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Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing?, Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Fabien Cholet reports financial support was provided by Microbiology Society. Cindy Smith reports financial support was provided by Science Foundation Ireland Starting Investigator Award. Cindy Smith reports financial support was provided by Royal Academy of Engineering. Cindy Smith reports financial support was provided by Engineering and Physical Sciences Research Council. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Fermented foods, including cheeses, have garnered increased interest in recent years for their potential health benefits. This study explores the biological properties of eight French raw-milk cheeses-goat cheese, Saint-Nectaire, Cantal, Bleu d'Auvergne, Roquefort, Comté, Brie de Meaux, and Epoisses-on oxidative processes using both in vivo ( Caenorhabditis elegans ) and in vitro (human leukocytes) models. A cheese fractionation protocol was adapted to study four fractions for each cheese: a freeze-dried fraction (FDC) corresponding to whole cheese, an apolar (ApE), and two polar extracts (W40 and W70). We showed that all cheese fractions significantly improved Caenorhabditis elegans ( C. elegans ) survival rates when exposed to oxidative conditions by up to five times compared to the control, regardless of the fractionation protocol and the cheese type. They were also all able to reduce the in vivo accumulation of reactive oxygen species (ROS) by up to 70% under oxidative conditions, thereby safeguarding C. elegans from oxidative damage. These beneficial effects were explained by a reduction in ROS production up to 50% in vitro in human leukocytes and overexpression of antioxidant factor-encoding genes ( daf-16 , skn-1 , ctl-2 , and sod-3 ) in C. elegans .

Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Selenium-79 is considered as a critical radionuclide in safety assessment of high-level radioactive waste deep geological repository in clay-rich formations, owing to its long half-life and its anionic form in three relevant oxidation states (VI, IV,-II). An in-depth understanding of the diffusive transport properties of Se is therefore essential, especially due to its high sensitivity to oxido-reduction conditions. Here, the mobility of selenite and selenate in claystone samples (Callovo-Oxfordian, East of Paris Basin, France) under anoxic conditions is assessed by combining batch and diffusion experiments, and synchrotron-based spectroscopic mapping of diffusion fronts. Results showed that selenite and selenate behaved distinctly. Selenate diffused similarly to the reference anionic tracer, 36Cl−, without significant sorption or reduction. Selenite showed a sorption behaviour that increased with the decrease of the initial concentration from 10−3 to 10−6 mol L−1, values of distribution ratio (R d) from batch experiments ranging from 10 to about 250 mL g−1. Selenite in-diffusion experiments showed that a pure diffusion model with reversible sorption was able to roughly reproduce the evolution of dissolved selenite in solution over time. However, additional reactions were required to properly describe the irregular shape of the selenite diffusion profiles in the solid. Mapping of Se oxidation state in diffusion fronts within the claystone coupons showed the presence of reduced Se (Se (0), Se(-I) and/or Se(-II)) along a fringe located at about 2 mm beneath the surface, possibly explaining the irregular shape of diffusion profiles. In the superficial zone (0–2 mm), oxidizing perturbations are assumed to account for the preservation of selenite under this oxidation state. These perturbations would also bias batch results in the same manner. Deeper in the claystone sample, diffusing selenite was observed, with a content steadily decreasing up to 7 mm from the inlet. The results suggest that, even after more than 500 days of diffusion, Se reduction would occur progressively along the diffusion pathways. • Selenate diffused similarly to 36Cl−, without significant sorption or reduction. • Selenite sorption increases with [Se(IV)] 0 decreasing from 10−3 to 10−6 mol L−1 • Oxidation state of selenium diffusing in clay rock was mapped using micro-XAS. • Irregular shape of Se(IV) diffusion profile is related to oxido-reduction processes. • In the first 2 mm of rock oxidizing artifacts preserve Se(IV) under this oxidation state. [ABSTRACT FROM AUTHOR]

The oxidation of sulfide ores is a common phenomenon. To better understand the current development and status of oxidation studies of sulfide ores (OSSO), a bibliometric analysis of OSSO was conducted by mapping the spatiotemporal distribution of the knowledge domain and the research focus using VOSviewer and Citespace tools. The data were derived from the Web of Science (WOS) core collection database from 2000 to 2018. Study emphases covered publication outputs, countries/regions, organizations, top journals, research focus and keyword co-occurrence network, and theme development. The results include the following findings: (1) The line of the 3-year moving average of publications (3-year MAP), h-index (3-year MAH), and authors (3-year MAA) increased from 2001 to 2018. Conversely, the h-index continuously declined. (2) Asia had the most publications, with 1052, followed by Europe, with 923, and America, with 767. China, the USA, and Australia are the most active countries. (3) The top 10 organizations with the most publications are five Chinese organizations and one organization from each of the following countries: Russia, Australia, France, and India. (4) Hydrometallurgy, Minerals Engineering, Ore Geology Reviews, Geochimica Et Cosmochimica Acta, and Economic Geology are among the top 10 journals that researchers are most concerned about. (5) Cooperation among different organization or different countries is the most effective way to produce the most influential papers. (6) The OSSO is still focused on the process of oxidation by using different methods and techniques. In future work, it is necessary to progress new methods to understand the process of self-heating and prevent spontaneous combustion disaster of sulfide ore which result from OSSO.

Mangroves are tidal wetlands that are often under strong anthropogenic pressures, despite the numerous ecosystem services they provide. Pollution from urban runoffs is one such threats, yet some mangroves are used as a bioremediation tool for wastewater (WW) treatment. This practice can impact mangrove crabs, which are key engineer species of the ecosystem. Using an experimental area with controlled WW releases, this study aimed to determine from an ecological and ecotoxicological perspective, the effects of WW on the red mangrove crab Neosarmatium africanum. Burrow density and salinity levels (used as a proxy of WW dispersion) were recorded, and a 3-week caging experiment was performed. Hemolymph osmolality, gill Na + /K + -ATPase (NKA) activity and gill redox balance were assessed in anterior and posterior gills of N. africanum. Burrow density decreased according to salinity decreases around the discharged area. Crabs from the impacted area had a lower osmoregulatory capacity despite gill NKA activity remaining undisturbed. The decrease of the superoxide dismutase activity indicates changes in redox metabolism. However, both catalase activity and oxidative damage remained unchanged in both areas but were higher in posterior gills. These results indicate that WW release may induce osmoregulatory and redox imbalances, potentially explaining the decrease in crab density. Based on these results we conclude that WW release should be carefully monitored as crabs are key players involved in the bioremediation process., (Copyright © 2019 Elsevier B.V. All rights reserved.)

