Transfer of La, Ce, Sm and Yb to alfalfa and ryegrass from spiked soil and the role of Funneliformis mosseae

Rare earth elements (REEs) are widely used in high-tech industries, and REE waste emissions have become a concern for ecosystems, food quality and human beings. Arbuscular mycorrhizal fungi (AMF) have repeatedly been reported to alleviate plant stress in metal-contaminated soils. To date, little information is available concerning the role of AMF in REE-contaminated soils. We recently showed that there was no transfer of Sm to alfalfa by Funneliformis mosseae, but only a single REE was examined, while light and heavy REEs are present in contaminated soils. To understand the role of AMF on the transfer of REEs to plants, we carried out an experiment using alfalfa (Medicago sativa) and ryegrass (Lolium perenne) in compartmented pots with separate bottom compartments that only were accessible by F. mosseae fungal hyphae. The bottom compartments contained a mixture of four REEs at equal concentrations (La, Ce, Sm and Yb). The concentration of REEs in plants was higher in roots than in shoots with higher REE soil-root than root-shoot transfer factors. Moreover, significantly higher light-REEs La and Ce were transferred to ryegrass shoots than Sm and the heavy-REE Yb, but this was not observed for alfalfa. Alfalfa dry weight was significantly increased by F. mosseae inoculation, but not ryegrass dry weight. For both plant species, there was significantly higher P uptake by the mycorrhizal plants than the nonmycorrhizal plants, but there was no significant transfer of La, Ce, Sm or Yb to alfalfa and ryegrass roots or shoots due to F. mosseae inoculation.

Altered fungal communities in contaminated soils from French industrial brownfields

Polycyclic aromatic hydrocarbons (PAHs) and metals are contaminants of industrial brownfield soils. Pollutants can have harmful effects on fungi, which are major actors of soil functioning. Our objective was to highlight fungal selection following long-term contamination of soils. Fungal diversity was assessed on 30 top-soil samples from ten sites gathered in three groups with different contamination levels and physico-chemical characteristics: 1) uncontaminated controls, 2) slag heaps displaying high PAH and moderate metal contaminations, and 3) settling ponds displaying high metal and intermediate PAH contaminations. Although fungal abundance and richness were similar among the soil groups, the diversity and evenness indices were lower for the slag heap group. Fungal diversity differed among soil groups at the phylum and OTU levels, and indicator species were identified. The relative abundance of Agaricomycetes, Saccharomycetes, Leotiomycetes and Chytridiomycota was higher in the control soils than in the two groups of contaminated soils. Cryptomycota LKM11 representatives were favoured in the slag heap and settling pond groups, and their relative abundance was correlated to the zinc and lead contamination levels. Dothideomycetes - positively linked to PAH contamination - and Eurotiomycetes were specific to the slag heap group. Pucciniomycetes and especially Gymnosporangium members were favoured in the settling pond soils.

Bioavailability and transfer of elevated Sm concentration to alfalfa in spiked soils

Rare earth elements (REEs) have been widely used in recent decades, and their exploitation has led to industrial REE emission and to contaminated soils especially in former mining areas. This raised people concerns on the accumulation and toxicity of REEs in soils and plants, and consequences on plant health. Although many studies dealt with REE in soils and plants, there is still a need to precise their toxicity, bioavailability and transfer to plants in contaminated sites in order to restore such ecosystems. We studied the bioavailability and transfer of a REE to Medicago sativa grown on two contaminated soils differing in their chemical characteristics. A pot experiment was set up in a growth chamber where two natural soils were spiked or not with samarium (Sm) as a model REE. Two chemical extractants were tested to estimate the bioavailability of Sm in the soil, its decrease with time and its transfer to the plants. Results showed that DTPA extractable Sm was well correlated with Sm uptake in alfalfa shoots. The experiment pointed out a significant ageing effect since DTPA extractable Sm significantly decreased within 2 weeks in the soils and was significantly lower in the less acidic soil than in the other. The uptake of Sm from soil to alfalfa shoots depended on the soil pH and on the spiking concentration. The soil to plant transfer factor was low (< 0.08), but a 30% reduction of alfalfa biomass was observed when the soils were spiked with 100 to 200 mg kg^-1 of Sm.

No significant transfer of the rare earth element samarium from spiked soil to alfalfa by Funneliformis mosseae

Rare earth elements including samarium have been widely used in modern technologies in recent decades. Following over-exploitation and soil contamination, they can accumulate in plants and be toxic at high concentrations. Arbuscular mycorrhizae benefit plants in metal-contaminated soils by improving their survival and growth and alleviating metal toxicity, but little information is available about soil contaminated by rare earth elements. We performed two experiments using samarium to study the role of arbuscular mycorrhizal fungi on plant growth and samarium transfer to alfalfa in a samarium-spiked soil. A pot experiment was conducted in a soil spiked with two concentrations of samarium and a non-spiked control, inoculated or not with a metal-tolerant Funneliformis mosseae. A compartmented pot experiment was then performed with a separated compartment containing samarium-spiked sand only accessible by F. mosseae fungal hyphae to further study the transport of samarium from the soil to alfalfa. The biomass of alfalfa grown on samarium-spiked soil was reduced, while it was significantly higher following arbuscular mycorrhiza inoculation in the pot experiment, both in the control and samarium-spiked soil. Although mycorrhizal plants had a higher phosphorus content than non-mycorrhizal ones, there was no significant difference in samarium concentrations between mycorrhizal and non-mycorrhizal plants. The compartment experiment confirmed that there was no significant samarium transfer to the plant by F. mosseae. Other fungi and plants should be tested, and field experiments performed, but our results suggest that arbuscular mycorrhizal plants might be considered in phytorestoration of rare-earth-contaminated soils.

