Application of a three-dimensional model for assessing effects of small clear-cuttings on radiation and soil temperature

A three-dimensional model Mixfor-3D of soil–vegetation–atmosphere transfer (SVAT) was developed and applied to estimate possible effects of tree clear-cutting on radiation and soil temperature regimes of a forest ecosystem. The Mixfor-3D model consists of several closely coupled 3D sub-models describing: forest stand structure; radiative transfer in a forest canopy; turbulent transfer of sensible heat, H₂O and CO₂ between ground surface and the atmospheric surface layer; evapotranspiration of ground surface vegetation and soil; heat and moisture transfer in soil. The model operates with the horizontal grid resolution, 2 m × 2 m; vertical resolution, 1 m and primary time step, 1 h.     

Simulation of NO and N2O emissions from a spruce forest during a freeze/thaw event using an N-flux submodel from the PnET-N-DNDC model integrated to CoupModel

The amount of nitrogen gases (N₂O, NO and N₂) emitted from forest soils depends on interactions between soil properties, climatic factors and soil management. To increase the understanding of nitrogen processes in soil ecosystems, two dynamic models, CoupModel (coupled heat and mass transfer model for soil–plant–atmosphere systems) and the denitrification–decomposition (DNDC) model were selected. Both are dynamic models with different submodels for soil, vegetation, hydrology and climate system. CoupModel has a higher degree of detail on soil physical and abiotic components, whereas the DNDC model contains details of microbiological processes involved in production of nitrogen gases. To improve the previous simple submodel of nitrogen emission in CoupModel, we included a submodel corresponding to the forest version of DNDC containing photosynthesis/evapotranspiration-nitrogen (PnET-N-DNDC model).     

Vegetation competition model for water and light limitation. I: Model description, one-dimensional competition and the influence of groundwater

Vegetation growth models often concentrate on the interaction of vegetation with soil moisture but usually omit the influence of groundwater. However the proximity of groundwater can have a profound effect on vegetation growth, because it strongly influences the spatial and temporal distribution of soil moisture and therefore water and oxygen stress of vegetation. In two papers we describe the behavior of a coupled vegetation-groundwater-soil water model including the competition for water and light. In this first paper we describe the vegetation model, compare the model to measured flux data and show the influence of water and light competition in one dimension. In the second paper we focus on the influence of lateral groundwater flow and spatial patterns along a hillslope. The vegetation model is based on a biophysical representation of the soil-plant-atmosphere continuum. Transpiration and stomatal conductance depend both on atmospheric forcing and soil moisture content. Carbon assimilation depends on environmental conditions, stomatal conductance and biochemical processes. Light competition is driven by tree height and water competition is driven by root water uptake and its water and oxygen stress reaction. The modeled and measured H₂O and CO₂ fluxes compare well to observations on both a diurnal and a yearly timescale. Using an upscaling procedure long simulation runs were performed. These show the importance of light competition in temperate forests: once a tree is established under slightly unfavorable soil moisture conditions it can not be outcompeted by smaller trees with better soil moisture uptake capabilities, both in dry as in wet conditions. Performing the long simulation runs with a background mortality rate reproduces realistic densities of wet and dry adapted tree species along a wet to dry gradient. These simulations show that the influence of groundwater is apparent for a large range of groundwater depths, by both capillary rise and water logging. They also show that species composition and biomass have a larger influence on the water balance in eco-hydrological systems than soil and groundwater alone.     

Plant acclimation to elevated CO2—From simple regularities to biogeographic chaos

