Structural root architecture of 5-year-old Pinus pinaster measured by 3D digitising and analysed with AMAPmod

Pinus pinaster (Ait.) is a high yielding forest tree, producing nearly a fourth of French marketed timber essentially from intensively managed stands located in southwestern France, in the Landes Forest. This species has generally a poor stem straightness, especially when it grows in poor sandy podzol of the Landes Forest, affected by summer droughts and winter floods. Above- and below-ground architecture and biomass as well as stem straightness were measured on twenty-nine 5-year-old planted trees uprooted by pulling with a lumbering crane. A very precise numeric representation of the geometry and topology of structural root architecture was gained using a low-magnetic-field digitising device (Danjon et al., 1998; Sinoquet and Rivet, 1997). Data were analysed with AMAPmod, a database software designed to analyse plant topological structures (Godin et al., 1997). Several characteristics of root architecture were extracted by queries including root number, length, diameter, volume, spatial position, ramification order, branching angle and inter-laterals length. Differences between root systems originated from their dimensions, but also from the proportion of deep roots and the taproot size, which represented 8% of the total root volume. The proportion of root volume in the zone of rapid taper was negatively correlated with the proportion of root volume in the taproot indicating a compensation between taproot and main lateral root volume. Among all studied root characteristics the maximal rooting depth, the proportion of deep roots and the root partitioning coefficient were correlated with stem straightness. This revised version was published online in June 2006 with corrections to the Cover Date.     

Root architecture and wind-firmness of mature Pinus pinaster

This study aims to link three-dimensional coarse root architecture to tree stability in mature timber trees with an average of 1-m rooting depth. Undamaged and uprooted trees were sampled in a stand damaged by a storm. Root architecture was measured by three-dimensional (3-D) digitizing. The distribution of root volume by root type and in wind-oriented sectors was analysed. Mature Pinus pinaster root systems were organized in a rigid 'cage' composed of a taproot, the zone of rapid taper of horizontal surface roots and numerous sinkers and deep roots, imprisoning a large mass of soil and guyed by long horizontal surface roots. Key compartments for stability exhibited strong selective leeward or windward reinforcement. Uprooted trees showed a lower cage volume, a larger proportion of oblique and intermediate depth horizontal roots and less wind-oriented root reinforcement. Pinus pinaster stability on moderately deep soils is optimized through a typical rooting pattern and a considerable structural adaptation to the prevailing wind and soil profile.     

稻茬麦根系构型的定向分型分析

为探索稻茬麦根构型的方向性,使用田间数字化仪实现稻茬麦根系的数值化,将根系数据导入Pro-E重构出根系的空间状态图,然后将根构型每隔10°进行各向投影,计算根系构型在18个维度的分形维数与分形丰度.结果表明:小麦苗期根构型在各维度的分形特征具有较强的规律性,表明根系在土体中的分布具有明显的方向性.在苗期到返青期,根构型在18个维度的分形指标波动性大,表明这一时期内根系生长处于持续的动态变化过程.在拔节期,根构型在各维度的分形再次呈现出一定的规律性,表明根系在土体中的分布重新表现出明显的方向性.该研究方法可以精准描述和分析植物根系在田间环境中的分布状况.     

Modelling the influence of assimilate availability on root growth and architecture

A model has been designed to simulate rubber seedling root development as related to assimilate availability. Each root of the system is defined both as an element of a network of axes, characterized by its order, position and connections and as an individual sink competing for assimilates. At each time step, the growth of each root is calculated as a function of its own growth potential and of assimilate availability calculated within the whole plant. The potential elongation rate of a root is estimated by its apical diameter, which reflects the size of the meristem. When a root is initiated, the apical diameter depends on root type, but it varies thereafter according to assimilate availability. Thus, the latter controls both current and potential elongation. The model was able to simulate periodicity in root development as related to shoot growth and to reproduce differences in sensitivity to assimilate availability related to root type. It thereby validated the hypothesis that root growth but also root system architecture depend on assimilate allocation and that apical diameter is a good indicator of root growth potential. Provided that specific calibration is done, this model may be used for other species.     