Unravelling the Role of Melanin in Cd and Zn Tolerance and Accumulation of Three Dark Septate Endophytic Species

Dark septate endophytes (DSEs) are often trace element (TE)-tolerant fungi and are abundant in TE-polluted environments. The production of melanin, a black polymer found in cell walls, was hypothesized by several authors to play a role in the TE tolerance of DSEs. To test this hypothesis, we established a series of experiments using albino strains and melanin inhibitors and examined the responses to Cd and Zn. Six DSEs belonging to genera Cadophora sp., Leptodontidium sp. and Phialophora mustea, were evaluated. The strains mainly produced 1,8-dihydroxynaphthalene (DHN) melanin whereas 3,4-dihydroxyphenylalanin melanin was also synthetized. Cd and Zn decreased melanin synthesis in most of the strains. A reduction in melanin concentration in hyphae through the use of tricyclazole, an inhibitor of DHN-melanin synthesis, did not reduce the tolerance of the strains to Cd and Zn. Similarly, albino mutants of Leptodontidium sp. were not more sensitive to Cd and Zn than the WT strain. Moreover, tricyclazole-treated colonies accumulated less Cd but more Zn compared to untreated colonies. The Cd and Zn contents of Leptodontidium albino strains were variable and similar to that of the WT. The results suggest that melanin production is not an important functional trait that contributes to Cd and Zn tolerance, but might contribute to Cd accumulation.

DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

Interactions between dark septate endophytes, ectomycorrhizal fungi and root pathogens in vitro

Dark septate endophytes (DSEs) are widely distributed worldwide and can promote plant growth. Therefore, they are considered potentially important plant allies, especially in stressful environments. Previous studies have reported that DSEs cohabit roots with other microorganisms such as ectomycorrhizal (ECM), endophytic and pathogenic fungi/oomycetes. However, interactions between different DSE species have not yet been reported, and studies on the interactions between DSEs and other fungi are scarce. Using a simple and reproducible pairwise growth assay in vitro, we studied the synergistic/antagonistic interactions between eight DSEs, two ECM fungi and three root pathogens. Most of the DSE/DSE outcomes were neutral. Interestingly, we identified several DSE strains acting in synergy with other strains, as well as strains that could potentially act as biocontrol agents. Notably, three metal-tolerant DSE strains, namely, Cadophora sp., Leptodontidium sp. and Phialophora mustea, could decrease the growth of the root phytopathogens Pythium intermedium, Phytophthora citricola and Heterobasidion annosum. The present data are discussed in the general context of the use of fungal consortia as inocula in the tree-based phytomanagement of marginal lands.

Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient

The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.

High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil

PAH biodegradation in plant rhizosphere has been investigated in many studies, but the timescale of degradation and degrading bacteria activity was rarely considered. We explored the impact of plants on the temporal variability of PAH degradation, microbial abundance, activity, and bacterial community structure in a rhizotron experiment. A historically contaminated soil was spiked with PAHs, planted or not with alfalfa, over 22 days with sampling once a week. In both conditions, most of the spiked PAHs were dissipated during the first week, conducting to polar polycyclic aromatic compound production and to decreased richness and diversity of bacterial communities. We showed a rapid impact of the rhizosphere on PAH degradation via the increased activity of PAH-degrading bacteria. After 12 days, PAH degradation was significantly higher in the planted (100% degradation) than in unplanted (70%) soil. Gram-negative (Proteobacteria) PAH-dioxygenase genes and transcripts were higher in planted than unplanted soil and were correlated to the spiked PAH degradation. Conversely, Gram-positive (Actinobacteria) PAH-dioxygenase gene transcription was constant over time in both conditions. At 12 days, plant growth favored the activity of many Gammaproteobacteria (Pseudomonadaceae, Stenotrophomonas, and Acinetobacter) while in unplanted soil Alphaproteobacteria (Sphingomonadaceae, Sphingobium, and Magnetospirillum) and Actinobacteria (Iamia, Geodermatophilaceae, and Solirubrobacterales) were more active.

Co-inoculation of Lolium perenne with Funneliformis mosseae and the dark septate endophyte Cadophora sp. in a trace element-polluted soil

The presence of dark septate endophytes (DSEs) or arbuscular mycorrhizal fungi (AMF) in plant roots and their effects on plant fitness have been extensively described. However, little is known about their interactions when they are simultaneously colonizing a plant root, especially in trace element (TE)-polluted soils. We therefore investigated the effects of Cadophora sp. and Funneliformis mosseae on ryegrass (Lolium perenne) growth and element uptake in a Cd/Zn/Pb-polluted soil. The experiment included four treatments, i.e., inoculation with Cadophora sp., inoculation with F. mosseae, co-inoculation with Cadophora sp. and F. mosseae, and no inoculation. Ryegrass biomass and shoot Na, P, K, and Mg concentrations significantly increased following AMF inoculation as compared to non-inoculated controls. Similarly, DSE inoculation increased shoot Na concentration, whereas dual inoculation significantly decreased shoot Cd concentration. Moreover, oxidative stress determined by ryegrass leaf malondialdehyde concentration was alleviated both in the AMF and dual inoculation treatments. We used quantitative PCR and microscope observations to quantify colonization rates. They demonstrated that DSEs had no effect on AMF colonization, while AMF colonization slightly decreased DSE frequency. We also monitored fluorescein diacetate (FDA) hydrolysis and alkaline phosphatase (AP) activity in the rhizosphere soils. FDA hydrolysis remained unchanged in the three inoculated treatments, but AMF colonization increased AP activity and P mobility in the soil whereas DSE colonization did not alter AP activity. In this experiment, we unveiled the interactions between two ecologically important fungal groups likely to occur in roots which involved a decrease of oxidative stress and Cd accumulation in shoots. These results open promising perspectives on the fungal-based phytomanagement of TE-contaminated sites by the production of uncontaminated and marketable plant biomass.

