Laboratoire Interdisciplinaire des Environnements Continentaux

Organic chemicals can contribute to local and regional losses of freshwater biodiversity and ecosystem services. However, their overall relevance regarding larger spatial scales remains unknown. Here, we present, to our knowledge, the first risk assessment of organic chemicals on the continental scale comprising 4,000 European monitoring sites. Organic chemicals were likely to exert acute lethal and chronic long-term effects on sensitive fish, invertebrate, or algae species in 14% and 42% of the sites, respectively. Of the 223 chemicals monitored, pesticides, tributyltin, polycyclic aromatic hydrocarbons, and brominated flame retardants were the major contributors to the chemical risk. Their presence was related to agricultural and urban areas in the upstream catchment. The risk of potential acute lethal and chronic long-term effects increased with the number of ecotoxicologically relevant chemicals analyzed at each site. As most monitoring programs considered in this study only included a subset of these chemicals, our assessment likely underestimates the actual risk. Increasing chemical risk was associated with deterioration in the quality status of fish and invertebrate communities. Our results clearly indicate that chemical pollution is a large-scale environmental problem and requires far-reaching, holistic mitigation measures to preserve and restore ecosystem health.

Growth factors mediate their diverse biologic responses (regulation of cellular proliferation, differentiation, migration and survival) by binding to and activating cell-surface receptors with intrinsic protein kinase activity named receptor tyrosine kinases (RTKs). About 60 RTKs have been identified and can be classified into more than 16 different receptor families. Their activity is normally tightly controlled and regulated. Overexpression of RTK proteins or functional alterations caused by mutations in the corresponding genes or abnormal stimulation by autocrine growth factor loops contribute to constitutive RTK signaling, resulting in alterations in the physiological activities of cells. The ErbB receptor family of RTKs comprises four distinct receptors: the EGFR (also known as ErbB1/HER1), ErbB2 (neu, HER2), ErbB3 (HER3) and ErbB4 (HER4). ErbB family members are often overexpressed, amplified, or mutated in many forms of cancer, making them important therapeutic targets. EGFR has been found to be amplified in gliomas and non-small-cell lung carcinoma while ErbB2 amplifications are seen in breast, ovarian, bladder, non-small-cell lung carcinoma, as well as several other tumor types. Several data have shown that ErbB receptor family and its downstream pathway regulate epithelial-mesenchymal transition, migration, and tumor invasion by modulating extracellular matrix (ECM) components. Recent findings indicate that ECM components such as matrikines bind specifically to EGF receptor and promote cell invasion. In this review, we will present an in-depth overview of the structure, mechanisms, cell signaling, and functions of ErbB family receptors in cell adhesion and migration. Furthermore, we will describe in a last part the new strategies developed in anti-cancer therapy to inhibit ErbB family receptor activation.

Present knowledge concerning the ecotoxic effects of nano-materials is very limited and merits to be documented more fully. For this purpose, we appraised the toxicity of nine metallic nano-powders (copper zinc iron oxide, nickel zinc iron oxide, yttrium iron oxide, titanium dioxide, strontium ferrite, indium tin oxide, samarium oxide, erbium oxide, and holmium oxide) and of two organic nano- powders (fullerene-C60 and single-walled carbon nanotube or SWCNT). After a simple process where nano-powders (NPs) were prepared in aqueous solution and filtered, they were then bioassayed across several taxonomic groups including decomposers (bacteria), primary producers (micro-algae), as well as primary and secondary consumers (micro-invertebrates and fish). Toxicity data generated on the 11 NPs reflected a wide spectrum of sensitivity that was biological level-, test-, and endpoint-specific. With all acute and chronic tests confounded for these 11 NPs, toxicity responses spanned over three orders of magnitude: >463 mg/L (24 h LC50 of the invertebrate Thamnoplatyurus platyurus for fullerene-C60) / 0.3 mg/L (96 h EC50 of the invertebrate Hydra attenuata for indium tin oxide), that is a ratio of 1543. On the basis of the MARA (Microbial Array for Risk Assessment) assay toxic fingerprint concept, it is intimated that NPs may have different modes of toxic action. When mixed in a 1:1 ratio with a certified reference material (CRM) sediment, two solid phase assays and an elutriate assay, respectively, showed that five NPs (copper zinc iron oxide, samarium oxide, erbium oxide, holmium oxide, and SWCNT) were able to increase both CRM sediment toxicity and its elutriate toxicity. This initial investigation suggests that chemicals emerging from nanotechnology may pose a risk to aquatic life in water column and sediment compartments and that further studies on their adverse effects are to be encouraged.

