Circadian rhythms regulate the environmental responses of net CO2 exchange in bean and cotton canopies

Studies on the dependence of the rates of ecosystem gas exchange on environmental parameters often rely on the up-scaling of leaf-level response curves ('bottom-up' approach), and/or the down-scaling of ecosystem fluxes ('top-down' approach), where one takes advantage of the natural diurnal covariation between the parameter of interest and photosynthesis rates. Partly independent from environmental variation, molecular circadian clocks drive ∼24 h oscillations in leaf-level photosynthesis, stomatal conductance and other physiological processes in plants under controlled laboratory conditions. If present and of sufficient magnitude at ecosystem scales, circadian regulation could lead to different results when using the bottom-up approach (where circadian regulation exerts a negligible influence over fluxes because the environment is modified rapidly) relative to the top-down approach (where circadian regulation could affect fluxes as it requires the passage of a few hours). Here we dissected the drivers of diurnal net CO2 exchange in canopies of an annual herb (bean) and of a perennial shrub (cotton) through a set of experimental manipulations to test for the importance of circadian regulation of net canopy CO2 exchange, relative to that of temperature and vapor pressure deficit, and to understand whether circadian regulation could affect the derivation of environmental flux dependencies. Contrary to conventional wisdom, we observed how circadian regulation exerted controls over net CO2 exchange that were of similar magnitude to the controls exerted by direct physiological responses to temperature and vapor pressure deficit. Diurnal patterns of net CO2 exchange could only be explained by considering effects of environmental responses combined with circadian effects. Consequently, we observed significantly different results when inferring the dependence of photosynthesis over temperature and vapor pressure deficit when using the top-down and the bottom up approaches.We remain indebted to E. Gerardeau, D. Dessauw, J. Jean, P. Prudent (Aïda CIRAD), J.-J. Drevon, C. Pernot (Eco&Sol INRA), B. Buatois, A. Rocheteau (CEFE CNRS), A. Pra, A. Mokhtar and the full Ecotron team, in particular C. Escape, for outstanding technical assistance during experiment set-up, plant cultivation and measurements. Earlier versions of the manuscript benefitted from comments by M. Dietze, B. Medlyn, R. Duursma and Y.-S. Lin. This study benefited from the CNRS human and technical resources allocated to the ECOTRONS Research Infrastructures as well as from the state allocation ‘Investissement d'Avenir’ ANR-11-INBS-0001, ExpeER Transnational Access program, Ramón y Cajal fellowships (RYC-2012-10970 to VRD and RYC-2008-02050 to JPF), the Erasmus Mundus Master Course Mediterranean Forestry and Natural Resources Management (MEDfOR) and internal grants from UWS-HIE to VRD and ZALF to AG. We thank the Associate Editor T. Vesala and two anonymous reviewers for their help to improve this manuscript

TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses

ABSTRACTThe advent of NGS has intensified the need for robust pipelines to perform high-performance automated analyses. The required softwares depend on the sequencing method used to produce raw data (e.g. Whole genome sequencing, Genotyping By Sequencing, RNASeq) as well as the kind of analyses to carry on (GWAS, population structure, differential expression). These tools have to be generic and scalable, and should meet the biologists needs.Here, we present the new version of TOGGLe (Toolbox for Generic NGS Analyses), a simple and highly flexible framework to easily and quickly generate pipelines for large-scale second- and third-generation sequencing analyses, including multi-sample and multi-threading support. TOGGLe is a workflow manager designed to be as effortless as possible to use for biologists, so the focus can remain on the analyses. Pipelines are easily customizable and supported analyses are reproducible and shareable. TOGGLe is designed as a generic, adaptable and fast evolutive solution, and has been tested and used in large-scale projects on various organisms. It is freely available at http://toggle.southgreen.fr/, under the GNU GPLv3/CeCill-C licenses) and can be deployed onto HPC clusters as well as on local machines