Assessment of derelict soil quality: Abiotic, biotic and functional approaches

The intensification and subsequent closing down of industrial activities during the last century has left behind large surfaces of derelict lands. Derelict soils have low fertility, can be contaminated, and many of them remain unused. However, with the increasing demand of soil surfaces, they might be considered as a resource, for example for non-food biomass production. The study of their physico-chemical properties and of their biodiversity and biological activity may provide indications for their potential re-use. The objective of our study was to investigate the quality of six derelict soils, considering abiotic, biotic, and functional parameters. We studied (i) the soil bacteria, fungi, meso- and macro-fauna and plant communities of six different derelict soils (two from coking plants, one from a settling pond, two constructed ones made from different substrates and remediated soil, and an inert waste storage one), and (ii) their decomposition function based on the decomposer trophic network, enzyme activities, mineralization activity, and organic pollutant degradation. Biodiversity levels in these soils were high, but all biotic parameters, except the mycorrhizal colonization level, discriminated them. Multivariate analysis showed that biotic parameters co-varied more with fertility proxies than with soil contamination parameters. Similarly, functional parameters significantly co-varied with abiotic parameters. Among functional parameters, macro-decomposer proportion, enzyme activity, average mineralization capacity, and microbial polycyclic aromatic hydrocarbon degraders were useful to discriminate the soils. We assessed their quality by combining abiotic, biotic, and functional parameters: the compost-amended constructed soil displayed the highest quality, while the settling pond soil and the contaminated constructed soil displayed the lowest. Although differences among the soils were highlighted, this study shows that derelict soils may provide a biodiversity ecosystem service and are functional for decomposition.

Differential growth promotion of poplar and birch inoculated with three dark septate endophytes in two trace element-contaminated soils

Dark septate endophytes (DSEs) are abundant in stressful environments, including trace element (TE)-enriched soils. However, knowledge about the effects of DSEs on plant growth in such soils is poor compared to the well-known mycorrhizal fungi. The aim of this work was to evaluate the effects of three DSE strains isolated from TE-contaminated soils on the growth and mineral nutrition of Betula pendula and Populus tremula x alba grown on two contrasting TE-polluted soils. The three DSEs evenly colonized the two plant species in both soils. Nevertheless, plant responses to DSE inoculation varied from neutral to beneficial depending on soil properties. Depending on fungal strain and plant species, different factors seemed to contribute to plant growth promotion. Phialophora mustea Pr27 and Leptodontidium Pr30 decreased lipid peroxidation in birch shoots. Chlorophyll, K, and P concentrations increased in the shoots of Leptodontidium Pr30-inoculated trees, whereas Cd concentration decreased in Cadophora Fe06-inoculated birch. The absence of a general DSE-mediated plant growth-promoting behavior could represent a limiting factor for a generic use of DSEs in the tree-based phytomanagement of TE-contaminated soils. Our results suggest that the selection of strains adapted to particular edaphic conditions should not be overlooked within the framework of phytomanagement.

Rhizosphere effect is stronger than PAH concentration on shaping spatial bacterial assemblages along centimetre-scale depth gradients

At centimetre scale, soil bacterial assemblages are shaped by both abiotic (edaphic characteristics and pollutants) and biotic parameters. In a rhizobox experiment carried out on planted industrial soil contaminated with polycyclic aromatic hydrocarbons (PAHs), we previously showed that pollution was distributed randomly with hot and cold spots. Therefore, in the present study, we investigated the effect of this patchy PAH distribution on the bacterial community assemblage and compared it with that of root depth gradients found in the rhizosphere of either alfalfa or ryegrass. Sequencing of 16S rRNA amplicons revealed a higher bacterial diversity in ryegrass rhizosphere and enrichment in specific taxa by the 2 plant species. Indeed, Bacteroidetes, Firmicutes, and Gammaproteobacteria were globally favored in alfalfa, whereas Acidimicrobiia, Chloroflexi, Alpha-, and Betaproteobacteria were globally favored in ryegrass rhizosphere. The presence of alfalfa created depth gradients of root biomass, carbohydrate, and pH, and actually shaped the bacterial assemblage, favoring Actinobacteria near the surface and Gemmatimonadetes and Proteobacteria at greater depths. Contrarily, the bacterial assemblage was homogeneous all along depths of the ryegrass root system. With both plant species, the PAH content and random distribution had no significant effect on bacterial assemblage. Globally, at centimeter scale, bacterial community assemblages were mostly shaped by soil physical and chemical depth gradients induced by root growth but not by patchy PAH content.

Dynamics of PAHs and derived organic compounds in a soil-plant mesocosm spiked with 13C-phenanthrene

Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous and persistent soil pollutants. Their fate and the influence of the plant rhizosphere on their dynamics has been extensively studied, but studies mainly focused on their dissipation rate. We conducted a plant-soil mesocosm experiment to study the fate and distribution of PAHs or derived compounds in the extractable fraction, the residual soil, the shoot biomass and the root biomass. The experiment was conducted for 21 days using ryegrass and a forest soil spiked with ¹³C-labeled phenanthrene (PHE), using combined IRMS and NanoSIMS for analyses. Almost 90% of the initial extractable PHE content was dissipated within 3 weeks, but no rhizospheric effect was highlighted on PHE dissipation. More than 40% of ¹³C-PHE was still in the soil at the end of the experiment, but not as PHE or PAH-derived compounds. Therefore it was under the form of new compounds (metabolites) and/or had been incorporated into the microbial biomass. About 0.36% of the initial ¹³C-PHE was recovered in the root and shoot tissues, representing similar ¹³C enrichment (E¹³C) as in the soil (E¹³C ≈ 0.04 at.%). Using NanoSIMS, ¹³C was also localized at the microscale in the roots and their close environment. Global ¹³C enrichment confirmed the results obtained by IRMS. Some hotspots of ¹³C enrichment were found, with a high ³²S/¹²C¹⁴N ratio. Comparing the ratios, sizes and shapes of these hotspots suggested that they could be bacteria.