Modelling and predicting the spatial distribution of tree root density in heterogeneous forest ecosystems

Background and Aims In mountain ecosystems, predicting root density in three dimensions (3-D) is highly challenging due to the spatial heterogeneity of forest communities. This study presents a simple and semi-mechanistic model, named ChaMRoots, that predicts root interception density (RID, number of roots m^–2). ChaMRoots hypothesizes that RID at a given point is affected by the presence of roots from surrounding trees forming a polygon shape.Methods The model comprises three sub-models for predicting: (1) the spatial heterogeneity – RID of the finest roots in the top soil layer as a function of tree basal area at breast height, and the distance between the tree and a given point; (2) the diameter spectrum – the distribution of RID as a function of root diameter up to 50 mm thick; and (3) the vertical profile – the distribution of RID as a function of soil depth. The RID data used for fitting in the model were measured in two uneven-aged mountain forest ecosystems in the French Alps. These sites differ in tree density and species composition.Key Results In general, the validation of each sub-model indicated that all sub-models of ChaMRoots had good fits. The model achieved a highly satisfactory compromise between the number of aerial input parameters and the fit to the observed data.Conclusions The semi-mechanistic ChaMRoots model focuses on the spatial distribution of root density at the tree cluster scale, in contrast to the majority of published root models, which function at the level of the individual. Based on easy-to-measure characteristics, simple forest inventory protocols and three sub-models, it achieves a good compromise between the complexity of the case study area and that of the global model structure. ChaMRoots can be easily coupled with spatially explicit individual-based forest dynamics models and thus provides a highly transferable approach for modelling 3-D root spatial distribution in complex forest ecosystems.     

Rice morphogenesis and plant architecture: measurement, specification and the reconstruction of structural development by 3D architectural modelling

BACKGROUND AND AIMS: The morphogenesis and architecture of a rice plant, Oryza sativa, are critical factors in the yield equation, but they are not well studied because of the lack of appropriate tools for 3D measurement. The architecture of rice plants is characterized by a large number of tillers and leaves. The aims of this study were to specify rice plant architecture and to find appropriate functions to represent the 3D growth across all growth stages. METHODS: A japonica type rice, 'Namaga', was grown in pots under outdoor conditions. A 3D digitizer was used to measure the rice plant structure at intervals from the young seedling stage to maturity. The L-system formalism was applied to create '3D virtual rice' plants, incorporating models of phenological development and leaf emergence period as a function of temperature and photoperiod, which were used to determine the timing of tiller emergence. KEY RESULTS: The relationships between the nodal positions and leaf lengths, leaf angles and tiller angles were analysed and used to determine growth functions for the models. The '3D virtual rice' reproduces the structural development of isolated plants and provides a good estimation of the tillering process, and of the accumulation of leaves. CONCLUSIONS: The results indicated that the '3D virtual rice' has a possibility to demonstrate the differences in the structure and development between cultivars and under different environmental conditions. Future work, necessary to reflect both cultivar and environmental effects on the model performance, and to link with physiological models, is proposed in the discussion.     

Analysis of the plant architecture via tree-structured statistical models: the hidden Markov tree models

Plant architecture is the result of repetitions that occur through growth and branching processes. During plant ontogeny, changes in the morphological characteristics of plant entities are interpreted as the indirect translation of different physiological states of the meristems. Thus connected entities can exhibit either similar or very contrasted characteristics. We propose a statistical model to reveal and characterize homogeneous zones and transitions between zones within tree-structured data: the hidden Markov tree (HMT) model. This model leads to a clustering of the entities into classes sharing the same 'hidden state'. The application of the HMT model to two plant sets (apple trees and bush willows), measured at annual shoot scale, highlights ordered states defined by different morphological characteristics. The model provides a synthetic overview of state locations, pointing out homogeneous zones or ruptures. It also illustrates where within branching structures, and when during plant ontogeny, morphological changes occur. However, the labelling exhibits some patterns that cannot be described by the model parameters. Some of these limitations are addressed by two alternative HMT families.     

