Root foraging elicits niche complementarity-dependent yield advantage in the ancient 'three sisters' (maize/bean/squash) polyculture

Biocultural diversity and crop improvement

Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.

Competition and co-association, but not phosphorous availability, shape the benefits of phosphate-solubilizing root bacteria for maize (Zea mays)

Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilizing rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. We used maize-associated rhizobacteria with varying phosphate solubilization ability in experiments in soil, sterilized soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated the intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: the beneficial effects of one Serratia isolate were only detectable when plants were inoculated with a single strain and the beneficial effects of a competition-sensitive Rhizobium was only detectable in sterilized soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilization may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.

Large root cortical cells and reduced cortical cell files improve growth under suboptimal nitrogen in silico

Suboptimal nitrogen availability is a primary constraint to plant growth. We used OpenSimRoot, a functional-structural plant/soil model, to test the hypothesis that larger root cortical cell size (CCS), reduced cortical cell file number (CCFN), and their interactions with root cortical aerenchyma (RCA) and lateral root branching density (LRBD) are useful adaptations to suboptimal soil nitrogen availability in maize (Zea mays). Reduced CCFN increased shoot dry weight over 80%. Reduced respiration, reduced nitrogen content, and reduced root diameter accounted for 23%, 20%, and 33% of increased shoot biomass, respectively. Large CCS increased shoot biomass by 24% compared with small CCS. When simulated independently, reduced respiration and reduced nutrient content increased the shoot biomass by 14% and 3%, respectively. However, increased root diameter resulting from large CCS decreased shoot biomass by 4% due to an increase in root metabolic cost. Under moderate N stress, integrated phenotypes with reduced CCFN, large CCS, and high RCA improved shoot biomass in silt loam and loamy sand soils. In contrast, integrated phenotypes composed of reduced CCFN, large CCS and reduced lateral root branching density had the greatest growth in silt loam, while phenotypes with reduced CCFN, large CCS and high LRBD were the best performers in loamy sands. Our results support the hypothesis that larger CCS, reduced CCFN, and their interactions with RCA and LRBD could increase nitrogen acquisition by reducing root respiration and root nutrient demand. Phene synergisms may exist between CCS, CCFN, and LRBD. CCS and CCFN merit consideration for breeding cereal crops with improved nitrogen acquisition, which is critical for global food security.

Complementary effects of phosphorus supply and planting density on maize growth and phosphorus use efficiency

Phosphorus (P) supply and planting density regulate plant growth by altering root morphological traits and soil P dynamics. However, the compensatory effects of P supply and planting density on maize (Zea mays L.) growth and P use efficiency remain unknown. In this study, we conducted pot experiments of approximately 60 days to determine the effect of P supply, i.e., no P (CK), single superphosphate (SSP), and monoammonium phosphate (MAP), and different planting densities (low: two plants per pot; and high: four plants per pot) on maize growth. A similar shoot biomass accumulation was observed at high planting density under CK treatment (91.5 g plot^-1) and low planting density under SSP treatment (94.3 g plot^-1), with similar trends in P uptake, root morphological traits, and arbuscular mycorrhizal colonization. There was no significant difference in shoot biomass between high planting density under SSP (107.3 g plot^-1) and low planting density under MAP (105.2 g plot^-1); the corresponding P uptake, root growth, and P fraction in the soil showed the same trend. These results suggest that improved P supply could compensate for the limitations of low planting density by regulating the interaction between root morphological traits and soil P dynamics. Furthermore, under the same P supply, the limitations of low planting density could be compensated for by substituting MAP for SSP. Our results indicate that maize growth and P use efficiency could be improved by harnessing the compensatory effects of P supply and planting density to alter root plasticity and soil P dynamics.

Grasses procure key soil nutrients for clovers

Rhizobial nitrogen fixation in legumes provides spillover benefits to neighbouring plants such as pasture grasses. Generally, it is understood to be unidirectional between plant functional groups, providing a benefit from legumes to grasses. We question whether bidirectional complementarity also exists in terms of exploiting the wider soil nutrient pool. We test this hypothesis using soil cores with their component vegetation assemblages sampled from a hill country pasture in South Island, New Zealand. The soil was deficient in key essential elements: P, S, B, Mo and Ni. Facilitation from grasses to clovers was evident; legume-grass mixtures procured more nutrients from the soil than when either species was growing alone. When grasses and clover grow together in unfertilized grassland, more nitrogen is procured by the plant community, and other limiting plant nutrients in the soil are better exploited. Coexistence with grasses is favourable to clovers in terms of soil biogeochemistry.

