Root responses to neighbouring plants in common bean are mediated by nutrient concentration rather than self/non-self recognition

Root phenotypes for improved nitrogen capture

Background

Suboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer.

Scope

Intraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes.

Conclusions

Substantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.

Changes in the Amount and Distribution of Soil Nutrients and Neighbours Have Differential Impacts on Root and Shoot Architecture in Wheat (Triticum aestivum)

Plants exhibit differential behaviours through changes in biomass development and distribution in response to environmental cues, which may impact crops uniquely. We conducted a mesocosm experiment in pots to determine the root and shoot behavioural responses of wheat, T. aestivum. Plants were grown in homogeneous or heterogeneous and heavily or lightly fertilized soil, and alone or with a neighbour of the same or different genetic identity (cultivars: CDC Titanium, Carberry, Glenn, Go Early, and Lillian). Contrary to predictions, wheat did not alter relative reproductive effort in the presence of neighbours, more nutrients, or homogenous soil. Above and below ground, the plants' tendency to use potentially shared space exhibited high levels of plasticity. Above ground, they generally avoided shared, central aerial space when grown with neighbours. Unexpectedly, nutrient amount and distribution also impacted shoots; plants that grew in fertile or homogenous environments increased shared space use. Below ground, plants grown with related neighbours indicated no difference in neighbour avoidance. Those in homogenous soil produced relatively even roots, and plants in heterogeneous treatments produced more roots in nutrient patches. Additionally, less fertile soil resulted in pot-level decreases in root foraging precision. Our findings illustrate that explicit coordination between above- and belowground biomass in wheat may not exist.

In silico evidence for the utility of parsimonious root phenotypes for improved vegetative growth and carbon sequestration under drought

Drought is a primary constraint to crop yields and climate change is expected to increase the frequency and severity of drought stress in the future. It has been hypothesized that crops can be made more resistant to drought and better able to sequester atmospheric carbon in the soil by selecting appropriate root phenotypes. We introduce OpenSimRoot_v2, an upgraded version of the functional-structural plant/soil model OpenSimRoot, and use it to test the utility of a maize root phenotype with fewer and steeper axial roots, reduced lateral root branching density, and more aerenchyma formation (i.e. the 'Steep, Cheap, and Deep' (SCD) ideotype) and different combinations of underlying SCD root phene states under rainfed and drought conditions in three distinct maize growing pedoclimatic environments in the USA, Nigeria, and Mexico. In all environments where plants are subjected to drought stress the SCD ideotype as well as several intermediate phenotypes lead to greater shoot biomass after 42 days. As an additional advantage, the amount of carbon deposited below 50 cm in the soil is twice as great for the SCD phenotype as for the reference phenotype in 5 out of 6 simulated environments. We conclude that crop growth and deep soil carbon deposition can be improved by breeding maize plants with fewer axial roots, reduced lateral root branching density, and more aerenchyma formation.

No neighbour-induced increase in root growth of soybean and sunflower in mesh-divider experiments after controlling for nutrient concentration and soil volume

Root competition is a key factor determining plant performance, community structure and ecosystem productivity. To adequately estimate the extent of root proliferation of plants in response to neighbours independently of nutrient availability, one should use a set-up that can simultaneously control for both nutrient concentration and soil volume at plant individual level. With a mesh-divider design, which was suggested as a promising solution for this problem, we conducted two intraspecific root competition experiments: one with soybean (Glycine max) and the other with sunflower (Helianthus annuus). We found no response of root growth or biomass allocation to intraspecific neighbours, i.e. an 'ideal free distribution' (IFD) norm, in soybean; and even a reduced growth as a negative response in sunflower. These responses are all inconsistent with the hypothesis that plants should produce more roots even at the expense of reduced fitness in response to neighbours, i.e. root over-proliferation. Our results suggest that neighbour-induced root over-proliferation is not a ubiquitous feature in plants. By integrating the findings with results from other soybean studies, we conclude that for some species this response could be a genotype-dependent response as a result of natural or artificial selection, or a context-dependent response so that plants can switch from root over-proliferation to IFD depending on the environment of competition. We also critically discuss whether the mesh-divider design is an ideal solution for root competition experiments.

