Along with diverse bioactive metabolites produced by symbiotic fungi, this creates the possibility of controlling a wide range of pests (Wang et al., 2023), including plant-parasitic nematodes and herbivorous insects (Akram et al., 2023). When mycorrhizal and endophytic fungi are used as biocontrol agents, they yield inconsistent results, including both negative and positive outcomes among studies. This could be due to the condition of the tested environment and differences in the techniques and methodologies followed; however, it is crystal clear that fungi can control phytopathogens and improve plant health (Table 1). On the other hand, most of the works conducted by researchers are limited to the control environment/laboratory scale, and the need for field evaluation needs to be highlighted (Suebrasri et al., 2020; Azuddin et al., 2021; Mota et al., 2021). In a study, Yanan et al. (2015) recognized the enhanced resistance of strawberry plants when inoculated with Glomus mosseae against Fusarium wilt caused by Funneliformis mosseae. The authors found that an increase in cell wall lignin and HRGP (hydroxyproline-rich glycoprotein) proteins, along with changes in the activities of catalase, peroxidase, and superoxide dismutase enzymes, leads to such resistance. Wang et al. (2022a) emphasized the importance of Rhizophagus irregularis against F. oxysporum, as they trigger the plant defense mechanism, induce expression of the JA synthesis genes, such as allene oxide cyclase gene (AOC) and lipoxygenase D gene (LOXD), and increase activities of polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL). Khruengsai et al. (2021) showed that Daldinia eschscholtzii MFLUCC 19–0493 isolated from Barleria prionitis inhibits the anthracnose disease fungi Colletotrichum acutatum, through the production of various other volatile compounds—3,5-dimethyl-4-heptanone, benzaldehyde dimethyl acetal, elemicin, ethyl sorbate, methyl geranate, and trans-sabinene hydrate. In contrast to previous works, Odunayo Joseph and Victor Olumide (2022) aimed to identify the additional benefits provided by the fungi beyond pest resistance. Odunayo Joseph and Victor Olumide (2022) showed the importance of Glomus clarum in controlling the tomato early blight disease caused by Alternaria solani. Their results showed that once inoculated with G. clarum, the plants exhibited enhanced resistance to the pathogenic fungus. Moreover, with the enhanced nutrient supply, the crop showed increased production of flowers, fruit weight per plant, leaf condition, and stem growth.

In their in vitro assay, Suebrasri et al. (2020) showed that several endophytes, Diaporthe phaseolorum BUP3/1 and Macrophomina phaseolina BUP2/3, isolated from Jerusalem artichoke (Helianthus tuberosus) and D. eschscholtzii 2NTYL11 and Trichoderma erinaceum ST-KKU2, isolated from Stemona root (Stemona tuberosa) and ginger (Zingiber officinale), control the stem rot fungi (mycelial growth) Sclerotium rolfsii impressively at 76.00, 41.20, 66.67, and 63.63%, respectively. Furthermore, the pot experiment showed that T. erinaceum ST-KKU2 and D. eschscholtzii 2NTYL11 control the disease at a higher level (58.14%) than the others. Furthermore, they have observed predatory mechanisms, and the production of polyketide groups (6-n-pentyl-2H-pyran-2-one/6PAP and 2,3-dihydro-5-hydroxy-2-methyl-4H-1-benzopyran-4-one/DHMB) is a primary factor in controlling the pathogens. Many other studies have also shown the effects of various endophytic fungi in significantly controlling major devastating phytopathogens in crops, e.g., Induratia coffeana inhibits Colletotrichum lindemuthianum at 99.64 ± 0.57 (Mota et al., 2021); T. harzianum inhibits Colletotrichum scovellei at 85.80 ± 5.47 (Azuddin et al., 2021); and Annulohypoxylon sp. inhibits Penicillium digitatum at 72.96 ± 0.58 (Du et al., 2022). The symbiotic fungi also produce various antibacterial compounds, such as acetic acid, acetol, and hexanoic acid, among others (Rashid, 2021). Similarly, a number of compounds produced by symbiotic fungi also control the plant parasitic nematodes, for example, 3-methoxyepicoccone, 4,5,6-trihydroxy-7-methylphthalide, chaetoglobosin A, chaetoglobosin B, and flavoring isolated from Chaetomium globosum YSC5 found to be working against Meloidogyne javanica (Khan et al., 2019). The application of endophytic fungi also exhibits good nematocidal effects due to these compounds. In a study by Yao et al. (2023), it was found that Acremonium sclerotigenum effectively controls M. incognita, with a mortality rate of up to 95.5% in the juvenile (J2 stage) and significant inhibition of egg hatching of up to 43%. Schouteden et al. (2015) emphasized the importance of AMF in controlling nematodes. Adding value to this, Bell et al. (2023) highlighted the effectiveness of various AMFs in controlling potato cyst nematode Globodera pallida. In turn, the importance of symbiotic fungi against plant viruses is still less of a concern. However, available studies have shown their significance (Fakhro et al., 2010; Jaber and Salem, 2014; Kiarie et al., 2020).

