Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The mechanism for tree orientation in angiosperms is based on the production of high tensile stress on the upper side of the inclined axis. In many species, the stress level is strongly related to the presence of a peculiar layer, called G-layer, in the fibre wall. The structure of G-layer has been recently described as a hydrogel thanks to N2 adsorption-desorption isotherms of supercritically dried samples showing a high mesoporosity (pores size from 2 to 50 nm). This led us to revisit the concept of G-layer that was until now only described from anatomical observation. Adsorption isotherms of both normal wood and tension wood have been measured on six tropical species. Measurements show that mesoporosity is high in tension wood with typical thick G-layer while it is much less with thinner G-layer, sometimes no more than normal wood. The mesoporosity of tension wood species without G-layer is as low as in normal wood. Not depending on the amount of pores, the pore sizes distribution are always centred around 6-12 nm. These results suggest that, among species producing fibres with G-layer, large structural differences of G-layer exist between species
ISSN: 0022-0957

hal-00387861
https://hal.archives-ouvertes.fr/hal-00387861
DOI : 10.1093/jxp/erp133

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
We predict the IR-TO, IR-LO and Raman modes (wave numbers and intensities) of magnesite (MgCO3) up to 50 GPa, at T = 0 K, using the density-functional perturbation theory up to a third order perturbation, under the harmonic assumption. The predicted IR-TO and Raman mode wave numbers, the mode Grüneisen parameters and the Davydov splittings are systematically compared with experimental data for all modes up to the pressures of 10-30 GPa and for some modes up to 50 GPa. Existing experiments allow extending this comparison only to IR-LO wave numbers of the E u (ν3) asymmetric-stretch mode, confirming the odd experimental behavior of this mode at very high pressures. Predicted IR-TO, IR-LO and Raman intensities up to 50 GPa are just tabulated, but data are missing for their comparison with precise experiments. However, the generally good agreement observed between numerical results and experimental data, when their comparison is possible, suggests that first-principles methods are a major help to predict the entire spectrum up to very high pressures.
ISSN: 0342-1791

hal-00527834
https://hal.archives-ouvertes.fr/hal-00527834
DOI : 10.1007/s00269-010-0395-y

Éditeur(s) : HAL CCSD Cambridge University Press (CUP)
Résumé : Nodulated legume trees comprised 43% of the stand basal area in the low, most frequently flooded microsites, and 23% in higher, drier microsites in a tropical freshwater swamp forest in French Guiana. Dinitrogen fixation in Pterocarpus officinalis, Hydrochorea corymbosa and Inga pilosula was confirmed by acetylene reduction assay (ARA), presence of leghaemoglobin in nodules and the N-15 natural abundance method. The results for Zygia cataractae were inconclusive but suggested N-2 fixation in drier microsites. Nodulated Inga disticha had a N-15-to-N-14 ratio similar to non-N-2-fixing trees, but ARA indicated nitrogenase activity and leghaemoglobin was present in nodules. All bacterial strains were identified as Bradyrhizobium spp. according to the partial 16S rDNA sequences, and they were infective in vitro in the model species Macroptilium atropurpuretan. About 35-50% of N in the leaves of P. officinalis, H. corymbosa and I. pilosula was fixed from the atmosphere. Dinitrogen fixation was estimated to contribute at least 8-13% and 1728% to whole-canopy N in high and low microsites, respectively. Symbiotic N, fixation appears to provide both a competitive advantage to legume trees under N-limited, flooded conditions and an important N input to neotropical freshwater swamp forests.
ISSN: 0266-4674

hal-01189191
https://hal.archives-ouvertes.fr/hal-01189191
PRODINRA : 13151
DOI : 10.1017/S0266467403006059

