into brown spots with reddish-brown halos, culminating in shoot dieback [137]. Geotrichum candidum is an economically significant pathogen, causing sour rot in numerous fruit and vegetable crops [138]. Similarly, bitter rot, caused by Colletotrichum spp., also affects pears and apples. In the early stage of fruit infection, small gray–brown spots appear. Small black spots arrange in a circular pattern after enlargement, with pink mucus overflowing when wet [111,139]. Botryosphaeria dothidea causes ring rot in apples and pears. There are slight concave lesions and brown rings on the fruit, which ultimately lead to decay, seriously affecting the yield and quality of fruits [140,141]. Brown rot (Monilinia fructicola and M. laxa) affects fruits of peach, producing concentric brown lesions with mold rings on mature fruits that either abscise prematurely or mummify, while immature fruits develop arrested necrotic spots [142].

Fungi are the main pathogenic microorganisms influencing the quality of seeds [143]. Infections associated with seeds can cause seed degradation. The infections decrease germination and vitality of seeds. Finally, seed and plant mortality would occur, which ultimately reduces yields of horticultural crops (see Figure 1).

4. Techniques and Applications of Spectral Analysis for Detecting Fungi in Horticultural Crops

4.1. Techniques of Spectral Analysis for Detecting Fungi in Horticultural Crops

Many conventional techniques for the detection and identification of fungal pathogens have been applied to agricultural products. Methods like visual inspection and microscopy are effective for identifying visible symptoms. More advanced molecular and biochemical methods like Polymerase Chain Reaction (PCR), Enzyme-Linked Immunosorbent Assay (ELISA), and chromatographic techniques offer high sensitivity and specificity, albeit at higher cost and complexity [144,145]. Emerging technologies like spectral analysis (e.g., Infrared and Raman spectroscopy) offer rapid and non-destructive methods for fungal pathogen detection and characterization [146,147]. Spectral analysis, a powerful and nondestructive sensor technology, is a valuable tool for analyzing entire crops, active pathogens, and interactions between plants and pathogens [138]. When combined with multivariate analysis through data preprocessing, constructing efficient fungal detection models, feature extraction, and practical applications, it can be used to detect and characterize the presence of fungi in a variety of environments. Spectral techniques also work for large-scale screening, which significantly expands their application in agriculture [148].

Infrared Spectroscopy (IR) has been recognized as a highly effective spectral technique for the detection of fungi [149,150]. Fourier Transform Infrared Spectroscopy (FTIR) is the common analytical technique for IR. It is often employed to identify fungal metabolites and mycotoxins, providing a non-destructive means of assessing contamination. The identification of typical constituents in horticultural crops, including flavonoids, glucose, sucrose, and starch, has been successfully performed by IR [151,152]. Moreover, IR has been effectively applied to track plant diseases [153]. For instance, the deterioration of strawberries can be detected at 3040–2830 cm⁻¹ [154]. Specifically, the infrared method is highly sensitive to leaf diseases. A smart detection and spraying system was designed and developed to recognize rose powdery mildew and gray mold diseases using a combination of thermal and visible images [155]. Many injuries and infections produce unique spectral signatures that reflect common stress responses in fruits. These spectral characteristics hence allow both direct and indirect non-destructive autonomous detection. Currently, they have been successfully applied to the identification of various fungal diseases in horticultural crops, such as grapes, tomatoes, potatoes, and figs [156,157] (see

Table 1. Examples of various spectral detection methods and their applications in identifying fungal pathogens in horticultural crops.

