Breathing air to save energy--new insights into the ecophysiological role of high-affinity [NiFe]-hydrogenase in Streptomyces avermitilis.

International audienceThe Streptomyces avermitilis genome encodes a putative high-affinity [NiFe]-hydrogenase conferring the ability to oxidize tropospheric H2 in mature spores. Here, we used a combination of transcriptomic and mutagenesis approaches to shed light on the potential ecophysiological role of the enzyme. First, S. avermitilis was either exposed to low or hydrogenase-saturating levels of H2 to investigate the impact of H2 on spore transcriptome. In total, 1293 genes were differentially expressed, with 1127 and 166 showing lower and higher expression under elevated H2 concentration, respectively. High H2 exposure lowered the expression of the Sec protein secretion pathway and ATP-binding cassette-transporters, with increased expression of genes encoding proteins directing carbon metabolism toward sugar anabolism and lower expression of NADH dehydrogenase in the respiratory chain. Overall, the expression of relA responsible for the synthesis of the pleiotropic alarmone ppGpp decreased upon elevated H2 exposure, which likely explained the reduced expression of antibiotic synthesis and stress response genes. Finally, deletion of hhySL genes resulted in a loss of H2 uptake activity and a dramatic loss of viability in spores. We propose that H2 is restricted to support the seed bank of Streptomyces under a unique survival-mixotrophic energy mode and discuss important ecological implications of this finding

Detection and Isolation of Plant-Associated Bacteria Scavenging Atmospheric Molecular Hydrogen.

International audienceHigh-affinity H2 -oxidizing bacteria possessing group 5 [NiFe]-hydrogenase genes are important contributors to atmospheric hydrogen (H2 ) uptake in soil environments. Although previous studies reported the occurrence of a significant H2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. Here, we show the existence of plant-associated bacteria with the ability to consume atmospheric H2 that may be a potential energy source required for their persistence in plants. Detection of the gene hhyL - encoding the large subunit of group 5 [NiFe]-hydrogenase - in plant tissues showed that plant-associated high-affinity H2 -oxidizing bacteria are widely distributed in herbaceous plants. Among a collection of 145 endophytic isolates, 7 Streptomyces strains were shown to possess hhyL gene and exhibit high- or intermediate-affinity H2 uptake activity. Inoculation of Arabidopsis thaliana (thale cress) and Oryza sativa (rice) seedlings with selected isolates resulted in an internalization of the bacteria in plant tissues. H2 uptake activity per bacterial cells was comparable between plant and soil, demonstrating that both environments are favorable for the H2 uptake activity of streptomycetes. This study first demonstrated the occurrence of plant-associated high-affinity H2 -oxidizing bacteria and proposed their potential contribution as a sink for atmospheric H2

Surveying the endomicrobiome and ectomicrobiome of bark beetles: The case of Dendroctonus simplex.

International audienceMany bark beetles belonging to the Dendroctonus genus carry bacterial and fungal microbiota, forming a symbiotic complex that helps the insect to colonize the subcortical environment of the host tree. However, the biodiversity of those bacteria at the surface of the cuticle or inside the body parts of bark beetles is not well established. The aim of this study was to characterize the bacterial microbiome associated with the eastern larch beetle, Dendroctonus simplex, using bacterial 16S rRNA gene pyrosequencing. The ecto- and endomicrobiome and the subcortical galleries were investigated. Several bacterial genera were identified, among which Pseudomonas, Serratia and Yersinia are associated with the surface of the beetle cuticle, and genera belonging to Enterobacteriaceae and Gammaproteobacteria with the interior of the insect body. The index of dissimilarity indicates that the bacterial microbiome associated with each environment constitutes exclusive groups. These results suggest the presence of distinct bacterial microbiota on the surface of the cuticle and the interior of D. simplex body. Additionally, the bacterial diversity identified in the galleries is substantially different from the ectomicrobiome, which could indicate a selection by the insect. This study reports for the first time the identification of the eastern larch beetle microbiome

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.

