Diversity, function and assembly of the Trifolium repens L. root-associated microbiome under lead stress

• Published in: Journal of hazardous materials 2022-09, Vol.438, p.129510-129510, Article 129510
• Main Authors: Wang, Lei, Gong, Li, Gan, Deping, Li, Xinying, Yao, Jiaxuan, Qu, Jianhua, Cong, Jingmin, Zhang, Ying
• Format: Article
• Language: English
• Subjects: Heavy metal; Microbial interactions; Phytoremediation; Root endosphere; T. repens
• ISSN: 0304-3894; 1873-3336
• DOI: 10.1016/j.jhazmat.2022.129510

Root-associated microbial layers provide unique niches that drive specific microbe assemblies. While the rhizosphere microbiome has long received much attention, endophytic microbes remain largely elusive. Characterizing metal-tolerant plants’ strategies for assembling different root-associated microbial layers is important for optimizing phytoremediation. Here, a pre-stratified rhizo-box assay was conducted with Trifolium repens L. under greenhouse conditions with artificial Pb-contaminated soil. Cultivation compensated for the pollution-driven loss of soil microbial biomass carbon, enzyme activities and abundance. The acid-soluble Pb proportion increased in the rhizosphere (from 6.5–13.7% to 7.1–18.0%) compared with bulk soil. Under stress, root-layer variants were a considerable source of variation in the microbiome, with the endosphere representing a unique and independent niche. A core set of root microbes were selected by T. repens, with Proteobacteria and Actinobacteria composed of diverse plant-growth-promoting bacteria (PGPBs) and metal-tolerant members. Cluster analysis revealed endosphere-enriched genera, with Rhizobium, Nocardioides, Novosphingobium, Phyllobacterium, and Sphingomonas being the most dominant. Finally, inferred microbial metabolic pathways suggested that these potential metal-tolerant PGPB species provide critical services to hosts, enabling them to tolerate and even flourish in contaminated soil. Our results provide novel insights for understanding how root-associated microbes help metal-tolerant plants cope with abiotic stress. [Display omitted] •Cultivation of T. repens rejuvenates the performance of Pb-contaminated soil.•Rejuvenation relies on changes to interaction with microbes, not Pb immobilization.•Root-associated compartments showed a specific degree of niche specificity.•A core-root microbiome referred to as metal-tolerant PGPB is selected by T. repens.