Reuniting the Three Sisters: collaborative science with Native growers to improve soil and community health

Before Euro-American settlement, many Native American nations intercropped maize (Zea mays), beans (Phaseolus vulgaris), and squash (Cucurbita pepo) in what is colloquially called the "Three Sisters." Here we review the historic importance and consequences of rejuvenation of Three Sisters intercropping (3SI), outline a framework to engage Native growers in community science with positive feedbacks to university research, and present preliminary findings from ethnography and a randomized, replicated 3SI experiment. We developed mutually beneficial collaborative research agendas with four Midwestern US Native American nations. Ethnographic data highlighted a culturally based respect for 3SI as living beings, the importance it holds for all cultural facets of these Native nations, and the critical impact the practice has on environmental sustainability. One concern expressed by Native growers during ethnographic research was improving soil health-part of the rationale for establishing the 3SI agronomic experiment. To address this, we collaboratively designed a 3SI experiment. After 1 year, 3SI increased short-term soil respiration by 24%, decreased salt-extractable nitrate by 54%, had no effect on soil microbial biomass (but increased its carbon-to-nitrogen ratio by 32%) compared to the average of monoculture crops. The overarching purpose of this collaborative project is to develop a deeper understanding of 3SI, its cultural importance to Native communities, and how reinvigorating the practice-and intercropping in general-can make agroecosystems more sustainable for people and the environment.

Plant biodiversity promotes sustainable agriculture directly and via belowground effects

While the positive relationship between plant biodiversity and ecosystem functioning (BEF) is well established, the extent to which this is mediated via belowground microbial processes is poorly understood. Growing evidence suggests that plant community structure influences soil microbial diversity, which in turn promotes functions desired for sustainable agriculture. Here, we outline the 'plant-directed' and soil microbe-mediated mechanisms expected to promote positive BEF. We identify how this knowledge can be utilized in plant diversification schemes to maximize ecosystem functioning in agroecosystems, which are typically species poor and sensitive to biotic and abiotic stressors. In the face of resource overexploitation and global change, bridging the gaps between biodiversity science and agricultural practices is crucial to meet food security in the Anthropocene.

Shift in beneficial interactions during crop evolution

Plant domestication can be viewed as a form of co‐evolved interspecific mutualism between humans and crops for the benefit of the two partners. Here, we ask how this plant–human mutualism has, in turn, impacted beneficial interactions within crop species, between crop species, and between crops and their associated microbial partners. We focus on beneficial interactions resulting from three main mechanisms that can be promoted by manipulating genetic diversity in agrosystems: niche partitioning, facilitation, and kin selection. We show that a combination of factors has impacted either directly or indirectly plant–plant interactions during domestication and breeding, with a trend toward reduced benefits arising from niche partitioning and facilitation. Such factors include marked decrease of molecular and functional diversity of crops and other organisms present in the agroecosystem, mass selection, and increased use of chemical inputs. For example, the latter has likely contributed to the relaxation of selection pressures on nutrient‐mobilizing traits such as those associated to root exudation and plant nutrient exchanges via microbial partners. In contrast, we show that beneficial interactions arising from kin selection have likely been promoted since the advent of modern breeding. We highlight several issues that need further investigation such as whether crop phenotypic plasticity has evolved and could trigger beneficial interactions in crops, and whether human‐mediated selection has impacted cooperation via kin recognition. Finally, we discuss how plant breeding and agricultural practices can help promoting beneficial interactions within and between species in the context of agroecology where the mobilization of diversity and complexity of crop interactions is viewed as a keystone of agroecosystem sustainability.