A field-pilot bioreactor exploiting microbial iron (Fe) oxidation and subsequent arsenic (As) and Fe co-precipitation was monitored during 6 months for the passive treatment of As-rich acid mine drainage (AMD). It was implemented at the Carnoulès mining site (southern France) where AMD contained 790-1315 mg L -1 Fe(II) and 84-152 mg L -1 As, mainly as As(III) (78-83%). The bioreactor consisted in five shallow trays of 1.5 m 2 in series, continuously fed with AMD by natural flow. We monitored the flow rate and the water physico-chemistry including redox Fe and As speciation. Hydraulic retention time (HRT) was calculated and the precipitates formed inside the bioreactor were characterized (mineralogy, Fe and As content, As redox state). Since As(III) oxidation improves As retention onto Fe minerals, bacteria with the capacity to oxidize As(III) were quantified through their marker gene aioA. Arsenic removal yields in the pilot ranged between 3% and 97% (average rate (1.8 ± 0.8) ✕ 10 -8  mol L -1 s -1 ), and were positively correlated to HRT and inlet water dissolved oxygen concentration. Fe removal yields did not exceed 11% (average rate (7 ± 5) ✕ 10 -8  mol L -1 s -1 ). In the first 32 days the precipitate contained tooeleite, a rare arsenite ferric sulfate mineral. Then, it evolved toward an amorphous ferric arsenate phase. The As/Fe molar ratio and As(V) to total As proportion increased from 0.29 to 0.86 and from ∼20% to 99%, respectively. The number of bacterial aioA gene copies increased ten-fold during the first 48 days and stabilized thereafter. These results and the monitoring of arsenic speciation in the inlet and the outlet water, provide evidences that As(III) oxidized in the pilot. The biotreatment system we designed proved to be suitable for high As DMA. The formation of sludge highly enriched into As(V) rather than As(III) is advantageous in the perspective of long term storage., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Wetlands have been proposed to naturally attenuate U transfers in the environment via U complexation by organic matter and potential U reduction. However, U mobility may depend on the identity of particulate/dissolved uranium source materials and their redox sensitivity. Here, we examined the fate of uranium in a highly contaminated wetland (up to 4500 mg·kg -1 U) impacted by former mine water discharges. Bulk U L III -EXAFS and (micro-)XANES combined with SEM-EDXS analyses of undisturbed soil cores show a sharp U redox boundary at the water table, together with a major U redistribution from U(IV)-minerals to U(VI)-organic matter complexes. Above the water table, U is fully oxidized into mono- and bidentate U(VI)-carboxyl and monodentate U(VI)-phosphoryl complexes. Minute amounts of U(VI)-phosphate minerals are also observed. Below the water table, U is fully reduced and is partitioned between U(IV)-phosphate minerals (i.e., ningyoite and a lermontovite-like phase), and bidentate U(IV)-phosphoryl and monodentate U(IV)-carboxyl complexes. Such a U redistribution from U-minerals inherited from mine water discharge deposits could result from redox cycling nearby the water table fluctuation zone. Oxidative dissolution of U(IV)-phosphate minerals could have led to U(VI)-organic matter complexation, followed by subsequent reduction into U(IV)-organic complexes. However, uranium(IV) minerals could have been preserved in permanently waterlogged soil.

Molecular speciation of atmospheric organic matter was investigated during a short summer field campaign performed in a citrus fruit field in northern Corsica (June 2011). Aimed at assessing the performance on the field of newly developed analytical protocols, this work focuses on the molecular composition of both gas and particulate phases and provides an insight into partitioning behavior of the semi-volatile oxygenated fraction. Limonene ozonolysis tracers were specifically searched for, according to gas chromatography-mass spectrometry (GC-MS) data previously recorded for smog chamber experiments. A screening of other oxygenated species present in the field atmosphere was also performed. About sixty polar molecules were positively or tentatively identified in gas and/or particle phases. These molecules comprise a wide range of branched and linear, mono and di-carbonyls (C3-C7), mono and di-carboxylic acids (C3-C18), and compounds bearing up to three functionalities. Among these compounds, some can be specifically attributed to limonene oxidation and others can be related to α- or β-pinene oxidation. This provides an original snapshot of the organic matter composition at a Mediterranean site in summer. Furthermore, for compounds identified and quantified in both gaseous and particulate phases, an experimental gas/particle partitioning coefficient was determined. Several volatile products, which are not expected in the particulate phase assuming thermodynamic equilibrium, were nonetheless present in significant concentrations. Hypotheses are proposed to explain these observations, such as the possible aerosol viscosity that could hinder the theoretical equilibrium to be rapidly reached., (Copyright © 2015. Published by Elsevier B.V.)

This is the premier study designed to evaluate the impact of thermal pre-treatment on the availability of polycyclic aromatic hydrocarbons (PAHs) for successive removal by chemical oxidation. Experiments were conducted in two soils having different PAH distribution originating from former coking plant sites (Homécourt, H, and Neuves Maisons, NM) located in northeast of France. Soil samples were pre-heated at 60, 100, and 150 °C for 1 week under inert atmosphere (N2). Pre-heating resulted in slight removal of PAHs (<10%) and loss of extractable organic matter (EOM). Then, these pre-heated soil samples were subjected to Fenton-like oxidation (H2O2 and magnetite) at room temperature. Chemical oxidation in soil without any pre-treatment showed almost no PAH degradation underscoring the unavailability of PAHs. However, chemical oxidation in pre-heated soils showed significant PAH degradation (19, 29, and 43% in NM soil and 31, 36, and 47% in H soil pre-treated at 60, 100, and 150 °C, respectively). No preferential removal of PAHs was observed after chemical oxidation in both soils. These results indicated the significant impact of pre-heating temperature on the availability of PAHs in contaminated soils and therefore may have strong implications in the remediation of contaminated soils especially where pollutant availability is a limiting factor.

A new laboratory-made Zn-ferrite (ZnFe2O4) binding gel is fully tested using Diffusive Gradient in Thin films (DGT) probes to measure total As [including inorganic As(III) and As(V), as well as MonoMethyl Arsenic Acid (MMAA(V)) and DiMethyl Arsenic Acid (DMAA(V))] in river waters and sediment pore waters. The synthesis of the binding gel is easy, cheap and its insertion into the acrylamide gel is not problematic. An important series of triplicate tests have been carried out to validate the use of the Zn-ferrite binding gel in routine for several environmental matrixes studies, in order to test: (i) the effect of pH on the accumulation efficiency of inorganic As species; (ii) the reproducibility of the results; (iii) the accumulation efficiency of As species; (iv) the effects of the ionic strength and possible competitive anions; and (v) the uptake and the elution efficiency of As species after accumulation in the binding gel. All experimental conditions have been reproduced using two other existing binding gels for comparison: ferrihydrite and Metsorb® HMRP 50. We clearly demonstrate that the Zn-ferrite binding gel is at least as good as the two other binding gels, especially for pH values higher than 8. In addition, by taking into consideration the diffusion rates of As(III) and As(V) in the gel, combining the 3-mercaptopropyl [accumulating only As(III)] with the Zn-ferrite binding gels allows for performing speciation studies. An environmental study along the Marque River finally illustrates the ability of the new binding gel to be used for field studies., (Copyright © 2015. Published by Elsevier B.V.)

The pigments responsible for the yellow-orange coloration of apple juices have remained largely unknown up to now. Four French cider apple juices were produced in conditions similar to those used in the cider-making industry. The oxidized juices, characterized using the CIE L a b parameters, displayed various colors depending on the apple variety and native phenolic composition. HPLC-DAD-MS revealed contrasting pigment profiles related to oxidized tanning and nontanning molecules. The latter were divided into two groups according to their polarity and their visible spectra. With regard to phenolic classes, flavanol monomers and hydroxycinnamic acids played an essential role in the formation of oxidation products. Interestingly, dihydrochalcones appeared to include precursors of some yellow compounds. Indeed, the yellow pigment phloretin xyloglucoside oxidation product (PXGOPj), derived from phloretin xyloglucoside, was clearly identified in apple juices as a xyloglucose analogue of the yellow pigment phloridzin oxidation product (POPj), previously characterized in a model solution by Le Guernevé et al. (Tetrahedron Lett. 2004, 45 (35), 6673-6677).

