Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade‐offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions.     

Microbial enhancement of crop resource use efficiency

Naturally occurring soil microbes may be used as inoculants to maintain crop yields despite decreased resource (water and nutrient) inputs. Plant symbiotic relationships with mycorrhizal fungi alter root aquaporin gene expression and greatly increase the surface area over which plant root systems take up water and nutrients. Soil bacteria on the root surface alter root phytohormone status thereby increasing growth, and can make nutrients more available to the plant. Combining different classes of soil organism within one inoculant can potentially take advantage of multiple plant growth-promoting mechanisms, but biological interactions between inoculant constituents and the plant are difficult to predict. Whether the yield benefits of such inocula allow modified nutrient and water management continues to challenge crop biotechnologists.     

Root Development and Nutrient Uptake

Root system formation proceeds in close coordination with shoot growth. Accordingly, root growth and its functions are regulated tightly by the shoot through materials cycling between roots and shoots. A plant root system consists of different kinds of roots that differ in morphology and functions. The spatial configuration and distribution of these roots determine root system architecture in the soil, which in turn primarily regulates the acquisition of soil resources like nutrients and water. Morphological and physiological properties of each root and the concomitant tissues further affect nutrient uptake and transport, while the root traits that are related to such acquisition also depend on the kinds of nutrients and their mobility in the soil. In addition, mechanisms involved in the uptake and transport of mineral nutrients recently have been elucidated at the molecular level. A number of genes for acquisition and transport of various mineral nutrients have been identified in model plant systems such as Arabidopsis thaliana, and rice, and in other plant species. An integration of studies on nutrient behavior in soils and the morphological and physiological functions of root systems will further elucidate the mechanism of plant nutrient uptake and transport by roots, and offer a real possibility of genetically improving crop productivity in problem soils.

     

Root development and configuration in intensively managed radiata pine plantations

Summary In south-east Australia, where radiata pine (Pinus radiata D. Don) is grown on sandy soils low in nutrients and short of water, early establishment, and rapid growth to canopy closure lead to increased productivity. At this stage demands for nutrients and water are high, and trees respond vigorously to silvicultural inputs.For several months after transplanting in winter roots are confined within a narrow planting wedge, low temperature restricts new root growth and slows recovery from water stress in plants. From spring, depending upon the configuration and vigour of the roots transplanted, lateral roots extend radially throughout the soil.Although there were small decreases in concentration of roots radially from the stems of very young trees, such spatial differences disappeared between ages 2 and 3, so that rooting density was independent of distance from the stem. The pattern of vertical distribution of lateral roots was not influenced by age and 80–90% of the lateral roots were within the top 30 cm soil. Roots developed rapidly as the trees grew towards canopy closure, but in general the rooting densities of these pines are among the lowest reported for plants. In rapidly growing trees approaching canopy closure, the secondary thickening of the lateral roots was sufficient to double the weight of roots without altering root length.Knowledge about root growth and root configuration during the early phase of plantation development will assist management decisions where intensive silviculture is practiced, and hence ensure the most efficient use of nutrients and water.     

Not a load of rubbish: simulated field trials in large‐scale containers

Assessment of yield performance under fluctuating environmental conditions is a major aim of crop breeders. Unfortunately, results from controlled‐environment evaluations of complex agronomic traits rarely translate to field performance. A major cause is that crops grown over their complete lifecycle in a greenhouse or growth chamber are generally constricted in their root growth, which influences their response to important abiotic constraints like water or nutrient availability. To overcome this poor transferability, we established a plant growth system comprising large refuse containers (120 L ‘wheelie bins’) that allow detailed phenotyping of small field‐crop populations under semi‐controlled growth conditions. Diverse winter oilseed rape cultivars were grown at field densities throughout the crop lifecycle, in different experiments over 2 years, to compare seed yields from individual containers to plot yields from multi‐environment field trials. We found that we were able to predict yields in the field with high accuracy from container‐grown plants. The container system proved suitable for detailed studies of stress response physiology and performance in pre‐breeding populations. Investment in automated large‐container systems may help breeders improve field transferability of greenhouse experiments, enabling screening of pre‐breeding materials for abiotic stress response traits with a positive influence on yield.     

