Endophytic Microbial Community Structure and Dynamics Influence Agarwood Formation in Aquilaria malaccensis Lam

Aquilaria malaccensis Lam., an Agarwood-producing tree native to Southeast Asia, secretes oleoresin, a resin with diverse applications, in response to injuries. To explore the role of endosphere microbial communities during Agarwood development, we utilized a metagenomics approach across three stages: non-symptomatic (NC), symptomatic early (IN), and symptomatic mature (IN1). The NC metagenome was dominated by Bacillus (19.15%), Klebsiella (13.25%), and Pantoea (12.46%) among bacteria and Saccharomyces (15.92%) among fungi. Notably, bacterial chemotaxis pathway genes were more prevalent in NC (2.14%) compared to IN (0.92%) and IN1 (1.16%), suggesting microbial chemotactic behavior. In the IN stage, Klebsiella (27.05%) and Saccharomyces (34.81%) were the dominant genera. The IN1 metagenome featured Pantoea (8.92%) and Neurospora (8.24%) as leading bacterial and fungal genera, respectively. Functional genes associated with defense mechanisms, lipid transport, and secondary metabolite biosynthesis were increasingly represented in IN1, indicating an enhanced microbial response as infection progresses. Ecological indices, including a high Shannon-Wiener index (H' = 4.467) and Simpson's dominance (1 - D = 0.9697), alongside Pielou's evenness index (J = 0.7034), highlighted a dynamic and diverse microbial community at the mature infection stage, reflecting the complex interactions within the Aquilaria endosphere during Agarwood formation.