Éditeur(s) : HAL CCSD Springer International Publishing
Résumé : The intensive farming practices that have been developed over the past 60 years are based mainly on the use of chemical inputs such as fertilisers and pesticides, mechanical tillage and monoculture. The limitations of these methods are now clear: long-term degradation of soil fertility, impacts on the environment and human health, high consumption of fossil fuels, low efficiency of inputs and threats to food security in a context of climate change. Would farming practices that rely on the activation of ecological processes be an alternative to achieve a balance between high productivity and environmental preservation? While many studies suggest a positive relationship between soil biodiversity and ecosystem services, there is considerable debate on the form such agricultural systems should take. This study reviewed the state of current knowledge and identified aspects requiring further research to achieve the aim of sustainable intensification of agriculture. The following major points emerged: 1) Most studies focused on the evaluation of individual practices. However, changes in farmers’ cropping practices to take advantage of soil biodiversity services would need to manage not only the interactions between various practices but also the trade-off between the technical and socio economic constraints of cropping systems. Advances in agricultural system design approaches may help to ensure appropriate trade-offs. 2) More attention should be given to drawing on knowledge from different sources: laboratory studies focusing on the ecological functions of soil biodiversity, experimental surveys on farmers’ fields to rank the farming practices and processes to be included in site-specific models, and on- station experiments to test hypotheses and acquire additional reference material. 3) Whereas advances in technical and scientific knowledge provide an increasing number of relevant indicators for characterizing biodiversity and ecological functions, studies are rarely targeted at the development of indicators that are accessible to farmers or their technical advisors. The lack of indicators accessible to grassroots players for evaluating the impacts of their decisions on soil biodiversity remains a serious obstacle to the development of innovative agro-ecological systems.
Sustainable Agriculture Reviews 14

ISBN : 978-3-319-06015-6
hal-01268743
https://hal.archives-ouvertes.fr/hal-01268743
DOI : 10.1007/978-3-319-06016-3_5
PRODINRA : 270786

Éditeur(s) : HAL CCSD Springer Verlag (Germany) Springer Verlag
Résumé : Production rates in horizontal shale gas wells display declines that are controlled by the low permeability and the intrinsic heterogeneity of the shale matrix. We present an original multi-continuum approach that yields a physical model able to reproduce the complexity of the decreasing gas rates. The model describes the dynamics of gas rate as function of the physical reservoir parameters and geometry, while the shale matrix heterogeneity is accounted for by a stochastic description of transmissivity field. From the 3D (Dimensional) problem setting, including the heterogeneous shale matrix, the fractures generated by the hydrofracking operations, as well as the production well characteristics, we establish an effective upscaled 1D model for the gas pressures in fracture and matrix as well as the volumetric flux. We analyse the decline curves behaviour, and we identify the time scales that characterize the dynamics of the gas rate decline using explicit analytical Laplace space solutions of the upscaled process model. Asymptotically, the flux curves decrease exponentially, while in an intermediate regime we find a power-law behaviour, in which the flux scales with a power law in time as (t^{-beta }), where (beta ) reflects the medium heterogeneity. We use this solution to fit a set of real data displaying distinctly different decline trends and study the sensitivity of the model to the reservoir parameters in order to identify their respective controls at the different stages of the decline curve dynamics. Results indicate that the initial value of the gas rate is determined by the transmissivity of the fractures and the initial pressure of the gas in the shale matrix. The latter causes mainly a shift in the entire decline curve. The early time of decline curve shape is primarily controlled by the fracture properties (compressibility and transmissivity). During the main part of the economically valuable production times, i.e. before the production rate drops exponentially, the decline curve is strongly controlled by the properties of the shale rocks including their heterogeneity, which is modelled by two parameters describing the non-Fickian pressure diffusion effects in a stochastic framework.
ISSN: 0169-3913

hal-01217247
https://hal.archives-ouvertes.fr/hal-01217247
DOI : 10.1007/s11242-015-0504-y