Traits and selection strategies to improve root systems and water uptake in water-limited wheat crops

Wheat yields globally will depend increasingly on good management to conserve rainfall and new varieties that use water efficiently for grain production. Here we propose an approach for developing new varieties to make better use of deep stored water. We focus on water-limited wheat production in the summer-dominant rainfall regions of India and Australia, but the approach is generally applicable to other environments and root-based constraints. Use of stored deep water is valuable because it is more predictable than variable in-season rainfall and can be measured prior to sowing. Further, this moisture is converted into grain with twice the efficiently of in-season rainfall since it is taken up later in crop growth during the grain-filling period when the roots reach deeper layers. We propose that wheat varieties with a deeper root system, a redistribution of branch root density from the surface to depth, and with greater radial hydraulic conductivity at depth would have higher yields in rainfed systems where crops rely on deep water for grain fill. Developing selection systems for mature root system traits is challenging as there are limited high-throughput phenotyping methods for roots in the field, and there is a risk that traits selected in the lab on young plants will not translate into mature root system traits in the field. We give an example of a breeding programme that combines laboratory and field phenotyping with proof of concept evaluation of the trait at the beginning of the selection programme. This would greatly enhance confidence in a high-throughput laboratory or field screen, and avoid investment in screens without yield value. This approach requires careful selection of field sites and years that allow expression of deep roots and increased yield. It also requires careful selection and crossing of germplasm to allow comparison of root expression among genotypes that are similar for other traits, especially flowering time and disease and toxicity resistances. Such a programme with field and laboratory evaluation at the outset will speed up delivery of varieties with improved root systems for higher yield.     

Root-targeted biotechnology to mediate hormonal signalling and improve crop stress tolerance

Since plant root systems capture both water and nutrients essential for the formation of crop yield, there has been renewed biotechnological focus on root system improvement. Although water and nutrient uptake can be facilitated by membrane proteins known as aquaporins and nutrient transporters, respectively, there is a little evidence that root-localised overexpression of these proteins improves plant growth or stress tolerance. Recent work suggests that the major classes of phytohormones are involved not only in regulating aquaporin and nutrient transporter expression and activity, but also in sculpting root system architecture. Root-specific expression of plant and bacterial phytohormone-related genes, using either root-specific or root-inducible promoters or grafting non-transformed plants onto constitutive hormone producing rootstocks, has examined the role of root hormone production in mediating crop stress tolerance. Root-specific traits such as root system architecture, sensing of edaphic stress and root-to-shoot communication can be exploited to improve resource (water and nutrients) capture and plant development under resource-limited conditions. Thus, root system engineering provides new opportunities to maintain sustainable crop production under changing environmental conditions.     

New insights to lateral rooting: Differential responses to heterogeneous nitrogen availability among maize root types

Historical domestication and the "Green revolution" have both contributed to the evolution of modern, high-performance crops. Together with increased irrigation and application of chemical fertilizers, these efforts have generated sufficient food for the growing global population. Root architecture, and in particular root branching, plays an important role in the acquisition of water and nutrients, plant performance, and crop yield. Better understanding of root growth and responses to the belowground environment could contribute to overcoming the challenges faced by agriculture today. Manipulating the abilities of crop root systems to explore and exploit the soil environment could enable plants to make the most of soil resources, increase stress tolerance and improve grain yields, while simultaneously reducing environmental degradation. In this article it is noted that the control of root branching, and the responses of root architecture to nitrate availability, differ between root types and between plant species. Since the control of root branching depends upon both plant species and root type, further work is urgently required to determine the appropriate genes to manipulate to improve resource acquisition by specific crops.     

间套作提高农田水分利用效率的节水机理

综合国内外多学科的研究成果,从地表水向土壤水的转化效率、农田水分的有效性、植物冠层结构、灌溉用水量和作物产量等方面,论述了间套作提高农田水分利用效率的节水机理.结果表明:间套作能够促进植物根系对农田水分的充分利用,有利于增加根层土壤的贮水量;间套作一方面减小棵间蒸发、抑制无效蒸腾,另一方面优化作物系统的源-库关系,创造出有利于植物生长发育的小气候,为资源在时间和空间上的集约利用和高产打好基础,在不增加农田灌溉水的同时大幅度提高单位面积产量,促进作物水分利用效率明显提高.     

