Rhizosphere water content drives hydraulic redistribution : Implications of pore-scale heterogeneity to modeling diurnal transpiration in water-limited ecosystems

Trees typically survive prolonged droughts by absorbing water from deeper layers. Where soils are shallow, roots may be extract water from the underlying fractured bedrocks. In dry seasons, surface-soil moisture dynamics reflect hydraulic redistribution (HR). HR is usually estimated based on the gradient of mean, or bulk, soil water potential among layers in the rooting zone (HRB). This approach neglects the potential effect of spatial heterogeneity of water content at the millimeter scale between the rhizosphere and bulk soil. We proposed to account for the rhizosphere water balance, estimating HR to the rhizosphere (HRR) of the dry surface soil from the underlying fractured rock. The model was evaluated using a 15-year dataset collected in Sardinia. When the typical approach, based on moisture gradients among bulk soil layers, was used for estimating HRB, tree transpiration was underpredicted in all seasons, especially in spring and summer. Forcing the model with measured tree transpiration, HRB decreased during spring and summer, while the contribution of the underlying rock layer to tree transpiration was threefold that estimated using HRR-based model. The average water content of the bulk surface soil layer was very low, reaching 0.06 in the driest summers while showing little diurnal dynamics; however, concentrating water in roughly estimated rhizosphere volume, produced rhizosphere water content appreciably higher (approximate to 0.16), and much more dynamic. Predicted HRR dominated evapotranspiration (60% - 65%) in dry springs and summers reaching 80% of tree transpiration. Most importantly, the proposed rhizosphere-HR model correctly predicts the diurnal dynamics of tree transpiration year-round, and the grass transpiration in its active spring period. Eco-hydrological models operating at sub-daily scale should consider partitioning the soil to rhizosphere volume, thus allowing both diagnostic and prognostic estimates of diurnal biosphere-atmosphere mass and energy exchanges.Peer reviewe

Isospectral graphs with identical nodal counts

According to a recent conjecture, isospectral objects have different nodal count sequences. We study generalized Laplacians on discrete graphs, and use them to construct the first non-trivial counter-examples to this conjecture. In addition, these examples demonstrate a surprising connection between isospectral discrete and quantum graphs

Stand sapwood basal area : an indicator of tree vigor

The control that stand leaf area exerts upon individual tree vigor was tested on a heterogeneous, even-aged Douglas-fir stand infected by Phellinus root rot. Tree vigor, or growth efficiency ratio, was defined as the current basal area growth per unit of leaf area. Because of a close relationship between sapwood basal area and tree leaf area, stand sapwood basal area was used as an indirect estimator of competing leaf area to test changes in growth efficiency at different levels of canopy density. It was hypothesized that the growth efficiency ratio would decrease linearly with increasing stand sapwood basal area. No significant relationships were found between stand sapwood basal area and either average or individual tree growth efficiency. However, the maximum efficiency of trees recorded under specified levels of canopy competition (upper boundary) did follow the expected trends. No significant difference was found between the slope of the upper boundary linear equation and the slope of the line which described the relationship between mean growth efficiency and stand sapwood basal area in another homogeneous stand in the Oregon Coastal Range. Several explanations for the lack of the general hypothesized relationship were offered, including the need for more refined measurement methods of sapwood basal area and basal area growth. Still, the most reasonable explanation is that root rot continued to reduce growth below the potential and induced unmeasured continuous changes in the canopy which affected individual tree response differently

Leaf area index and specific leaf weight : keys to interpreting canopy photosynthesis and stand growth

Two physiological factors are of major importance to tree and stand growth: (1) the photosynthetic rate of foliage and (2) the amount of foliage. If carbohydrate allocation patterns remain constant, stand growth should be related directly to total canopy photosynthesis. From a literature analysis I assess methods of relating photosynthetic rates to biochemical, anatomical, and structural characteristics of foliage. A number of these foliage characteristics were found to be interrelated. Specific leaf weight was shown to be a valuable index for comparing photosynthesis by various parts of a tree canopy over a season or throughout an entire year. Mean annual photosynthetic rate in five separate portions of a spruce canopy was directly proportional to observed differences in specific leaf weight (r2 = 0.99). Annual carbon uptake was a function of total foliage biomass (r2 = 0.96). When foliage biomass at each crown segment was adjusted for differences in specific leaf weight, reflecting differences in photosynthetic rates, the predictive equation further improved C r2 = 0.99). Specific leaf weight is recommended as an index for comparing the relative effects of various silvicultural treatments on photosynthesis. I then evaluated how stand growth and canopy leaf area were related by analyzing 24 years of growth records from a Pinus ponderosa (Laws.) experiment. The experiment included a wide range in initial stocking and partial control of understory vegetation (Barrett 1982). I found that treatment effects on tree growth can be evaluated at low values of stand leaf area from comparison of growth efficiencies (wood produced per unit leaf area) among plots of similar canopy leaf area. By comparing stand growth with stand leaf area, I concluded that the major effect of removing understory vegetation was to speed the development of the canopy. This interpretation was also supported by a comparison of the rate of leaf area development on plots with and without understory vegetation at comparable levels of canopy leaf area. Comparing stands at a similar canopy leaf area is advised for assessing how treatment affects stand development. This is a valuable alternative to analyzing treatment effects at one point in time and helps to explain the results of many fertilization experiments

