Automatic Root Length Estimation from Images Acquired In Situ without Segmentation

Image-based root phenotyping technologies, including the minirhizotron (MR), have expanded our understanding of the in situ root responses to changing environmental conditions. The conventional manual methods used to analyze MR images are time-consuming, limiting their implementation. This study presents an adaptation of our previously developed convolutional neural network-based models to estimate the total (cumulative) root length (TRL) per MR image without requiring segmentation. Training data were derived from manual annotations in Rootfly, commonly used software for MR image analysis. We compared TRL estimation with 2 models, a regression-based model and a detection-based model that detects the annotated points along the roots. Notably, the detection-based model can assist in examining human annotations by providing a visual inspection of roots in MR images. The models were trained and tested with 4,015 images acquired using 2 MR system types (manual and automated) and from 4 crop species (corn, pepper, melon, and tomato) grown under various abiotic stresses. These datasets are made publicly available as part of this publication. The coefficients of determination (R2), between the measurements made using Rootfly and the suggested TRL estimation models were 0.929 to 0.986 for the main datasets, demonstrating that this tool is accurate and robust. Additional analyses were conducted to examine the effects of (a) the data acquisition system and thus the image quality on the models' performance, (b) automated differentiation between images with and without roots, and (c) the use of the transfer learning technique. These approaches can support precision agriculture by providing real-time root growth information.

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

BACKGROUND

Manual analysis of (mini-)rhizotron (MR) images is tedious. Several methods have been proposed for semantic root segmentation based on homogeneous, single-source MR datasets. Recent advances in deep learning (DL) have enabled automated feature extraction, but comparisons of segmentation accuracy, false positives and transferability are virtually lacking. Here we compare six state-of-the-art methods and propose two improved DL models for semantic root segmentation using a large MR dataset with and without augmented data. We determine the performance of the methods on a homogeneous maize dataset, and a mixed dataset of > 8 species (mixtures), 6 soil types and 4 imaging systems. The generalisation potential of the derived DL models is determined on a distinct, unseen dataset.

RESULTS

The best performance was achieved by the U-Net models; the more complex the encoder the better the accuracy and generalisation of the model. The heterogeneous mixed MR dataset was a particularly challenging for the non-U-Net techniques. Data augmentation enhanced model performance. We demonstrated the improved performance of deep meta-architectures and feature extractors, and a reduction in the number of false positives.

CONCLUSIONS

Although correction factors are still required to match human labelled root lengths, neural network architectures greatly reduce the time required to compute the root length. The more complex architectures illustrate how future improvements in root segmentation within MR images can be achieved, particularly reaching higher segmentation accuracies and model generalisation when analysing real-world datasets with artefacts-limiting the need for model retraining.

Root system response to salt stress in grapevines (Vitis spp.): A link between root structure and salt exclusion

Accessing freshwater resources for agriculture becomes more complex due to increasing demands and declining water quality. Alternative water sources, such as saline water, require ad hoc solutions. Therefore, understanding roots' response to saline water is crucial for future agriculture. We examined the response of three grapevine rootstocks (Paulsen 1103, Richter 110 and SO4) to salt stress. The rootstocks were subjected to two salinity treatments: 10 mM and 30 mM NaCl (EC = 2 and 4 ds/m, respectively). Root and shoot samples were taken at the end of the experiment for morphologic and ionomic analyses. The specific root area (SRA) increased in response to salinity for all three rootstocks due to root tissue density and average root diameter reductions. Salinity also led to increased root Na⁺ and Cl^- contents and reduced root K⁺/Na⁺ ratio, parallel to increased leaf Cl^- but not Na⁺ contents. SO4 showed improved chloride and sodium exclusion, concomitant with its highest SRA, resulting from the increase in its thin roots' contribution to the total root system surface area. We suggest that enhanced SRA combined with decreased root tissue density and diameter may improve grapevines' salt exclusion by less salt uptake from the soil.

