Plants as Sources of Airborne Bacteria, Including Ice Nucleation-Active Bacteria

Vertical wind shear and concentration gradients of viable, airborne bacteria were used to calculate the upward flux of viable cells above bare soil and canopies of several crops. Concentrations at soil or canopy height varied from 46 colony-forming units per m³ over young corn and wet soil to 663 colony-forming units per m³ over dry soil and 6,500 colony-forming units per m³ over a closed wheat canopy. In simultaneous samples, concentrations of viable bacteria in the air 10 m inside an alfalfa field were fourfold higher than those over a field with dry, bare soil immediately upwind. The upward flux of viable bacteria over alfalfa was three- to fourfold greater than over dry soil. Concentrations of ice nucleation-active bacteria were higher over plants than over soil. Thus, plant canopies may constitute a major source of bacteria, including ice nucleation-active bacteria, in the air.     

RATP: a model for simulating the spatial distribution of radiation absorption, transpiration and photosynthesis within canopies: application to an isolated tree crown

The model RATP (radiation absorption, transpiration and photosynthesis) is presented. The model was designed to simulate the spatial distribution of radiation and leaf-gas exchanges within vegetation canopies as a function of canopy structure, canopy microclimate within the canopy and physical and physiological leaf properties. The model uses a three-dimensional (3D) representation of the canopy (i.e. an array of 3D cells, each characterized by a leaf area density). Radiation transfer is computed by a turbid medium analogy, transpiration by the leaf energy budget approach, and photosynthesis by the Farquhar model, each applied for sunlit and shaded leaves at the individual 3D cell-scale. The model typically operates at a 20–30 min time step. The RATP model was applied to an isolated, 20-year-old walnut tree grown in the field. The spatial distribution of wind speed, stomatal response to environmental variables, and light acclimation of leaf photosynthetic properties were taken into account. Model outputs were compared with data acquired in the field. The model was shown to simulate satisfactorily the intracrown distribution of radiation regime, transpiration and photosynthetic rates, at shoot or branch scales.     

When will plant morphology affect the shape of a seed dispersal "kernel"?

Most models of dispersal assume that plants are point sources. In reality, the scale in height over which seed sources are distributed is often of the same order as the scale in distance over which most individual seeds are dispersed. But is this sufficient to affect the fundamental shapes of dispersal frequency distributions? Most published conclusions about the effects of canopy structure on dispersal are subjective. A model is developed to explore the consequences of plant canopies for the shapes of whole-plant seed dispersal "kernels". The canopies were described by simple geometric shapes, while an empirical probability density function (PDF) was used for dispersal from a point source. It was found that the resulting whole-plant PDF for dispersal distance was almost invariably peaked, whereas the PDF for the density of seed rain (as would be measured by pitfall traps) could either be peaked or monotonic according to the canopy shape, position of seeds in the canopy, and mean dispersal distance. The shapes of kernels from whole plants (distributed seed sources) can be very different from those derived from a point source under certain circumstances.     

Morphological responses of Datura ferox L. seedlings to the presence of neighbours

Summary We studied the effects of density on the dynamics of seedling growth and canopy microclimate within experimental stands composed of Datura ferox L. seedlings grown in individual pots. Interception of photosynthetically active radiation (PAR) by seedlings was evaluated either indirectly, by measuring leaf area, proportion of leaf area shaded by neighbouring individuals and laminar orientation with respect to sunlight, or directly, by measuring PAR at individual leaves at their natural angle of display. An integrating cylinder, with a geometry approximating that of a stem, was used within the canopies to measure the red:far-red (R:FR) ratio of the light flux from all compass points parallel to the soil surface. Seedlings responded rapidly (i.e. 1–2 weeks) to increased density by producing longer internodes and partitioning more dry matter to stems relative to leaves. These responses were observed before either PAR interception of growth rate were reduced by the presence of neighbours. Conversely, morphogenetic adjustment was preceded by a consistent effect of plant density on the R:FR ratio of the light received by the integrating cylinder. Air and soil temperature were not affected by density in these experiments. Differences in wind velocity within the canopy associated with plant density were avoided by the experimental procedure. The results support the idea that the drop in R:FR ratio of the light flux parallel to the ground — e.g. reflected sunlight — is an early signal that allows rapid adjustment of plant form to changes in canopy structure.     