Friends, neighbours and enemies: an overview of the communal and social biology of plants

Plants were traditionally seen as rather passive actors in their environment, interacting with each other only in so far as they competed for the same resources. In the last 30 years, this view has been spectacularly overturned, with a wealth of evidence showing that plants actively detect and respond to their neighbours. Moreover, there is evidence that these responses depend on the identity of the neighbour, and that plants may cooperate with their kin, displaying social behaviour as complex as that observed in animals. These plant-plant interactions play a vital role in shaping natural ecosystems, and are also very important in determining agricultural productivity. However, in terms of mechanistic understanding, we have only just begun to scratch the surface, and many aspects of plant-plant interactions remain poorly understood. In this review, we aim to provide an overview of the field of plant-plant interactions, covering the communal interactions of plants with their neighbours as well as the social behaviour of plants towards their kin, and the consequences of these interactions. We particularly focus on the mechanisms that underpin neighbour detection and response, highlighting both progress and gaps in our understanding of these fascinating but previously overlooked interactions.

Wheat plants sense substrate volume and root density to proactively modulate shoot growth

Plants must carefully coordinate their growth and development with respect to prevailing environmental conditions. To do this, plants can use a range of nutritional and non-nutritional information that allows them to proactively modulate their growth to avoid resource limitations. As is well-known to gardeners and horticulturists alike, substrate volume strongly influences plant growth, and maybe a key source of non-nutritional information for plants. However, the mechanisms by which these substrate volume effects occur remain unclear. Here, we show that wheat plants proactively modulate their shoot growth with respect to substrate volume, independent of nutrient availability. We show that these effects occur in two phases; in the first phase, the dilution of a mobile 'substrate volume-sensing signal' (SVS) allows plants to match their shoot (but not root) growth to the total size of the substrate, irrespective of how much of this they can occupy with their roots. In the second phase, the dilution of a less mobile 'root density-sensing signal' (RDS) allows plants to match root growth to actual rooting volume, with corresponding effects on shoot growth. We show that the effects of soil volume and plant density are largely interchangeable and that plants may use both SVS and RDS to detect their neighbours and to integrate growth responses to both volume and the presence of neighbours. Our work demonstrates the remarkable ability of plants to make proactive decisions about their growth, and has implications for mitigating the effects of dense sowing of crops in agricultural practice.

Competition at the soybean V6 stage affects root morphology and biochemical composition

The experiment was conducted in the 2016/17 crop season in a greenhouse at Passo Fundo University, Brazil. We hypothesised that the morphological characteristics and biochemical and anatomical composition of soybean roots and shoots, when competing with weeds during different growth periods, are negatively affected, so current concepts of competition between plants should also consider changes in plant roots. The soybean cultivar P 95R51 and horseweed (Conyza bonariensis) were used. The treatments consisted of the presence or absence of weeds during different coexistence periods of soybean with horseweed. The periods were V0-V3, V0-V6, V0-R2, V3-R6, V6-R6 and R2-R6, where V0 was the date of soybean sowing and V3, V6, R2 and R6 were phenological stages of the crop. Two fresh roots were used to examine morphological traits. Four roots were used for quantification of dry matter and secondary metabolites. Root length was reduced by 21%, 14% and 20% when competing with a weed in the V0-V3, V0-V6 and R2-R6 coexistence periods, respectively. Total phenol content in the V0-V6 and V0-R2 periods was reduced when plants were in competition with weeds; a similar trend was found for flavonoids in the V0-V6 period. Soybean-horseweed competition from crop emergence to the V6 stage, in general, affects shoot and root morphological traits and the biochemical composition of the soybean roots. The presence of horseweed at the V3, V6 and R2 stages does not negatively alter the traits evaluated. Root anatomical composition is not modified during all coexistence periods with horseweed.