Pseudomonas xanthomarina S11 is an arsenite-oxidizing bacterium isolated from an arsenic-contaminated former gold mine in Salsigne, France. This bacterium showed high resistance to arsenite and was able to oxidize arsenite to arsenate at concentrations up to 42.72 mM As[III]. The genome of this strain was sequenced and revealed the presence of three ars clusters. One of them is located on a plasmid and is organized as an "arsenic island" harbouring an aio operon and genes involved in phosphorous metabolism, in addition to the ars genes. Neither the aioXRS genes nor a specific sigma-54-dependent promoter located upstream of aioBA genes, both involved in regulation of arsenite oxidase expression in other arsenite-oxidizing bacteria, could be identified in the genome. This observation is in accordance with the fact that no difference was observed in expression of arsenite oxidase in P. xanthomarina S11, whether or not the strain was grown in the presence of As[III]., (Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.)

BOD5 dates back to 1912 when the Royal Commission decided to use the mean residence time of water in the rivers of England, 5 days, as a standard to measure the biochemical oxygen demand. Initially designed to protect the quality of river waters from extensive sewage discharge, the use of BOD5 has been quickly extended to waste water treatment plants (WWTPs) to monitor their efficiency on a daily basis. The measurement has been automatized but remains a tedious, time- and resource-consuming analysis. We have cross-validated a surrogate BOD5 method on two sites in France and in the USA with a total of 109 samples. This method uses a fluorescent redox indicator on a 96-well microplate to measure microbial catabolic activity for a large number of samples simultaneously. Three statistical tests were used to compare surrogate and reference methods and showed robust equivalence.

After a crude oil spill caused by a broken pipeline in 2009 to a gravel aquifer in southern France, degradation processes under various redox conditions progressively established, but at rates that predict a long life-time of the source under natural attenuation after partial source removal. In this study, we aimed at identifying the rate-limiting factors for each redox condition, with special emphasis on phosphate as limiting nutrient. The study was conducted in laboratory microcosms assembled with material collected on site: sediments, water from monitoring wells, oil and microbial sludge. Redox conditions were promoted by adding electron acceptors (either oxygen, nitrate, limonite (FeO(OH)), cryptomelane (K(Mn(4+),Mn(2+))8O16), or sulfate). For each condition, the role of phosphate was studied by repeated additions for up to 290days. The results showed a very strong stimulation of aerobic and denitrifying rates of oil degradation by phosphate, provided that oxygen and nitrate were repeatedly supplied. Phosphate caused also a marked stimulation of methanogenic degradation, and a relatively small stimulation of metal reduction. These anaerobic processes started only after marked lag phases, and phosphate shortened the lag phase for methanogenic degradation. Degradation of aromatic and aliphatic hydrocarbons with less than 8 carbons, including benzene, was confirmed even under unstimulated conditions. It is concluded that degradation rates at the site are limited by both, availability of electron acceptors and availability of phosphate needed for promoting microbial growth., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Producers of processed anchovies have developed hazard analysis and critical control points (HACCP) to guarantee the quality of their products. Nonetheless there is a lack of objective data to determine products' shelf life. The quality of a product is usually established on the basis of its safety and organoleptic properties. These parameters were assessed by monitoring the profiles of volatile compounds and quantitating six biogenic amines in samples of two types of processed anchovies during their shelf life. With regard to biogenic amines, quantities were below the regulatory limits throughout shelf life, except when a temperature abuse was applied for marinated samples. Moreover, this work highlights an optimum volatile profile at 5 and 6 months of storage for salted and marinated anchovies, respectively. This is the result of a higher content of six aldehyde and nine ketone compounds, mainly from lipid oxidation.

Aim: Fat mass localization affects lipid metabolism differently at rest and during exercise in overweight and normal-weight subjects. The aim of this study was to investigate the impact of a low vs high ratio of abdominal to lower-body fat mass (index of adipose tissue distribution) on the exercise intensity (Lipox(max)) that elicits the maximum lipid oxidation rate in normal-weight women., Methods: Twenty-one normal-weight women (22.0 ± 0.6 years, 22.3 ± 0.1 kg.m(-2)) were separated into two groups of either a low or high abdominal to lower-body fat mass ratio [L-A/LB (n = 11) or H-A/LB (n = 10), respectively]. Lipox(max) and maximum lipid oxidation rate (MLOR) were determined during a submaximum incremental exercise test. Abdominal and lower-body fat mass were determined from DXA scans., Results: The two groups did not differ in aerobic fitness, total fat mass, or total and localized fat-free mass. Lipox(max) and MLOR were significantly lower in H-A/LB vs L-A/LB women (43 ± 3% VO(2max) vs 54 ± 4% VO(2max), and 4.8 ± 0.6 mg min(-1)kg FFM(-1)vs 8.4 ± 0.9 mg min(-1)kg FFM(-1), respectively; P < 0.001). Total and abdominal fat mass measurements were negatively associated with Lipox(max) (r = -0.57 and r = -0.64, respectively; P < 0.01) and MLOR [r = -0.63 (P < 0.01) and r = -0.76 (P < 0.001), respectively]., Conclusion: These findings indicate that, in normal-weight women, a predominantly abdominal fat mass distribution compared with a predominantly peripheral fat mass distribution is associated with a lower capacity to maximize lipid oxidation during exercise, as evidenced by their lower Lipox(max) and MLOR., (Copyright © 2014 Elsevier Masson SAS. All rights reserved.)

The hydroxyl (OH) radical is the most important oxidant in the atmosphere since it controls its self-oxidizing capacity. The main sources of OH radicals are the photolysis of ozone and the photolysis of nitrous acid (HONO). Due to the attenuation of solar radiation in the indoor environment, the possibility of OH formation through photolytic pathways indoors has been ignored up to now. In the indoor air, the ozonolysis of alkenes has been suggested as an alternative route of OH formation. Models and indirect measurements performed up to now according to this hypothesis suggest concentrations of OH radicals on the order of 10(4)-10(5) molecules per cubic centimeter. Here, we present direct measurements of significant amounts of OH radicals of up to 1.8⋅10(6) molecules per cubic centimeter during an experimental campaign carried out in a school classroom in Marseille. This concentration is on the same order of magnitude of outdoor OH levels in the urban scenario. We also show that photolysis of HONO is an important source of OH radicals indoors under certain conditions (i.e., direct solar irradiation inside the room). Additionally, the OH concentrations were found to follow a linear dependence with the product J(HONO)⋅[HONO]. This was also supported by using a simple quasiphotostationary state model on the OH radical budget. These findings force a change in our understanding of indoor air quality because the reactivity linked to OH would involve formation of secondary species through chemical reactions that are potentially more hazardous than the primary pollutants in the indoor air.