A model of canopy photosynthesis incorporating protein distribution through the canopy and its acclimation to light, temperature and CO2

Background and Aims

The distribution of photosynthetic enzymes, or nitrogen, through the canopy affects canopy photosynthesis, as well as plant quality and nitrogen demand. Most canopy photosynthesis models assume an exponential distribution of nitrogen, or protein, through the canopy, although this is rarely consistent with experimental observation. Previous optimization schemes to derive the nitrogen distribution through the canopy generally focus on the distribution of a fixed amount of total nitrogen, which fails to account for the variation in both the actual quantity of nitrogen in response to environmental conditions and the interaction of photosynthesis and respiration at similar levels of complexity.

Model

A model of canopy photosynthesis is presented for C₃ and C₄ canopies that considers a balanced approach between photosynthesis and respiration as well as plant carbon partitioning. Protein distribution is related to irradiance in the canopy by a flexible equation for which the exponential distribution is a special case. The model is designed to be simple to parameterize for crop, pasture and ecosystem studies. The amount and distribution of protein that maximizes canopy net photosynthesis is calculated.

Key Results

The optimum protein distribution is not exponential, but is quite linear near the top of the canopy, which is consistent with experimental observations. The overall concentration within the canopy is dependent on environmental conditions, including the distribution of direct and diffuse components of irradiance.

Conclusions

The widely used exponential distribution of nitrogen or protein through the canopy is generally inappropriate. The model derives the optimum distribution with characteristics that are consistent with observation, so overcoming limitations of using the exponential distribution. Although canopies may not always operate at an optimum, optimization analysis provides valuable insight into plant acclimation to environmental conditions. Protein distribution has implications for the prediction of carbon assimilation, plant quality and nitrogen demand.     

A mechanistic analysis of light and carbon use efficiencies

We explore the extent to which a simple mechanistic model of short-term plant carbon (C) dynamics can account for a number of generally observed plant phenomena. For an individual, fully expanded leaf, the model predicts that the fast-turnover labile C, starch and protein pools are driven into an approximate or moving steady state that is proportional to the average leaf absorbed irradiance on a time-scale of days to weeks, even under realistic variable light conditions, in qualitative agreement with general patterns of leaf acclimation to light observed both temporally within the growing season and spatially within plant canopies. When the fast-turnover pools throughout the whole plant (including stems and roots) also follow this moving steady state, the model predicts that the time-averaged whole-plant net primary productivity is proportional to the time-averaged canopy absorbed irradiance and to gross canopy photosynthesis, and thus suggests a mechanistic explanation of the observed approximate constancy of plant light-use efficiency (LUE) and carbon-use efficiency. Under variable light conditions, the fast-turnover pool sizes and the LUE are predicted to depend negatively on the coefficient of variation of irradiance. We also show that the LUE has a maximum with respect to the fraction of leaf labile C allocated to leaf protein synthesis ( a_lp ), reflecting a trade-off between leaf photosynthesis and leaf respiration. The optimal value of a_lp is predicted to decrease at elevated [CO₂] _a , suggesting an adaptive interpretation of leaf acclimation to CO₂. The model therefore brings together a number of empirical observations within a common mechanistic framework.     

Structure is more important than physiology for estimating intracanopy distributions of leaf temperatures

Estimating leaf temperature distributions (LTDs) in canopies is crucial in forest ecology. Leaf temperature affects the exchange of heat, water, and gases, and it alters the performance of leaf‐dwelling species such as arthropods, including pests and invaders. LTDs provide spatial variation that may allow arthropods to thermoregulate in the face of long‐term changes in mean temperature or incidence of extreme temperatures. Yet, recording LTDs for entire canopies remains challenging. Here, we use an energy‐exchange model (RATP) to examine the relative roles of climatic, structural, and physiological factors in influencing three‐dimensional LTDs in tree canopies. A Morris sensitivity analysis of 13 parameters showed, not surprisingly, that climatic factors had the greatest overall effect on LTDs. In addition, however, structural parameters had greater effects on LTDs than did leaf physiological parameters. Our results suggest that it is possible to infer forest canopy LTDs from the LTDs measured or simulated just at the surface of the canopy cover over a reasonable range of parameter values. This conclusion suggests that remote sensing data can be used to estimate 3D patterns of temperature variation from 2D images of vegetation surface temperatures. Synthesis and applications. Estimating the effects of LTDs on natural plant–insect communities will require extending canopy models beyond their current focus on individual species or crops. These models, however, contain many parameters, and applying the models to new species or to mixed natural canopies depends on identifying the parameters that matter most. Our results suggest that canopy structural parameters are more important determinants of LTDs than are the physiological parameters that tend to receive the most empirical attention.     

