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To understand and predict soil moisture dynamics it is essential to take the role of the vegetation into account. For example, hydrological processes in agricultural soils are strongly affected by seasonal vegetation dynamics in terms of rooting depth and root distribution. Here we present a new approach to monitor and model root dynamics and its influence on soil moisture in the critical zone using mini-rhizotrons combined with phenological observations. The setup in the field observatory consists of a portable root scanner connected to a tablet computer and a number of acrylic glass tubes with a diameter of two inches that are inserted into the soil at the start of the growing season of selected crops. 360-degrees-scans of soil and roots are taken regularly at different depths in the tubes. Root parameters such as length, diameter, surface and density are identified automatically from the data for each soil layer. Complementary observations of aboveground plant phenology, obtained either by visual inspection in-situ or by remote sensing techniques, are related to the root parameters. Results from mini-rhizotron data collected at two observatories in Germany show that vertical root distribution and maximum rooting depth in agricultural soils, which varies with plant species and phenology, weather patterns, soil type and management, irrigation etc., are crucial parameters to explain the observed temporal variability and vertical gradients in soil moisture satisfactorily. Deriving these parameters from above-ground phenology and incorporating them into a soil water model led to a significant improvement when compared to a model version based on reference rooting depths from the literature. Thus, we argue that mini-rhizotrons constitute a useful supplement to hydrological observatories and can help understand and predict soil moisture dynamics in the critical zone.

The project AgriSens Demmin 4.0 aims to explore applications of remote sensing products for the agricultural sector. The developed methods and acquired knowledge will be made available for farmers and the public. Experiments and case studies are carried out in the project area, which is located about 180 kilometres north of Berlin and covers approximately 800 square kilometres with a large part of arable farming land. For this area, a rich collection of different data sources exists: Besides remote sensing data (from satellites, aircrafts and UAV systems), meteorological and soil data is collected by a dense network of environmental measuring stations. Additionally, comprehensive field measurement campaigns are conducted.In the project, the agrometeorological department of the German National Meteorological Service prepares and processes the meteorological data and provides agrometeorological simulations to the project partners. The basis for these simulations is the SVAT model AMBAV (AgrarMeteorologische Berechnung der Aktuellen Verdunstung), which computes estimates for soil moisture and evapotranspiration based on the atmospheric conditions, soil types and current vegetation.The above-mentioned richness of data for the project area enables the comparison of soil moisture estimates of different sources, each having specific scales, strengths, and weaknesses: Soil cores for gravimetric soil moisture samples have a high degree of accuracy, but only have limited spatial and temporal validity because of their sparsity. Installed soil sensors offer time-continuous measurements, but are prone to calibration errors and offsets. Satellite-derived products promise extensive monitoring of areas of interest, but provide only indirect and area-integrated measurements of surface soil water, which have limited informative value for deeper soil layers. Soil moisture modelling can be used to bridge the gap in scales since it is more flexible and may provide soil moisture estimation in arbitrary resolution if the relevant input data is available.In our study, we compare in-situ soil moisture measurements and AMBAV model estimates for the AgriSens Demmin 4.0 area in order to evaluate the model but also asses the comparability of the different data sources. Preliminary results show that intercomparisons of soil core samples and AMBAV model results are satisfactory when there is good knowledge about the soil texture, whereas the agreement with automatic soil sensors remains problematic, most likely due to installation and calibration aspects.High-quality in-situ data is generally important for the adjustment and verification of remote sensing products, and this includes the area of soil-vegetation-atmosphere transfer of water. Model validation and development is viewed as critical in order to provide an efficient linkage between the two domains.

Evapotranspiration (ET) from wetlands is often considered to occur at a potential rate. However, depending on the structural and physiological traits of the dominating plant species, actual ET can deviate substantially from potential ET. Here we present a case study from a restored wetland in north-western Germany which is dominated by moor grass (Molinia caerulea). ET was measured over three years by means of the Bowen Ratio method, leaf transpiration and leaf resistance of moor grass were measured with a porometer, and both green and total leaf area index were measured optically and manually.Whilst actual and potential ET were practically similar during the period from late summer to the end of winter, they differed significantly from the beginning of spring to early summer and on hot summer days. Two likely reasons for this marked seasonality could be identified. (1) Molinia leaves responded very sensitively to the vapour pressure deficit of the air, independent of the unlimited water supply to its roots. (2) A thick mat of dead leaves covered the surface in spring before and while the new leaves emerged and acted as an efficient protection cover against evaporation.The SVAT model ‘AMBAV’ was developed by the German Meteorological Service and is operationally used in agrometeorological applications. Based on the Bowen Ratio and in-situ plant physiological data, it was newly parameterised for the investigated type of wetland. If run with weather data from a nearby station, AMBAV could verify the observed seasonal pattern of actual ET from the moor grass dominated wetland. The results demonstrate that the present vegetation reduces wetland ET and thus contributes to the maintenance of a high water table in the restored wetland.

The ACASA (Advanced Canopy-Atmosphere-Soil Algorithm) model, with a higher order closure for tall vegetation, has already been successfully tested and validated for spruce forests. The aim of this paper is the further application for a clearing with a heterogeneous structure of the underlying surface. The comparison with flux data shows a good agreement with a footprint aggregated tile approach of the model. However, the results of a comparison with a tile approach on the basis of the mean land use classification of the clearing is not significantly different. It is assumed that the footprint model is not accurate enough to separate small scale heterogeneities. All measured fluxes are corrected for energy balance closure with a Bowen ratio and a buoyancy flux correction method. The comparison with the model – where the energy balance is closed – shows that the buoyancy correction for Bowen ratios > 1.5 better fits the measured data. For lower Bowen ratios, the correction probably lies between both methods, but the amount of available data was too small to make a conclusion. With an assumption of a similarity between water and carbon dioxide fluxes, no correction of the net ecosystem exchange is necessary for Bowen ratios > 1.5.

