Root biology never sleeps

Natural ecosystems and agricultural production have been threatened by multifaceted global environmental changes. Soil degradation, extreme drought and flooding events, shifting climatic patterns and other challenges have prompted many disciplines within plant science to pivot to find solutions. Accordingly, root research has expanded from fundamental studies on roots, as providers of physical support, water and essential nutrients uptake, towards identification of beneficial traits for stress adaptation and control of key biological soil processes. Advances in trait identification, data acquisition, management and modelling are enabling root researchers to develop predictive models to support ecosystems in these changing environments. Through technical presentations, posters, industry exhibits and a root phenotyping workshop, the international, jointly presented, completely virtual International Society of Root Research (ISRR)11/Rooting2021 meeting provided a unique platform for researchers across disciplines to share recent advances in root biology, from molecular to ecosystem-level scales, in agricultural and natural ecosystems, addressing critical questions in response to climate change and its impact on crop productivity and ecosystem services. In this report, the 2021 ISRR Ambassador cohort provides an overview of the current root research landscape and reflection on the importance of frontier research for a more sustainable future. In response to global travel restrictions imposed by the COVID-19 pandemic, the 11th Symposium of the International Society of Root Research (ISRR11, https://www.rootresearch.org/) and the 9th International Symposium on Root Development (Rooting2021) merged into a single online event co-organised by the Interdisciplinary Plant Group at the University of Missouri (Columbia, MO, USA) and the University of Nottingham (UK). Over 700 participants representing academia, government and industry from more than 53 countries (Supporting Information Fig. S1) joined the virtual event held 24–28 May 2021. The schedule ran almost uninterrupted across international time zones, featuring 74 talks (10 plenaries, 16 keynotes, and 48 invited) and c. 300 posters, spanning a broad range of disciplines. In addition, the 2021 ISRR Lifetime Achievement Award was presented to Wendy Silk, Emeritus Professor at the University of California-Davis (USA). ISRR11/Rooting2021 hosted the 3rd ISRR Ambassador Program, a unique platform for early-career root researchers. The virtual ISRR11/Rooting2021 Ambassador Program provided networking activities, experience with conference organisation, interaction with professionals in diverse career areas, and opportunities to discuss advances in the field with a broadly multidisciplinary cohort (Notes S1). Ambassador tasks at the ISRR11/Rooting 2021 meeting included session note-taking, the production of this Meeting report, and a set of recommendations for diversity and inclusion in future scientific events (Notes S2). The ISRR11/Rooting2021 meeting concluded with a root phenotyping workshop with virtual tours of major root phenotyping facilities and demonstrations of methods. Organised by Larry York (Oak Ridge National Laboratory, TN, USA) and Darren Wells (University of Nottingham, UK), in collaboration with other experts and the ISRR Ambassadors, the workshop with a Q&A format was used to discuss the latest advances in root phenotyping techniques. The potential complementarity of image analysis software tools emerged as a key topic as depicted in Fig. S2. The availability of standardised protocols for root collection and trait measurement was also highlighted by the participants of the online survey, organised by the Ambassadors in addition to the Symposium (Delory et al., 2022) and the workshop as an important issue for future research. The Root Ecology Handbook recently published in New Phytologist provides a comprehensive guide on root sampling, processing and measuring for a wide variety of traits in a standardised manner (Freschet et al., 2021). Root phenotyping for traits related to crop performance or ecosystem services has been a main focus in the field of root biology since the 1970s (Hurd, 1974). However, quantitative analysis of plant phenotypes and their linkages to plant functions remains a major bottleneck. ISRR11/Rooting2021 highlighted the current emphasis on phenotyping root traits that will provide resilience to changing environmental conditions (Fig. 1), including traits related to root–microbial interactions (Kawasaki et al., 2021). Rhizosphere processes related to root stress responses are key for sustainable food production systems, as they impact soil functioning and resource use efficiency. The impact of drought and limited nutrient supply on