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
In cyclic females, FSH stimulates ovarian estradiol (E2) production and follicular growth up to the terminal stage. A transient elevation in circulating FSH and E2 levels occurs shortly after birth. But what could be the action of FSH on the ovary during this period, and in particular how it stimulates ovarian steroidogenesis without supporting terminal follicular maturation is intriguing. By experimentally manipulating FSH levels, we demonstrate in mice that the mid-infantile elevation in FSH is mandatory for E2 production by the immature ovary, but that it does not stimulate follicle growth. Importantly, FSH increases aromatase expression to stimulate E2 synthesis, however it becomes unable to induce cyclin D2, a major driver of granulosa cell proliferation. Besides, although FSH prematurely induces luteinizing hormone (LH) receptor expression in granulosa cells, LH pathway is not functional in these cells to induce their terminal differentiation. In line with these results, supplying infantile mice with a superovulation regimen exacerbates E2 production, but it does not stimulate the growth of follicles and it does not induce ovulation. Overall, our findings unveil a regulation whereby high postnatal FSH concentrations ensure the supply of E2 required for programming adult reproductive function without inducing follicular maturation before puberty.
ISSN: 2045-2322

hal-01516023
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01516023
DOI : 10.1038/srep46222
PUBMED : 28397811
PUBMEDCENTRAL : PMC5387682

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : HAL CCSD Wiley
Résumé :  
Pollination ecology and reproductive success of Jack-in-the-pulpit (Arisaema triphyllum) were studied in two natural populations in Québec, Canada. Individual A. triphyllum plants can be of three types: male, female or bisexual. In both populations studied, the presence of bisexual inflorescences was not negligible (13%), where 'female' and 'male' bisexual plants were categorised according to the relative number of stamens and ovaries. 'Male bisexual' plants produce only pollen and 'female bisexual' plants produce only fruit. Hence, A. triphyllum is a true dioecious plant, as each plant only reproduces through either the male or the female function. 'Female bisexual' plants were equivalent to female plants in terms of visitation rate by insects, fructification rate and production of berries and seeds. Neither agamospermy in female plants nor self-pollination in 'female bisexual' plants was found, thus A. triphyllum relies on insects for cross-pollination. Despite the long flowering cycle, a low visitation rate was documented: only 20-40% of inflorescences were visited, according to gender, by a mean of 1.5 insects. In this study, Mycetophilidae represented the most generically diversified and abundant family, as well as the most efficient insect pollinator, especially the genera Docosia and Mycetophila.
ISSN: 1435-8603

hal-01032127
https://hal.archives-ouvertes.fr/hal-01032127
DOI : 10.1111/j.1438-8677.2009.00192.x

Éditeur(s) : HAL CCSD
Résumé : International audience
The Corinth Rift is the most seismically active zone in Europe. Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary natural observatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studies have improved our view about fault geometry and mechanics within CRL but there is still a critical need for a better knowledge of the structure at depth.In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by using recently developed methodologies of structural imaging in order to determine, with high resolution, the local 3D structure and the earthquake locations. We perform an iterative joint determination of 3D velocity model and earthquake coordinates. P and S velocity models are estimated through a first arrival traveltime tomography by using the adjoint state method proposed by Taillandier et al. (2009). It consists in the minimization of the cost function between observed and theoretical arrival times,which is achieved by estimating the gradient of the cost function. Earthquake locations are also estimated with a linearized inversion approach by computing the gradient of the misfit function. Iterations are repeated until the cost function no longer decreases. We present preliminary results consisting in: (1) the adjustment of a 1D velocity model that is used as initial model of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity model and earthquake locations.We also perform a preliminary receiver function analysis of teleseismic data recorded by the broadband stations of the CRL network. The multiscale approach (Gesret et. al., 2010) analysis of teleseismic P to S converted waves allows to analyze the signal toward the higher frequencies and thus to characterize the structure at depth with a high resolution. Our multiscale approach should give us reliable depth of interfaces beneath seismometers in the CRL area. In this first attempt, we adjust the 1D velocity model that produces a synthetic RF as similar as possible to the stack of observed RF for a subset of data. The identified interfaces could then be compared with heterogeneities imaged by the tomography.
AGU Fall Meeting
San Fransico, United States