Plant growth promotion, metabolite production and metal tolerance of dark septate endophytes isolated from metal-polluted poplar phytomanagement sites

Numerous studies address the distribution and the diversity of dark septate endophytes (DSEs) in the literature, but little is known about their ecological role and their effect on host plants, especially in metal-polluted soils. Seven DSE strains belonging to Cadophora, Leptodontidium, Phialophora and Phialocephala were isolated from roots of poplar trees from metal-polluted sites. All strains developed on a wide range of carbohydrates, including cell-wall-related compounds. The strains evenly colonized birch, eucalyptus and ryegrass roots in re-synthesis experiments. Root and shoot growth promotion was observed and was both plant and strain dependent. Two Phialophora and Leptodontidium strains particularly improved plant growth. However, there was no correlation between the level of root colonization by DSEs and the intensity of growth promotion. All strains produced auxin and six also stimulated plant growth through the release of volatile organic compounds (VOCs). SPME-GC/MS analyses revealed four major VOCs emitted by Cadophora and Leptodontidium The strains exhibited growth at high concentrations of several metals. The ability of metal-resistant DSE strains to produce both soluble and volatile compounds for plant growth promotion indicates interesting microbial resources with high potential to support sustainable production of bioenergy crops within the context of the phytomanagement of metal-contaminated sites.

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters

Industrial wasteland soils with aged PAH and heavy metal contaminations are environments where pollutant toxicity has been maintained for decades. Although the communities may be well adapted to the presence of stressors, knowledge about microbial diversity in such soils is scarce. Soil microbial community dynamics can be driven by the presence of plants, but the impact of plant development on selection or diversification of microorganisms in these soils has not been established yet. To test these hypotheses, aged-contaminated soil samples from a field trial were collected. Plots planted with alfalfa were compared to bare soil plots, and bacterial and fungal diversity and abundance were assessed after 2 and 6 years. Using pyrosequencing of 16S rRNA gene and ITS amplicons, we showed that the bacterial community was dominated by Proteobacteria, Actinobacteria, and Bacteroidetes and was characterized by low Acidobacteria abundance, while the fungal community was mainly represented by members of the Ascomycota. The short-term toxic impact of pollutants usually reduces the microbial diversity, yet in our samples bacterial and fungal species richness and diversity was high suggesting that the community structure and diversity adapted to the contaminated soil over decades. The presence of plants induced higher bacterial and fungal diversity than in bare soil. It also increased the relative abundance of bacterial members of the Actinomycetales, Rhizobiales, and Xanthomonadales orders and of most fungal orders. Multivariate analysis showed correlations between microbial community structure and heavy metal and PAH concentrations over time, but also with edaphic parameters (C/N, pH, phosphorus, and nitrogen concentrations).

Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants

Rhizoremediation uses root development and exudation to favor microbial activity. Thus it can enhance polycyclic aromatic hydrocarbon (PAH) biodegradation in contaminated soils. Spatial heterogeneity of rhizosphere processes, mainly linked to the root development stage and to the plant species, could explain the contrasted rhizoremediation efficiency levels reported in the literature. Aim of the present study was to test if spatial variability in the whole plant rhizosphere, explored at the centimetre-scale, would influence the abundance of microorganisms (bacteria and fungi), and the abundance and activity of PAH-degrading bacteria, leading to spatial variability in PAH concentrations. Two contrasted rhizospheres were compared after 37 days of alfalfa or ryegrass growth in independent rhizotron devices. Almost all spiked PAHs were degraded, and the density of the PAH-degrading bacterial populations increased in both rhizospheres during the incubation period. Mapping of multiparametric data through geostatistical estimation (kriging) revealed that although root biomass was spatially structured, PAH distribution was not. However a greater variability of the PAH content was observed in the rhizosphere of alfalfa. Yet, in the ryegrass-planted rhizotron, the Gram-positive PAH-degraders followed a reverse depth gradient to root biomass, but were positively correlated to the soil pH and carbohydrate concentrations. The two rhizospheres structured the microbial community differently: a fungus-to-bacterium depth gradient similar to the root biomass gradient only formed in the alfalfa rhizotron.

Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils

The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the development of PAH-degrading bacteria holding Gram-negative PAH-ring hydroxylating dioxygenase, catechol-1,2-dioxygenase and catechol-2,3-dioxygenase genes. Regarding the total community structure, bacteria closely related to Thiobacillus (β-Proteobacteria) and Steroidobacter (γ-Proteobacteria) genera were favoured by wood sawdust amendment. In both soils, plant rhizospheres induced the development of fungi belonging to Ascomycota and related to Alternaria and Fusarium genera. Bacteria closely related to Luteolibacter (Verrucomicrobia) and Microbacterium (Actinobacteria) were favoured in alfalfa and ryegrass rhizosphere.

Environmental fate and ecotoxicity of lanthanides: are they a uniform group beyond chemistry?