A comparison of soil core sampling and minirhizotrons to quantify root development of field-grown potatoes

Root growth of potato (Solanum tuberosum L.) is sensitive to soil conditions. A reduced root system size can result in reduced uptake of water and/or nutrients, leading to impaired crop growth. To understand the mechanisms by which soil conditions affect crop growth, study of temporal and spatial development of roots is required.In field experiments, effects of soil temperature, soil compaction and potato cyst nematodes (Globodera pallida) on root growth of potato cultivars were studied using two methods: core sampling and vertically oriented minirhizotrons.Minirhizotrons showed relatively more roots in deeper soil layers than core sampling, probably because of preferential root growth along the tube. Spatial distribution of roots should therefore be analysed by core sampling.To eliminate differences in spatial distribution, total root systems as measured by both methods were compared. Nematodes, cultivars and time did not affect the relationship between both methods. Soil compaction, however, affected it because of a strong response of root length in bulk soil and small differences in root number against the minirhizotron, suggesting that soil coring has to be used to study effects of different bulk densities.With both methods, sequential measurements of roots give the net effect of root growth and decay. Data on root turnover can only be obtained with minirhizotrons by comparing video recordings of different dates. Other information obtained with minirhizotrons is the average orientation of roots. Moreover, the minirhizotron method has the advantage of demanding less labour.     

Impact of climate change on crop nutrient and water use efficiencies

Implicit in discussions of plant nutrition and climate change is the assumption that we know what to do relative to nutrient management here and now but that these strategies might not apply in a changed climate. We review existing knowledge on interactive influences of atmospheric carbon dioxide concentration, temperature and soil moisture on plant growth, development and yield as well as on plant water use efficiency (WUE) and physiological and uptake efficiencies of soil-immobile nutrients. Elevated atmospheric CO₂ will increase leaf and canopy photosynthesis, especially in C3 plants, with minor changes in dark respiration. Additional CO₂ will increase biomass without marked alteration in dry matter partitioning, reduce transpiration of most plants and improve WUE. However, spatiotemporal variation in these attributes will impact agronomic performance and crop water use in a site-specific manner. Nutrient acquisition is closely associated with overall biomass and strongly influenced by root surface area. When climate change alters soil factors to restrict root growth, nutrient stress will occur. Plant size may also change but nutrient concentration will remain relatively unchanged; therefore, nutrient removal will scale with growth. Changes in regional nutrient requirements will be most remarkable where we alter cropping systems to accommodate shifts in ecozones or alter farming systems to capture new uses from existing systems. For regions and systems where we currently do an adequate job managing nutrients, we stand a good chance of continued optimization under a changed climate. If we can and should do better, climate change will not help us.     

植物根系质外体屏障研究进展

根是植物吸收水分和矿质营养以维持生命活动的重要器官。根系的构型和超微结构具有物种特异性, 对水分和矿质营养的吸收有不同程度的影响。其中, 内、外皮层的木栓层和凯氏带是2种重要的质外体屏障, 可非定向地阻断水分和离子运输, 在植物生长发育及响应逆境胁迫中发挥重要作用。尽管如此, 植物根系质外体屏障的结构、化学组成、生理功能、生物合成及其调控仅在模式植物拟南芥(Arabidopsis thaliana)中被广泛研究。近年来, 关于作物大麦(Hordeum vulgare)、水稻(Oryza sativa)以及部分牧草的根系质外体屏障研究报道逐渐增多。该文系统比较了拟南芥、大麦、水稻以及部分牧草根系质外体屏障的异同, 提出今后的研究方向, 以期为深入探索禾本科作物和牧草根系质外体屏障在生长发育和逆境适应中的作用奠定理论基础, 并为作物和牧草育种工作提供新思路。     

Mechanism of plant growth promotion by rhizobacteria

Plant growth results from interaction of roots and shoots with the environment. The environment for roots is the soil or planting medium which provide structural support as well as water and nutrients to the plant. Roots also support the growth and functions of a complex of microorganisms that can have a profound effect on the growth anti survival of plants. These microorganisms constitute rhizosphere microflora and can be categorized as deleterious, beneficial, or neutral with respect to root/plant health. Beneficial interactions between roots and microbes do occur in rhizosphere and can be enhanced. Increased plant growth and crop yield can be obtained upon inoculating seeds or roots with certain specific root-colonizing bacteria- 'plant growth promoting rhizobacteria'. In this review, we discuss the mechanisms by which plant growth promoting rhizobacteria may stimulate plant growth.     