Detection Method	Crops Affected	Pathogen Fungus	References
ATR-IR	strawberry	Podosphaera aphanis	[158]
ATR-Mid-IR	tomato	Geotrichum candidum	[138]
IR	rose	Podosphaera pannosa, Botrytis cinerea	[155]
FTIR	tomato	Geotrichum candidum	[138]
	potato	Fusarium spp., Rhizoctonia solani	[159]
	grape	Aspergillus spp., Botrytis cinerea, Penicillium expansum	[157]
	fig	Aspergillus flavus	[156]
NIR	apple	Venturia inaequalis	[160]
	date fruit (Phoenix dactylifera)	Aspergillus flavus	[161]
	tomato	Penicillium, Aspergillus, Mucor	[162]
	grapes	Botrytis cinerea	[163]
	plum	Monilinia fructigena	[164]
Vis-NIR	lettuce	Aspergillus niger, Fusarium oxysporum, Alternaria alternata	[165]
	mango	Colletotrichum gloeosporioides	[166]
UV-Vis	fig	Aspergillus flavus	[167]
Raman	apple	Rhizopus stolonifer, Botrytis cinerea	[168]
	banana	Fusarium oxysporum f. sp. cubense	[169,170]
Fluorescence	citrus	Penicillium digitatum	[171]

Attenuated Total Reflection Infrared Spectroscopy (ATR-IR); Attenuated Total Reflection Mid-Infrared Spectroscopy (ATR-Mid-IR); Near-Infrared Spectroscopy (NIR); Visible and near-infrared Spectroscopy (Vis-NIR); Ultraviolet-Visible Spectroscopy (UV-Vis).

).

The spectral technique is based on the absorption of infrared light, which has an energy equivalent to molecular vibrations. The chemical and structural organization of a sample will be reflected in the IR absorption spectrum [172,173]. Basal stem rot (BSR) is a disease caused by Ganoderma boninense [174]. A 92% overall classification accuracy in the prediction of mild, moderate, and severe phases of BSR illness made it possible using principal component analysis based on IR spectra. Further, ATR-IR has also been successfully employed to identify various stages of powdery mildew infection in strawberry leaves [158]. Using ATR mid-IR, the sour rot infection in tomato fruits caused by G. candidum can be detected non-invasively and with high accuracy [138]. Mid-IR has demonstrated the ability to identify structural alterations in the cuticle that can be attributed to pectin, lignin, other polysaccharides, or cutin. These spectral changes may indicate the presence of the sour rot disease during both the early and late stages of fruit development.

NIR is used for rapid screening of fungal presence and biomass. It measures the absorbance of near-infrared light, which can be correlated with the concentration of fungal biomass in substrates. By scanning the NIR spectrum of the sample, information about the hydrogen-containing groups of the organic molecules in the sample can be obtained. The interaction of these substances with light produces specific spectral peaks and bands that can be used to determine chemical composition and material structure [168]. Differences in the chemical composition between healthy and fungus-infected materials result in spectral differences [161]. For instance, hyperspectral imaging in the NIR region has been applied to the rapid screening of fungal infections, especially in fruits. The technique has been proven to help postharvest handlers minimize anthracnose disease damage to mango [175]. It enabled early detection of Aspergillus flavus on date fruits and differentiated healthy and infected apple leaves, with scab positions clearly observable in images [160,161]. Additionally, a combination of NIR hyperspectral imaging (1000–1700 nm), data preprocessing pipeline, and machine learning-based modeling predicted the susceptibility of freshly harvested tomato sepals to future infections by fungi such as Penicillium, Aspergillus, and Mucor [162]. Spectral detection demonstrated an excellent aptitude in detecting different vibrational behaviors of the grape berry molecules affected by B. cinerea. The easy and non-invasive identification of specific temporal stages of infection could represent a proficient tool for monitoring B. cinerea development in grape berries intended for high-quality wine production [163]. Furthermore, combining NIR and electronic tongue (E-tongue) technology allowed the detection of Monilinia fructigena in plum before visible symptoms, achieving high accuracy in quantifying fungal levels [164].

The visible and near-infrared spectroscopy (Vis–NIR) and vegetation index approaches have been applied test aquaponically cultivated lettuce infected with various fungal pathogens (Aspergillus niger, F. oxysporum, and Alternaria alternata). In the near-infrared spectral range, infected leaves exhibit lower reflectance values compared to controls, indicating structural changes in cells caused by fungal infection, enabling effective detection [165]. Anthracnose, a major disease in mango crops affecting 60% of production, can be detected by Vis–NIR hyperspectral imaging [166]. Early detection of myrtle rust on rose apple trees was achieved by using indices derived from thermal imagery and visible-to-short-infrared spectroscopy [176]. Vis-NIR could also be used to identify banana fruits infected with Colletotrichum musae [177].

