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

## TL;DR

This study shows how the root microbiome of pine seedlings shifts toward slower-growing bacteria as the plants develop, affecting forest ecosystem stability.

## Contribution

The study reveals how bacterial growth strategies in pine seedling roots change over time, independent of nitrogen availability.

## Key findings

- Root-associated bacteria show increased genome size and decreased ribosomal RNA operon copy number, indicating a shift to slow-growth strategies.
- Later-colonizing bacteria like Bradyrhizobium are nitrogen-insensitive, while early colonizers like Herbaspirillum are nitrogen-sensitive.
- Discrepancies exist between predicted nitrogen fixation and actual nifH gene measurements, highlighting limitations in functional predictions.

## Abstract

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.