It is also important to note that the majority of studies have focused on the application of endophytic fungi to control insect pests, rather than mycorrhizal fungi, despite showing their undeniable importance (Vannette and Hunter, 2009; Jiang et al., 2021). Control of insect pests using fungi has a long history, dating back to the 1980s. Beauveria bassiana is the earliest identified and most recognized entomopathogenic endophyte in controlling a wide range of pests (Islam et al., 2023). Today, in addition to B. bassiana, several other entomopathogenic fungi, including Metarhizium, Isaria, and Lecanicillium, have been used to control insect pests. However, such utilization is still in its early stages of development and requires considerable further study, particularly in identifying new infectious fungal species and strains (Bamisile et al., 2023). Suebrasri et al. (2020) examined the effect of B. bassiana and Purpureocillium lilacinum against the cotton aphid, Aphis gossypii. They have recognized that fungi have an impact on the host’s reproduction. They have found the significant control of aphids by B. bassiana, while P. lilacinum shows considerable but not significant control. Agbessenou et al. (2020) studied the controlling ability of Lepidopteran Tuta absoluta using tomato (Solanum lycopersicum) and nightshade (Solanum scabrum) Trichoderma asperellum M2RT4, B. bassiana ICIPE 706, and Hypocrea lixii F3ST1. They have found the effectiveness of those fungi in reducing the number of eggs laid, mines developed, pupae formed, and adults emerged. In contrast to the above two studies, Pappas et al. (2018) recognized the indirect control of pests by endophytic fungi in their study on Fusarium solani strain K against two-spotted spider mites (Tetranychus urticae) in tomato. They have studied the expression of genes GGPS1, JIP-21, LOXD, PPO-D, PPO-F, PR-1A, PR-P6, and WIPI-II in the pest after fungi colonization, which is important for host defense mechanisms against pests. However, according to their findings, the fungi significantly upregulated the expression of WIPI-II and PPO-D. At the same time, no effects were observed on other mite-defense-related genes, such as GGPS1, JIP-21, LOXD, PPO-F, PR-1A, and PR-P6. The indirect effect was also recognized through the alteration of the plant’s volatile compound emissions, such as decanal, 5-heptene-2-one-6-methyl, and geranyl acetone.

Heavy metal pollutants such as arsenic (As), cadmium (Cd), cobalt (Co), copper (Cu), lead (Pb), magnesium (Mg), manganous (Mn), nickel (Ni), strontium (Sr), and zinc (Zn) are known to be a major threat to agriculture today. The excessive release of heavy metals into the environment leads to biological toxicity and direct environmental pollution (Borymski et al., 2018; Asiminicesei et al., 2024). Furthermore, those metals that are injurious to plants also alter metabolite activities and reduce total productivity (Jańczak-Pieniążek et al., 2022). Moreover, it has been understood that heavy metals impede seed germination, shorten roots and shoots, and lower respiration and photosynthesis rates (Majhi and Sikdar, 2023). A major problem occurs when crops absorb heavy metals, and human consumption of these contaminated crops leads to life-threatening diseases (Boluspayeva et al., 2022). In early studies, microbes and plants have been used separately to eliminate those heavy metal pollutants from the soil prominently; nevertheless, understanding the importance of plant–fungal interactions, combined application of both plants and fungi became a catchier topic nowadays (Flemming et al., 1990; Joshi-Tope and Francis, 1995; Boorboori and Zhang, 2022). The plant-based approach to removing heavy metals, known as phytoremediation, involves the application of selected species that are resistant to heavy metals and accumulate high levels of metal (loid)s in their plant bodies, primarily in the roots and shoots. The plants are selected based on the two assignments: bioconcentration factor (BCF) and translocation factor (TF). The shoot-to-root ratio of heavy metal and the root-to-soil ratio of heavy metal (Sharma et al., 2023).

In general, vascular plants typically have a marginally higher tolerance to heavy metals (Fasani et al., 2022). Plants can alter the number of polysaccharides in their cell walls to withstand the stress caused by heavy metals. The main proteins in cell walls that are involved in cell wall dynamics and plant responses to stressors are called peroxidases. As plant roots grow, they release secretions into the soil, including low-molecular-weight organic acids, which break down soil minerals and release metals (Boorboori and Zhang, 2022). Mycoremediation, the removal of heavy metal stress by fungi, could be a more effective approach because fungi can move across and penetrate toxic or unfavorable zones to reach substrates and nutrients (Antón-Herrero et al., 2023). The underlying mechanism for mitigating the heavy metal threats is not yet well understood (Fan et al., 2022). Nevertheless, according to the findings, the homeostatic systems of fungi regulate the import, export, storage, and transport of heavy metals. It is also known that oxalate crystals produced by mycorrhiza fungi immobilise and detoxify heavy metals. The filamentous hyphae of these fungi enter the deeper soil aggregates and chelate or adsorb heavy metals (Mishra et al., 2017). In more detail, for example, ATP-binding cassette (ABC) transporters regulate several heavy metals, including Cd (Víglaš and Olejníková, 2021); CtrA2, CtrC, and CtrB transporters coordinately work on Cu (Raffa et al., 2019); and SMF1 and SMF2 function on Mn (Mori et al., 2018). Cytoplasmic compounds in fungi transform hazardous metals into less or non-toxic forms, which can then be segregated within the vacuole. Metallothioneins (MTs), a major class of intracellular peptide chelators of metal ions, play a crucial role in cellular tolerance to and detoxification of heavy metals (Gajewska et al., 2022). Moreover, it has been recognized that fungi’s genetic mechanisms of adaptation, or modifying their expression patterns, result in different profiles of gene expression (Traxler et al., 2022). The MT genes of fungi can be induced even by a single heavy metal, triggering the detoxification mechanism (Gajewska et al., 2022).