hal-01417184
https://hal-mines-paristech.archives-ouvertes.fr/hal-01417184

Éditeur(s) : John Wiley & Sons
Résumé : 1. Transitional waters, described as critical transition zones because of their position at terrestrial, freshwater and marine interfaces, provide essential goods and services to the biosphere including human populations. These ecotones face increasing human influence mainly due to population density increase in coastal areas. 2. Transitional water bodies have, to date, received little attention in the development of ecological status indicators, this is a critical deficiency when trying to meet the Water Framework Directive objective of all significant water bodies achieving good ecological status by the year 2015. 3. In order to assess changes in transitional water communities many taxonomic-based indicators have already been proposed but there are a number of concerns for their use such as taxonomic classification difficulties, their unsuitability for multi-site comparisons and their inconsistent relationships with disturbance or stress. 4. Alternative methods based on body size, abundance distribution among functional groups, functional diversity and productivity descriptors are proposed. These methods offer the opportunity to compare sites with different taxonomic compositions and allow derivation of indicators related to ecological status of communities under scrutiny. 5. Finally, the suitability of these taxonomic-free descriptors to provide relevant information for each of the four main biotic compartments in coastal lagoons is discussed. The use of biomass distribution among functional groups for fish, benthos and macrophyte and to use body-size distribution for benthos and plankton is proposed. Copyright (c) 2006 John Wiley and Sons, Ltd.
Aquatic Conservation: Marine and Freshwater Ecosystems (1052-7613) (John Wiley & Sons), 2006-07 , Vol. 16 , N. 5 , P. 469-482

Droits : 2006 John Wiley & Sons, Ltd
http://archimer.ifremer.fr/doc/2006/publication-1849.pdf
DOI:10.1002/aqc.769
http://archimer.ifremer.fr/doc/00000/1849/

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Under physiological conditions, the liver sinusoidal endothelial cells (LSECs) mediate hepatic immune tolerance toward self or foreign antigens through constitutive expression of anti-inflammatory mediators. However, upon viral infection or Toll-like receptor 2 (TLR2) activation, LSECs can achieve proinflammatory functions, but their role in hepatic inflammation during acute viral hepatitis is unknown. Using the highly virulent mouse hepatitis virus type 3 (MHV3) and the attenuated variants 51.6-MHV3 and YAC-MHV3, exhibiting lower tropism for LSECs, we investigated in vivo and in vitro the consequence of LSEC infection on their proinflammatory profiles and the aggravation of acute hepatitis process. In vivo infection with virulent MHV3, in comparison to attenuated strains, resulted in fulminant hepatitis associated with higher hepatic viral load, tissue necrosis, and levels of inflammatory mediators and earlier recruitment of inflammatory cells. Such hepatic inflammatory disorders correlated with disturbed production of interleukin-10 (IL-10) and vascular factors by LSECs. We next showed in vitro that infection of LSECs by the virulent MHV3 strain altered their production of anti-inflammatory cytokines and promoted higher release of proinflammatory and procoagulant factors and earlier cell damage than infection by attenuated strains. This higher replication and proinflammatory activation in LSECs by the virulent MHV3 strain was associated with a specific activation of TLR2 signaling by the virus. We provide evidence that TLR2 activation of LSCEs by MHV3 is an aggravating factor of hepatic inflammation and correlates with the severity of hepatitis. Taken together, these results indicate that preservation of the immunotolerant properties of LSECs during acute viral hepatitis is imperative in order to limit hepatic inflammation and damage. IMPORTANCE Viral hepatitis B and C infections are serious health problems affecting over 350 million and 170 million people worldwide, respectively. It has been suggested that a balance between protection and liver damage mediated by the host's immune response during the acute phase of infection would be determinant in hepatitis outcome. Thus, it appears crucial to identify the factors that predispose in exacerbating liver inflammation to limit hepatocyte injury. Liver sinusoidal endothelial cells (LSECs) can express both anti- and proinflammatory functions, but their role in acute viral hepatitis has never been investigated. Using mouse hepatitis virus (MHV) infections as animal models of viral hepatitis, we report for the first time that in vitro and in vivo infection of LSECs by the pathogenic MHV3 serotype leads to a reversion of their intrinsic anti-inflammatory phenotype toward a proinflammatory profile as well to as disorders in vascular factors, correlating with the severity of hepatitis. These results highlight a new virus-promoted mechanism of exacerbation of liver inflammatory response during acute hepatitis.
ISSN: 0022-538X

hal-01390974
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974/file/Mouse%20Hepatitis%20Virus%20Infection_accepted.pdf
DOI : 10.1128/JVI.01069-16