Éditeur(s) : HAL CCSD EDP Sciences
Résumé : International audience
This paper presents a comparison of models for extreme rainfall and flood values. Based on a large set of thousands of rainfall and discharge data, the French ExtraFlo project showed that design estimate of extreme values based on the fitting of a distribution on a limited sample of maximum values is very inaccurate when only a few decades of observation are available. Some interesting alternatives are possible, using a regional approach, or historical data when available, or simulation methods, or sedimentological or geochemical signatures of flood deposits.
Cette communication présente les principaux résultats du projet ExtraFlo sur l'estimation des pluies et crues extrêmes. A partir d'un jeu de données conséquent de plusieurs milliers de stations, une procédure d'inter-comparaison a permis d'évaluer les performances d'une trentaine d'implémentations différentes issues de différentes combinaisons (modèle probabiliste, méthode d'estimation, cadre local / régional / mixte local et régional). Le projet ExtraFlo a permis de mettre en évidence le manque de robustesse des approches basées sur le traitement statistique d'une série de quelques dizaines d'années d'observation. Des alternatives intéressantes existent, basées sur l'exploitation des records de pluie et de débit à l'échelle d'une région, de la collecte de données historiques quand cela est possible, de méthodes de simulation basées sur le couplage d'un générateur d'averses avec un modèle hydrologique pour la transformation des pluies en débit, ou des traces morphologiques laissées par les crues anciennes.
ISSN: 0018-6368

hal-01128341
https://hal.archives-ouvertes.fr/hal-01128341
https://hal.archives-ouvertes.fr/hal-01128341/document
https://hal.archives-ouvertes.fr/hal-01128341/file/ly2014-pub00041933.pdf
DOI : 10.1051/lhb/2014010

Éditeur(s) : HAL CCSD Le Cherche midi CNRS
Résumé : 192 pages
National audience
https://hal.archives-ouvertes.fr/hal-01118878

ISBN : 978-2-7491-4075-9
hal-01118878
https://hal.archives-ouvertes.fr/hal-01118878

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The paper presents coastal structures design in the presence of waves by the minimization of a cost function. It aims to show that shape optimization can be efficiently applied to ocean engineering. This is an underlying guiding principle for the design of harbors or offshore breakwaters. We compute the solution of a specific simplified boundary value problem describing the short wave propagation toward a vertical sea cliff or vertical wall and modify accordingly the shape of defense structures in order to minimize a pre-defined cost function taking into account the strength (energy) of the water waves. The optimization procedure relies on a global semi-deterministic search algorithm able to escape from local minima.
ISSN: 0378-3839

hal-00411905
https://hal.archives-ouvertes.fr/hal-00411905
DOI : 10.1016/j.coastaleng.2007.06.006

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Wood has a hierarchical structure involving several levels of organisation. The stiffness of wood relies on its capacity to transfer mechanical stress to its stiffest element at the lowest scale, namely crystalline cellulose. This study aims at quantifying to what extend crystalline cellulose contributes to wood stiffness depending on its moisture content. The crystal strains of cellulose were measured using X-ray diffraction on wet and dry specimens of spruce, based on a previously published methodology. The comparison between crystal strain and macroscopic strain shows that, during elastic loading, cellulose strain is lower than macroscopic strain. The means ratio of crystal/macroscopic strain amounts 0.85 for dry specimens and 0.64 for wet specimens. This strain ratio cannot be explained just by the projection effect due to the difference in orientation between cellulose microfibrils and cell wall, but results from deformation mechanisms in series with cellulose. Analysis shows that this series contribution represents a non-negligible contribution to wood compliance and is strongly moisture-dependent. This contribution amounts 9% for dry specimens and 33% for wet specimens, corresponding to a 4-fold increase in compliance for the series contribution. The origin of these strains is ascribed to mechanisms involving bending or shear strain at different scales, due to the fact that reinforcing element are neither perfectly straight nor infinitely long.
ISSN: 0266-3538

hal-01425031
https://hal.archives-ouvertes.fr/hal-01425031
https://hal.archives-ouvertes.fr/hal-01425031/document
https://hal.archives-ouvertes.fr/hal-01425031/file/Art_Almeras_al_Contribution_cellulose_moisture-dependent_elastic_behavior_2017.pdf
DOI : 10.1016/j.compscitech.2016.11.025