Lorenzo-Gutiérrez et al. (2019) demonstrated the role of mt1 in conferring tolerance to F. oxysporum against Cd, Cu, and Zn. Gautam et al. (2023) recently showed the metal-binding and heavy metal tolerance mechanisms of metallothionein OsMT-I-Id. Furthermore, their evidence shows the ability of fungi to induce OsMT-I-Id in rice against As, Cd, and Cu. It has also been identified that other genes, particularly ChrA, ChrB, and ChrR, function in response to a specific heavy metal. Those genes facilitate the fungi to tolerate Cr pollutants (Chi et al., 2021; He et al., 2021). In a recent study, Chi et al. (2021) analyzed the genome of P1 in Penicillium janthinellum and annotated 23 genes related to heavy metals.

Substantial investigation has been conducted to examine the significance of fungi in tolerating/degrading heavy metals. Ahmad et al. (2006) found that Aspergillus niger (also Penicillium sp.) tolerates heavy metals like Ni, Cr, and Cd. They have further recognized that fungi tolerance is not just under single-metal conditions but also under multi-metal conditions. Acosta-Rodríguez et al. (2018) later found the tolerability of A. niger against 2,000 ppm of Cr, Zn, Pb, and Hg, 1,200 and 1,000 ppm of Cu, As (III) and (VI), 600 ppm of Co, and 400 ppm of Cd.

Further, their study evident that, for instance, the ability of the fungus to eliminate Zn and Cr (VI) by 100%, followed by Hg (83.2%), Co (71.4%), As (V) (69%), As (III) (66%), Pb (59%), Cd (57%), and Cu (37%). In addition, Acosta-Rodríguez et al. (2018) gave an in-depth understanding of the mycoremediation potential of fungi. They highlighted that A. niger is not always superior in removing heavy metals, as it may remove specific metals (and certain concentrations) that could also depend on temperature and pH of the substrate. In a separate study, Mohamadhasani and Rahimi (2022) found that Pleurotus species grew more under low concentrations of the tested heavy metals (Co and Cu), indicating potential for heavy metal removal. It is noteworthy that when a fungus-like AMF establishes a direct relationship with plants, it increases the immobilization, conversion, detoxification, and extraction of heavy metals (Boorboori and Zhang, 2022). It is also recorded that a wide range of AMF can withstand highly polluted soils, thus, offering future possibilities for finding novel AMF species with greater mycoremediation ability (Suárez et al., 2023).

In a study, Iram et al. (2019) used several Aspergillus spp. (A. niger, A. terreus, and A. flavus) and Penicillium (P. chrysogenum) to remediate the Cr, Cu, Pb, and Cd associated with wheat and sunflower (Helianthus annuus). Plant–fungal interaction significantly helps remove the tested contaminants, enhanced by Aspergillus sp. (Cr < Cu < Pb < Cd). Furthermore, the researchers found that the interaction of P. chrysogenum leads to the storage of a higher amount of Pb in the plant shoot compared to other metals. Fan et al. (2022) found that A. niger (TL-F2) and A. flavus (TL-F3) facilitated the accumulation/subcellular distribution of Cd by annual ryegrass. Further, the researchers observed that ryegrass roots (17.8–37.1 μg pot⁻¹) were significantly more capable of absorbing Cd than the shoots (1.66–5.45 μg pot⁻¹). Overall, it was observed that the accumulation of Cd in different subcellular fractions increased with Cd concentration from 1.96 to 10.2 mg kg⁻¹. Nevertheless, compared with non-fungus ryegrass, cell wall and soluble Cd fractions in fungus-inoculated roots increased by 13.5–44% and decreased by 21.5–26.4%. Additionally, the authors recognized that fungal interaction significantly increases the plant’s biomass. For example, the biomass increases of fungus-inoculated roots range from 14 to 43%. Regarding the increasing Cd solution, in non-fungus-inoculated plants, the dry biomass is decreased by 10–40%. Chen et al. (2007) demonstrated the role of F. mosseae, in removing the effect of Phosphorus (P) and As associated with alfalfa. They inoculated the fungus and observed the increase in dry weight of both shoots and roots of the plants. Furthermore, Chen et al. (2007) observed that F. mosseae significantly decreased As concentrations in both plant shoots and roots, which also correlated with the fungus’s colonization. While fungus significantly increases the P supply to the alfalfa, proving that hyphal uptake of As and Chaturvedi et al. (2021) studied the Pea (Pisum sativum) F. mosseae symbiosis for phytoremediation of soil contaminated with Cd, Pb, and As. It has been found that F. mosseae led to an increase in plant growth, concentration of photosynthetic pigments, carbohydrates, nitrogen (N), and defense antioxidants, as well as a decrease in proline, all of which were statistically significant. Ultimately, those changes also help to protect the plant against hazardous pollutants. Furthermore, this association resulted in the removal of those pollutants from the soil to a considerable extent.

