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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Martin, Olivier; Fernandez-Diclo, Yasmil; Coville, Jérôme; Soubeyrand, Samuel;

    International audience; Insect-borne diseases are diseases carried by insects affecting humans, animals or plants. They have the potential to generate massive outbreaks such as the Zika epidemic in 2015-2016 mostly distributed in the Americas, the Pacific and Southeast Asia, and the multi-foci outbreak caused by the bacterium {\it Xylella fastidiosa} in Europe in the 2010s. In this article, we propose and analyze the behavior of a spatially-explicit compartmental model adapted to pathosystems with fixed hosts and mobile vectors disseminating the disease. The behavior of this model based on a system of partial differential equations is complementarily characterized via a theoretical study of its equilibrium states and a numerical study of its transitive phase using global sensitivity analysis. The results are discussed in terms of implications concerning the surveillance and control of the disease over a medium-to-long temporal horizon.

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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Nonlinear Analysis Real World Applications
    Other literature type . Article . 2021 . Peer-reviewed
    License: Elsevier TDM
    https://doi.org/10.48550/arxiv...
    Article . 2020
    License: arXiv Non-Exclusive Distribution
    Data sources: Datacite
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  • Authors: Sessa, Valentina; Assoumou, Edi; Bossy, Mireille; Carvalho, Sílvia; +1 Authors

    A big challenge of sustainable power systems is the integration of climate variability into the operational and long-term planning processes. In this paper, we focus on the run-of-river based hydropower generation on a European scale. In particular, we deal with the modeling of this form of power production based on climate variables. Translating time series of climate data (precipitation and air temperature) into time series of run-of-river based hydropower generation is not an easy task as it is necessary to capture the complex relationship between the availability of water and the generation of electricity. Indeed, this kind of electricity generation is limited by the flow of the river in which the power plants are located. Moreover, the water flow is a nonlinear function of the climate variables and the geographical characteristics of the river basins. Finally, the impact of the climate variables on the runoff may occur with a certain delay, whose determination depends on physically based phenomena (e.g., melting snow-local temperature). In this work, we first compare well-established machine learning regression algorithms to be used for modeling the run-of-river hydropower generation. Then, the technique showing to have the best performance is used for producing long-term estimates of hydropower capacity factors based on future climate scenarios for each European country.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Cornacchia, Ivano; Tomas, Séverine; Douzals, Jean-Paul; Courault, Dominique;

    [Departement_IRSTEA]Ecotechnologies [TR1_IRSTEA]INSPIRE [ADD1_IRSTEA]Équiper l'agriculture; The reuse of treated wastewater (TWW) for sprinkler irrigation could potentially diffuse pathogen-containing droplets off the application area. Wind and other unfavorable climatic factors enhance irrigation drift and bioaerosol dispersion, exposing humans to potentially severe health risks including the spread of diseases. Few studies have quantified bioaerosols during both spraying and airborne transport phases. Studies of effective sampling strategies to better qualify the dispersion process are also required. This paper presents experimentsconducted in a wind tunnel for a deeper understanding of the effects of wind and temperature on pathogen or contaminant airborne dispersal and transport. It is the first time that passive collectors [polyvinyl chloride (PVC) lines] and active samplers (AGI-4 impinger) have been compared under analogous wind conditions using a fluorescent tracer. Droplet-size distribution was also investigated at 12 m from the boomwith a NanoMoudi 122-NR cascade impactor in increasing wind conditions from 1 to 3 ms−1. PVC lines return a detailed evolution of the sprayed volume within a short range from the boom and for concentrated fluxes. Transport assessment of PVC lines indicates that transport and permanently airborne condition of the spray notably grow with increasing wind, resulting in a more compact and concentrated plume; mean transport increases from 0.13 to 1.18 Lh−1 m−2 at 7.7 m from the nozzle as the wind velocity increases from 1 to 3 ms−1. AGI-4 appears more suitable to assess finely aerosolized conditions because of its greater sensitivity compared to PVC lines as shown for sample values less than 1 Lh−1 m−2. The comparison between the AGI-4 and PVC lines shows higher values of recovery for the active samplers compared to the PVC lines. The total volume collected by the impingers was 2.93% of the sprayed volume, approximately twice that collected by PVC lines under analogous conditions, even though their sampling surface was only 1.54% that of PVC lines. Droplet-size distributions from the cascade impactor denote a median volume diameter from 1.1 to 2 μm, for the nozzle type used, and a relevant reduction in recovery at stronger wind velocities. An empirical relation time of flight is proposed as a first step in developing decision models that can be used to make sprinkler irrigation safe and to define standards for TWW reuse in agricultural practices (e.g., safe distance of application depending upon wind conditions and droplet-size distribution).

