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In the environment, abiotic (climatic conditions, physico-chemical parameters), biotic (interactions between microorganisms, vegetation and fauna), and anthropogenic (stress, pollution) filters are driving the microbial diversity observed locally. A key question in microbial ecology is to understand the impact of these filters on bacterial diversity and ecosystem functioning. To highlight the responses of bacterial assemblages to these ecological filters, a new approach based on bacterial functional traits has been developed. This approach provides a functional picture of bacterial assemblages using morphological, physiological, and genomic traits as proxies of functions, and leads to a generalizable approach over a larger range of ecosystems with different bacterial diversities. We have created a user-friendly database of bacterial functional traits, thanks to the properties of 19,455 bacterial strains. This database has been called BactoTraits. For example, oxygen preference, size and shape of bacteria, motility, optimum and range of pH and temperature, genome GC percent and trophic type are among the 19 traits included in BactoTraits. Based on the best-informed strains in the database, we identified five functional groups (i.e. mesophiles, competitors, colonizers, stress-sensitives and stress-tolerants) exhibiting a wide strain taxonomic diversity but with quite similar trait profile combinations. As an example of application, BactoTraits was used to characterize the traits and functional diversity of bacterial assemblages in soil samples from 10 sites with different physico-chemical properties and various levels of metal and polycyclic aromatic hydrocarbon (PAH) contaminations. Inference of functional traits was based on taxonomic diversity information obtained by high-throughput sequencing of 16S rDNA. This trait-based approach has allowed to discriminate soils according to their physico-chemical properties and levels of contamination and to go further into the description of the bacterial assemblages. Several bacterial traits were identified as indicators of specific contaminants such as metals (e.g. filament shape, microaerophile and temperature optimum/range higher than 40 °C) or PAHs (e.g. spherical shape, facultative anaerobe/aerobe, no spore production, pH optimum ≥ 8, low temperature optimum but high temperature variation tolerance). Inferring trait values from a taxonomy-based approach can be extended readily to other microbial systems and contexts such as (i) studies on soils and aquatic ecosystems, (ii) microbial ecology along various environmental gradients, (iii) human, plant and animal microbiotes, as well as (iv) trophic interactions between bacterial communities and their predators.

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.

In iron-deficient conditions, most bacteria and fungi are known to release siderophores, iron-chelating compounds. Most plants do not produce siderophores, but seem to use microbial siderophores as iron sources. Although ectomycorrhizal fungi have been found to release siderophores in pure culture, little research has addressed production by mycorrhizas and the consequences for plant iron nutrition. The objectives of this study were to determine the effect of an ectomycorrhizal fungus [Pisolithus tinctorius (Pers.) Coker and Couch] on the utilization of siderophore (ferrioxamine B) by slash pine (Pinus elliottii Engelm.) roots grown under iron-deficient or iron-sufficient conditions. Experiments were conducted with excised roots and whole seedlings. Uptake of 55 Fe from ferrioxamine B was lower by mycorrhizal roots than non-mycorrhizal roots. Growth under iron-deficient conditions had little effect on iron uptake by non-mycorrhizal roots but increased the uptake by mycorrhizal roots. Uptake of iron from a non-purified siderophore isolated from a pure culture of P. tinctorius was also lower by mycorrhizal roots. The uptake of iron was not dependent on the pH of the uptake solution. Differential responses could be attributed to different mechanisms of iron uptake between fungal cells and root cells. However, the higher iron content of mycorrhizal roots may indicate a negative feedback effect on uptake.

International audience; 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.

International audience

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.

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.

International audience; 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's 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 two 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 (

International audience; 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.

