Microbial processes can be involved in the remobilization of uranium (U) from reduced sediments under O2 reoxidation events such as water table fluctuations. Such reactions could be typically encountered after U-bearing sediment dredging operations. Solid U(IV) species may thus reoxidize into U(VI) that can be released in pore waters in the form of aqueous complexes with organic and inorganic ligands. Non-uraninite U(IV) species may be especially sensitive to reoxidation and remobilization processes. Nevertheless, little is known regarding the effect of microbially mediated processes on the behaviour of U under these conditions.

Transcriptome contigs of Dreissena rostriformis bugensis in fasta format

Temperature is known to stimulate metabolism with cascading effects on multiple biological processes. These effects may, however, vary across processes, types of organisms or levels of biological organisation. They can also vary with nutrient availability, with potentially stronger temperature effects when nutrients are not limiting. This context dependence of temperature effects on processes challenges our ability to anticipate their consequences on ecosystems in a changing world. In headwater streams, the decomposition of allochthonous leaf litter, driven by both microbial decomposers and invertebrates, is known to respond to both temperature and nutrient availability. These food webs are highly tractable and a useful model system to investigate the variations of temperature effects on processes across types of organisms (microbes versus invertebrates), resource availability levels (nutrient concentration), and levels of biological organisation (from individual to ecosystem). In a microcosm experiment, we measured the effects of temperature and nitrogen availability (four levels each) on respiration rates of litter-consuming microbes and invertebrates and their decomposition activity in different contexts of food web complexity. The latter included one treatment without invertebrate detritivore (microbial decomposers only), three single invertebrate taxa (Gammarus, Potamophylax, and Sericostoma) treatments, and one mixed invertebrate taxa treatment (three‐species altogether). Microbial processes increased nearly exponentially with temperature (Arrhenius model, activation energy (± 95% confidence interval) = 0.56 ± 0.53 and 1.00 ± 0.23 eV for litter decomposition and respiration), while invertebrate‐driven processes increased (activation energy from 0.47–1.15 eV) up to a maximal value at an intermediate temperature (c. 11–15°C depending on species and process), above which process rates decreased. By contrast, litter consumption in mixed invertebrate species treatments was not significantly influenced by temperature, because of a negative effect of species mixing occurring above 12°C. Nitrogen had a weaker influence, only slightly stimulating litter consumption by mixed‐species invertebrates, which limited the scope for synergies with temperature effects. Our results raise issues about how aquatic litter consumers meet their energy requirements at high temperature and suggest that a general consequence of warming could be loss of carbon through mineralisation in headwater stream food webs. In several aspects, our results deviate from expectations based on universal relationships between temperature and individual metabolism (e.g. metabolic theory of ecology), suggesting that we may need to develop less simplistic assumptions to predict the consequence of warming on ecosystem processes.

In addition to global warming, aquatic ecosystems are currently facing multiple global changes among which include changes in nitrogen (N) loads. While several studies have investigated both temperature and N impacts on aquatic ecosystems independently, knowledge on their interactive effects remains scarce. In forested headwater streams, decomposition of leaf litter represents the main process ensuring the transfer of nutrients and energy to higher trophic levels, followed by autochthonous primary production, mainly ensured by phototrophic biofilms. The main aim of this study was to disentangle the independent and combined effects of temperature increase and nutrient availability on the relative importance of brown and green processes involved in stream functioning. We hypothesised that water temperature and nutrients would lead to a general increase in leaf-litter decomposition and primary production, but that the intensity of these effects would be largely modulated by competitive interactions arising between microorganisms as well as by the top-down control of microorganisms by macro-invertebrates. Macro-invertebrates would, in turn, be bottom-up controlled by microbial resources quality. To test these hypotheses, we conducted a 56-day experiment in artificial streams containing leaf litter, microbial decomposers and biofilm inoculum, and an assemblage of macro-invertebrates. Two water inorganic N:phosphorus (P) ratios (33 and 100, molar ratios) and two temperatures (ambient, +2 degrees C) were manipulated, each treatment being replicated three times. Fungal and biofilm growth as well as leaf-litter decomposition and primary production were quantified. Top-down impacts of invertebrate primary consumers on brown and green compartments were evaluated using exclosures while bottom-up control was evaluated through the measurement of resource stoichiometry and fatty acid profiles, as well as quantification of macro-invertebrate growth and survival. Contrary to expectations, microbial decomposition was not significantly stimulated by nutrient or temperature manipulations, while primary production was only improved under ambient temperature. In the + 2 degrees C treatment with high N:P, greater biofilm biomass was associated with lower fungal development, which indicates competition for nutrients in these conditions. Temperature increased macro-invertebrate growth and leaf-litter consumption, but this effect was independent of any improvement of basal resource quality, suggesting that temperature mediated changes in consumer metabolism and activity was the main mechanism involved. Most of our hypotheses that were based on simplified laboratory observations have been rejected in our semi-controlled mesocosms. Our study suggests that the complexity of biological communities might greatly affect the response of ecosystems to multiple stressors, and that interactions between organisms must be explicitly taken into account when investigating the impacts of global change on ecosystem functioning.

