Background Soil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is usually performed using metagenomic sequences acquired for the same sample. However, such hugely diverse metagenomic datasets are difficult to assemble; in parallel, theoretical proteomes from isolates available in generic databases are of high quality. Both these factors advocate for the use of theoretical proteomes in metaproteomics interpretation pipelines. Here, we examined a number of database construction strategies with a view to increasing the outputs of metaproteomics studies performed on soil samples. Results The number of peptide-spectrum matches was found to be of comparable magnitude when using public or sample-specific metagenomics-derived databases. However, numbers were significantly increased when a combination of both types of information was used in a two-step cascaded search. Our data also indicate that the functional annotation of the metaproteomics dataset can be maximized by using a combination of both types of databases. Conclusions A two-step strategy combining sample-specific metagenome database and public databases such as the non-redundant NCBI database and a massive soil gene catalog allows maximizing the metaproteomic interpretation both in terms of ratio of assigned spectra and retrieval of function-derived information.

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Sedimentary archives provide long-term records of particulate-bound pollutants (e.g. trace metal elements, PAHs). We present the results obtained on a set of selected cores from alluvial deposits within the Seine River basin, integrating the entire area's land uses upstream of the core location, collected upstream and downstream of Paris megacity and in the estuary. Some of these cores go back to the 1910s. These records are complemented by in-depth studies of the related pollution emissions, their regulation and other environmental regulations, thereby establishing contaminant trajectories. They are representative of a wide range of contamination intensities resulting from industrial, urban and agricultural activities and their temporal evolution over a 75,000 km 2 territory. A wide set of contaminants, including metals, radionuclides, pharmaceuticals and up to 50 persistent organic pollutants, have been analysed based on the Seine River sediment archives. Altogether, more than 70 particulate contaminants, most of them regulated or banned (OSPAR convention, European Water Framework Directive (WFD 2000/60/EC)), were measured in dated cores collected at 7 sites, resulting in a large data set. After drawing a picture of the literature devoted to sedimentary archives, the findings resulting from several decades of research devoted to the Seine River basin will be used, together with other studies on other French and foreign rivers, to illustrate the outstanding potential of sedimentary archives. The limitations of using sedimentary archives for inter-site comparison and the approaches developed in the PIREN-Seine to overcome such limitations such as selecting pertinent indicators (specific fluxes, per capita release, leakage rate, etc.) will be described. The very complex interactions between humans and their environment will be addressed through questions such as the impact on the spatial and temporal trajectories of contaminants of factors such as wastewater management, deindustrialisation within the Seine River basin, implementation of national and EU environmental regulations, etc. This chapter will show how such studies can reveal the persistence of the contamination and the emergence of new pollutants, e.g. antibiotics. It will propose indicators for the evaluation of the environment resilience and the efficiency of environmental policies.

Abstract. Environmental pollution by polychlorinated biphenyls (PCBs) is a key cause for concern about river quality because of their low degradation rates leading to their accumulation in sediments and living organisms. An original interdisciplinary work was conducted along the four main French rivers (Seine, Rhône, Loire and Garonne rivers), which flow into major European seas. We completed a dataset based on sediment analyses provided by monitoring agencies, port authorities and research teams on different solid matrices (sediment cores, bed and flood deposits, suspended particulate matter and dredged sediments). This dataset focused on the seven indicator PCBs and their sum (ΣPCBi) from 1945 to 2018 (nΣPCBi =1416). Special effort was put into the quality control to provide robust spatio-temporal information. Taking into account hydrological and human drivers, we outlined two main pollution trends: (1) from 1945 to 1975, a quick increase in ΣPCBi (up to 4 mg kg−1 dry weight, dw) and a sharp decrease in the 1980s on the Seine and Loire rivers and (2) increasing but moderate ΣPCBi levels (50 to 150 µg kg−1 dw) followed by a decline after the 1990s on the Rhône and Garonne rivers. In addition to these patterns, PCB emissions from urban and industrial areas or accidental events were significant in each river. Finally, when calculating specific flux, the Rhône exhibited the uppermost ΣPCBi load (up to 12 µgm-2yr-1 in 1977–1987), at least 25 % higher than those of the Seine and Loire rivers, while the Garonne showed a very low flux. In western Europe, we confirmed that the Rhône, Seine and Loire rivers contribute significantly to the PCB contamination of the seas, while French specific ΣPCBi fluxes are 2 orders of magnitude lower than those found in American or Asian rivers. The dataset is available at https://doi.org/10.1594/PANGAEA.904277 (Dendievel et al., 2019).

Abstract. Environmental pollution by Polychlorinated Biphenyls (PCBs) is a key concern about river quality because of their low degradation rates leading to their accumulation in sediments or living organisms. This original interdisciplinary work was conducted at a large scale along the four main French rivers (Seine, Rhône, Loire and Garonne Rivers), which flow into major European seas. We completed a dataset based on sediment analyses provided by monitoring agencies, port authorities and research teams on different solid matrices (cores, bed and flood sediments, suspended particulate matters, dredged sediments). This dataset (n=1416) focused on the seven indicator PCBs and their sum (∑PCBi) from 1945 to 2018. Special effort was put on the quality control to provide robust spatio-temporal information. Taking into account hydrological and human drivers, we outlined two main pollution trends: (1) from 1945 to 1975, a quick increase of ∑PCBi (up to 4 mg.kg−1 dry weight, dw) and a sharp decrease in the 1980s on the Seine and Loire Rivers; (2) increasing but moderate ∑PCBi levels (50 to 150 µg.kg−1 dw) followed by a decline after the 1990s on the Rhône and Garonne Rivers. In addition to these patterns, PCBs emissions from urban and industrial areas or accidental events were significant on each river. Finally, when calculating specific fluxes, the Rhône River exhibited the biggest ∑PCBi load (up to 12 µg.m−2.year−1 in 1977–1987), at least 25 % higher than those of the Seine and Loire Rivers, while the Garonne River showed very low fluxes. French specific ∑PCBi fluxes are two orders of magnitude lower than those found in American or Asian Rivers. In Europe, we confirmed that the Rhone and Seine Rivers provide a major supply of PCBi to the Western Mediterranean and the English Channel, respectively. The dataset is available at https://doi.pangaea.de/10.1594/PANGAEA.904277.

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Thanks to the use of filters collected daily in the west of Paris, we confirm the passage of the lead-laden plume following the fire on the roof and spire of Notre-Dame Cathedral in April 2019. The measured concentrations on the filter (Pb = 1.4 μg m −3 ), scanning electron microscopy and Hysplit simulation, correspond to an estimate of a few hundred kilograms of lead that would have been volatilized and then oxidized in the form of micronic and submicronic aerosols. The concentrations found in the plume are, however, much lower than those found in the environment in the 1980s and 1990s but are 100 times higher than those found in times prior to and after the fire. The isotopic signature of the plume is almost identical to that of the fine Pb dust found inside the Notre-Dame building. It is different from the isotopic signature of the Parisian atmosphere before and after the fire, but it is similar to that of the atmospheric Pb legacy recorded by peat cores over the last 300 years in France. The presence of very fine lead-bearing particles makes them potentially transportable over long distances after large urban fires. Our study shows the value of daily aerosol sampling to retrospectively trace the plumes of air pollutants from industrial accidents but also from historical monument fires such as Notre-Dame in 2019.