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Nicholas K. Geitner; Christine Ogilvie Hendren; Geert Cornelis; Ralf Kaegi; +37 Authors

    International audience; The chemical composition and properties of environmental media determine nanomaterial (NM) transport, fate, biouptake, and organism response. To compare and interpret experimental data, it is essential that sufficient context be provided for describing the physical and chemical characteristics of the setting in which a nanomaterial may be present. While the nanomaterial environmental, health and safety (NanoEHS) field has begun harmonization to allow data comparison and re-use (e.g. using standardized materials, defining a minimum set of required material characterizations), there is limited guidance for standardizing test media. Since most of the NM properties driving environmental behaviour and toxicity are medium-dependent, harmonization of media is critical. A workshop in March 2016 at Duke University identified five categories of test media: aquatic testing media, soil and sediment testing media, biological testing media, engineered systems testing media and product matrix testing media. For each category of test media, a minimum set of medium characteristics to report in all NM tests is recommended. Definitions and detail level of the recommendations for specific standardized media vary across these media categories. This reflects the variation in the maturity of their use as a test medium and associated measurement techniques, variation in utility and relevance of standardizing medium properties, ability to simplify standardizing reporting requirements, and in the availability of established standard reference media. Adoption of these media harmonization recommendations will facilitate the generation of integrated comparable datasets on NM fate and effects. This will in turn allow testing of the predictive utility of functional assay measurements on NMs in relevant media, support investigation of first principles approaches to understand behavioral mechanisms, and support categorization strategies to guide research, commercial development, and policy.

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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Article . 2019
    Data sources: NARCIS
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  • Authors: Camilo Corrales, David; Baranger, Alain; Jumel, Stephane; Leclerc, Melen; +5 Authors

    International audience

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    Authors: Barillé, Laurent; Bris, Anthony Le; Goulletquer, Philippe; Thomas, Yoann; +7 Authors

    International audience; Oyster production has historically taken place in intertidal zones, and shellfish farms already occupy large extents of the French intertidal space. The expansion of French shellfish aquaculture within intertidal areas is therefore spatially limited, and moving production to the subtidal offshore environment is considered to be a possible solution to this problem. Finding new sites along the French Atlantic coast was studied here from the perspective of small oyster companies run by young farmers, who are interested in offshore bivalve aquaculture expansion compatible with their investment capacity. In assessing the feasibility of such offshore production, we considered three main issues: (1) bivalve growth potential and (2) technical feasibility and conflicting uses, both within a spatial framework, as well as (3) the steps and barriers of the administrative licensing process. Oyster spat in an experimental offshore cage showed significantly faster growth, in terms of both weight and length, compared to those in an intertidal cage, mainly due to lower turbidity and full-time feeding capacity (i.e., constant immersion in the water). A combination of Earth Observation data and bivalve ecophysiological modelling was then used to obtain spatial distribution maps of growth potential, which confirmed that offshore sites have better potential for oyster growth than the traditionally oyster-farmed intertidal sites overall, but that this is highly spatially variable. Small-scale producers indicated two technical factors constraining where farms could be located: bathymetry must be between 5 and 20 m and the distance from a harbor no more than five nautical miles. These were included along with maps of various environmental and socioeconomic constraints in a Spatial Multi-Criteria Evaluation (SMCE). Touristic traffic and bottom trawling by fisherman were found to be the two other most restrictive variables. The GIS-based SMCE developed in this study showed that there is almost 400 km 2 of highly-to very highly-suitable area within which to develop offshore aquaculture using simple, low-cost bottom-cage techniques, and can be used to assist the shellfish industry in the Marine Spatial Planning decision-making process, still in progress in this coastal area. However, the complexity of the administrative processes necessary to obtain an offshore license is perceived as a stronger barrier by farmers owning small companies than site selection, technical feasibility, and required investments, and will be crucial to address in order to realistically proceed to offshore cultivation. The process demonstrated here, and the results are relevant to other coastal and offshore locations throughout the world and can be adapted for other species.