Upon exposure to altered levels of CO₂, plants express a variety of acclimations to CO₂ directly, over and above acclimations to indirect changes in temperature and water regimes. These acclimations commonly include increased photosynthetic CO₂ assimilation and increased water-use efficiency with reduced N content and reduced stomatal conductance. The robust generic acclimations are explicable by combining simple models of carboxylation, stomatal control, energy balance, and functional balance. Species- or genotype-specific acclimations are overlaid on these generic acclimations. Several such specific acclimations that are often seen are readily incorporated in an extended model. These specific acclimations generate a great spread of values in key performance measures of photosynthesis, water- and N-use efficiencies, and rates of water and N use, even among C₃ species that are the focus of this work. These performance measures contribute strongly to relative fitness and thus to evolving biogeographic distributions. The spread in fitness values is so large as to impend “chaotic” shifts in biogeography (and, ultimately, evolution) that are not understandable with models specific to species or functional groups; rather, a systematic study of key physiological and developmental parameters is merited. Also merited is a coherent extension of the model used here, or similar models, to include other phenomena, including mycorrhizal associations, transience in resource availability, etc. The composition of useful approximate fitness functions from physiological and allocational responses is a major challenge, with some leads originating from the model. In the search to extract patterns of responses, arguments based on the responses being close to optimal or adaptive will be misleading, in view of the absence of selection pressure to perform adaptively at high CO₂ for over 20 million years. I offer suggestions for more useful research designs.     

Effects of experimental protocol on global vegetation model accuracy: A comparison of simulated and observed vegetation patterns for Asia

Prognostic vegetation models have been widely used to study the interactions between environmental change and biological systems. This study examines the sensitivity of vegetation model simulations to: (i) the selection of input climatologies representing different time periods and their associated atmospheric CO₂ concentrations, (ii) the choice of observed vegetation data for evaluating the model results, and (iii) the methods used to compare simulated and observed vegetation. We use vegetation simulated for Asia by the equilibrium vegetation model BIOME4 as a typical example of vegetation model output. BIOME4 was run using 19 different climatologies and their associated atmospheric CO₂ concentrations. The Kappa statistic, Fuzzy Kappa statistic and a newly developed map-comparison method, the Nomad index, were used to quantify the agreement between the biomes simulated under each scenario and the observed vegetation from three different global land- and tree-cover data sets: the global Potential Natural Vegetation data set (PNV), the Global Land Cover Characteristics data set (GLCC), and the Global Land Cover Facility data set (GLCF). The results indicate that the 30-year mean climatology (and its associated atmospheric CO₂ concentration) for the time period immediately preceding the collection date of the observed vegetation data produce the most accurate vegetation simulations when compared with all three observed vegetation data sets. The study also indicates that the BIOME4-simulated vegetation for Asia more closely matches the PNV data than the other two observed vegetation data sets. Given the same observed data, the accuracy assessments of the BIOME4 simulations made using the Kappa, Fuzzy Kappa and Nomad index map-comparison methods agree well when the compared vegetation types consist of a large number of spatially continuous grid cells. The results of this analysis can assist model users in designing experimental protocols for simulating vegetation.     

Does the canopy mixing layer model apply to highly flexible aquatic vegetation? Insights from numerical modelling

Vegetation is a characteristic feature of shallow aquatic flows such as rivers, lakes and coastal waters. Flow through and above aquatic vegetation canopies is commonly described using a canopy mixing layer analogy which provides a canonical framework for assessing key hydraulic characteristics such as velocity profiles, large-scale coherent turbulent structures and mixing and transport processes for solutes and sediments. This theory is well developed for the case of semi-rigid terrestrial vegetation and has more recently been applied to the case of aquatic vegetation. However, aquatic vegetation often displays key differences in morphology and biomechanics to terrestrial vegetation due to the different environment it inhabits. Here we investigate the effect of plant morphology and biomechanical properties on flow–vegetation interactions through the application of a coupled LES-biomechanical model. We present results from two simulations of aquatic vegetated flows: one assuming a semi-rigid canopy and the other a highly flexible canopy and provide a comparison of the associated flow regimes. Our results show that while both cases display canopy mixing layers, there are also clear differences in the shear layer characteristics and turbulent processes between the two, suggesting that the semi-rigid approximation may not provide a complete representation of flow–vegetation interactions.     