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
STUDY QUESTION: Can protein biomarkers of the male genital tract be identified in human seminal plasma? SUMMARY ANSWER: We identified potential biomarkers for each of the organs participating in the secretions of the human seminal plasma. WHAT IS KNOWN ALREADY: The seminal plasma fulfills critical functions for fertility by providing spermatozoa with a protective milieu, promoting their final maturation and modulating the immune responsiveness of the female reproductive tract. It is also considered to be a promising source of biomarkers of male infertility and/or pathologies of the male genital tract. STUDY DESIGN, SIZE, DURATION: This study combines proteomic analyses of normal seminal plasma together with transcriptomic gene expression profiling of human healthy tissues. MATERIALS, SETTING, METHODS: Non-liquefied seminal plasma proteins from a healthy donor were prefractionated using two sequential Proteominer™ libraries. Eight subproteome fractions were collected, trypsin digested and subjected to three successive mass spectrometry analyses for peptide characterization. The list of identified proteins was compared with and merged with other available data sets of the human seminal plasma proteome. The expression of corresponding genes was then investigated using tissue transcriptome profiles to determine where, along the male reproductive tract, these proteins were produced. Finally, tissue specificity of a selected subset of biomarker candidates was validated on human tissues. MAIN RESULTS AND THE ROLE OF CHANCE: We first performed a proteomic analysis of the human seminal plasma and identified 699 proteins. By comparing our protein list with other previous proteomic data sets, we found that 2545 unique proteins have been described so far in the human seminal plasma. We then profiled their expression at the gene level and identified 83 testis, 42 epididymis, 7 seminal vesicle and 17 prostate candidate protein markers. For a subset of testis-specific candidates, i.e. TKTL1, LDHC and PGK2, we further validated their germ cell expression and demonstrated that such markers could distinguish between semen from fertile and infertile men. LIMITATIONS, REASONS FOR CAUTION: While some of the markers we identified are well-known tissue-specific products, further dedicated studies to validate the biomarker status of new candidates will be required. Additionally, whether or not the abundance of these proteins is indeed decreased in some specific pathological situations remains to be determined. WIDER IMPLICATIONS OF THE FINDINGS: Using an integrative genomics approach, we identified biomarker candidates for each of the organs participating in the seminal plasma production. In this study, we essentially focused on germ cell markers and their potential application for the diagnosis of male infertility. Other types of markers also deserve a focused attention given their potential predictive value for various reproductive disorders, notably for prostate cancers. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the Proteomics Core Facility at Biogenouest and was funded by Conseil Régional de Bretagne, IBiSA and Agence de la Biomédecine grants. The authors declare that there exists a competing financial interest in this work that is related to a patent application on the use of identified germ cell-specific proteins in an antibody-based assay (Fertichip™) to predict the successful testicular biopsy outcomes in human non-obstructive azoospermia.
ISSN: 0268-1161

inserm-00814146
http://www.hal.inserm.fr/inserm-00814146
DOI : 10.1093/humrep/des360
PUBMED : 23024119

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The equilibrium phase relations of a mafic durbachite (53 wt.% SiO2) from the TA (TM) ebi pluton, representative of the Variscan ultrapotassic magmatism of the Bohemian Massif (338-335 Ma), have been determined as a function of temperature (900-1,100A degrees C), pressure (100-200 MPa), and H2O activity (1.1-6.1 wt.% H2O in the melt). Two oxygen fugacity ranges were investigated: close to the Ni-NiO (NNO) buffer and 2.6 log unit above NNO buffer (a dagger NNO + 2.6). At 1,100A degrees C, olivine is the liquidus phase and co-crystallized with phlogopite and augite at 1,000A degrees C for the whole range of investigated pressure and water content in the melt. At 900A degrees C, the mineral assemblage consists of augite and phlogopite, whereas olivine is not stable. The stability field of both alkali feldspar and plagioclase is restricted to low pressure (100 MPa) at nearly water-saturated conditions (< 3-4 wt.% H2O) and T < 900A degrees C. A comparison between experimental products and natural minerals indicates that mafic durbachites have a near-liquidus assemblage of olivine, augite, Ti-rich phlogopite, apatite and zircon, followed by alkali feldspar and plagioclase, similar to the mineral assemblage of minette magma. Natural amphibole, diopside and orthopyroxene were not reproduced experimentally and probably result from sub-solidus reactions, whereas biotite re-equilibrated at low temperature. The crystallization sequence olivine followed by phlogopite and augite reproduces the sequence inferred in many mica-lamprophyre rocks. The similar fractionation trends observed for durbachites and minettes indicate that mafic durbachites are probably the plutonic equivalents of minettes and that K- and Mg-rich magmas in the Bohemian Massif may have been generated from partial melting of a phlogopite-clinopyroxene-bearing metasomatized peridotite. Experimental melt compositions also suggest that felsic durbachites can be generated by simple fractionation of a more mafic parent and mixing with mantle-derived components at mid crustal pressures.
ISSN: 0010-7999