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    Horizon / Pleins textes
    Other literature type . 2020
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    https://doi.org/10.1016/j.aqua...
    Other literature type . Article . 2020 . Peer-reviewed
    License: Elsevier TDM
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    Authors: Richter, Daniel J.; Watteaux, Romain; Vannier, Thomas; Leconte, Jade; +45 Authors

    We thank the commitment of the following people and sponsors who made this expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Paris Sciences et Lettres (PSL) Research University (ANR-11-IDEX-0001–02), the French Government ANR (projects FRANCE GENOMIQUE/ANR-10-INBS-09, MEMO LIFE/ANR-10-LABX-54, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, MAPPI/ANR-2010-COSI-004, TARA-GIRUS/ANR-09-PCS-GENM-218), US NSF grant DEB-1031049, FWO, BIO5, Biosphere 2, Agnès b., the Veolia Environment Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. The bulk of genomic computations were performed using the Airain HPC machine provided through GENCI- [TGCC/CINES/IDRIS] (grants t2011076389, t2012076389, t2013036389, t2014036389, t2015036389 and t2016036389). We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted us sampling permissions. Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

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    eLife
    Article . 2022 . Peer-reviewed
    License: CC BY
    Data sources: Sygma; Crossref
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    MPG.PuRe
    Article . 2022
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    Article . 2022
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    https://www.biorxiv.org/conten...
    Preprint
    License: CC BY NC
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    eLife
    Article . 2022
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    Article . 2022
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    HAL AMU
    Article . 2022
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Madhav P. Thakur; Helen Phillips; Ulrich Brose; Franciska T. de Vries; +23 Authors

    Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity. Published version M.P.T. acknowledges funding from the GermanResearch Foundation (DFG, TH 2307/1-1). H.R.P.P.was supported by the sDiv (DFG FZT 118). M.L.was supported by the TULIP Laboratory of Excellence(ANR-10-LABX-41). M.C.R. and W.H.V.d.P. acknowledgesupport from ERC Advanced Grants [grant number:ERC-ADV 694368 and ERC-ADV 323020 (SPECIALS),respectively]. F.T.D.V. is supported by a BBSRC DavidPhillips Fellowship (BB/L02456X/1). N.E. and O.F.acknowledge funding by the European Research Council(ERC Starting Grant 677232, ECOWORM). C.A.G. issupported by the European Union’s Horizon 2020 researchand innovation programme under grant agreement No641762-ECOPOTENTIAL. E.K.C. acknowledges fundingfrom the Academy of Finland (285882) and the NaturalSciences and Engineering Research Council of Canada(postdoctoral fellowship 471903 and RGPIN-2019-05758).

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    NARCIS; Research@WUR
    Other literature type . Article . 2020
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    Biological Reviews
    Other literature type . Article . 2020 . 2019 . Peer-reviewed
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    Biological Reviews
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    Article . 2019
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    https://doi.org/10.17169/refub...
    Other literature type . 2019
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ IRIS - Università de...arrow_drop_down
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      Other literature type . Article . 2020
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      Biological Reviews
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      Biological Reviews
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      https://doi.org/10.17169/refub...
      Other literature type . 2019
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Meryl Vila Nova; Kevin Durimel; Kévin La; Arnaud Felten; +4 Authors

    AbstractBackgroundSalmonella entericasubsp.enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440Salmonellagenomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).ResultsBased on a genome dataset includingSalmonellaserovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively.ConclusionsOur results suggest that the genetic and metabolic determinants ofSalmonellaadaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.