Sap flow measurements of trees are today the most common method to determine transpiration at the tree and the forest canopy level. They provide independent measurements for flux comparisons and model validation. Sap flow measurements of Norway spruce (Picea abies) which were conducted in the mountain range of the Fichtelgebirge (Germany) are reviewed with respect to analyses of structure-function relationships, atmospheric control and horizontal heterogeneity of stand transpiration in the Lehstenbach catchment, and local vertical gradients from the forest floor over various heights in the tree up to the atmosphere above. It is concluded that sap flow measurements have importance for the analysis of physiologically controlled plant process at the organism and community level and could first demonstrate age dependence of managed forest stands. The measurements also supplement long-term micrometeorological measurements and have the potential for cross validation of independent measurements of water vapor fluxes and the water equivalent of latent heat fluxes from eddy covariance technique. For short-term comparisons, the time lag between sap flow and evaporation and effects of changes in tree water storage need to be considered.

Complexity of flow structures and turbulent transports in heterogeneous forest landscapes was investigated by means of a high-resolution large-eddy simulation of the Waldstein–Weidenbrunnen site. The simulation setup was based on experiment data of a daytime situation, collected during the EGER project in summer 2011. The forest structure on site was represented in the simulation based on airborne laser scanning data and forest inventory measurements. It was found that due to patchiness of the forest and variations in tree density, individual horizontal and vertical flow patterns develop across and along forest edges, as well as in gaps and forest aisles. These flow patterns directly affect the spatial distribution of scalars such as temperature and tracers, while the temperature field itself is heterogeneous owing to the PAI-dependent heat storage capacity of the heterogeneous forest stand. This in turn affects the spreading of tracers. Overall, the mechanical and thermodynamical effects of the 3d-heterogeneous forest structure locally alter the energy and mass exchange between forest and atmosphere, complicating the estimation of a representative net ecosystem exchange based on single-point measurements. This study emphasizes the need for further sophisticated joined measuring-modelling approaches in order to improve our understanding of exchange processes in heterogeneous forest landscapes.

Within micrometeorology the term modeling is not uniquely defined. It refers to various methods covering a range of complexity extending from simple regressions up to complicated numerical models . In applied meteorology (agro meteorology and hydro meteorology) simple analytical models are very common. Modeling of evaporation is particularly important but sophisticated numerical methods are not yet widely used in this research area. The following chapter describes different types of models and their limitations beginning with simple analytical methods up to numerical models of near-surface energy and matter transport. The application of models in heterogeneous terrain receives special attention and related flux averaging approaches are addressed in a separate subchapter.

Eddy covariance flux towers measure net exchange of land–atmosphere flux. For the flux of carbon dioxide, this net ecosystem exchange (NEE) is governed by two processes, gross primary production (GPP) and a sum of autotrophic and heterotrophic respiration components known as ecosystem respiration (RE). A number of statistical flux-partitioning methods, often developed to fill missing NEE data, can also be used to estimate GPP and RE from NEE time series. Here we present results of the first comprehensive, multi-site comparison of these partitioning methods. An initial test was performed with a subset of methods in retrieving GPP and RE from NEE generated by an ecosystem model, which was also degraded with realistic noise. All methods produced GPP and RE estimates that were highly correlated with the synthetic data at the daily and annual timescales, but most were biased low, including a parameter inversion of the original model. We then applied 23 different methods to 10 site years of temperate forest flux data, including 10 different artificial gap scenarios (10% removal of observations), in order to investigate the effects of partitioning method choice, data gaps, and intersite variability on estimated GPP and RE. Most methods differed by less than 10% in estimates of both GPP and RE. Gaps added an additional 6–7% variability, but did not result in additional bias. ANOVA showed that most methods were consistent in identifying differences in GPP and RE across sites, leading to increased confidence in previously published multi-site comparisons and syntheses. Several methods produced outliers at some sites, and some methods were systematically biased against the ensemble mean. Larger model spread was found for Mediterranean sites compared to temperate or boreal sites. For both real and synthetic data, high variability was found in modeling of the diurnal RE cycle, suggesting that additional study of diurnal RE mechanisms could help to improve partitioning algorithms.