Interaction between flow, transport and vegetation spatial structure

This paper summarizes recent advances in vegetation hydrodynamics and uses the new concepts to explore not only how vegetation impacts flow and transport, but also how flow feedbacks can influence vegetation spatial structure. Sparse and dense submerged canopies are defined based on the relative contribution of turbulent stress and canopy drag to the momentum balance. In sparse canopies turbulent stress remains elevated within the canopy and suspended sediment concentration is comparable to that in unvegetated regions. In dense canopies turbulent stress is reduced by canopy drag and suspended sediment concentration is also reduced. Further, for dense canopies, the length-scale of turbulence penetration into the canopy, δ _e , is shown to predict both the roughness height and the displacement height of the overflow profile. In a second case study, the relation between flow speed and spatial structure of a seagrass meadow gives insight into the stability of different spatial structures, defined by the area fraction covered by vegetation. In the last case study, a momentum balance suggests that in natural channels the total resistance is set predominantly by the area fraction occupied by vegetation, called the blockage factor, with little direct dependence on the specific canopy morphology.     

Large-eddy simulation of low-level jet-like flow in a canopy

The computational method of Large-Eddy Simulations has been used to study the weak, neutrally stable drainage flow within tree canopies. The computational results show that a secondary velocity maximum that resembles a jet is formed within the canopy under the nocturnal flow conditions. This jet-like flow is important in the analysis and measurements of the net ecosystem-atmosphere exchange (NEE) for carbon dioxide (CO₂). A uniformly distributed, plane source was placed within the canopy in order to simulate the nocturnal production of CO₂. The NEE is calculated as the sum of the integration of the rate of change of the concentration of CO₂ over the computational domain, the vertical turbulent flux measured directly by eddy-covariance (EC) method, and the advection terms, which are not taken into account in the EC method. Numerical results of the velocity and concentration fields, within and above the canopy, are presented and their impact on the CO₂ transport is investigated in detail. The computational results show that 15–20% of NEE is drained out by the advection process under the canopy. The results also show that the turbulent fluctuations in the lateral direction are also significant and may result in 2–5% CO₂ transport.     

14C of grasses as an indicator of fossil fuel CO2 pollution

Measuring the amount of fossil fuel carbon stored in the vegetation is now crucial to understand the mechanisms ruling climate changes. In this respect, highly polluted areas such as major towns represent “natural” laboratories because fossil fuel CO₂ (¹⁴C-free) is isotopically distinct from mean atmospheric CO₂ (¹⁴C-labeled). Here, a¹⁴C study of urban grasses near a major highway in Paris, France, shows that plants store up to 13% of fossil fuel carbon. The ¹⁴C composition of urban grasses is thus a novel parameter to assess the fossil fuel CO₂ pollution.     

Recruitment limitation in Dungeness crab populations is driven by variation in atmospheric forcing

Ecologists have long debated the relative importance of biotic interactions vs. abiotic forces on the population dynamics of both marine and terrestrial organisms. Investigation of stock size in Dungeness crab (Cancer magister) is a classic example of this debate. We first tested the hypothesis that adult population size was set by larval success. We found that during a five-year sampling period, adult crab population size from Oregon through central California, USA, as measured by the commercial catch, varied directly with the number of terminal-stage larvae (megalopae) returning to Coos Bay, Oregon, four years earlier; adult population size was largely determined (> 90% of the variation) by success during the larval stage. We then tested whether biotic interactions or abiotic forces caused the variation in larval success. Most of the variation (> 90%) in the number of returning megalopae is explained by the timing of the spring transition, a seasonal shift in atmospheric forcing that drives ocean currents along the west coast of the United States. Early spring transitions lead to larger numbers of returning Dungeness megalopae, while in four other crab taxa, species with very different life history characteristics, early-spring transitions lead to lower numbers of returning megalopae. During the past roughly 30 years, the size of the commercial catch of Dungeness crab is significantly and negatively correlated with the date of the spring transition throughout the California Current system. Long-term variation in the date of the spring transition may explain a major crash in the Dungeness crab fishery in central California, which began in the late 1950s. The data suggest that Dungeness crab population size is determined by variation in larval success and that a significant portion of this variation is due to the timing of the spring transition, a large-scale climatic forcer.     

