Experimental Microbial Evolution of Extremophiles

Experimental microbial evolutions (EME) involves studying closely a microbial population after it has been through a large number of generations under controlled conditions (Kussell 2013). Adaptive laboratory evolution (ALE) selects for fitness under experimentally imposed conditions (Bennett and Hughes 2009; Dragosits and Mattanovich 2013). However, experimental evolution studies focusing on the contributions of genetic drift and natural mutation rates to evolution are conducted under non-selective conditions to avoid changes imposed by selection (Hindré et al. 2012). To understand the application of experimental evolutionary methods to extremophiles it is essential to consider the recent growth in this field over the last decade using model non-extremophilic microorganisms. This growth reflects both a greater appreciation of the power of experimental evolution for testing evolutionary hypotheses and, especially recently, the new power of genomic methods for analyzing changes in experimentally evolved lineages. Since many crucial processes are driven by microorganisms in nature, it is essential to understand and appreciate how microbial communities function, particularly with relevance to selection. However, many theories developed to understand microbial ecological patterns focus on the distribution and the structure of diversity within a microbial population comprised of single species (Prosser et al. 2007). Therefore an understanding of the concept of species is needed. A common definition of species using a genetic concept is a group of interbreeding individuals that is isolated from other such groups by barriers of recombination (Prosser et al. 2007). An alternative ecological species concept defines a species as set of individuals that can be considered identical in all relevant ecological traits (Cohan 2001). This is particularly important because of the abundance and deep phylogenetic complexity of microbial communities. Cohan postulated that “bacteria occupy discrete niches and that periodic selection will purge genetic variation within each niche without preventing divergence between the inhabitants of different niches”. The importance of gene exchange mechanisms likely in bacteria and archaea and therefore extremophiles, arises from the fact that their genomes are divided into two distinct parts, the core genome and the accessory genome (Cohan 2001). The core genome consists of genes that are crucial for the functioning of an organism and the accessory genome consists of genes that are capable of adapting to the changing ecosystem through gain and loss of function. Strains that belong to the same species can differ in the composition of accessory genes and therefore their capability to adapt to changing ecosystems (Cohan 2001; Tettelin et al. 2005; Gill et al. 2005). Additional ecological diversity exists in plasmids, transposons and pathogenicity islands as they can be easily shared in a favorable environment but still be absent in the same species found elsewhere (Wertz et al. 2003). This poses a major challenge for studying ALE and community microbial ecology indicating a continued need to develop a fitting theory that connects the fluid nature of microbial communities to their ecology (Wertz et al. 2003; Coleman et al. 2006). Understanding the nature and contribution of different processes that determine the frequencies of genes in any population is the biggest concern in population and evolutionary genetics (Prosser et al. 2007) and it is critical for an understanding of experimental evolution

Dynamical matrix eigenvectors in crystals : experimental determination for naphthalene and anthracene

A method is proposed for the determination of the dynamical matrix eigenvectors in crystals from the Raman scattering relative intensities of the lattice modes. Numerical applications are performed for naphthalene and anthracene whose low frequency Raman scattering lines are reinvestigated (for both single crystals and polycrystalline sample spectra). Molecular anisotropies in crystals are used. Due to the uncertainties of the experimental intensities a relatively good agreement is observed between these eigenvectors and those given by the solution of the Lagrangian problem. Moreover, the method clearly shows that these eigenvectors are highly temperature dependent.Nous présentons une méthode permettant de déterminer les vecteurs propres des matrices dynamiques à partir des intensités relatives des raies de diffusion Raman caractérisant les modes de vibration de réseau. Nous appliquons cette méthode aux cristaux de naphtalène et d'anthracène dont les propriétés spectrales de basse fréquence ont été analysées de nouveau (tant pour des échantillons monocristallins que pulvérulents). Nous soulignons l'importance de considérer les anisotropies des molécules dans le cristal et non celles qui sont relatives aux molécules isolées. Compte tenu des imprecisions d'une part dues aux mesures des intensités, d'autre part celles inhérentes à la méthode de calcul, nous trouvons néanmoins un accord satisfaisant entre les vecteurs propres déterminés ainsi, avec ceux donnés directement par la résolution du déterminant séculaire. De plus, cette méthode montre que ces vecteurs propres sont extrêmement sensibles à la température

Inferring CO2 sources and sinks from satellite observations: Method and application to TOVS data

International audienceProperly handling satellite data to constrain the inversion of CO2 sources and sinks at the Earth surface is a challenge motivated by the limitations of the current surface observation network. In this paper we present a Bayesian inference scheme to tackle this issue. It is based on the same theoretical principles as most inversions of the flask network but uses a variational formulation rather than a pure matrix-based one in order to cope with the large amount of satellite data. The minimization algorithm iteratively computes the optimum solution to the inference problem as well as an estimation of its error characteristics and some quantitative measures of the observation information content. A global climate model, guided by analyzed winds, provides information about the atmospheric transport to the inversion scheme. A surface flux climatology regularizes the inference problem. This new system has been applied to 1 year's worth of retrievals of vertically integrated CO2 concentrations from the Television Infrared Observation Satellite Operational Vertical Sounder (TOVS). Consistent with a recent study that identified regional biases in the TOVS retrievals, the inferred fluxes are not useful for biogeochemical analyses. In addition to the detrimental impact of these biases, we find a sensitivity of the results to the formulation of the prior uncertainty and to the accuracy of the transport model. Notwithstanding these difficulties, four-dimensional inversion schemes of the type presented here could form the basis of multisensor data assimilation systems for the estimation of the surface fluxes of key atmospheric compounds

Interaction of micro and nanoplastics with proteins: How the adsorption of biolomolecules on plastics control their biological and environmental identity ?

