Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Rapid impact of phenanthrene and arsenic on bacterial community structure and activities in sand batches.

The impact of both organic and inorganic pollution on the structure of soil microbial communities is poorly documented. A short-time batch experiment (6 days) was conducted to study the impact of both types of pollutants on the taxonomic, metabolic and functional diversity of soil bacteria. For this purpose sand spiked with phenanthrene (500 mg kg(-1) sand) or arsenic (arsenite 0.66 mM and arsenate 12.5 mM) was supplemented with artificial root exudates and was inoculated with bacteria originated from an aged PAH and heavy-metal-polluted soil. The bacterial community was characterised using bacterial strain isolation, TTGE fingerprinting and proteomics. Without pollutant, or with phenanthrene or arsenic, there were no significant differences in the abundance of bacteria and the communities were dominated by Pseudomonas and Paenibacillus genera. However, at the concentrations used, both phenanthrene or arsenic were toxic as shown by the decrease in mineralisation activities. Using community-level physiological profiles (Biolog Ecoplates™) or differential proteomics, we observed that the pollutants had an impact on the community physiology, in particular phenanthrene induced a general cellular stress response with changes in the central metabolism and membrane protein synthesis. Real-time PCR quantification of functional genes and transcripts revealed that arsenic induced the transcription of functional arsenic resistance and speciation genes (arsB, ACR3 and aioA), while no transcription of PAH-degradation genes (PAH-dioxygenase and catechol-dioxygenase) was detected with phenanthrene. Altogether, in our tested conditions, pollutants do not have a major effect on community abundance or taxonomic composition but rather have an impact on metabolic and functional bacterial properties.

Low effect of phenanthrene bioaccessibility on its biodegradation in diffusely contaminated soil.

This study focused on the role of bioaccessibility in the phenanthrene (PHE) biodegradation in diffusely contaminated soil, by combining chemical and microbiological approaches. First, we determined PHE dissipation rates and PHE sorption/desorption isotherms for two soils (PPY and Pv) presenting similar chronic PAH contamination, but different physico-chemical properties. Our results revealed that the PHE dissipation rate was significantly higher in the Pv soil compared to the PPY soil, while PHE sorption/desorption isotherms were similar. Interestingly, increases of PHE desorption and potentially of PHE bioaccessibility were observed for both soils when adding rhamnolipids (biosurfactants produced by Pseudomonas aeruginosa). Second, using 13C-PHE incubated in the same soils, we analyzed the PHE degrading bacterial communities. The combination of stable isotope probing (DNA-SIP) and 16S rRNA gene pyrosequencing revealed that Betaproteobacteria were the main PHE degraders in the Pv soil, while a higher bacterial diversity (Alpha-, Beta-, Gammaproteobacteria and Actinobacteria) was involved in PHE degradation in the PPY soil. The amendment of biosurfactants commonly used in biostimulation methods (i.e. rhamnolipids) to the two soils clearly modified the PHE sorption/desorption isotherms, but had no significant impact on PHE degradation rates and PHE-degraders identity. These results demonstrated that increasing the bioaccessibility of PHE has a low impact on its degradation and on the functional populations involved in this degradation.

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities.

The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.

Oxidation of a PAH polluted soil using modified Fenton reaction in unsaturated condition affects biological and physico-chemical properties.

A batch experiment was conducted to assess the impact of chemical oxidation using modified Fenton reaction on PAH content and on physico-chemical and biological parameters of an industrial PAH contaminated soil in unsaturated condition. Two levels of oxidant (H(2)O(2), 6 and 65 g kg(-1)) and FeSO(4) were applied. Agronomic parameters, bacterial and fungal density, microbial activity, seed germination and ryegrass growth were assessed. Partial removal of PAHs (14% and 22%) was obtained with the addition of oxidant. The impact of chemical oxidation on PAH removal and soil physico-chemical and biological parameters differed depending on the level of reagent. The treatment with the highest concentration of oxidant decreased soil pH, cation exchange capacity and extractable phosphorus content. Bacterial, fungal, and PAH degrading bacteria densities were also lower in oxidized soil. However a rebound of microbial populations and an increased microbial activity in oxidized soil were measured after 5 weeks of incubation. Plant growth on soil treated by the highest level of oxidant was negatively affected.

In situ assessment of phytotechnologies for multicontaminated soil management.

Due to human activities, large volumes of soils are contaminated with organic pollutants such as polycyclic aromatic hydrocarbons, and very often by metallic pollutants as well. Multipolluted soils are therefore a key concern for remediation. This work presents a long-term evaluation of the fate and environmental impact of the organic and metallic contaminants of an industrially polluted soil under natural and plant-assisted conditions. A field trial was followed for four years according to six treatments in four replicates: unplanted, planted with alfalfa with or without mycorrhizal inoculation, planted with Noccaea caerulescens, naturally colonized by indigenous plants, and thermally treated soil planted with alfalfa. Leaching water volumes and composition, PAH concentrations in soil and solutions, soil fauna and microbial diversity, soil and solution toxicity using standardized bioassays, plant biomass, mycorrhizal colonization, were monitored. Results showed that plant cover alone did not affect total contaminant concentrations in soil. However, it was most efficient in improving the contamination impact on the environment and in increasing the biological diversity. Leaching water quality remained an issue because of its high toxicity shown by micro-algae testing. In this matter, prior treatment of the soil by thermal desorption proved to be the only effective treatment.

Water and phosphorus content affect PAH dissipation in spiked soil planted with mycorrhizal alfalfa and tall fescue.

Polycyclic aromatic hydrocarbon (PAH) dissipation efficiency can be increased in the plant rhizosphere, but may be affected by various environmental factors. We investigated the effects of the watering regime and phosphorus concentration on PAH dissipation in the rhizosphere of mycorrhizal plants in a pot experiment. Two plant species, alfalfa (Medicago sativa) and tall fescue (Festuca arundinacea), were co-cultured and inoculated with an arbuscular mycorrhizal (AM) fungus (Glomus intraradices) in PAH (phenanthrene (PHE)=500 mg kg(-1), pyrene (PYR)=500 mg kg(-1), dibenzo(a,h)anthracene (DBA)=65 mg kg(-1)) spiked agricultural soil for 6 weeks. Treatments with different phosphorus concentrations and watering regimes were compared. The PHE dissipation reached 90% in all treatments and was not affected by the treatments. The major finding was the significant positive impact of mycorrhizal plants on the dissipation of high molecular weight PAH (DBA) in high-water low-phosphorus treatment. Such an effect was not observed in high-water high-phosphorus and low-water low-phosphorus treatments, where AM colonization was very low. A positive linear relationship was detected between PYR dissipation and the percentage of Gram-positive PAH-ring hydroxylating dioxygenase genes in high-water high-phosphorus treatments, but not in the other two treatments with lower phosphorus concentrations and water contents. Such results indicated that the phosphorus and water regime were important parameters for the dissipation of HMW-PAH.