Root microbiome dynamics favor slow-growth strategies during Pinus seedling development

Microbial functional trait dynamics during seedling development-a critical yet underexplored driver of forest ecosystem establish, develop, and stability-remain poorly understood. We investigated bacterial genomic traits dynamics in subtropical Pinus massoniana seedlings over a growing season. Leaf-associated bacteria showed minimal temporal shifts, whereas root-associated bacteria exhibited pronounced trends: average genome size increased (independent of nitrogen addition), whereas ribosomal RNA operon copy number (RRN) declined under ambient nitrogen, indicating a transition from fast-growing to slow-growing strategies. These trajectories reflect the differential turnover of later, nitrogen-insensitive taxa (e.g. large-genome, low-RRN Bradyrhizobium) relative to earlier, nitrogen-sensitive taxa (e.g. small-genome, high-RRN Herbaspirillum) during colonization and establishment from an aerial source onto a developing host. Additionally, we detected a discrepancy between the temporal dynamics of predicted nitrogen fixation potential and quantitative real-time PCR-based nifH quantification, underscoring the need for caution when interpreting prediction-based functional potentials. These findings identify trait-mediated assembly as a key driver of early root microbiome dynamics in pine seedlings and highlight the need for temporally resolved, ground-truthed functional inference when predicting ecosystem processes.