First-order turbulence closure for modelling complex canopy flows

Simple first-order closure remains an attractive way of formulating equations for complex canopy flows when the aim is to find analytic or simple numerical solutions to illustrate fundamental physical processes. Nevertheless, the limitations of such closures must be understood if the resulting models are to illuminate rather than mislead. We propose five conditions that first-order closures must satisfy then test two widely used closures against them. The first is the eddy diffusivity based on a mixing length. We discuss the origins of this approach, its use in simple canopy flows and extensions to more complex flows. We find that it satisfies most of the conditions and, because the reasons for its failures are well understood, it is a reliable methodology. The second is the velocity-squared closure that relates shear stress to the square of mean velocity. Again we discuss the origins of this closure and show that it is based on incorrect physical principles and fails to satisfy any of the five conditions in complex canopy flows; consequently its use can lead to actively misleading conclusions.

CHP toolkit: case study of LAIe sensitivity to discontinuity of canopy cover in fruit plantations

This paper presents an open-source canopy height profile (CHP) toolkit designed for processing small-footprint full-waveform LiDAR data to obtain the estimates of effective leaf area index (LAIe) and CHPs. The use of the toolkit is presented with a case study of LAIe estimation in discontinuous-canopy fruit plantations. The experiments are carried out in two study areas, namely, orange and almond plantations, with different percentages of canopy cover (48% and 40%, respectively). For comparison, two commonly used discrete-point LAIe estimation methods are also tested. The LiDAR LAIe values are first computed for each of the sites and each method as a whole, providing “apparent” site-level LAIe, which disregards the discontinuity of the plantations’ canopies. Since the toolkit allows for the calculation of the study area LAIe at different spatial scales, between-tree-level clumpingcan be easily accounted for and is then used to illustrate the impact of the discontinuity of canopy cover on LAIe retrieval. The LiDAR LAIe estimates are therefore computed at smaller scales as a mean of LAIe in various grid-cell sizes, providing estimates of “actual” site-level LAIe. Subsequently, the LiDAR LAIe results are compared with theoretical models of “apparent” LAIe versus “actual” LAIe, based on known percent canopy cover in each site. The comparison of those models to LiDAR LAIe derived from the smallest grid-cell sizes against the estimates of LAIe for the whole site has shown that the LAIe estimates obtained from the CHP toolkit provided values that are closest to those of theoretical models.

Modeling study of the aspect ratio influence on urban canopy energy fluxes with a modified wall-canyon energy budget scheme

The influence of the aspect ratio (building height/street canyon width) and the mean building height of cities on local energy fluxes and temperatures is studied by means of an Urban Canopy Model (UCM) coupled with a one-dimensional second-order turbulence closure model. The UCM presented is similar to the Town Energy Balance (TEB) model in most of its features but differs in a few important aspects. In particular, the street canyon walls are treated separately which leads to a different budget of radiation within the street canyon walls. The UCM has been calibrated using observations of incoming global and diffuse solar radiation, incoming long-wave radiation and air temperature at a site in So Paulo, Brazil. Sensitivity studies with various aspect ratios have been performed to assess their impact on urban temperatures and energy fluxes at the top of the canopy layer. In these simulations, it is assumed that the anthropogenic heat flux and latent heat fluxes are negligible. Results show that the simulated net radiation and sensible heat fluxes at the top of the canopy decrease and the stored heat increases as the aspect ratio increases. The simulated air temperature follows the behavior of the sensible heat flux. (C) 2010 Elsevier Ltd. All rights reserved.