Éditeur(s) : HAL CCSD European Geosciences Union (EGU)
Résumé : International audience
Holocene climate fluctuations and human activity since the Neolithic have shaped present-day Mediter-ranean environments. Separating anthropogenic effects from climatic impacts to better understand Mediterranean pale-oenvironmental changes over the last millennia remains a challenging issue. High-resolution pollen analyses were un-dertaken on two cores from the Palavasian lagoon system (Hérault, southern France). These records allow reconstruction of vegetation dynamics over the last 4500 years. Results are compared with climatic, historical and archeological archives. A long-term aridification trend is highlighted during the late Holocene, and three superimposed arid events are recorded at 4600–4300, 2800–2400 and 1300–1100 cal BP. These periods of high-frequency climate variability coincide in time with the rapid climatic events observed in the Atlantic Ocean (Bond et al., 2001). From the Bronze Age (4000 cal BP) to the end of the Iron Age (around 2000 cal BP), the spread of sclerophyllous taxa and loss of forest cover result from anthropogenic impact. Classical Antiquity is characterized by a major reforestation event related to the concentration of rural activity and populations in coastal plains leading to forest recovery in the mountains. A major regional deforestation occurred at the beginning of the High Middle Ages. Around 1000 cal BP, forest cover is minimal while the cover of olive, chestnut and walnut expands in relation to increasing human influence. The present-day vegetation dominated by Mediterranean shrubland and pines has been in existence since the beginning of the 20th century.
ISSN: 1814-9324

hal-01447627
https://hal-univ-tlse2.archives-ouvertes.fr/hal-01447627
https://hal-univ-tlse2.archives-ouvertes.fr/hal-01447627/document
https://hal-univ-tlse2.archives-ouvertes.fr/hal-01447627/file/Azuara%20et%20al%202015_cor.pdf
DOI : 10.5194/cp-11-1769-2015

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
ISSN: 0927-7757

hal-00360381
https://hal.archives-ouvertes.fr/hal-00360381
DOI : 10.1016/j.colsurfa.2007.10.002

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : This paper presents an inversion method using the interseismic velocity field to determine effective rigidity of the lithosphere. The method is based on the minimization of a cost function defined as the quadratic measure of the difference between measured and modelled velocity fields on a discrete set of points. The continuous mapping of the rigidity is fulfilled with a limited set of parameters and the forward solution is achieved using a plane stress finite element code. The computation of the cost function gradient in the parameters' space allows one to iteratively find the best parameters set through a suitable optimization algorithm.;We first design a benchmark including an abrupt rigidity variation that cannot be described by a continuous function. For such a case, we show that increasing the number of parameters is a way to accurately describe sharp variations of the rigidity map. Then, we use a dense GPS velocity field over the southwestern United States to estimate the corresponding rigidity variations for different spatial resolutions of the parameters' grid. We analyse the conceptual and practical difficulties associated with our methodology. Finally, rigidity maps obtained by our inversion method in southwestern United States and particularly across the San Andreas Fault System are reviewed and compared to current plate rigidity estimates and geophysical data over this area.
ISSN: 0956-540X

hal-00669897
https://hal.archives-ouvertes.fr/hal-00669897
DOI : 10.1111/j.1365-246X.2011.05192.x

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : The distribution of water and ions in nanoporous membranes, in particular close to their surfaces with external reservoirs, is investigated by means of molecular dynamics (MD) simulations using classical polarizable force fields. A sodium iodide (NaI) aqueous solution is considered in uncharged weakly hydrophilic (WH) and highly hydrophilic (HH) nanoporous materials modeled by a single truncated nanopore in contact with two reservoirs. In the inner part of the nanopore, the spatial distribution of water and ions is obtained by coupling semi-infinitesimal longitudinal and semi-infinitesimal radial descriptions. In the HH material, in contrast with the WH material, species are no longer uniformly distributed in the inner nanopore and water molecules are distributed in a nearly frozen axially periodic corona-like structure which leads to the formation of ionic tunnels. In the reservoirs, water molecules and ions attracted by the membrane surface create a necking of the confined solution which acts as a barrier at the entrance of the nanopore. In the WH nanopore subsurface, close to the surface of the membrane, the species distribution is analogous to the interface distribution between an aqueous electrolyte solution and air. In the HH nanopore subsurface, this distribution is modulated by the water corona-like structure. These results provide useful information for predicting properties of nanoporous membranes, in particular the drastic reduction of diffusion coefficients in HH materials, and give a guide to designing synthetic membranes for applications in nanofiltration, etc.
ISSN: 1932-7447

hal-00682155
https://hal.archives-ouvertes.fr/hal-00682155
DOI : 10.1021/jp2078924