The Key Role of Variety and Method of Sowing Selection in Pea Roots’ Parameters Development under Sustainable Practice

The selection of varieties is extremely important for decreasing fertilizer consumption. However, little attention is devoted to assessing the effectiveness of row spacing in tandem with types of varieties of pea on root development in the context of limited nutrition. As essential knowledge in this area is lacking, a study was conducted with two objectives using an ordinal regression model. (i): To determine whether qualitative variables (cultivar, fertilization, and row spacing) or quantitative variables (root parameters) affect the root dry mass density, and (ii): To assess the variation in root architecture of two pea cultivars (fodder vs. edible type) grown under different P supply levels (0, 45, and 90 kg P2O5) and row spacing (narrow—15 cm—and wide—30 cm). The ordinal regression model showed that row spacing and cultivar type are meaningful predictors of root dry mass density (RDMD). The root dry mass density increased at wider row spacing in the fodder pea cultivar. As root surface area density (RSAD) and SRL-specific root length (SRL) most accurately describe root mass, it was concluded that the cultivar type and row spacing are crucial factors for increasing root plasticity, which can improve soil utilization.

Co-optimization of axial root phenotypes for nitrogen and phosphorus acquisition in common bean

Background and Aims

Root architecture is a primary determinant of soil resource acquisition. We hypothesized that root architectural phenes will display both positive and negative interactions with each other for soil resource capture because of competition for internal resources and functional trade-offs in soil exploration.

Methods

We employed the functional-structural plant model SimRoot to explore how interactions among architectural phenes in common bean determine the acquisition of phosphate and nitrate, two key soil resources contrasting in mobility. We evaluated the utility of basal root whorl number (BRWN) when basal root growth angle, hypocotyl-borne roots and lateral root branching density (LRBD) were varied, under varying availability of phosphate and nitrate.

Key Results

Three basal root whorls were optimal in most phenotypes. This optimum shifted towards greater values when LRBD decreased and to smaller numbers when LRBD increased. The maximum biomass accumulated for a given BRWN phenotype in a given limiting nutrient scenario depended upon root growth angle. Under phosphorus stress shallow phenotypes grew best, whereas under nitrate stress fanned phenotypes grew best. The effect of increased hypocotyl-borne roots depended upon BRWN as well as the limiting nutrient. Greater production of axial roots due to BRWN or hypocotyl-borne roots reduced rooting depth, leading to reduced biomass under nitrate-limiting conditions. Increased BRWN as well as greater LRBD increased root carbon consumption, resulting in reduced shoot biomass.

Conclusions

We conclude that the utility of a root architectural phenotype is determined by whether the constituent phenes are synergistic or antagonistic. Competition for internal resources and trade-offs for external resources result in multiple phenotypes being optimal under a given nutrient regime. We also find that no single phenotype is optimal across contrasting environments. These results have implications for understanding plant evolution and also for the breeding of more stress-tolerant crop phenotypes.

Bluejoint Is an Effective Bio-Barrier Species on Mine Covers

Covers with capillary barrier effects (CCBE) are used to prevent acid mine drainage from mine wastes in the short term. However, the long-term efficiency of CCBE can be affected by trees because their roots may reduce the ability of covers to limit oxygen migration and also physically damage the CCBE. Two plant species that are native to boreal Canada, bluejoint () and sheep laurel (, were selected as bio-barrier species (BBS) to test if they reduce the growth and root system architecture of trees established on mine covers (balsam poplar [], willow [ spp], and black spruce []). The experiment was established in 2008 on a mine tailings impoundment located in northwestern Quebec, Canada. Trees were measured for height, diameter, and biomass. Coarse roots were excavated from the plots and digitized in three dimensions. Compared with the control (no BBS), bluejoint strongly decreased tree height and diameter increment, biomass, maximum root depth and radial extension, total root length and volume, and number of second- and third-order tree roots. Height and diameter increment, biomass, maximum root depth and volume, and number of second-order roots of balsam poplar increased with sheep laurel compared with control conditions, whereas willow showed no response to this treatment. Most characteristics of black spruce (except root-to-shoot ratio and number of second-order roots) improved in the presence of sheep laurel compared with the control. Thus, bluejoint was a more efficient BBS than sheep laurel. Bio-barriers comprised of bluejoint can be used as a countermeasure for controlling tree invasion of CCBE.