International audience; In the last decades, anthropogenic disturbances have altered the ability of soils to provide diverse functions. Certain anthropogenic soils, with a low fertility level and often contaminated, ended up underused and derelict. Although derelict for humans, these soils may be refuges for biodiversity, but their biological functioning remains poorly understood. To this end, a trait-based approach of soil invertebrate communities might be an effective predictor of ecosystem state. The present work aims to highlight the in situ links between the abiotic characteristics of derelict soils and the taxonomic and functional structure and composition (through a trait-based approach) of macrofauna and Collembola communities inhabiting these soils. We studied 6 different derelict soils: two soils from coking plants, one soil from a settling pond, two constructed soils, and an inert waste storage soil. We measured fifteen abiotic soil parameters that inform on fertility and contamination. We took into account sixteen traits and ecological preferences to characterize the functional structure and composition of Collembola and macrofauna communities. Soil fertility (organic matter content, C:N ratio, P, Ca and Mg concentrations, cation-exchange capacity, and clay content) and moderate contamination (Pb, Cd, Zn, and PAH concentrations) altered the taxonomic and functional composition of Collembola and macrofauna communities by selecting traits such as body length, pigmentation, vertical distribution, diet type, and habitat preference. Compost-amended constructed soil properties selected taxonomic and functional community composition of slightly disturbed soil. In contrast, metal-contaminated constructed soil harbored a higher proportion of Collembola displaying the traits and ecological preferences of instable ecosystems. The study of functional profiles of Collembola and macrofauna communities in the derelict soils evidenced that they support different communities with more or less wide functional potential. It underlines the interest of multiple biotic component studies to reach a better ecosystem description.

Le fort developpement industriel du debut du XXe siecle, puis son declin a la fin du siecle dernier, ont fortement impacte des surfaces considerables de sol. Dans un contexte de rarefaction des sols et de pressions foncieres croissantes, la remediation et la rehabilitation de ces sols fortement anthropises sont des enjeux forts. Au-dela de la necessite d’eliminer la pollution presente et les risques associes pour l’environnement et la sante, la restauration et la refonctionnalisation de ces friches et sols delaisses meritent d’etre prises en consideration. La possibilite de valoriser ces sols non seulement pour des usages comme la production de biomasse non alimentaire, mais aussi comme reserve de biodiversite est mise en avant dans cet article. Souvent percues au depart comme un handicap, les friches industrielles peuvent ainsi devenir un veritable atout qu’il convient de valoriser.

International audience; 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.

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.

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.

International audience

International audience

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.

National audience

International audience

International audience; 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.

International audience; 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).

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.

EA BIOME INRA; National audience

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.

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.

International audience; Dark septate endophytes (DSEs) are melanin-enriched ascomycetous fungi that are abundant in stressed environments. However, little is known about their physiology and metabolism, and DSE genes have not been functionally characterized yet. Therefore developing molecular genetic tools to investigate the biological function of genes of interest in DSEs is of major significance. We investigated Agrobacterium tumefaciens-mediated transformation (ATMT) efficiency in eight DSE strains belonging to Cadophora sp., Cadophora malorum, Leptodontidium sp., Phialophora mustea, and Cladosporium cladosporioides. ATMT efficiency was DSE-dependent and ranged from 0.6% to 125 %. The transformants were mitotically stable and expressed the gfp marker. The patterns of transformant appearance as a function of time were diverse and also strain-dependent. We further focused on the effect of mycelium ageing on ATMT efficiency. Leptodontidium sp. Me07, Leptodontidium sp. Pr30, and C. cladosporioides CBS 101367 were significantly more transformed using fifteen-day-old mycelium (44.5, 6.9, and 1.1%, respectively) as compared to two-day-old mycelium (121, 28.7, and 25.1, respectively), whereas P. mustea Pr29 was more transformed using young mycelium (21.5% compared to 5.3% for the old mycelium). Finally, we focused on the effect of melanin content on ATMT efficiency. Melanin content in mycelium ranged from 0.9 to 3.2 mg per gram of dry weight. Tricyclazole, an inhibitor of melanin biosynthesis, negatively modulated melanin content, while copper, an inducer of melanin biosynthesis, positively modulated them. However there was no correlation between hyphal melanin content and ATMT efficiency.