The use of antibiotics in both human and veterinary medicine has led to increased presence of these compounds and antibiotic resistance in the environment. In this study, the effect of low, environmentally relevant (mg L(-1)) concentrations of vancomycin (VA), flumequine (FLU), and sulfamethoxazole (SMX) on nitrate reduction rates was studied in river sediments. Nitrate reduction rates were determined by supplying intact sediments for several weeks with both nitrate and antibiotics (ng L(-1), μg L(-1), and mg L(-1) concentrations), including a non-amended control. Furthermore the concentrations of the three investigated antibiotics were measured in the initial (natural) sediments and the sediments supplied with the antibiotics. The antibiotic concentrations in the sediments decreased (on average 62% for FLU and 93% for SMX) during the experiments, indicating loss of antibiotics due to sorption or (bio) degradation. Nitrate reduction rates were not affected by environmental concentrations of VA, FLU and SMX. FLU and SMX only partially inhibited nitrate reduction rates at high, therapeutic concentrations by 41 and 39% respectively. The three tested antibiotics significantly enhanced the production of nitrite, an intermediate in dissimilatory nitrate reduction. Nitrite production increased 1.9 and 1.4 fold for environmental VA concentrations (107 and 187 μg L(-1) respectively), application of 58 mg L(-1) SMX resulted in a 7.5 fold increase and augmented 16 and 8.5 fold in the presence of respectively 13 μg L(-1) and 52 mg L(-1) FLU. Even though inhibition of nitrate reduction rates was observed at therapeutic antibiotic concentrations, nitrate reduction proceeded under all experimental conditions, indicating the presence of resistance toward these antibiotics among the nitrate reducing bacteria. The accumulation of nitrite suggests that the nitrite reduction step was more affected than the overall nitrate reduction process., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Thaumarchaeota have been recognized as the main drivers of aerobic ammonia oxidation in many ecosystems. However, little is known about the role of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in lacustrine ecosystems. In this study, the photic zone of three contrasted freshwater ecosystems located in France was sampled during two periods: winter homothermy (H) and summer thermal stratification (TS), to investigate the distribution of planktonic AOA and AOB. We showed that AOB were predominant in nutrient-rich ecosystems, whereas AOA dominated when ammonia concentrations were the lowest and during winter, which could provide a favorable environment for their growth. Moreover, analyses of archaeal libraries revealed the ubiquity of the thaumarchaeal I.1a clade associated with higher diversity of AOA in the most nutrient-poor lake. More generally, this work assesses the presence of AOA in lakes, but also highlights the existence of clades typically associated with lacustrine and hot spring ecosystems and specific ecological niches occupied by these microorganisms., (Copyright © 2013. Published by Elsevier Masson SAS.)

Stable isotopic tracer methodologies now allow the evaluation of the reactivity of the endogenous (ambient) and exogenous (added) Hg to further predict the potential effect of Hg inputs in ecosystems. The differential reactivity of endogenous and exogenous Hg was compared in superficial sediments collected in a coastal lagoon (Arcachon Bay) and in an estuary (Adour River) from the Bay of Biscay (SW France). All Hg species (gaseous, aqueous, and solid fraction) and ancillary data were measured during time course slurry experiments under variable redox conditions. The average endogenous methylation yield was higher in the estuarine (1.2 %) than in the lagoonal sediment (0.5 %), although both methylation and demethylation rates were higher in the lagoonal sediment in relation with a higher sulfate-reducing activity. Demethylation was overall more consistent than methylation in both sediments. The endogenous and exogenous Hg behaviors were always correlated but the exogenous inorganic Hg (IHg) partitioning into water was 2.0-4.3 times higher than the endogenous one. Its methylation was just slightly higher (1.4) in the estuarine sediment while the difference in the lagoonal sediment was much larger (3.6). The relative endogenous and exogenous methylation yields were not correlated to IHg partitioning, demonstrating that the bioavailable species distributions were different for the two IHg pools. In both sediments, the exogenous IHg partitioning equaled the endogenous one within a week, while its higher methylation lasted for months. Such results provide an original assessment approach to compare coastal sediment response to Hg inputs.

Within cloud water, microorganisms are metabolically active and, thus, are expected to contribute to the atmospheric chemistry. This article investigates the interactions between microorganisms and the reactive oxygenated species that are present in cloud water because these chemical compounds drive the oxidant capacity of the cloud system. Real cloud water samples with contrasting features (marine, continental, and urban) were taken from the puy de Dôme mountain (France). The samples exhibited a high microbial biodiversity and complex chemical composition. The media were incubated in the dark and subjected to UV radiation in specifically designed photo-bioreactors. The concentrations of H(2)O(2), organic compounds, and the ATP/ADP ratio were monitored during the incubation period. The microorganisms remained metabolically active in the presence of ()OH radicals that were photo-produced from H(2)O(2). This oxidant and major carbon compounds (formaldehyde and carboxylic acids) were biodegraded by the endogenous microflora. This work suggests that microorganisms could play a double role in atmospheric chemistry; first, they could directly metabolize organic carbon species, and second, they could reduce the available source of radicals through their oxidative metabolism. Consequently, molecules such as H(2)O(2) would no longer be available for photochemical or other chemical reactions, which would decrease the cloud oxidant capacity.

Introduction: This article recalls and demonstrates that heterogeneous photocatalysis belongs to heterogeneous catalysis according to its initial history. There are criteria, which have to be imperatively taken into account to deal with true (photo-)catalytic reactions. The photocatalytic activity, chosen as the reaction rate, is governed by five physical parameters (mass of catalyst, wavelength, initial concentrations (or pressures) of the reactants, temperature (around room temperature), and radiant flux)., Discussion: Once performed in optimal conditions, the reaction has to be characterized with (a) its quantum yield (ratio of the reaction rate to the incident photon flux), (b) the turnover number (number of molecules converted per active site during a given time), and (c) the turnover frequency ( per second). The true catalytic nature demands that the conversion provides a number of converted molecules higher than the "stoichiometric threshold" defined as the number of the active sites initially present on the catalyst, i.e., that be much greater than 1, and possibly than at least two or three orders of magnitude. Eventually, a complete mass balance determination should be established for all elements. It is shown that the main reaction intermediates are radicals. All these concepts and principles are illustrated by various examples (selective mild oxidation reactions, water pollutants elimination, and air purification), leading to a list of recommendations for performing really true catalytic reactions.

Background: Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-independent approaches performed in the AMD of Carnoulès (France) confirmed this low species richness. However, very little is known about the cultured bacteria in this ecosystem. The aims of the study were firstly to apply novel culture methods in order to access to the largest cultured bacterial diversity, and secondly to better define the robustness of the community for 3 important functions: As(III) oxidation, cellulose degradation and cobalamine biosynthesis., Results: Despite the oligotrophic and acidic conditions found in AMDs, the newly designed media covered a large range of nutrient concentrations and a pH range from 3.5 to 9.8, in order to target also non-acidophilic bacteria. These approaches generated 49 isolates representing 19 genera belonging to 4 different phyla. Importantly, overall diversity gained 16 extra genera never detected in Carnoulès. Among the 19 genera, 3 were previously uncultured, one of them being novel in databases. This strategy increased the overall diversity in the Carnoulès sediment by 70% when compared with previous culture-independent approaches, as specific phylogenetic groups (e.g. the subclass Actinobacteridae or the order Rhizobiales) were only detected by culture. Cobalamin auxotrophy, cellulose degradation and As(III)-oxidation are 3 crucial functions in this ecosystem, and a previous meta- and proteo-genomic work attributed each function to only one taxon. Here, we demonstrate that other members of this community can also assume these functions, thus increasing the overall community robustness., Conclusions: This work highlights that bacterial diversity in AMDs is much higher than previously envisaged, thus pointing out that the AMD system is functionally more robust than expected. The isolated bacteria may be part of the rare biosphere which remained previously undetected due to molecular biases. No matter their current ecological relevance, the exploration of the full diversity remains crucial to decipher the function and dynamic of any community. This work also underlines the importance to associate culture-dependent and -independent approaches to gain an integrative view of the community function.