In contrast, a study conducted by Gu et al. (2017) yielded mixed results regarding the interactions between mycorrhizae and plants. Their study showed that showy stonecrop (Hylotelephium spectabile) and Purple Heart (Tradescantia pallida) survive under heavy metal-polluted soil, along with a mycorrhizal association, while exhibiting increased biomass in both roots and shoots. For example, when compared to the non-inoculated condition, stonecrop showed the most significant growth response to mycorrhizal inoculation, with increases in shoot and root biomass of 196 and 263%, respectively. The researchers measured the concentrations of Cd, Cu, Pb, and Zn in the plant’s tissues and recognized that metal concentrations in stonecrop shoots were unaffected by mycorrhiza. In contrast, Pb, Cu, Cd, and Zn concentrations in roots rose considerably by 108, 112, 34, and 19%, in comparison to the non-inoculated control. Furthermore, the study results indicated that the AMF inoculation did not affect the purple Heart plant’s shoot or root metal uptake, except for a 36 and 136% increase in Zn and Cd, respectively, in the roots. The outcomes also showed that AMF had a minimal effect on the uptake of Zn and Cu by the shoots of both plants.

Endophytes solubilize micro- and macronutrients available in the soil, supporting the mobilization and uptake of these nutrients by plants. The activity of endophytic fungi is well recognized in reducing the incidence of Fe deficiency in plants. Around the roots of non-graminaceous plants, certain endophytes synthesize and excrete phytosiderophores that solubilize Fe (III) by binding to mugineic acids (MA). This conjugation results in the formation of Fe (III)-MA, eliminating the need for plants to reduce Fe (III) to Fe (II) in order to absorb rhizospheric metals (Watts et al., 2023). Those fungi are also important in N fixation, as they fix more N within the plant, which is a more favorable environment for N fixation due to the low partial oxygen pressure (Rana et al., 2020). In legume plants, endophytic fungi also promote nodulation and N fixation even under low N availability (Xie et al., 2019). According to the literature, rather than the endophyte associations, the benefits of mycorrhizae in organic N and P accumulation for plants have been well studied. When AMF interacts with plants, it increases the availability of nutrients, particularly P, and with EcM—organic N, P, and other nutrients even under hazardous environmental conditions, promoting greater plant growth (Procter et al., 2014). More precisely, mycorrhizal fungi have been found to enhance crop productivity, increasing plant height, leaf area, biomass, and seed yield, even under lower soil nutrient content (Beslemes et al., 2023). Therefore, numerous studies have been conducted to date on mycorrhizal fungi; thus, here, we primarily discuss the alterations in crop-mycorrhizal interactions, particularly those involving AMF.

In a study, Zhu et al. (2016) demonstrated the response of AMF community composition to fertilization in the rhizosphere soil of maize crops. The findings suggested various fertilization regimes had a considerable impact on AMF diversity in the maize rhizosphere. Furthermore, the addition of organic manure is the most significant factor positively influencing the composition of AMF. Notably, the input of N and P fertilizers is also recognized as the next driving factor for the AMF composition. Furthermore, testing with 2-ethylnaphthalene and 2,6,10-trimethyltetradecane showed an adverse effect on AMF—Glomus relative abundance; however, 3-methylbiphenyl showed a positive correlation with Rhizophagus. This implies that changes in fungal composition may also impact their interaction with host plants. In a separate study, Beslemes et al. (2023) investigated the contribution of AMF inoculation on the growth and productivity of two-rowed barley crops in conventional and organic cropping systems. The researchers also obtained similar results to those of Zhu et al. (2016), as the organic cropping system supports the significant influence of AMF colonization on host plants, leading to increased crop productivity. According to the findings, nutrient availability is sometimes not affected by community composition, particularly in the case of root-associated fungi. However, the effect on plant growth is also supported by the fungal associations, which supply higher nutrients to the plants than those regularly taken (Maciá-Vicente et al., 2022). It is noteworthy to highlight the results of the study conducted by Wang et al. (2022b), as their findings provide additional support for the points discussed above. Here, the researchers have tested different AMF inoculations on cherry tomato crops under varied nutritional conditions, attempting to understand their effect on AMF and host-plant interactions. In their pot experiment, Wang et al. (2022b), used three different nutritional treatments: high nutrition level (1:1, volume ratio of peat soil to sand), medium nutrition level (1:2, volume ratio of peat soil to sand), and low nutrition level (1:3, volume ratio of peat soil to sand). The four fungal inoculation treatments included F. mosseae, Glomus versiforme, Rhizophagus intraradices, and an equal mixture of all three fungi. They have recognized highly significant differences between the various AMF inoculation treatments in the root mycorrhizal infection of cherry tomatoes. Furthermore, Wang et al. (2022b), found that the amount of nutrients in the soil, the type of fungi inoculation, and their interactions all had a significant impact on the accumulation of N and P in S. lycopersicum. Overall, at medium and low nutrient levels, the infection rates of G. versiforme and the mixture were significantly greater than those of F. mosseae and Rp. intraradices, and at high nutrient levels, the infection rates of G. versiforme exceeded those of F. mosseae. Additionally, it is reported that the crop exhibits different growth performances under four fungal treatments and three nutrient levels. Wang et al. (2022a) also observed that the treatments had significant effects on flower number, fruit number, fruit biomass, and reproductive allocation of the crop. By accounting for all these results, the researchers concluded that the nutritional level directly alters the plant-AMF interaction.