Lanthanides are a chemically uniform group of metals (La-Lu) that, together with yttrium (Y) and scandium (Sc), form the group of rare earth elements (REEs). Because of their many applications (e.g., agriculture, medicine, motor industry), their global production has increased exponentially in the last decades and their biogeochemical cycles are being disrupted by human uses (e.g., gadolinium anomalies in freshwater and tap water, REEs enrichment of soils as a consequence of agricultural practices). However, ecotoxicological effects and mechanism of action of these elements are still poorly understood. In particular, there is no consensus as to lanthanides showing a coherent and predictable pattern of (eco)toxicity in the same way as their atomic properties. For aquatic organisms, contradictory conclusions on this issue can be found in the bibliography. This review shows that the variable composition of culture media used in ecotoxicology, and the associated differences in lanthanide's speciation, are the most likely cause for such discrepancies. In particular, the formation of insoluble species in some highly complexing media likely leads to changes in the soluble concentration of lanthanide during some tests; with the potential for a generalized underestimation of their toxicity at the present state of knowledge. For terrestrial organisms, suitable studies to establish trends in lanthanides' toxicity are practically nonexistent; with most research focusing on the effects of REE mixtures. Molecular level studies to elucidate the mechanisms of action of lanthanides are essentially limited to La, pointing to the need for further research to identify common mechanisms of action or modes of action across lanthanides. Overall, agreement on the correct procedures to follow to obtain reliable and comparable data for individual lanthanide is the first action to take in order to arrive at a reliable risk assessment for this group of elements in both aquatic and terrestrial systems.

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.

Experimental increase in availability of a PAH complex organic contamination from an aged contaminated soil: consequences on biodegradation

Although high PAH content and detection of PAH-degraders, the PAH biodegradation is limited in aged-contaminated soils due to low PAH availability (i.e., 1%). Here, we tried to experimentally increase the soil PAH availability by keeping both soil properties and contamination composition. Organic extract was first removed and then re-incorporated in the raw soil as fresh contaminants. Though drastic, this procedure only allowed a 6-time increase in the PAH availability suggesting that the organic constituents more than ageing were responsible for low availability. In the re-contaminated soil, the mineralization rate was twice more important, the proportion of 5-6 cycles PAH was higher indicating a preferential degradation of lower molecular weight PAH. The extraction treatment induced bacterial and fungal community structures modifications, Pseudomonas and Fusarium solani species were favoured, and the relative quantity of fungi increased. In re-contaminated soil the percentage of PAH-dioxygenase gene increased, with 10 times more Gram negative representatives.

PAH oxidation in aged and spiked soils investigated by column experiments

Soils of former steel-making or coking plants have been contaminated for decades by PAHs. These soils could be cleaned up by In situ chemical oxidation (ISCO) but the low PAH availability may be a drawback. The objective of the present contribution was to study the efficiency of PAH oxidation in two aged soils compared to a spiked soil in dynamic conditions. Column experiments were performed with two oxidants: hydrogen peroxide used in modified Fenton's reaction and activated persulfate. The oxidant doses were moderate to ensure the feasibility of process upscaling. Besides, the availability of PAHs in these soils was measured by extraction with a cyclodextrin. Our results showed that oxidation was limited: the higher PAH degradation rate was 30% with the aged soils and 55% with the spiked one. PAH availability was a parameter explaining these results but no direct correlation was found between PAH extractability by the cyclodextrin and oxidation efficiency. Other parameters were also involved, such as the organic carbon content, the calcite content and the pH. This study was a first achievement before studying the influence of a number of parameters on the efficiency of PAH oxidation in aged soils.

Long-term in situ dynamics of the fungal communities in a multi-contaminated soil are mainly driven by plants

The fungal communities of a multi-contaminated soil polluted by polycyclic aromatic hydrocarbons and heavy metals (NM) were studied within a long-term in situ experiment of natural attenuation assisted by plants. Three treatments were monitored: bare soil (NM-BS), soil planted with alfalfa and inoculated with mycorrhizal fungi (NM-Msm), and soil with spontaneous vegetation (NM-SV). The same soil after thermal desorption (TD) was planted with alfalfa and inoculated with mycorrhizal fungi (TD-Msm). Twice a year for 5 years, the fungal abundance and the community structure were evaluated by real-time PCR and temporal temperature gradient gel electrophoresis targeting 18S rRNA genes. The fungal abundance increased over time and was higher in planted than in bare NM soil and in TD than in NM soil. The Shannon diversity index (H') increased during the first 2 years with the emergence of more than 30 ribotypes, but decreased after 3 years with the selection of a few competitive species, mostly Ascomycetes. H' was higher under complex plant assemblage (NM-SV) than in the NM-BS plots but did not differ between NM and TD soils planted with alfalfa. These results indicated that even in a highly polluted soil, the plant cover was the main driver of the fungal community structure.

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.

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples"

Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, as well as the abundance and genetic structure of the total bacterial community in the DNA extracted from 12 different soils by the 13 laboratories. High quality DNA was successfully extracted from all 12 soils, despite different physical and chemical characteristics and a range of origins from arable soils, through forests to industrial sites. Quantification of the 16S rRNA gene abundances by real time PCR and analysis of the total bacterial community structure by automated ribosomal intergenic spacer analysis (A-RISA) showed acceptable to good levels of reproducibility. Based on the results of both ring-tests, the method was unanimously approved by the ISO as an international standard method and the normative protocol will now be disseminated within the scientific community. Standardization of a soil DNA extraction method will improve data comparison, facilitating our understanding of soil microbial diversity and soil quality monitoring.

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.

Root exudates modify bacterial diversity of phenanthrene degraders in PAH-polluted soil but not phenanthrene degradation rates

To determine whether the diversity of phenanthrene-degrading bacteria in an aged polycyclic aromatic hydrocarbon (PAH) contaminated soil is affected by the addition of plant root exudates, DNA stable isotope probing (SIP) was used. Microcosms of soil with and without addition of ryegrass exudates and with ¹³C-labelled phenanthrene (PHE) were monitored over 12 days. PHE degradation was slightly delayed in the presence of added exudate after 4 days of incubation. After 12 days, 68% of added PHE disappeared both with and without exudate. Carbon balance using isotopic analyses indicated that a part of the ¹³C-PHE was not totally mineralized as ¹³CO₂ but unidentified ¹³C-compounds (i.e. ¹³C-PHE or ¹³C-labelled metabolites) were trapped into the soil matrix. Temporal thermal gradient gel electrophoresis (TTGE) analyses of 16S rRNA genes were performed on recovered ¹³C-enriched DNA fractions. 16S rRNA gene banding showed the impact of root exudates on diversity of PHE-degrading bacteria. With PHE as a fresh sole carbon source, Pseudoxanthomonas sp. and Microbacterium sp. were the major PHE degraders, while in the presence of exudates, Pseudomonas sp. and Arthrobacter sp. were favoured. These two different PHE-degrading bacterial populations were also distinguished through detection of PAH-ring hydroxylating dioxygenase (PAH-RHD(α)) genes by real-time PCR. Root exudates favoured the development of a higher diversity of bacteria and increased the abundance of bacteria containing known PAH-RHD(α) genes.