We are presenting here a multi-isotope approach (δ¹³C and δ¹⁸O of CO₂; δ¹³C and δD of CH₄) to assess (i) the level(s) of methane oxidation during waste biodegradation and its migration through a landfill cover in Sonzay (France), and (ii) its contribution to the atmospheric CO₂ levels above the surface. The isotope approach is compared to the more conventional mass balance approach. Results from the two techniques are comparable and show that the CH₄ oxidation under the landfill cover is heterogenous, with low oxidation percentages in samples showing high biogas fluxes, which was expected in clay covers presenting fissures, through which CH₄ is rapidly transported. At shallow depth, more immobile biogas pockets show a higher level of CH₄ oxidation by the methanotrophic bacteria. δ¹³C of CO₂ samples taken at different heights (from below the cover up to 8m above the ground level) were also used to identify and assess the relative contributions of its main sources both under the landfill cover and in the surrounding atmosphere., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

A novel strictly anaerobic bacterium designated SPDX02-08(T) was isolated from a deep terrestrial geothermal spring located in southwest France. Cells (1-2 × 2-6 μm) were non-motile, non sporulating and stained Gram negative. Strain SPDX02-08(T) grew at a temperature between 40 and 60°C (optimum 55°C), pH between 6.3 and 7.3 (optimum 7.2) and a NaCl concentration between 0 and 5 g/l (optimum 2 g/l). Sulfate, thiosulfate and sulfite were used as terminal electron acceptors, but not elemental sulfur, nitrate, nitrite, Fe (III) or fumarate. In the presence of sulfate, strain SPDX02-08(T) completely oxidized pyruvate, propionate, butyrate, isobutyrate, valerate, isovalerate and hexadecanoate. Stoichiometric measurements revealed a complete oxidation of part of lactate (0.125 mol of acetate produced per mole lactate oxidized). Strain SPDX02-08(T) required yeast extract to oxidize formate and H(2) but did not grow autotrophically on H(2). Among the substrates tested, only pyruvate was fermented. The G+C content of the genomic DNA was 57.6 mol%. Major cellular fatty acids of strain SPDX02-08(T) were iso-C(15:0), C(15:0), and C(16:0). Phylogenetic analysis of the 16S small-subunit (SSU) ribosomal RNA gene sequence indicated that strain SPDX02-08(T) belongs to the genus Desulfosoma, family Syntrophobacteraceae, having Desulfosoma caldarium as its closest phylogenetic relative (97.6% similarity). The mean DNA/DNA reassociation value between strain SPDX02-08(T) and Desulfosoma caldarium was 16.9 ± 2.7%. Based on the polyphasic differences, strain SPDX02-08(T) is proposed to be assigned as a new species of the genus Desulfosoma, Desulfosoma profundi sp. nov. (DSM 22937(T) = JCM 16410(T)). GenBank accession number for the 16S rRNA gene sequence of strain SPDX02-08(T) is HM056226.

Magnetotactic bacteria (MTB) mineralize nanosized magnetite or greigite crystals within cells and thus play an important role in the biogeochemical process. Despite decades of research, knowledge of MTB distribution and ecology, notably in areas subjected to oil industry activities, is still limited. In the present study, we investigated the presence of MTB in the Gulf of Fos, French Mediterranean coast, which is subjected to intensive oil industry activities. Microcosms containing sediments/water (1:2, v/v) from several sampling sites were monitored over several weeks. The presence of MTB was revealed in five of eight sites. Diverse and numerous MTB were revealed particularly from one site (named CAR), whilst temporal variations of a homogenous magnetotactic cocci population was shown within the LAV site microcosm over a 4-month period. Phylogenetic analysis revealed that they belonged to Alphaproteobacteria, and a novel genus from the LAV site was evidenced. Among the physicochemical parameters measured, a correlation was shown between the variation of MTB abundance in microcosms and the redox state of sulphur compounds.

In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities.

Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) were successfully developed to monitor functional aoxB genes as markers of aerobic arsenite oxidizers. DGGE profiles showed a shift in the structure of the aoxB-carrying bacterial population, composed of members of the Alpha-, Beta- and Gammaproteobacteria, depending on arsenic (As) and E(h) levels in Upper Isle River Basin waters. The highest aoxB gene densities were found in the most As-polluted oxic surface waters but without any significant correlation with environmental factors. Arsenite oxidizers seem to play a key role in As mobility in As-impacted waters.

Microbial mats are stratified microbial communities composed by highly inter-related populations and therefore are frequently chosen as model systems to study diversity and ecophysiological strategies. The present study describes an integrated approach to analyze microbial quinones and intact polar lipids (IPLs) in microbial mats within layers as thin as 500 microm by liquid chromatography-tandem mass spectrometry. Quinone profiles revealed important depth-related differences in community composition in two mat systems. The higher abundance of ubiquinones, compared to menaquinones, reflected the clear predominance of microorganisms belonging to aerobic alpha-, beta-, and gamma-Proteobacteria in Ebro delta estuarine mats. Hypersaline photosynthetic Camargue mats (France) showed a predominance of menaquinone-9 at the top of the mat, which is consistent with an important contribution of facultative aerobic or anaerobic bacteria in its photic zone. Quinone indices also indicated a higher diversity of non-phototrophs and a more anaerobic character in the hypersaline mats. Besides, the dissimilarity index suggested that the samples were greatly influenced by a depth-related redox state gradient. In the analysis of IPLs, there was a predominance of phosphatidylglycerols and sulfoquinovosyldiacylglycerols, the latter being an abundant biomarker of Cyanobacteria. This combined approach based on quinone and IPL analysis has proven to be a useful method to establish differences in the microbial diversity and redox state of highly structure microbial mat systems at a fine-scale level.

A significant amount of nitrogen entering river basins is denitrified in riparian zones. The aim of this study was to evaluate the influence of nitrate and carbon concentrations on the kinetic parameters of nitrate reduction as well as nitrous oxide emissions in river sediments in a tributary of the Marne (the Seine basin, France). In order to determine these rates, we used flow-through reactors (FTRs) and slurry incubations; flow-through reactors allow determination of rates on intact sediment slices under controlled conditions compared to sediment homogenization in the often used slurry technique. Maximum nitrate reduction rates (R(m)) ranged between 3.0 and 7.1microg Ng(-1)h(-1), and affinity constant (K(m)) ranged from 7.4 to 30.7mg N-NO(3)(-)L(-1). These values were higher in slurry incubations with an R(m) of 37.9microg Ng(-1)h(-1) and a K(m) of 104mg N-NO(3)(-)L(-1). Nitrous oxide production rates did not follow Michaelis-Menten kinetics, and we deduced a rate constant with an average of 0.7 and 5.4ng Ng(-1)h(-1) for FTR and slurry experiments respectively. The addition of carbon (as acetate) showed that carbon was not limiting nitrate reduction rates in these sediments. Similar rates were obtained for FTR and slurries with carbon addition, confirming the hypothesis that homogenization increases rates due to release of and increasing access to carbon in slurries. Nitrous oxide production rates in FTR with carbon additions were low and represented less than 0.01% of the nitrate reduction rates and were even negligible in slurries. Maximum nitrate reduction rates revealed seasonality with high potential rates in fall and winter and low rates in late spring and summer. Under optimal conditions (anoxia, non-limiting nitrate and carbon), nitrous oxide emission rates were low, but significant (0.01% of the nitrate reduction rates)., (Copyright 2009 Elsevier Ltd. All rights reserved.)