Dreissenids are established model species for ecological and ecotoxicological studies, since they are sessile and filter feeder organisms and reflect in situ freshwater quality. Despite this strong interest for hydrosystem biomonitoring, omics data are still scarce. In the present study, we achieved full de novo assembly transcriptomes of digestive glands to gain insight into Dreissena polymorpha and D. rostriformis bugensis molecular knowledge. Transcriptomes were obtained by Illumina RNA sequencing of seventy-nine organisms issued from fifteen populations inhabiting sites that exhibits multiple freshwater contamination levels and different hydrosystem topographies (open or closed systems). Based on a recent de novo assembly algorithm, we carried out a complete, quality-checked and annotated transcriptomes. The power of the present study lies in the completeness of transcriptomes gathering multipopulational organisms sequencing and its full availability through an open access interface that gives a friendly and ready-to-use access to data. The use of such data for proteogenomic and targeted biological pathway investigations purpose is promising as they are first full transcriptomes for this two Dreissena species.

Carbon cycling in headwater streams is mostly driven by the decomposition of allochthonous organic matter, and to a lesser extent by primary production. Quantifying the influence of temperature on these processes is therefore essential to better anticipate the consequences of global warming for stream ecological functioning. In this study, we measured alder litter microbial decomposition and associated fungal biomass and diversity, using leaf discs enclosed in fine-mesh bags along a natural geothermal temperature gradient, in both spring and winter. We monitored the chlorophyll-a accrual in biofilms growing on ceramic tiles. The temperature gradient, from upstream to downstream, ranged from 15.3 to 14.2 °C in spring and 18.2 to 13.2 °C in winter. Autotrophs and heterotrophs exhibited contrasting responses to temperature. The expected positive effect of temperature was actually observed for chlorophyll-a accrual only, while an apparent temperature-independence of litter decomposition rate was found. Moreover, temperature effects on heterotrophic and autotrophic organisms depended on the season, with higher litter decomposition rates, sporulation rates, fungal biomass and chlorophyll-a in spring, despite a lower mean water temperature than in winter. Together, these results suggest that the influence of temperature remained largely overrode by seasonal effects. This result is likely due to annual variations in light availability, and may involve indirect positive interactions between microbial primary producers and decomposers.

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).

We combined microscopic and molecular methods to investigate fungal assemblages on alder leaf litter exposed in the benthic and hyporheic zones of five streams across a gradient of increasing acidification for 4 weeks. The results showed that acidification and elevated Al concentrations strongly depressed sporulating aquatic hyphomycetes diversity in both zones of streams, while fungal diversity assessed by denaturing gradient gel electrophoresis (DGGE) appeared unaffected. Clone library analyses revealed that fungal communities on leaves were dominated by members of Ascomycetes and to a lesser extent by Basidiomycetes and Chytridiomycetes. An important contribution of terrestrial fungi was observed in both zones of the most acidified stream and in the hyporheic zone of the reference circumneutral stream. The highest leaf breakdown rate was observed in the circumneutral stream and occurred in the presence of both the highest diversity of sporulating aquatic hyphomycetes and the highest contribution to clone libraries of sequences affiliated with aquatic hyphomycetes. Both methods underline the major role played by aquatic hyphomycetes in leaf decomposition process. Our findings also bring out new highlights on the identity of leaf-associated fungal communities and their responses to anthropogenic alteration of running water ecosystems.

