Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps.

Industrial waste dumps are rarely colonized by vegetation after they have been abandoned, indicating biological infertility. Revegetation of industrial tailings dumps is thus necessary to prevent wind erosion, metal leaching and has been shown to restore soil functions and ecosystem services. However, little is known about the microbial colonization and community structure of vegetated tailings following the application of restoration technologies. In this study, we investigated the rhizosphere and phyllosphere bacterial communities of a poplar tree plantation within a phytomanagement-based restoration program of a Hg-contaminated site. We used Illumina-based sequencing combined with culture-dependent approaches to describe plant-associated bacterial communities and to isolate growth-promoting bacteria (PGPB) and Hg-resistant bacteria. The genus Streptomyces was highly specific to the root community, accounting for 24.4% of the relative abundance but only representing 0.8% of the soil community, whereas OTUs from the Chloroflexi phylum were essentially detected in the soil community. Aboveground habitats were dominated by bacteria from the Deinococcus-Thermus phylum, which were not detected in belowground habitats. Leaf and stem habitats were characterized by several dominant OTUs, such as those from the phylum Firmicutes in the stems or from the genera Methylobacterium, Kineococcus, Sphingomonas and Hymenobacter in the leaves. Belowground habitats hosted more cultivable Hg-resistant bacteria than aboveground habitats and more Hg-resistant bacteria were found on the episphere than in endospheric habitats. Hg-resistant isolates exhibiting plant growth-promoting (PGP) traits, when used as inoculants of Capsicum annuum, were shown to increase its root dry biomass but not Hg concentration. The N-fixing and Hg-resistant species Pseudomonas graminis, observed in the poplar phyllosphere, may be a key microorganism for the restoration of industrial tailings dumps.