A novel anaerobic, chemo-organotrophic bacterium, designated VNs36(T), was isolated from a well that collected water from a deep saline aquifer used for underground gas storage at a depth of 830 m in the Paris Basin, France. Cells were curved motile rods or vibrios (3.0-5.0x0.5 microm). Strain VNs36(T) grew at temperatures between 20 and 50 degrees C (optimum 37 degrees C) and at pH values between 5.0 and 9.0 (optimum 6.9). It did not require salt for growth, but tolerated up to 20 g NaCl l(-1) (optimum 2 g l(-1)). In the presence of sulfate, strain VNs36(T) used lactate, formate and pyruvate as carbon and energy sources. The main fermentation products from lactate were acetate, H(2) and CO(2). Sulfate, thiosulfate and sulfite were used as electron acceptors, but not sulfur. The genomic DNA G+C content of strain VNs36(T) was 67.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs36(T) was affiliated with the family Desulfovibrionaceae within the class Deltaproteobacteria. On the basis of 16S rRNA gene sequence comparisons, DNA G+C content and the absence of desulfoviridin in cell extracts, it is proposed that strain VNs36(T) be assigned to a new genus, Desulfocurvus gen. nov., as a representative of a novel species, Desulfocurvus vexinensis sp. nov. The type species of this genus is Desulfocurvus vexinensis with the type strain VNs36(T) (=DSM 17965(T)=JCM 14038(T)).

In this study, we examined fat oxidation rates during exercise in obese pubescent boys. Three groups of pubescent boys (16 pre-pubescent, Tanner's stage I; 16 pubescent, Tanner's stage III; and 14 post-pubescent, Tanner's stage V) performed a graded test on a leg cycle ergometer. The first step of the test was fixed at 30 W and power was gradually increased by 20 W every 3.5 min. Oxygen consumption (VO(2)) and carbon dioxide production (VCO(2)) were determined as the means of measurements during the last 30 s of each step, which allowed us to calculate fat oxidation rates versus exercise intensity. Between 20 and 50% of peak oxygen consumption (VO(2peak)), fat oxidation rate in relative values (mg . min(-1) . kg FFM(-1)) decreased continuously with pubertal development. In the same way, the maximum rate of fat oxidation occurred at a lower percentage of VO(2peak) (pre-pubescent: 49.47 +/- 1.62%; pubescent: 47.43 +/- 1.26%; post-pubescent: 45.00 +/- 0.97%). Our results confirm that puberty is responsible for a decrease in fat free mass capacities to use fat during exercise. The results suggest that post-pubescent obese boys need to practise physical activity at a lower intensity than pre-pubescent boys to enhance lipolysis and diminish adipose tissue and the consequences of obesity.

A 3 year study of the infiltration of Lot River water into a well field located in an adjacent gravel and clay alluvial aquifer was conducted to assess the importance of organic matter regarding the redox processes which influence groundwater quality in a positive (denitrification) or negative (Mn dissolution) manner. Chloride was used to quantify the mixing of river water with groundwater. According to modeling with PHREEQC, the biodegradation of the infiltrated dissolved organic carbon (DOCi) is not sufficient to explain the observed consequences of the redox reactions (dissolved O2 depletion, denitrification, Mn dissolution). Another electron donor source must therefore be involved: we propose solid organic carbon (SOC) as a likely candidate, if made available for degradation by prior hydrolysis. Its contribution to redox reactions could be significant (30-80% of the total organic carbon consumed by redox reactions during river bank filtration). We show here also that even though the first few meters of infiltration are highly reactive, significant redox reactions can take place further in the aquifer, possibly affecting groundwater quality away from the river bank.

In addition to methane (CH(4)) and carbon dioxide (CO(2)), landfill gas may contain more than 200 non-methane organic compounds (NMOCs) including C(2+)-alkanes, aromatics, and halogenated hydrocarbons. Although the trace components make up less than 1% v/v of typical landfill gas, they may exert a disproportionate environmental burden. The objective of this work was to study the dynamics of CH(4) and NMOCs in the landfill cover soils overlying two types of gas collection systems: a conventional gas collection system with vertical wells and an innovative horizontal gas collection layer consisting of permeable gravel with a geomembrane above it. The 47 NMOCs quantified in the landfill gas samples included primarily alkanes (C(2)-C(10)), alkenes (C(2)-C(4)), halogenated hydrocarbons (including (hydro)chlorofluorocarbons ((H)CFCs)), and aromatic hydrocarbons (BTEXs). In general, both CH(4) and NMOC fluxes were all very small with positive and negative fluxes. The highest percentages of positive fluxes in this study (considering all quantified species) were observed at the hotspots, located mainly along cell perimeters of the conventional cell. The capacity of the cover soil for NMOC oxidation was investigated in microcosms incubated with CH(4) and oxygen (O(2)). The cover soil showed a relatively high capacity for CH(4) oxidation and simultaneous co-oxidation of the halogenated aliphatic compounds, especially at the conventional cell. Fully substituted carbons (TeCM, PCE, CFC-11, CFC-12, CFC-113, HFC-134a, and HCFC-141b) were not degraded in the presence of CH(4) and O(2). Benzene and toluene were also degraded with relative high rates. This study demonstrates that landfill soil covers show a significant potential for CH(4) oxidation and co-oxidation of NMOCs.

High resolution profiles of Mn, Tl and Fe concentrations have been assessed in the pore waters of river Leie sediments at Warneton and Menen (at the border of Belgium and France) by DET (Diffusive Equilibrium in Thin Films) and DGT (Diffusive Gradients in Thin Films) techniques. The oxidized, solid Mn (IV), Tl (III) and Fe (III) compounds were reduced in the suboxic (+255 to -20 mV versus Standard Hydrogen Electrode (SHE)) riverine sediments and since these reduced species are much more soluble also they are released into the pore waters. The highest DET (total dissolved) concentrations of Fe (76 mg l(-1)), Mn (2 mg l(-1)) were observed at the station of Menen, while Tl maxima differed only slightly between the 3 surveys (21 to 27 microg l(-1)). The average ratios of Fe/Mn/Tl in the pore waters at the 3 sampling stations are fairly constant for both the DET and DGT samplings. However, the results indicate that compared to Fe and Tl a greater proportion of the Mn measured by DET is accumulated by DGT, reflecting the ready supply of Mn from solid phase to solution.