Recovering the Metabolic, Self-Thinning, and Constant Final Yield Rules in Mono-Specific Stands

Competition among plants of the same species often results in power-law relations between measures of crowding, such as plant density, and average size, such as individual biomass. Yoda's self-thinning rule, the constant final yield rule, and metabolic scaling, all link individual plant biomass to plant density and are widely applied in crop, forest, and ecosystem management. These dictate how plant biomass increases with decreasing plant density following a given power-law exponent and a constant of proportionality. While the exponent has been proposed to be universal and thus independent of species, age, environmental, and edaphic conditions, different theoretical mechanisms yield absolute values ranging from less than 1 to nearly 2. Here, eight hypothetical mechanisms linking the exponent to constraints imposed on plant competition are featured and contrasted. Using dimensional considerations applied to plants growing isometrically, the predicted exponent is -3/2 (Yoda's rule). Other theories based on metabolic arguments and network transport predict an exponent of -4/3. These rules, which describe stand dynamics over time, differ from the "rule of constant final yield" that predicts an exponent of -1 between the initial planting density and the final yield attained across stands. The latter can be recovered from statistical arguments applied at the time scale in which the site carrying capacity is approached. Numerical models of plant competition produce plant biomass-density scaling relations with an exponent between -0.9 and -1.8 depending on the mechanism and strength of plant-plant interaction. These different mechanisms are framed here as a generic dynamical system describing the scaled-up carbon economy of all plants in an ecosystem subject to differing constraints. The implications of these mechanisms for forest management under a changing climate are discussed and recent research on the effects of changing aridity and site "quality" on self-thinning are highlighted.Peer reviewe

Organic nitrogen enhances nitrogen nutrition and early growth of Pinus sylvestris seedlings

Boreal trees are capable of taking up organic nitrogen (N) as effectively as inorganic N. Depending on the abundance of soil N forms, plants may adjust physiological and morphological traits to optimize N uptake. However, the link between these traits and N uptake in response to soil N sources is poorly understood. We examined Pinus sylvestris L. seedlings' biomass growth and allocation, transpiration and N uptake in response to additions of organic N (the amino acid arginine) or inorganic N (ammonium nitrate). We also monitored in situ soil N fluxes in the pots following an addition of N, using a microdialysis system. Supplying organic N resulted in a stable soil N flux, whereas the inorganic N resulted in a sharp increase of nitrate flux followed by a rapid decline, demonstrating a fluctuating N supply and a risk for loss of nitrate from the growth medium. Seedlings supplied with organic N achieved a greater biomass with a higher N content, thus reaching a higher N recovery compared with those supplied inorganic N. In spite of a higher N concentration in organic N seedlings, root-to-shoot ratio and transpiration per unit leaf area were similar to those of inorganic N seedlings. We conclude that enhanced seedlings' nutrition and growth under the organic N source may be attributed to a stable supply of N, owing to a strong retention rate in the soil medium

Rock Water as a Key Resource for Patchy Ecosystems on Shallow Soils : Digging Deep Tree Clumps Subsidize Surrounding Surficial Grass

Mediterranean mountainous areas of shallow soil often display a mosaic of tree clumps surrounded by grass. The combined role and dynamics of water extracted from the underlying rock, and the competition between adjacent patches of trees and grass, has not been investigated. We quantified the role rock water plays in the seasonal dynamics of evapotranspiration (ET), over a patchy landscape in the context of current and past seasonal climate changes, and land-cover change strategies. Soil water budget suggests deep water uptake by roots of trees (0.8-0.9 mm/d), penetrating into the fractured basalt, subsidized grass transpiration in spring through hydraulic redistribution. However, in summer trees used all the rock water absorbed (0.79 mm/d). A 15-year data set shows that, with increasing seasonal drought-severity (potential ET/precipitation) to >1.04, the vertical water flux through the bottom of the thin soil layer transitions from drainage to uptake in support of ET. A hypothetical grass-covered landscape, with no access to deep water, would require 0.68-0.85 mm/d more than is available, forcing shortened growing season and/or reduced leaf area. Long-term decreasing winter precipitation and increasing spring potential ET suggest drying climate, so far with stable vegetation mosaic but progressively earlier peak of grass leaf area. Intervention policies to increase water yield by reducing tree cover will curtail grass access to rock moisture, while attempting to increase tree-related products (including carbon sequestration) by increasing forest cover will limit water availability per tree leaf area. Both changes may further reduce ecosystem stability.Peer reviewe

