Nocturnal Intermittent Coupling Between the Interior of a Pine Forest and the Air Above It

A 1-year set of measurements of CO₂ and energy turbulent fluxes above and within a 25-m pine forest in southern Brazil is analyzed. The study focuses on the coupling state between two levels and its impact on flux determination by the eddy-covariance method. The turbulent series are split in their typical temporal scales using the multiresolution decomposition, a method that allows proper identification of the time scales of the turbulent events. Initially, four case studies are presented: a continually turbulent, a continually calm, a calm then turbulent, and an intermittent night. During transitions from calm to turbulent, large scalar fluxes of opposing signs occur at both levels, suggesting the transference of air accumulated in the canopy during the stagnant period both upwards and downwards. Average fluxes are shown for the entire period as a function of turbulence intensity and a canopy Richardson number, used as an indicator of the canopy coupling state. Above the canopy, CO₂ and sensible heat fluxes decrease in magnitude both at the neutral and at the very stable limit, while below the canopy they increase monotonically with the canopy Richardson number. Latent heat fluxes decrease at both levels as the canopy air becomes more stable. The average temporal scales of the turbulent fluxes at both levels approach each other in neutral conditions, indicating that the levels are coupled in that case. Average CO₂ fluxes during turbulent periods that succeed very calm ones are appreciably larger than the overall average above the canopy and smaller than the average or negative within the canopy, indicating that the transfer of air accumulated during calm portions at later turbulent intervals affects the flux average. The implications of this process for mean flux determination are discussed.     

A lagrangian random-walk model for simulating water vapor,CO2 and sensible heat flux densities and scalar profiles over and within a soybean canopy

An integrated canopy micrometeorological model is described for calculating CO₂, water vapor and sensible heat exchange rates and scalar concentration profiles over and within a crop canopy. The integrated model employs a Lagrangian random walk algorithm to calculate turbulent diffusion. The integrated model extends previous Lagrangian modelling efforts by employing biochemical, physiological and micrometeorological principles to evaluate vegetative sources and sinks. Model simulations of water vapor, CO₂ and sensible heat flux densities are tested against measurements made over a soybean canopy, while calculations of scalar profiles are tested against measurements made above and within the canopy. The model simulates energy and mass fluxes and scalar profiles above the canopy successfully. On the other hand, model calculations of scalar profiles inside the canopy do not match measurements.The tested Lagrangian model is also used to evaluate simpler modelling schemes, as needed for regional and global applications. Simple, half-order closure modelling schemes (which assume a constant scalar profile in the canopy) do not yield large errors in the computation of latent heat (LE) and CO₂ (F _c ) flux densities. Small errors occur because the source-sink formulation of LE andF _c are relatively insensitive to changes in scalar concentrations and the scalar gradients are small. On the other hand, complicated modelling frames may be needed to calculate sensible heat flux densities; the source-sink formulation of sensible heat is closely coupled to the within-canopy air temperature profile.     

Evaluation of Two Energy Balance Closure Parametrizations

A general lack of energy balance closure indicates that tower-based eddy-covariance (EC) measurements underestimate turbulent heat fluxes, which calls for robust correction schemes. Two parametrization approaches that can be found in the literature were tested using data from the Canadian Twin Otter research aircraft and from tower-based measurements of the German Terrestrial Environmental Observatories (TERENO) programme. Our analysis shows that the approach of Huang et al. (Boundary-Layer Meteorol 127:273–292, 2008), based on large-eddy simulation, is not applicable to typical near-surface flux measurements because it was developed for heights above the surface layer and over homogeneous terrain. The biggest shortcoming of this parametrization is that the grid resolution of the model was too coarse so that the surface layer, where EC measurements are usually made, is not properly resolved. The empirical approach of Panin and Bernhofer (Izvestiya Atmos Oceanic Phys 44:701–716, 2008) considers landscape-level roughness heterogeneities that induce secondary circulations and at least gives a qualitative estimate of the energy balance closure. However, it does not consider any feature of landscape-scale heterogeneity other than surface roughness, such as surface temperature, surface moisture or topography. The failures of both approaches might indicate that the influence of mesoscale structures is not a sufficient explanation for the energy balance closure problem. However, our analysis of different wind-direction sectors shows that the upwind landscape-scale heterogeneity indeed influences the energy balance closure determined from tower flux data. We also analyzed the aircraft measurements with respect to the partitioning of the “missing energy” between sensible and latent heat fluxes and we could confirm the assumption of scalar similarity only for Bowen ratios $\approx $ 1.     