Fine root architecture, morphology, and biomass of different branch orders of two Chinese temperate tree species

We have limited understanding of architecture and morphology of fine root systems in large woody trees. This study investigated architecture, morphology, and biomass of different fine root branch orders of two temperate tree species from Northeastern China—Larix gmelinii Rupr and Fraxinus mandshurica Rupr —by sampling up to five fine root branch orders three times during the 2003 growing season from two soil depths (i.e., 0–10 and.10–20 cm). Branching ratio (R _b) differed with the level of branching: R _b values from the fifth to the second order of branching were approximately three in both species, but markedly higher for the first two orders of branching, reaching a value of 10.4 for L. gmelinii and 18.6 for F. mandshurica. Fine root diameter, length, SRL and root length density not only had systematic changes with root order, but also varied significantly with season and soil depth. Total biomass per order did not change systematically with branch order. Compared to the second, third and/or fourth order, the first order roots exhibited higher biomass throughout the growing season and soil depths, a pattern related to consistently higher R _b values for the first two orders of branching than the other levels of branching. Moreover, the differences in architecture and morphology across order, season, and soil depth between the two species were consistent with the morphological disparity between gymnosperms and angiosperms reported previously. The results of this study suggest that root architecture and morphology, especially those of the first order roots, should be important for understanding the complexity and multi-functionality of tree fine roots with respect to root nutrient and water uptake, and fine root dynamics in forest ecosystems.     

Relations between root length densities and root intersections with horizontal and vertical planes using root growth modelling in 3-dimensions

The root growth simulation model of Diggle (ROOTMAP; 1988) was modified to allow the numerical output of data on root intersections with horizontal and vertical planes. ROOTMAP was used to generate two three-dimensional model structures of fibrous root systems. The lateral roots were oriented randomly (geotropism index=0) but the main axes were positively gravitropic (geotropism index=0.6). The mean density of root intersections (n, cm^-2) with the sides of a series of 5×5×5 cm cubic volumes was related approximately linearly to the root length density (L_t cm^-2) within each volume by the equation L_t=2.3n (correlation coefficient, r=0.981). This compared with the relation of L_t=2n predicted theoretically for randomly oriented lines (Melhuish and Lang, 1968). Root length density was related to the intersection density by the equation L_t=2.43n_v (r=0.940) for the vertical faces and L_t=1.88n_h (r=0.984) for the horizontal faces. L_t/n_v was greater than L_t/n_h because of the preferential vertical orientation of the main root axes. The Melhuish and Lang (1968) equation does not generally give accurate prediction of root length density from field experiment data. Under field conditions, values have been reported in the ranges of 1.4 to 16 for L_t/n_h, and 3.8 to 9 for L_t/n_v. The most likely explanation for this difference is that only a small proportion (e.g. about 20–30%) of the actual number of roots are counted using the core-break and root mapping (including the trench wall) methods, due to the practical experimental difficulties of identifying individual fine roots under field conditions. Detailed experimental studies are needed to identify what portion of the root system is recorded using these field techniques (e.g. whether the main root axes are counted while the fine lateral roots remain undetected). Three-dimensional models of root growth provide a new method of studying the relations between L_t, n_v and n_h for root systems generated stochastically according to known geometrical rules. Using these models it will be possible to determine the effects of the degree of gravitropism and of root branching on the value and on the variability of L_t/n_h and L_t/n_v. The effectiveness of the statistical corrections that have been developed to correct for non-random root orientation can also be evaluated, as can the effects of sample position.     

Geometrical properties of simulated maize root systems: consequences for length density and intersection density

The spatial distribution of root length density (RLD) is important because it affects water and nutrient uptake. It is difficult to obtain reliable estimates of RLD because root systems are very variable and heterogeneous. We identified systematic trends, clustering, and anisotropy as geometrical properties of root systems, and studied their consequences for the sampling and observation of roots. We determined the degree of clustering by comparing the coefficient of variation of a simulated root system with that of a Boolean model. We also present an alternative theoretical derivation of the relation between RLD and root intersection density (RID) based on the theory of random processes of fibres. We show how systematic trends, clustering and anisotropy affect the theoretical relation between RLD and RID, and the consequences this has for measurement of RID in the field. We simulated the root systems of one hundred maize crops grown for a thermal time of 600 K d, and analysed the distribution of RLD and root intersection density RID on regular grids of locations throughout the simulated root systems. Systematic trends were most important in the surface layers, decreasing with depth. Clustering and anisotropy both increased with depth. Roots at depth had a bimodal distribution of root orientation, causing changes in the ratio of RLD/RID. The close proximity of the emerging lateral roots and the parent axis caused clustering which increased the coefficient of variation.     