hal-00618418
https://hal.archives-ouvertes.fr/hal-00618418
DOI : 10.1007/s00410-009-0430-5

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
High sea surface temperature accompanied by high levels of solar irradiance is responsible for the disruption of the symbiosis between cnidarians and their symbiotic dinoflagellates from the genus Symbiodinium. This phenomenon, known as coral bleaching, is one of the major threats affecting coral reefs around the world. Because an important molecular trigger to bleaching appears related to the production of reactive oxygen species (ROS), it is critical to understand the function of the antioxidant network of Symbiodinium species. In this study we investigated the response of two Symbiodinium species, from contrasting environments, to a chemically induced oxidative stress. ROS produced during this oxidative burst reduced photosynthesis by 30 to 50% and significantly decreased the activity of superoxide dismutase. Lipid peroxidation levels and carotenoid concentrations, especially diatoxanthin, confirm that these molecules act as antioxidants and contribute to the stabilization of membrane lipids. The comparative analysis between the two Symbiodinium species allowed us to highlight that Symbiodinium sp. clade A temperate was more tolerant to oxidative stress than the tropical S. kawagutii clade F. These differences are very likely a consequence of adaptation to their natural environment, with the temperate species experiencing conditions of temperature and irradiance much more variable and extreme.
ISSN: 0140-7791

hal-01546161
https://hal.archives-ouvertes.fr/hal-01546161
DOI : 10.1111/pce.12825