Aeroponic systems: A unique tool for estimating plant water relations and NO3 uptake in response to salinity stress

The study of transpiration, water, and nutrient uptake during abiotic stress in the root zone is hindered because of the hidden nature of the root zone. In this study, a modified aeroponic system was used to evaluate whole plant transpiration, nitrate and water uptake in the growth and development of tomato plants in response to salinity. Tomato seedlings were exposed to three levels of salinity (1.5, 4.5, and 9 dSm-1) and three levels of nitrate (1, 4, and 8 mM NO3) in a separate experiments conducted concurrently. Whole plant transpiration, water and nitrate uptake were estimated. Our study revealed that ~30 to 35 days after treatment (DAT), water uptake rate per plant increased from a common initial rate of about 0.05 to 1.1, 0.6, and 0.4 kg/day at 1.5, 4.5, and 9 dSm-1 respectively. The NO3 uptake rates in tomatoes grown in 1 and 4 mM NO3 were 5.5 and 22% respectively, of the uptake of tomatoes grown in 8 mM NO3. The estimation of nitrate uptake and lower sensitivity to salinity stress in the aeroponic showed the effectiveness and cost efficiency of the system in the cultivation of vegetables during abiotic stresses. The novelty of the system described is the continuous estimation of root and nutrient uptake by the whole plant at any given time.

Wide vessels sustain marginal transpiration flux and do not optimize inefficient gas exchange activity under impaired hydraulic control and salinity

Plants optimize water use and carbon assimilation via transient regulation of stomata resistance and by limiting hydraulic conductivity in a long-term response of xylem anatomy. We postulated that without effective hydraulic regulation plants would permanently restrain water loss and photosynthetic productivity under salt stress conditions. We compared wild-type tomatoes to a transgenic type (TT) with impaired stomatal control. Gas exchange activity, biomass, starch content, leaf area and root traits, mineral composition and main stems xylem anatomy and hydraulic conductivity were analyzed in plants exposed to salinities of 1 and 4 dS m^-1 over 60 days. As the xylem cannot easily readjust to different environmental conditions, shifts in its anatomy and the permanent effect on plant hydraulic conductivity kept transpiration at lower levels under unstressed conditions and maintained it under salt-stress, while sustaining higher but inefficient assimilation rates, leading to starch accumulation and decreased plant biomass, leaf and root area and root length. Narrow conduits in unstressed TT plants were related to permanent restrain of hydraulic conductivity and plant transpiration. Under salinity, TT plants followed the atmospheric water demand, sustained similar transpiration rate from unstressed to salt-stressed conditions and possibly maintained hydraulic integrity, due to likely impaired hydraulic regulation, wider conduits and higher hydraulic conductivity. The accumulation of salts and starch in the TT plants was a strong evidence of salinity tolerance via osmotic regulation, also thought to help to maintain the assimilation rates and transpiration flux under salinity, although it was not translated into higher growth.

Optimizing root yield of cassava under fertigation and the masked effect of atmospheric temperature

BACKGROUND

Fertigation is a rare and an expensive method of fertilizer application to cassava, and hence there is a need to optimize its efficiency for profitability. This study's objective was to optimize root yield of cassava through fertigation using a logistic model.

RESULTS

The field treatments were six fertigation concentrations against three cassava varieties, selected according to their maturity period. The logistic model predicted 52%, 116% and 281% benefit of fertigation for the varieties Mweru, Kampolombo and Nalumino, respectively. Furthermore, only half of the amount of fertilizer applied for Mweru was required to achieve twice the root yield of Kampolombo. During the experiment, an unknown importance of atmospheric temperature to cassava and its relationship to fertigation was observed. An elevation of 3.7 °C in atmospheric temperature led to 226%, 364% and 265% increase in root yield of Mweru, Kampolombo and Nalumino, respectively. Conversely, shoot biomass and root yield declined when the average atmospheric temperatures dropped by 3.6 °C. However, the cold temperatures affected the short-growth-duration (Mweru) and medium-growth-duration (Kampolombo) varieties earlier, 22 days after the drop, than the long-growth-duration variety (Nalumino) - 50 days after the drop.

