**3. Biodiversity and Ecology of Endophytes Associated with Crops Belonging to the Amaryllidaceae Family**

The endophytic symbiosis could be an implementation of the microorganisms' strategy aimed at reducing the effects of the external changeable environment through the long-term coevolution with plants providing a stable niche in their tissues [47]. The leaf surface is an attractive habitat for endophytic fungi, which are influenced by the possibility of colonization through the epidermal structures, by leaf health and nutritional status, and by competition with the other microorganisms. Several studies have been carried out to characterize the mycobiota of *A. cepa* rhizosphere and phyllosphere, but much less research has been focused on fungi colonizing internal tissues. Abdel-Gawad et al. [48] isolated and identified, based on macro- and microscopic characters, 24 genera and 38 species of fungi from the rhizoplane of onion, with dominating *Aspergillus* spp., *Cladosporium* spp. and *Penicillium* spp., and 17 genera and 35 species from the phylloplane, with dominating *Aspergillus* and *Penicillium* spp. The root and leaf surface of onion hosted a broader spectrum of species than internal tissues, confirming that plants selectively recruit endophytic microorganisms. Moreover, aboveground plant tissues are exposed to rapid fluctuations in temperature, humidity, and solar radiation, so microorganisms colonizing leaves are also affected by abiotic stress, exceeding sometimes their tolerance thresholds. Abdel-Gawad et al. [48] evidenced that the onion's fungal microbiota dependent on temperature, namely the species *Humicola grisea* (current name *Trichocladium griseum*), *Penicillium mirabile* (current name *Talaromyces verruculosus*), and *Rhizoctonia solani*, were isolated from leaves at 19 ◦C, whereas other species, such as *Chaetomium brasiliense* (current name *Ovatospora brasiliensis*) and *Zopfiella latipes*, at 28 ◦C. Moreover, the mentioned species were not specific for onion but isolated from roots of the other crops in the investigated region, namely Assiut Governorate in Egypt. Only one species, *Z. latipes*, was isolated from onion leaves for the first time in Egypt [49]. A red spider lily (*Lycoris radiata*) and golden spider lily (*L. aurea*) are ornamentals of Asian origin, introduced into many countries all over the world because of decorative flowers, but their bulbs are known as poisonous in traditional medicine systems. Zhou et al. [50] identified, using molecular (polymerase chain reaction—PCR) and morphological characteristics, 27 species of fungal endophytes belonging to 14 genera from *L. radiata*. Only *Fusarium* developed hyphae in all organs; *Stagonosporopsis* and *Glomerella* (current name *Colletotrichum*) were isolated from leaf tissues; *Phoma* from the bulb; *Galactomyces*, *Metacordyceps* (current name *Metarhizium*) and *Diaporthe* from root tissues. *Aspergillus*, *Colletotrichum*, *Diaporthe*, *Fusarium*, *Penicillium*, *Phoma*, and *Phyllosticta* were commonly isolated from a wide range of hosts but *Cylindrocarpon*, *Galactomyces*, *Sarocladium*, and *Stagonosporopsis* were described as endophytes of specific plants. In earlier studies, despite the mentioned species, *Trichoderma* sp. was isolated from a bulb of *L. radiata* [51] and *Mucor* sp. from the bulb of *L. aurea* [52]. Notably, *Metarhizium* sp., which was reported as a soil fungus [53], was isolated from *L. radiata* tissues, so this fungus seems to colonize plants occasionally [50].

The relationships between the endophyte fungi and host plant are very diversified and dynamically change from mutualism, symbiosis, and commensalism to pathogenic during plant ontogeny [54,55]. For example, *Colletotrichum*, *Diaporthe*, *Fusarium*, *Phyllosticta*, and *Phoma*, isolated from healthy tissues of *L. radiata* are commonly recognized as pathogenic, so the antifungal alkaloids can enforce symbiotic lifestyle in plants, maintaining a balance between host and its endophytes/parasites. Regarding endophytes colonization during onion's ontogeny, Mueva et al. [56] stated that the seed inoculation was more effective than seedling inoculation in terms of endophytes recovery in subsequent stages of plant development. Indeed, endophytes inoculated at the seed surface colonized seed radicle and plumule and developed internal mycelia in growing tissues. The fungal colonization and distribution in onion tissues firstly depended on inoculation technique and secondly on the endophyte selection by the host. Independently on the inoculation technique, most of the investigated endophytes, for example *Clonostachys rosea*, *Hypocrea lixii* (current name *Trichoderma lixii*), *Trichoderma asperellum*,

*T. atroviride*, *T. harzianum*, and *Fusarium* spp., were isolated from onion roots, followed by stems and leaves. These differences could be due to tissue morphology and physiology, microbiome interactions, and the influence of external conditions [56,57]. Onions have shallow, weakly branched root systems with sparse root hairs, inefficient in the use of soil nutrient resources. The root endophytic and mycorrhizal fungi play a significant role in supporting onions with mineral salts, that is why this species is among the most symbiosis-dependent crops [7]. Focusing on endophytic fungi colonizing shallot roots, Priyadharsini et al. [58] found that the percent of root length with fungal microsclerotia was significantly and negatively correlated with soil phosphorus level. Similarly, percents of root length with dark septate hyphae and dark septate endophyte total colonization were negatively correlated with soil zinc and copper contents. It can be concluded that colonization of shallot roots by fungal endophytes was reduced in soils rich in mineral salts. Wu et al. [59] hypothesized that the endophytic fungal community may be helpful to symbiotic plants (i.a. *Allium mongolicum*) for surviving in the extreme environments of Asian deserts. The mycobiota associated with photosynthesizing or storage leaves, for example *T. harzianum* and *T. koningii*, could act antagonistically to phytopathogens. On the other side, leaves with disease symptoms, with damaged epidermal cells and the lamellar seta shed releasing nutrients, could be secondarily colonized by opportunistic fungi such as *Botrytis cinerea*, *Penicillium aurantiogriseum*, *Alternaria alternata*, and *Cladosporium* spp. [20].

Plant storage tissues, including sugar-rich onions' bulbs, can contain specific endophytes, actively reproducing in these tissues without visible damage [60]. One of the main chemoecological roles of Amaryllidaceae alkaloids is the protection of nutrient-rich bulbs against phytopathogens and herbivores. Xiang et al. [61] isolated and sequenced six fungal endophytes from *Narcissus pseudonarcissus* bulb and only two from leaf tissues. Zhou et al. [19] found that bulbs of *L. radiata* were exclusively colonized at a higher degree than other tissues, probably because of the perennial life cycle of bulbs and annual cycle of other plant parts [62] and because of the space and carbohydrates provided by bulbs as storage sinks [63].