Éditeur(s) : HAL CCSD Editions Paralia CFL
Résumé : Le lido de Villeneuve-lès-Maguelone (Languedoc-Roussillon) est un archétype de littoral microtidal, dominé par la houle, en érosion, et largement affecté par la submersion marine lors des tempêtes. Les observations réalisées dans le cadre du Système d'Observation Littoral - Trait de Côte (SO LTC) concernent l'hydrodynamique et le transport sédimentaire dans l'avant-côte et la lagune. La tache d'observation MAGOBS (Observatoire Aresquiers-Maguelone-Palavas) de cet observatoire regroupe un dispositif instrumental automatisé composé de 30 points d'acquisition en temps réel entre 6 mètres de profondeur et le haut de plage (à terre) ainsi que dans la lagune. Le dispositif est opérationnel depuis mai 2011. Son déploiement a permis de déverrouiller les difficultés techniques liées à la mesure temps réel en zone littorale : choix du type des appareils de mesure, de la technologie embarquée, des cadences d'acquisition, résolution des questions du transfert de la donnée. Le dispositif produit 2 Tera-octets de données par an. Les données sont stockées sur un ensemble de serveurs dédiés. Les données sont mises en ligne sur le site du SO-LTC (www.soltc.org), immédiatement après premiers traitements et qualification. Elles commencent à être utilisées pour des calculs de niveau d'eau à la côte, et dansdes outils de prédiction des vagues et des niveaux à la côte associant mesure et modélisation.
ISSN: 1760-8716

hal-00854410
https://hal.archives-ouvertes.fr/hal-00854410
DOI : 10.5150/jngcgc.2012.064-G

Éditeur(s) : HAL CCSD EDP Sciences
Résumé : International audience
Understanding mechanisms in DSSCs is fundamental for their improvement; this includes the nanocrystalline semiconducting layer behaviour. Different mesoporous TiO2 layers are fabricated and analyzed for possible use in DSSC solar cells. The preparations included the addition of P123 triblock copolymer as structuring agent to the synthesized anatase sol. This preparation was also mixed with Degussa P25 TiO2 nanoparticles in one case and polystyrene latex in another. Mesoporous mixed TiO2-SiO2 thin layers were also analyzed. The diverse morphologies and features are studied by microscopic techniques and by means of spectral quantum efficiency of a photoelectrochemical cell (PEC) that uses as photoelectrode the unsensitized porous TiO2 layer. Contact angle measurements are also performed. We have found that a very high specific area due to very small nanocrystals and small pores can hinder electrolyte penetration in the pores formed by TiO2 nanograins, affecting photoelectrodes efficiency. © EDP Sciences, 2015.
ISSN: 1286-0042

hal-01683213
https://hal.univ-antilles.fr/hal-01683213
DOI : 10.1051/epjap/2015150221

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The present study reports data on CO2-rich geothermal waters and their associated carbonate deposits from the SW part of the Permian Lodève Basin (South of France). Both waters and carbonates are enriched in 226Ra, with activities up to 2.2 Bq/L and 3.5 Bq/g respectively. A series of carbonate samples precipitated around the studied wells since 1990 were dated through the 226Ra-210Pb and 228Ra-228Th methods, and the results are discussed in a new Concordia diagram. While both methods give comparable dates for many samples, Ra-Pb ages are sometimes much older than Ra-Th ages. We propose that these discrepancies result from the adsorption of 222Rn daughter nuclides in such a Rn-rich environment. The (228Ra/226Ra)0 activity ratios calculated at the time of deposition are remarkably constant for about 12 years, suggesting the presence of a steady-state aquifer. The low (228Ra/226Ra)0 ratios (0.348 ± 0.008) are best explained if most of the Ra derives from the Cambrian carbonate series (mainly dolostone) underlying the Permian Basin, which have low Th/U and similar (228Ra/226Ra) ratios. This study suggests that Ra and other alkaline-earth elements do not necessarily originate from the rocks surrounding the deep geothermal reservoir, but rather may be introduced into the CO2-rich water during its transfer towards the surface and interaction with carbonate rocks.
ISSN: 0009-2541

hal-01053715
https://hal.archives-ouvertes.fr/hal-01053715
DOI : 10.1016/j.chemgeo.2014.02.008