International audience

International audience

International audience; Despite many studies on the impact of arable land conversion to Short Rotation Coppice (SRC), few studies have been carried out on soil biota. This study aims at assessing biological and physico-chemical soil properties that are affected by SRC compared to forestry, grassland and an agrosystem.All samples were collected in the Aisne valley (France), from the same type of soil, with four land uses, i.e. willow SRC, agrosystem, grassland and alluvial forest, 3 years after SRC was planted. We studied fertility, the biological community (earthworm diversity, density and biomass, bacterial and fungal density and community structures) and biochemical parameters (enzyme activities, basal respiration and nitrification).After 3 years' growth, soil biological parameters (fungal abundance, laccase activity, anecic earthworm proportion and earthworm diversity) and CEC were higher in the SRC than in the agrosystem soil. In parallel, fungal abundance was higher in SRC than in forest and grassland soils.Compared to annual arable crops, SRC promoted biological properties. However, in the short term, the parameters we measured were lower than in the forest and grassland soils. The use of certain parameters as indicators of soil functioning/quality assessment to discriminate the four land uses is discussed.

International audience; 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 (TM)) 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.

International audience; Although high PAH content and detection of PAH-degraders, the PAH biodegradation is limited in aged-contaminated soils due to low PAR 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.

International audience; 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.

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

International audience

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.

International audience; This study aimed at evaluating potential arsenic (As) mobility in an industrially contaminatedsoil (64 mg As kg-1) of the Meuse River basin, and at identifying key bacterial groups that drive soil As dynamics. Both speciation and release of As from this soil was followed under anaerobicconditions using a laboratory batch experiment. In the presence of exogenous carbon sources,AsV initially present in the soil matrix and/or adsorbed on synthetic hydrous ferric oxides wassolubilized and mainly reduced into AsIII by indigenous soil microfora. After a one-monthincubation period in these biotic conditions, AsIII accounted for 80-85% of the total dissolved Asand more than 60% of the solid-phase As. Bacterial community structure (i.e. 16S rDNA-basedCE-SSCP profiles) changed with incubation time and As amendment. The detection of distantlyrelated arsenate respiratory reductase genes (arrA), as functional markers of AsV-respirers,indicates that novel dissimilatory AsV-reducing bacteria may be involved in Asbiotransformation and mobility in anoxic soils. Since As and iron were concomitantly released, acrucial role of indirect As-mobilizing bacteria on As behavior was also revealed. Our results show that the majority of As within the soil matrix was bioavailable and bioaccessible forheterotrophic AsV reduction to AsIII, which may increase As toxicity and mobility in thecontaminated soils.

cited By 0; International audience; Chloride is often considered as the main chlorine form in soils. However, recent studies show that chlorine is mostly present in soils as naturally produced organically bound molecules. The relative contribution of biotic, including microbial, and abiotic processes to formation of organically bound chlorine remains poorly understood. We performed a37Cl spiking batch experiment with a forest soil incubated under abiotic and biotic conditions over two time periods to simultaneously monitor the formation of organically bound chlorine from natural and tracer chlorine. To compare biotic and abiotic conditions without biased effect of sterilization technique for abiotic control, the soil was irradiated and reinoculated or not with soil microflora. Fifteen days after microbial inoculation, the natural non-extractable organic chlorine content in the inoculated soil was significantly higher than in the sterile soil, showing that microbial activity contributed to formation of organically bound chlorine. However, no significant difference was noted between the two incubation periods. The same trend was noted for tracer chlorine, yet without a significant difference. The present study shows that chlorination is mediated by microbial activity, but there is also some indication of abiotic formation of organically bound chlorine, with a non-extractable organic tracer chlorine formation of about 6% just after spiking in abiotic conditions. © 2016 Elsevier Ltd

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.

The polycyclic aromatic hydrocarbon (PAH) dissipation potential of Fusarium solani MM1 and Arthrobacter oxydans MsHM11, isolated from a PAH-polluted soil, was investigated in liquid cultures containing 500, 500, and 50 mg l −1 of phenanthrene (PHE), pyrene (PYR), and dibenz(a,h)anthracene (DBA), respectively. The contributions of adsorption, absorption and biotransformation were evaluated separately by extracting and analysing PAHs from the biomass and from the culture medium. In the pure culture, F. solani dissipated approximately 30% of each tested PAH in 28 days when glucose was supplied as the carbon source. PAH adsorption on F. solani hyphae was negligible, whereas absorption was found to account for one-third of the dissipation. Absorbed PAHs, reaching 3% of the fungal dry biomass, could be visualised in autofluorescent intracellular vesicles. In contrast, A. oxydans grew on PAHs as sole carbon source and led to 55% dissipation of PHE in 28 days without any significant absorption. This dissipation potential was inhibited by the presence of glucose, and the PYR and DBA contents were never dissipated in the bacterial pure culture. In the mixed co-culture, the PAH dissipation rates were lower, showing that antagonistic interactions, such as pH changes or competition for carbon source, indirectly inhibited both microbial potentials.

