The methodology, implementation, and analysis of the isotopic composition of soil respired CO₂ in forest ecological research

Soils are the largest terrestrial pool of carbon, therefore it is critical to understand what controls soil carbon efflux to the atmosphere in light of current climate uncertainty. The primary efflux of carbon from soil is soil respiration which is typically categorized into autotrophic and heterotrophic respiration. These two components have different responses to changes in the environment, thus necessitating a means to quantify the contributions of each. Natural abundance ¹³C can identify autotrophic and heterotrophic sources of respiration, but there is a paucity of research concerning the soil isotope methodology and the subsequent analysis. This dissertation documents my contributions to the advancement of understanding carbon metabolism in forest ecosystems of the Pacific Northwest through the use of the natural abundance carbon isotopic signature of soil respiration. The results of this research represent significant progress in the use of ¹³C in forest ecology. I show in a laboratory setting that a change in the isotopic signature of soil gas can take at least 48 hours to reach equilibrium. A change in the isotopic source of respiration is one mechanism behind non steady-state conditions while another mechanism is dynamic gas transport. I explored the impact of a negative pressure potential across the soil surface by inducing advection and found the isotopic signature of respiration to be 1‰ less than the theoretical steady-state value. I performed a source partitioning experiment in which I identified a highly depleted source of carbon contributing to respiration. I also considered the impacts of the potential errors associated with collecting and measuring isotopic samples on mixing-models currently used to identify the isotopic signature of respiration. I found that the effect of CO₂ and δ¹³C measurement error on large CO₂ concentration regime to be substantially different than small concentration regimes, necessitating a unique mixing-model and regression-model combination for estimating the isotopic signal of respiration. Finally, I built upon the progress made in the previous experiments and analyze almost two years of soil respiration and its isotopic signature to determine potential environmental and biological drivers. I found that: transpiration was highly correlated with both respiration and the carbon isotopic signature; soil moisture primarily influenced tree processes related to respiration; and I found evidence of soil respiration under isotopic non steady-state conditions

Visualizing land‐use and management complexity within biogeochemical cycles of an agricultural landscape

Crop fields are cultivated across continuities of soil, topography, and local climate that drive biological processes and nutrient cycling at the landscape scale; yet land management and agricultural research are often performed at the field scale, potentially neglecting the context of the surrounding landscape. Adding to this complexity is the overlap of ecosystems and their biogeochemical legacies, as a patchwork of crops fields, natural grasslands, and forests develops across the landscape. Furthermore, as new technologies and policies are introduced, management practices change, including fertilization strategies, which further alter biological productivity and nutrient cycling. All of these environmental, biological, and historical legacies are potentially recorded in the isotopic signal of plant, soil, and sediment organic matter across the landscape. We mapped over 1500 plant, soil, and sediment isotopic values and generated an isotopic landscape (isoscape) over a 40-km² agricultural site in NE Germany. We observed distinct patterns in the isotopic composition of organic matter sampled from the landscape that clearly reflect the landscape complexity. C₃ crop intrinsic water-use efficiency reflected a precipitation gradient, while native forest and grassland plant species did not, suggesting that native plants are more adapted to predominant climatic conditions. δ¹³Csoil patterns reflected both the long-term input of plant organic matter, which was affected by the local climate conditions, and the repeated cultivation of corn. Soil organic matter ¹⁵N isotopic values also revealed spatial differences in fertilization regimes. Forest fragments, in which the nitrogen cycle was relatively open, were more water-use efficient. Sediments from small water bodies received substantial inputs from surrounding field vegetation but were also affected by seasonal drying. These isotopic maps can be used to visualize large spatial heterogeneity and complexity, and they are a powerful means to interpret past and current trends in agricultural landscapes

The impact of snow cover on nutrients dynamics in Western Siberia territories

International audienc

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

Circadian rhythms have significant effects on leaf-to-canopy scale gas exchange under field conditions

Background Molecular clocks drive oscillations in leaf photosynthesis, stomatal conductance, and other cell and leaf-level processes over ~24 h under controlled laboratory conditions. The influence of such circadian regulation over whole-canopy fluxes remains uncertain; diurnal CO2 and H2O vapor flux dynamics in the field are currently interpreted as resulting almost exclusively from direct physiological responses to variations in light, temperature and other environmental factors. We tested whether circadian regulation would affect plant and canopy gas exchange at the Montpellier European Ecotron. Canopy and leaf-level fluxes were constantly monitored under field-like environmental conditions, and under constant environmental conditions (no variation in temperature, radiation, or other environmental cues). Results We show direct experimental evidence at canopy scales of the circadian regulation of daytime gas exchange: 20–79 % of the daily variation range in CO2 and H2O fluxes occurred under circadian entrainment in canopies of an annual herb (bean) and of a perennial shrub (cotton). We also observed that considering circadian regulation improved performance by 8–17 % in commonly used stomatal conductance models. Conclusions Our results show that circadian controls affect diurnal CO2 and H2O flux patterns in entire canopies in field-like conditions, and its consideration significantly improves model performance. Circadian controls act as a ‘memory’ of the past conditions experienced by the plant, which synchronizes metabolism across entire plant canopies

Night and day - Circadian regulation of night-time dark respiration and light-enhanced dark respiration in plant leaves and canopies

The potential of the vegetation to sequester C is determined by the balance between assimilation and respiration. Respiration is under environmental and substrate-driven control, but the circadian clock might also contribute. To assess circadian control on night-time dark respiration (RD) and on light enhanced dark respiration (LEDR) - the latter providing information on the metabolic reorganization in the leaf during light-dark transitions - we performed experiments in macrocosms hosting canopies of bean and cotton. Under constant darkness (plus constant air temperature and air humidity), we tested whether circadian regulation of RD scaled from leaf to canopy respiration. Under constant light (plus constant air temperature and air humidity), we assessed the potential for leaf-level circadian regulation of LEDR. There was a clear circadian oscillation of leaf-level RD in both species and circadian patterns scaled to the canopy. LEDR was under circadian control in cotton, but not in bean indicating species-specific controls. The circadian rhythm of LEDR in cotton might indicate variable suppression of the normal cyclic function of the tricarboxylic-acid-cycle in the light. Since circadian regulation is assumed to act as an adaptive memory to adjust plant metabolism based on environmental conditions from previous days, circadian control of RD may help to explain temporal variability of ecosystem respiration.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’ AnaEE-France 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 MEDfOR, internal grants from UWS-HIE to VRD and ZALF to AG and Juan de la Cierva-fellowships (IJCI-2014-21393 to JGA). 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

Genotypic variability enhances the reproducibility of an ecological study

Many scientific disciplines are currently experiencing a “reproducibility crisis” because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduces reproducibility by amplifying impacts of lab-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. We tested this hypothesis using a multi-laboratory microcosm study in which the same ecological experiment was repeated in 14 laboratories across Europe. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the “reproducibility crisis”, deliberately including genetic variation may be a simple solution for increasing the reproducibility of ecological studies performed in controlled environments

GROUP SELECTION EDGE EFFECTS ON THE VASCULAR PLANT COMMUNITY OF A SIERRA NEVADA OLD-GROWTH FOREST

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