CONCLUSION

Fertigation induced resilience of the shoot biomass production to cold which was most pronounced in the root yield of Mweru in response to the highest fertigation concentration. Thus, while fertigation improved cassava's resilience to cold, it only did so effectively for short-growth-duration variety, Mweru. Also, enhanced performance of cassava under increased atmospheric temperature indicated its importance as a climate-smart crop. © 2020 Society of Chemical Industry.

Environmental Tradeoffs between Nutrient Recycling and Greenhouse Gases Emissions in an Integrated Aquaculture-Agriculture System

The unlimited nitrogen (N) availability that has characterized crop production in the last few decades is accompanied by environmental burdens, including the greenhouse gas (GHG) emissions associated with fertilizer production, post-application nitrate (NO₃^-) pollution of water bodies, and emissions of reactive gaseous N forms into the atmosphere. Here, we quantified the environmental tradeoffs of replacing mineral N fertilizer with NO₃^- and ammonium (NH₄⁺) originating from effluent water of aquaculture in a cucumber (Cucumis sativus) cultivation system. While the yield, nitrogen use efficiency (NUE), and NO₃^- leaching were similar between the cucumbers fertilized and irrigated (fertigated) by aquaculture effluent water containing 100 mg of NO₃^--N L^-1 (AN), by aquaculture effluent water supplemented with NH₄⁺ (AN+), or by tap water with NO₃^- and NH₄⁺ added (FN+), there were significant differences in the nitrous oxide (N₂O) emissions between the systems. The N₂O emissions peaked after each irrigation event followed by an exponential decline. The cumulative N₂O emissions were between 60 and 600 g N₂O-N ha^-1, smaller than predicted based on a fertilizer application rate of 600 kg N ha^-1 and were in the order AN+ ≫ FN+ > AN.

Potassium and storage root development: focusing on photosynthesis, metabolites and soluble carbohydrates in cassava

The linkage between K and the development of storage roots in root crops is partially understood, hence this experiment determined some of the mechanisms involved in cassava. The effects of 10, 40, 70, 100, 150 and 200 mg K l^-1 fertigation on photosynthetic attributes, soluble carbohydrates, starch, metabolites, growth and yield were studied in a greenhouse. Storage root yield, number of storage roots, stomatal conductance and net photosynthesis reached maximum at 150 mg K l^-1 . However, soluble carbohydrates and starch in the leaves significantly declined with an increasing concentration of K solution, similarly to the trend of glycerol in the leaves. Conversely, malic acid, citric acid and propionic acid gradually increased reaching maximum at 150, 150 and 70 mg K l^-1 respectively. Combined, these results suggest that sugars were transported from the leaves to a stronger sink - the bulking storage roots. This and the increase of intermediate metabolites of tricarboxylic acid cycle provided the energy required for the bulking process and the development of the storage roots. Although the measured parameters indirectly link K to storage root development, they nonetheless form a basis for studies on direct interactions.

High Nitrogen Availability Limits Photosynthesis and Compromises Carbohydrate Allocation to Storage in Roots of Manihot esculenta Crantz

Cassava (M. esculenta Crantz), feeding countless people and attracting markets worldwide, is a model for traditional crops that need physiology-based fertigation (fertilization through irrigation) standards in intensive cultivation. Hence, we studied the effects of 10 to 200 mg L^-1 nitrogen (N) fertigation on growth and yields of cassava and targeted alterations in their photosynthetic, transpiration, and carbohydrate management. We found that increasing irrigation N from 10 to 70 mg L^-1 increased cassava's photosynthesis and transpiration but supported only the canopy's growth. At 100 mg N L^-1 cassava reached a threshold of sugar in leaves (∼47 mg g^-1), began to accumulate starch and supported higher yields. Yet, at 200 mg N L^-1, the canopy became too demanding and plants had to restrain transpiration, reduce photosynthesis, decrease carbohydrates, and finally lower yields. We concluded that the phases of cassava response to nitrogen are: 1) growth that does not support yields at low N, 2) productive N application, and 3) excessive use of N. Yet traditional leaf mineral analyses fail to exhibit these responses, and therefore we propose a simple and inexpensive carbohydrate measurement to guide a precise use of N.