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The chemical investigations of Dicorynia guianensis heartwood led to the isolation of four new indole alkaloids for the first time in this plant. Compound (1) identified as spiroindolone 20,30,40,90-tetrahydrospiro [indoline-3,10pyrido[3,4-b]-indol]-2-one, and compound (3) described as nitrone 1-methyl-4,9-dihydro-3H-pyrido [3,4-b] indole 2-oxide and were isolated for the first time as natural products. ABTS antioxidant activity guided their isolation.
ISSN: 1874-3900

hal-01138910
https://hal.archives-ouvertes.fr/hal-01138910
DOI : 10.1016/j.phytol.2015.03

Éditeur(s) : HAL CCSD Inter-Research
Résumé : Precise knowledge of lifetime migrations is vital in exploited fish species, since all essential habitats must be protected to maintain sustainable stock levels. The present study used multi-element otolith fingerprints of the gilthead sea bream Sparus aurata (L.) to discriminate its main juvenile and adult habitats in the Languedoc-Roussillon region (Gulf of Lions, northwest Mediterranean) and infer the lifetime migrations of 12 individuals from the area (11 from the present day and 1 from the Roman era). This allowed for the first time the identification of key habitats for the successful completion of the species' life cycle in the Gulf of Lions, and the connectivity between them. Our results revealed that lagoon use by S. aurata is probably ancient (>2500 yr) and confirmed its current commonness. Yet, although most observed migration patterns were in accordance with the migratory behavior previously described for the species, strong inter-individual variations and new patterns in habitat use were detected. At the juvenile stage, a preference for shallow lagoons with low salinities was evidenced. Nevertheless, the first year of life can also be successfully completed in marine conditions. At the adult stage, lagoon use was shown to occur until at least age 4 yr, with periods of lagoon residency of up to 11 mo in a year, often including winter months. Because overwintering in the lagoons was previously thought to be impossible for S. aurata due to low temperatures, this finding has important implications for future stock management, especially since the species breeds in winter.
Marine Ecology Progress Series

hal-00682003
https://hal.archives-ouvertes.fr/hal-00682003
DOI : 10.3354/meps09444

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Anisotropy of low-field magnetic susceptibility (AMS) of basaltic lava flows can give some clues about post-emplacement tilting occurring in volcanic sequences. Such a study has been carried out on a sequence of 19 successive lava flows from Kerguelen Archipelago. Surprisingly, two different patterns were observed. The first one - herein called normal fabric - is consistent with the lava-flow direction inferred from geological observations, whereas the second one observed for about 70 per cent of the analysed samples - herein called abnormal fabric - appears to be unrelated to the shear history of the lava flows during their emplacements. These abnormal fabrics are not strictly inverse fabric but seem to have a more complex origin. The unusual nature of these abnormal fabrics has been confirmed by lattice preferred orientation of plagioclases obtained from high-resolution electron backscattered diffraction measurements. The aim of this study is to propose a physical interpretation of these fabrics. A first step in our understanding was to clearly identify the nature and the magnetic properties of the Fe-Ti oxides assemblage. Thus, we present a comprehensive rock magnetic analysis relying on low- and high-temperature thermomagnetic curves (K-T), crossover diagrams, first-order reversal curves, ore-microscopy, Mössbauer measurements and electron backscattered images. We found that in the present case the abnormal fabrics are probably linked to a mixture of prevailing single domain (SD) strongly interacting grains population and a subsidiary multidomain grains population. SD grains are identified as small magnetite crystallized within the interstitial glass in globular aggregates along the silicate framework. Then a question arises: to what extent such SD interacting grains in globular aggregates can affect the magnetic susceptibility and its anisotropy? To answer this question, we developed a physical model in which the total energy density of an SD grain with an uniaxial anisotropy is minimized. In this model, the distribution function of the direction of the magnetic interaction field is comprised between two boundary states. It is either isotropic, which formally corresponds to the thermal demagnetized state, or it is ordered, which formally corresponds to the Alternative Field demagnetized state. We show that in both cases the degree of anisotropy decreases as the interaction field increases. Thus, we conclude that the abnormal fabric encountered in this study can be simply explained by strong magnetostatic interactions that would explain the large scattering of AMS often observed in basaltic lava flows.
ISSN: 0956-540X

hal-00716449
https://hal.archives-ouvertes.fr/hal-00716449
https://hal.archives-ouvertes.fr/hal-00716449/document
https://hal.archives-ouvertes.fr/hal-00716449/file/gji-S-12-HAL.pdf
DOI : 10.1111/J.1365-246X.2012.05421.X