Éditeur(s) : Université d'Angers
Résumé : In oyster farming areas, organic matter fluxes toward sediment is increased. Pacific oysters (Crassostrea gigas) reject organic-rich faeces and pseudofaeces as a result of filtration process. Organic matter can be consumed by benthic fauna, but in excess it can entails the reduction of benthic faunal species richness, abundance and biomass. Organic matter degradation also induces hypoxic (or anoxic) conditions in the sediment, and production of ammonia and sulfides in toxic concentrations. The main objective of this study is to assess the effects of oyster farming on benthic intertidal ecosystems in the Pertuis Charentais. Benthic macrofauna, living (stained) foraminifera, and physicochemical characteristics of the water column and sediment were used as indicators to evaluate these effects. A multidisciplinary approach was conducted across the Pertuis Charentais at 3 different spatial scales: an oyster trestle (micro-scale), an oyster culture area (meso-scale) and various sites across the Pertuis Charentais (macro-scale). The study was also realised at 4 different temporal scales: some months for the spatial micro-scale, every two weeks for 2 years at meso-scale and once per season during one year at macro-scale. In this study, I found that oyster farming enriches sediment in fine particles, organic matter (up to 12 %), particulate organic carbon (15-20 µg mg 1) and leads to high microphytobenthic biomass. Moreover, the association of seasonnal warming (during spring and summer), remineralisation of accumulated organic matter and short-term hypoxic conditions leads to sulfides and ammonium production. Consequently, the benthic biodiversity decreases and the population dynamic is disturbed. The population dynamic disturbance is characterised by fast abundance rises followed by high mortality rates. In these conditions, tolerant benthic macrofaunal (Cirratulidae, Spionidae and Capitellidae) and foraminiferal (Ammonia tepida and Cribroelphidium gunteri) species are promoted. AMBI index confirms "medium" ecological quality of oyster farming areas. On the contrary, across the control sites, sensible species are maintained (Amphipods, Rosalina cf. vilardeboana). Comparison of oyster farming techniques shows that on-bottom culture is less disturbing for benthic ecosystem than off-bottom culture. Axial tomodensitometry, an innovative method, was used to describe in 3D the sedimentary column organisation. I show that oyster farming modifies the sedimentary column functioning. Indeed, the macrofaunal diversity decrease leads to the modification of the functional diversity of assemblages. Thus, the vertical distribution of living foraminifera is limited in oyster farming areas, because their distribution is tightly related to macrofaunal bioturbating modes.
Dans les zones ostréicoles, les flux de matière organique sont importants, l'huître Crasssotrea gigas rejetant sous forme de pseudo-fécès et de fécès de grandes quantités de matière organique. De ce fait, bien que cette matière organique puisse être consommée par la faune benthique, sa surabondance peut provoquer une réduction de la richesse spécifique, de l'abondance et de la biomasse et provoquer sur le plan des processus biogéochimiques des déplétions en oxygène et l'apparition de substances comme l'ammonium et les sulfures dont les concentrations peuvent devenir toxiques. L'objectif principal de cette étude était donc de déterminer l'impact de l'ostréiculture, grâce à plusieurs indicateurs, sur le compartiment benthique d'un écosystème littoral comme les pertuis charentais. Pour évaluer ces effets, la macrofaune benthique et les foraminifères vivants benthiques ont été utilisés en association avec des mesures des paramètres physico-chimiques de la colonne d'eau et du sédiment. Une approche pluridisciplinaire a ainsi été menée dans les pertuis charentais à trois échelles spatiales différentes : à l'échelle d'une table ostréicole (micro-échelle), à l'échelle d'un site ostréicole (méso-échelle) et à l'échelle des pertuis charentais (macro-échelle). Dans les trois cas, un suivi dans le temps a été associé à une étude de distribution spatiale, quelques mois à micro-échelle, tous les quinze jours pendant deux années à méso-échelle et une fois par saison pendant une année à macro-échelle. Ces différentes approches ont permis d'avoir une vision pertinente de la dynamique et de la réponse fonctionnelle de la faune benthique aux changements induits par la présence de l'ostréiculture. La présence des cultures ostréicoles dans les pertuis charentais enrichit les sédiments en particules fines, en matière organique (12 %), en carbone organique particulaire (15-20 µg mg-1) et favorise une production microphytobenthique élevée. Pendant la période chaude de l'année printemps-été, la reminéralisation de la matière organique accumulée associée à des hypoxies temporaires a favorisé la production de sulfures et d'ammonium. Dans les stations soumises à l'ostréiculture, la diversité des assemblages diminue. La dynamique des espèces est caractérisée par des augmentations rapides des abondances suivies d'épisodes de mortalité. Les espèces tolérantes de la macrofaune benthique (Cirratulidae, Spionidae et Capitellidae) et des foraminifères vivants benthiques (Ammonia tepida et Cribroelphidium gunteri) sont favorisées. Le calcul de l'indice AMBI confirme la qualité écologique moyenne de ces sites. Au contraire, dans la station témoin, les espèces sensibles sont favorisées (Amphipodes, Rosalina cf. vilardeboana). La comparaison de la technique de culture sur table et de culture à plat a montré que la culture des huîtres à plat est moins perturbante pour le milieu. L'étude de la bioturbation a montré l'influence qui existe entre le mode de bioturbation des différents groupes de la macrofaune et la répartition verticale des foraminifères vivants dans la colonne sédimentaire. La diminution de la diversité des assemblages de la macrofaune dans les zones soumises à l'ostréiculture modifient la diversité fonctionnelle de ces assemblages et affectent le fonctionnement de la colonne sédimentaire, limitant la répartition verticale des foraminifères dans ces zones.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-2582.pdf
http://archimer.ifremer.fr/doc/00000/2582/