Arguments for and against self and non-self root recognition in plants

Root-root interaction research gained more and more attention over the past few years. Roots are pivotal for plant survival because they ensure uptake of water and nutrients. Therefore, detection of adjacent roots might lead to competitive advantages. Several lines of experimental evidence suggest that roots have ways to discriminate non-related roots, kin, and-importantly-that they can sense self/non-self roots to avoid intra-plant competition. In this mini-review, the existence of self/non-self recognition in plant roots will be discussed and the current knowledge on the mechanisms that could be involved will be summarized. Although the process of identity recognition is still not completely understood, interesting data are available and emerging new technologies will certainly aid to better understand this research field that can have an important biological, ecological, and agricultural impact.

Integration of root phenes for soil resource acquisition

Suboptimal availability of water and nutrients is a primary limitation to plant growth in terrestrial ecosystems. The acquisition of soil resources by plant roots is therefore an important component of plant fitness and agricultural productivity. Plant root systems comprise a set of phenes, or traits, that interact. Phenes are the units of the plant phenotype, and phene states represent the variation in form and function a particular phene may take. Root phenes can be classified as affecting resource acquisition or utilization, influencing acquisition through exploration or exploitation, and in being metabolically influential or neutral. These classifications determine how one phene will interact with another phene, whether through foraging mechanisms or metabolic economics. Phenes that influence one another through foraging mechanisms are likely to operate within a phene module, a group of interacting phenes, that may be co-selected. Examples of root phene interactions discussed are: (1) root hair length × root hair density, (2) lateral branching × root cortical aerenchyma (RCA), (3) adventitious root number × adventitious root respiration and basal root growth angle (BRGA), (4) nodal root number × RCA, and (5) BRGA × root hair length and density. Progress in the study of phenes and phene interactions will be facilitated by employing simulation modeling and near-isophenic lines that allow the study of specific phenes and phene combinations within a common phenotypic background. Developing a robust understanding of the phenome at the organismal level will require new lines of inquiry into how phenotypic integration influences plant function in diverse environments. A better understanding of how root phenes interact to affect soil resource acquisition will be an important tool in the breeding of crops with superior stress tolerance and reduced dependence on intensive use of inputs.

Belowground neighbor perception in Arabidopsis thaliana studied by transcriptome analysis: roots of Hieracium pilosella cause biotic stress

Root-root interactions are much more sophisticated than previously thought, yet the mechanisms of belowground neighbor perception remain largely obscure. Genome-wide transcriptome analyses allow detailed insight into plant reactions to environmental cues. A root interaction trial was set up to explore both morphological and whole genome transcriptional responses in roots of Arabidopsis thaliana in the presence or absence of an inferior competitor, Hieracium pilosella. Neighbor perception was indicated by Arabidopsis roots predominantly growing away from the neighbor (segregation), while solitary plants placed more roots toward the middle of the pot. Total biomass remained unaffected. Database comparisons in transcriptome analysis revealed considerable similarity between Arabidopsis root reactions to neighbors and reactions to pathogens. Detailed analyses of the functional category "biotic stress" using MapMan tools found the sub-category "pathogenesis-related proteins" highly significantly induced. A comparison to a study on intraspecific competition brought forward a core of genes consistently involved in reactions to neighbor roots. We conclude that beyond resource depletion roots perceive neighboring roots or their associated microorganisms by a relatively uniform mechanism that involves the strong induction of pathogenesis-related proteins. In an ecological context the findings reveal that belowground neighbor detection may occur independently of resource depletion, allowing for a time advantage for the root to prepare for potential interactions.

Effects of nutrient heterogeneity and competition on root architecture of spruce seedlings: implications for an essential feature of root foraging

BACKGROUND

We have limited understanding of root foraging responses when plants were simultaneously exposed to nutrient heterogeneity and competition, and our goal was to determine whether and how plants integrate information about nutrients and neighbors in root foraging processes.