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    BMC Genomics
    Other literature type . Article . 2019 . Peer-reviewed
    License: CC BY
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    ProdInra
    Article . 2019
    License: CC BY
    Data sources: ProdInra
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    BMC Genomics
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    BMC Genomics
    Article . 2019
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Radomski, Nicolas; Cadel-Six, Sabrina; Cherchame, Emeline; Felten, Arnaud; +7 Authors

    International audience; The investigation of foodborne outbreaks (FBOs) from genomic data typically relies on inspecting the relatedness of samples through a phylogenomic tree computed on either SNPs, genes, kmers, or alleles (i.e., cgMLST and wgMLST). The phylogenomic reconstruction is often time-consuming, computation-intensive and depends on hidden assumptions, pipelines implementation and their parameterization. In the context of FBO investigations, robust links between isolates are required in a timely manner to trigger appropriate management actions. Here, we propose a non-parametric statistical method to assert the relatedness of samples (i.e., outbreak cases) or whether to reject them (i.e., non-outbreak cases). With typical computation running within minutes on a desktop computer, we benchmarked the ability of three non-parametric statistical tests (i.e., Wilcoxon rank-sum, Kolmogorov-Smirnov and Kruskal-Wallis) on six different genomic features (i.e., SNPs, SNPs excluding recombination events, genes, kmers, cgMLST alleles, and wgMLST alleles) to discriminate outbreak cases (i.e., positive control: C+) from non-outbreak cases (i.e., negative control: C−). We leveraged four well-characterized and retrospectively investigated FBOs of Salmonella Typhimurium and its monophasic variant S. 1,4,[5],12:i:-from France, setting positive and negative controls in all the assays. We show that the approaches relying on pairwise SNP differences distinguished all four considered outbreaks in contrast to the other tested genomic features (i.e., genes, kmers, cgMLST alleles, and wgMLST alleles). The freely available non-parametric method written in R has been designed to be independent of both the phylogenomic reconstruction and the detection methods of genomic features (i.e., SNPs, genes, kmers, or alleles), making it widely and easily usable to anybody working on genomic data from suspected samples.

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    Frontiers in Microbiology
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Frontiers in Microbi...arrow_drop_down
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Martin, Olivier; Fernandez-Diclo, Yasmil; Coville, Jérôme; Soubeyrand, Samuel;

    International audience; Insect-borne diseases are diseases carried by insects affecting humans, animals or plants. They have the potential to generate massive outbreaks such as the Zika epidemic in 2015-2016 mostly distributed in the Americas, the Pacific and Southeast Asia, and the multi-foci outbreak caused by the bacterium {\it Xylella fastidiosa} in Europe in the 2010s. In this article, we propose and analyze the behavior of a spatially-explicit compartmental model adapted to pathosystems with fixed hosts and mobile vectors disseminating the disease. The behavior of this model based on a system of partial differential equations is complementarily characterized via a theoretical study of its equilibrium states and a numerical study of its transitive phase using global sensitivity analysis. The results are discussed in terms of implications concerning the surveillance and control of the disease over a medium-to-long temporal horizon.

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    Nonlinear Analysis Real World Applications
    Other literature type . Article . 2021 . Peer-reviewed
    License: Elsevier TDM
    https://doi.org/10.48550/arxiv...
    Article . 2020
    License: arXiv Non-Exclusive Distribution
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  • Authors: Sessa, Valentina; Assoumou, Edi; Bossy, Mireille; Carvalho, Sílvia; +1 Authors

    A big challenge of sustainable power systems is the integration of climate variability into the operational and long-term planning processes. In this paper, we focus on the run-of-river based hydropower generation on a European scale. In particular, we deal with the modeling of this form of power production based on climate variables. Translating time series of climate data (precipitation and air temperature) into time series of run-of-river based hydropower generation is not an easy task as it is necessary to capture the complex relationship between the availability of water and the generation of electricity. Indeed, this kind of electricity generation is limited by the flow of the river in which the power plants are located. Moreover, the water flow is a nonlinear function of the climate variables and the geographical characteristics of the river basins. Finally, the impact of the climate variables on the runoff may occur with a certain delay, whose determination depends on physically based phenomena (e.g., melting snow-local temperature). In this work, we first compare well-established machine learning regression algorithms to be used for modeling the run-of-river hydropower generation. Then, the technique showing to have the best performance is used for producing long-term estimates of hydropower capacity factors based on future climate scenarios for each European country.