Within-canopy sesquiterpene ozonolysis in Amazonia

Through rapid reactions with ozone, which can initiate the formation of secondary organic aerosols, the emission of sesquiterpenes from vegetation in Amazonia may have significant impacts on tropospheric chemistry and climate. Little is known, however, about sesquiterpene emissions, transport, and chemistry within plant canopies owing to analytical difficulties stemming from very low ambient concentrations, high reactivities, and sampling losses. Here, we present ambient sesquiterpene concentration measurements obtained during the 2010 dry season within and above a primary tropical forest canopy in Amazonia. We show that by peaking at night instead of during the day, and near the ground instead of within the canopy, sesquiterpene concentrations followed a pattern different from that of monoterpenes, suggesting that unlike monoterpene emissions, which are mainly light dependent, sesquiterpene emissions are mainly temperature dependent. In addition, we observed that sesquiterpene concentrations were inversely related with ozone (with respect to time of day and vertical concentration), suggesting that ambient concentrations are highly sensitive to ozone. These conclusions are supported by experiments in a tropical rain forest mesocosm, where little atmospheric oxidation occurs and sesquiterpene and monoterpene concentrations followed similar diurnal patterns. We estimate that the daytime dry season ozone flux of -0.6 to -1.5 nmol m(-2) s(-1) due to in-canopy sesquiterpene reactivity could account for 7%-28% of the net ozone flux. Our study provides experimental evidence that a large fraction of total plant sesquiterpene emissions (46%-61% by mass) undergo within-canopy ozonolysis, which may benefit plants by reducing ozone uptake and its associated oxidative damage.

Aerosol properties, in-canopy gradients, turbulent fluxes and VOC concentrations at a pristine forest site in Amazonia

Aerosol physical and chemical properties were measured in a forest site in central Amazonia (Cuieiras reservation, 2.61S; 60.21W) during the dry season of 2004 (Aug-Oct). Aerosol light scattering and absorption, mass concentration, elemental composition and size distributions were measured at three tower levels (Ground: 2 m; Canopy: 28 m, and Top: 40 m). For the first time, simultaneous eddy covariance fluxes of fine mode particles and volatile organic compounds (VOC) were measured above the Amazonian forest canopy. Aerosol fluxes were measured by eddy covariance using a Condensation Particle Counter (CPC) and a sonic anemometer. VOC fluxes were measured by disjunct eddy covariance using a Proton Transfer Reaction Mass Spectrometer (PTR-MS). At nighttime, a strong vertical gradient of phosphorus and potassium in the aerosol coarse mode was observed, with higher concentrations at Ground level. This suggests a source of primary biogenic particles below the canopy. Equivalent black carbon measurements indicate the presence of light-absorbing aerosols from biogenic origin. Aerosol number size distributions typically consisted of superimposed Aitken (76 nm) and accumulation modes (144 nm), without clear events of new particle formation. Isoprene and monoterpene fluxes reached respectively 7.4 and 0.82 mg m(-2) s(-1) around noon. An average fine particle flux of 0.05 +/- 0.10 10(6) m(-2) s(-1) was calculated, denoting an equilibrium between emission and deposition fluxes of fine mode particles at daytime. No significant correlations were found between VOC and fine mode aerosol concentrations or fluxes. (C) 2009 Elsevier Ltd. All rights reserved.

Habitat use, reproductive traits and social interactions in a stream-dweller treefrog endemic to the Brazilian Cerrado

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Sward canopy structure and performance of beef heifers under supplementation in Brachiaria brizantha cv. Marandu pastures maintained with three grazing intensities in a continuous stocking system

The objective of this study was to assess the sward canopy structure of Brachiaria brizantha cv. Marandu pastures maintained in three grazing intensities under continuous stocking system during the rainy season, along with the behavior and performance of grazing beef heifers supplemented with mineral salt or an energy/protein supplement. Three levels of forage allowance were assessed: 2.0, 2.5 and 3.0 kg of forage/kg of live weight, combined with two supplements (ad libitum mineral salt, and an energy/protein supplement at 0.3% of live weight/day, supplied daily). The experiment was designed as a randomized block study with two replications. The supplements did not influence the variables related to the canopy structure. Canopy height was greater at higher forage allowances during the late summer and early fall. Similarly, the stem mass was greater in pastures with higher forage allowances. Animals fed protein supplement spent less time grazing than animals supplemented with mineral salt. Stocking rate was higher in pastures with lower forage allowance levels, which increased the live weight gain per grazing area. Daily weight gain did not vary according to the forage allowance levels. The use of an energy/protein supplement did not affect the stocking rate; however, it increased individual live weight gain and live weight gain per grazing area compared with mineral salt supplementation. The use of energy/protein supplements is an efficient alternative to enhance animal performance and production under grazing systems during the rainy season