The Effect of the Screen on the Mass, Momentum, and Energy Exchange Rates of a Uniform Crop Situated in an Extensive Screenhouse

The area of crops cultivated in extensive screenhouses is rapidly growing, especially in semi-arid and arid regions. Water vapour, carbon dioxide, and sensible heat released or taken up by crops within such protected environments can substantially alter the immediate micro-environment, which in turn, affects these fluxes. This amplified interaction between plants and their microclimate challenges simple assessments on how partially covering the crop by a screen modifies plant water uptake and photosynthesis. Via a newly proposed higher-order closure model, the effects of a screen on the mean flow field, turbulent stresses, radiative and energy fluxes, as well as scalar sources, sinks, fluxes, and mean scalar concentration within screenhouses are explored. As a starting point, an extensive screenhouse is assumed thereby reducing the sensitivity of the model results to the precise geometric configuration of the screenhouse. The model findings for the screenhouse are presented and referenced against their open field counterpart. The radiation modulation and changes to turbulent transport due to the presence of the screen are investigated. In general, the presence of a screen results in a warmer and more humid environment inside the screenhouse, promoting reductions in both canopy photosynthesis and transpiration. However, the overall effect of the screen is to enhance water-use efficiency thereby resulting in water savings for the same amount of gross primary production.     

CFD simulation of airflow over a regular array of cubes. Part II: analysis of spatial average properties

In the first part of this study, results of a computational fluid dynamics simulation over an array of cubes have been validated against a set of wind-tunnel measurements. In Part II, such numerical results are used to investigate spatially-averaged properties of the flow and passive tracer dispersion that are of interest for high resolution urban mesoscale modelling (e.g. non resolved obstacle approaches). The results show that vertical profiles of mean horizontal wind are linear within the canopy and logarithmic above. The drag coefficient, derived from the numerical results using the classical formula for the drag force, is height dependent (it decreases with height). However, a modification of the formula is proposed (accounting for subgrid velocity scales) that makes the drag coefficient constant with height. Results also show that the dispersive fluxes are similar in magnitude to the turbulent fluxes, and that they play a very important role within the canopy. Vertical profiles of turbulent length scales (to be used in k–l closure schemes, where k is the turbulent kinetic energy and l a turbulent length scale) are also derived. Finally the distribution of the values around the mean over the reference volumes are analysed for wind and tracer concentrations.     

Modelling Vegetation-Atmosphere Co2 Exchange By A Coupled Eulerian-Langrangian Approach

A Eulerian-Lagrangian canopy microclimate model wasdeveloped with the aim of discerning physical frombiophysical controls of CO₂ and H₂O fluxes. The model couples radiation attenuation with mass,energy, and momentum exchange at different canopylevels. A unique feature of the model is its abilityto combine higher order Eulerian closure approachesthat compute velocity statistics with Lagrangianscalar dispersion approaches within the canopy volume. Explicit accounting for within-canopy CO₂,H₂O, and heat storage is resolved by consideringnon-steadiness in mean scalar concentration andtemperature. A seven-day experiment was conducted inAugust 1998 to investigate whether the proposedmodel can reproduce temporal evolution of scalar(CO₂, H₂O and heat) fluxes, sources andsinks, and concentration profiles within and above auniform 15-year old pine forest. The modelreproduced well the measured depth-averaged canopy surfacetemperature, CO₂ and H₂O concentrationprofiles within the canopy volume, CO₂ storageflux, net radiation above the canopy, and heat andmass fluxes above the canopy, as well as the velocitystatistics near the canopy-atmosphere interface. Implications for scaling measured leaf-levelbiophysical functions to ecosystem scale are alsodiscussed.     