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    Authors: Cornacchia, Ivano; Tomas, Séverine; Douzals, Jean-Paul; Courault, Dominique;

    [Departement_IRSTEA]Ecotechnologies [TR1_IRSTEA]INSPIRE [ADD1_IRSTEA]Équiper l'agriculture; The reuse of treated wastewater (TWW) for sprinkler irrigation could potentially diffuse pathogen-containing droplets off the application area. Wind and other unfavorable climatic factors enhance irrigation drift and bioaerosol dispersion, exposing humans to potentially severe health risks including the spread of diseases. Few studies have quantified bioaerosols during both spraying and airborne transport phases. Studies of effective sampling strategies to better qualify the dispersion process are also required. This paper presents experimentsconducted in a wind tunnel for a deeper understanding of the effects of wind and temperature on pathogen or contaminant airborne dispersal and transport. It is the first time that passive collectors [polyvinyl chloride (PVC) lines] and active samplers (AGI-4 impinger) have been compared under analogous wind conditions using a fluorescent tracer. Droplet-size distribution was also investigated at 12 m from the boomwith a NanoMoudi 122-NR cascade impactor in increasing wind conditions from 1 to 3 ms−1. PVC lines return a detailed evolution of the sprayed volume within a short range from the boom and for concentrated fluxes. Transport assessment of PVC lines indicates that transport and permanently airborne condition of the spray notably grow with increasing wind, resulting in a more compact and concentrated plume; mean transport increases from 0.13 to 1.18 Lh−1 m−2 at 7.7 m from the nozzle as the wind velocity increases from 1 to 3 ms−1. AGI-4 appears more suitable to assess finely aerosolized conditions because of its greater sensitivity compared to PVC lines as shown for sample values less than 1 Lh−1 m−2. The comparison between the AGI-4 and PVC lines shows higher values of recovery for the active samplers compared to the PVC lines. The total volume collected by the impingers was 2.93% of the sprayed volume, approximately twice that collected by PVC lines under analogous conditions, even though their sampling surface was only 1.54% that of PVC lines. Droplet-size distributions from the cascade impactor denote a median volume diameter from 1.1 to 2 μm, for the nozzle type used, and a relevant reduction in recovery at stronger wind velocities. An empirical relation time of flight is proposed as a first step in developing decision models that can be used to make sprinkler irrigation safe and to define standards for TWW reuse in agricultural practices (e.g., safe distance of application depending upon wind conditions and droplet-size distribution).

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    Authors: Nicholas K. Geitner; Christine Ogilvie Hendren; Geert Cornelis; Ralf Kaegi; +37 Authors

    International audience; The chemical composition and properties of environmental media determine nanomaterial (NM) transport, fate, biouptake, and organism response. To compare and interpret experimental data, it is essential that sufficient context be provided for describing the physical and chemical characteristics of the setting in which a nanomaterial may be present. While the nanomaterial environmental, health and safety (NanoEHS) field has begun harmonization to allow data comparison and re-use (e.g. using standardized materials, defining a minimum set of required material characterizations), there is limited guidance for standardizing test media. Since most of the NM properties driving environmental behaviour and toxicity are medium-dependent, harmonization of media is critical. A workshop in March 2016 at Duke University identified five categories of test media: aquatic testing media, soil and sediment testing media, biological testing media, engineered systems testing media and product matrix testing media. For each category of test media, a minimum set of medium characteristics to report in all NM tests is recommended. Definitions and detail level of the recommendations for specific standardized media vary across these media categories. This reflects the variation in the maturity of their use as a test medium and associated measurement techniques, variation in utility and relevance of standardizing medium properties, ability to simplify standardizing reporting requirements, and in the availability of established standard reference media. Adoption of these media harmonization recommendations will facilitate the generation of integrated comparable datasets on NM fate and effects. This will in turn allow testing of the predictive utility of functional assay measurements on NMs in relevant media, support investigation of first principles approaches to understand behavioral mechanisms, and support categorization strategies to guide research, commercial development, and policy.