Physiology and metabolism of grafted bell pepper in response to low root-zone temperature

Low temperature is a prominent limiting factor for tropical originated crops production in temperate regions, particularly during cool-season production. The diverse response of two rootstocks (Canon-sensitive and S103-tolerant to low root-zone temperature) was studied when exposed to aeroponically different temperature regimes at the root zone: constant low temperature of 14°C low root-zone temperature (LRZT), transient exposure to LRZT of 27-14-27°C and control temperature of 27°C. Gas exchange, shoot dry mass, and root morphology were measured. Shifts in central and secondary metabolite levels in the leaves and roots were examined by gas chromatography-mass spectrometry (GC-MS). Low root-zone temperature inhibited photosynthesis and transpiration of both grafted bell pepper plants; however, self-grafted Canon physiology was impeded to a greater extent compared with Canon grafted onto rootstock S103. Rootstock S103 demonstrated higher sink potential contributing to milder reduction of photosynthesis and transpiration during stress compared with self-grafted Canon. This reduction of gas exchange led to a significant reduction of root maximum length and root dry mass in self-grafted Canon in response to the stress at 14°C compared with Canon grafted onto rootstock S103. In response to stress, GC-MS metabolite profiling showed enhance metabolism in both cultivars' leaves, as well as in the roots irrespective of the developmental stage of the plant. This evidence combined indicates enhance gas exchange and carbon assimilation when bell pepper is grafted on S103 under low root-zone temperature.

Swift metabolite changes and leaf shedding are milestones in the acclimation process of grapevine under prolonged water stress

BACKGROUND

Grape leaves provide the biochemical substrates for berry development. Thus, understanding the regulation of grapevine leaf metabolism can aid in discerning processes fundamental to fruit development and berry quality. Here, the temporal alterations in leaf metabolism in Merlot grapevine grown under sufficient irrigation and water deficit were monitored from veraison until harvest.

RESULTS

The vines mediated water stress gradually and involving multiple strategies: osmotic adjustment, transcript-metabolite alteration and leaf shedding. Initially stomatal conductance and leaf water potential showed a steep decrease together with the induction of stress related metabolism, e.g. up-regulation of proline and GABA metabolism and stress related sugars, and the down-regulation of developmental processes. Later, progressive soil drying was associated with an incremental contribution of Ca²⁺ and sucrose to the osmotic adjustment concomitant with the initiation of leaf shedding. Last, towards harvest under progressive stress conditions following leaf shedding, incremental changes in leaf water potential were measured, while the magnitude of perturbation in leaf metabolism lessened.

CONCLUSIONS

The data present evidence that over time grapevine acclimation to water stress diversifies in temporal responses encompassing the alteration of central metabolism and gene expression, osmotic adjustments and reduction in leaf area. Together these processes mitigate leaf water stress and aid in maintaining the berry-ripening program.

A bell pepper cultivar tolerant to chilling enhanced nitrogen allocation and stress-related metabolite accumulation in the roots in response to low root-zone temperature

Two bell pepper (Capsicum annuum) cultivars, differing in their response to chilling, were exposed to three levels of root-zone temperatures. Gas exchange, shoot and root phenology, and the pattern of change of the central metabolites and secondary metabolites caffeate and benzoate in the leaves and roots were profiled. Low root-zone temperature significantly inhibited gaseous exchange, with a greater effect on the sensitive commercial pepper hybrid (Canon) than on the new hybrid bred to enhance abiotic stress tolerance (S103). The latter was less affected by the treatment with respect to plant height, shoot dry mass, root maximum length, root projected area, number of root tips and root dry mass. More carbon was allocated to the leaves of S103 than nitrogen at 17°C, while in the roots at 17°C, more nitrogen was allocated and the ratio between C/N decreased. Metabolite profiling showed greater increase in the root than in the leaves. Leaf response between the two cultivars differed significantly. The roots accumulated stress-related metabolites including γ-aminobutyric acid (GABA), proline, galactinol and raffinose and at chilling (7°C) resulted in an increase of sugars in both cultivars. Our results suggest that the enhanced tolerance of S103 to root cold stress, reflected in the relative maintenance of shoot and root growth, is likely linked to a more effective regulation of photosynthesis facilitated by the induction of stress-related metabolism.