Temperature plays a crucial role in the metabolite activities of plants, and increased temperature may have a deleterious effect on their physiological functions and growth. Climate change and the temperature rise are among the pressing issues in the agricultural sector, as evidenced by the failure of crop farming and the inability to achieve the expected harvest (Habib-Ur-Rahman et al., 2022; Janni et al., 2023). Moreover, the temperature rise alters the plant–fungal interaction both positive and negative ways, depending on the lifestyle of the plant and the fungus. When plants are associated with pathogens, the disease caused by the fungi may be more prevalent due to an increase in the virulence of the pathogenic fungi, this has been greatly presented by Waheed et al. (2023) in their review. Note that there is an optimum temperature range in each of the plant–fungal interactions at which the disease develops, for instance, 23.8°C is the optimum temperature for the White Rot disease in grape berries caused by Coniella diplodiella (Ji et al., 2021), while 30°C is the optimum temperature for root rot fungi F. solani, and 15°C is the optimum temperature for F. tricinctum to cause the disease in cotyledons, soybean (Yan and Nelson Jr, 2020).

In an earlier study, Park (1990) attempted to understand the infection of Puccinia striiformis in wheat seedlings, as well as the effects of temperature changes under both laboratory and field conditions. Based on the laboratory study, the researchers expected that no infection would occur at or above 20.8 + 0.2°C, where infection declined from 100% at 15.4°C to 0.8% at 20.5°C. However, under field conditions, the infection rate is higher between 19 and 30°C, showing difficulties in predicting which temperature range can exactly influence significant changes in plant–fungal interaction. The molecular-based answer for such changes is still lacking. Onaga et al. (2017) observed that M. oryzae plant fungal biomass is significantly higher at 35°C than at 28°C and also recognized the elevated level of putative fungal effector genes in plants exposed to 35°C, compared to lower temperatures. Considering all those, Onaga et al. (2017) highlighted that raising the temperature may facilitate M. oryzae infection by weakening plant resistance and hastening the pathogen’s colonization of plant tissues.

The adaptation of pathogens to global warming has been reported; however, the patterns and mechanisms of such adaptations in many plant pathogens remain to be understood. To fill this gap, Wu et al. (2022) tested the genotypes of Phytophthora infestans under five temperature regimes. They have noted that phenotypic plasticity contributes ~10 times more than heritability measured by genetic variance. Additionally, the expression of genetic variation and the relationship between local temperature and pathogen aggressiveness have been found to be altered by the experimental temperatures. The variance in aggressiveness is exacerbated by raising the experimental temperature. Pathogens from warmer climates caused less disease than those from cooler climates at low experimental temperatures, whereas the opposite was true at higher experimental temperatures. On the other hand, fungal symbionts provide more benefits to their host plants by protecting them from temperature fluctuations. Mathur et al. (2021) investigated the impact of high-temperature stress on plant physiological traits and mycorrhizal symbiosis in maize. It has been recorded that the vegetative and reproductive growth of maize, from germination to grain filling, is impacted by higher temperatures (35°C and above). The results of their experiment show that AMF interaction helps improve the plant’s photosynthesis rate by increasing N and Mg content, along with enhanced carbohydrate and sugar accumulation. The researchers further reported that AMF prevents damage to the photosynthetic apparatus (PSI and PSII) of the host plant due to the higher temperatures. Furthermore, Mathur et al. (2021) reported that enhanced photosynthesis, accompanied by improved soil quality and crop growth, leads to the mitigation of multiple malformations in the physiological characteristics of the host plant.

Both fungal communities and plants respond directly to the soil water regime, thereby affecting their interactions (Erlandson et al., 2016; Xiao et al., 2022; Chen et al., 2023). On one hand, plants generally increase their susceptibility to phytopathogens due to drought stress. On the other hand, they also increase their resistance against those phytopathogens. The morphological characteristics of the plant root are one of the factors that determine its relationship with fungi. It has been recognized that plants with thin root systems exhibit lower dependence on AMFs for water uptake, due to their ability to acquire water efficiently (Lozano et al., 2021). Most EcMFs typically form rhizomorphs and hydrophobic mycelia, which help plants mitigate the impact of drought (Castaño et al., 2023).

Boczoń et al. (2021) described in detail how the plant–fungal interactions change under water scarcity (drought) due to climate change. According to them, drought reduced the overall prominence of mycorrhizal associations with the plants, leading to reduced further water uptake and alterations in metabolic pathways due to ATP and nutritional deficiencies. Next, impairment of plant tissues and chlorosis of the leaves occur, leading to a switch in the fungus’s endophytic lifestyle to pathogenic, causing disease in the hosts. In addition, Boczoń et al. (2021) noted that these changes weaken the plant’s defensive system, even against pests, and make it more susceptible to invertebrate attacks.

