*3.1. Biochemistry and Functions of Fungal Endophytes Associated with Allioidae Crops*

Abdel-Hafez et al. [20] investigated endophytes colonizing *A. cepa* leaves, both healthy and infected by purple blotch (*Alternaria porri*). Fungi were isolated and identified according to their macroscopic and microscopic characteristics. Despite the strains detected from healthy and diseased leaves, belonging to genera *Cladosporium*, *Alternaria*, *Penicillium*, and *Stemphylium*, five species, namely *Absidia corymbifera* (current name *Lichtheimia corymbifera*), *B. cinerea*, *P. aurantiogriseum*, *P. glabrum*, and *Syncephalastrum racemosum*, were isolated only from infected leaves, while three species (*Fusarium oxysporum*, *Trichoderma harzianum*, and *T. koningii*) were isolated only from healthy ones (Table 1). *Trichoderma* spp. showed antagonistic potential against *A. porri*, through competition, lysis, antibiosis, and parasitism [64,65]. The antagonistic effect of *Epicoccum nigrum*, *Penicillium oxalicum*, and *Stachybotrys chartarum* against *A. porri* was antibiosis caused by effective lytic, as well as antimicrobial secondary metabolites produced by endophytic fungi [20]. Previously, Flori and Roberti [66] noticed the antifungal activity of the endophyte *Beauveria bassiana*, inoculated to onion roots, against *F. oxysporum* f. sp. *cepae*, causing basal rot of onion. The antifungal potential of the endophyte *Talaromyces pinophilus* (current name *Penicillium pinophilum*) against *B. cinerea* was described by Abdel-Rahim and Abo-Elyousr [67]. *T. pinophilus* was isolated from onion's inflorescences and identified with PCR amplification of the ribosomal internal transcribed spacer (ITS) region. The mycelium of *T. pinophilus* penetrated intercellularly the hyphae of *B. cinerea*, involving cell wall degrading enzymes (chitinase, lipase, and protease) in the mycoparasitic process.


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Muvea et al. [56,68] showed the effect of onion inoculation with some strains of endophytic fungi on the proportion of thrips due to reduced feeding and oviposition, caused by antixenotic repellence or higher death rate of thrips. Moreover, the reduced feeding of thrips on endophyte-colonized onions could reduce the transmission of virus diseases, spread by insects.

Among endophytes of garlic that can produce bioactive compounds, Shentu et al. [71] isolated and identified, based on morphological and molecular procedures, *Trichoderma brevicompactum* with strong antifungal activities. Trichodermin, an antifungal compound of *T. brevicompactum* inhibited mycelial growth of *R. solani*, with an EC50 of 0.25 μg mL<sup>−</sup>1, and *B. cinerea*, with an EC50 of 2.02 μg mL−<sup>1</sup> (Table 2). A weak inhibition was noted against *Colletotrichum lindemuthianum* (EC50 = 25.60 μg mL<sup>−</sup>1). The authors underlined that the relationship between *T. brevicompactum* and the garlic plant remained unclear. Espinoza et al. [72] investigated the chive's growth parameters and secondary metabolites as affected by inoculation with the endophyte fungus *B. bassiana*. The fungus applied to the rhizosphere, colonized plant tissues, and finally was isolated from roots and leaves, affecting total alkaloids content but not leaves yield. Koul et al. [73] isolated and morphologically and molecularly identified the fungus *Penicillium pinophilum*, from bulbs of chive's population native to snow mountain regions of India. *P. pinophilum* was a source of anticancer anthraquinones, dicatenarin, and skyrin. Both compounds inhibited human pancreatic cancer (MIA PaCa-2) cells with least IC50 values of 12 μg mL−<sup>1</sup> and 27 μg mL−<sup>1</sup> respectively, through mitochondrial-mediated apoptotic pathway. Dicatenarin cytotoxic/proapoptotic activity was more pronounced than skyrin due to the presence of an additional phenolic hydroxyl group at C-4, which increased reactive oxygen species generation [73].