The carbon bonus of organic nitrogen enhances nitrogen use efficiency of plants

The importance of organic nitrogen (N) for plant nutrition and productivity is increasingly being recognized. Here we show that it is not only the availability in the soil that matters, but also the effects on plant growth. The chemical form of N taken up, whether inorganic (such as nitrate) or organic (such as amino acids), may significantly influence plant shoot and root growth, and nitrogen use efficiency (NUE). We analysed these effects by synthesizing results from multiple laboratory experiments on small seedlings (Arabidopsis, poplar, pine and spruce) based on a tractable plant growth model. A key point is that the carbon cost of assimilating organic N into proteins is lower than that of inorganic N, mainly because of its carbon content. This carbon bonus makes it more beneficial for plants to take up organic than inorganic N, even when its availability to the roots is much lower - up to 70% lower for Arabidopsis seedlings. At equal growth rate, root:shoot ratio was up to three times higher and nitrogen productivity up to 20% higher for organic than inorganic N, which both are factors that may contribute to higher NUE in crop production

A Lagrangian dispersion model for predicting CO\u3csub\u3e2\u3c/sub\u3e sources, sinks, and fluxes in a uniform loblolly pine (\u3ci\u3ePinus taeda\u3c/i\u3e L.) stand

A canopy Lagrangian turbulent scalar transport model for predicting scalar fluxes, sources, and sinks within a forested canopy was tested using CO2 concentration and flux measurements. The model formulation is based on the localized near-field theory (LNF) proposed by Raupach [1989a, b]. Using the measured mean CO2 concentration profile, the vertical velocity variance profile, and the Lagrangian integral timescale profile within and above a forested canopy, the proposed model predicted the CO2 flux and source (or sink) profiles. The model testing was carried out using eddy correlation measurements at 9 m in a uniform 13 m tall Pinus taeda L . (loblolly pine) stand at the Blackwood division of the Duke Forest near Durham, North Carolina. The tree heightand spacing are relatively uniform throughout. The measured vertical profile leaf area index (LAI) was characterized by three peaks, with a maximum LAI occurring at 6.5 m, in qualitative agreement with the LNF source-sink predicted profile. The LNF CO2 flux predictions were in better agreement with eddy correlation measurements (coefficient of determinatior r2=0.58; and standard error of estimate equal to 0.16m kg-1 m s-1) than K theory. The model reproduced the mean diurnal CO2 flux, suggesting better performance over longer averaging time periods. Two key simplifications to the LNF formulation were considered, namely, the near-Gaussian approximation to the verticalvelocity and the absence of longitudinal advection. It was found that both of these assumptions were violated throughout the day, but the resulting CO2 flux error at 9 m was not strongly related to these approximations. In contrast to the forward LNF approach utilized by other studies, this investigation demonstrated that the inverse LNF approach is sensitive to near-field corrections

Overlapping Splicing Regulatory Motifs—Combinatorial Effects on Splicing

Regulation of splicing in eukaryotes occurs through the coordinated action of multiple splicing factors. Exons and introns contain numerous putative binding sites for splicing regulatory proteins. Regulation of splicing is presumably achieved by the combinatorial output of the binding of splicing factors to the corresponding binding sites. Although putative regulatory sites often overlap, no extensive study has examined whether overlapping regulatory sequences provide yet another dimension to splicing regulation. Here we analyzed experimentally-identified splicing regulatory sequences using a computational method based on the natural distribution of nucleotides and splicing regulatory sequences. We uncovered positive and negative interplay between overlapping regulatory sequences. Examination of these overlapping motifs revealed a unique spatial distribution, especially near splice donor sites of exons with weak splice donor sites. The positively selected overlapping splicing regulatory motifs were highly conserved among different species, implying functionality. Overall, these results suggest that overlap of two splicing regulatory binding sites is an evolutionary conserved widespread mechanism of splicing regulation. Finally, over-abundant motif overlaps were experimentally tested in a reporting minigene revealing that overlaps may facilitate a mode of splicing that did not occur in the presence of only one of the two regulatory sequences that comprise it