This study describes the biodegradation of phenanthrene in aqueous media in the presence and in the absence of a surfactant, Brij 30. Biodegradations were performed using either Pseudomonas putida DSMZ 8368 or a bacterial consortium Pyr01 isolated from one PAHs-polluted site. P . putida degraded phenanthrene to form 1-hydroxy-2-naphthoic acid (1H2Na) as the major metabolite. LC–MS analysis revealed the production of complementary intermediates in the presence of Brij 30, showing intense ions at mass-to-charge ratios ( m/z ) 97 and 195. Higher phenanthrene biodegradation rate was obtained in the presence of Brij 30. Conversely, in the case of Pyr01consortium, the addition of Brij 30 (0.5 g L −1 ) had a negative effect on biodegradation: no phenanthrene biodegradation products were detected in the medium, whereas a production of several intermediates ( m/z 97, 195 and 293) was obtained without surfactant. New results on phenanthrene metabolism by P . putida DSMZ 8368 and Pyr01 consortium in the presence and in the absence of Brij 30 we obtained. They confirm that the knowledge of the effect of a surfactant on bacterial cultures is crucial for the optimization of surfactant-enhanced PAHs biodegradation.

To counteract forest decline due to anthropogenic acidification, two catchments located on granite and on sandstone bedrock were limed (2.5 t/ha). The catchments are located in strongly affected areas in the Vosges Mountains of northeastern France. Four years after liming, structure of soil bacterial communities and community-level physiological profiling (CLPP) were investigated at two seasons. Bacterial communities were compared with those of two reference adjacent catchments to highlight changes induced by liming. Denaturing gradient gel electrophoresis (DGGE) and Biolog Ecoplate™ analysis revealed that liming modified the structure of bacterial communities and the CLPPs, suggesting that moderate large-scale liming has a sustainable impact on bacterial communities of forest soils. Moreover, significantly higher responses from limed soils were observed for a larger number of Biolog Ecoplate substrates compared to control soils. Analysis of 16S rRNA gene clone libraries showed that taxonomic diversity was slightly lower in limed soils, particularly within acidobacterial and Gram-positive groups, whereas proteobacterial diversity increased in limed soils. The relative abundance of dominant taxa showed that the ratio between Proteobacteria and Acidobacteria was higher in limed soils. This large-scale field study documents the effects of a four year old liming on bacterial communities of forest soils by providing a common indicator based on analysis of metabolic potential activities of heterotroph communities and by identifying major taxonomic changes in bacterial community structure. The results confirm previous observations showing that the ratio between Proteobacteria and Acidobacteria could be a microbial indicator of soil quality improvement.

Anthropogenic acidification in headwater streams is known to affect microbial assemblages involved in leaf litter breakdown. Far less is known about its potential effects on microbial enzyme activities. To assess the effects of acidification on microbial activities associated with decaying leaves, a 70-day litter bag experiment was conducted in headwater streams at six sites across an acidification gradient. The results revealed that microbial leaf decomposition was strongly and negatively correlated with total Al concentrations (r = −0.99, p < 0.001) and positively correlated with Ca2+ concentrations (r = 0.94, p = 0.005) and pH (r = 0.93, p = 0.008). Denaturing gradient gel electrophoresis analyses showed that microbial assemblages differed between non-impacted and impacted sites, whereas fungal biomass associated with decaying leaves was unaffected. The nutrient content of leaf detritus and ecoenzymatic activities of carbon (C), nitrogen (N) and phosphorus (P) acquisition revealed that N acquisition was unaltered, while P acquisition was significantly reduced across the acidification gradient. The P content of leaf litter was negatively correlated with total Al concentrations (r = −0.94, p < 0.01) and positively correlated with decomposition rates (r = 0.95, p < 0.01). This potential P limitation of microbial decomposers in impacted sites was confirmed by the particularly high turnover activity for phosphatase and imbalanced ratios between the ecoenzymatic activities of C and P acquisition. The toxic form of Al has well-known direct effects on aquatic biota under acidic conditions, but in this study, Al was found to also potentially affect microbially mediated leaf processing by interfering with the P cycle. These effects may in turn have repercussions on higher trophic levels and whole ecosystem functioning.