Whole-plant phenotypic engineering: moving beyond ratios for multi-objective optimization of nutrient use efficiency

Nutrient use efficiency (NUE) is typically measured as the ratio of yield to soil nutrient availability but ignores contributions of underlying plant traits. Relevant plant traits can be grouped as root acquisition efficiency, shoot radiation use efficiency, and plant metabolic efficiency. The intentional integration of these traits will lead to synergistic improvements of NUE. Recent progress in trait-focused research includes phenotyping root nutrient uptake rates and respiration, engineering reduced photorespiration, and identification of nutrient assimilation pathways. Traits need to be conceptualized in agricultural systems contexts to improve synchrony of plant demand and soil supply of nutrients, including consideration of crop mixtures. Use of simulation modeling and multi-objective optimization will allow accelerating NUE gains beyond selection for a single ratio.

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.

Transcriptomic Responses of Rhizobium phaseoli to Root Exudates Reflect Its Capacity to Colonize Maize and Common Bean in an Intercropping System

Corn and common bean have been cultivated together in Mesoamerica for thousands of years in an intercropping system called "milpa," where the roots are intermingled, favoring the exchange of their microbiota, including symbionts such as rhizobia. In this work, we studied the genomic expression of Rhizobium phaseoli Ch24-10 (by RNA-seq) after a 2-h treatment in the presence of root exudates of maize and bean grown in monoculture and milpa system under hydroponic conditions. In bean exudates, rhizobial genes for nodulation and degradation of aromatic compounds were induced; while in maize, a response of genes for degradation of mucilage and ferulic acid was observed, as well as those for the transport of sugars, dicarboxylic acids and iron. Ch24-10 transcriptomes in milpa resembled those of beans because they both showed high expression of nodulation genes; some genes that were expressed in corn exudates were also induced by the intercropping system, especially those for the degradation of ferulic acid and pectin. Beans grown in milpa system formed nitrogen-fixing nodules similar to monocultured beans; therefore, the presence of maize did not interfere with Rhizobium-bean symbiosis. Genes for the metabolism of sugars and amino acids, flavonoid and phytoalexin tolerance, and a T3SS were expressed in both monocultures and milpa system, which reveals the adaptive capacity of rhizobia to colonize both legumes and cereals. Transcriptional fusions of the putA gene, which participates in proline metabolism, and of a gene encoding a polygalacturonase were used to validate their participation in plant-microbe interactions. We determined the enzymatic activity of carbonic anhydrase whose gene was also overexpressed in response to root exudates.

Facilitation and plant phenotypic evolution

While antagonistic interactions between plants have been a major topic of eco-evolutionary research, little evidence exists on the evolution of positive plant interactions (i.e., plant facilitation). Here, we first summarize the existing empirical evidence on the role of facilitation as a selection pressure on plants. Then, we develop a theoretical eco-evolutionary framework based on fitness-trait functions and interaction effectiveness that provides predictions for how facilitation-related traits may evolve. As evolution may act at levels beyond the individual (such as groups or species), we discuss the subject of the units of evolutionary selection through facilitation. Finally, we use the proposed formal evolutionary framework for facilitation to identify areas of future research based on the knowledge gaps detected.

Maize intercropping in the milpa system. Diversity, extent and importance for nutritional security in the Western Highlands of Guatemala

We present an assessment of the extent, diversity, and nutritional contribution of the milpa through a quantitative analysis of data from a survey conducted in 989 small scale farm households in the Western Highlands of Guatemala (WHG). The milpa is a traditional agricultural system in which maize is intercropped with other species, such as common beans, faba beans, squashes or potatoes. Our study shows that more than two-thirds of the 1,205 plots recorded were under the milpa system, with a great diversity of crop combinations. As shown with the 357 plots for which specific yields were available, milpa systems present higher total productivity than monocropped maize, expressed as total energy yield of the harvested crops in the respective system, and were also better at providing the recommended daily allowances of fourteen essential nutrients, based on a Potential Nutrient Adequacy (PNA) indicator. Maize-bean-potato, maize-potato, and maize-bean-faba intercrops had the highest PNAs, and monocropped maize, the lowest. These results support the implementation of milpa systems tailored to different agro-ecologies in order to improve nutrition in the WHG and a variety of similar regions.