Nitrified leachate recirculation has been proposed as a promising strategy for sustainable landfill management. In four test reactors, nitrate or nitrite was added (250 mg N-NO(x)(-)L(-1)) during municipal solid waste biodegradation. Nitrogen-oxides reduction reactions were monitored. Denitrification was the main nitrogen reducing reaction observed. On one hand, during the acidogenic waste degradation phase, as high amounts of volatile fatty acids (VFA) were present, nitrogen-oxides reductions were interpreted as heterotrophic denitrifications. On the other hand, denitrification reactions occurring during the late methanogenic phase were accompanied by sulphate productions and, as VFA were not detected, it was probably an autotrophic reaction. Denitrification inhibition was observed once. Ammonium concentration increased suggesting the occurrence of a dissimilatory nitrate reduction to ammonium (DNRA). Statistical treatment of analytical data revealed that only H(2)S concentration had a significant negative effect on N(2) production in our system. NO production was observed once when nitrite was injected during the acidogenic phase resulting in a total waste degradation inhibition. These results indicate that the consequences of nitrified leachate recirculation in full-scale landfills need to be carefully examined especially during the acidogenic phase or in the presence of waste containing high quantities of sulphur.

The techniques of DET (diffusive equilibrium in thin films) and DGT (diffusive gradients in thin films) were applied to obtain high-resolution vertical profiles of trace metals in freshwater sediments. In the framework of the EU-Interreg project Stardust (http://www.vliz.be/projects/stardust/) between France and Belgium, in which the mobility of sediment bound metals is investigated, sediment samples were collected from the Upper Scheldt River (at Helkijn, Belgium) and the Leie River (at Warneton, located at the Belgian-French border). Intra- and inter-laboratory comparisons of the gel techniques were carried out between the two laboratories involved. In general, a good agreement was observed, taking sediment heterogeneity into account. At both stations, metal pore water profiles show more or less similar tendencies although the sediment at Warneton was more anoxic than at Helkijn. A strong correlation between Fe and Co was found at Helkijn as well as at Warneton. The metal gradients at the water/sediment interface were calculated from the high resolution profiles and the conventional, low resolution profiles. Significant differences were observed.

Many developed countries have targeted landfill methane recovery among greenhouse gas mitigation strategies, since methane is the second most important greenhouse gas after carbon dioxide. Major questions remain with respect to actual methane production rates in field settings and the relative mass of methane that is recovered, emitted, oxidized by methanotrophic bacteria, laterally migrated, or temporarily stored within the landfill volume. This paper presents the results of extensive field campaigns at three landfill sites to elucidate the total methane balance and provide field measurements to quantify these pathways. We assessed the overall methane mass balance in field cells with a variety of designs, cover materials, and gas management strategies. Sites included different cell configurations, including temporary clay cover, final clay cover, geosynthetic clay liners, and geomembrane composite covers, and cells with and without gas collection systems. Methane emission rates ranged from -2.2 to >10,000 mg CH(4) m(-2) d(-1). Total methane oxidation rates ranged from 4% to 50% of the methane flux through the cover at sites with positive emissions. Oxidation of atmospheric methane was occurring in vegetated soils above a geomembrane. The results of these studies were used as the basis for guidelines by the French environment agency (ADEME) for default values for percent recovery: 35% for an operating cell with an active landfill gas (LFG) recovery system, 65% for a temporary covered cell with an active LFG recovery system, 85% for a cell with clay final cover and active LFG recovery, and 90% for a cell with a geomembrane final cover and active LFG recovery.

Pollution from agriculture and urban effluents influences the ecology and biochemical functioning of the Seine River. Nitrification dominates nitrogen transformations downstream of the effluents of the Paris wastewater treatment plant (WWTP) at Achères, treating, by activated sludge the wastewater of 6.5 million inhabitant equivalents from Paris and its suburbs, without nitrification and denitrification treatment. It discharges effluents containing large amounts of nitrogen, ammonium mostly (approximately 30 mg L(-1) N-NH(4+) L(-1)), on average 45 mg L(-1) of suspended particulate matter, high quantities of total organic carbon (approximately 30 mg C L(-1)) largely biodegradable (40%), and high concentration in total phosphorus ( approximately 3 mg Tot P L(-1)), as well as microorganisms. Ammonium, brought into the river system, is slowly nitrified in the lower Seine River and especially in the freshwater estuary. The nitrifying activities can be observed by measuring inorganic nitrogen compound concentrations and potential activities. To understand the contributions of the WWTP effluents, the upstream agricultural runoff water and the Seine tributaries, it is useful to investigate the bacterial community. Whereas ammonia oxidation has been widely studied, the second step, i.e. nitrite oxidation, is less well understood. We have previously analysed the ammonium-oxidizing bacterial (AOB) community in the Seine (Cébron, A., Berthe, T., Garnier, J., 2003. Nitrification and nitrifying bacteria in the lower Seine River and estuary (France). Appl. Environ. Microbiol. 69, 7091-7100; Cébron, A., Coci, M., Garnier, J., Laanbroek, H.J., 2004. DGGE analysis of the ammonia oxidizing bacterial community structure in the lower Seine River: impact of the Paris wastewater effluents. Appl. Environ. Microbiol. 70, 6726-6737), and focus here on the composition of the nitrite-oxidizing bacterial (NOB) community. As no general molecular probe targeting all known NOBs is currently available, we chose to target and quantify (by competitive PCR) the two genera Nitrobacter and Nitrospira assumed to be the major players in nitrite oxidation in freshwater environments. Nitrobacter species were dominant in the upstream Seine River basin but Nitrospira was the dominant NOB downstream of the WWTP. These two genera were equally represented in WWTP effluents. In the Seine River estuary, especially in the salinity gradient, the Nitrobacter proportion increases and that of Nitrospira disappears, possibly due dilution by seawater.

Reigous acid creek originating from the Carnoulès tailings impoundment supplies high concentrations of arsenic under soluble (up to approximately 4 mg/l) and particulate (up to 150 mgAs/g) phases to the Amous river, situated at the drainage basin of the Rhône river (Southern France). The metalloid is present as As(III) (>95%) in Reigous creek water while As(V) predominates (50-80%) in the solid phase, i.e. schwertmannite. At the confluence between acid (pH<5) creek and alkaline Amous river, As(III) concentrations decrease ten-fold through dilution and formation of As-rich ferrihydrite (As/Fe=0.02-0.1) containing 10-30% As(III). However, these attenuation processes are not efficient in the summer heatwave of 2003 since As concentrations in Amous river water (>or=20 microg/l) and As/Fe ratios in particulate matter (>or=0.07) are closed to those of Reigous creek (

A novel sulfate-reducing bacterium was isolated from a well that collected water from a deep aquifer at a depth of 430 m in the Paris Basin, France. The strain, designated B7-43T, was made up of vibrioid cells that were motile by means of a single polar flagellum. Cells contained desulfoviridin. In the presence of sulfate, the following substrates were used as energy and carbon sources: lactate, pyruvate, malate, fumarate, ethanol, butanol, acetate/H2 and glycine. Sulfite and thiosulfate were also used as electron acceptors in the presence of lactate. In the absence of electron acceptors, pyruvate, malate and fumarate were fermented. Optimal growth was obtained in 1 g NaCl l(-1) and at pH 7. On the basis of 16S rRNA gene sequence analysis, the isolate was most closely related to members of the genus Desulfovibrio (90 % similarity). It is thus proposed that strain B7-43T (=DSM 16056T=ATCC BAA-905T) represents a novel species within this genus, Desulfovibrio putealis sp. nov.