UV-Vis spectroscopy measures the absorption of ultraviolet and visible light by fungal compounds. This technique is useful for detecting specific pigments or metabolites produced by fungi. For example, aflatoxin contaminated figs may show a bright greenish-yellow fluorescence (BGYF) under ultraviolet (UV) light at a wavelength of 365 nm [167].

Raman spectroscopy reveals detailed information on the structure as well as molecular vibrations of the examined object. Since each molecule has its unique set of vibrational energy levels, the Raman spectrum can reveal essential details about the dynamics, environment, and structure of molecules. Plant diseases have been effectively detected non-destructively using Raman spectroscopy [178]. Different from infrared spectra, Raman spectra are produced by gathering inelastically scattered photons from samples of interest. One of the advantages of Raman spectroscopy in biological applications is its ability to extract highly informative spectra from undamaged tissues [179,180]. Thus, biological materials can be thoroughly analyzed chemically even though they are highly complicated [181]. With these benefits, Raman spectroscopy is among the most promising tools/techniques in agriculture for identifying and detecting fungal infections. However, fluorescence may cause a low signal/noise ratio [182]. Raman spectroscopy, as an objective, real, and efficient fungal pathogen detection tool, has been proven to be used to detect horticultural crop fungal diseases, such as apple mold heart disease and fusarium wilt in bananas [168,169,170]. Combined with modeling technology, they provided a non-destructive, rapid, and accurate identification of apple fruit damage [183].

Over the last two decades, surface-enhanced Raman scattering (SERS) has been developed as a fast and sensitive analytical technique with the ability to identify various substances. SERS improves substrate performance because the electromagnetic field is near the roughened surface of metal nanostructures [184]. This offers a viable method for label-free, quick, sensitive, and nondestructive identification of microorganisms in samples. The use of colloidal Au nanoparticles (AuNPs) as an improved substrate for amplifying fungal Raman signals may be attributed to its great sensitivity, exceptional biocompatibility, and user-friendliness. Using SERS, the molecular fingerprints of A. niger, S. cerevisiae, F. moniliforme, and T. viride in crops have been successfully identified. To further distinguish between the various kinds of fungi, multivariate statistical analysis was also used. The characteristics of the various fungal species will help in the early assessment of grain crops so that their spread may be controlled. Apart from its diagnostic uses, this technique may also be beneficial for enhancing understanding of the many categories of fungal infection and figuring out how to store crops [185].

Fluorescence spectroscopy detects the natural fluorescence of fungal cells or the fluorescence induced by specific dyes. It can be useful for identifying live fungi in various substrates. As an illustration, the fluorescence level of 104 varieties of oranges and tangerines was studied and determined by using hyperspectral and color imaging. Citrus rot lesions caused by Penicillium digitatum emit fluorescence when illuminated with UV light [170].

The spectrum of X-rays ranges from 0.01 to 10 nm, falling between ultraviolet and gamma rays. Most horticultural products are penetrable by X-ray, and the amount of X-ray energy that passes through them is determined by the density of targets, incident energy, and absorption coefficient. Thus, X-ray imaging can be used to assess the quality, maturity, and internal defects of horticultural plants. For example, X-ray irradiation with convergent chemicals like sodium dichloroisocyanurate (NaDCC) or nano-silver particles has been used to treat leaf blight on cut lilies [186].

The key topics covered by NMR methods include ripeness, maturity, internal defects, and damage, as well as physiological illnesses caused by pre- and postharvest circumstances that manifest during storage. MRI has been used to examine fungal infections in various fruits, including nectarines, strawberries, grapes, tangerines, oranges, and coconuts [187].