Modelling canopy CO2 fluxes: are ‘big‐leaf’ simplifications justified?

• 1 The ‘big‐leaf’ approach to calculating the carbon balance of plant canopies is evaluated for inclusion in the ETEMA model framework. This approach assumes that canopy carbon fluxes have the same relative responses to the environment as any single leaf, and that the scaling from leaf to canopy is therefore linear.
• 2 A series of model simulations was performed with two models of leaf photosynthesis, three distributions of canopy nitrogen, and two levels of canopy radiation detail. Leaf‐ and canopy‐level responses to light and nitrogen, both as instantaneous rates and daily integrals, are presented.
• 3 Observed leaf nitrogen contents of unshaded leaves are over 40% lower than the big‐leaf approach requires. Scaling from these leaves to the canopy using the big‐leaf approach may underestimate canopy photosynthesis by ~20%. A leaf photosynthesis model that treats within‐leaf light extinction displays characteristics that contradict the big‐leaf theory. Observed distributions of canopy nitrogen are closer to those required to optimize this model than the homogeneous model used in the big‐leaf approach.
• 4 It is theoretically consistent to use the big‐leaf approach with the homogeneous photosynthesis model to estimate canopy carbon fluxes if canopy nitrogen and leaf area are known and if the distribution of nitrogen is assumed optimal. However, real nitrogen profiles are not optimal for this photosynthesis model, and caution is necessary in using the big‐leaf approach to scale satellite estimates of leaf physiology to canopies. Accurate prediction of canopy carbon fluxes requires canopy nitrogen, leaf area, declining nitrogen with canopy depth, the heterogeneous model of leaf photosynthesis and the separation of sunlit and shaded leaves. The exact nitrogen profile is not critical, but realistic distributions can be predicted using a simple model of canopy nitrogen allocation.

     

Photomorphogenesis and canopy dynamics. Phytochrome-mediated proximity perception accounts for the growth dynamics of canopies of Populus trichocarpa × deltoides'Beaupré'

The phytochrome family of signal-transducing photoreceptors provides plants with the capacity to perceive variations in the relative fluxes of red (R) and far-red (FR) radiation. This capacity has been proposed to be of ecological value in the perception of the proximity of neighbouring plants and the consequent induction of shade avoidance responses. The work reported here has evaluated this potential by determining quantitatively the effect of neighbour proximity on the growth of canopies of Populus trichocarpa×deltoides‘Beaupré’ trees, and relating the measured variables to the long-term vectoral radiation quality inside each canopy. The spectral distribution of radiation inside four canopies of Populus trichocarpa×deltoides‘Beaupre’ of different densities was monitored throughout the growing season. Spectral distributions inside the canopies were measured in 10° wedges at different heights and angles. The results are presented as PFD over 400–700 nm (PFD400–700) and PFD over 400–800 nm (PFD400–700). Results are also presented for the calculated phytochrome photoequilibrium (Pfr/P) and red:far-red ratio (R:FR). Data are presented as in-canopy angular and height profiles, and as diurnal and seasonal variations. PFD_400–700 and Pfr/P were found to be reduced inside each canopy, the reduction being greatest in the most dense canopy, and least in the most open canopy. At any height within each canopy, calculated Pfr/P decreased linearly with time throughout the growing season, until leaf senescence began. The reduction was greater in the denser canopies and was found to be similar for three consecutive field seasons. Linear relationships were found between plant stem growth rate, plant spacing and Pfr/P calculated from radiation propagated approximately horizontally within the canopies. The findings support the role of phytochrome in proximity perception in the natural environment and provide a quantitative basis for investigating the competitive interactions between plants growing in dense stands. The hypothesis is proposed that the dynamics of developing or regenerating canopies can be accounted for on the basis of phytochrome-mediated perception of the proximity of neighbouring plants.     