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    Article . 2019
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  • Authors: Camilo Corrales, David; Baranger, Alain; Jumel, Stephane; Leclerc, Melen; +5 Authors

    International audience

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    Authors: Barillé, Laurent; Bris, Anthony Le; Goulletquer, Philippe; Thomas, Yoann; +7 Authors

    International audience; Oyster production has historically taken place in intertidal zones, and shellfish farms already occupy large extents of the French intertidal space. The expansion of French shellfish aquaculture within intertidal areas is therefore spatially limited, and moving production to the subtidal offshore environment is considered to be a possible solution to this problem. Finding new sites along the French Atlantic coast was studied here from the perspective of small oyster companies run by young farmers, who are interested in offshore bivalve aquaculture expansion compatible with their investment capacity. In assessing the feasibility of such offshore production, we considered three main issues: (1) bivalve growth potential and (2) technical feasibility and conflicting uses, both within a spatial framework, as well as (3) the steps and barriers of the administrative licensing process. Oyster spat in an experimental offshore cage showed significantly faster growth, in terms of both weight and length, compared to those in an intertidal cage, mainly due to lower turbidity and full-time feeding capacity (i.e., constant immersion in the water). A combination of Earth Observation data and bivalve ecophysiological modelling was then used to obtain spatial distribution maps of growth potential, which confirmed that offshore sites have better potential for oyster growth than the traditionally oyster-farmed intertidal sites overall, but that this is highly spatially variable. Small-scale producers indicated two technical factors constraining where farms could be located: bathymetry must be between 5 and 20 m and the distance from a harbor no more than five nautical miles. These were included along with maps of various environmental and socioeconomic constraints in a Spatial Multi-Criteria Evaluation (SMCE). Touristic traffic and bottom trawling by fisherman were found to be the two other most restrictive variables. The GIS-based SMCE developed in this study showed that there is almost 400 km 2 of highly-to very highly-suitable area within which to develop offshore aquaculture using simple, low-cost bottom-cage techniques, and can be used to assist the shellfish industry in the Marine Spatial Planning decision-making process, still in progress in this coastal area. However, the complexity of the administrative processes necessary to obtain an offshore license is perceived as a stronger barrier by farmers owning small companies than site selection, technical feasibility, and required investments, and will be crucial to address in order to realistically proceed to offshore cultivation. The process demonstrated here, and the results are relevant to other coastal and offshore locations throughout the world and can be adapted for other species.

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    Horizon / Pleins textes
    Other literature type . 2020
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    https://doi.org/10.1016/j.aqua...
    Other literature type . Article . 2020 . Peer-reviewed
    License: Elsevier TDM
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    Authors: Richter, Daniel J.; Watteaux, Romain; Vannier, Thomas; Leconte, Jade; +45 Authors

    We thank the commitment of the following people and sponsors who made this expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Paris Sciences et Lettres (PSL) Research University (ANR-11-IDEX-0001–02), the French Government ANR (projects FRANCE GENOMIQUE/ANR-10-INBS-09, MEMO LIFE/ANR-10-LABX-54, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, MAPPI/ANR-2010-COSI-004, TARA-GIRUS/ANR-09-PCS-GENM-218), US NSF grant DEB-1031049, FWO, BIO5, Biosphere 2, Agnès b., the Veolia Environment Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. The bulk of genomic computations were performed using the Airain HPC machine provided through GENCI- [TGCC/CINES/IDRIS] (grants t2011076389, t2012076389, t2013036389, t2014036389, t2015036389 and t2016036389). We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted us sampling permissions. Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

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    eLife
    Article . 2022 . Peer-reviewed
    License: CC BY
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    Article . 2022
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    https://www.biorxiv.org/conten...
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    eLife
    Article . 2022
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    Article . 2022
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    HAL AMU
    Article . 2022
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    Authors: Madhav P. Thakur; Helen Phillips; Ulrich Brose; Franciska T. de Vries; +23 Authors

    Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity. Published version M.P.T. acknowledges funding from the GermanResearch Foundation (DFG, TH 2307/1-1). H.R.P.P.was supported by the sDiv (DFG FZT 118). M.L.was supported by the TULIP Laboratory of Excellence(ANR-10-LABX-41). M.C.R. and W.H.V.d.P. acknowledgesupport from ERC Advanced Grants [grant number:ERC-ADV 694368 and ERC-ADV 323020 (SPECIALS),respectively]. F.T.D.V. is supported by a BBSRC DavidPhillips Fellowship (BB/L02456X/1). N.E. and O.F.acknowledge funding by the European Research Council(ERC Starting Grant 677232, ECOWORM). C.A.G. issupported by the European Union’s Horizon 2020 researchand innovation programme under grant agreement No641762-ECOPOTENTIAL. E.K.C. acknowledges fundingfrom the Academy of Finland (285882) and the NaturalSciences and Engineering Research Council of Canada(postdoctoral fellowship 471903 and RGPIN-2019-05758).

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    NARCIS; Research@WUR
    Other literature type . Article . 2020
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    Biological Reviews
    Other literature type . Article . 2020 . 2019 . Peer-reviewed
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    Biological Reviews
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    Article . 2019
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    https://doi.org/10.17169/refub...
    Other literature type . 2019
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      NARCIS; Research@WUR
      Other literature type . Article . 2020
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      Biological Reviews
      Other literature type . Article . 2020 . 2019 . Peer-reviewed
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      Article . 2019
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      https://doi.org/10.17169/refub...
      Other literature type . 2019
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    Authors: Meryl Vila Nova; Kevin Durimel; Kévin La; Arnaud Felten; +4 Authors

    AbstractBackgroundSalmonella entericasubsp.enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440Salmonellagenomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).ResultsBased on a genome dataset includingSalmonellaserovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively.ConclusionsOur results suggest that the genetic and metabolic determinants ofSalmonellaadaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.

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    BMC Genomics
    Other literature type . Article . 2019 . Peer-reviewed
    License: CC BY
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    ProdInra
    Article . 2019
    License: CC BY
    Data sources: ProdInra
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    BMC Genomics
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    BMC Genomics
    Article . 2019
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    Article . 2019
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    Authors: Radomski, Nicolas; Cadel-Six, Sabrina; Cherchame, Emeline; Felten, Arnaud; +7 Authors

    International audience; The investigation of foodborne outbreaks (FBOs) from genomic data typically relies on inspecting the relatedness of samples through a phylogenomic tree computed on either SNPs, genes, kmers, or alleles (i.e., cgMLST and wgMLST). The phylogenomic reconstruction is often time-consuming, computation-intensive and depends on hidden assumptions, pipelines implementation and their parameterization. In the context of FBO investigations, robust links between isolates are required in a timely manner to trigger appropriate management actions. Here, we propose a non-parametric statistical method to assert the relatedness of samples (i.e., outbreak cases) or whether to reject them (i.e., non-outbreak cases). With typical computation running within minutes on a desktop computer, we benchmarked the ability of three non-parametric statistical tests (i.e., Wilcoxon rank-sum, Kolmogorov-Smirnov and Kruskal-Wallis) on six different genomic features (i.e., SNPs, SNPs excluding recombination events, genes, kmers, cgMLST alleles, and wgMLST alleles) to discriminate outbreak cases (i.e., positive control: C+) from non-outbreak cases (i.e., negative control: C−). We leveraged four well-characterized and retrospectively investigated FBOs of Salmonella Typhimurium and its monophasic variant S. 1,4,[5],12:i:-from France, setting positive and negative controls in all the assays. We show that the approaches relying on pairwise SNP differences distinguished all four considered outbreaks in contrast to the other tested genomic features (i.e., genes, kmers, cgMLST alleles, and wgMLST alleles). The freely available non-parametric method written in R has been designed to be independent of both the phylogenomic reconstruction and the detection methods of genomic features (i.e., SNPs, genes, kmers, or alleles), making it widely and easily usable to anybody working on genomic data from suspected samples.

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    Article . 2019
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    Frontiers in Microbiology
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    Article . 2019
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      Frontiers in Microbiology
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