Beneficial traits of root endophytes and rhizobacteria associated with plants growing in phytomanaged soils with mixed trace metal-polycyclic aromatic hydrocarbon contamination.

The diversity of cultivable bacteria associated with plants from phytomanaged soils with mixed trace metal (TM) and polycyclic aromatic hydrocarbon (PAH) contamination in Pierrelaye (France) was evaluated. The emphasis was on the cultivable bacterial community since the overall objective is to obtain inoculants to improve the remediation of this type of contaminated site. Root endophytic and rhizosphere soil bacterial counts were determined, and isolates were pooled by amplified rDNA restriction analysis and identified by 16S rDNA sequencing. Isolates were further characterized for the production of plant growth-promoting (PGP) substances, and resistance to TM. The selected strains were evaluated for their ability to degrade PAHs. The potential of cell-free microbial supernatant to increase the mobilisation of PAHs from the polluted soil of Pierrelaye was also evaluated. Proteobacteria and Actinobacteria dominated the collection of isolates, and differences in taxonomic diversity were observed between plant species (Populus or Zea mays) and depending on the remediation treatment (Populus inoculation with mycorrhizae or Populus intercropping with Alnus). The majority of isolates exhibited at least one of the tested PGP traits, as well as resistance to more than one TM. Several rhizosphere, endophyte and even one bulk soil isolate showed high rates of fluoranthene and pyrene reduction. The endophyte Rhizobium strain MR28 isolated from maize and degrading pyrene produced bioemulsifying molecules capable of improving the availability of PAHs from the soil of Pierrelaye. A selection of the most interesting strains was made for further re-inoculation experiments in order to assess their potential in rhizoremediation processes.

Pioneer trees of Betula pendula at a red gypsum landfill harbour specific structure and composition of root-associated microbial communities.

The study of root-associated microbial communities is important to understand the natural processes involved in plant recolonisation at degraded areas. Root associated bacterial and fungal communities of woody species colonising a red gypsum landfill (a metal-enriched environment) were characterised through metabarcoding. Among trees naturally growing on the landfill, Betula pendula is the only tree species in the centre of the area, whereas companion tree species such as Populus nigra, P. tremula and Salix purpurea were present on the edges. The bacterial community was dominated by Proteobacteria (38%), Actinobacteria (35%) and Bacteroidetes (20%) and the most abundant bacterial OTU belonged to the family Streptomycetaceae. The fungal community was dominated by Ascomycota (60%) and Basidiomycota (30%) and the most abundant family was Pyronemataceae. Analysis of similarities, heatmap and hierarchical cluster analysis showed that B. pendula grown in the centre of the landfill harboured a specific microbial community, which was unique and different, not only from other tree species (Populus or Salix spp.), but also from other B. pendula growing at the edges. Our findings on relevant indicator OTUs associated to the birches located in the centre of the landfill (such as Otu00716 Catellatospora sp. (family Micromonosporaceae, phylum Actinobacteria) or Otu4_35502 Russula sp. (family Russulaceae, phylum Basidiomycota)) may have important implications for the successful revegetation of these harsh environments using microbial-based phytostabilisation approaches.

Streptomyces Dominate the Soil Under Betula Trees That Have Naturally Colonized a Red Gypsum Landfill.

The successful restoration of well-engineered tailings storage facilities is needed to avoid mine tailings problems. This study characterized the bacterial communities from vegetated and non-vegetated soils from a red gypsum landfill resulting from the industrial extraction of titanium. A set of 275 bacteria was isolated from vegetated soil and non-vegetated soil areas and taxonomically characterized using BOX-PCR. The study also evaluated the ability of a subset of 88 isolated bacteria on their ability to produce plant growth promoting (PGP) traits [indoleacetic acid (IAA) production, phosphate solubilization, and siderophore production] and their tolerance to potentially toxic elements (PTEs). Twenty strains were chosen for further analysis to produce inoculum for birch-challenging experiments. Principal component analysis (PCA) showed that the set of pedological parameters (pH, granulometry, carbon, organic matter, and Mg content) alone explained approximately 40% of the differences between the two soils. The highest density of total culturable bacteria was found in the vegetated soil, and it was much higher than that in the non-vegetated soil. The Actinobacteria phyla dominated the culturable soil community (70% in vegetated soil and 95% in non-vegetated soil), while the phyla Firmicutes (including the genus Bacillus) and Bacteroides (including the genera Pedobacter and Olivibacter) were found only in the vegetated soil fraction. Additional genera (Rhizobium, Variovorax, and Ensifer) were found solely in the vegetated soil. The vegetated soil bacteria harbored the most beneficial PGP bacteria with 12% of the isolates showing three or more PGP traits. The strains with higher metal tolerances in our study were Phyllobacterium sp. WR140 (RO1.15), Phyllobacterium sp. WR140 (R01.34), and Streptomyces sp. (R04.15), all isolated from the vegetated soil. Among the isolates tested in challenging experiments, Phyllobacterium (R01.34) and Streptomyces sp. (R05.33) have the greatest potential to act as PGP rhizobacteria and therefore to be used in the biological restoration of tailings dumps.

Bacterial diversity associated with poplar trees grown on a Hg-contaminated site: Community characterization and isolation of Hg-resistant plant growth-promoting bacteria.

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 N2-fixing and Hg-resistant species Pseudomonas graminis, observed in the poplar phyllosphere, may be a key microorganism for the restoration of industrial tailings dumps.

Agronomic Practices for Improving Gentle Remediation of Trace Element-Contaminated Soils.

The last few decades have seen the rise of Gentle soil Remediation Options (GRO), which notably include in situ contaminant stabilization ("inactivation") and plant-based (generally termed "phytoremediation") options. For trace element (TE)-contaminated sites, GRO aim to either decrease their labile pool and/or total content in the soil, thereby reducing related pollutant linkages. Much research has been dedicated to the screening and selection of TE-tolerant plant species and genotypes for application in GRO. However, the number of field trials demonstrating successful GRO remains well below the number of studies carried out at a greenhouse level. The move from greenhouse to field conditions requires incorporating agronomical knowledge into the remediation process and the ecological restoration of ecosystem services. This review summarizes agronomic practices against their demonstrated or potential positive effect on GRO performance, including plant selection, soil management practices, crop rotation, short rotation coppice, intercropping/row cropping, planting methods and plant densities, harvest and fertilization management, pest and weed control and irrigation management. Potentially negative effects of GRO, e.g., the introduction of potentially invasive species, are also discussed. Lessons learnt from long-term European field case sites are given for aiding the choice of appropriate management practices and plant species.