Foliage randomness and light interception in 3-D digitized trees: an analysis from multiscale discretization of the canopy

Light models for vegetation canopies based on the turbid medium analogy are usually limited by the basic assumption of random foliage dispersion in the canopy space. The objective of this paper was to assess the effect of three possible sources of non-randomness in tree canopies on light interception properties. For this purpose, four three-dimensional (3-D) digitized trees and four theoretical canopies – one random and three built from fractal rules – were used to compute canopy structure parameters and light interception, namely the sky-vault averaged STAR (Silhouette to Total Area Ratio). STAR values were computed from (1) images of the 3-D plants, and (2) from a 3-D turbid medium model using space discretization at different scales. For all trees, departure from randomness was mainly due to the spatial variations in leaf area density within the canopy volume. Indeed STAR estimations, based on turbid medium assumption, using the finest space discretization were very close to STAR values computed from the plant images. At this finest scale, foliage dispersion was slightly clumped, except one theoretical fractal canopy, which showed a marked regular dispersion. Taking into account a non-infinitely small leaf size, whose effect is theoretically to shorten self-shading, had a minor effect on STAR computations. STAR values computed from the 3-D turbid medium were very sensitive to plant lacunarity, a parameter introduced in the context of fractal studies to characterize the distribution of gaps in porous media at different scales. This study shows that 3-D turbid medium models based on space discretization are able to give correct estimation of light interception by 3-D isolated trees, provided that the 3-D grid is properly defined, that is, discretization maximizes plant lacunarity.     

Do bryophyte shoot systems function like vascular plant leaves or canopies? Functional trait relationships in Sphagnum mosses (Sphagnaceae)

Vascular plant leaf traits that influence photosynthetic function form the basis of mechanistic models of carbon exchange. Given their unique tissue organization, bryophytes may not express similar patterns. We investigated relationships among tissue, shoot, and canopy traits, and their associations with photosynthetic characteristics in 10 Sphagnum species. Trait relationships were organized around a primary dimension accounting for 43% of variation in 12 traits. There was no significant relationship between nitrogen content of shoot systems and maximum photosynthesis expressed on mass (A(mass)) or area (A(area)) bases due to nitrogen sequestration and storage within the canopy interior. This pattern differs from the distribution of nitrogen in vascular plant canopies. Thus, nitrogen and its relationship to carbon uptake in Sphagnum shoots does not conform to patterns of either vascular plant leaves or canopies. Species that concentrate biomass and nitrogen in the capitulum have enhanced rates of A(mass) and A(area). Consequently, A(area) was positively associated with N(area) of the capitulum only. Overall, water content and carotenoid concentration were the strongest predictors of both A(mass) and A(area) and these were expressed as inverse relationships. The relationships of plant traits in Sphagnum defines a principal trade-off between species that tolerate environmental stress and those that maximize carbon assimilation.     

Optimal nitrogen distribution within a leaf canopy under direct and diffuse light

Nitrogen distribution within a leaf canopy is an important determinant of canopy carbon gain. Previous theoretical studies have predicted that canopy photosynthesis is maximized when the amount of photosynthetic nitrogen is proportionally allocated to the absorbed light. However, most of such studies used a simple Beer's law for light extinction to calculate optimal distribution, and it is not known whether this holds true when direct and diffuse light are considered together. Here, using an analytical solution and model simulations, optimal nitrogen distribution is shown to be very different between models using Beer's law and direct–diffuse light. The presented results demonstrate that optimal nitrogen distribution under direct–diffuse light is steeper than that under diffuse light only. The whole‐canopy carbon gain is considerably increased by optimizing nitrogen distribution compared with that in actual canopies in which nitrogen distribution is not optimized. This suggests that optimization of nitrogen distribution can be an effective target trait for improving plant productivity.     

