The architecture of the branched root system of plants is a major determinant of vigor. Water availability is known to impact root physiology and growth; however, the spatial scale at which this stimulus influences root architecture is poorly understood. Here we reveal that differences in the availability of water across the circumferential axis of the root create spatial cues that determine the position of lateral root branches. We show that roots of several plant species can distinguish between a wet surface and air environments and that this also impacts the patterning of root hairs, anthocyanins, and aerenchyma in a phenomenon we describe as hydropatterning. This environmental response is distinct from a touch response and requires available water to induce lateral roots along a contacted surface. X-ray microscale computed tomography and 3D reconstruction of soil-grown root systems demonstrate that such responses also occur under physiologically relevant conditions. Using early-stage lateral root markers, we show that hydropatterning acts before the initiation stage and likely determines the circumferential position at which lateral root founder cells are specified. Hydropatterning is independent of endogenous abscisic acid signaling, distinguishing it from a classic water-stress response. Higher water availability induces the biosynthesis and transport of the lateral root-inductive signal auxin through local regulation of TRYPTO-PHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 and PIN-FORMED 3, both of which are necessary for normal hydropatterning. Our work suggests that water availability is sensed and interpreted at the suborgan level and locally patterns a wide variety of developmental processes in the root. moisture regulation | root development | root system architecture | adaptive root response | auxin-regulated root patterning

X-ray microcomputed tomography (mCT) is an invaluable tool for visualizing plant root systems within their natural soil environment noninvasively. However, variations in the x-ray attenuation values of root material and the overlap in attenuation values between roots and soil caused by water and organic materials represent major challenges to data recovery. We report the development of automatic root segmentation methods and software that view mCT data as a sequence of images through which root objects appear to move as the x-y cross sections are traversed along the z axis of the image stack. Previous approaches have employed significant levels of user interaction and/or fixed criteria to distinguish root and nonroot material. RooTrak exploits multiple, local models of root appearance, each built while tracking a specific segment, to identify new root material. It requires minimal user interaction and is able to adapt to changing root density estimates. The model-guided search for root material arising from the adoption of a visual-tracking framework makes RooTrak less sensitive to the natural ambiguity of x-ray attenuation data. We demonstrate the utility of RooTrak using mCT scans of maize (Zea mays), wheat (Triticum aestivum), and tomato (Solanum lycopersicum) grown in a range of contrasting soil textures. Our results demonstrate that RooTrak can successfully extract a range of root architectures from the surrounding soil and promises to facilitate future root phenotyping efforts.

2Plants can acclimate by using tropisms to link the direction of growth to 41 environmental conditions. Hydrotropism allows roots to forage for water, a process 42 known to depend on abscisic acid (ABA) but whose molecular and cellular basis 43 remains unclear. Here, we show that hydrotropism still occurs in roots after laser 44 ablation removed the meristem and root cap. Additionally, targeted expression 45 studies reveal that hydrotropism depends on the ABA signalling kinase, SnRK2.2, and 46 the hydrotropism-specific MIZ1, both acting specifically in elongation zone cortical 47 cells. Conversely, hydrotropism, but not gravitropism, is inhibited by preventing 48 differential cell-length increases in the cortex, but not in other cell types. We conclude 49 that root tropic responses to gravity and water are driven by distinct tissue-based 50 mechanisms. In addition, unlike its role in root gravitropism, the elongation zone 51 performs a dual function during a hydrotropic response, both sensing a water 52 potential gradient and subsequently undergoing differential growth. 53 3 Tropic responses are differential growth mechanisms that roots use to explore the 54 surrounding soil efficiently. In general, a tropic response can be divided into several steps, 55 comprising perception, signal transduction, and differential growth. All of these steps have 56 been well characterized for gravitropism, where gravity sensing cells in the columella of the 57 root cap generate a lateral auxin gradient, whilst adjacent lateral root cap cells transport 58 auxin to epidermal cells in the elongation zone, thereby triggering the differential growth that 59 drives bending [1][2][3][4] . In gravi-stimulated roots, the lateral auxin gradient is transported 60 principally by AUX1 and PIN carriers [3][4][5] . 61Compared with gravitropism, the tropic response to asymmetric water availability, i.e., 62 hydrotropism, has been far less studied. Previously, it was reported that surgical removal or 63 ablation of the root cap reduces hydrotropic bending in pea [6][7][8] and Arabidopsis thaliana 9 , 64suggesting that the machinery for sensing moisture gradients resides in the root cap. It has 65 also been reported that hydrotropic bending occurs due to differential growth in the 66 elongation zone 7,10 . However unlike gravitropism, hydrotropism in A. thaliana is independent 67 of AUX1 and PIN-mediated auxin transport 11,12 . Indeed, roots bend hydrotropically in the 68 absence of any redistribution of auxin detectable by auxin-responsive reporters 13,14 . 18,19 . 83However it is unclear whether this broad expression pattern is necessary for MIZ1's function 84 in hydrotropism or whether ABA signal transduction components in general have to be 85 expressed in specific root tip tissues for a hydrotropic response. The present study describes 86 a series of experiments in A. thaliana designed to identify the root tissues essential for a 87 hydrotropic response. We report that MIZ1 and a key ABA signal-transduction component 88SnRK2....