The significance of metal hyperaccumulation for biotic interactions

Metal hyperaccumulating plants contain very high metal contents. Because of the general toxicity of metals, chemically-mediated biotic interactions involving hyperaccumulating plants may differ greatly from those of non-hyperaccumulators. Recent research has demonstrated a defensive function for hyperaccumulated metals against herbivores and pathogens. We predict that some herbivore/pathogen species have evolved metal tolerance, and suggest that resulting high metal levels in herbivores/pathogens may defend them against their own predators. Little is known regarding interference and commensal interactions involving hyperaccumulating plants. Decreased competition may occur through an interference interaction similar to allelopathy, in which enrichment of metal in the soil under a hyperaccumulator plant's canopy may inhibit another plant species, thus resulting in “elemental allelopathy”. Metal enrichment of soil under hyperaccumulators also may result in commensalism if another plant species (possibly another hyperaccumulator) derives a benefit from growing in the metal-enriched soil under the canopy of a hyperaccumulating overstory plant. It seems likely that high-metal plant litter will host a specialized microflora of decomposers and may affect nutrient cycling rates. Mutualist biotic interactions also may be affected by the elevated metal contents of hyperaccumulating species. Mycorrhizal fungi may form mutualisms with hyperaccumulators, but the phenomenon is poorly-explored. The few cases investigated to date have not detected mycorrhizae. Pollination and seed dispersal mechanisms may require biotic vectors that might be affected by plant metal content. Hyperaccumulating plants may have solved this dilemma in three ways. First, some may rely on abiotic vectors for pollen or seed dispersal. Second, biotic vectors used by these species may have varied diets and thus dilute metal intake to non-toxic levels. Finally, biotic vectors may have evolved tolerance of elevated dietary levels of metals, and perhaps have become specialists on hyperaccumulator species. Received 7 November 1997; accepted 28 December 1997.     

The theory behind,and the challenges of,conserving nature's stage in a time of rapid change

Most conservation planning to date has focused on protecting today's biodiversity with the assumption that it will be tomorrow's biodiversity. However, modern climate change has already resulted in distributional shifts of some species and is projected to result in many more shifts in the coming decades. As species redistribute and biotic communities reorganize, conservation plans based on current patterns of biodiversity may fail to adequately protect species in the future. One approach for addressing this issue is to focus on conserving a range of abiotic conditions in the conservation‐planning process. By doing so, it may be possible to conserve an abiotically diverse “stage” upon which evolution will play out and support many actors (biodiversity). We reviewed the fundamental underpinnings of the concept of conserving the abiotic stage, starting with the early observations of von Humboldt, who mapped the concordance of abiotic conditions and vegetation, and progressing to the concept of the ecological niche. We discuss challenges posed by issues of spatial and temporal scale, the role of biotic drivers of species distributions, and latitudinal and topographic variation in relationships between climate and landform. For example, abiotic conditions are not static, but change through time—albeit at different and often relatively slow rates. In some places, biotic interactions play a substantial role in structuring patterns of biodiversity, meaning that patterns of biodiversity may be less tightly linked to the abiotic stage. Furthermore, abiotic drivers of biodiversity can change with latitude and topographic position, meaning that the abiotic stage may need to be defined differently in different places. We conclude that protecting a diversity of abiotic conditions will likely best conserve biodiversity into the future in places where abiotic drivers of species distributions are strong relative to biotic drivers, where the diversity of abiotic settings will be conserved through time, and where connectivity allows for movement among areas providing different abiotic conditions.     

Using a biogeochemistry model in simulating forests productivity responses to climatic change and [CO2] increase: example of Pinus halepensis in Provence (south-east France)