Grape Metabolic Response to Postveraison Water Deficit Is Affected by Interseason Weather Variability

Postveraison water deficit is a common strategy implemented to improve fruit composition in many wine-growing regions. However, contrasting results are often reported on fruit size and composition, a challenge for generalizing the positive impact of this technique. Our research investigated the effect of water deficit (WD) imposed at veraison on Merlot grapevines, during two experimental seasons (2014-2015). In both years WD resulted in reduced carbon assimilation rates and leaf shedding. However, the treatment effect on the analyzed berry parameters varied between seasons. Modification of skin metabolites was more evident in 2015 than in 2014, despite the similar soil water content and water stress physiological parameters (gas exchange, water potential) recorded in the two experimental years. Higher solar radiation and air temperature in 2015 than in 2014 hint for the involvement of atmospheric parameters in fulfilling the potential effect of WD. Our results suggest that the interaction between water availability and weather conditions plays a crucial role in modulating the grape berry composition.

Paclobutrazol induces tolerance in tomato to deficit irrigation through diversified effects on plant morphology, physiology and metabolism

Dwindling water resources combined with meeting the demands for food security require maximizing water use efficiency (WUE) both in rainfed and irrigated agriculture. In this regard, deficit irrigation (DI), defined as the administration of water below full crop-water requirements (evapotranspiration), is a valuable practice to contain irrigation water use. In this study, the mechanism of paclobutrazol (Pbz)-mediated improvement in tolerance to water deficit in tomato was thoroughly investigated. Tomato plants were subjected to normal irrigated and deficit irrigated conditions plus Pbz application (0.8 and 1.6 ppm). A comprehensive morpho-physiological, metabolomics and molecular analysis was undertaken. Findings revealed that Pbz application reduced plant height, improved stem diameter and leaf number, altered root architecture, enhanced photosynthetic rates and WUE of tomato plants under deficit irrigation. Pbz differentially induced expression of genes and accumulation of metabolites of the tricarboxylic acid (TCA) cycle, γ-aminobutyric acid (GABA-shunt pathway), glutathione ascorbate (GSH-ASC)-cycle, cell wall and sugar metabolism, abscisic acid (ABA), spermidine (Spd) content and expression of an aquaporin (AP) protein under deficit irrigation. Our results suggest that Pbz application could significantly improve tolerance in tomato plants under limited water availability through selective changes in morpho-physiology and induction of stress-related molecular processes.

Tolerance to high soil temperature in foxtail millet (Setaria italica L.) is related to shoot and root growth and metabolism

Roots play important roles in regulating whole-plant carbon and water relations in response to extreme soil temperature. Three foxtail millet (Setaria italica L.) lines (448-Ames 21521, 463-P1391643 and 523-P1219619) were subjected to two different soil temperatures (28 and 38 °C). The gas exchange, chlorophyll fluorescence, root morphology and central metabolism of leaves and roots were studied at the grain-filling stage. High soil temperature (38 °C) significantly influenced the shoot transpiration, stomatal conductance, photosynthesis, root growth and metabolism of all lines. The root length and area were significantly reduced in lines 448 and 463 in response to the stress, while only a small non-specific reduction was observed in line 523 in response to the treatment. The shift of root metabolites in response to high soil temperature was also genotype specific. In response to high soil temperature, glutamate, proline and pyroglutamate were reduced in line 448, and alanine, aspartate, glycine, pyroglutamate, serine, threonine and valine were accumulated in line 463. In the roots of line 523, serine, threonine, valine, isomaltose, maltose, raffinose, malate and itaconate were accumulated. Root tolerance to high soil temperature was evident in line 523, in its roots growth potential, lower photosynthesis and stomatal conductance rates, and effective utilization and assimilation of membrane carbon and nitrogen, coupled with the accumulation of protective metabolites.

