Root-Associated Bacterial Community Assembly and Functional Divergence of Four Native Halophytes in the Yellow River...

Coastal salt-marsh wetlands sustain diverse native halophytes whose root-associated microbiomes mediate plant adaptation to saline-alkaline environments. Host filtering and niche differentiation between rhizosphere soil and root endosphere jointly shape bacterial community assembly, yet comparative information for co-existing native halophytes in the northern Yellow River Delta remains limited. Here, we collected 80 rhizosphere soil and root tissue samples from replicated plots in the Binzhou coastal salt-marsh wetland (northern Yellow River Delta), and applied Illumina MiSeq 16S rRNA sequencing to compare bacterial communities of four native pioneer halophytes (Phragmites australis, Suaeda salsa, Tamarix chinensis, Cynanchum chinense). Rhizosphere soils had markedly higher alpha diversity than root endospheres, with C. chinense rhizosphere reaching the highest diversity; Proteobacteria dominated roots, whereas Actinobacteriota, Bacteroidota and Chloroflexi accumulated in rhizosphere habitats. Root bacterial communities displayed greater interspecific divergence, and rhizospheres of S. salsa and P. australis possessed enhanced nitrogen metabolism and hydrocarbon degradation. LEfSe identified host-specific biomarkers, and Chloroflexi Subgroup_10 functioned as a core hub whereas no shared keystone genus existed across root endosphere networks, underscoring stronger host filtering in endophytic habitats. This study advances our understanding of host-driven bacterial assembly of native halophytes and provides baseline references for microbiome-assisted wetland restoration in the northern Yellow River Delta.