Integrated metabolomic and transcriptomic analysis unveils the molecular mechanism of tobacco growth promotion mediated by endophytic fungi

Climate change and long-term monoculture cropping have caused a continuous reduction in tobacco production. Plant endophytic fungal fertilizer has been widely used for crop cultivation and management; however, its application in tobacco cultivation remains rare in China. In this study, a total of 317 endophytic fungi were isolated and characterized from two main flue-cured tobacco cultivars (Yunyan 87 and K326), comprising 63 species across 32 genera (Yunyan 87) and 104 species across 33 genera (K326), respectively. Five endophytic fungi were finally screened and exhibited a significant growth-promoting effect after inoculating seedlings of four tobacco varieties. The molecular mechanisms of the most potent endophytic fungi, Fusarium oxysporum , Aspergillus terrestris , and Cladosporium tenuissimum , were further investigated. The results showed that these fungi regulated indole-3-acetic acid (IAA) biosynthesis by enhancing the conversion of 3-indoleacetamide (IAM) into IAA while inhibiting the conversion of IAA into IAA-aspartate (IAA-Asp). qRT-PCR analysis revealed that the relative expression levels of AMI1 and FAAH were up-regulated, whereas that of GH3.1 was down-regulated following fungal treatment. This study highlights the molecular mechanism and potential application of endophytic fungi as microbial fertilizers in the tobacco cultivation industry. • A total of 317 endophytic fungi were isolated and identified from two main flue-cured tobacco varieties in China. • Five strains of endophytic fungi significantly promoted the growth of four major cultivated tobacco varieties. • These fungi can enhance the conversion of IAM into IAA, while inhibiting the conversion of IAA into IAA-Asp.