Plant compartments and regional variations shape the community structures and functional composition of endophytic fungi of Citrus aurantium

Although <i>Citrus aurantium</i> has enormous medicinal and ecological value in southern China, little research has been conducted into the composition and functions of endophytic fungi in it. To better explore the characteristics of the endophytic fungal community in <i>C. auranti</i><i>um</i>, ITS rRNA gene analyses were used to characterize the endophytic fungal microbiome across three plant compartments and three regions. The results showed that a total of 12 109 OTUs were obtained and further divided into 15 phyla and 768 genera. Ascomycota was the dominant phylum. <i>Fusarium, Alternaria, Mortierella, Plectosphaerella, Cladosporium, Colletotrichum, Trichomerium, Botryotrichum</i>, and <i>Aspergillus</i> were the dominant genera. The endemic and dominant genera of endophytic fungi in <i>C. aurantium</i> exhibited plant compartment specificity. The assembly of endophytic fungal communities was dominated by homogeneous selection of deterministic processes. The endophytic fungal genera of <i>C. aurantium</i> predominantly exhibited positive interactions (with a proportion > 99%). The dominant functions of endophytic fungi in <i>C. aurantium</i> were pathotroph and saprotroph. The composition (niche: <i>R</i>²= 0.09, <i>P</i> = 0.001; site: <i>R</i>²= 0.06, <i>P</i> = 0.021) and functional components (niche: <i>R</i>²= 0.117, <i>P</i> = 0.002; site: <i>R</i>²= 0.122, <i>P</i> = 0.006) exhibited significant plant compartment and region specificity. The results of this study reveal the characteristics of the endophytic fungal community of <i>C. aurantium</i>, and provide a theoretical reference for the further development and utilization of endophytic fungal resources.