4.2. Application of Fungi in Horticultural Crops

To promote growth of crops, biotechnology products known as “biofertilizers” involve the application of microorganisms to soil, seeds, or plant surfaces [188,189]. The efficacy of biofertilizers depends on microbial functions, such as nitrogen fixation and phosphorus solubilization. By lowering usage of chemical fertilizers, their applications improve soil health and help mitigate climate change impact. To improve the availability of nutrients in the soil, biofertilizers incorporate beneficial microbial inoculants. Combining biofertilizers and chemical fertilizers optimizes plant development and increases the availability of macronutrients, thus boosting fertilizer efficiency [190]. Furthermore, microbial consortia in fertilizers can influence the carbon cycle, causing the development of more efficient and eco-friendly fertilizers [191]. For instance, incorporating AMF into biofertilizers can reduce the need for external phosphorus fertilizers [192]. Over the past few decades, employing soil microorganisms as biofertilizers has led to enhanced crop yields, improved disease control, higher quality, and promoted plant growth [193,194]. Biological fertilizer has high microbial activity due to the existence of fungi that can produce plant growth regulators [195]. For example, it improved the yield and fruit physicochemical quality of papaya [196].

Microbial pesticides have emerged as a cornerstone of sustainable agriculture, recently garnering significant attention due to their target specificity, environmental safety, efficacy, biodegradability, and usage in integrated pest management programs over conventional chemical counterparts. These pesticides are primarily made from naturally occurring microorganisms, including bacteria, fungi, and viruses [197]. It has been documented that Trichoderma sp. inhibits the activity of many soil-borne fungal diseases [198]. The occurrences of root rot, green and black gram in chickpeas, and groundnuts may all be reduced. Some fungi have been applied to plant pest management as well, such as mycoinsecticide, a microbial insecticide containing living fungi. Certain strains of this fungus have an antagonistic impact on insects and other arthropod pests, leading to the release of metabolites that can either kill or damage them [199]. Mycoinsecticides work in six broad phases, i.e., attachment, germination, penetration, invasion, reproduction, and host death. It has been observed that horticultural crops infested with thrips, beetles, weevils, aphids, whiteflies, and mites can be controlled by Beauveria bassiana and Metarhizium brunneum [200]. Their utility spans both greenhouse and open-field environments, offering a viable control option particularly in situations where chemical pesticides are restricted or where pest resistance has become problematic.

The fact that limited fungal strains have been developed into marketable mycoinsecticides suggests that the field is still in its early stages of development.

5. Perspectives for Future Research and Applications

Fungi hold immense potential for revolutionizing horticultural practices, yet further exploration is needed to maximize their benefits.

The integration of multiple fungal species into bioformulations represents an innovative solution to address multifaceted agricultural challenges. In the future, it is necessary to further reveal the molecular mechanisms of fungal pathogenicity, providing a theoretical basis for the development of new antifungal drugs and disease-resistant varieties. Optimizing these combinations for stability, efficacy, and scalability, particularly under varying field conditions, should be encouraged. These formulations could significantly reduce chemical inputs while enhancing crop yields and soil health.

The symbiotic relationship between mycorrhizal fungi and horticultural crops has a significant impact on plant growth and nutrient absorption. Endophytic fungi can enhance plant stress resistance and promote plant growth. By utilizing the decomposition effect of fungi, new types of fungal fertilizers can be developed to convert organic waste into nutrients that can be utilized by plants. Further study would be encouraged to investigate the diversity, ecological functions, and interaction mechanisms with host plants of mycorrhizal fungi in order to provide a scientific basis for optimizing the application of mycorrhizal fungi. Secondly, explore the potential application of endophytic fungi in horticultural crops to improve plant disease resistance, drought tolerance, and salt tolerance. Meanwhile, the stability of fertilizer efficiency and their environmental friendliness require attention.

On the commercial side, scaling up the production of fungal biofertilizers and biopesticides, while addressing regulatory hurdles, is essential for broader application. Collaborative efforts between academics, industry, and policymakers will be critical to transforming fungi into a cornerstone of sustainable horticulture.

Technological advancements in non-destructive fungal pathogen detection, such as infrared and Raman spectroscopy, present promising avenues for early and precise disease diagnosis. Refining these technologies for affordability and integration with artificial intelligence could lead to user-friendly systems for real-time monitoring. In the future, it is necessary to pay attention to their sensitivity and specificity and enhance the accuracy and efficiency of detection. Big data and artificial intelligence can integrate with detection technologies. Ultimately, they help us to achieve real-time monitoring, warning, and prevention of fungal diseases in horticultural crops.