Summary Scientific understanding of acidification in aquatic ecosystems relies on effective assessment, which at present is mostly limited to chemical and sometimes structural biological variables. Effects on ecosystem functioning are, in contrast, largely neglected. Litter breakdown is a potentially useful, highly integrative and crucial process that could enhance such assessment programmes. Breakdown rates of beech Fagus sylvatica leaves were determined in 25 woodland headwater streams along an acidification gradient in the Vosges Mountains, France. Additional data relating to micro‐organisms (microbial respiration, fungal biomass and degree of conditioning measured as leaf palatability) and macroinvertebrates (shredder diversity, abundance and biomass) associated with decomposing leaves were collected to elucidate the mechanisms underlying leaf breakdown. Breakdown rates varied more than 20‐fold between the most acidified and circumneutral sites ( k = 0·0002–0·0055 day −1 ). Stream water alkalinity and total Al concentration together accounted for 88% of the variation in litter breakdown rates among streams. Microbial factors associated with decaying leaves, particularly microbial respiration, declined with increasing stream acidity and were significantly related to Ca 2+ and total Al concentrations. Total abundance, biomass and richness of leaf‐shredding invertebrates associated with decomposing leaves were not related to stream acidity. However, the abundance and biomass of the amphipod Gammarus fossarum , an acid‐sensitive and particularly efficient leaf‐shredder, showed a strong positive relationship with leaf breakdown rate. Gammarus abundance and microbial respiration together accounted for 85% of the variation in litter breakdown rates among streams. Synthesis and applications . These results indicate that leaf‐litter breakdown responds strongly to stream acidification, with both microbial decomposers and invertebrate detritivores markedly affected. Measuring leaf breakdown rate may be developed into a simple, powerful and low‐cost tool for assessing a critical component of ecosystem functioning. We advocate further investigation of this approach for the routine biomonitoring of freshwaters affected by, or recovering from, other anthropogenic stresses.

River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.

Abstract Aquatic ecologists face challenges in identifying the general rules of the functioning of ecosystems. A common framework, including freshwater, marine, benthic, and pelagic ecologists, is needed to bridge communication gaps and foster knowledge sharing. This framework should transcend local specificities and taxonomy in order to provide a common ground and shareable tools to address common scientific challenges. Here, we advocate the use of functional trait‐based approaches (FTBAs) for aquatic ecologists and propose concrete paths to go forward. Firstly, we propose to unify existing definitions in FTBAs to adopt a common language. Secondly, we list the numerous databases referencing functional traits for aquatic organisms. Thirdly, we present a synthesis on traditional as well as recent promising methods for the study of aquatic functional traits, including imaging and genomics. Finally, we conclude with a highlight on scientific challenges and promising venues for which FTBAs should foster opportunities for future research. By offering practical tools, our framework provides a clear path forward to the adoption of trait‐based approaches in aquatic ecology.

ABSTRACT The oxidation of alcohols and aldehydes is crucial for detoxification and efficient catabolism of various volatile organic compounds (VOCs). Thus, many Gram-negative bacteria have evolved periplasmic oxidation systems based on pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) that are often functionally redundant. Here we report the first description and characterization of a lanthanide-dependent PQQ-ADH (PedH) in a nonmethylotrophic bacterium based on the use of purified enzymes from the soil-dwelling model organism Pseudomonas putida KT2440. PedH (PP_2679) exhibits enzyme activity on a range of substrates similar to that of its Ca 2+ -dependent counterpart PedE (PP_2674), including linear and aromatic primary and secondary alcohols, as well as aldehydes, but only in the presence of lanthanide ions, including La 3+ , Ce 3+ , Pr 3+ , Sm 3+ , or Nd 3+ . Reporter assays revealed that PedH not only has a catalytic function but is also involved in the transcriptional regulation of pedE and pedH , most likely acting as a sensory module. Notably, the underlying regulatory network is responsive to as little as 1 to 10 nM lanthanum, a concentration assumed to be of ecological relevance. The present study further demonstrates that the PQQ-dependent oxidation system is crucial for efficient growth with a variety of volatile alcohols. From these results, we conclude that functional redundancy and inverse regulation of PedE and PedH represent an adaptive strategy of P. putida KT2440 to optimize growth with volatile alcohols in response to the availability of different lanthanides. IMPORTANCE Because of their low bioavailability, lanthanides have long been considered biologically inert. In recent years, however, the identification of lanthanides as a cofactor in methylotrophic bacteria has attracted tremendous interest among various biological fields. The present study reveals that one of the two PQQ-ADHs produced by the model organism P. putida KT2440 also utilizes lanthanides as a cofactor, thus expanding the scope of lanthanide-employing bacteria beyond the methylotrophs. Similar to the system described in methylotrophic bacteria, a complex regulatory network is involved in lanthanide-responsive switching between the two PQQ-ADHs encoded by P. putida KT2440. We further show that the functional production of at least one of the enzymes is crucial for efficient growth with several volatile alcohols. Overall, our study provides a novel understanding of the redundancy of PQQ-ADHs observed in many organisms and further highlights the importance of lanthanides for bacterial metabolism, particularly in soil environments.