Éditeur(s) : HAL CCSD
Résumé : International audience
Semantic web standards, tools, ontologies and related technologies have considerably matured in the recent years. Nowadays, accessing a wide catalogue of biological, social, environmental, and ecological data sources helps stakeholders working on biodiversity to answer their complex questions. Will the real time access to web resources effectively support the definition of strategies to conserve and manage biodiversity? How might semantic web technologies help us to handle the complex and heterogeneous big data related to biodiversity? The workshop aims to identify the key challenges faced by the bioinformatics community, discuss potential solutions and identify the opportunities emerging from the trans-disciplinary interactions between Plant Science and Informatics experts. Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from biology, agriculture, agro-ecology, genomics, environmental studies, to social sciences, citizen sciences. Research papers presenting various aspects of semantic web technologies applied to biodiversity data, ranging from position papers to implemented systems descriptions and their evaluation, will be selected. We are particularly interested in the use of the semantic technologies to design and develop systems that supports research on agricultural and wild biodiversity conservation and management for food security. Examples may include strategies for resilience to climate change pressures, sustainability of productive ecosystems, ecosystems services monitoring or territories management, rather than systems supporting only research on climate patterns or soil erosion.
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757

lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757/document

Éditeur(s) : HAL CCSD
Résumé : The presence of biological matter (biofilms) in deep geological sites for storage of, for instance, toxic elements or groundwater in aquifers was clearly proved. That biomass triggers physical and chemical processes which greatly modify the durability and the sustainability of the sites. These processes, mainly from oxidative/reductive reactions, are poorly understood. This is mainly due to the fact that former studies were done at the macroscopic level far away from the micrometric scale where relevant processes induced by bacteria take place. Investigations at microscopic level are needed. Thus, we developed an experimental set-up based on the combined use of optical microscopy (transmission), atomic force microscopy (AFM) and electrical and electro-chemical AFM microscopy (EC_AFM) in order to get simultaneous information on topographic and electro-chemical processes. The first highly sensitive step was to use AFM with biological samples in liquid environment: wepresent here a study about AFM imaging of living, moving or self-immobilized bacteria, in their genuine physiological liquid medium and in true in vivo conditions. No external immobilization protocol, neither chemical nor mechanical was needed. For the first time, the native gliding movements of Gram negative Nostoc cyanobacteria upon the surface were studied by AFM. AFM height and mechanical stiffness data were simultaneously acquired. From these, mechanical parameters, inner turgor pressure and Young modulus, were derived for different bacterial species (Anabaenopsis circularis, Rhodococcus wratislaviensis). Our study revealed that AFM imaging is thus possible on moving living species. These results open a large window on new studies of both dynamical phenomena of practical and fundamental interests such as the formation of biofilms and dynamic properties of bacteria in real physiological conditions. The second delicate step was to combine AFM and optical measurements with electrical ones. We mounted a new experimental set-up coupling real-time (i) monitoring of optical properties as the optical density (OD) evolution related to bulk bacterial growth in liquid or as the counting of number of bacteria adhering on the surface of the sample as well and (ii) electrical and electrochemical measurements. Furthermore, these results will shortly be applied to the optimized monitoring of the in-situ activity of bacteria consuming oil pollutants, following this way, in real-time, the bioremediation of an oilcontaminated soil (ANR ECOTECH_BIOPHY program).
La présence de matière biologique (biofilms) dans les sites de stockage géologique profond, d'éléments toxiques ou encore de l'eau potable des aquifères est maintenant clairement démontrée. Cette biomasse est à l'origine de processus physiques et chimiques qui modifient considérablement la durabilité et la pérennité des sites concernés. Ces processus, principalement de type oxydo-réductif, sont encore mal compris. Ceci est principalement dû aux méthodes d'investigation, principalement macroscopiques, loin de l'échelle micrométrique caractéristique des bactéries. Seules des études, basées sur des méthodes d'investigation locale, peuvent apporter les informations requises. Ainsi, nous avons développé un dispositif expérimental basé sur l'utilisation combinée de la microscopie optique (en transmission), la microscopie à force atomique (AFM) et la microscopie AFM en mode électrique et électrochimique (EC_AFM) afin d'obtenir des informations simultanées sur la topographie de l'échantillon et sur les processus électrochimiques à l'échelle des bactéries. La première étape sensible consistait à utiliser l'AFM sur des échantillons biologiques en milieu liquide: nous présentons ici les résultats de l'imagerie AFM en milieu liquide de plusieurs types de bactéries dans leurs conditions physiologiques naturelles (conditions in vivo). Aucun protocole d'immobilisation, ni chimique ni mécanique, n'a été nécessaire; et pour la première fois, les mouvements de reptation de cyanobactéries Nostoc ont été étudiés par l'AFM. Les études AFM ont permis d'acquérir des données topographiques mais aussi mécaniques : nous avons pu ainsi mesurer le module d'Young, la pression de turgescence de différentes souches bactériennes (Anabaenopsis circularis, Rhodococcus wratislaviensis). Cette étude complète, a révélé que l'imagerie AFM est donc possible sur des espèces vivantes en mouvement. Ces résultats ouvrent une grande fenêtre sur de nouvelles études d'intérêts tels que la formation de biofilms et les propriétés dynamiques de bactéries dans des conditions physiologiques réelles. La deuxième étape délicate était de combiner l'AFM aux mesures optiques et électriques. Nous avons développé un nouveau dispositif expérimental permettant (i) le suivi de l'évolution de la croissance bactérienne par la mesure des propriétés optiques comme la densité optique DO (pour le développement bactérien en volume - milieu planctonique) , ou l'analyse de l'image du substrat par comptage du nombre de bactéries sur la surface de l'échantillon (biofilm), et (ii) les mesures électriques et électrochimiques. L'ensemble de ces résultats sera prochainement appliqué au développement de nouveaux outils de surveillance d'une biodépollution de terrain contaminé par les hydrocarbures, par le suivi in situ et en temps réel de l'activité de bactéries dépolluantes (ECOTECH_BIOPHY ANR).
https://tel.archives-ouvertes.fr/tel-01044714