In situ microsensor measurements were combined with biogeochemical methods to determine oxygen, sulfur, and carbon cycling in microbial mats growing in a solar saltern (Salin-de-Giraud, France). Sulfate reduction rates closely followed the daily temperature changes and were highest during the day at 25 degrees C and lowest during the night at 11 degrees C, most probably fueled by direct substrate interactions between cyanobacteria and sulfate-reducing bacteria. Sulfate reduction was the major mineralization process during the night and the contribution of aerobic respiration to nighttime DIC production decreased. This decrease of aerobic respiration led to an increasing contribution of sulfide (and iron) oxidation to nighttime O2 consumption. A peak of elemental sulfur in a layer of high sulfate reduction at low sulfide concentration underneath the oxic zone indicated anoxygenic photosynthesis and/or sulfide oxidation by iron, which strongly contributed to sulfide consumption. We found a significant internal carbon cycling in the mat, and sulfate reduction directly supplied DIC for photosynthesis. The mats were characterized by a high iron content of 56 micromol Fe cm(-3), and iron cycling strongly controlled the sulfur cycle in the mat. This included sulfide precipitation resulting in high FeS contents with depth, and reactions of iron oxides with sulfide, especially after sunset, leading to a pronounced gap between oxygen and sulfide gradients and an unusual persistence of a pH peak in the uppermost mat layer until midnight.

The Seine River is strongly affected by the effluents from the Acheres wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study was to investigate the diversity of the ammonia-oxidizing bacterial population by identifying autochthonous bacteria from upstream and/or allochthonous ammonia-oxidizing bacteria from the WWTP effluents. Measurements of potential nitrifying activity, competitive PCR, and denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments specific to ammonia-oxidizing bacteria (AOB) were used to explore the succession and shifts of the ammonia-oxidizing community in the lower Seine River and to analyze the temporal and spatial functioning of the system at several different sampling dates. A major revelation was the stability of the patterns. The CTO primers used in this study (G. A. Kowalchuk, J. R. Stephen, W. D. Boer, J. I. Prosser, T. M. Embley, and J. W. Woldendorp, Appl. Environ. Microbiol. 63:1489-1497, 1997) were shown not to be completely specific to AOB of the beta subclass of Proteobacteria. We further demonstrated that when DGGE patterns are interpreted, all the different bands must be sequenced, as one major DGGE band proved to be affiliated with a group of non-AOB in the beta subclass of Proteobacteria. The majority of AOB (75 to 90%) present in the lower Seine river downstream of the effluent output belong to lineage 6a, represented by Nitrosomonas oligotropha- and Nitrosomonas ureae-like bacteria. This dominant lineage was represented by three bands on the DGGE gel. The major lineage-6a AOB species, introduced by the WWTP effluents, survived and might have grown in the receiving medium far downstream, in the estuary; it represented about 40% of the whole AOB population. The other two species belonging to lineage 6a seem to be autochthonous bacteria. One of them developed a few kilometers downstream of the WWTP effluent input in an ammonia-enriched environment, and the other appeared in the freshwater part of the estuary and was apparently more adapted to estuarine conditions, i.e., an increase in the amount of suspended matter, a low ammonia concentration, and high turnover of organic matter. The rest of the AOB population was represented in equal proportions by Nitrosospira- and Nitrosococcus mobilis-like species.

An alkene-degrading, sulfate-reducing bacterium, strain PF2803T, was isolated from oil-polluted sediments (Fos Harbour, France). The cells were found to be Gram-negative, non-sporulating, non-motile and to have a slightly curved rod shape. Optimum growth occurred at 1 % (w/v) NaCl, pH 6.8 and 28-30 degrees C. Strain PF2803T oxidized alkenes (from C8 to C23). The G + C content of the genomic DNA was 57.8 mol% (HPLC). On the basis of 16S rRNA gene sequence analyses, strain PF2803T belongs to the family 'Desulfobacteraceae' in the class 'Deltaproteobacteria', with Desulfatibacillum aliphaticivorans as its closest relative (99.6 % identity). Comparative sequence analyses of the dissimilatory sulfite reductase (dsrAB) gene supported the affiliation of strain PF2803T to the genus Desulfatibacillum. DNA-DNA hybridization with its closest taxon demonstrated 48.4 % similarity. On the basis of the results of physiological and genetic analyses, strain PF2803T is identified as a novel species of the genus Desulfatibacillum, for which the name Desulfatibacillum alkenivorans sp. nov. is proposed. The type strain is PF2803T (= DSM 16219T = ATCC BAA-924T).

The potential impact of indigenous bacterial processes on the release of heavy metals from dredged sediment deposits was investigated. Batch re-suspension experiments were conducted in order to investigate the release of Zn, Cd, Cu and Pb from a polluted anoxic sediment submitted to oxidative perturbations. The concentrations of heavy metals, sulphate and dissolved organic carbon (DOC) were periodically recorded, and cell counts were performed to follow the evolution of several bacterial species. The specific effects of microbial processes were quantified by performing re-suspension assays on sterilised samples. Moreover, the effect of an initial acidification of the system was studied. The results showed that metal release was mainly due to oxidation of sulphide minerals contained in the sediment. Sulphur-oxidising bacteria such as Acidithiobacillus thiooxidans were identified to play a major role in the process, by enhancing the oxidation kinetic. However, the acid production resulting from these reactions was almost totally buffered by the dissolution of the calcite present in the sediment. Copper was released to a lesser extent, and a strong association with organic matter was observed. Lead was not observed in solution, because of its low solubility at neutral conditions and of its re-adsorption on the solid phase. The initial acidification of the system resulted in an faster growth of the acidophilic A. thiooxidans. A subsequent pH drop originating from microbial processes was then observed during the first stages of the experiment. As a consequence, drastic increases in metal (Zn, Cd) release were observed.

Total dissolved trace and major metals and their partitioning in porewater sediment have been investigated at two sites in the Seine River estuary (France). For this purpose, solid phase extraction (SPE) has been employed using specific chelating resins for the separation and preconcentration of organic and inorganic forms of studied metals under controlled (N2) inert atmosphere. In fact, the study is focused on the development of a method for sample collection and handling under inert atmosphere in order to avoid some potential artefacts of the extracted porewater, to preserve the samples from possible chemical oxidation changes and to determine metals partitioning between organic and inorganic forms. For this point, a separation and preconcentration method using two columns in series (chelamine and C18 columns) was used. The trace and major metals fixed on the two resins for all determinations were stripped by nitric acid (2 M) and analyzed by Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES) and Zeeman Graphite Furnace Atomic Absorption Spectroscopy (ZGF-AAS). The relationship between the distribution of metals and physico-chemical parameters such as pH and Eh (redox potential) as a function of depth was discussed. Some tendency in the distributions and seasonal variability of these traces and major metals are improved. The concentrations for all studied metals decreased as a function of depth where iron and manganese were found at mg L(-1) levels and other metals were found at [micro sign]g L(-1) levels, as well as there were significant fractions of all metals (except of manganese) which were complexed by organic matter. The comparison of data for the major elements (Fe and Mn), obtained by direct determination (without preconcentration) and preconcentration, show a very good recovery.