Tree-ring chronologies provide long-term records of growth in natural environmental conditions and may be used to evaluate the impacts of climatic change and [CO₂] increase on forest productivity. This study focuses on 21 Pinus halepensis forest stands in calcareous Provence (in the south-east France). Changes in productivity are simulated using the global biogeochemistry model BIOME3, that we have adapted to run with chronological data. Tree-ring data (width and density) were used to estimate, for each stand, an observed series of changes in productivity. Simulated and observed productivity changes are then compared to validate the chronological biogeochemistry model BIOME3C. Variations in productivity were well reconstructed at 15 sites. After this validation, BIOME3C was used to simulate forest productivity changes for a 2×CO₂ scenario. The 2×CO₂ climate used as input was obtained using results from Météo-France’s ARPEGE atmospheric general circulation model (AGCM), downscaled to local meteorological stations. Productivity increases moderately for all stands (from 17 to 24%) when climatic changes alone were taken into account. The main factor responsible for this increase is a reduction in summer drought severity. Productivity increases highly for all stands (from 72 to 86%) when the physiological fertilising effect of the [CO₂] increase is considered separately. When both climatic changes and the [CO₂] increase were taken into account, productivity increases highly, from 107% (for Moustier) to 141% (for La Ciotat). The direct fertilising effect of [CO₂] increase has a greater influence on the forest stands productivity than the indirect climatic changes effect. These results also exhibit the importance of the synergy between the effects of climate change and [CO₂] increase, as the increase in productivity resulting from the combined effects are more than the sum of the individual CO₂ and climate effects. Although the detected effects of global change during the 20th century were slight, acceleration of these changes is likely to lead to great changes in the future productivity of P. halepensis forests.     

A note on the sufficiency of low resolution ecosystem models

Analysis of a system of non-linear differential equations illustrates the effects of interactions between biotic and abiotic components of a complex aquatic ecosystem model. A stochastic analysis shows that the variance of the abiotic variables is related in a simple manner to the autocorrelation function of the biotic variables. The results suggest that for oligotrophic and eutrophic conditions, relatively simple ecosystem models may be sufficient for studies of an aquatic environment. Under mesotrophic conditions, the high state variable resolution of a complex model may be necessary.     

Modeling plant competition along an environmental gradient

The effect of an environmental gradient on inter-specific plant competitive interactions is modeled in a simple empirical model with biologically interpretable parameters. The model allows testing of hypotheses on the effect of the gradient on plant competitive interactions, as well as making ecological predictions from simple competition experiments using standard statistical procedures. The model, which is general and can be applied to different abiotic and biotic environmental gradients, is applied to a specific case of two competing Arabidopsis thaliana genotypes along a gradient of the general fungal pathogen Peronospora parasitica. One of the A. thaliana genotype is susceptible to the fungal pathogen P. parasitica and the other genotype is resistant. The Bayesian posterior distribution of the probability that the resistant genotype outcompetes the susceptible genotype is calculated as a function of the pathogen level. The design of the studied A. thaliana competition experiments is the minimum required experimental design needed to apply the model.     

The Structure of the Shear Layer in Flows over Rigid and Flexible Canopies

Flume experiments were conducted with rigid and flexible model vegetation to study the structure of coherent vortices (a manifestation of the Kelvin–Helmholtz instability) and vertical transport in shallow vegetated shear flows. The vortex street in a vegetated shear layer creates a pronounced oscillation in the velocity profile, with the velocity near the top of a model canopy varying by a factor of three during vortex passage. In turn, this velocity oscillation drives the coherent waving of flexible canopies. Relative to flows over rigid vegetation, the oscillation in canopy geometry has the effect of decreasing the amount of turbulent vertical momentum transport in the shear layer. Using a waving plant to determine phase in the vortex cycle, each vortex is shown to consist of a strong sweep at its front (during which the canopy is most deflected), followed by a weak ejection at its rear (when the canopy height is at a maximum). Whereas in unobstructed mixing layers the vortices span the entire layer, they encompass only 70% of the flexibly obstructed shear layer studied here.     

A Fine-Scale <Emphasis Type="Italic">k</Emphasis>−ε Model for Atmospheric Flow over Heterogeneous Landscapes

A multi-purpose model for small-scale atmospheric flows over heterogeneous landscapes is being developed. The aim of this research is to build a tool able to predict the dynamical (wind, turbulence) and diffusive (gases, particles) fields over landscapes characterised by heterogeneous plant cover. In its present stage of development the model is based on the numerical integration of neutral atmospheric flow equations, using an energy-dissipation closure scheme and over a domain that may include vegetation layers. Three validation cases of the model are presented: (i) response of the airflow to a change in surface roughness; (ii) airflow within and above a horizontally homogeneous plant canopy; (iii) airflow over two complex forest-to-clearing and clearing-to-forest transitions. All simulations provide results in good agreement with the experimental data, except for turbulent kinetic energy just after a clearing-to-forest transition. This result is not surprising for a statistical k– model in a flow region characterised by strong distorsion and intermittent turbulence. However the overall good performance of the model is promising for environmental research at fine scales over heterogeneous landscapes.     