Allometry, root/shoot ratio and root architecture in understory saplings of deciduous dicotyledonous trees in central Japan

Plant allometry that is related to plant architecture and biomass allocation strongly influences a plants ability to grow in shaded forest understory. Some allometric traits can change with plant size. The present study compared crown and trunk allometries, root/shoot biomass allometry, and root architecture among understory saplings (0.25--5m height, except for two trees > 5 < 7 m) of seven deciduous dicotyledonous species in central Japan. Associations of the crown and trunk allometries with several plant morphological attributes were analyzed. Branch morphology (plagiotropyvs orthotropy) and life size were correlated with sapling crown and trunk allometries. Both large leaves and orthotropic branches were associated with a narrow small crown and slender trunk. The root/shoot ratio decreased rapidly with increasing plant height for saplings shorter than about 1.5 m. Less shade-tolerant species tended to have smaller root/shoot ratios for saplings taller than 1.5 m. With an increase in plant height, the branch/trunk biomass ratio decreased for saplings with plagiotropic branches but increased for saplings with orthotropic branches. Four subcanopy species (Acer distylum, Carpinus cordata, Fraxinus lanuginosa and Acanthopanax sciadophylloides) had superficial root systems; a common understory species (Sapium japonica) had a deep tap root system; and a canopy species (Magnolia obovata) and a subcanopy species (Acer tenuifolium) had heart root systems of intermediate depth. The root depth was not related to shade tolerance. Among species of the same height, the difference in fine root length can be 30-fold.     

Role of cytokinin and auxin in shaping root architecture: regulating vascular differentiation, lateral root initiation, root apical dominance and root gravitropism

BACKGROUND AND AIMS: Development and architecture of plant roots are regulated by phytohormones. Cytokinin (CK), synthesized in the root cap, promotes cytokinesis, vascular cambium sensitivity, vascular differentiation and root apical dominance. Auxin (indole-3-acetic acid, IAA), produced in young shoot organs, promotes root development and induces vascular differentiation. Both IAA and CK regulate root gravitropism. The aims of this study were to analyse the hormonal mechanisms that induce the root's primary vascular system, explain how differentiating-protoxylem vessels promote lateral root initiation, propose the concept of CK-dependent root apical dominance, and visualize the CK and IAA regulation of root gravitropiosm. KEY ISSUES: The hormonal analysis and proposed mechanisms yield new insights and extend previous concepts: how the radial pattern of the root protoxylem vs. protophloem strands is induced by alternating polar streams of high IAA vs. low IAA concentrations, respectively; how differentiating-protoxylem vessel elements stimulate lateral root initiation by auxin-ethylene-auxin signalling; and how root apical dominance is regulated by the root-cap-synthesized CK, which gives priority to the primary root in competition with its own lateral roots. CONCLUSIONS: CK and IAA are key hormones that regulate root development, its vascular differentiation and root gravitropism; these two hormones, together with ethylene, regulate lateral root initiation.     

A stochastic model of tree architecture and biomass partitioning: application to Mongolian Scots pines

Background and Aims

Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal species used for windbreak and sand stabilization in arid and semi-arid areas in northern China. A model-assisted analysis of its canopy architectural development and functions is valuable for better understanding its behaviour and roles in fragile ecosystems. However, due to the intrinsic complexity and variability of trees, the parametric identification of such models is currently a major obstacle to their evaluation and their validation with respect to real data. The aim of this paper was to present the mathematical framework of a stochastic functional–structural model (GL2) and its parameterization for Mongolian Scots pines, taking into account inter-plant variability in terms of topological development and biomass partitioning.