Joachin et al. (2023) studied how water availability influences the effective specialization of a fungal pathogen in its interactions with plants. Under low, average, and high-water treatments, they established paired congeners of three native and three non-native species of coastal prairie plants, with or without the pathogenic soil fungus Fusarium incarnatum-equiseti species complex 6b. The Fusarium treatment demonstrated greater adverse and species-specific effects on plant biomass at high water availability than at low water availability for all examined plant species. Furthermore, the results of Joachin et al. (2023) supported the discussions by Benítez et al. (2013). They have emphasized that the effective specialization of pathogens promotes the coexistence of plant species, for instance, via negative plant–soil feedback or the Janzen-Connell hypothesis (Comita et al., 2014). Under water scarcity, endophytic and mycorrhizal fungi show various alterations to host plants, depending on the species and the combination of other environmental factors (Dastogeer, 2018; Ahlawat et al., 2022; Frew, 2023). For instance, drought conditions may lead to the production of various plant biochemical compounds, also with the help of fungi, which mitigates water stress conditions (Boczoń et al., 2021). Hubbard et al. (2014) demonstrated that endophytic Ascomycetous fungi enhance the heat and drought tolerance of wheat (Triticum turgidum) in terms of grain yield and second-generation seed viability. Later, in a more comprehensive study, Miranda et al. (2023) found that the endophytic fungus Zopfiella erostrate substantially colonizes wheat and tomato roots, contributing to enhanced plant nutrient mineralization and water uptake under water deficiency. Their study showed the significant effect of the fungus on plant growth; however, the researchers did not observe any considerable changes in fungal root colonization under water-deficient conditions compared with the well-watered plants. Nevertheless, the fungus exhibited higher photosynthetic efficiency, decreased enzymatic activity (catalase and ascorbate peroxidase), altered glutathione reductase activity, lower hydrogen peroxide concentrations, and a significant drop in lipid peroxide accumulation. The studies indicated that such a change or activation of antioxidant compounds and enzymatic activities worked against oxidative damage generated by water-deficient conditions (Piri et al., 2019; Kaur and Saxena, 2023).

In an experiment with F. mosseae on tomato, Bitterlich et al. (2018) emphasized the importance of AMF in alleviating the drought impact on the plants. They recognized the considerable amount of available water content reserved by F. mosseae. To a great extent, fungal restoration of plant hydraulic status and increased plant transpiration were also observed with the decline in soil water content. In addition to water scarcity, soil waterlogging conditions also influence plant–fungal interactions. According to the study by Calvo-Polanco et al. (2014), the fungus R. irregularis benefits tomato plants under flooded conditions. They have gained a molecular-level understanding, as evidenced by the increase in root hydraulic conductivity due to the fungus, which is related to the upregulation of aquaporin gene expression, specifically GintAQP1 and SlPIP1;7. Further studies have demonstrated that mycorrhizal fungi stimulate the production of 1-aminocyclopropane-1-carboxylic acid (ACC) and ethylene (Et) in plants, thereby enhancing their resistance to flooded conditions (Cruz et al., 2000).

The rise of atmospheric CO₂ has been observed over recent decades, which is linked to climatic changes. Elevated CO₂ (eCO₂) is beneficial for crops, as it increases the efficiency of photosynthesis and growth; however, the overall impact is not entirely understood. Furthermore, the interaction between plants and fungi is also affected by changes in CO₂ (Smith and Luna, 2023).