plants under global climate change, and the mechanisms of root response from molecular to field scales, have prompted focussed advances on well established areas in the field of root research. Therefore, the role of auxin and cytokinin in molecular crosstalk has prompted the rise of the ‘hormonics’ to explore their functions in root development under drought stress (Rodriguez-Alonso et al., 2018), and to identify signalling pathways that link nutrient availability to root developmental parameters (Shahzad & Amtmann, 2017). Hormonal signalling also underlies ‘nutritropism’, an extension of ‘chemotropism’ (Newcombe & Rhodes, 1904), which can now be explored with advanced imaging and microscopy technology (T. Fujiwara, University of Tokyo, Japan). Root-related strategies to mitigate drought stress related to root hydraulic architecture and water transport were also discussed (Maurel & Nacry, 2020). Root-system-level traits linked with water and nutrient use efficiency such as wheat root axial conductance (Hendel et al., 2021), architectural traits in rice (Ruangsiri et al., 2021) and maize (Kistler et al., 2018) have been identified with a combination of shovelomics, phenotyping, functional genomics and modelling. The long-standing challenges of grafting for the introduction of root traits related to stress tolerance have been partially overcome by recent progress on our understanding of graft compatibility and cell-to-cell adhesion (Notaguchi et al., 2020). Advancing our understanding of grafting mechanisms will certainly provide new avenues to understand the effects of specific root genotypes and/or traits on other parts of the plant body (J. Cantillo, Donald Danforth Plant Science Center, MO, USA). Current trends in root research seek to integrate stress responses inside the root system with a better understanding of these root–soil–microbe interactions. ISRR11/Rooting2021 highlighted the role of the rhizosphere microbiome in nutrient homeostasis, for example, in root diffusion (Salas-González et al., 2021), or during nitrogen acquisition (Arsova et al., 2012). Root exudates were introduced as potential targets for rhizosphere engineering to promote beneficial microbiome functionalities (Kawasaki et al., 2021) or to control harmful species. Novel studies looking into root–microbiome interactions have become possible due to precision genome editing, production of knocked-down lines and reconstruction of biosynthetic metabolic pathways (Huang et al., 2019), and advanced imaging techniques such as positron emission tomography (Schmidt et al., 2020). Recent advances in imaging techniques and image analysis (Fig. 1) can support high-throughput root phenotyping of relevant structural features within the root architecture (Fig. 2). Detailed image-based root phenotyping techniques such as X-ray computed tomography (CT) scanning can improve our interpretation of in-field studies (C. Topp, Donald Danforth Plant Science Center, MO, USA). Current advances allow high-resolution and/or high-throughput phenotyping studies, even in mature crops and under field conditions (Gore et al., 2020; Rich et al., 2020), although methodological challenges remain (Delory et al., 2022). For example, root phenotyping of rooting depth and its significance for deep water or nitrate uptake is being addressed with large-scale field experiments using minirhizotrons or soil coring on maize (A. Leakey, University of Illinois, USA), wheat (J. Christopher, University of Queensland, Australia) and potatoes (O. Popovic, Copenhagen University, Denmark). Automated, high-resolution minirhizotrons are also used for visualising the dynamics of roots and fungi interaction in experimentally warmed peatlands (C. Iversen, Oak Ridge National Laboratory, TN, USA; Defrenne et al., 2020). These imaging advances are complemented by the development of free, open source and high-performance image analysis software (Fig. S2). Pairing 3D imaging techniques (e.g. X-ray CT) with mathematical modelling is a powerful way to study plant–soil interactions on different scales, from soil pores to growing root systems (Roose et al., 2016). This hybrid approach has resulted in key milestones by allowing the elucidation of how root architecture and exudation jointly affect P mobilisation and uptake (McKay Fletcher et al., 2020), and to quantify the extent to which the dissolution of N fertiliser granules affects soil microbial activity (Ruiz et al., 2020). Imaging techniques can also be used for traits related to root–microbe interactions (Fig. 1), complementing other multidisciplinary approaches that seek to better understand the complex dialogue between roots, the associated microbiome and soil processes. Mathematical modelling complements phenotyping advances by overcoming the challenges of experimental