# Developmental Stage-Driven Niche Differentiation and Assembly of Rhizosphere and Endophytic Bacterial Communities in Helianthus annuus Under Saline–Alkaline Stress

## TL;DR

This study explores how sunflower root and soil bacterial communities change during plant development under saline-alkaline stress, revealing distinct assembly patterns and potential for agricultural applications.

## Contribution

The study reveals stage-dependent assembly dynamics and functional shifts in sunflower root microbiomes under saline-alkaline stress.

## Key findings

- Rhizosphere communities showed higher diversity and complex interaction networks compared to root endosphere communities.
- Endophytic bacterial communities progressively converged toward a Proteobacteria-dominated core, especially Pseudomonas, during plant development.
- Functional predictions indicated enhanced nitrogen-related metabolic potential during flowering, linked to Pseudomonas enrichment.

## Abstract

Soil salinization severely constrains agricultural productivity, while root-associated microbiota contribute to plant adaptation to saline–alkali stress. However, developmental assembly dynamics of rhizosphere and root endosphere bacterial communities remain insufficiently characterized in irrigation-driven saline–alkali agroecosystems such as the Hetao Plain of northern China. Here, Helianthus annuus plants were sampled at seedling, squaring, and flowering stages, and rhizosphere and root microbiota were analyzed using high-throughput amplicon sequencing integrated with soil physicochemical measurements, beta nearest taxon index–based community assembly inference, and co-occurrence network analysis. The rhizosphere maintained higher diversity, broader taxonomic heterogeneity, and persistently complex interaction networks, whereas the root endosphere exhibited progressive diversity reduction and compositional convergence during plant development. Developmental progression drove contrasting successional trajectories, with increasing rhizosphere complexity and endophytic convergence toward a Proteobacteria-dominated core, particularly Pseudomonas. Beta nearest taxon index analysis indicated mixed stochastic and dispersal-related processes in the rhizosphere but drift-dominated assembly in late-stage roots. Functional predictions revealed enhanced nitrogen-related metabolic potential during flowering, coinciding with enrichment and network centrality of Pseudomonas. These findings demonstrate stage-dependent spatial reorganization of sunflower root microbiomes under saline–alkali stress and provide a framework for identifying functionally relevant microbial groups for targeted microbiome-based agricultural management.