Direct in vivo evidence of immense stem water exploitation in irrigated date palms

During the summer, evaporative demand at midday often exceeds the transport capacity of most desert plants. However, date palms maintain their ecological dominance with sustained and uniquely high rates of transpiration. This high rate of flow cannot be attributed to soil water supply alone. In order to quantify intra-plant water allocation in irrigated date palms, three water-sensing techniques have been incorporated: heat dissipation, gravimetric sampling, and time domain reflectrometry. Each of these methods has known limitations but their integration resulted in a quantitative in vivo accounting of the date palm diurnal and seasonal water mass balance. By incorporating these methods it was possible to determine that date palms substantially rely on the exploitation and recharge of the stem reservoir in their water budget. The stem of mature date palms can hold up to 1 m(3) of water and supply 25% of daily transpiration (i.e. 5000 l of water in 100 d of summer). The internal stem water reservoir is consistently recharged by over 50 l per night which allows for successive daytime reuse throughout the entire growing season. More broadly, these findings suggest that internal water allocation and night-time soil-water availability could provide useful information for improving date palm irrigation practices.

Estimating sap flux densities in date palm trees using the heat dissipation method and weighing lysimeters

In a world of diminishing water reservoirs and a rising demand for food, the practice and development of water stress indicators and sensors are in rapid progress. The heat dissipation method, originally established by Granier, is herein applied and modified to enable sap flow measurements in date palm trees in the southern Arava desert of Israel. A long and tough sensor was constructed to withstand insertion into the date palm's hard exterior stem. This stem is wide and fibrous, surrounded by an even tougher external non-conducting layer of dead leaf bases. Furthermore, being a monocot species, water flow does not necessarily occur through the outer part of the palm's stem, as in most trees. Therefore, it is highly important to investigate the variations of the sap flux densities and determine the preferable location for sap flow sensing within the stem. Once installed into fully grown date palm trees stationed on weighing lysimeters, sap flow as measured by the modified sensors was compared with the actual transpiration. Sap flow was found to be well correlated with transpiration, especially when using a recent calibration equation rather than the original Granier equation. Furthermore, inducing the axial variability of the sap flux densities was found to be highly important for accurate assessments of transpiration by sap flow measurements. The sensors indicated no transpiration at night, a high increase of transpiration from 06:00 to 09:00, maximum transpiration at 12:00, followed by a moderate reduction until 08:00; when transpiration ceased. These results were reinforced by the lysimeters' output. Reduced sap flux densities were detected at the stem's mantle when compared with its center. These results were reinforced by mechanistic measurements of the stem's specific hydraulic conductivity. Variance on the vertical axis was also observed, indicating an accelerated flow towards the upper parts of the tree and raising a hypothesis concerning dehydrating mechanisms of the date palm tree. Finally, the sensors indicated reduction in flow almost immediately after irrigation of field-grown trees was withheld, at a time when no climatic or phenological conditions could have led to reduction in transpiration.

Drainage water reuse: biological, physical, and technological considerations for system management

Previous reviews of drainage water reuse have discussed principles of water reuse and disposal; provided examples of reuse practices; offered reuse criteria for salinity, for trace elements, and for bacteria; discussed mitigation of dissolved trace elements in reuse strategies; and summarized the California experience with a focus on discussion of salinity, sodicity, B, Mo, and Se issues. This review emphasizes recent literature contributing to understanding physical and biological constraints to drainage water reuse. The potential for drip irrigation and, particularly, low-flow/high-frequency systems to enhance the use of drainage water while minimizing the deleterious effects on yield and on water and soil resources is examined using the numeric HYRDUS-2d model. Additionally, an analytical model is used to illustrate physical and biological limitations to drainage water management that result from the self-regulating nature of the soil-plant-water system. The models suggest that crop, soil, irrigation frequency, and delivery systems might be manipulated to reduce the quantity of drainage water, but they also suggest that the nature of the system may seriously constrain the amount of reduction that might be achieved.