Functional significance of variation in bryophyte canopy structure

In most bryophytes, the thickness of boundary layers (i.e., unstirred layers) that surrounds plant surfaces governs rates of water loss. Architectural features of canopies that influence boundary layer thickness affect the water balance of bryophytes. Using field samples (9.3 cm diameter cushions) from 12 populations (11 species) of mosses and liverworts, we evaluated the relationship between canopy structure and boundary layer properties. Canopy structure was characterized using a contact surface probe to measure canopy depth along perpendicular transects at spatial scales ranging from 0.8 to 30 mm on 186 points per sample. Semivariance in depth measurements at different spatial scales was used to estimate three architectural properties: surface roughness (L(r)), the scale of roughness elements (S(r)), and fine-scale surface texture, the latter characterized by the fractal dimension (D) of the canopy profile. Boundary layer properties were assessed by evaporation of ethanol from samples in a wind-tunnel at wind speeds from 0.6 to 4.2 m/s and applied to characterize mass transfer using principles of dynamic similarity (i.e., using dimensionless representations of conductance and flow). In addition, particle image velocimetry (PIV) was used to visualize and quantify flow over two species. All cushions exhibited the characteristics of turbulent as opposed to laminar boundary layers, and conductance increased with surface roughness. Bryophyte canopies with higher L(r) had greater conductances at all wind speeds. Particle image velocimetry analysis verified that roughness elements interacted with flow and caused turbulent eddies to enter canopies, enhancing evaporation. All three morphological features were significantly associated with evaporation. When L(r), S(r), and D were incorporated with a flow parameter into a conductance model using multiple linear regression, the model accounted for 91% of the variation in mass transfer.     

Velocity gradients and turbulence around macrophyte stands in streams

1. Submerged macrophytes strongly modify water flow in small lowland streams. The present study investigated turbulence and vertical velocity gradients using small hot-wire anemometers in the vicinity and within the canopies of four macrophyte species with the objective of evaluating: (a) how plant canopies influence velocity gradients and shear force on the surfaces of the plants and the stream bed; and (b) how the presence and morphology of plants influence the intensity of turbulence. 2. Water velocity was often relatively constant with water depth both outside and inside the plant canopies, but the velocity declined steeply immediately above the unvegetated stream bed. Steep vertical velocity profiles were also observed in the transition to the surface of the macrophyte canopy of three of the plant species forming a dense shielding structure of high biomass. Less steep vertical profiles were observed at the open canopy surface of the fourth plant species, growing from a basal meristem and having the biomass more homogeneously distributed with depth. The complex distribution of hydraulic roughness between the stream bed, the banks and the plants resulted in velocity profiles which often fitted better to a linear than to a logarithmic function of distance above the sediment and canopy surfaces. 3. Turbulence increased in proportion to the mean flow velocity, but the slope of the relationships differed in a predictable manner among positions outside and inside the canopies of the different species, suggesting that their morphology and movements influenced the intensity of turbulence. Turbulence was maintained in the attenuated flow inside the plant canopies, despite estimates of low Reynolds numbers, demonstrating that reliable evaluation of flow patterns requires direct measurements. The mean velocity inside plant canopies mostly exceeded 2 cm s^??1 and turbulence intensity remained above 0.2 cm s^??1, which should be sufficient to prevent carbon limitation of photosynthesis in CO₂-rich streams, while plant growth may benefit from the reduced physical disturbance and the retention of nutrient-rich sediment particles. 4. Flow patterns were highly reproducible within canopies of the individual species despite differences in stand size and location among streams. We propose that individual plant stands are suitable functional units for analysing the influence of submerged macrophytes on flow patterns, retention of particles and biological communities in lowland streams.     