Éditeur(s) : HAL CCSD CRC Press
Résumé : Among the ecosystem services provided by forests, wood provisioning takes a central position. Wood and derived products have played a critical role in the evolution of human kind and demand for raw material is increasing in a foreseeable future. Wood is used for energy production, construction and a wide variety of products for which different properties are required. Anatomical, chemical and physical properties of wood are determined through a complex process called xylogenesis controlled by internal and external signals and occurring during the life of the tree. In this chapter we describe i/how wood is formed and ii/the different factors controlling this developmental process with emphasis on the molecular machinery involved, iii/the functions of wood and iv/the biotechnology approaches developed to improve wood biomass production and properties genetically.
Tree Biotechnology

ISBN : 978-1466597143
hal-01032436
https://hal.archives-ouvertes.fr/hal-01032436

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour. Results: We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance. Conclusions: This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
ISSN: 1754-6834

Droits : http://creativecommons.org/licenses/by/
hal-01112360
http://hal.upmc.fr/hal-01112360
http://hal.upmc.fr/hal-01112360/document
http://hal.upmc.fr/hal-01112360/file/Poggi-Parodi_2014_Kinetic.pdf
DOI : 10.1186/s13068-014-0173-z

Éditeur(s) : Inter-research
Résumé : Mixed beds of Ophiocomina nigra and Ophiothrix fragilis (Echinodermata, Ophiuroidea) are usually predominated by O. fragilis and are reported to be stable over time. The Bay of Brest (Brittany, France) is a highly productive ecosystem where both species co-occur in the main central part. Using a geostatistical approach, we tested for changes in O. nigra and O. fragilis density and total biomass patterns between 1987 and 2011. Our results highlighted an increase in O. nigra population size and the induction of a spatial shift of the co-occurring O. fragilis. O. nigra increased similar to 5 times in density and covered almost all the study area, while its density-dependent biomass increased similar to 3 times (22 t km(-2), ash-free dry mass) between 1987 and 2011. Overall, the O. fragilis population decreased in density by similar to 30%, but its total biomass did not change over time. The current distribution pattern revealed a clear spatial exclusion of O. fragilis from the central part of the study area toward the southern part, overlapping beds of dead slipper limpet Crepidula fornicata, which were formerly considered to be the dominant suspension-feeder species in the bay. The success of O. nigra colonization is linked to its biological and functional traits, as well as deep changes in food supply over the studied period. Ecological consequences of such a large change in the benthic compartment of the bay are explored in the light of associated changes in environmental patterns.
Marine Ecology-progress Series (0171-8630) (Inter-research), 2012 , Vol. 460 , P. 79-90

Droits : 2012 Inter-Research
http://archimer.ifremer.fr/doc/00090/20136/17782.pdf
DOI:10.3354/meps09784
http://archimer.ifremer.fr/doc/00090/20136/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
We explored the relationship between soil processes, estimated through soil respiration (Rsoil), and the spatial variation in forest structure, assessed through the distribution of tree size, in order to understand the determinism of spatial variations in Rsoil in a tropical forest. The influence of tree size was examined using an index (Ic) calculated for each tree as a function of (1) the trunk cross section area and (2) the distance from the measurement point. We investigated the relationships between Ic and litterfall,root mass and Rsoil, respectively. Strong significant relationships were found between Ic and both litterfall and root mass. Rsoil showed a large range of variations over the 1-ha experimental plot, from 1.5 to 12.6 gC m−2 d−1. The best relationship between Ic and Rsoil only explained 17% of the spatial variation in Rsoil. These results support the assumption that local spatial patterns in litter production and root mass depend on tree distribution in tropical forests. Our study also emphasizes the modest contribution of tree size distribution-which is mainly influenced by the presence of the biggest trees (among the large range size of the inventoried trees greater than 10 cm diameter at 1.30 m above ground level or at 0.5 m above the buttresses)-in explaining spatial variations in Rsoil.
ISSN: 0032-079X

hal-00797064
https://hal.archives-ouvertes.fr/hal-00797064

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The correlation between the flow turbulence and the performances of a ma- rine current turbine is studied. First, the incoming flow encountered in the flume tank is characterized in the framework of fully developed turbulent cascades in the inertial range. The Reynolds number, the Kolmogorov dissipation scale and the integral scale, are estimated from flow measurements. The intermittency of the turbulence is characterized in the lognormal multifractal framework, and the influence of the turbulent flow on the turbine power is assessed. The rotor speed control unit characteristics used for the turbine regulation induces non-negligible effects on the turbine behavior under fluctuations loads. Even if the power spectrum does not reveal any scale invariance, a multiscale analysis allows us to show the correlations between the turbulence time se- ries and the power produced. The classical Mean Square Coherency function shows that for scales larger than 10 seconds, the upstream velocity and power have large correlations. In the framework of the Empirical Mode Decomposition method, such correlations are studied using the time-dependence intrinsic corre- lation analysis method. This method allows to zoom into time-frequency scales where the flow perturbations induced some modifications in power production
ISSN: 0960-1481