The influence of thermal desorption on genotoxicity of multipolluted soil

A multipolluted soil sampled from a former coking plant in Lorraine (France) was evaluated for its genotoxic effects on coelomocytes of the Eisenia fetida earthworm using the comet assay. The biological efficiency of thermal desorption of the contaminated soil was also investigated. The untreated polluted soil was shown to be genotoxic to earthworms. Although thermal desorption reduced the concentration of PAHs by 94% (Sigma(16 PAHs)=1846 and 101 mg/kg before and after thermal desorption, respectively), the treatment did not eliminate the genotoxicity of soil pollutants to earthworms but increased it. The concentration of non-volatile metals did not change after thermal desorption. Among metals found in the treated soil, cadmium, chromium and nickel could explain the genotoxicity of the contaminated soil after thermal desorption. The treatment could increase the bioavailability and genotoxicity of heavy metals, through a modification of the soil's organic matter, the speciation of heavy metals and their binding to organic matter. This study underlines the importance of measuring biological effects, in order to evaluate the risk associated with formerly contaminated soils and the efficiency of remediation.

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.

Differential effects of AM fungal isolates on Medicago truncatula growth and metal uptake in a multimetallic (Cd, Zn, Pb) contaminated agricultural soil

Toxic metal accumulation in soils of agricultural interest is a serious problem needing more attention, and investigations on soil-plant metal transfer must be pursued to better understand the processes involved in metal uptake. Arbuscular mycorrhizal (AM) fungi are known to influence metal transfer in plants by increasing plant biomass and reducing metal toxicity to plants even if diverging results were reported. The effects of five AM fungi isolated from metal contaminated or non-contaminated soils on metal (Cd, Zn) uptake by plant and transfer to leachates was assessed with Medicago truncatula grown in a multimetallic contaminated agricultural soil. Fungi isolated from metal-contaminated soils were more effective to reduce shoot Cd concentration. Metal uptake capacity differed between AM fungi and depended on the origin of the isolate. Not only fungal tolerance and ability to reduce metal concentrations in plant but also interactions with rhizobacteria affected heavy metal transfer and plant growth. Indeed, thanks to association with nodulating rhizobacteria, one Glomus intraradices inoculum increased particularly plant biomass which allowed exporting twofold more Cd and Zn in shoots as compared to non-mycorrhizal treatment. Cd concentrations in leachates were variable among fungal treatments, but can be significantly influenced by AM inoculation. The differential strategies of AM fungal colonisation in metal stress conditions are also discussed.

Effects of thermal desorption on the composition of two coking plant soils: impact on solvent extractable organic compounds and metal bioavailability

To evaluate the efficiency and the influence of thermal desorption on the soil organic compartment, contaminated soils from coking plant sites (NM and H) were compared to their counterparts treated with thermodesorption. The extractable organic matter, and the metal content and distribution with soil compartments were studied. In both thermodesorbed soils, PAH (polycyclic aromatic hydrocarbon) degradation exceeded 90%. However, the thermal desorption led not only to a volatilization of the organic compounds but also to the condensation of extractable organic matter. The treatments only affected the Fe and Zn distribution within the more stable fractions, whereas the organic compound degradation did not affect their mobility and availability.

Role and influence of mycorrhizal fungi on radiocesium accumulation by plants

This review summarizes current knowledge on the contribution of mycorrhizal fungi to radiocesium immobilization and plant accumulation. These root symbionts develop extended hyphae in soils and readily contribute to the soil-to-plant transfer of some nutrients. Available data show that ecto-mycorrhizal (ECM) fungi can accumulate high concentration of radiocesium in their extraradical phase while radiocesium uptake and accumulation by arbuscular mycorrhizal (AM) fungi is limited. Yet, both ECM and AM fungi can transport radiocesium to their host plants, but this transport is low. In addition, mycorrhizal fungi could thus either store radiocesium in their intraradical phase or limit its root-to-shoot translocation. The review discusses the impact of soil characteristics, and fungal and plant transporters on radiocesium uptake and accumulation in plants, as well as the potential role of mycorrhizal fungi in phytoremediation strategies.

Impact of arbuscular mycorrhizal fungi on uranium accumulation by plants

Contamination by uranium (U) occurs principally at U mining and processing sites. Uranium can have tremendous environmental consequences, as it is highly toxic to a broad range of organisms and can be dispersed in both terrestrial and aquatic environments. Remediation strategies of U-contaminated soils have included physical and chemical procedures, which may be beneficial, but are costly and can lead to further environmental damage. Phytoremediation has been proposed as a promising alternative, which relies on the capacity of plants and their associated microorganisms to stabilize or extract contaminants from soils. In this paper, we review the role of a group of plant symbiotic fungi, i.e. arbuscular mycorrhizal fungi, which constitute an essential link between the soil and the roots. These fungi participate in U immobilization in soils and within plant roots and they can reduce root-to-shoot translocation of U. However, there is a need to evaluate these observations in terms of their importance for phytostabilization strategies.

Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDalpha) genes from Gram positive and Gram negative bacteria in soil and sediment samples

Real-Time PCR based assays were developed to quantify Gram positive (GP) and Gram negative (GN) bacterial populations that are capable of degrading the polycyclic aromatic hydrocarbons (PAH) in soil and sediment samples with contrasting contamination levels. These specific and sensitive Real-Time PCR assays were based on the quantification of the copy number of the gene that encodes the alpha subunit of the PAH-ring hydroxylating dioxygenases (PAH-RHDalpha), involved in the initial step of the aerobic metabolism of PAH. The PAH-RHDalpha-GP primer set was designed against the different allele types present in the data base (narAa, phdA/pdoA2, nidA/pdoA1, nidA3/fadA1) common to the Gram positive PAH degraders such as Rhodococcus, Mycobacterium, Nocardioides and Terrabacter strains. The PAH-RHDalpha-GN primer set was designed against the genes (nahAc, nahA3, nagAc, ndoB, ndoC2, pahAc, pahA3, phnAc, phnA1, bphAc, bphA1, dntAc and arhA1) common to the Gram negative PAH degraders such as Pseudomonas, Ralstonia, Commamonas, Burkholderia, Sphingomonas, Alcaligenes, Polaromonas strains. The PCR clones for DNA extracted from soil and sediment samples using the designed primers showed 100% relatedness to the PAH-RHDalpha genes targeted. Deduced from highly sensitive Real-Time PCR quantification, the ratio of PAH-RHDalpha gene relative to the 16S rRNA gene copy number showed that the PAH-bacterial degraders could represent up to 1% of the total bacterial community in the PAH-contaminated sites. This ratio highlighted a positive correlation between the PAH-bacterial biodegradation potential and the PAH-contamination level in the environmental samples studied.

Selenium bioavailability and uptake as affected by four different plants in a loamy clay soil with particular attention to mycorrhizae inoculated ryegrass

The aim of this study was to investigate the influence of plant species, especially of their rhizosphere soil, and of inoculation with an arbuscular mycorrhizal (AM) fungus on the bioavailability of selenium and its transfer in soil-plant systems. A pot experiment was performed with a loamy clay soil and four plant species: maize, lettuce, radish and ryegrass, the last one being inoculated or not with an arbuscular mycorrhizal fungus (Glomus mosseae). Plant biomass and Se concentration in shoots and roots were estimated at harvest. Se bioavailability in rhizosphere and unplanted soil was evaluated using sequential extractions. Plant biomass and selenium uptake varied with plant species. The quantity of rhizosphere soil also differed between plants and was not proportional to plant biomass. The highest plant biomass, Se concentration in plants, and soil to plant transfer factor were obtained with radish. The lowest Se transfer factors were obtained with ryegrass. For the latter, mycorrhizal inoculation did not significantly affect plant growth, but reduced selenium transfer from soil to plant by 30%. In unplanted soil after 65 days aging, more than 90% of added Se was water-extractable. On the contrary, Se concentration in water extracts of rhizosphere soil represented less than 1% and 20% of added Se for ryegrass and maize, respectively. No correlation was found between the water-extractable fraction and Se concentration in plants. The speciation of selenium in the water extracts indicated that selenate was reduced, may be under organic forms, in the rhizosphere soil.

Ectomycorrhizas impede phytoremediation of polycyclic aromatic hydrocarbons (PAHs) both within and beyond the rhizosphere

Exploitation of mycorrhizas to enhance phytoremediation of organic pollutants has received attention recently due to their positive effects on establishment of plants in polluted soils. Some evidence exist that ectomycorrhizas enhance the degradation of pollutants of low recalcitrance, while less easily degradable polyaromatic molecules have been degraded only by some of these fungi in vitro. Natural polyaromatic (humic) substances are degraded more slowly in soil where ectomycorrhizal fungi are present, thus phytoremediation of recalcitrant pollutants may not benefit from the presence of these fungi. Using a soil spiked with three polycyclic aromatic hydrocarbons (PAHs) and an industrially polluted soil (1 g kg(-1) of summation operator12 PAHs), we show that the ectomycorrhizal fungus Suillus bovinus, forming hydrophobic mycelium in soil that would easily enter into contact with hydrophobic pollutants, impedes rather than promotes PAH degradation. This result is likely to be a nutrient depletion effect caused by fungal scavenging of mineral nutrients.

Evaluation of matrices for the sorption and biodegradation of phenanthrene

Permeable reactive barriers (PRBs), a new cost effective technology for the remediation of contaminated groundwater, have rarely been considered for PAH contamination. We evaluated three candidate matrices (activated carbon (AC), pouzzolana coated (PzF) or not (Pz) with heavy fuel oil) for phenanthrene (PHE) sorption capacity and the biodegradation of adsorbed PHE. Adsorption-desorption batch experiments showed higher sorption capacity of AC than PzF (60 fold) and Pz (1,500 fold). Sorption isotherms were not linear for all matrices as described by a Freundlich model. Phenanthrene desorption from AC and PzF within 48 h was limited (1-3%). Mineralization of (14)C-PHE by a PAH-degrading bacterial strain increased in the presence of AC and Pz (+16 and +12%). Among the three matrices, AC may be a good candidate for PRBs due to high adsorption, low desorption and increased PHE degradation.