Effects of Wind Waves versus Ship Waves on Tidal Marsh Plants: A Flume Study on Different Life Stages of Scirpus maritimus

Recent research indicates that many ecosystems, including intertidal marshes, follow the alternative stable states theory. This theory implies that thresholds of environmental factors can mark a limit between two opposing stable ecosystem states, e.g. vegetated marshes and bare mudflats. While elevation relative to mean sea level is considered as the overall threshold condition for colonization of mudflats by vegetation, little is known about the individual driving mechanisms, in particular the impact of waves, and more specifically of wave period. We studied the impact of different wave regimes on plants in a full scale flume experiment. Seedlings and adult shoots of the pioneer Scirpus maritimus were subjected to two wave periods at two water levels. Drag forces acting on, and sediment scouring occurring around the plants were quantified, as these are the two main mechanisms determining plant establishment and survival. Depending on life stage, two distinct survival strategies emerge: seedlings present a stress avoidance strategy by being extremely flexible, thus limiting the drag forces and thereby the risk of breaking. Adult shoots present a stress tolerance strategy by having stiffer stems, which gives them a higher resistance to breaking. These strategies work well under natural, short period wind wave conditions. For long period waves, however, caused e.g. by ships, these survival strategies have a high chance to fail as the flexibility of seedlings and stiffness of adults lead to plant tissue failure and extreme drag forces respectively. This results in both cases in strongly bent plant stems, potentially limiting their survival.     

Vibrational Dynamics of Icosahedrally Symmetric Biomolecular Assemblies Compared with Predictions Based on Continuum Elasticity

Coarse-grained elastic network models elucidate the fluctuation dynamics of proteins around their native conformations. Low-frequency collective motions derived by simplified normal mode analysis are usually involved in biological function, and these motions often possess noteworthy symmetries related to the overall shape of the molecule. Here, insights into these motions and their frequencies are sought by considering continuum models with appropriate symmetry and boundary conditions to approximately represent the true atomistic molecular structure. We solve the elastic wave equations analytically for the case of spherical symmetry, yielding a symmetry-based classification of molecular motions together with explicit predictions for their vibrational frequencies. We address the case of icosahedral symmetry as a perturbation to the spherical case. Applications to lumazine synthase, satellite tobacco mosaic virus, and brome mosaic virus show that the spherical elastic model efficiently provides insights on collective motions that are otherwise obtained by detailed elastic network models. A major utility of the continuum models is the possibility of estimating macroscopic material properties such as the Young's modulus or Poisson's ratio for different types of viruses.     

Leaf nitrogen, photosynthesis, conductance and transpiration: scaling from leaves to canopies

A model is presented which solves simultaneously for leaf-scale stomatal conductance, CO₂ assimilation and the energy balance as a function of leaf position within canopies of well-watered vegetation. Fluxes and conductances were calculated separately for sunlit and shaded leaves. A linear dependence of photosynthetic capacity on leaf nitrogen content was assumed, while leaf nitrogen content and light intensity were assumed to decrease exponentially within canopies. Separate extinction coefficients were used for diffuse and direct beam radiation. An efficient Gaussian integration technique was used to compute fluxes and mean conductances for the canopy. The multilayer model synthesizes current knowledge of radiation penetration, leaf physiology and the physics of evaporation and provides insights into the response of whole canopies to multiple, interacting factors. The model was also used to explore sources of variation in the slopes of two simple parametric models (nitrogen- and light-use efficiency), and to set bounds on the magnitudes of the parameters. For canopies low in total N, daily assimilation rates are ～10% lower when leaf N is distributed uniformly than when the same total N is distributed according to the exponentially decreasing profile of absorbed radiation. However, gains are negligible for plants with high N concentrations. Canopy conductance, G_c should be calculated as G_c=Aσ(f_slg_sl+f_shg_sh), where Δ is leaf area index, f_si and f_sh are the fractions of sunlit and shaded leaves at each level, and g_si and g_sh are the corresponding stomatal conductances. Simple addition of conductances without this weighting causes errors in transpiration calculated using the ‘big-leaf’ version of the Penman-Monteith equation. Partitioning of available energy between sensible and latent heat is very responsive to the parameter describing the sensitivity of stomata to the atmospheric humidity deficit. This parameter also affects canopy conductance, but has a relatively small impact on canopy assimilation. Simple parametric models are useful for extrapolating understanding from small to large scales, but the complexity of real ecosystems is thus subsumed in unexplained variations in parameter values. Simulations with the multilayer model show that both nitrogen- and radiation-use efficiencies depend on plant nutritional status and the diffuse component of incident radiation, causing a 2- to 3-fold variation in these efficiencies.