Molecular hydrogen from water radiolysis as an energy source for bacterial growth in a basin containing irradiating waste

Although being deionized, filtered and therefore normally deeply oligotrophic, the water from a basin containing irradiating waste presented relatively high bacterial concentrations (ca 10(5) cfu ml(-1)) and biofilm development at its surface and on the walls. This water was characterized by a high concentration of molecular H2 due to water radiolysis, while its electrochemical potential was around +400 mV due the presence of dissolved O2 and active oxygen compounds. This combination of H2 availability and of an oxidant environment is completely original and not described in nature. From surface and wall biofilms, we enumerated the autotrophic populations ( approximately 10(5) bacteria ml(-1)) able to grow in presence of H2 as energy source and CO2 as carbon source, and we isolated the most abundant ones among cultivable bacteria. They efficiently grew on a mineral medium, in the presence of H2, O2 and CO2, the presence of the three gases being indispensable. Two strains were selected and identified using their rrs gene sequence as Ralstonia sp. GGLH002 and Burkholderia sp. GGLH005. In pure culture and using isotope exchange between hydrogen and deuterium, we demonstrated that these strains are able to oxidize hydrogen as energy source, using oxygen as an electron acceptor, and to use carbon dioxide as carbon source. These chemoautotroph hydrogen-oxidizing bacteria probably represent the pioneer bacterial populations in this basin and could be primary producers in the bacterial community.     

Quantitative SUMO-1 modification of a vaccinia virus protein is required for its specific localization and prevents its self-association

Vaccinia virus (VV), the prototype member of the Poxviridae, a family of large DNA viruses, carries out DNA replication in specialized cytoplasmic sites that are enclosed by the rough endoplasmic reticulum (ER). We show that the VV gene product of A40R is quantitatively modified by SUMO-1, which is required for its localization to the ER-enclosed replication sites. Expression of A40R lacking SUMO-1 induced the formation of rod-shaped cytoplasmic aggregates. The latter likely consisted of polymers of nonsumoylated protein, because unmodified A40R interacted with itself, but not with the SUMO-1-conjugated protein. Using a bacterial sumoylation system, we furthermore show that unmodified A40R is mostly insoluble, whereas the modified form is completely soluble. By electron microscopy, the A40R rods seen in cells were associated with the cytosolic side of the ER and induced the apposition of several ER cisternae. A40R is the first example of a poxvirus protein to acquire SUMO-1. Its quantitative SUMO-1 modification is required for its proper localization to the viral "mini-nuclei" and prevents its self-association. The ability of the nonsumoylated A40R to bring ER membranes close together could suggest a role in the fusion of ER cisternae when these coalesce to enclose the VV replication sites.     

The back-calculation of size and growth from otoliths: Validation and comparison of models at an individual level

Multiple internal and external tagging experiments tested the applicability of five back-calculation models (Biological Intercept, Modified-Fry, Body Proportional Hypothesis, Time-Varying Growth, and an Age-Effects model) as predictors of individual growth trajectories of two marine cleaning gobies, Elacatinus evelynae and E. prochilos, that were raised in aquaria under conditions that resulted in variable growth. Mixed-effect model analyses of longitudinal records of otoliths and somatic growth collected at the individual level revealed that E. evelynae and E. prochilos produced daily increments on their otoliths for up to two months post-settlement and that the Modified-Fry model provided the most accurate size-at-age estimates despite the presence of age, growth and time-varying growth effects in the dataset. Very large errors in predicted size were produced by the Age-Effects model. The four other back-calculation models all provided slightly biased estimates of back-calculated size-at-age, with the Modified-Fry model providing the least biased estimates. Regardless of bias, both experimental and theoretical evidence indicated that back-calculated size was a better proxy of fish length than otoliths radius. Relationships between fish length and otoliths radius were allometric at the level of individuals, which explained why the Modified-Fry model performed better. However, this allometry was undetectable at the population level. This study represents the first attempt to validate modern back-calculation models using longitudinal data collected and analysed at the individual level. Our results suggest the use of the Modified-Fry model as a conservative approach in routine back-calculations of fish size at age from otoliths.     

Defining Mediterranean and Black Sea Biogeochemical Subprovinces and Synthetic Ocean Indicators Using Mesoscale Oceanographic Features

The Mediterranean and Black Seas are semi-enclosed basins characterized by high environmental variability and growing anthropogenic pressure. This has led to an increasing need for a bioregionalization of the oceanic environment at local and regional scales that can be used for managerial applications as a geographical reference. We aim to identify biogeochemical subprovinces within this domain, and develop synthetic indices of the key oceanographic dynamics of each subprovince to quantify baselines from which to assess variability and change. To do this, we compile a data set of 101 months (2002–2010) of a variety of both “classical” (i.e., sea surface temperature, surface chlorophyll-a, and bathymetry) and “mesoscale” (i.e., eddy kinetic energy, finite-size Lyapunov exponents, and surface frontal gradients) ocean features that we use to characterize the surface ocean variability. We employ a k-means clustering algorithm to objectively define biogeochemical subprovinces based on classical features, and, for the first time, on mesoscale features, and on a combination of both classical and mesoscale features. Principal components analysis is then performed on the oceanographic variables to define integrative indices to monitor the environmental changes within each resultant subprovince at monthly resolutions. Using both the classical and mesoscale features, we find five biogeochemical subprovinces for the Mediterranean and Black Seas. Interestingly, the use of mesoscale variables contributes highly in the delineation of the open ocean. The first axis of the principal component analysis is explained primarily by classical ocean features and the second axis is explained by mesoscale features. Biogeochemical subprovinces identified by the present study can be useful within the European management framework as an objective geographical framework of the Mediterranean and Black Seas, and the synthetic ocean indicators developed here can be used to monitor variability and long-term change.     