We review 15 techniques for estimating missing values of net ecosystem CO 2 exchange (NEE) in eddy covariance time series and evaluate their performance for different artificial gap scenarios based on a set of 10 benchmark datasets from six forested sites in Europe. The goal of gap filling is the reproduction of the NEE time series and hence this present work focuses on estimating missing NEE values, not on editing or the removal of suspect values in these time series due to systematic errors in the measurements (e.g., nighttime flux, advection). The gap filling was examined by generating 50 secondary datasets with artificial gaps (ranging in length from single half-hours to 12 consecutive days) for each benchmark dataset and evaluating the performance with a variety of statistical metrics. The performance of the gap filling varied among sites and depended on the level of aggregation (native half-hourly time step versus daily), long gaps were more difficult to fill than short gaps, and differences among the techniques were more pronounced during the day than at night. The non-linear regression techniques (NLRs), the look-up table (LUT), marginal distribution sampling (MDS), and the semi-parametric model (SPM) generally showed good overall performance. The artificial neural network based techniques (ANNs) were generally, if only slightly, superior to the other techniques. The simple interpolation technique of mean diurnal variation (MDV) showed a moderate but consistent performance. Several sophisticated techniques, the dual unscented Kalman filter (UKF), the multiple imputation method (MIM), the terrestrial biosphere model (BETHY), but also one of the ANNs and one of the NLRs showed high biases which resulted in a low reliability of the annual sums, indicating that additional development might be needed. An uncertainty analysis comparing the estimated random error in the 10 benchmark datasets with the artificial gap residuals suggested that the techniques are already at or very close to the noise limit of the measurements. Based on the techniques and site data examined here, the effect of gap filling on the annual sums of NEE is modest, with most techniques falling within a range of ±25 g C m −2 year −1 .

Flux measurements from eight global FLUXNET sites were used to estimate parameters in a process-based, land-surface model (CSIRO Biosphere Model (CBM), using nonlinear parameter estimation techniques. The parameters examined were the maximum photosynthetic carboxylation rate (vcmax;25) the potential photosynthetic electron transport rate (jmax,25) of the leaf at the top of the canopy, and basal soil respiration (rs,25), all at a reference temperature of 251C. Eddy covariance measurements used in the analysis were from four evergreen forests, three deciduous forests and an oak-grass savanna. Optimal estimates of model parameters were obtained by minimizing the weighted differences between the observed and predicted flux densities of latent heat, sensible heat and net ecosystem CO2 exchange for each year. Values of maximum carboxylation rates obtained from the flux measurements were in good agreement with independent estimates from leaf gas exchange measurements at all evergreen forest sites. A seasonally varying vcmax;25 and jmax,25 in CBM yielded better predictions of net ecosystem CO2 exchange than a constant vcmax;25 and jmax,25 for all three deciduous forests and one savanna site. Differences in the seasonal variation of vcmax;25 and jmax,25 among the three deciduous forests are related to leaf phenology. At the tree-grass savanna site, seasonal variation of vcmax;25 and jmax,25 was affected by interactions between soil water and temperature, resulting in vcmax;25 and jmax,25 reaching maximal values before the onset of summer drought at canopy scale. Optimizing the photosynthetic parameters in the model allowed CBM to predict quite well the fluxes of water vapor and CO2 but sensible heat fluxes were systematically underestimated by up to 75Wm � 2 .

This paper examines long-term eddy covariance data from 18 European and 17 North American and Asian forest, wetland, tundra, grassland, and cropland sites under non-water-stressed conditions with an empirical rectangular hyperbolic light response model and a single layer two light-class carboxylase-based model. Relationships according to ecosystem functional type are demonstrated between empirical and physiological parameters, suggesting linkages between easily estimated parameters and those with greater potential for process interpretation. Relatively sparse documentation of leaf area index dynamics at flux tower sites is found to be a major difficulty in model inversion and flux interpretation. Therefore, a simplification of the physiological model is carried out for a subset of European network sites with extensive ancillary data. The results from these selected sites are used to derive a new parameter and means for comparing empirical and physiologically based methods across all sites, regardless of ancillary data. The results from the European analysis are then compared with results from the other Northern Hemisphere sites and similar relationships for the simplified process-based parameter were found to hold for European, North American, and Asian temperate and boreal climate zones. This parameter is useful for bridging between flux network observations and continental scale spatial simulations of vegetation/atmosphere carbon dioxide exchange.

Latent heat, which plays a major role in the energy balance of ecosystems, is usually calculated in different types of models, e.g., water balance approaches, aggregated “big-leaf” models, multi-layer ecosystem process models, that can be generally catalogued as Soil–Vegetation–Atmosphere–Transport models (SVATs) in a broader sense, etc. In this study, four (multi-) layered models (PLant-ATmosphere INteraction model (PLATIN), MixFor-SVAT, SVAT-CN, PnET-N-DNDC) and an atmospheric boundary layer model including vegetation (HIgh Resolution Vegetation Atmosphere Coupler (HIRVAC)) were used to predict latent heat (LE) and sensible heat (H) exchange in the target area of VERTIKO, a research project on vertical transports of energy and trace gases and their spatial/temporal extrapolation under complex natural conditions. Investigated vegetation types were a Norway spruce forest, and two grassland sites in Brandenburg and Saxony (Germany) during field campaigns in 2001 and 2002. Four models had half-hourly to hourly time steps, but PnET-N-DNDC had a daily time step. All models used meteorological conditions above the canopy as input, and computed LE and H independently, or H as the residual of the energy balance. Intercomparisons Abbreviations: b, offset of linear regression; [CO 2], CO2 concentration; DoY, day of year; EC, eddy covariance; ET, evapotranspiration; E0, potential evaporation; FB, fractional bias; IA, index of agreement; LW, longwave radiation; m, slope of linear regression; MAE, mean absolute error; NIR, near infrared radiation; P, air pressure; PAR, photosynthetic active radiation; PPT, precipitation; R.H., relative humidity; Rg, global radiation, incoming shortwave radiation; RMSE, root mean square error; Rn, net radiation; S.E. of y, standard error for the y estimate; S.E., standard error of parameter; Ta, air temperature; u, wind speed