In detritus-based ecosystems, autochthonous primary production contributes very little to the detritus pool. Yet primary producers may still influence the functioning of these ecosystems through complex interactions with decomposers and detritivores. Recent studies have suggested that, in aquatic systems, small amounts of labile carbon (C) (e.g., producer exudates), could increase the mineralization of more recalcitrant organic-matter pools (e.g., leaf litter). This process, called priming effect, should be exacerbated under low-nutrient conditions and may alter the nature of interactions among microbial groups, from competition under low-nutrient conditions to indirect mutualism under high-nutrient conditions. Theoretical models further predict that primary producers may be competitively excluded when allochthonous C sources enter an ecosystem. In this study, the effects of a benthic diatom on aquatic hyphomycetes, bacteria, and leaf litter decomposition were investigated under two nutrient levels in a factorial microcosm experiment simulating detritus-based, headwater stream ecosystems. Contrary to theoretical expectations, diatoms and decomposers were able to coexist under both nutrient conditions. Under low-nutrient conditions, diatoms increased leaf litter decomposition rate by 20% compared to treatments where they were absent. No effect was observed under high-nutrient conditions. The increase in leaf litter mineralization rate induced a positive feedback on diatom densities. We attribute these results to the priming effect of labile C exudates from primary producers. The presence of diatoms in combination with fungal decomposers also promoted decomposer diversity and, under low-nutrient conditions, led to a significant decrease in leaf litter C:P ratio that could improve secondary production. Results from our microcosm experiment suggest new mechanisms by which primary producers may influence organic matter dynamics even in ecosystems where autochthonous primary production is low.

* Ammonium and nitrate are the prevalent nitrogen sources for growth and development of higher plants. Here, we report on the characterization of the ammonium transporter (AMT) family in the perennial species Populus trichocarpa. * In silico analysis and expression analysis of AMT genes from poplar was performed. In addition, AMT1;2 and AMT1;6 function was studied in detail by heterologous expression in yeast. * The P. trichocarpa genome contains 14 putative AMTs, which is more than twice the number of AMTs in Arabidopsis. In roots, the high-affinity AMT1;2 strongly increased upon mycorrhiza formation and might be partly responsible for the high-affinity ammonium uptake component measured in poplar. Transcript level for the high-affinity AMT1;6 was strongly affected by the diurnal cycle. AMT3;1 was exclusively expressed in senescing poplar leaves. Remarkably AMT2;1 was highly expressed in leaves while AMT2;2 was mostly expressed in petioles. Specific expression of AMT1;5 in stamen and of AMT1;6 in female flower indicate that they have key functions in reproductive organ development in poplar. * The present study provides basic genomic and transcriptomic information for the poplar AMT family and will pave the way for deciphering the precise role of AMTs in poplar physiology.

Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.

Dispersal is an essential process in population and community dynamics, but is difficult to measure in the field. In freshwater ecosystems, information on biological traits related to organisms' morphology, life history and behaviour provides useful dispersal proxies, but information remains scattered or unpublished for many taxa. We compiled information on multiple dispersal-related biological traits of European aquatic macroinvertebrates in a unique resource, the DISPERSE database. DISPERSE includes nine dispersal-related traits subdivided into 39 trait categories for 480 taxa, including Annelida, Mollusca, Platyhelminthes, and Arthropoda such as Crustacea and Insecta, generally at the genus level. Information within DISPERSE can be used to address fundamental research questions in metapopulation ecology, metacommunity ecology, macroecology and evolutionary ecology. Information on dispersal proxies can be applied to improve predictions of ecological responses to global change, and to inform improvements to biomonitoring, conservation and management strategies. The diverse sources used in DISPERSE complement existing trait databases by providing new information on dispersal traits, most of which would not otherwise be accessible to the scientific community.

or Aqua Regia that under- and overestimate the reactive element contents, respectively. Low concentrations of oxyanions in our data set and structural underestimation of their reactive concentrations warrant further investigation.