Estimating Co2 Source/Sink Distributions Within A Rice Canopy Using Higher-Order Closure Model

Source/sink strengths and vertical fluxdistributions of carbon dioxide within and above arice canopy were modelled using measured meanconcentration profiles collected during aninternational rice experiment in Okayama, Japan (IREX96). The model utilizes an Eulerian higher-orderclosure approach that permits coupling of scalar andmomentum transport within vegetation to infer sourcesand sinks from mean scalar concentration profiles; theso-called `inverse problem'. To compute the requiredvelocity statistics, a Eulerian second-order closuremodel was considered. The model well reproducedmeasured first and second moment velocity statisticsinside the canopy. Using these modelled velocitystatistics, scalar fluxes within and above the canopywere computed and compared with CO<sub>2</sub>eddy-correlation measurements above the canopy. Goodagreement was obtained between model calculations offluxes at the top of the canopy and measurements. Close to the ground, the model predicted higherrespiratory fluxes when the paddy was drained comparedto when it was flooded. This is consistent with thefloodwater providing a barrier to diffusion ofCO<sub>2</sub> from the soil to the atmosphere. TheEulerian sources and flux calculations were alsocompared to source and flux distributions estimatedindependently using a Lagrangian Localized Near Fieldtheory, the first study to make such a comparison.Some differences in source distributions werepredicted by these analyses. Despite this, thecalculated fluxes by the two approaches compared wellprovided a closure constant, accounting for theinfluence of `near-field' sources in the Eulerian fluxtransport term, was given a value of 1.5 instead ofthe value of 8 found in laboratory studies.     

Effects of Unstable Thermal Stratification on Vertical Fluxes of Heat and Momentum in Urban Areas

A Reynolds-averaged Navier–Stokes microscale model is used for the simulation of the effect of unstable thermal stratification on the flow within an aligned configuration of building-like cubes as used in Santiago et al. (Urban Clim 9:115–133, 2014). The spatially-averaged results show increased dispersive fluxes, turbulent length scales and sectional drag coefficient. An extension of K-theory is presented to parametrize the sum of the turbulent and dispersive fluxes, and the length scale and drag coefficient increases are parametrized as functions of the ratio of buoyant and inertial forces. This approach improves the results of urban canopy parametrization simulations inside and above the urban canyon and represents the first attempt to account for the dispersive fluxes and the effect of solar radiation on the flow.     

Influence of Nocturnal Low-level Jets on Eddy-covariance Fluxes over a Tall Forest Canopy

Observations of low-level jets (LLJs) at the Howland AmeriFlux site in the USA and the jet’s impact on nocturnal turbulent exchange and scalar fluxes over a tall forest canopy are discussed. Low-frequency motions and turbulent bursts characterize moderately strong LLJs, whereas low-frequency motions are suppressed during periods with strong LLJs and enhanced shear. An analysis based on the shear-sheltering hypothesis seeks to elucidate the effect of LLJs on flux measurements. In the absence of shear sheltering, large eddies penetrate the roughness sublayer causing enhanced mixing while during periods with shear sheltering, mixing is reduced. In the absence of the latter, ‘upside-down’ eddies are primarily responsible for the enhanced velocity variances, scalar and momentum fluxes. The integral length scales over the canopy are greater than the canopy height. The variance spectra and cospectra from the wavelet analysis indicate that large eddies (spatial scale greater than the low-level jet height) interact with active canopy-scale turbulence, contributing to counter-gradient scalar fluxes.     

Consequences of Incomplete Surface Energy Balance Closure for CO2 Fluxes from Open-Path CO2/H2O Infrared Gas Analysers

We present an approach for assessing the impact of systematic biases in measured energy fluxes on CO₂ flux estimates obtained from open-path eddy-covariance systems. In our analysis, we present equations to analyse the propagation of errors through the Webb, Pearman, and Leuning (WPL) algorithm [Quart. J. Roy. Meteorol. Soc. 106, 85–100, 1980] that is widely used to account for density fluctuations on CO₂ flux measurements. Our results suggest that incomplete energy balance closure does not necessarily lead to an underestimation of CO₂ fluxes despite the existence of surface energy imbalance; either an overestimation or underestimation of CO₂ fluxes is possible depending on local atmospheric conditions and measurement errors in the sensible heat, latent heat, and CO₂ fluxes. We use open-path eddy-covariance fluxes measured over a black spruce forest in interior Alaska to explore several energy imbalance scenarios and their consequences for CO₂ fluxes.     