METHODOLOGY/PRINCIPAL FINDINGS

The experiment was conducted in split-containers, wherein half of the roots of spruce (Picea asperata) seedlings were subjected to intraspecific root competition (the vegetated half), while the other half experienced no competition (the non-vegetated half). Experimental treatments included fertilization in the vegetated half (FV), the non-vegetated half (FNV), and both compartments (F), as well as no fertilization (NF). The root architecture indicators consisted of the number of root tips over the root surface (RTRS), the length percentage of diameter-based fine root subclasses to total fine root (SRLP), and the length percentage of each root order to total fine root (ROLP). The target plants used novel root foraging behaviors under different combinations of neighboring plant and localized fertilization. In addition, the significant increase in the RTRS of 0-0.2 mm fine roots after fertilization of the vegetated half alone and its significant decrease in fertilizer was applied throughout the plant clearly showed that plant root foraging behavior was regulated by local responses coupled with systemic control mechanisms.

CONCLUSIONS/SIGNIFICANCE

We measured the root foraging ability for woody plants by means of root architecture indicators constructed by the roots possessing essential nutrient uptake ability (i.e., the first three root orders), and provided new evidence that plants integrate multiple forms of environmental information, such as nutrient status and neighboring competitors, in a non-additive manner during the root foraging process. The interplay between the responses of individual root modules (repetitive root units) to localized environmental signals and the systemic control of these responses may well account for the non-additive features of the root foraging process.

Genotypic recognition and spatial responses by rice roots

Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent to which the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.

Complementarity in root architecture for nutrient uptake in ancient maize/bean and maize/bean/squash polycultures

BACKGROUND AND AIMS

During their domestication, maize, bean and squash evolved in polycultures grown by small-scale farmers in the Americas. Polycultures often overyield on low-fertility soils, which are a primary production constraint in low-input agriculture. We hypothesized that root architectural differences among these crops causes niche complementarity and thereby greater nutrient acquisition than corresponding monocultures.

METHODS

A functional-structural plant model, SimRoot, was used to simulate the first 40 d of growth of these crops in monoculture and polyculture and to determine the effects of root competition on nutrient uptake and biomass production of each plant on low-nitrogen, -phosphorus and -potassium soils.

KEY RESULTS

Squash, the earliest domesticated crop, was most sensitive to low soil fertility, while bean, the most recently domesticated crop, was least sensitive to low soil fertility. Nitrate uptake and biomass production were up to 7 % greater in the polycultures than in the monocultures, but only when root architecture was taken into account. Enhanced nitrogen capture in polycultures was independent of nitrogen fixation by bean. Root competition had negligible effects on phosphorus or potassium uptake or biomass production.

CONCLUSIONS

We conclude that spatial niche differentiation caused by differences in root architecture allows polycultures to overyield when plants are competing for mobile soil resources. However, direct competition for immobile resources might be negligible in agricultural systems. Interspecies root spacing may also be too large to allow maize to benefit from root exudates of bean or squash. Above-ground competition for light, however, may have strong feedbacks on root foraging for immobile nutrients, which may increase cereal growth more than it will decrease the growth of the other crops. We note that the order of domestication of crops correlates with increasing nutrient efficiency, rather than production potential.

Why not beans?

Changes in climate and urbanisation rapidly affecting human livelihood are particularly threatening to developing nations in tropical regions. Food production crises have focused the global development agenda on agricultural research, a proven approach for increasing crop yield. A few crops benefit from private investment, but improvement of most crops will rely on limited public funding that must be deployed strategically, pushing forward both proven approaches and new ideas. Why not invest in beans? More than 300 million people rely on this crop, considered to be the most important grain legume for human consumption. Yet the yield of beans, especially in poor regions or marginal soils, is reduced by abiotic stresses such as phosphorus deficiency, aluminum toxicity and especially drought. Is it possible to assemble resources, including genetic diversity in beans, breeding expertise, genomic information and tools, and physiological insight to generate rapid progress in developing new lines of beans more tolerant to abiotic stress? A workshop to address this question was held in November 2010 at the International Center for Tropical Agriculture (CIAT) in Colombia. The resulting 'call to action' is presented in this issue which also includes research papers focused on tolerance of beans to stress.