To quantify the effects of soil temperature (Tsoil), and relative soil water content (RSWC) on soil N2O emission we measured N2O soil efflux with a closed dynamic chamber in situ in the field and from soil cores in a controlled climate chamber experiment. Additionally we analysed the effect of soil acidity, ammonium, and nitrate concentration in the field. The analysis was performed on three meadows, two bare soils and in one forest. We identified soil water content, soil temperature, soil nitrogen content, and pH as the main parameters influencing soil N2O emission. The response of N2O emission to soil temperature and relative soil water content was analysed for the field and climate chamber measurements. A non-linear regression model (DenNit) was developed for the field data to describe soil N2O efflux as a function of soil temperature, soil moisture, pH value, and ammonium and nitrate concentration. The model could explain 81% of the variability in soil N2O emission of all individual field measurements, except for data with short-term soil water changes, namely during and up to 2 h after rain stopped. We validated the model with an independent dataset. For this additional meadow site 73% of the flux variation could be explained with the model.

To quantify the effects of soil temperature (Tsoil), and relative soil water content (RSWC) on soil respiration we measured CO2 soil efflux with a closed dynamic chamber in situ in the field and from soil cores in a controlled climate chamber experiment. Additionally we analysed the effect of soil acidity and fine root mass in the field. The analysis was performed on three meadow, two bare fallow and one forest sites. The influence of soil temperature on CO2 emissions was highly significant with all land-use types, except for one field campaign with continuous rain. Where soil temperature had a significant influence, the percentage of variance explained by soil temperature varied from site to site from 13–46% in the field and 35–66% in the climate chamber. Changes of soil moisture influenced only the CO2 efflux on meadow soils in field and climate chamber (14–34% explained variance), whereas on the bare soil and the forest soil there was no visible effect. The spatial variation of soil CO2 emission in the field correlated significantly with the soil pH and fine root mass, explaining up to 24% and 31% of the variability. A non-linear regression model was developed to describe soil CO2 efflux as a function of soil temperature, soil moisture, pH-value and root mass. With the model we could explain 60% of the variability in soil CO2 emission of all individual field chamber measurements. Through the model analysis we highlight the temporal influence of rain events. The model overestimated the observed fluxes during and within four hours of the last rain event. Conversely, after more than 72h without rain the model underestimated the fluxes. Between four and 72 h after rainfall, the regression model of soil CO2 emission explained up to 91% of the variance.

In order to quantify the effects of temperature and soil water content on soil respiration, during June and July 2002 CO2 soil efflux was measured with a closed chamber (non-steady state, flow through) system in the field. The amount of CO2 emission was highly dependent on the land-use in the observation area, which consisted of meadow soil and brownfield. The CO2 emission from the brownfield ranged from 0.9 to 5.5 µmol CO2 m−2 s−1, and that for meadow soil from 1.1 to 12.6 µmol CO2 m−2 s−1. Soil respiration, as a function of soil temperature (Tsoil), relative soil water content (RSWC), soil pH, and the soil carbon/nitrogen ratio (C/N), was analysed by a modified closed non-linear regression model. Between 63% and 81% of the variation of soil CO2 emission could be explained with changes of Tsoil, RSWC, pH, and C/N for the individual chambers on the brownfield.

Observations of ecosystem net carbon dioxide exchange obtained with eddy covariance techniques over a 4-year period at spruce, beech and pine forest sites were used to derive time series data for gross primary production (GPP) and ecosystem respiration (Reco). A detailed canopy gas exchange model (PROXELNEE) was inverted at half-hour time step to estimate seasonal changes in carboxylation capacity and light utilization efficiency of the forest canopies. The parameter estimates were then used further to develop a time-dependent modifier of physiological activity in the daily time step gas exchange model of Chen et al. (1999), previously used for regional simulations in BOREAS. The daily model was run under a variety of assumptions and the results emphasize the need in future analyses: (1) to focus on time-dependent seasonal changes in canopy physiology as well as in leaf area index, (2) to compare time courses of physiological change in different habitats in terms of recognizable cardinal points in the seasonal course, and (3) to develop methods for utilizing information on seasonal changes in physiology in regional and continental carbon budget simulations. The results suggest that the daily model with appropriate seasonal adjustments for physiological process regulation should be an efficient tool for use in conjunction with remote sensing for regional evaluation of global change scenarios.

Differences in the seasonal pattern of assimilatory and respiratory processes are responsible for divergences in seasonal net carbon exchange among ecosystems. Using FLUXNET data ( http://www.eosdis.ornl.gov/FLUXNET ) we have analyzed seasonal patterns of gross primary productivity (FGPP), and ecosystem respiration (FRE) of boreal and temperate, deciduous and coniferous forests, Mediterranean evergreen systems, a rainforest, temperate grasslands, and C3 and C4 crops. Based on generalized seasonal patterns classifications of ecosystems into vegetation functional types can be evaluated for use in global productivity and climate change models. The results of this study contribute to our understanding of respiratory costs of assimilated carbon in various ecosystems. Seasonal variability of FGPP and FRE of the investigated sites increased in the order tropical Mediterranean temperate coniferous temperate deciduous boreal forests . Together with the boreal forest sites, the managed grasslands and crops show the largest seasonal variability. In the temperate coniferous forests, seasonal patterns of FGPP and FRE are in phase, in the temperate deciduous and boreal coniferous forests FRE was delayed compared to FGPP, resulting in the greatest imbalance between respiratory and assimilatory fluxes early in the growing season. FGPP adjusted for the length of the carbon uptake period decreased at the sampling sites across functional types in the order C4 crops, temperate and boreal deciduous forests (7.5–8.3 g C m −2 per day )> temperate conifers, C3 grassland and crops (5.7–6.9 g C m −2 per day )> boreal conifers (4.6 g C m−2 per day). Annual FGPP and net ecosystem productivity (FNEP) decreased across climate zones in the order tropical>temperate>boreal. However, the decrease in FNEP with latitude was greater than the decrease in FGPP, indicating a larger contribution of respiratory (especially heterotrophic) processes in boreal systems.