BACKGROUND:Di-(2-ethylhexyl)-phthalate (DEHP) is a commonly used plasticizer in polyvinylchloride (PVC) formulations and a potentially non-genotoxic carcinogen. The aim of this study was to identify genes whose level of expression is altered by DEHP by using a global wide-genome approach in Syrian hamster embryo (SHE) cells, a model similar to human cells regarding their responses to this type of carcinogen. With mRNA Differential Display (DD), we analysed the transcriptional regulation of SHE cells exposed to 0, 12.5, 25 and 50 μM of DEHP for 24 hrs, conditions which induced neoplastic transformation of these cells. A real-time quantitative polymerase chain reaction (qPCR) was used to confirm differential expression of genes identified by DD.RESULTS:Gene expression profiling showed 178 differentially-expressed fragments corresponding to 122 genes after tblastx comparisons, 79 up-regulated and 43 down-regulated. The genes of interest were involved in many biological pathways, including signal transduction, regulation of the cytoskeleton, xenobiotic metabolism, apoptosis, lipidogenesis, protein conformation, transport and cell cycle. We then focused particularly on genes involved in the regulation of the cytoskeleton, one of the processes occurring during carcinogenesis and in the early steps of neoplastic transformation. Twenty one cytoskeleton-related genes were studied by qPCR. The down-regulated genes were involved in focal adhesion or cell junction. The up-regulated genes were involved in the regulation of the actin cytoskeleton and this would suggest a role of cellular plasticity in the mechanism of chemical carcinogenesis. The gene expression changes identified in the present study were PPAR-independent.CONCLUSION:This study identified a set of genes whose expression is altered by DEHP exposure in mammalian embryo cells. This is the first study that elucidates the genomic changes of DEHP involved in the organization of the cytoskeleton. The latter genes may be candidates as biomarkers predictive of early events in the multistep carcinogenic process.

ABSTRACT The arsenic resistance gene cluster of Microbacterium sp. A33 contains a novel pair of genes ( arsTX ) encoding a thioredoxin system that are cotranscribed with an unusual arsRC2 fusion gene, ACR3 , and arsC1 in an operon divergent from arsC3 . The whole ars gene cluster is required to complement an Escherichia coli ars mutant. ArsRC2 negatively regulates the expression of the pentacistronic operon. ArsC1 and ArsC3 are related to thioredoxin-dependent arsenate reductases; however, ArsC3 lacks the two distal catalytic cysteine residues of this class of enzymes.

Mycobacterium sp. strain SNP11 is able to grow with pyrene, fluoranthene, phenanthrene and fluorene the sole carbon and energy sources. A probe based on the previously described gene pdoA2, which encodes the alpha subunit of a PAH ring-hydroxylating dioxygenase in Mycobacterium sp. strain 6PY1 [S. Krivobok et al., Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases, J. Bacteriol. 185(13) (2003) 3828-3841], was used to isolate a 14 kb DNA fragment from strain SNP11. Twelve putative open reading frames (ORFs), divided into two groups by a promoter intergenic region, were detected in this DNA sequence. The first gene cluster, located upstream of the promoter region, showed low but significant deduced amino acid sequence homologies with enzymes involved in aromatic degradation. The second gene cluster, under control of the promoter, contained pdoA2 (designated phdA in this study) and several other ORFs with deduced amino acid sequences closely related to enzymes involved in the phenanthrene-degrading pathway of Nocardioides sp. strain KP7. Gene expression analysis in Mycobacterium smegmatis mc(2)155 revealed broad substrate specificity of the ring-hydroxylating dioxygenase, since transformant cells containing phdAB strongly oxidized fluoranthene, phenanthrene, anthracene, fluorine and dibenzofuran. Laser desorption/ionization time-of-flight mass spectrometry (LDI-ToF MS) analyses of culture media after PAH degradation by M. smegmatis transformants also revealed that the second gene cluster, located downstream of the promoter, takes an active share in initial phenanthrene and anthracene degradation by allowing transformation of these two PAHs in aromatic ring-cleaved metabolites. (c) 2006 Elsevier Masson SAS. All rights reserved.

Mycobacterium sp. SNP11 has a high PAH biodegradation potential. In this paper, the toxicity of pyrene, fluoranthene, phenanthrene, and their dead-end metabolites, accumulated in the media after biodegradation by Mycobacterium sp. SNP11, were evaluated by a screening battery of acute, chronic, and genotoxic tests. According to the bioassays, performed on bacteria (Vibrio fischeri, Salmonella typhimurium strains TA1535/pSK1002, TA97a, TA98, TA100), algae (Pseudokirchneriella subcapitata), and crustaceans (Daphnia magna, Ceriodaphnia dubia), total disappearance or a very significant reduction of the (geno)toxic potential was observed after PAH degradation by Mycobacterium sp. SNP11.