Acid mine drainage (AMD) is considered as one of the most important global environmental challenges. Therefore, understanding the impact of AMD on the diversity of microbial communities associated with native plants is important for phytoremediation. In this study, the community assembly and microbial diversity associated with native plants growing along an AMD impact gradient was investigated using metabarcoding and high throughput iChip technique. The study revealed that across both domains of bacteria and fungi, richness and species diversity decreased according to AMD impact. Bacterial species diversity was more stratified according to the pH gradient than fungi, and the AMD impact on the plant-associated microbial diversity decreased towards the plant roots. The microbial community composition of the undisturbed site was significantly different from the AMD impacted sites, and the communities in the AMD impacted sites were further stratified according to the degree of impact. The overall microbial diversity was mediated by the AMD impact, niche differences and plant species differences. Dispersal limitation was the most important community assembly process in the undisturbed site, while the homogenous selection of Burkholderia, Actinospica, Puia and Bradyrhizobium increased along the AMD impact gradient. Differential abundance analysis further revealed that Umbelopsis, Burkholderia and Sphingomonas were among the biomarkers of the AMD impacted sites. Several strains of some of these responsive genera were subsequently isolated using the iChip. Overall, this study presents novel insight into the ecology of plant-associated microbial communities that are relevant for environmental monitoring and for enhancing the revegetation of AMD impacted sites.
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