The effects of disturbance history, climate, and changes in atmospheric carbon dioxide (CO2) concentration and nitrogen deposition (Ndep) on carbon and water fluxes in seven North American evergreen forests are assessed using a coupled water–carbon–nitrogen model, canopy-scale flux observations, and descriptions of the vegetation type, management practices, and disturbance histories at each site. The effects of interannual climate variability, disturbance history, and vegetation ecophysiology on carbon and water fluxes and storage are integrated by the ecosystem process model Biome-BGC, with results compared to site biometric analyses and eddy covariance observations aggregated by month and year. Model results suggest that variation between sites in net ecosystem carbon exchange (NEE) is largely a function of disturbance history, with important secondary effects from site climate, vegetation ecophysiology, and changing atmospheric CO2 and Ndep. The timing and magnitude of fluxes following disturbance depend on disturbance type and intensity, and on post-harvest management treatments such as burning, fertilization and replanting. The modeled effects of increasing atmospheric CO 2 on NEE are generally limited by N availability, but are greatly increased following disturbance due to increased N mineralization and reduced plant N demand. Modeled rates of carbon sequestration over the past 200 years are driven by the rate of change in CO2 concentration for old sites experiencing low rates of N dep. The model produced good estimates of between-site variation in leaf area index, with mixed performance for between- and within-site variation in evapotranspiration. There is a model bias

Tree canopy water use and foliage net CO2 uptake (NPP) were simulated for a 31-year-old Pinus sylvestris (Scots pine) plantation near Hartheim, in the Upper Rhine Valley, Germany with a mechanistically-based, three-dimensional stand gas-exchange model (STANDFLUX) for a ten-day period during spring 1992. STANDFLUX was formulated to include the effects of penumbra caused by the fine structure of the needles on light distribution within crowns. Good correspondence was found between simulated rates of tree canopy water use when including penumbral effects and eddy-covariance ET and sap flow transpiration measurements. Water use was 8–13% lower and NPP was 10–17% lower in simulations for the ten-day period when penumbral effects were not included.

At present a network of over 100 field sites are measuring carbon dioxide, water vapor and sensible heat fluxes between the biosphere and atmosphere, on a nearly continuous basis. Gaps in the long term measurements of evaporation and sensible heat flux must be filled before these data can be used for hydrological and meteorological applications. We adapted methods of gap filling for NEE (net ecosystem exchange of carbon) to energy fluxes and applied them to data sets available from the EUROFLUX and AmeriFlux eddy covariance databases. The average data coverage for the sites selected was 69% and 75% for latent heat (λE) and sensible heat (H). The methods were based on mean diurnal variations (half-hourly binned means of fluxes based on previous and subsequent days, MDV) and look-up tables for fluxes during assorted meteorological conditions (LookUp), and the impact of different gap filling methods on the annual sum of λE and H is investigated. The difference between annual λE filled by MDV and λE filled by LookUp ranged from - 120 to 210 MJ m-2 per year, i.e. -48 to +86 mm per year, or -13 to +39% of the annual sum. For annual sums of H differences between -140 and + 140 MJ m-2 per year or -12 to +19% of the annual sum were found.

The advent of long-term studies on CO2 and water vapor exchange provides us with new information on how the atmosphere and biosphere interact. Conventional time series analysis suggests that temporal fluctuations of weather variables and mass and energy flux densities occur on numerous time scales. The time scales of variance that are associated with annual time series of meteorological variables, scalar flux densities and their covariance with one another, however, remain unquantified. We applied Fourier analysis to time series (4 years in duration) of photon flux density, air temperature, wind speed, pressure and the flux densities of CO 2 and water vapor. At the daily time scale, strong spectral peaks occurred in the meteorological and flux density records at periods of 12 and 24 h, due to the daily rising and setting of the sun. At the synoptic time scale (3‐7 days) the periodic passage of weather fronts alter available sunlight and temperature. In turn, variations in these state variables affect carbon assimilation, respiration and transpiration. At the seasonal and semi-annual time scales, a broad spectral peak occurs due to seasonal changes in weather and plant functionality and phenology. In general, 21% of the variance of CO2 exchange is associated with the annual cycle, 43% of the variance is associated with the diurnal cycle and 9% is associated with the semi-annual time scale. A pronounced spectral gap was associated with periods 3‐4 weeks long. Interactions between CO2 flux density ( Fc) and sunlight, air temperature and latent heat flux density were quantified using co-spectral, coherence and phase angle analyzes. Coherent and in-phase spectral peaks occur between CO2 exchange rates and water vapor exchange on annual, seasonal and daily time scales. A 180 phase shift occurs between Fc and photon flux density (Qp) on seasonal and daily time scales because the temporal course of sunlight corresponds with the withdrawal of CO2 from the atmosphere, a flux that possesses a negative sign. Covariations between Fc and Tair experience a 180 phase shift with one another at the seasonal time scale because rising temperatures are associated with more carbon uptake. At daily time scales the phase angle between Fc and Tair is on the order of 130. This phase lag can be explained by the strong dependence of canopy photosynthesis on available light and the 2‐3 h lags, which occur between the daily course of sunlight and air temperature.

