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.

Biosciences Division and Center for Bioenergy Innovation Oak Ridge National Laboratory Oak Ridge TN 37831 USA

Cary Institute of Ecosystem Studies Millbrook NY 12545 USA

CEFE Univ Montpellier CNRS EPHE IRD 1919 route de Mende Montpellier 34293 France

Center for Tree Science Morton Arboretum 4100 Illinois Rt 53 Lisle IL 60532 USA

Department of Biological Sciences Macquarie University North Ryde NSW 2109 Australia

Department of Botany Institute of Biological Sciences Federal University of Goiás 19 74690 900 Goiânia Goiás Brazil

Department of Ecological Science Faculty of Science Vrije Universiteit Amsterdam De Boelelaan 1085 Amsterdam 1081 HV the Netherlands

Department of Ecology Evolution and Behavior University of Minnesota St Paul MN 55108 USA

Department of Forest and Soil Sciences University of Natural Resources and Life Sciences Vienna 1190 Austria

Department of Functional Ecology Institute of Botany CAS Dukelska 135 37901 Trebon Czech Republic

Department of General Botany Institute of Experimental Biology Faculty of Biology Adam Mickiewicz University Uniwersytetu Poznańskiego 6 61 614 Poznań Poland

Department of Plant and Environmental Sciences Clemson University Clemson SC 29634 USA

Department of Plant Sciences The Pennsylvania State University University Park PA 16802 USA

Environmental Biology Department Institute of Environmental Sciences CML Leiden University Leiden 2300 RA the Netherlands

Environmental Sciences Division and Climate Change Science Institute Oak Ridge National Laboratory Oak Ridge TN 37831 USA

Forest Dynamics Swiss Federal Research Institute WSL Zürcherstr 111 8903 Birmensdorf Switzerland

Forest Soils and Biogeochemistry Swiss Federal Research Institute WSL Zürcherstr 111 8903 Birmensdorf Switzerland

Functional Forest Ecology University of Hamburg Haidkrugsweg 1 22885 Barsbütel Germany

Geobotany Faculty of Biology University of Freiburg Schänzlestr 1 79104 Freiburg Germany

INRAE AMAP CIRAD IRD CNRS University of Montpellier Montpellier 34000 France

Institute of Applied Ecology Chinese Academy of Sciences Shenyang 110016 China

Institute of Dendrology Polish Academy of Sciences Parkowa 5 62 035 Kórnik Poland

Institute of Terrestrial Ecosystems ETH Zurich 8092 Zurich Switzerland

International Center for Tropical Botany Department of Biological Sciences Florida International University Miami FL 33199 USA

Laurentian University 935 Ramsey Lake Road Sudbury ON P3E 2C6 Canada

Noble Research Institute LLC 2510 Sam Noble Parkway Ardmore OK 73401 USA

Odum School of Ecology University of Georgia 140 E Green Street Athens GA 30602 USA

Plant Ecology and Nature Conservation Group Department of Environmental Sciences Wageningen University and Research PO Box 47 6700 AA Wageningen the Netherlands

Plant Sciences Forschungszentrum Jülich GmbH D 52425 Jülich Germany

School of Biological Sciences The University of Western Australia 35 Stirling Highway Crawley WA 6009 Australia

School of Biological Sciences The University of Western Australia Crawley WA Australia

School of Geography and Priestley International Centre for Climate University of Leeds Leeds LS2 9JT UK

School of Science and Engineering University of Dundee Dundee DD1 4HN UK

Senckenberg Biodiversity and Climate Research Centre Senckenberganlage 25 60325 Frankfurt am Main Germany

Station d'Ecologie Théorique et Expérimentale CNRS 2 route du CNRS 09200 Moulis France

Systematic Botany and Functional Biodiversity Institute of Biology Leipzig University Johannisallee 21 23 Leipzig 04103 Germany

The James Hutton Institute Invergowrie Dundee DD2 5DA UK

Université Clermont Auvergne INRAE VetAgro Sup UREP 63000 Clermont Ferrand France

UR 1115 PSH Centre PACA site Agroparc INRAE 84914 Avignon cedex 9 France

USDA ARS Water Management Research Unit 2150 Centre Avenue Bldg D Suite 320 Fort Collins CO 80526 USA

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Semantic segmentation of plant roots from RGB (mini-) rhizotron images-generalisation potential and false positives of established methods and advanced deep-learning models

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