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 (H2O2, 6 and 65 g kg(-1)) and FeSO4 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. (C) 2011 Elsevier Ltd. All rights reserved.

A large number of soil bioindicators were used to assess biological diversity and activity in soil polluted with polycyclic aromatic hydrocarbons (PAHs) and the same soil after thermal desorption (TD) treatment. Abundance and biodiversity of bacteria, fungi, protozoa, nematodes and microarthropods, as well as functional parameters such as enzymatic activities and soil respiration, were assessed during a two year period of in situ monitoring. We investigated the influence of vegetation (spontaneous vegetation and Medicago sativa) and TD treatment on biological functioning. Multivariate analysis was performed to analyze the whole data set. A principal response curve (PRC) technique was used to evaluate the different treatments (various vegetation and contaminated vs. TD soil) contrasted with control (bare) soil over time. Our results indicated the value of using a number of complementary bioindicators, describing both diversity and functions, to assess the influence of vegetation on soil and discriminate polluted from thermal desorption (TD)-treated soil. Plants had an influence on the abundance and activity of all organisms examined in our study, favoring the whole trophic chain development. However, although TD-treated soil had a high abundance and diversity of microorganisms and fauna, enzymatic activities were weak because of the strong physical and chemical modifications of this soil. (C) 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Polycyclic aromatic hydrocarbon (PAH) degradation may be increased in plant rhizosphere, but the role of plants in PAH degradation is not clearly understood. We investigated the effect of ryegrass root exudates on phenanthrene (PHE) degradation, PHE degrading bacterial population and functional gene expression in sand microcosms inoculated with bacteria from an industrial PAH polluted soil. Dominant bacteria were identified using 16S rDNA based temporal thermal gradient electrophoresis (TTGE). Functional PAH-ring hydroxylating dioxygenase (PAH-RHD α ) genes (DNA) and transcripts (RNA) were quantified through real-time PCR and RT-PCR. Without root exudates PHE degradation was rapid and complete within 5 days. Herbaspirillum sp. and Pseudomonas putida were the dominant strains. Percentage of PAH-RHD α relative to 16S rRNA, both for genes and transcripts, was the highest after only two days and then decreased. With phenanthrene and root exudates as carbon sources, only 50% of the PHE was degraded in 10 days. P. putida -related bacteria were also detected with other strains related to Pseudomonas sp. and Paenibacillus . PHE degradation was reduced, and the percentage of PAH-RHD α transcripts was lower with root exudates than with only PHE, but increased over the incubation, while PAH-RHD α gene copy number was higher.

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 13CO(2) 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(alpha)) 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(alpha) genes.

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% ([summation operator]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.

The objectives of this study were to determine whether the invasive plant Amaranthus viridis influenced soil microbial and chemical properties and to assess the consequences of these modifications on native plant growth. The experiment was conducted in Senegal at two sites: one invaded by A. viridis and the other covered by other plant species. Soil nutrient contents as well as microbial community density, diversity and functions were measured. Additionally, five sahelian Acacia species were grown in (1) soil disinfected or not collected from both sites, (2) uninvaded soil exposed to an A. viridis plant aqueous extract and (3) soil collected from invaded and uninvaded sites and inoculated or not with the arbuscular mycorrhizal (AM) fungus Glomus intraradices. The results showed that the invasion of A. viridis increased soil nutrient availability, bacterial abundance and microbial activities. In contrast, AM fungi and rhizobial development and the growth of Acacia species were severely reduced in A. viridis-invaded soil. Amaranthus viridis aqueous extract also exhibited an inhibitory effect on rhizobial growth, indicating an antibacterial activity of this plant extract. However, the inoculation of G. intraradices was highly beneficial to the growth and nodulation of Acacia species. These results highlight the role of AM symbiosis in the processes involved in plant coexistence and in ecosystem management programs that target preservation of native plant diversity.