Tree xylem sapflow rates of 140-year-old Norway spruce (Picea abies) were scaled to the stand level and compared to canopy transpiration predicted by the stand gas exchange model STANDFLUX. Variation in sapflux densities between individual sensors was high (coef- ficient of variance = 0.4) and included both variation within and between trees, but it was not dif- ferent between two applied sapflow methodologies (radial flowmeter according to Granier, vari- able heating tissue heat balance method according to Cermak and Kucera). During the morning, a time-lag of typically 2 h elapsed between sapflow (Eand predicted canopy transpiration rate (EDuring this time total water use was as high as 0.3 mm, which was less than the estimated capacity of easily available water in the tree canopy (0.45 mm, on average 14 L per tree). Canopy conductance derived from stand sapflow rates (gand from STANDFLUX (g was in the same range (g10 mm sbut a stronger decline with increasing vapor pressure deficit of the air

Quantification of an ecosystem's carbon balance and its components is pivotal for understanding both ecosystem functioning and global cycling. Several methods are being applied in parallel to estimate the different components of the CO2 balance. However, different methods are subject to different sources of error. Therefore, it is necessary that site level component estimates are cross-checked against each other before being reported. Here we present a two-step approach for testing the accuracy and consistency of eddy covariance–based gross primary production (GPP) and ecosystem respiration (Re) estimates with biometric measurements of net primary production (NPP), autotrophic (Ra) and heterotrophic (Rh) respiration. The test starts with closing the CO2 balance to account for reasonable errors in each of the component fluxes. Failure to do so within the constraints will classify the flux estimates on the site level as inconsistent. If the CO2 balance can be closed, the test continues by comparing the closed site level Ra/GPP with the Rh/GPP ratio. The consistency of these ratios is then judged against expert knowledge. Flux estimates of sites that pass both steps are considered consistent. An inconsistent ratio is not necessarily incorrect but provides a signal for careful data screening that may require further analysis to identify the possible biological reasons of the unexpected ratios. We reviewed the literature and found 16 sites, out of a total of 529 research forest sites, that met the data requirements for the consistency test. Thirteen of these sites passed both steps of the consistency cross-check. Subsequently, flux ratios (NPP/GPP, Rh/NPP, Rh/Re, and Re/GPP) were calculated for the consistent sites. Similar ratios were observed at sites which lacked information to check consistency, indicating that the flux data that are currently used for validating models and testing ecological hypotheses are largely consistent across a wide range of site productivities. Confidence in the output of flux networks could be further enhanced if the required fluxes are independently estimated at all sites for multiple years and harmonized methods are used.

We tested the hypothesis that the date of the onset of net carbon uptake by temperate deciduous forest canopies corresponds with the time when the mean daily soil temperature equals the mean annual air temperature. The hypothesis was tested using over 30 site-years of data from 12 field sites where CO(2) exchange is being measured continuously with the eddy covariance method. The sites spanned the geographic range of Europe, North America and Asia and spanned a climate space of 16 degrees C in mean annual temperature. The tested phenology rule was robust and worked well over a 75 day range of the initiation of carbon uptake, starting as early as day 88 near Ione, California to as late as day 147 near Takayama, Japan. Overall, we observed that 64% of variance in the timing when net carbon uptake started was explained by the date when soil temperature matched the mean annual air temperature. We also observed a strong correlation between mean annual air temperature and the day that a deciduous forest starts to be a carbon sink. Consequently we are able to provide a simple phenological rule that can be implemented in regional carbon balance models and be assessed with soil and temperature outputs produced by climate and weather models.

[1] Data from a network of eddy covariance stations in Europe and North America (FLUXNET) were analyzed to examine the diurnal patterns of surface energy and carbon fluxes during the summer period across a range of ecosystems and climates. Diurnal trends were quantified by assessing the time of day surface fluxes and meteorological variable reached peak values, using the “diurnal centroid” method; the diurnal centroid enabled us to discern whether the peak activity of the variable of interest is weighted more toward the morning or afternoon. In this paper, diurnal centroid estimates were used to diagnose which atmospheric and physiological processes controlled carbon dioxide, water vapor, and sensible heat fluxes across different ecosystems and climates. Sensitivity tests suggested that the diurnal centroids for latent (LE) and sensible (H) heat flux depend on atmospheric resistance, static stability in the free atmosphere, stomatal response to vapor pressure deficit, and advection. With respect to diurnal trends of surface energy fluxes at FLUXNET sites, maximum LE occurred later in the day relative to H at most tall forests with continental climates. The lag between LE and H was reduced or reversed at sites that were influenced by advection or by afternoon stomatal closure. The time of peak carbon uptake of temperate forests occurred earlier relative to the temporal peak of photosynthetically active radiation, as compared to boreal forests. The timing of this peak occurred earlier during periods with low soil water content, as it did during the summer in Mediterranean climates. In this case, the diurnal centroid for the CO2 flux was influenced by the response of respiration and photosynthesis to increasing afternoon temperature and by afternoon stomatal closure.