Emerging high-throughput approaches to analyze bioremediation of sites contaminated with hazardous and/or recalcitrant wastes

Sustainable development requires the promotion of environmental management and a constant search for new technologies to treat a wide range of aquatic and terrestrial habitats contaminated by increasing anthropogenic activities. Bioremediation, i.e. the elimination of natural or xenobiotic pollutants by living organisms, is an environmentally friendly and cost-effective alternative to physico-chemical cleanup options. However, the strategy and outcome of bioremediation in open systems or confined environments depend on a variety of physico-chemical and biological factors that need to be assessed and monitored. In particular, microorganisms are key players in bioremediation applications, yet their catabolic potential and their dynamics in situ remain poorly characterized. To perform a comprehensive assessment of the biodegradative potential of a contaminated site and efficiently monitor changes in the structure and activities of microbial communities involved in bioremediation processes, sensitive, fast and large-scale methods are needed. Over the last few years, the scientific literature has revealed the progressive emergence of genomic high-throughput technologies in environmental microbiology and biotechnology. In this review, we discuss various high--throughput techniques and their possible--or already demonstrated-application to assess biotreatment of contaminated environments.     

Genetic determinism of reproductive fitness traits under drought stress in the model legume <Emphasis Type="Italic">Medicago truncatula</Emphasis>

Fitness traits that determine the reproductive ability of individuals and the persistence of populations are affected by drought stress. Medicago truncatula that commonly encounters drought stress in its natural area, and for which large natural diversity and genetic tools are available, is a suitable species to investigate genetic determinism of fitness traits under stress. In a common garden, three successive cycles of short drought stress were applied after flowering, during the reproductive stage that is the most susceptible to drought for that species. Ten genotypes derived from natural populations and a mapping population were used to investigate the genetic determinism of vegetative and reproductive traits as components of fitness. A large genetic variation was observed and transgressive genotypes (more resistant or more susceptible than the parental genotypes) were found in the mapping population. Fitness traits were reduced by 5–74% in drought condition compared to well-watered condition. The most affected characters were total pod number per plant and total pod weight per plant. A total of 49 QTL, explaining between 6 and 38% of phenotypic variation for vegetative and reproductive fitness traits, were detected on all chromosomes except chromosome 6. A major QTL for flowering date (R ² of 19 and 38%) that co-located with QTL for reproductive fitness traits were found on chromosome 7. In this study, no major QTL specific to drought-stressed or well-watered conditions were detected. We, thus, showed that QTL explaining fitness traits were numerous with small effects, in accordance with the genetic determinism of a complex trait.     

Seasonal, daily and diurnal variations in the stable carbon isotope composition of carbon dioxide respired by tree trunks in a deciduous oak forest

The stable C isotope composition (δ¹³C) of CO₂ respired by trunks was examined in a mature temperate deciduous oak forest (Quercus petraea). Month-to-month, day-to-day and diurnal, measurements were made to determine the range of variations at different temporal scales. Trunk growth and respiration rates were assessed. Phloem tissue was sampled and was analysed for total organic matter and soluble sugar ¹³C composition. The CO₂ respired by trunk was always enriched in ¹³C relative to the total organic matter, sometimes by as much as 5‰. The δ¹³C of respired CO₂ exhibited a large seasonal variation (3.3‰), with a relative maximum at the beginning of the growth period. The lowest values occurred in summer when the respiration rates were maximal. After the cessation of radial trunk growth, the respired CO₂ δ¹³C values showed a progressive increase, which was linked to a parallel increase in soluble sugar content in the phloem tissue (R = 0.95; P < 0.01). At the same time, the respiration rates declined. This limited use of the substrate pool might allow the discrimination during respiration to be more strongly expressed. The late-season increase in CO₂ δ¹³C might also be linked to a shift from recently assimilated C to reserves. At the seasonal scale, CO₂ δ¹³C was negatively correlated with air temperature (R = −0.80; P < 0.01). The diurnal variation sometimes reached 3‰, but the range and the pattern depended on the period within the growing season. Contrary to expectations, diurnal variations were maximal in winter and spring when the leaves were missing or not totally functional. By contrast to the seasonal scale, these diurnal variations were not related to air temperature or sugar content. Our study shows that seasonal and diurnal variations of respired ¹³C exhibited a similar large range but were probably explained by different mechanisms.     

Flanking sequence tags in Arabidopsis thaliana T-DNA insertion lines: a pilot study

Eight hundred and fifty Arabidopsis thaliana T-DNA insertion lines have been selected on a phenotypic basis. The T-DNA flanking sequences (FST) have been isolated using a PCR amplification procedure and sequenced. Seven hundred plant DNA sequences have been obtained revealing a T-DNA insertion in, or in the immediate vicinity of 482 annotated genes. Limited deletions of plant DNA have been observed at the site of insertion of T-DNA as well as in its left (LB) and right (RB) T-DNA signal sequences. The distribution of the T-DNA insertions along the chromosomes shows that they are essentially absent from the centrometric and pericentrometric regions.