Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics.

Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.

Reflections on the Predictability of Evolution: Toward a Conceptual Framework.

Evolution is generally considered to be unpredictable because genetic variations are known to occur randomly. However, remarkable patterns of repeated convergent evolution are observed, for instance, loss of pigments by organisms living in caves. Analogous phenotypes appear in similar environments, sometimes in response to similar constraints. Alongside randomness, a certain evolutionary determinism also exists, for instance, the selection of particular phenotypes subjected to particular environmental constraints in the "evolutionary funnel." We pursue the idea that eco-evolutionary specialization is in some way determinist. The conceptual framework of phenotypic changes entailing specialization presented in this essay explains how evolution can be predicted. We also discuss how the predictability of evolution could be tested using the case of metabolic specialization through gene losses. We also put forward that microorganisms could be key models to test and possibly make headway evolutionary predictions and knowledge about evolution.

Beyond the Black Queen Hypothesis.

The Black Queen Hypothesis, recently proposed to explain an evolution of dependency based on gene loss, is gaining ground. This paper focuses on how the evolution of dependency transforms interactions and the community. Using agent-based modeling we suggest that species specializing in the consumption of a common good escape competition and therefore favor coexistence. This evolutionary trajectory could open the way for novel long-lasting interactions and a need to revisit the classically accepted assembly rules. Such evolutionary events also reshape the structure and dynamics of communities, depending on the spatial heterogeneity of the common good production. Let Black be the new black!

Nutrient fluxes toward phytoplankton: is it useful to consider turbulence intermittency?

The Influence of turbulence on nutrient fluxes towards phytoplankton cells has been previously estimated, but those studies did not take into account the intermittent nature of turbulent processes. This has been investigated here comparing the nutrient fluxes obtained using both mean and instantaneous turbulent energy dissipation rates. This approach shows that the size of cell potentially influenced by turbulence is lower than previously indicated, and that the spectral average estimate of the turbulence effect overestimates the flux. The capacity of cell to use such intermittent flux is then discussed.

Structural stability of a stage structured model of fish: the case of the anchovy (Engraulis encrasicolus L.) in the Bay of Biscay.

A study of stage structured model of fish population is presented. This model focuse on the anchovy population in the Bay of Biscay (Engraulis encrasicolus L.) is presented. The method of study is based on an intermediate complexity mathematical model, taking into account the spatialisation, the environmental conditions and the stage-structure of the fishes. First, to test the model, we show mathematical properties, such as unicity of the solution of structural stability. Then we provide numerical simulations, to validate the model and to test the dynamics according to the variations of the parameters.