Structural development and assembly patterns of the root-associated microbiomes during phytoremediation

Highlights: • Root-associated microbiomes assemble specifically during phytoremediation. • A core root microbiome is selected by the metal-tolerant plant H. cannabinus. • Metal-tolerant PGPB species are keystone members in the metal-contaminated soil. Successful in situ phytoremediation depends on beneficial interactions between roots and microbes. However, the assembly strategies of root-associated microbiome during phytoremediation are not well known. Here we investigated the assembly patterns of root-associated microbiomes during phytoremediation as well as its regulation by both plants and heavy metals. Plant cultivation and soil amendment increased microbial diversity and restructured microbial communities. Rhizo-compartmentalization was the largest source of variation in root-associated microbiomes, with endosphere being the most independent and exclusive compartment. Soil type explained a larger amount of microbiomes variation in bulk soil and rhizosphere than that in endosphere. A specific core root microbiome was likely to be selected by the metal-tolerant plant H. cannabinus, with Enterobacteriaceae, Pseudomonadaceae and Comamonadaceae which contain a large number of metal-tolerant and plant growth-promoting bacteria (PGPB) being the most abundant families. The root-associated microbial community tended to proceed a niche-assembled patterns and formed a smaller bacterial pool dominant by Proteobacteria, Actinobacteria and Chloroflexi under metal-contaminated conditions. Among these genera, potential metal-tolerant PGPB species have taken up the keystone positions in the microbial co-occurrence networks, revealing their key roles in metal-contaminated environment due to niche selection. We also detected a keystone functional group reducing metal bioavailability which might work as vanguards and devote to maintaining the structure and function of the whole microbial community. In conclusion, this study suggested a specific assembly pattern of root-associated microbiomes of the metal-tolerant plant H. cannabinus during phytoremediation, showing the directional selections of the associated microbiomes by both the plant and metal-contaminated conditions in such a system.