Methods

In GL2, plant organogenesis is determined by the realization of random variables representing the behaviour of axillary or apical buds. The associated probabilities are calibrated for Mongolian Scots pines using experimental data including means and variances of the numbers of organs per plant in each order-based class. The functional part of the model relies on the principles of source–sink regulation and is parameterized by direct observations of living trees and the inversion method using measured data for organ mass and dimensions.

Key Results

The final calibration accuracy satisfies both organogenetic and morphogenetic processes. Our hypothesis for the number of organs following a binomial distribution is found to be consistent with the real data. Based on the calibrated parameters, stochastic simulations of the growth of Mongolian Scots pines in plantations are generated by the Monte Carlo method, allowing analysis of the inter-individual variability of the number of organs and biomass partitioning. Three-dimensional (3D) architectures of young Mongolian Scots pines were simulated for 4-, 6- and 8-year-old trees.

Conclusions

This work provides a new method for characterizing tree structures and biomass allocation that can be used to build a 3D virtual Mongolian Scots pine forest. The work paves the way for bridging the gap between a single-plant model and a stand model.     

The architecture of Picea sitchensis structural root systems on horizontal and sloping terrain

The coarse root systems of 24 Sitka spruce (Picea sitchensis (Bong.) Carr.) trees, from a 40-year-old plantation in west Scotland, were extracted, digitised in three dimensions, and root topology was recorded. Roots were from trees grown on a steep (ca. 30°) north-facing slope, and from an adjacent horizontal area with similar gleyed mineral soil. The prevailing wind was across-slope from the west. Analysis of below-ground parts of the trees in comparison with those above-ground revealed a positive linear relationship between coarse root volume and stem volume. Most non-directional characteristics of the root systems were similar between trees on the slope and on flat terrain. Allocation of root mass around trees was examined in relation to the slope and the prevailing wind direction. Trees on the horizontal area had more root mass in leeward sectors than other sectors, but trees on the slopes had more root mass in the windward sectors than other sectors. Centres of mass of the root systems from the horizontal part of the site were not significantly clustered in any direction, but root systems of trees on the slope had centres of mass significantly clustered across the slope in the windward direction. For trees on the slope, the mean direction of the largest sector without structural roots was 4° from north, i.e. downslope. The results are discussed in relation to soil characteristics and the biomechanical behaviour of trees on slopes.     

A generic 3D finite element model of tree anchorage integrating soil mechanics and real root system architecture

Understanding the mechanism of tree anchorage in a forest is a priority because of the increase in wind storms in recent years and their projected recurrence as a consequence of global warming. To characterize anchorage mechanisms during tree uprooting, we developed a generic finite element model where real three-dimensional (3D) root system architectures were represented in a 3D soil. The model was used to simulate tree overturning during wind loading, and results compared with real data from two poplar species (Populus trichocarpa and P. deltoides). These trees were winched sideways until failure, and uprooting force and root architecture measured. The uprooting force was higher for P. deltoides than P. trichocarpa, probably due to its higher root volume and thicker lateral roots. Results from the model showed that soil type influences failure modes. In frictional soils, e.g., sandy soils, plastic failure of the soil occurred mainly on the windward side of the tree. In cohesive soils, e.g., clay soils, a more symmetrical slip surface was formed. Root systems were more resistant to uprooting in cohesive soil than in frictional soil. Applications of this generic model include virtual uprooting experiments, where each component of anchorage can be tested individually.     

SimRoot: Modelling and visualization of root systems

SimRoot, a geometric simulation model of plant root systems, is described. This model employs a data structure titled the Extensible Tree, which is well suited to the type of data required to model root systems. As implemented on Silicon Graphics workstations, the data structure and visualization code provides for continuous viewing of the simulated root system during growth. SimRoot differs from existing models in the explicit treatment of spatial heterogeneity of physiological processes in the root system, and by inclusion of a kinematic treatment of root axes. Examples are provided of the utility of the model in estimating the fractal geometry of simulated root systems in 1, 2, and 3 dimensional space. We envision continued development of the model to incorporate competition from neighboring root systems, linkage with crop simulation models to simulate root-shoot interactions, explicit treatment of soil heterogeneity, and plasticity of root responses to soil factors such as presence of mycorrhizal associations.