Chakraborty and Datta (2003) evaluated the aggressiveness of Colletotrichum gloeosporioides in shrubby stylo (Stylosanthes scabra) that causes anthracnose disease. Considering their 22-year field experiment period, Chakraborty and Datta (2003) found a fourfold difference in disease severity levels between isolates with the lowest and highest disease severity levels. Prior to 1987, both weakly (severity < 0.6) and moderately aggressive (severity 0.6–0.8) isolates were found; however, between 1991 and 1999, the distribution became more uniform, with aggressive isolates (severity 0.8–1.2) and highly aggressive isolates (severity > 1.2) towards the host plant. They have recognized that these changes mainly happen due to the eCO₂. Further, they have correlated this scenario with the controlled environment study. The experiment demonstrates that increasing CO₂ levels (from 400 ppm to 700 ppm) enhances the pathogen’s aggressiveness. In their experiment, Karnosky et al. (2002) observed that eCO₂ (560 ppm, 200 ppm)/O₃ (1.5x ambient) occurrence and severity of leaf rust caused by Melampsora medusae on trembling aspen (Populus tremuloides). They have found that seasonal exposures to O₃ and CO_2, as well as O₃ alone, both resulted in significantly increased rust occurrence and severity, three to five times. Leaf surface topography, microroughness, and physicochemical characteristics (e.g., chemical composition and epicuticular wax structure) collectively determine leaf surface properties, such as wettability, and this is recognized as a key consideration for changes in host-fungus interactions. The wettability of the leaf surface significantly increases the incidence of M. medusae by positively influencing the fungal attachment and further infection process. In the contest, some studies reported enhanced disease resistance under eCO₂. For instance, Hibberd et al. (1996) and Mikkelsen et al. (2015) found that eCO₂ (700 ppm) shows resistance against the Erysiphe graminis and Blumeria graminis, respectively, associated with barley. Williams et al. (2018) recognized the increased resistance of Arabidopsis thaliana against necrotrophic Plectosphaerella cucumerina infection under the eCO₂ (1,200 ppm). Furthermore, the study by Williams et al. (2018) added value to Karnosky et al. (2002), as it considered in-depth biochemical mechanisms and molecular bases to explain disease resistance. Of this, Williams et al. (2018) noted a 69.3 and 69.4% increase in SA and JA accumulation under eCO₂, respectively. They have further identified that eCO₂ alters basal and SA-induced PR1 gene expression, which is responsible for stress resistance. In line with this, Mhamdi and Noctor (2016) also recognized increased disease resistance in A. thaliana (along with other plants, such as Phaseolus vulgaris, or beans) against B. cinerea under 3,000 ppm of CO₂. They have also highlighted that eCO₂ triggers SA accumulation and is partially linked to metabolic effects involving redox signaling. This is supported by the fact that complete priming of the SA pathway and the corresponding resistance to high CO₂ are prevented by genetic modification of redox components, including glutathione levels and NADPH-generating enzymes. Furthermore, they have emphasized that this is also true for other crop plants studied, such as beans. In addition, working with Cochliobolus miyabeanus that infects rice, Dorneles et al. (2020) recognized (under 700 ppm of CO₂) higher activity of the enzyme’s ascorbate peroxidase, catalase, chitinase, peroxidase, polyphenoloxidase, superoxide dismutase, enhanced phenolic compounds, and lignin concentration, indicating defense responses.

The interaction between plants and endophytic fungi may vary in response to eCO₂. According to their experiment, Christian et al. (2021) found that a community of endophytic fungi declined with eCO₂, which is opposite to the findings of Alberton et al. (2010). Liu et al. (2023) investigated the diversity and colonization of eCO₂ and AMF. They have recognized that with eCO₂, the diversity of AMF increases, while decreasing root colonization with host plants, such as maize and wheat.

The study of multiomic techniques, including the integration of genome, metagenomics, metabolomics, volatilomics, and spectranomics data, in plant–fungal interactions appears to be scarce. However, such an application will provide an in-depth understanding of the biology and physiology of both the plant and the fungus when they are associated (Shakeel et al., 2022). These multiomic strategies can unravel the functional roles of different fungal species within agricultural ecosystems, improve our understanding of how co-infecting fungi may synergistically modulate the plant’s defense mechanisms, often leading to enhanced pathogenicity and altered nutrient acquisition strategies. Analyzing the microbial community dynamics beneath the plant surface through this methodology sheds light on how co-infection scenarios can lead to unique fungal interactions that ultimately impact plant productivity and health, including the identification of microbial modulation of key plants’ genetic potentials and metabolic pathways (Hori et al., 2021; Doni et al., 2022; Luo et al., 2022). Also, multiomics can facilitate the discovery of novel bioactive compounds produced during interaction, further expanding the toolkit for sustainable agriculture (Kumar et al., 2023). For instance, genomics studies can identify genes in microbes that are responsible for nutrient acquisition or phytohormone production, which in turn enhance plant growth (Wójcik et al., 2023). Transcriptomics investigations reveal how plants respond to microbes at the gene expression level, highlighting signaling pathways activated during symbiosis or pathogen defense (Van Dillewijn, 2008; Mukherjee, 2022). There are several limitations to using multiomic approaches. Such as in gene expression, replication of environmental conditions, complexity of microbial communities, and difficulties in obtaining sufficient materials (e.g., Rhizosphere fungi), its wide use is restricted (Chiquito-Contreras et al., 2024). Overall, in multitopic approaches, several limitations exist, including gaps in taxonomic or chemical compound databases, which can make comparison and verification challenging. Instead, higher costs for sample analysis, advanced technologies with specific infrastructure facilities, and a lack of expertise are the main considerations, particularly in developing countries. Those factors further restricted the application of multiomic techniques (Crandall et al., 2020).

Network mappings of plant–fungal interactions are crucial for understanding how microbes influence plant metabolism, stress responses, and immune systems (He et al., 2021). Of this, genome-wide association studies (GWAS) have been a recent focus; for example, Bergelson et al. (2019) identified a few significant Quantitative Trait Loci (QTLs) associated with Arabidopsis thaliana root microbial species richness and community structure. These QTLs are implicated in plant immunity, cell wall integrity, and the development of roots and root hairs. A study by He et al. (2021) developed a behavioral ecology model to define the strengths of mutualism, antagonism, aggression, and altruism between each pair of root microbes of A. thaliana. It showed the importance of such studies in selecting microbes that benefit sustainable plant growth. De Vries et al. (2018) indicated that the inherent mechanisms of microbial relationships in response to environmental disturbances can be uncovered by examining the properties of co-occurrence networks. Agler et al. (2016) noted that recognizing network hubs and their significance in microbial community structure has important implications for understanding interactions between microbes and can aid in the development of targeted biocontrol strategies in the future.