Impact of Eddy Characteristics on Turbulent Heat and Momentum Fluxes in the Urban Roughness Sublayer

Eddy-covariance observations above the densely built-up Centre of Nanjing were made from December 2011 to August 2012. Separate eddy-covariance systems installed at two levels on a 36-m tower located on a rooftop were operated simultaneously, and observations grouped into two sectors (A, B) according to the prevalent wind directions. For sector A, where the nearby buildings are all below the lower measurement level, the sensible heat and momentum fluxes are generally greater at the upper level. For sector B, where several high-rise buildings are located upwind, the sensible heat and momentum fluxes at the upper level are close to those at the lower level. The analysis shows that the turbulent eddy characteristics differ between the two wind sectors, leading to a different behaviour of turbulent exchange between the two levels. A hypothesis is proposed that addresses the vertical variation of turbulent fluxes in the urban roughness sublayer (RSL). For sector A, the buildings block the flow, change the trajectory of scalars, and distort the footprint of scalar fluxes; this ‘blocking effect’ is believed to lead to a smaller sensible heat flux above the canopy layer. Such an effect should decrease with height in the RSL, explaining the increase of the observed turbulent heat flux with height. In addition, the presence of non-uniform building heights adversely affects turbulence organization around the canopy top, and likely elevates the inflection point of the mean flow to a higher elevation close to the upper measurement level, where larger shear results in a larger momentum flux. For sector B, wake effects from the nearby high-rise buildings strongly reduce turbulence organization at higher elevations, leading to similar sensible heat and momentum fluxes at both measurement levels.     

Structure Function Analysis of Two-Scale Scalar Ramps. Part II: Ramp Characteristics and Surface Renewal Flux Estimation

Ramp features in the turbulent scalar field are associated with turbulent coherent structures, which dominate energy and mass fluxes in the atmospheric surface layer. Although finer scale ramp-like shapes embedded within larger scale ramp-like shapes can readily be perceived in turbulent scalar traces, their presence has largely been overlooked in the literature. We demonstrate the signature of more than one ramp scale in structure functions of the turbulent scalar field measured from above bare ground and two types of short plant canopies, using structure-function time lags ranging in scale from isotropic to larger than the characteristic coherent structures. Spectral analysis of structure functions was used to characterize different scales of turbulent structures. By expanding structure function analysis to include two ramp scales, we characterized the intermittency, duration, and surface renewal flux contribution of the smallest (i.e., Scale One) and the dominant (i.e., Scale Two) coherent structure scales. The frequencies of the coherent structure scales increase with mean wind shear, implying that both Scale One and Scale Two are shear-driven. The embedded Scale One turbulent structure scale is ineffectual in the surface-layer energy and mass transport process. The new method reported here for obtaining surface renewal-based scalar exchange works well over bare ground and short canopies under unstable conditions, effectively eliminating the α calibration for these conditions and forming the foundation for analysis over taller and more complex surfaces.     

Scalar Transport over Forested Hills

Numerical simulations of scalar transport in neutral flow over forested ridges are performed using both a 1.5-order mixing-length closure scheme and a large-eddy simulation. Such scalar transport (particularly of CO₂) has been a significant motivation for dynamical studies of forest canopy–atmosphere interactions. Results from the 1.5-order mixing-length simulations show that hills for which there is significant mean flow into and out of the canopy are more efficient at transporting scalars from the canopy to the boundary layer above. For the case with a source in the canopy this leads to lower mean concentrations of tracer within the canopy, although they can be very large horizontal variations over the hill. These variations are closed linked to flow separation and recirculation in the canopy and can lead to maximum concentrations near the separation point that exceed those over flat ground. Simple scaling arguments building on the analytical model of Finnigan and Belcher (Q J Roy Meteorol Soc 130:1–29, 2004) successfully predict the variations in scalar concentration near the canopy top over a range of hills. Interestingly this analysis suggests that variations in the components of the turbulent transport term, rather than advection, give rise to the leading order variations in scalar concentration. The scaling arguments provide a quantitative measure of the role of advection, and suggest that for smaller/steeper hills and deeper/sparser canopies advection will be more important. This agrees well with results from the numerical simulations. A large-eddy simulation is used to support the results from the mixing-length closure model and to allow more detailed investigation of the turbulent transport of scalars within and above the canopy. Scalar concentration profiles are very similar in both models, despite the fact that there are significant differences in the turbulent transport, highlighted by the strong variations in the turbulent Schmidt number both in the vertical and across the hill in the large-eddy simulation that are not represented in the mixing-length model.     