Intercropping Competition between Apple Trees and Crops in Agroforestry Systems on the Loess Plateau of China

Agroforestry has been widely practiced in the Loess Plateau region of China because of its prominent effects in reducing soil and water losses, improving land-use efficiency and increasing economic returns. However, the agroforestry practices may lead to competition between crops and trees for underground soil moisture and nutrients, and the trees on the canopy layer may also lead to shortage of light for crops. In order to minimize interspecific competition and maximize the benefits of tree-based intercropping systems, we studied photosynthesis, growth and yield of soybean (Glycine max L. Merr.) and peanut (Arachis hypogaea L.) by measuring photosynthetically active radiation, net photosynthetic rate, soil moisture and soil nutrients in a plantation of apple (Malus pumila M.) at a spacing of 4 m × 5 m on the Loess Plateau of China. The results showed that for both intercropping systems in the study region, soil moisture was the primary factor affecting the crop yields followed by light. Deficiency of the soil nutrients also had a significant impact on crop yields. Compared with soybean, peanut was more suitable for intercropping with apple trees to obtain economic benefits in the region. We concluded that apple-soybean and apple-peanut intercropping systems can be practical and beneficial in the region. However, the distance between crops and tree rows should be adjusted to minimize interspecies competition. Agronomic measures such as regular canopy pruning, root barriers, additional irrigation and fertilization also should be applied in the intercropping systems.     

根区交替控制灌溉条件下玉米根系吸水规律

为了阐明根区交替控制灌溉(CRDAI)条件下玉米根系吸水规律,通过田间试验,在沟灌垄植模式下采用根区交替控制灌溉研究玉米根区不同点位(沟位、坡位和垄位)的根长密度(RLD)及根系吸水动态。研究表明,根区土壤水分的干湿交替引起玉米RLD的空间动态变化,在垄位两侧不对称分布,并存在层间差异;土壤水分和RLD是根区交替控制灌溉下根系吸水速率的主要限制因素。在同一土层,根系吸水贡献率以垄位最大,沟位最低;玉米营养生长阶段,10—30 cm土层的根系吸水速率最大;玉米生殖生长阶段,20—70 cm为根系吸水速率最大的土层,根系吸水贡献率为43.21%—55.48%。研究阐明了交替控制灌溉下根系吸水与土壤水分、RLD间相互作用的动态规律,对控制灌溉下水分调控机理研究具有理论意义。     

Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, phosphorus, sulfate and trace elements that plants acquire from the soil. If we want to develop sustainable approaches to producing high crop yield, we need to better understand how the root develops, takes up a wide spectrum of nutrients, and interacts with symbiotic and pathogenic organisms. To accomplish these goals, we need to be able to explore roots in microscopic detail over time periods ranging from minutes to days.We developed the RootChip, a polydimethylsiloxane (PDMS)- based microfluidic device, which allows us to grow and image roots from Arabidopsis seedlings while avoiding any physical stress to roots during preparation for imaging¹ (Figure 1). The device contains a bifurcated channel structure featuring micromechanical valves to guide the fluid flow from solution inlets to each of the eight observation chambers². This perfusion system allows the root microenvironment to be controlled and modified with precision and speed. The volume of the chambers is approximately 400 nl, thus requiring only minimal amounts of test solution.Here we provide a detailed protocol for studying root biology on the RootChip using imaging-based approaches with real time resolution. Roots can be analyzed over several days using time lapse microscopy. Roots can be perfused with nutrient solutions or inhibitors, and up to eight seedlings can be analyzed in parallel. This system has the potential for a wide range of applications, including analysis of root growth in the presence or absence of chemicals, fluorescence-based analysis of gene expression, and the analysis of biosensors, e.g. FRET nanosensors³.     

Contribution of adventitious vs initial roots to growth and physiology of black spruce seedlings

Black spruce (Picea mariana [Mill.] BSP) is a boreal tree species characterized by the formation of an adventitious root system. Unlike initial roots from seed germination, adventitious roots gradually appear above the root collar, until they constitute most of mature black spruce root system. Little is known about the physiological role they play and their influence on tree growth relative to initial roots. We hypothesized that adventitious roots present an advantage over initial roots in acquiring water and nutrients. To test this hypothesis, the absorptive capacities of the two root systems were explored in a controlled environment during one growing season. Black spruce seedlings were placed in a double‐pot system allowing irrigation (25 and 100% water container capacity) and fertilization (with or without fertilizer) inputs independent to initial and adventitious roots. After 14 weeks, growth parameters (height, diameter, biomass), physiology (net photosynthetic rate, stomatal conductance, shoot water potential) and nutrient content (N, P, K, Ca and Mg foliar content) were compared. Most measured parameters showed no difference for the same treatment on adventitious or initial roots, except for root biomass. Indeed, fertilized black spruce seedlings invested heavily in adventitious root production, twice as much as initial roots. This was also the case when adventitious roots alone were irrigated, while seedlings with adventitious roots subjected to low irrigation produced initial root biomass equivalent to that of adventitious roots. We conclude that black spruce seedlings perform equally well through adventitious and initial roots, but if resources are abundant, they strongly promote development of adventitious roots.     

