Soil heavy metals and phytoremediation by Populus deltoides alter the structure and function of bacterial community in mine ecosystems

Despite the fact that microbes act as key indicators of soil heavy metal (HMs) toxicity, their variations and adaptation to the long-term HMs pollution in mine ecosystems, particularly field study knowledge of the effects of phytoremediation, remain insufficient. A comparative study on microbiota of the rhizosphere and endosphere of Populus deltoides and their structural and functional variations in response to composite HMs pollution was conducted. Results suggested that habitat niche was the driving force in shaping bacterial composition as shown by distinctive niche differentiation of 48 core species. Among all factors, HM explained 43% of the bacterial variability that constituted the key determinant for all microbiota structures. Further redundancy analysis revealed Cd and Pb were the main drivers of soil microbiota distribution, while none of HMs significantly affected the structure of endophytes. The responses of microbiota to HM stress varied in different habitats. The diversity (Shannon) and richness (Chao) of bare soil (CS) was significantly deteriorated by HM, but richness of rhizosphere (CRS) was greatly increased than CS, indicating the beneficial effects of phytoremediation to bacterial composition. Functional genes were also enriched in contaminated samples related to multiple cell defence mechanisms including extracellular binding, transmembrane transport, and antioxidant protection. Metabolic pathways related to plant signaling compounds and energy-rich nucleotides were enriched in endophytes, inferring the potential for stress protection and plant growth promotion. This study indicated that shifts of microbial organization and function strengthened their HM stress adaptability; plant associated microbiome contributed to the phytoremediation efficiency, which could provide the basis for soil evaluation after phytoremediation and further exploration of host-microbe interactions in mine ecosystems.