Turbulent transport of scalar quantities within and above a paddy field

An experiment was conducted to study turbulent transport processes of scalar quantities within and above a rice plant canopy. A sonic anemometer-thermometer and a Lyman- humidiometer were used to measure the turbulent fluxes of sensible and latent heat and related turbulence statistics within a paddy field. The sensible and latent heat fluxes measured at two heights within and above the plant canopy showed that the upper layer of this plant canopy was an active source region and that the source strength of sensible and latent heat depended on the solar radiation and physiology of rice plants. Analysis of joint probability distributions of w and T and of w and q within this plant canopy showed that downdrafts were remarkably efficient for upward transport of sensible and latent heat in the daytime. The vertical fluxes of temperature and humidity variance were also divergent from the upper layer of plant canopies. The power spectra of temperature and humidity within the plant canopy decreased rapidly in the high frequency range, compared with the - 2/3 law relationship of nS(n) vs log n observed above plant canopies.     

Concurrency of Coherent Structures and Conditionally Sampled Daytime Sub-canopy Respiration

We investigated an alternative means for quantifying daytime ecosystem respiration from eddy-covariance data in three forests with different canopy architecture. Our hypothesis was that the turbulent transport by coherent structures is the main pathway for carrying detectable sub-canopy respiration signals through the canopy. The study extends previously published work by incorporating state-of-the-art wavelet decomposition techniques for the detection of coherent structures. Further, we investigated spatial and temporal variability of the respiration signal and coherent exchange at multiple heights, for three mature forest sites with varying canopy and terrain properties for one summer month. A connection between the coherent structures and identified sub-canopy respiration signal was clearly determined. Although not always visible in signals collected above the canopy, certain cases showed a clear link between conditionally sampled respiration events and coherent structures. The dominant time scales of the coherent structure ejection phase (20?C30 s), relative timing of maximum coincidence between respiration events and the coherent structure ejection phase (at approximately ?10 s from detection) and vertical transport upward through the canopy were shown to be consistent in time, across measurement heights and across the different forest sites. Best results were observed for an open canopy pine site. We conclude that the presented method is likely to be applicable at more open rather than dense (closed) canopies. The results provided a confirmation of the connection between below- and above-canopy scalar time series, and may help the development or refinement of direct methods for the determination of component fluxes from observations above the canopy.     

A spectral and lag-correlation analysis of turbulence in a deciduous forest canopy

The processes influencing turbulence in a deciduous forest and the relevant length and time scales are investigated with spectral and cross-correlation analysis. Wind velocity power spectra were computed from three-dimensional wind velocity measurements made at six levels inside the plant canopy and at one level above the canopy. Velocity spectra measured within the plant canopy differ from those measured in the surface boundary layer. Noted features associated with the within-canopy turbulence spectra are: (a) power spectra measured in the canopy crown peak at higher wavenumbers than do those measured in the subcanopy trunkspace and above the canopy; (b) peak spectral values collapse to a relatively universal value when scaled according to a non-dimensional frequency comprised of the product of the natural frequency and the Eulerian time scale for vertical velocity; (c) at wavenumbers exceeding the spectral peak, the slopes of the power spectra are more negative than those observed in the surface boundary layer; (d) Eulerian length scales decrease with depth into the canopy crown, then increase with further depth into the canopy; (e) turbulent events below crown closure are more correlated with turbulent events above the canopy than are those occurring in the canopy crown; and (f) Taylor's frozen eddy hypothesis is not valid in a plant canopy. Interactions between plant elements and the mean wind and turbulence alter the processes that produce, transport and remove turbulent kinetic energy and account for the noted observations.     

Verification of a One-Dimensional Model of $$\hbox {CO}_{2}$$ Atmospheric Transport Inside and Above a Forest Canopy Using Observations at the Norunda Research Station

