Integrating Multiple Omics Identifies Phaeoacremonium rubrigenum Acting as Aquilaria sinensis Marker Fungus to Promote Agarwood Sesquiterpene Accumulation by Inducing Plant Host Phosphorylation

The present study aimed to explore the factors that promote persistent agarwood accumulation. To this end, we first investigated the morphological changes and volatile compound distribution in five layers of “Guan Xiang” agarwood. The agarwood-normal transition layer (TL), an essential layer of persistent agarwood accumulation, showed clear metabolic differences by microscopy and GC-MS analysis. Microbiome analysis revealed that Phaeocremonium rubrigenum was the predominant biomarker fungus in the TL of “Guan Xiang” agarwood samples. Among the seven isolated fungi, P. rubrigenum exhibited a significantly heightened ability to induce the production in Aquilaria sinensis seedlings, especially for sesquiterpene. Tracing the proteome profile changes in P. rubrigenum-induced A. sinensis calli for 18 ds showed that the fungus-induced sesquiterpene biosynthesis increased mainly through the mevalonate (MVA) pathway. Specifically, the phosphorylation modification level, instead of the protein abundance of transcription factors (TFs), showed corresponding changes during sesquiterpene biosynthesis, thus indicating that induced phosphorylation is the key reason for enhanced sesquiterpene production. IMPORTANCE Agarwood is an expensive resinous portion derived from Aquilaria plants and has been widely used as medicine, incense, and perfume. The factors involved in steady agarwood accumulation remain elusive. Our current study suggests that as a TL marker fungus, P. rubrigenum could persistently promote agarwood sesquiterpene accumulation by inducing phosphorylation of the TFs-MVA network in A. sinensis. Moreover, our work provides strategies to improve agarwood industry management and sheds light on the potential molecular mechanisms of plant adaptation to native microbial conditions.