hal-01528296
https://hal.archives-ouvertes.fr/hal-01528296
DOI : 10.1016/j.renene.2017.05.024

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background : Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a.Results : In QM9136, we detected a surprisingly low number of mutagenic events in the promoter and coding regions of genes, i.e. only eight indels and six single nucleotide variants. One of these indels led to a frame-shift in the Zn2Cys6 transcription factor XYR1, the general regulator of cellulase and xylanase expression, and resulted in its C-terminal truncation by 140 amino acids. Retransformation of strain QM9136 with the wild-type xyr1 allele fully recovered the ability to produce cellulases, and is thus the reason for the cellulase-negative phenotype. Introduction of an engineered xyr1 allele containing the truncating point mutation into the moderate producer T. reesei QM9414 rendered this strain also cellulase-negative. The correspondingly truncated XYR1 protein was still able to enter the nucleus, but failed to be expressed over the basal constitutive level.Conclusion : The missing 140 C-terminal amino acids of XYR1 are therefore responsible for its previously observed auto-regulation which is essential for cellulases to be expressed. Our data present a working example of the use of genome sequencing leading to a functional explanation of the QM9136 cellulase-negative phenotype.
ISSN: 1471-2164

Droits : http://creativecommons.org/licenses/by/
hal-01149671
http://hal.upmc.fr/hal-01149671
http://hal.upmc.fr/hal-01149671/document
http://hal.upmc.fr/hal-01149671/file/Lichius_2015_Genome_sequencing.pdf
DOI : 10.1186/s12864-015-1526-0

Éditeur(s) : HAL CCSD Institute of Mathematics Polish Academy of Sciences
Résumé : International audience
In analogy to the classical isomorphism between L(D(Rn);D0(Rm)) and D0(Rm+n) (resp. L(S(Rn); S0(Rm)) and S0(Rm+n)), we show that a large class of moderate linear mappings acting between the space GC(Rn) of compactly supported generalized functions and G(Rn) of generalized functions (resp. the space GS(Rn) of Colombeau rapidly decreasing generalized functions and the space G (Rn) of temperate ones) admits generalized integral representations, with kernels belonging to specic regular subspaces of G(Rm+n) (resp. G (Rm+n)). The main novelty is to use accelerated -nets, which are unit elements for the convolution product in these regular subspaces, to construct the kernels. Finally, we establish a strong relationship between these results and the classical ones.
ISSN: 0137-6934

hal-01529541
https://hal.univ-antilles.fr/hal-01529541
https://hal.univ-antilles.fr/hal-01529541/document
https://hal.univ-antilles.fr/hal-01529541/file/delcroix.pdf
DOI : 10.4064/bc88-0-7

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Cross-species analyses of plant functional traits have shed light on factors contributing to differences in performance and distribution, but to date most studies have focused on either leaves or stems. We extend these tissue-specific analyses of functional strategy towards a whole-plant approach by integrating data on functional traits for 13 448 leaves and wood tissues from 4672 trees representing 668 species of Neotropical trees. Strong correlations amongst traits previously defined as the leaf economics spectrum reflect a tradeoff between investments in productive leaves with rapid turnover vs. costly physical leaf structure with a long revenue stream. A second axis of variation, the 'stem economics spectrum', defines a similar tradeoff at the stem level: dense wood vs. high wood water content and thick bark. Most importantly, these two axes are orthogonal, suggesting that tradeoffs operate independently at the leaf and at the stem levels. By simplifying the multivariate ecological strategies of tropical trees into positions along these two spectra, our results provide a basis to improve global vegetation models predicting responses of tropical forests to global change.
ISSN: 1461-023X

hal-00594040
https://hal.archives-ouvertes.fr/hal-00594040