A model of \(\hbox {CO}_{2}\) atmospheric transport in vegetated canopies is tested against measurements of the flow, as well as \(\hbox {CO}_{2}\) concentrations at the Norunda research station located inside a mixed pine–spruce forest. We present the results of simulations of wind-speed profiles and \(\hbox {CO}_{2}\) concentrations inside and above the forest canopy with a one-dimensional model of profiles of the turbulent diffusion coefficient above the canopy accounting for the influence of the roughness sub-layer on turbulent mixing according to Harman and Finnigan (Boundary-Layer Meteorol 129:323–351, 2008; hereafter HF08). Different modelling approaches are used to define the turbulent exchange coefficients for momentum and concentration inside the canopy: (1) the modified HF08 theory—numerical solution of the momentum and concentration equations with a non-constant distribution of leaf area per unit volume; (2) empirical parametrization of the turbulent diffusion coefficient using empirical data concerning the vertical profiles of the Lagrangian time scale and root-mean-square deviation of the vertical velocity component. For neutral, daytime conditions, the second-order turbulence model is also used. The flexibility of the empirical model enables the best fit of the simulated \(\hbox {CO}_{2}\) concentrations inside the canopy to the observations, with the results of simulations for daytime conditions inside the canopy layer only successful provided the respiration fluxes are properly considered. The application of the developed model for radiocarbon atmospheric transport released in the form of \(^{14}\hbox {CO}_{2}\) is presented and discussed.     

Momentum Transfer and Turbulent Kinetic Energy Budgets within a Dense Model Canopy

Second-order closure models for the canopy sublayer (CSL) employ aset of closure schemes developed for `free-air' flow equations andthen add extra terms to account for canopy related processes. Muchof the current research thrust in CSL closure has focused on thesecanopy modifications. Instead of offering new closure formulationshere, we propose a new mixing length model that accounts for basicenergetic modes within the CSL. Detailed flume experiments withcylindrical rods in dense arrays to represent a rigid canopy areconducted to test the closure model. We show that when this lengthscale model is combined with standard second-order closureschemes, first and second moments, triple velocity correlations,the mean turbulent kinetic energy dissipation rate, and the wakeproduction are all well reproduced within the CSL provided thedrag coefficient (C_D) is well parameterized. The maintheoretical novelty here is the analytical linkage betweengradient-diffusion closure schemes for the triple velocitycorrelation and non-local momentum transfer via cumulant expansionmethods. We showed that second-order closure models reproducereasonably well the relative importance of ejections and sweeps onmomentum transfer despite their local closure approximations.Hence, it is demonstrated that for simple canopy morphology (e.g.,cylindrical rods) with well-defined length scales, standard closureschemes can reproduce key flow statistics without much revision.When all these results are taken together, it appears that thepredictive skills of second-order closure models are not limitedby closure formulations; rather, they are limited by our abilityto independently connect the drag coefficient and the effectivemixing length to the canopy roughness density. With rapidadvancements in laser altimetry, the canopy roughness densitydistribution will become available for many terrestrialecosystems. Quantifying the sheltering effect, the homogeneity andisotropy of the drag coefficient, and more importantly, thecanonical mixing length, for such variable roughness density isstill lacking.     

An Analytical Model for the Distribution of CO2 Sources and Sinks, Fluxes, and Mean Concentration Within the Roughness Sub-Layer

A one-dimensional analytical model that predicts foliage CO₂ uptake rates, turbulent fluxes, and mean concentration throughout the roughness sub-layer (RSL), a layer that extends from the ground surface up to 5h, where h is canopy height, is proposed. The model combines the mean continuity equation for CO₂ with first-order closure principles for turbulent fluxes and simplified physiological and radiative transfer schemes for foliage uptake. This combination results in a second-order ordinary differential equation in which soil respiration (R) and CO₂ concentration well above the RSL are imposed as lower and upper boundary conditions, respectively. An inverse version of the model was tested against datasets from two contrasting ecosystems: a tropical forest (h = 40m) and a managed irrigated rice canopy (h = 0.7m), with good agreement noted between modelled and measured mean CO₂ concentration profiles within the entire RSL. Sensitivity analysis on the model parameters revealed a plausible scaling regime between them and a dimensionless parameter defined by the ratio between external (R) and internal (stomatal conductance) characteristics controlling the CO₂ exchange process. The model can be used to infer the thickness of the RSL for CO₂ exchange, the inequality in zero-plane displacement between CO₂ and momentum, and its consequences on modelled CO₂ fluxes. A simplified version of the solution is well suited for being incorporated into large-scale climate models. Furthermore, the model framework here can be used to a priori estimate relative contributions from the soil surface and the atmosphere to canopy-air CO₂ concentration, thereby making it synergetic to stable isotopes studies.