Inversion of plant dominance-diversity relationships along a latitudinal stress gradient

Species interactions affect plant diversity through the net effects of competition and facilitation, with the latter more prevalent in physically stressful environments when plant cover ameliorates abiotic stress. One explanation for species loss in invader-dominated systems is a shift in the competition-facilitation balance, with competition intensifying in areas formerly structured by facilitation. We test this possibility with a 10-site prairie meta-experiment along a 500-km latitudinal stress gradient, quantifying the relationships among abiotic stress, exotic dominance, and native plant recruitment over five years. The latitudinal gradient is inversely correlated with abiotic stress, with lower latitudes more moisture- and nutrient-limited. We observed strong negative effects by invasive dominant grasses on plant establishment, but only in northern sites with lower-stress environments. At these locations, disturbance was critical for recruitment by reducing the suppressive dominant (invasive) canopy. In more stressful environments to the south, the impacts of the dominant invaders on plant establishment became facilitative, and diversity was more limited by seed availability. Disturbance prevented recruitment because seedling survival depended on a protective plant canopy, presumably because the canopy reduced temperature or moisture stress. Seed limitation was similarly prevalent in all sites. Our work confirms the importance of facilitation as an organizing process for plants in higher-stress environments, even with transformations of species composition and dominance. It also demonstrates that the mechanisms regulating diversity, including invader impacts, can vary within the same plant community depending on environmental context. Because limits on native plant recruitment are environmentally contingent, management strategies that seek to increase diversity, including invader eradication, must account for site-level variations in the balance between biotic and abiotic constraints.     

Does defoliation induce chemical and morphological defenses in the leaves of silver birch seedlings under changing climate?

Summary.  We examined the effects of defoliation con-currently with elevated temperature and CO₂ on some chemical and morphological characteristics in the leaves of silver birch seedlings (Betula pendula). We also analyzed the consequent changes in the palatability of leaves for adult blue alder leaf beetles (Agelastica alni). Under the different climatic treatments, the seedlings were subjected to three fertilizer treatments (0 kg, 130 kg and 270 kg N ha⁻¹) and defoliation treatments (0%, 25% and 50% of the total leaf area). In each climatic treatment, fertilization increased the nitrogen content in the leaves, but decreased total concentrations of soluble phenolics, detected by high-performance liquid chromatography (HPLC), and insoluble condensed tannins. Defoliation, both independently and in combination with elevated temperature and CO₂, decreased the concentrations of the phenolics. Compared to the intact controls, the leaves of the defoliated seedlings were smaller and tougher. Under elevated temperature, the beetles consumed a smaller amount of the leaves of plants subjected to the high fertilization, while under ambient climatic conditions, fertilization increased the feeding. The total leaf consumption was higher under the ambient climatic conditions than under elevated temperature, elevated CO₂ or the combination of elevated temperature and CO₂.     

Influences of canopy structure and physiological traits on flux partitioning between understory and overstory in an eastern Siberian boreal larch forest

Boreal forests play an important role in the global balance of energy and CO₂. Our previous study of elaborate eddy covariance observations in a Siberian boreal larch forest, conducted both above the forest canopy and at the forest floor, revealed a significant contribution of latent heat flux (LE) from the cowberry understory to the whole ecosystem LE. Thus, in the present study, we examined what factors control the partitioning of whole ecosystem LE and CO₂ flux into the understory and overstory vegetation, using detailed leaf-level physiology (for both understory and overstory vegetation) and soil respiration property measurements as well as a multilayer soil-vegetation-atmosphere transfer (SVAT) model. The modeling results showed that the larch overstory's leaf area index (LAI) and vertical profile of leaf photosynthetic capacity were major factors determining the flux partitioning in this boreal forest ecosystem. This is unlike other forest ecosystems that tend to have dense LAI. We concluded that control of the larch overstory's LAI had a relationship with both the coexistence of the larch with the cowberry understory and with the water resources available to the total forest ecosystem.