tel-01044714
https://tel.archives-ouvertes.fr/tel-01044714
https://tel.archives-ouvertes.fr/tel-01044714/document
https://tel.archives-ouvertes.fr/tel-01044714/file/theseDhahri2013.pdf

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
AIMS: Virus detection has often been difficult due to a low concentration in water. In this study, we developed a new procedure based on concentration of virus particles on an innovative support: poly-L-lysine dendrigrafts (DGL), coupled with directed nucleic acid extraction and real-time PCR quantification. METHODS AND RESULTS: This method was evaluated using the bacteriophage MS2 as a model virus. This virus exhibited the size and structural properties of human pathogenic enteric viruses and has often been used to assess new supports of concentration. Moreover, this bacteriophage is also a faecal contamination indicator. In this study, many water filtration conditions were tested (volume of water, concentration, etc.), and more than 80% of bacteriophage were recovered after filtration on polymer, in most conditions. We demonstrated that the method was linear (slope = 0*99 ± 0*04 and Y intercept when x = -0*02 ± 0*28), valid (as manipulators, tested concentrations, volumes of sample and batch of polymer did not have any influence on concentration) and sensitive (allowing to concentrate up to 16,600-fold 1 l of sample and to detect and quantify down to 750 GC l(-1) and 7500 GC l(-1), respectively). CONCLUSIONS: To conclude, this support exhibits high interest to retain viruses and to allow to detect low concentration of virus in water. SIGNIFICANCE AND IMPACT OF THE STUDY: This study gives valuable advance in the methods of concentration and diagnosis of virus in water.
Journal of Applied Microbiology

hal-00828987
https://hal.archives-ouvertes.fr/hal-00828987
DOI : 10.1111/jam.12209
PUBMED : 23551794