Soil Nutrients and Host Filtering Jointly Shape Distinct Endophytic Bacterial Assemblages in Tropical Island Shrubs Across the South China Sea

Archipelagos in extreme climates offer ideal systems for studying species adaptations to harsh environments. Previously, properties of island soil microbial communities such as structures, diversities, and functions were under the main attentions. Nevertheless, how island edaphic properties shape endophytic bacterial assemblages in native shrubs and how these bacterial communities differentiate across neighboring islands remain poorly understood. In this study, we used high-throughput amplicon sequencing to investigate root endophytic bacterial communities in three dominant shrub species (Scaevola taccada, Guettarda speciosa, and Tournefortia argentea) across six islands of the South China Sea. Results revealed that host species and soil chemical composition such as organic carbon, nitrate nitrogen, and available phosphorus were the mutual factors shaping the structures of the bacterial communities. G. speciosa and T. argentea exhibited a higher α-diversity index than S. taccada. The bacterial phyla Proteobacteria and Actinobacteriota were dominant in all three shrubs. The distance between islands showed a negative effect on Bray–Curtis similarity of the endophytic bacterial communities in G. speciosa and T. argentea roots. Importantly, deterministic processes (82.53%–91.63%), particularly homogeneous selection, governed community assembly. The β-nearest taxon index trends differed between S. taccada (decreasing with distance) and G. speciosa (increasing with distance). The co-occurrence networks indicated greater stability in S. taccada bacterial communities than in other host species. These findings advance the understanding of how host plants, island edaphic factors, and spatial distances influence root-associated microbiome characteristics, offering insights for predicting shrub–microbe interactions under future biogeographical changes and guiding the conservation of fragile island ecosystems.