Stand age is an important structural determinant of canopy transpiration (E(c)) and carbon gain. Another more functional parameter of forest structure is the leaf area/sapwood area relationship, A(L)/A(S), which changes with site conditions and has been used to estimate leaf area index of forest canopies. The interpretation of age-related changes in A(L)/A(S) and the question of how A(L)/A(S) is related to forest functions are of current interest because they may help to explain forest canopy fluxes and growth. We conducted studies in mature stands of Picea abies (L.) Karst. varying in age from 40 to 140 years, in tree density from 1680 to 320 trees ha(-1), and in tree height from 15 to 30 m. Structural parameters were measured by biomass harvests of individual trees and stand biometry. We estimated E(c) from scaled-up xylem sap flux of trees, and canopy-level fluxes were predicted by a three-dimensional microclimate and gas exchange model (STANDFLUX). In contrast to pine species, A(L)/A(S) of P. abies increased with stand age from 0.26 to 0.48 m(2) cm(-2). Agreement between E(c) derived from scaled-up sap flux and modeled canopy transpiration was obtained with the same parameterization of needle physiology independent of stand age. Reduced light interception per leaf area and, as a consequence, reductions in net canopy photosynthesis (A(c)), canopy conductance (g(c)) and E(c) were predicted by the model in the older stands. Seasonal water-use efficiency (WUE = A(c)/E(c)), derived from scaled-up sap flux and stem growth as well as from model simulation, declined with increasing A(L)/A(S) and stand age. Based on the different behavior of age-related A(L)/A(S) in Norway spruce stands compared with other tree species, we conclude that WUE rather than A(L)/A(S) could represent a common age-related property of all species. We also conclude that, in addition to hydraulic limitations reducing carbon gain in old stands, a functional change in A(L)/A(S) that is related to reduced light interception per leaf area provides another potential explanation for reduced carbon gain in old stands of P. abies, even when hydraulic constraints increase in response to changes in canopy architecture and aging.

The warm season (mid-June through late August) partitioning between sensible (H) and latent (LE) heat flux, or the Bowen ratio (beta=H/LE), was investigated at 27 sites over 66 site years within the international network of eddy covariance sites (FLUXNET). Variability in beta across ecosystems and climates was analyzed by quantifying general climatic and surface characteristics that control flux partitioning. The climatic control on beta was quantified using the climatological resistance (R-i), which is proportional to the ratio of vapor pressure deficit (difference between saturation vapor pressure and atmospheric vapor pressure) to net radiation (large values of R-i decrease beta). The control of flux partitioning by the vegetation and underlying surface was quantified by computing the surface resistance to water vapor transport (R-c, with large values tending to increase beta). There was a considerable range in flux partitioning characteristics (R-c, R-i and beta) among sites, but it was possible to define some general differences between vegetation types and climates. Deciduous forest sites and the agricultural site had the lowest values of R-c and beta (0.25-0.50). Coniferous forests typically had a larger R-c and higher beta (typically between 0.50 and 1.00 but also much larger). However, there was notable variability in R-c and R-i between coniferous site years, most notably differences between oceanic and continental climates and sites with a distinct dry summer season (Mediterranean climate). Sites with Mediterranean climates generally had the highest net radiation, R-c, R-i, and beta. There was considerable variability in beta between grassland site years, primarily the result of interannual differences in soil water content and R-c

International audience; This paper examines long-term eddy covariance data from 18 European and 17 North American and Asian forest, wetland, tundra, grassland, and cropland sites under nonwater- stressed conditions with an empirical rectangular hyperbolic light response model and a single layer two light-class carboxylase-based model. Relationships according to ecosystem functional type are demonstrated between empirical and physiological parameters, suggesting linkages between easily estimated parameters and those with greater potential for process interpretation. Relatively sparse documentation of leaf area index dynamics at flux tower sites is found to be a major difficulty in model inversion and flux interpretation. Therefore, a simplification of the physiological model is carried out for a subset of European network sites with extensive ancillary data. The results from these selected sites are used to derive a new parameter and means for comparing empirical and physiologically based methods across all sites, regardless of ancillary data. The results from the European analysis are then compared with results from the other Northern Hemisphere sites and similar relationships for the simplified process-based parameter were found to hold for European, North American, and Asian temperate and boreal climate zones. This parameter is useful for bridging between flux network observations and continental scale spatial simulations of vegetation/atmosphere carbon dioxide exchange

[1] Clouds and aerosols alter the proportion of diffuse radiation in global solar radiation reaching the Earth's surface. It is known that diffuse and direct beam radiation differ in the way they transfer through plant canopies and affect the summation of nonlinear processes like photosynthesis differently than what would occur at the leaf scale. We compared the relative efficiencies of canopy photosynthesis to diffuse and direct photosynthetically active radiation (PAR) for a Scots pine forest, an aspen forest, a mixed deciduous forest, a tallgrass prairie and a winter wheat crop. The comparison was based on the seasonal patterns of the parameters that define the canopy photosynthetic responses to diffuse PAR and those that define the responses to direct PAR. These parameters were inferred from half-hourly tower CO2 flux measurements. We found that: (1) diffuse radiation results in higher light use efficiencies by plant canopies; (2) diffuse radiation has much less tendency to cause canopy photosynthetic saturation; (3) the advantages of diffuse radiation over direct radiation increase with radiation level; (4) temperature as well as vapor pressure deficit can cause different responses in diffuse and direct canopy photosynthesis, indicating that their impacts on terrestrial ecosystem carbon assimilation may depend on radiation regimes and thus sky conditions. These findings call for different treatments of diffuse and direct radiation in models of global primary production, and studies of the roles of clouds and aerosols in global carbon cycle.