A Comparative Analysis of Quantitative Metrics of Root Architecture

High throughput phenotyping is important to bridge the gap between genotype and phenotype. The methods used to describe the phenotype therefore should be robust to measurement errors, relatively stable over time, and most importantly, provide a reliable estimate of elementary phenotypic components. In this study, we use functional-structural modeling to evaluate quantitative phenotypic metrics used to describe root architecture to determine how they fit these criteria. Our results show that phenes such as root number, root diameter, and lateral root branching density are stable, reliable measures and are not affected by imaging method or plane. Metrics aggregating multiple phenes such as total length, total volume, convex hull volume, and bushiness index estimate different subsets of the constituent phenes; they however do not provide any information regarding the underlying phene states. Estimates of phene aggregates are not unique representations of underlying constituent phenes: multiple phenotypes having phenes in different states could have similar aggregate metrics. Root growth angle is an important phene which is susceptible to measurement errors when 2D projection methods are used. Metrics that aggregate phenes which are complex functions of root growth angle and other phenes are also subject to measurement errors when 2D projection methods are used. These results support the hypothesis that estimates of phenes are more useful than metrics aggregating multiple phenes for phenotyping root architecture. We propose that these concepts are broadly applicable in phenotyping and phenomics.

Aquaporins are main contributors to root hydraulic conductivity in pearl millet [Pennisetum glaucum (L) R. Br.]

Pearl millet is a key cereal for food security in arid and semi-arid regions but its yield is increasingly threatened by water stress. Physiological mechanisms relating to conservation of soil water or increased water use efficiency can alleviate that stress. Aquaporins (AQP) are water channels that mediate root water transport, thereby influencing plant hydraulics, transpiration and soil water conservation. However, AQP remain largely uncharacterized in pearl millet. Here, we studied AQP function in root water transport in two pearl millet lines contrasting for water use efficiency (WUE). We observed that these lines also contrasted for root hydraulic conductivity (Lpr) and AQP contribution to Lpr. The line with lower WUE showed significantly higher AQP contribution to Lpr. To investigate AQP isoforms contributing to Lpr, we developed genomic approaches to first identify the entire AQP family in pearl millet and secondly, characterize the plasma membrane intrinsic proteins (PIP) gene expression profile. We identified and annotated 33 AQP genes in pearl millet, among which ten encoded PIP isoforms. PgPIP1-3 and PgPIP1-4 were significantly more expressed in the line showing lower WUE, higher Lpr and higher AQP contribution to Lpr. Overall, our study suggests that the PIP1 AQP family are the main regulators of Lpr in pearl millet and may possibly be associated with mechanisms associated to whole plant water use. This study paves the way for further investigations on AQP functions in pearl millet hydraulics and adaptation to environmental stresses.

Variable Light Condition Improves Root Distribution Shallowness and P Uptake of Soybean in Maize/Soybean Relay Strip Intercropping System

In this study, soybean root distribution in an inter-cropping system was influenced by various environmental and biotic cues. However, it is still unknown how root development and distribution in inter-cropping responds to aboveground light conditions. Herein, soybeans were inter- and monocropped with P (phosphorus) treatments of 0 and 20 kg P ha yr⁻¹ (P0 and P20, respectively) in field experiment over 4 years. In 2019, a pot experiment was conducted as the supplement to the field experiment. Shade from sowing to V5 (Five trifoliolates unroll) and light (SL) was used to imitate the light condition of soybeans in a relay trip inter-cropping system, while light then shade from V5 to maturity (LS) was used to imitate the light condition of soybeans when monocropped. Compared to monocropping, P uptake and root distribution in the upper 0–15 cm soil layer increased when inter-cropped. Inter-cropped soybeans suffered serious shade by maize during a common-growth period, which resulted in the inhibition of primary root growth and a modified auxin synthesis center and response. During the solo-existing period, plant photosynthetic capacity and sucrose accumulation increased under ameliorated light in SL (shade-light). Increased light during the reproductive stage significantly decreased leaf P concentration in SL under both P-sufficient and P-deficient conditions. Transcripts of a P starvation response gene (GmPHR25) in leaves and genes (GmEXPB2) involved in root growth were upregulated by ameliorated light during the reproductive stage. Furthermore, during the reproductive stage, more light interception increased the auxin concentration and expression of GmYUCCA14 (encoding the auxin synthesis) and GmTIR1C (auxin receptor) in roots. Across the field and pot experiments, increased lateral root growth and shallower root distribution were associated with inhibited primary root growth during the seedling stage and ameliorated light conditions in the reproductive stage. Consequently, this improved topsoil foraging and P uptake of inter-cropped soybeans. It is suggested that the various light conditions (shade-light) mediating leaf P status and sucrose transport can regulate auxin synthesis and respond to root formation and distribution.