Biodegradation of phenanthrene, spatial distribution of bacterial populations and dioxygenase expression in the mycorrhizosphere of Lolium perenne inoculated with Glomus mosseae

Interactions between the plant and its microbial communities in the rhizosphere control microbial polycyclic aromatic hydrocarbons (PAH) biodegradation processes. Arbuscular mycorrhizal (AM) fungi can influence plant survival and PAH degradation in polluted soil. This work was aimed at studying the contribution of the mycorrhizosphere to PAH biodegradation in the presence of ryegrass (Lolium perenne L., cv. Barclay) inoculated with Glomus mosseae (BEG 69) by taking into account the structure and activity of bacterial communities, PAH degrading culturable bacteria as a function of the distance from roots. Ryegrass was grown in compartmentalized systems designed to harvest successive sections of rhizosphere in lateral compartments polluted or not with phenanthrene (PHE). Colonization of roots by G. mosseae (BEG 69) modified the structure and density of bacterial populations in the mycorrhizosphere, compared to the rhizosphere of non-mycorrhizal plants. G. mosseae increased the density of culturable heterotrophic and PAH degrading bacteria beyond the immediate rhizosphere in the presence of PHE, and increased the density of PAH degraders in the absence of the pollutant. Biodegradation was not significantly increased in the mycorrhizosphere, compared to control non-mycorrhizal plants, where PHE biodegradation already reached 92% after 6 weeks. However, dioxygenase transcriptional activity was found to be higher in the immediate mycorrhizosphere in the presence of G. mosseae (BEG 69).

Differential composition of bacterial communities as influenced by phenanthrene and dibenzo[a,h]anthracene in the rhizosphere of ryegrass (Lolium perenne L.)

Bioremediation technologies of Polycyclic Aromatic Hydrocarbons (PAH) are often limited by the recalcitrance to biodegradation of high molecular weight (HMW) PAH. Rhizosphere is known to increase the biodegradation of PAH but little is known about the biodegradability of these HMW compounds by rhizosphere bacteria. This study compared the effects of a 3 and a 5-ring PAH, phenanthrene (PHE) and dibenzo[a,h]anthracene (dBA) respectively, on the composition of bacterial community, the bacterial density and the biodegradation activity. Compartmentalized devices were designed to harvest three consecutive sections of the rhizosphere. Rhizosphere and non-rhizosphere compartments were filled with PHE or dBA spiked or unspiked sand and inoculated with a soil bacterial inoculum. Different bacterial communities and degradation values were found 5 weeks after spiking with PHE (41-76% biodegradation) and dBA (12-51% biodegradation). In sections closer to the root surface, bacterial populations differed as a function of the distance to roots and the PAH added, whereas in further rhizosphere sections, communities were closer to those of the non-planted treatments. Biodegradation of PHE was also a function of the distance to roots, and decreased from 76 to 42% within 9 mm from the roots. However, biodegradation of dBA was significantly higher in the middle section (3-6 mm from roots) than the others. Rhizosphere degradation of PAH varies with the nature of the PAH, and C fluxes from roots could limit the degradation of dBA.

Metal transfer to plants grown on a dredged sediment: use of radioactive isotope 203Hg and titanium

Improperly disposed of dredged sediments contaminated with metals may induce long-term leaching and an increase of metal concentrations in ground waters and vegetal cover plants. The objective of the study was to quantify the sediment-to-plant transfer of Cu, Pb, Hg and Zn with a particular focus on the pathway of Hg and to determine whether the establishment of vegetal cover modifies the metal availability. A pot experiment with rape (Brassica napus), cabbage (Brassica oleraccea) and red fescue (Festuca rubra) was set up using a sediment first spiked with the radioisotope 203Hg. Zinc concentrations (197-543 mg kg(-1) DM) in leaves were higher than Cu concentration (197-543 mg kg(-1) DM), Pb concentration (2.3-2.6 mg kg(-1) DM) and Hg concentration (0.9-1.7 mg kg(-1) DM). Leaves-to-sediment ratios decreased as follows: Zn > Cu > Hg > Pb. According to Ti measurements, metal contamination by dry deposition was less than 1%. Mercury concentration in plant leaves was higher than European and French thresholds. Foliar absorption of volatile Hg was a major pathway for Hg contamination with a root absorption of Hg higher in rape than in cabbage and red fescue. Growth of each species increased Cu solubility. Zinc solubility was increased only in the presence of rape. The highest increase of Cu solubility was observed for red fescue whereas this species largely decreased Zn solubility. Dissolved organic carbon (DOC) measurements suggested that Cu solubilisation could result from organic matter or release of natural plant exudates. Dissolved inorganic carbon (DIC) measures suggested that the high Zn solubility in the presence of rape could originate from a generation of acidity in rape rhizosphere and a subsequent dissolution of calcium carbonates. Consequently, emission of volatile Hg from contaminated dredged sediments and also the potential increase of metal solubility by a vegetal cover of grass when used in phytostabilisation must be taken into account by decision makers.

No significant contribution of arbuscular mycorrhizal fungi to transfer of radiocesium from soil to plants

The diffuse pollution by fission and activation products following nuclear accidents and weapons testing is of major public concern. Among the nuclides that pose a serious risk if they enter the human food chain are the cesium isotopes 137Cs and 134Cs (with half-lives of 30 and 2 years, respectively). The biogeochemical cycling of these isotopes in forest ecosystems is strongly affected by their preferential absorption in a range of ectomycorrhiza-forming basidiomycetes. An even more widely distributed group of symbiotic fungi are the arbuscular mycorrhizal fungi, which colonize most herbaceous plants, including many agricultural crops. These fungi are known to be more efficient than ectomycorrhizas in transporting mineral elements from soil to plants. Their role in the biogeochemical cycling of Cs is poorly known, in spite of the consequences that fungal Cs transport may have for transfer of Cs into the human food chain. This report presents the first data on transport of Cs by these fungi by use of radiotracers and compartmented growth systems where uptake by roots and mycorrhizal hyphae is distinguished. Independent experiments in three laboratories that used different combinations of fungi and host plants all demonstrated that these fungi do not contribute significantly to plant uptake of Cs. The implications of these findings for the bioavailability of radiocesium in different terrestrial ecosystems are discussed.

Spatial distribution of bacterial communities and phenanthrene degradation in the rhizosphere of Lolium perenne L

Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria.