Multi-omics reveals the involvement of endophytes in the growth of Moso bamboo (Phyllostachys edulis) shoots

Moso bamboo (Phyllostachys edulis) exhibits extraordinary speed of growth. While its anatomical and hormonal features have been well studied, the contribution of microbial interactions to its rapid growth remains largely unknown. Here, we integrated 16S rRNA and ITS amplicon sequencing, phytohormone measurements, and root transcriptome analysis across four developmental stages and three plant compartments (shoot top, shoot bottom, and root). We show that microbial diversity and network complexity were strongly shaped by tissue type and developmental stage, with early-stage roots and shoot meristems exhibiting strong immune filtering and later stages showing a marked increase in diversity. Network analysis revealed highly complex microbial associations in nutrient-limited shoot tops during dormancy, suggesting influenced cooperation among endophytes. In roots, hormone levels were tightly correlated with microbial dynamics, and transcriptome analysis identified 153 hormone-related genes that are differentially expressed across developmental stages, including stage-specific activation of AUX/IAA and SAUR families. A plant-microbe-hormone interaction network highlighted associations between auxin-related genes and growth-promoting genera such as Paenibacillus. Together, these findings reveal that endophytes likely modulate hormone signaling to facilitate rapid shoot elongation, providing insights into the unique developmental program of Moso bamboo.