Wild and endemic *Allium* species were also the object of investigation. In the latter respect, Abdulmyanova et al. [74] screened *Allium filidens* Regel and leaves of *A. longicuspis* Regel regarding endophytic fungi biodiversity and bioactivity. Among 16 isolates of endophytic fungi obtained from these plants and identified morphologically, the highest biodiversity was determined for bulbs of *A. filidens* and leaves of *A. longicuspis*. The *Penicillium* spp. were the most dominant symbionts of *A. filidens*, while *Aspergillus* spp. were commonly isolated from *A. longicuspis*. Beside cosmopolitan species, the rare endophytes *Alternaria tenuissima*, *Aspergillus spectabilis*, and *Cladosporium tenussimum* were also isolated. The endophytic fungi detected in the same host varied regarding bioactivity. For example, three strains of *Penicillium* sp. isolated from bulbs of *A. filidens* were different in cytotoxic, antibacterial, and antiamylase activity, two strains of *Alternaria* sp. from leaves of *A. longicuspis* exhibited only antibacterial activity [74,75]. Bulbs of both described *Allium* species, endemic in Afganistan, have been used in traditional Asian medicine [76].

## *3.2. Biochemistry and Functions of Fungal Endophytes Associated with Amaryllidoideae Crops*

Amarylidoideae alkaloids can be involved in chemical crosstalk between host plant and endophytes as communication molecules that are responsible for the shaping of plant-microbe interactions. This phenomenon was more widely investigated for endophytic bacteria, which can promote the synthesis of Amaryllidaceae alkaloids [77,78], but endophytic fungi are also involved in plant-endophyte and endophyte–endophyte interspecies communication. For example, Wang et al. [79] investigated endophytic fungi and bacteria in the bulbs of the Chinese sacred lily (*Narcissus tazetta*), widely used as an ornamental and medicinal plant in Asia [79]. The authors defined nine hexacyclopeptides produced by fungus and selectively accumulated by an endophytic bacterium *Achromobacter xylosoxidans* isolated from the same tissue (Table 2). The production of targeted hexacyclopeptides by *F. solani* was possible only in planta and decreased in vitro conditions. However, the ecological basis of this chemical cross-talk needs future investigations. Yang et al. [80] isolated and identified, using morphological and molecular methods, 18 strains of endophytic fungi from *Narcissus* sp. Three species, particularly *Rhinocladiella* sp., demonstrated significant inhibitory activity against acetylcholinesterase.

Onofri et al. [81] identified, using conventional taxonomic techniques, four strains of *Cryptococcus laurentii* (current name *Papiliotrema laurentii*), C1–C3 from root tips, C4 from outer bracts of bulb of daffodil (*N. pseudonarcissus*). The authors observed that lycorine, an alkaloid of *Narcissus* bulbs, inhibited the growth of C1–C3 but not C4 strains of fungi. The inhibition was due to destroying the cellular membranes and interfering with the substrate absorption and cell metabolism, namely blocking L-galactonic acid γ-lactone conversion into ascorbate by lycorine. In contrast, *C. laurentii*, isolated from the lycorine-containing bracts of the bulb, was able to degrade lycorine and to use decomposition products as growth stimulators.

*L. radiata* is the main source of Amaryllidaceae alkaloids but the low yield and high costs, resulting from its complex procedures and mixed stereoisomers, limit pharmaceutical development of plant-delivered drugs [50]. *Lycoris* spp. were objects of some investigations regarding endophyte microbiota and assessment of the biological activity of their metabolites. *Penicillium* sp. isolated from *L. aurea* was able to produce galanthamine in vitro [82], and the other nonidentified fungus strain L-10 possessed antibacterial and antifungal activity against *Staphylococcus aureus* and *Candida albicans*, respectively [52]. This phenomenon confirmed the antagonism between fungal and bacterial symbionts of this plant. Both novel and known compounds, especially alkaloids, could be produced by in vitro grown endophytic fungi isolated from *Lycorsis* spp. bulbs. Moreover, the inoculation with fungal endophytes enhanced the level of various alkaloids in *L. radiata*. So, inoculation with particular fungus or consortium of fungi can be used for increasing the content of targeted alkaloids during plant cultivation [50].

Li et al. [83] investigated drimane-type sesquiterpenoids of *Aspergillus versicolor*. Among the latter compounds, Versicalin A showed moderate cytotoxic activity against HL-60 tumor cells with an IC50 value of 5.6 μM, while proversilin C and E showed moderate cytotoxicity against human tumor HL-60, SMMC-7721, A-549, MCF-7, and SW-480 cell lines and the normal colonic epithelial cells NCM460 with IC50 values ranging from 7.3 to 28.4 μM [83,84]. The synthesis of the same chemical compounds by the plant host and endophytic fungus is the phenomenon described for some other species as an example of highly specified coevolution. Moreover, this phenomenon has a great significance in the detection and production of pharmaceutically valuable plant/endophyte derived drugs [85–87].


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