Effects of fluquinconazole and silthiofam, applied as seed treatments to single or consecutive crops of wheat, on take-all epidemic development and grain yields

Seed treatments containing fluquinconazole, silthiofam or a standard fungicide mixture with no activity against take‐all were compared in all combinations of sequences in successive second and third winter wheat crops in five field experiments and second to fourth crops in a sixth experiment. Compared with the standard treatment, silthiofam decreased take‐all more effectively than fluquinconazole when crops were sampled at tillering. In samples taken in summer, during grain filling, silthiofam often decreased the incidence of take‐all (percentage of plants with root symptoms) more than fluquinconazole, but fluquinconazole more effectively decreased the incidence of severe take‐all (percentage of plants with more than 75% of their root systems blackened). It is suggested that these differences are a consequence of more effective control of primary infection of roots by silthiofam and of secondary, root‐to‐root, infection by fluquinconazole. Silthiofam usually increased yield more than did fluquinconazole, perhaps as a consequence of better early protection during tiller and/or spikelet formation. Treatment with either of the fungicides affected epidemic development in the treated crop and in crops grown subsequently. In particular, decreased take‐all had the effect of delaying the year‐to‐year epidemic, so that nontreatment of a subsequent crop resulted in an upsurge in disease. Treatment with either take‐all fungicide of a crop grown after a treated crop was relatively effective if the epidemic in the comparable nontreated crop sequence was continuing to increase. It was, however, detrimental if the disease was approaching its peak in the first treated crop, particularly if a treated (fourth wheat) crop was being compared with a similar crop in a nontreated sequence in which take‐all decline had developed. These results provide a basis for recommendations for the use of seed treatment fungicides in sequences of wheat crops.     

Fine roots of <Emphasis Type="Italic">Prosopis flexuosa</Emphasis> trees in the field. Plant and soil variables that control their growth and depth distribution

Fine root growth in natural vegetation is difficult to predict due to its regulation by soil and plant factors. Field studies in arid ecosystems show a variety of root responses to soil resources and to plant aboveground phenology that sometimes differ from root responses predicted by controlled experiments. There is a pressing need to cover a greater diversity of plant species and ecological scenarios in field studies. In this paper, we have studied fine roots of Prosopis flexuosa trees living with or without access to phreatic water in an inter-dune valley and a dune flank, respectively, in the Central Monte Desert, Argentina. We have described fine root growth over time and at different depths by rhizotron observations and soil core auger samples in relation to soil water and nutrients, tree crown phenology, plant water and nutrient status. We have found that surface soil moisture from rainfall is the variable that best predicts seasonal topsoil fine root growth. Access to groundwater advanced leaf sprouting with respect to rainfall, but did not advance root growth that stayed linked to rainfall in valley and dune flank trees. Trees without access to phreatic water produced deeper and thicker or denser roots, which is consistent with the poor soil resource content of dunes. Variations in rainfall dynamics due to global climate change may have a particular impact on fine roots and ecosystem processes such as biogeochemistry and carbon budget in dune flank trees as well as in valley trees.     

Mechanisms of waterlogging tolerance in wheat – a review of root and shoot physiology

We review the detrimental effects of waterlogging on physiology, growth and yield of wheat. We highlight traits contributing to waterlogging tolerance and genetic diversity in wheat. Death of seminal roots and restriction of adventitious root length due to O₂ deficiency result in low root:shoot ratio. Genotypes differ in seminal root anoxia tolerance, but mechanisms remain to be established; ethanol production rates do not explain anoxia tolerance. Root tip survival is short‐term, and thereafter, seminal root re‐growth upon re‐aeration is limited. Genotypes differ in adventitious root numbers and in aerenchyma formation within these roots, resulting in varying waterlogging tolerances. Root extension is restricted by capacity for internal O₂ movement to the apex. Sub‐optimal O₂ restricts root N uptake and translocation to the shoots, with N deficiency causing reduced shoot growth and grain yield. Although photosynthesis declines, sugars typically accumulate in shoots of waterlogged plants. Mn or Fe toxicity might occur in shoots of wheat on strongly acidic soils, but probably not more widely. Future breeding for waterlogging tolerance should focus on root internal aeration and better N‐use efficiency; exploiting the genetic diversity in wheat for these and other traits should enable improvement of waterlogging tolerance.