International audienceSoil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities

Parametric identification of a functional-structural tree growth model and application to beech trees (Fagus sylvatica)

International audienceFunctional-structural models provide detailed representations of tree growth and their application to forestry seems full of prospects. However, owing to the complexity of tree architecture, parametric identification of such models remains a critical issue. We present the GreenLab approach for modelling tree growth. It simulates tree growth plasticity in response to changes of their internal level of trophic competition, especially topological development and cambial growth. The model includes a simplified representation of tree architecture, based on a species-specific description of branching patterns. We study whether those simplifications allow enough flexibility to reproduce with the same set of parameters the growth of two observed understorey beech trees (Fagus sylvatica L.) of different ages in different environmental conditions. The parametric identification of the model is global, i.e. all parameters are estimated simultaneously, potentially providing a better description of interactions between sub-processes. As a result, the source-sink dynamics throughout tree development is retrieved. Simulated and measured trees were compared for their trunk profiles (fresh masses and dimensions of every growth units, ring diameters at different heights) and compartment masses of their order 2 branches. Possible improvements of this method by including topological criteria are discussed

Estimation de contraintes résiduelles par la méthode du contour : application au soudage multipasse

Les procédés de soudage sont l'un des moyens d'assemblage les plus utilisés dans la construction navale. Pour des pièces de fortes épaisseurs, les joints soudés nécessitent plusieurs étapes successives (soudage multipasse) engendrant ainsi des contraintes et des déformations résiduelles. Dans cette étude deux méthodes de mesure de contraintes résiduelles (méthode du contour et méthode du trou profond) ont été appliquées sur un joint d'angle en Té en acier à haute limite d'élasticité

Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices.

International audienceThe impact of mechanical site preparation (MSP) on soil biogeochemical structure in young larch plantations was investigated. Soil samples were collected in replicated plots comprising simple trenching, double trenching, mounding and inverting site preparation. Unlogged natural mixed forest areas were used as a reference. Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots. However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest. A combination of the biological and physicochemical variables was used to define a multifunctional classification of the soil samples into four distinct groups categorized as a function of their deviation from baseline ecological conditions. According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level. No relationship was observed between MSP method and soil bacterial community structure as assessed by high-throughput sequencing of bacterial 16S rRNA gene; however, indicator genotypes were identified for each multifunctional soil class. This is the first identification of multifunctional molecular indicators for baseline and disturbed ecological conditions in soil, demonstrating the potential of applied microbial ecology to guide silvicultural practices and ecological risk assessment

Implementation of a new discrete Immersed Boundary Method in OpenFOAM

International audienceThe immersed boundary method proposed by Pinelli et al. (2010) has been implemented as a new object oriented library within the open source CFD solver OpenFOAM for incompressible bluff body fluid flows. The method encompasses the presence of fixed and moving solid obstacles in a computational mesh, without conforming to their boundaries. Standard Cartesian meshes are employed(uniform or stretched), which allows to use efficient and accurate flow solvers. The immersed obstacles are defined using a body force added on the conservation equations, and evaluated on Lagrangian markers that can move over the Eulerian mesh to capture the motion or the deformation of the body. The integration of the method in the finite-volume formalism and the succesfull integration of the method into the PISO algorithm will be detailed and a careful verification will be provided using a manufactured solution. The efficiency and the accuracy of the algorithm has been studied on various 2D and 3D simulations of flows around fixed and moving cylinder , including careful comparisons with available numerical and experimental results of the literature. Analysis of the computational cost, numerical behavior and accuracy of the numerical method show that the global properties of the OpenFOAM solver are not alterated. A quasi-linear scalability with the number of processors (up to 96) is obtained, with a slope slightly lower than the ideal scalability a feature that has been reported already in existing OpenFOAM studies. Work has been validated at Reynolds numbers in the range Re=30-500 and is in good agreement with reference data reported in the literature. Work is already in progress to extend the algorithm to the simulation of fluid structure interaction with induced oscillation and turbulent flows around bluff bodies for which preliminary results are in good agreement with reference data reported in the literature