The process-based simulation model STANDFLUX describes canopy water vapor and carbon dioxide exchange based on rates calculated for individual trees and as affected by local gradients in photon flux density (PFD), atmospheric humidity, atmospheric carbon dioxide concentration, and air temperature. Direct, diffuse, and reflected PFD incident on foliage elements within compartments of individual trees (defined by vertical layers and a series of concentric cylinders centered on the trunk) is calculated for a 3-dimensional matrix of points. Foliage element gas exchange rates are based on estimates of carboxylation, RuBP regeneration, and respiratory capacities as well as the correlated behavior found between stomatal conductance and assimilation rate. Because of the difficulties associated with effective sampling and description of spatial variation in structure and leaf level gas exchange parameters for trees comprising the forest canopy, the significance for canopy water and carbon dioxide exchange of varied representations of tree foliage distribution and of physiology is examined. The additional interactive effects encountered due to changes in tree density and, thus, spatial aggregation or disaggregation of foliage is also studied. The analysis is conducted within the context of observed structural and physiological variation encountered in Norway spruce (Picea abies) stands in the Fichtelgebirge region of central Germany. Potentials for simplifying the three-dimensional canopy gas exchange model without sizable influence on canopy flux rates were small. A relatively large number of sample points within the tree crowns is necessary to obtain consistent calculations of flux rates because of the non-linear relationship between PFD and net photosynthesis. Transpiration and net photosynthesis for stands with a low leaf area index (LAI) may be obtained from single tree estimates for each tree class weighted by class frequency, while 30 or more trees per class in differing relation to neighboring trees may be necessary to calculate reliable estimates of net photosynthesis in canopies with high LAI. The complexity in structure assumed for modeled trees was important, especially when overall canopy foliage area was either high or low due to spatial heterogeneity in clumping, e. g., potential canopy overlaps or side-lighting. Effects were greater for calculated net photosynthesis than for transpiration, reflecting higher sensitivity of net photosynthesis to differences in light distribution within individual trees. Accuracy in estimates of physiological parameters is equally important, and these characteristics have profound effects on estimated canopy gas exchange rates. While one-dimensional representations of canopy structure or approximations of tree physiological characteristics from other canopies or species may often be necessary in assessing vegetation/atmosphere exchanges, especially in the study of water balance of landscapes or regions, STANDFLUX provides a tool that can aid in evaluating the limitations of these simpler approaches.

Among the five EUROFLUX broad-leaved sites, four are beech stands and one is a poplar plantation. These sites are spread over a wide range of climatic conditions: mid-oceanic (France), continental (Germany) and subpolar (Iceland), and the elevation ranges from plain to mountain. Furthermore, these stands are of various ages: the poplar stand is a young plantation, the beech stand of Hesse is a young natural regeneration, while the other beech stands included in this study are much older (70 to 140 years).

FLUXNET is a global network of micrometeorological flux measurement site's that measure the exchanges of carbon dioxide, water vapor, and energy between the biosphere and atmosphere. At present over 140 sites are operating on a long- term and continuous basis. Vegetation under study includes temperate conifer and broadleaved (deciduous and evergreen) forests, tropical and boreal forests, crops, grasslands, chaparral, wetlands, and tundra. Sites exist on five continents and their latitudinal distribution ranges from 70 degreesN to 30 degreesS. FLUXNET has several primary functions. First, it provides infrastructure for compiling, archiving, and distributing carbon, water, and energy flux measurement, and meteorological, plant, and soil data to the science community. (Data and site information are available online at the FLUXNET Web site, http://www-eosdis.oml.gov/FLUXNTET/.) Second, the project supports calibration and flux intercomparison activities. This activity ensures that data from the regional networks are intercomparable. And third, FLUXNET supports the synthesis, discussion, and communication of ideas and data by supporting project scientists, workshops, and visiting scientists. The overarching goal is to provide information for validating computations of net primary productivity, evaporation, and energy absorption that are being generated by sensors mounted on the NASA Terra satellite. Data being compiled by FLUXNET are being used to quantify and compare magnitudes and dynamics of annual ecosystem carbon and water balances, to quantify the response of stand-scale carbon dioxide and water vapor flux densities to controlling biotic and abiotic factors, and to validate a hierarchy of soil-plant- atmosphere trace gas exchange models. Findings so far include 1) net CO2 exchange of temperate broadleaved forests increases by about 5.7 a C m(-2) day(-1) for each additional day that the growing season is extended; 2) the sensitivity of net ecosystem CO2 exchange to sunlight doubles if the sky is cloudy rather than clear; 3) the spectrum of CO2 flux density exhibits peaks at timescales of days, weeks, and years, and a spectral gap exists at the month timescale. 4) the optimal temperature of net CO2 exchange varies with mean summer temperature; and 5) stand age affects carbon dioxide and water vapor flux densities.

During the International Biological Program (IBP), systematic investigations of carbon flow through ecosystems and the structuring of carbon pools within ecosystems were carried out for the first time across the existing spectrum of biome types. Since then, concerted efforts have been made to understand the changes occurring in ecosystem carbon pools and carbon flow during aging and maturation of the system, in response to disturbances, and as symptomatic of ecosystem status or “health” (see review by Reiners 1983, Odum 1985). In other words, thorough knowledge of ecosystem carbon pools and carbon flow for a wide variety of ecosystem types and states is viewed as a key means by which better understanding of ecosystem response, resilience, and sustainable function maybe achieved.