Summary: 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 the literature in plant physiology, ecophysiology, ecology, agronomy and soil science, we reviewed 24 aspects of plant and ecosystem functioning and their relationships with a number of root system traits, including aspects of architecture, physiology, morphology, anatomy, chemistry, biomechanics and biotic interactions. Based on this assessment, we critically evaluated the current strengths and gaps in our knowledge, and identify future research challenges in the field of root ecology. Most importantly, we found that belowground traits with the broadest importance in plant and ecosystem functioning are not those most commonly measured. Also, the 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 the strongest links on functions, and to link genotypes to plant and ecosystem functioning.

Summary: In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting‐edge, meaningful and integrated knowledge. Consideration of the below‐ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below‐ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below‐ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine‐root vs coarse‐root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I–VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers’ views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

In a given root system, individual roots usually exhibit a rather homogeneous tip structure although highly different diameters and growth patterns, and this diversity is of prime importance in the definition of the whole root system architecture and foraging characteristics. In order to represent and predict this diversity, we built a simple and generic model at root tip level combining structural and functional knowledge on root elongation. The tip diameter, reflecting meristem size, is used as a driving variable of elongation. It varies, in response to the fluctuations of photo-assimilate availability, between two limits (minimal and maximal diameter). The elongation rate is assumed to be dependent on the transient value of the diameter. Elongation stops when the tip reaches the minimal diameter. The model could satisfactorily reproduce patterns of root elongation and tip diameter changes observed in various species at different scales. Although continuous, the model could generate divergent root classes as classically observed within populations of lateral roots. This model should help interpret the large plasticity of root elongation patterns which can be obtained in response to different combinations of endogenous and exogenous factors. The parameters could be used in phenotyping the root system.

Branching density (or the reciprocal: inter-branch distance) is an important trait which contributes to defining the number of roots in individual plants. The environmental and local variations in inter-branch distance have often been stressed, and simulations models have been put forward to take them into account within the dynamics of root system architecture (RSA). However, little is known about the interspecific and intra-plant variations of inter-branch distance. In this paper, we present an analysis which draws on 40 samples of plants belonging to 36 species collected in homogeneous soils, to address how the variations in inter-branch distance are structured within individual plants, and how this structure varies from one species to another. Using measurements of inter-branch distance on various roots of the same species and our knowledge of the branching process, we defined a simple and generic model dedicated to the simulation of the observed variations. This model distinguishes between two sub-processes: i) the longitudinal location of potential branching sites and ii) the effective emergence of lateral roots at these sites. Thus, it represents the variations in distance between the potential sites (with two parameters), and the probability of emergence of a lateral root at each site (one parameter). We show the ability of this model to account for the main variations in inter-branch distances with a limited number of parameters, and we estimated them for the different species. These parameters can be considered as promising traits to characterize—in a comprehensive and simple way—the genetic and environmental variations in the whole branching process at plant level. Based on the results, we make recommendations for carrying out comparable measurements of the branching density in developed plants. Moreover, we suggest the integration of this new model as a module in future RSA simulators, to improve their capacity to account for this important and highly variable characteristic of plant species.

In the recent years, many computational tools, such as image analysis, data management, process-based simulation and upscaling tools, were developed to help quantify and understand water flow in the soil-root system, at multiple scales (tissue, organ, plant and population). Several of these tools work together or, at least, are compatible. However, for the un-informed researcher, they might seem disconnected, forming a unclear and disorganised succession of tools. In this article, we present how different pieces of work can be further developed by connecting them to analyse soil-root-water relations in a comprehensive and structured network. This “explicit network of soil-root computational tools” informs the reader about existing tools and help them understand how their data (past and future) might fit within the network. We also demonstrate the novel possibilities of scale-consistent parameterizations made possible by the network with a set of case studies from the literature. Finally, we discuss existing gaps in the network and how we can move forward to fill them. Highlights: Many computational tools exist to quantify water flow in the soil-root system. These tools can be arranged in a comprehensive network that can be leveraged to better interpret experimental data.