approaches and benefits from the emerging field of functional phenomics (York, 2019). Highlights from the diversity of modelling approaches presented at ISRR/Rooting2021, in both spatial and temporal scales, include: a micro-hydrological model that describes a new symplastic water pumping mechanism (Couvreur et al., 2021); the dynamics and regulation of a fast brassinosteroid response pathway in Arabidopsis root tips (Großeholz et al., 2021); functional–structural plant (FSP) models to identify optimal root phenotypes for nutrient capture in contrasting environments (Rangarajan, 2021); and field-scale simulations of plant populations and communities (Postma et al., 2017; Schnepf et al., 2018; Faverjon et al., 2019). Future mathematical models will draw on larger, more complex, datasets incorporating novel imaging technology, high-throughput phenotyping and availability of relevant environmental data. The positive feedback cycles between these models and continued advances in phenotyping are what will surely advance the field of root science. To meet the challenges imposed by the global COVID-19 pandemic, online communication has provided new opportunities for international multidisciplinary cooperation. The ISRR11/Rooting2021 online event brought the root research community together to share knowledge on the latest developments in root and rhizosphere research, present new technological advances and identify pressing research questions that still require answers. The adoption of a holistic approach to root research, that is, one that takes into account all categories of root traits, from anatomy to root morphology, physiology and architecture, as well as interactions with the rhizosphere microbiota, was emphasised as a crucial step in facing the challenges posed by global change. We encourage root researchers to actively take advantage of the plethora of online resources currently available for plant phenotyping (https://quantitative-plant.org/), and to join the ISRR (https://www.rootresearch.org/). Collaborations to share knowledge, along with new technological advances, will help us further understand roots and rhizosphere processes. The authors thank the New Phytologist Foundation for supporting the Ambassador Program, and John Kirkegaard and Hallie Thompson for initiating the ISRR Ambassador Program in 2015. LAG acknowledges support from the Plant Genome Research Program, National Science Foundation (IOS-1444448). We thank Michelle Watt, Bob Sharp, Malcolm Bennett and the organisers of the ISRR11/Rooting2021 Symposium from the Interdisciplinary Plant Group at the University of Missouri (Columbia, USA) and the University of Nottingham (UK). In particular, the authors would like to thank Victoria Bryan as well as Jennifer Hartwick and her team for their exceptional support. We thank Larry York and Darren Wells for organising an excellent virtual root phenotyping workshop during the ISRR11/Rooting2021 conference with generous financial support from the International Plant Phenotyping Network. The ISRR Ambassadors are also very grateful to Charlie Messina, Michelle Watt, Genevieve Croft and Ronald Vargas for sharing their professional experience and for taking the time to discuss career opportunities for root scientists. The authors thank Christopher Topp, Larry York and Abraham Smith for their contributions to the preparation of the figures. Finally, thanks to all ISRR11/Rooting2021 participants for making this conference a success! See you at the next ISRR (organised in 2024 in Leipzig, Germany) and/or Rooting (organised in 2023 in Ghent, Belgium) conference. None declared. AJM, CNT, LAG and AT coordinated the ‘ISRR11 Ambassador Program’ and provided valuable feedback on the manuscript. The ISRR11 Ambassadors group (CNC, GC, KKD, BMD, AD, YD, APG, QH, P-WH, MCH-S, ML, JLPN, LM, JM-M, AER, JS, TSW, PW, XW, LX, CZ) compiled and collated minutes of the sessions throughout the meeting and wrote the initial draft and the revised versions. Ambassador JS prepared Notes S2 addressing diversity and inclusion at ISRR11/Rooting2021. Data sharing is not applicable to this article as no datasets were generated or analysed during the current study. Fig. S1 Map depicting the distribution and number of attendees to the joined Symposium ISRR11-Rooting2021. Fig. S2 Example of root image analysis pairing RootPainter and RhizoVision explorer. Notes S1 The ISRR11 3rd Graduate Student and Postdoc Ambassador Program. Notes S2 Diversity and inclusion at ISRR11/Rooting2021. Please note: Wiley Blackwell are not responsible for the content or functionality of any Supporting Information supplied by the authors. Any queries (other than missing material) should be directed to the New Phytologist Central Office. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.