Canopy characteristics and behavior of Nellore heifers in Brachiaria brizantha pastures under different grazing heights at a continuous stocking rate

The objective of this study was to evaluate the Brachiaria brizantha cv. Marandu canopy structure maintained at different grazing heights under a continuous stocking rate and with a dietary supplementation strategy for the animals during the rainy season. This study also intended to observe the relationships of these variables with the grazing behaviors of the heifers. The effects of three canopy heights (15, 25 and 35 cm) were evaluated in association with three types of supplements: one mineral and two protein/energy supplements, the first with a high rumen degradable protein and energy and the others with a low ratio. Both the protein/energy supplements were provided at 0.3% of body weight/day. The experimental design was completely randomized, with two replications and repeated measures, and took place during the period from January to April 2008. The supplementation strategies did not affect any variable related to the canopy structure. Total and green herbage masses and the ratio of green/dead material increased with canopy height. The leaf/stem ratio was higher in the lowest canopy height: 15 cm. Changes in the canopy structure caused variations in the grazing behavior of the animals. Animals maintained in the 15-cm-tall pasture grazed for a longer time, increasing the time for each meal, but the number of meals was lower than that of the animals grazing within the 35-cm-tall pasture. The grazing time of animals receiving the energy/protein supplement was lower only in the period of the day during which it was supplied. Canopy structure is affected by sward height, and changes animal behavior. Supplementation does not affect the canopy structure of the pastures with similar heights.

The specialized reproductive mode of the treefrog Aplastodiscus perviridis (Anura : Hylidae)

Males of the South American treefrog Aplastodiscus perviridis construct concealed subterranean nests. Using a complex courtship behavior that involves tactile stimuli and vocalizations, males guide the females to the subterranean nests where eggs are laid. Embryos and facultatively oophagous tadpoles (at least in stage 25) stay in subterranean nests until flooding transports them to ponds or streams. This is a rare reproductive mode previously known for few species in the Hyla albosignata and H. albofrenata complexes. Based on similarities of reproductive mode we suggest a monophyletic origin for Aplastodiscus and these complexes of Hyla.

Geographic Distribution and Morphological Variation of Striped and Nonstriped Populations of the Brazilian Atlantic Forest Treefrog Hypsiboas bischoffi (Anura: Hylidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Development of eleven polymorphic microsatellite markers for the Chaco Treefrog, Hypsiboas raniceps

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hylin a1, the first cytolytic peptide isolated from the arboreal South American frog Hypsiboas albopunctatus ('spotted treefrog')

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Canopy gap colonization in the Atlantic Montane Rain Forest

Na Floresta Pluvial Atlântica Montana do Sudeste Brasileiro, foi realizado um estudo para descrever e avaliar a colonização de clareiras. A composição de clareiras foi levantada através da cobertura do solo para as espécies herbáceas enquanto que todos os indivíduos lenhosos maiores que um metro de altura foram mensurados e identificados. Também foram coletadas informações sobre a estrutura das clareiras (área da clareira, número e diâmetro das quedas), posição topográfica e vegetação circundante. Dois gêneros de Marantaceae apresentaram considerável freqüência e abundância nas clareiras. As espécies lenhosas mais freqüentes e abundantes pertenceram ao grupo não-pioneiro e as famílias mais ricas encontradas nas clareiras não diferiram quando comparado à floresta como um todo. Como para as variáveis do estrato herbáceo e da vegetação circundante, os resultados revelaram que efeitos diretos e indiretos da topografia são importantes na determinação da composição interna de clareiras por espécies lenhosas. Estes resultados sugerem que a colonização de clareiras é influenciada não apenas pelas variáveis de estrutura, mas também pela posição topográfica e pelos indivíduos pré-estabelecidos.