International audienceDe grandes quantités de plastiques sont produites et rejetées dans la nature chaque année, certains étant ou devenant des Microplastiques ou des NanoPlastiques (regroupés dans MNP < 20 μm). Ces particules peuvent être introduites dans la chaîne alimentaire, et vont rapidement être entourées d’une couche de protéines appelée la corona. L’objectif de ce projet est d’étudier les interactions entre MNP et protéines pour comprendre le devenir et l’impact de ces matériaux polluants en milieux biologiques.Le premier axe d’étude porte sur des protéines isolées et bien connues. Actuellement nous avons mis des microparticules de polyéthylène et de polypropylène en contact avec de l’Albumine de sérum Bovin, ainsi qu’avec de l’hémoglobine porcine. L’utilisation de ces protéines modèles permet la compréhension des phénomènes qui régissent leur adsorption sur des MNP ainsi que l’observation éventuelle de l’altération de leur structure et de leur fonction.Le deuxième axe d’étude porte sur un système protéique plus complexe : un extrait protéique de levure (environ 5800 protéines). L’objectif est de comprendre, via des expériences de protéomique et des études statistiques, quels sont les déterminants physico-chimiques qui vont influer sur les interactions MNP/protéines.Ces deux axes nous permettront d’avoir une vision globale des interactions MNP/protéines : de la compréhension des mécanismes d’adsorption aux effets éventuels de ces particules sur les structures et fonctions biologiques des protéines

Interaction of micro and nanoplastics with proteins: How the adsorption of biolomolecules on plastics control their biological and environmental identity ?

International audienceDe grandes quantités de plastiques sont produites et rejetées dans la nature chaque année, certains étant ou devenant des Microplastiques ou des NanoPlastiques (regroupés dans MNP < 20 μm). Ces particules peuvent être introduites dans la chaîne alimentaire, et vont rapidement être entourées d’une couche de protéines appelée la corona. L’objectif de ce projet est d’étudier les interactions entre MNP et protéines pour comprendre le devenir et l’impact de ces matériaux polluants en milieux biologiques.Le premier axe d’étude porte sur des protéines isolées et bien connues. Actuellement nous avons mis des microparticules de polyéthylène et de polypropylène en contact avec de l’Albumine de sérum Bovin, ainsi qu’avec de l’hémoglobine porcine. L’utilisation de ces protéines modèles permet la compréhension des phénomènes qui régissent leur adsorption sur des MNP ainsi que l’observation éventuelle de l’altération de leur structure et de leur fonction.Le deuxième axe d’étude porte sur un système protéique plus complexe : un extrait protéique de levure (environ 5800 protéines). L’objectif est de comprendre, via des expériences de protéomique et des études statistiques, quels sont les déterminants physico-chimiques qui vont influer sur les interactions MNP/protéines.Ces deux axes nous permettront d’avoir une vision globale des interactions MNP/protéines : de la compréhension des mécanismes d’adsorption aux effets éventuels de ces particules sur les structures et fonctions biologiques des protéines

The greenhouse gas project of ESA’s climate change initiative (GHG-CCI): overview, achievements and future plans

International audienceThe GHG-CCI project (http://www.esa-ghg-cci.org/) is one of several projects of the European Space Agency's (ESA) Climate Change Initiative (CCI). The goal of the CCI is to generate and deliver data sets of various satellite-derived Essential Climate Variables (ECVs) in line with GCOS (Global Climate Observing System) requirements. The "ECV Greenhouse Gases" (ECV GHG) is the global distribution of important climate relevant gases-namely atmospheric CO 2 and CH 4-with a quality sufficient to obtain information on regional CO 2 and CH 4 sources and sinks. The main goal of GHG-CCI is to generate long-term highly accurate and precise time series of global near-surface-sensitive satellite observations of CO 2 and CH 4 , i.e., XCO 2 and XCH 4 , starting with the launch of ESA's ENVISAT satellite. These products are currently retrieved from SCIAMACHY/ENVISAT (2002-2012) and TANSO-FTS/GOSAT (2009-today) nadir mode observations in the near-infrared/shortwave-infrared spectral region. In addition, other sensors (e.g., IASI and MIPAS) and viewing modes (e.g., SCIAMACHY solar occultation) are also considered and in the future also data from other satellites. The GHG-CCI data products and related documentation are freely available via the GHG-CCI website and yearly updates are foreseen. Here we present an overview about the latest data set (Climate Research Data Package No. 2 (CRDP#2)) and summarize key findings from using satellite CO 2 and CH 4 retrievals to improve our understanding of the natural and anthropogenic sources and sinks of these important atmospheric greenhouse gases. We also shortly mention ongoing activities related to validation and initial user assessment of CRDP#2 and future plans