One of the overlooked aspects of plant–fungal interactions is the impact of indigenous fungi on plant growth and protection. Studying native fungi is limited, which could be due to their lower infection potential, and they may not be able to get sufficient inoculum that non-native fungi offer (Deguchi et al., 2021; Wu et al., 2021b). However, several studies have revealed that native fungi also have significant potential to enhance crop productivity in various dimensions, making their interaction with plants a crucial consideration (Koziol and Bever, 2023). One such example is the communication of plants through fungal mycelial networks. This is widely discussed in relation to mycorrhizal fungi; the fungal mycelia allow signals to be sent between plants. Recent research has demonstrated that these mycorrhizal networks serve as an information highway, facilitating the exchange of defense signals, allelochemicals, and nutritional resources (Luo et al., 2023). Nevertheless, this aspect has not been extensively discussed in the agricultural context, although it has been explored in other ecosystems (Gorzelak et al., 2015). On the one hand, this could be due to the shift in paradigm towards intensive, input-driven practices that prioritize high-yield crop production. Synthetic fertilizers and pesticides became the standard tools for increasing productivity, as they provided immediate and visible benefits to plant growth. However, these activities may alter soil properties and accumulate pollutants, which could negatively impact indigenous or native fungi, thereby hindering their potential benefits (Semenov et al., 2022; Steiner et al., 2024). On the other hand, the intricacy of biological interactions is not attracting researchers, as it is a challenging task (Aleklett et al., 2021).

It has long been recognized that the importance of fungal biocontrol agents is higher among academic communities (Wallis and Sisterson, 2024). In contrast, the commercial application is still not widely adopted worldwide due to its limitations, including a short shelf life, reduced efficacy, commercialization issues, and legislative procedures (Bamisile et al., 2021; Palmieri et al., 2022). Production quality control is one of the crucial steps in fungi formulations. The quality control process initiates with evaluating the inoculants, microbial strains, carriers, and the final product, as well as ensuring proper labeling and commercialization. To obtain legal acceptance, it is essential to properly identify fungi species or strains prior to mass cultivation. Furthermore, the cultures must be sterile, with high viability and germination capacity. Regulation regimes in the European Union and India specifically concern minimum viable spores and acceptable variation in microorganism concentrations (Ghorui et al., 2025).

When discussing commercial formulations, it has been recognized that the importance of developed fungal strains extends beyond indigenous fungi. In the current complex agricultural system, indigenous fungi may not be the most competitive option; however, it is also essential to identify more effective species for future formulations (Gohel et al., 2022; Díaz- Urbano et al., 2023; Erdoğan and Sağlan, 2023). Keep in mind that one of the foremost things to discuss in the fungal formulations is the viability of fungi. It is typically expected to be effective for at least 6 months and preferably for about 2 years. The formulation could be liquid-based or solid-based; however, both forms have their advantages and disadvantages. The liquid media could be easily controlled and supplemented with nutrients, although it required complex fermentation equipment. The solid-based formulations are relatively simple; in contrast, it is a challenge to supply the necessary nutrients to the fungi, and maintaining the viability of the fungal inoculum under low water content in the formulations can be complex (Teixidó et al., 2022). The researchers also made significant efforts to enhance the packaging and shelf life of fungal formulations. For example, Jeong et al. (2022) utilized modified atmosphere packaging (MAP) to prolong the shelf life of Metarhizium anisopliae conidia. They have found that MAP with 30% CO₂ + 70% N₂ retains 80.5% conidial viability after 28 days. However, the challenge here is the storage condition, as achieving higher shelf life with higher conidial viability requires cold storage facilities. Jeong et al. (2022) reported that MAP-treated conidia have a longer half-life when stored at 4°C compared to 25°C. In an independent study, Silva et al. (2024) attempted to extend the shelf life of a rice flour-granular formulation based on Trichoderma conidial biopesticide. Similar to the result of Jeong et al. (2022), Silva et al. (2024) evidenced that cold storage of the formulation is necessary for a longer shelf life (up to 24 months), which may not always be convenient for sellers or farmers in practice, particularly in developing countries.

Scientific evidence also indicated that the demerits of such applications—could be highly specialized against the targeted disease or the pathogen, and the controlling ability is highly dependent on the various biotic (e.g., host plant, metabolites and enzymes synthesized by host plant, and natural microflora of the host plant and their interaction) and abiotic (e.g., microelements, nutrients, pH, temperature, ultraviolet (UV) radiation, and water activity) conditions (Bonaterra et al., 2012). Therefore, the prediction of the effectiveness when applied to the field could be reduced, inconsistent, and dependent (Boro et al., 2022). For example, the study by Wei et al. (2019) can provide insight; the researchers tested the endophytic fungus Fusarium solani against Verticillium dahliae in Cotton plants. They have found that the biocontrol potential of the fungi is higher in efficacy in the greenhouse experiment. In contrast, when tested in the field, the efficacy decreased (Table 1). Nevertheless, numerous studies have shown that fungi biocontrol agents can be effective against phytopathogens; however, these findings are limited to greenhouse experiments (Herrera et al., 2020; Catambacan and Cumagun, 2021; Safari Motlagh et al., 2022).