Fused Filament Fabrication (FFF) is the process of 3D printing objects from melted plastic filament. The hot plastic exits a nozzle and fuses with the part just below, adding a layer of material to the object being formed. However, filament can only be deposited on top of an existing surface. Therefore, overhangs require a disposable support structure to be printed, temporarily supporting the threads of plastic that would otherwise hang in empty space. Existing techniques for support generation fall into two categories: The first allow for very reliable prints by enclosing the bottom of the object in a dense structure, at the expense of increased material usage and build times. The second generate thin hierarchical structures connecting to the surface in a sparse number of points. This uses less material, at the expense of reliability: the part might become unstable, the structure itself may become difficult to print, the bottom surface quality degrades. The user therefore has to correct the structure and its parameters for each new object. We propose to exploit the ability of FFF printers to print bridges across gaps. Since bridges are always supported by pillars at their extremities, they are both stronger and more stable than hierarchical tree structures. Our technique first selects the points to support based on overhang and part stability during the entire print process. It then optimizes for a printable scaffolding composed of bridges and vertical pillars, supporting all points. The result is an automated support generation technique using little material while ensuring fine surface quality and stability during the printing process.

The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium- and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a 'very high risk' of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate 'rapid' management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement.

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.

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

Large-scale production and incorporation of titanium dioxide nanoparticles (NP-TiO2 ) in consumer products leads to their potential release into the environment and raises the question of their toxicity. The bactericidal mechanism of NP-TiO2 under UV light is known to involve oxidative stress due to the generation of reactive oxygen species. In the dark, several studies revealed that NP-TiO2 can exert toxicological effects. However, the mode of action of these nanoparticles is still controversial. In the present study, we used a combination of fluorescent probes to show that NP-TiO2 causes Escherichia coli membrane depolarization and loss of integrity, leading to higher cell permeability. Using both transcriptomic and proteomic global approaches we showed that this phenomenon translates into a cellular response to osmotic stress, metabolism of cell envelope components and uptake/metabolism of endogenous and exogenous compounds. This primary mechanism of bacterial NP-TiO2 toxicity is supported by the observed massive cell leakage of K(+) /Mg(2+) concomitant with the entrance of extracellular Na(+), and by the depletion of intracellular ATP level.

Abstract Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.

A total diet study (TDS) was undertaken to estimate the chronic dietary exposure to pesticide residues and health risks for the French infants and young children below 3 years old. As a whole, 516 pesticides and metabolites were analysed in 309 food composite samples including 219 manufactured baby foods and 90 common foods, which cover 97% of infants and young children's diet. These composite samples were prepared using 5,484 food products purchased during all seasons from 2011 to 2012 and processed as consumed. Pesticide residues were detected in 67% of the samples and quantified in 27% of the baby food samples and in 60% of the common foods. Seventy-eight different pesticides were detected and 37 of these quantified at levels ranging from 0.02 to 594 µg/kg. The most frequently detected pesticides (greater than 5% samples) were (1) the fungicides 2-phenylphenol, azoxystrobin, boscalid, captan and its metabolite tetrahydrophthalimide, carbendazim, cyprodinil, difenoconazole, dodine, imazalil, metalaxyl, tebuconazole, thiabendazole, (2) the insecticides acetamiprid, pirimiphos-methyl and thiacloprid, (3) the herbicide metribuzin and (4) the synergist piperonyl butoxide. Dietary intakes were estimated for each of the 705 individuals studied and for 431 pesticides incl. 281 with a toxicological reference value (TRV). In the lower-bound scenario, which tends to underestimate the exposure, the TRV were never exceeded. In the upper-bound scenario that overestimates exposure, the estimated intakes exceeded the TRV for dieldrin and lindane (two persistent organic pollutants) and propylene thiourea, a metabolite of propineb. For these three substances, more sensitive analyses are needed to refine the assessment. For 17 other detected and/or prioritised pesticides, the risk could not be characterised due to the lack of a valid TRV, of certain food analyses or the absence of analytical standards for their metabolites.