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We present in this paper a novel, semiautomated image-analysis software to streamline the quantitative analysis of root growth and architecture of complex root systems. The software combines a vectorial representation of root objects with a powerful tracing algorithm that accommodates a wide range of image sources and quality. The root system is treated as a collection of roots (possibly connected) that are individually represented as parsimonious sets of connected segments. Pixel coordinates and gray level are therefore turned into intuitive biological attributes such as segment diameter and orientation as well as distance to any other segment or topological position. As a consequence, user interaction and data analysis directly operate on biological entities (roots) and are not hampered by the spatially discrete, pixel-based nature of the original image. The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements. The use of the software is illustrated with a time-lapse analysis of cluster root formation in lupin (Lupinus albus) and an architectural analysis of the maize (Zea mays) root system. The software, SmartRoot, is an operating system-independent freeware based on ImageJ and relies on cross-platform standards for communication with data-analysis software.

The effects of plants on the biosphere, atmosphere, and geosphere are key determinants of terrestrial ecosystem functioning. However, despite substantial progress made regarding plant belowground components, we are still only beginning to explore the complex relationships between root traits and functions. Drawing on literature in plant physiology, ecophysiology, ecology, agronomy and soil science, we review 24 aspects of plant and ecosystem functioning and their relationships with a number of traits of root systems, including aspects of architecture, physiology, morphology, anatomy, chemistry, biomechanics and biotic interactions. Based on this assessment, we critically evaluate the current strengths and gaps in our knowledge, and identify future research challenges in the field of root ecology. Most importantly, we found that below-ground traits with widest importance in plant and ecosystem Accepted Article This article is protected by copyright. All rights reserved functioning are not those most commonly measured. Also, the fair estimation of trait relative importance for functioning requires us to consider a more comprehensive range of functionally-relevant traits from a diverse range of species, across environments and over time series. We also advocate that establishing causal hierarchical links among root traits will provide a hypothesis-based framework to identify the most parsimonious sets of traits with strongest influence on the functions, and to link genotypes to plant and ecosystem functioning.

Soil water uptake by plant roots results from the complex interplay between plant and soil which modulates and determines transport processes at a range of spatial and temporal scales: at small scales, uptake rates are determined by local soil and root hydraulic properties but, at the plant scale, local processes interact within the root system and are integrated through the hydraulic architecture of the root system and plant transpiration. However, because of the inherent complexity of the root system (both structural and functional), plant roots are commonly account for with synthetic but over-simplifying descriptors, valid at a given spatial scale. In this article, we present a model describing both soil and plant processes involved in water uptake at the scale of the whole root system with explicit account of individual roots. This is achieved through the unifying concepts of root system architecture and hydraulic continuity between the soil and plant. The model is based on a combination of architectural, root system hydraulic and soil water transfer modelling. The model can reproduce qualitatively and quantitatively laboratory experimental data obtained from imaging of water uptake by light transmission (cf. Garrigues et al., Water uptake by plant roots: I-Formation and propagation of a water extraction front in mature root systems as evidenced by 2D light transmission imaging. Plant and soil (2006, this issue) or X-ray imaging for two soil types (a sand/clay mix and a sandy clay loam) and different narrow-leaf lupin root systems (taprooted and fibrous), using independently measured soil-plant parameters. Results of the experiments and modelling reported in this paper concur to show that a water extraction front formed on the root system. This uptake frontÕs spatial extension and propagation were closely related to the local dependence between root and soil hydraulic properties and root axial conductance. Hence, a sharp front formed in the sand/clay mix but was much more attenuated in the sandy loam. Comparison between taprooted and fibrous root systems grown in a sand/clay mix, show that the taprooted architecture induced a more spatially concentrated uptake zone (near the soil surface) with higher flux rates, but with xylem water potential at the base of the root system twice as low than in the fibrous architecture. Modelling provided evidence that hydraulic lift might have occurred when transpiration declined, particularly in soil prone to abrupt variations in soil water potential (sand/clay mix). Finally, such a model, explicitly coupling root system-soil water transfers, can be useful to study water uptake in relation with root architectural traits, distribution of root hydraulic conductance or influence of heterogeneous conditions (localised irrigation, root clumping).