Multiscale computational models can guide experimentation and targeted measurements for crop improvement

Computational models of plants have identified gaps in our understanding of biological systems, and have revealed ways to optimize cellular processes or organ-level architecture to increase productivity. Thus, computational models are learning tools that help direct experimentation and measurements. Models are simplifications of complex systems, and often simulate specific processes at single scales (e.g. temporal, spatial, organizational, etc.). Consequently, single-scale models are unable to capture the critical cross-scale interactions that result in emergent properties of the system. In this perspective article, we contend that to accurately predict how a plant will respond in an untested environment, it is necessary to integrate mathematical models across biological scales. Computationally mimicking the flow of biological information from the genome to the phenome is an important step in discovering new experimental strategies to improve crops. A key challenge is to connect models across biological, temporal and computational (e.g. CPU versus GPU) scales, and then to visualize and interpret integrated model outputs. We address this challenge by describing the efforts of the international Crops in silico consortium.

Multiple Integrated Root Phenotypes Are Associated with Improved Drought Tolerance

To test the hypothesis that multiple integrated root phenotypes would co-optimize drought tolerance, we phenotyped the root anatomy and architecture of 400 mature maize (Zea mays) genotypes under well-watered and water-stressed conditions in the field. We found substantial variation in all 23 root phenes measured. A phenotypic bulked segregant analysis revealed that bulks representing the best and worst performers in the field displayed distinct root phenotypes. In contrast to the worst bulk, the root phenotype of the best bulk under drought consisted of greater cortical aerenchyma formation, more numerous and narrower metaxylem vessels, and thicker nodal roots. Partition-against-medians clustering revealed several clusters of unique root phenotypes related to plant performance under water stress. Clusters associated with improved drought tolerance consisted of phene states that likely enable greater soil exploration by reallocating internal resources to greater root construction (increased aerenchyma content, larger cortical cells, fewer cortical cell files), restrict uptake of water to conserve soil moisture (reduced hydraulic conductance, narrow metaxylem vessels), and improve penetrability of hard, dry soils (thick roots with a larger proportion of stele, and smaller distal cortical cells). We propose that the most drought-tolerant-integrated phenotypes merit consideration as breeding ideotypes.

Should Root Plasticity Be a Crop Breeding Target?

Root phenotypic plasticity has been proposed as a target for the development of more productive crops in variable environments. However, the plasticity of root anatomical and architectural responses to environmental cues is highly complex, and the consequences of these responses for plant fitness are poorly understood. We propose that root phenotypic plasticity may be beneficial in natural or low-input systems in which the availability of soil resources is spatiotemporally dynamic. Crop ancestors and landraces were selected with multiple stresses, competition, significant root loss and heterogenous resource distribution which favored plasticity in response to resource availability. However, in high-input agroecosystems, the value of phenotypic plasticity is unclear, since human management has removed many of these constraints to root function. Further research is needed to understand the fitness landscape of plastic responses including understanding the value of plasticity in different environments, environmental signals that induce plastic responses, and the genetic architecture of plasticity before it is widely adopted in breeding programs. Phenotypic plasticity has many potential ecological, and physiological benefits, but its costs and adaptive value in high-input agricultural systems is poorly understood and merits further research.

Food Diversity and Indigenous Food Systems to Combat Diet-Linked Chronic Diseases

Improving food and nutritional diversity based on the diversity of traditional plant-based foods is an important dietary strategy to address the challenges of rapidly emerging diet- and lifestyle-linked noncommunicable chronic diseases (NCDs) of indigenous communities worldwide. Restoration of native ecosystems, revival of traditional food crop cultivation, and revival of traditional knowledge of food preparation, processing, and preservation are important steps to build dietary support strategies against an NCD epidemic of contemporary indigenous communities. Recent studies have indicated that many traditional plant-based foods of Native Americans provide a rich source of human health-relevant bioactive compounds with diverse health benefits. Based on this rationale of health benefits of traditional plant-based foods, the objective of this review is to present a state-of-the-art comprehensive framework for ecologically and culturally relevant sustainable strategies to restore and integrate the traditional plant food diversity of Native Americans to address the NCD challenges of indigenous and wider nonindigenous communities worldwide.

Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.)

BACKGROUND

Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation.

METHODS

An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored.

RESULTS

Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance.

CONCLUSIONS

The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.

Ameliorated light conditions increase the P uptake capability of soybean in a relay-strip intercropping system by altering root morphology and physiology in the areas with low solar radiation

Belowground interspecific facilitation and complementarity contribute to the phosphorus (P) uptake advantages in the cereal-legume intercropping system. However, the root morphological and physiological plasticity and, subsequently, the P uptake capability response to light conditions in intercropping systems remain unclear. Soybean was grown under two levels of P application rates in sole and intercropping systems (maize/soybean relay strip intercropping) from 2016 to 2018 in Renshou, southwest of China. As a supplement to the field experiment, soybean was also grown in L-S (simulating the light conditions of sole cropping in the field: light first and then shading) and S-L (simulating the light conditions of intercropping in the field: shading first and then light) light conditions with two levels of P application in 2018 in a pot experiment. After maize harvest (approximately 3/4 of the soybean growth period), light capture in intercropping was higher than sole (ameliorated light conditions in intercropping system), which resulted in an advantage of P uptake in intercropped soybean. Both low P supply and more light capture increased the total root length and root APase activity. The genes GmEXPB2 (which is associated with root growth) and GmACP1 (which is associated with exudation of APase) were highly expressed in plants that captured more light under both P-sufficient and P-deficient conditions. Additionally, more light capture increased the production of lateral roots and the proportion of in the upper 15 cm soil layer roots at the reproductive stage in the field. Across the field and pot experiments, increased root morphological and physiological plasticity were associated with lower P concentrations in the leaves and greater allocation of photosynthates to roots as sucrose. It is suggested that ameliorated light conditions can regulate soybean root growth plasticity and, consequently, P uptake in maize/soybean relay strip intercropping systems, especially in the areas with low solar radiation.

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.

Rightsizing root phenotypes for drought resistance

I propose that reduced root development would be advantageous for drought resistance in high-input agroecosystems. Selection regimes for crop ancestors and landraces include multiple stresses, intense competition, and variable resource distribution, which favored prolific root production, developmental plasticity in response to resource availability, and maintenance of unspecialized root tissues. High-input agroecosystems have removed many of these constraints to root function. Therefore, root phenotypes that focus on water capture at the expense of ancestral adaptations would be better suited to high-input agroecosystems. Parsimonious architectural phenotypes include fewer axial roots, reduced density of lateral roots, reduced growth responsiveness to local resource availability, and greater loss of roots that do not contribute to water capture. Parsimonious anatomical phenotypes include a reduced number of cortical cell files, greater loss of cortical parenchyma to aerenchyma and senescence, and larger cortical cell size. Parsimonious root phenotypes may be less useful in low-input agroecosystems, which are characterized by multiple challenges and trade-offs for root function in addition to water capture. Analysis of the fitness landscape of root phenotypes is a complex challenge that will be aided by the development of robust functional-structural models capable of simulating the dynamics of root-soil interactions.

Phosphorus acquisition by citrate- and phytase-exuding Nicotiana tabacum plant mixtures depends on soil phosphorus availability and root intermingling

Citrate and phytase root exudates contribute to improved phosphorus (P) acquisition efficiency in Nicotiana tabacum (tobacco) when both exudates are produced in a P deficient soil. To test the importance of root intermingling in the interaction of citrate and phytase exudates, Nicotiana tabacum plant-lines with constitutive expression of heterologous citrate (Cit) or fungal phytase (Phy) exudation traits were grown under two root treatments (roots separated or intermingled) and in two soils with contrasting soil P availability. Complementarity of plant mixtures varying in citrate efflux rate and mobility of the expressed phytase in soil was determined based on plant biomass and P accumulation. Soil P composition was evaluated using solution 31 P NMR spectroscopy. In the soil with limited available P, positive complementarity occurred in Cit+Phy mixtures with roots intermingled. Root separation eliminated positive interactions in mixtures expressing the less mobile phytase (Aspergillus niger PhyA) whereas positive complementarity persisted in mixtures that expressed the more mobile phytase (Peniophora lycii PhyA). Soils from Cit+Phy mixtures contained less inorganic P and more organic P compared to monocultures. Exudate-specific strategies for the acquisition of soil P were most effective in P-limited soil and depended on citrate efflux rate and the relative mobility of the expressed phytase in soil. Plant growth and soil P utilization in plant systems with complementary exudation strategies are expected to be greatest where exudates persist in soil and are expressed synchronously in space and time.