Root branching is critical for plants to secure anchorage and ensure the supply of water, minerals, and nutrients. To date, research on root branching has focused on lateral root development in young seedlings. However, many other programs of postembryonic root organogenesis exist in angiosperms. In cereal crops, the majority of the mature root system is composed of several classes of adventitious roots that include crown roots and brace roots. In this Update, we initially describe the diversity of postembryonic root forms. Next, we review recent advances in our understanding of the genes, signals, and mechanisms regulating lateral root and adventitious root branching in the plant models Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). While many common signals, regulatory components, and mechanisms have been identified that control the initiation, morphogenesis, and emergence of new lateral and adventitious root organs, much more remains to be done. We conclude by discussing the challenges and opportunities facing root branching research.

Soil compaction adversely affects root system architecture, influencing resource capture by limiting the volume of soil explored. Lateral roots formed later in plants grown in compacted soil and total root length and surface area were reduced. Root diameter was increased and swelling of the root tip occurred in compacted soil.

BackgroundX-ray micro-Computed Tomography (μCT) offers the ability to visualise the three-dimensional structure of plant roots growing in their natural environment – soil. Recovery of root architecture descriptions from X-ray CT data is, however, challenging. The X-ray attenuation values of roots and soil overlap, and the attenuation values of root material vary. Any successful root identification method must both explicitly target root material and be able to adapt to local changes in root properties.RooTrak meets these requirements by combining the level set method with a visual tracking framework and has been shown to be capable of segmenting a variety of plant roots from soil in X-ray μCT images. The approach provides high quality root descriptions, but tracks root systems top to bottom and so omits upward-growing (plagiotropic) branches.ResultsWe present an extension to RooTrak which allows it to extract plagiotropic roots. An additional backward-looking step revisits the previous image, marking possible upward-growing roots. These are then tracked, leading to efficient and more complete recovery of the root system. Results show clear improvement in root extraction, without which key architectural traits would be underestimated.ConclusionsThe visual tracking framework adopted in RooTrak provides the focus and flexibility needed to separate roots from soil in X-ray CT imagery and can be extended to detect plagiotropic roots. The extended software tool produces more complete descriptions of plant root structure and supports more accurate computation of architectural traits.

The rhizosphere is the zone of soil influenced by a plant root and is critical for plant health and nutrient acquisition. All below ground resources must pass through this dynamic zone prior to their capture by plant roots. However, researching the undisturbed rhizosphere has proved very challenging. Here we compare the temporal changes to the intact rhizosphere pore structure during the emergence of a developing root system in different soils. High resolution X-ray Computed Tomography (CT) was used to quantify the impact of root development on soil structural change, at scales relevant to individual micro-pores and aggregates (µm). A comparison of micro-scale structural evolution in homogenously packed soils highlighted the impacts of a penetrating root system in changing the surrounding porous architecture and morphology. Results indicate the structural zone of influence of a root can be more localised than previously reported (µm scale rather than mm scale). With time, growing roots significantly alter the soil physical environment in their immediate vicinity through reducing root-soil contact and crucially increasing porosity at the root-soil interface and not the converse as has often been postulated. This ‘rhizosphere pore structure’ and its impact on associated dynamics are discussed.

Summary Soil systems are characterized by the spatial and temporal distribution of organic and mineral particles, water and air within a soil profile. Investigations into the complex interactions between soil constituents have greatly benefited from the advent of non‐invasive techniques for structural analysis. In this paper we present a review of the application of one such technique, X‐ray computed tomography (CT), for studies of undisturbed soil systems, focusing on research during the last 10 years in particular. The ability to undertake three‐dimensional imaging has provided valuable insights regarding the quantitative assessment of soil features, in a way previously unachievable because of the opaque nature of soil. A dynamic approach to the evaluation of soil pore networks, hydro‐physical characteristics and soil faunal behaviour has seen numerous scanning methodologies employed and a diverse range of image analysis protocols used. This has shed light on functional processes across multiple scales whilst also bringing its own challenges. In particular, much work has been carried out to link a soil's porous architecture with hydraulic function, although new technical improvements allowing the characterization of organic matter and the influence of soil biota on structural development are showing great promise. Here we summarize the development of X‐ray CT in soil science, highlight the major issues relating to its use, outline some of the applications for overcoming these challenges and describe the potential of future technological advances for non‐invasive soil characterization through integration with other complementary techniques.