Niche-driven microbial assembly across the soil-root continuum of Casuarina equisetifolia under a heavy metal pollution gradient.

Abstract

Heavy metal pollution (HMP) threatens soil ecosystems and plant health. This study integrated 16S rRNA sequencing, network analysis, environmental mapping, and bacterial isolation to investigate how distinct ecological niches of Casuarina equisetifolia modulate microbial communities under metal stress. Results revealed a spatial pollution gradient, with Pb²⁺, Zn²⁺, and Cd²⁺ decreasing with distance from the mine, while As⁵⁺, Cr³ ⁺, and Ni²⁺ remained near background levels but displayed significant niche-dependent enrichment, especially for Cr³ ⁺, and Ni²⁺ in rhizosphere soil under medium and high pollution. Niche was the primary driver of microbial divergence, with only 0.56% of OTUs shared between the soil and root compartments. Rhizosphere soils harbored more unique OTUs and higher α-diversity than non-rhizosphere soils. Root endosphere and rhizosphere soil communities were consistently dominated by Actinobacteria across all pollution levels, whereas non-rhizosphere soil communities shifted from Proteobacteria (low pollution) to Actinobacteria (medium) and Chloroflexi (high). LEfSe identified niche-specific biomarkers from the phylum to genus levels, with high-pollution roots harboring the most diverse indicators. Heavy metals and soil properties (pH, CEC, and SOM) collectively shaped community assembly, with distinct drivers per niche: CEC and Enterobacter in non-rhizosphere soil, pH and Acidobacteriales in rhizosphere soil, and Zn as the central hub in the root endosphere network. Isolation yielded 63 metal-tolerant strains across eight genera, predominantly Bacillus cereus sensu lato group, whose niche origin shifted from the rhizosphere (low pollution) to the non-rhizosphere (medium) to the roots (high pollution), suggesting pollution-associated enrichment. These findings reveal niche-specific community assembly and pollution-driven enrichment of metal-tolerant Bacillus cereus s.l. in the root endosphere.