OpenSimRoot: widening the scope and application of root architectural models

OpenSimRoot is an open-source, functional-structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate the following: resource costs of developmental and anatomical traits; trait synergisms; and (interspecies) root competition. OpenSimRoot can model three-dimensional images from magnetic resonance imaging (MRI) and X-ray computed tomography (CT) of roots in soil. New modules include: soil water-dependent water uptake and xylem flow; tiller formation; evapotranspiration; simultaneous simulation of mobile solutes; mesh refinement; and root growth plasticity. OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and to gain a mechanistic understanding at system scales.

How Plant Root Exudates Shape the Nitrogen Cycle

Although the global nitrogen (N) cycle is largely driven by soil microbes, plant root exudates can profoundly modify soil microbial communities and influence their N transformations. A detailed understanding is now beginning to emerge regarding the control that root exudates exert over two major soil N processes - nitrification and N2 fixation. We discuss recent breakthroughs in this area, including the identification of root exudates as nitrification inhibitors and as signaling compounds facilitating N-acquisition symbioses. We indicate gaps in current knowledge, including questions of how root exudates affect newly discovered microbial players and N-cycle components. A better understanding of these processes is urgent given the widespread inefficiencies in agricultural N use and their links to N pollution and climate change.

Root Cortical Senescence Improves Growth under Suboptimal Availability of N, P, and K

Root cortical senescence (RCS) in Triticeae reduces nutrient uptake, nutrient content, respiration, and radial hydraulic conductance of root tissue. We used the functional-structural model SimRoot to evaluate the functional implications of RCS in barley (Hordeum vulgare) under suboptimal nitrate, phosphorus, and potassium availability. The utility of RCS was evaluated using sensitivity analyses in contrasting nutrient regimes. At flowering (80 d), RCS increased simulated plant growth by up to 52%, 73%, and 41% in nitrate-, phosphorus-, and potassium-limiting conditions, respectively. Plants with RCS had reduced nutrient requirement of root tissue for optimal plant growth, reduced total cumulative cortical respiration, and increased total carbon reserves. Nutrient reallocation during RCS had a greater effect on simulated plant growth than reduced respiration or nutrient uptake. Under low nutrient availability, RCS had greater benefit in plants with fewer tillers. RCS had greater benefit in phenotypes with fewer lateral roots at low nitrate availability, but the opposite was true in low phosphorus or potassium availability. Additionally, RCS was quantified in field-grown barley in different nitrogen regimes. Field and virtual soil coring simulation results demonstrated that living cortical volume per root length (an indicator of RCS) decreased with depth in younger plants, while roots of older plants had very little living cortical volume per root length. RCS may be an adaptive trait for nutrient acquisition by reallocating nutrients from senescing tissue and secondarily by reducing root respiration. These simulated results suggest that RCS merits investigation as a breeding target for enhanced soil resource acquisition and edaphic stress tolerance.

Response-based selection of barley cultivars and legume species for complementarity: Root morphology and exudation in relation to nutrient source

Phosphorus (P) and nitrogen (N) use efficiency may be improved through increased biodiversity in agroecosystems. Phenotypic variation in plants' response to nutrient deficiency may influence positive complementarity in intercropping systems. A multicomponent screening approach was used to assess the influence of P supply and N source on the phenotypic plasticity of nutrient foraging traits in barley (H. vulgare L.) and legume species. Root morphology and exudation were determined in six plant nutrient treatments. A clear divergence in the response of barley and legumes to the nutrient treatments was observed. Root morphology varied most among legumes, whereas exudate citrate and phytase activity were most variable in barley. Changes in root morphology were minimized in plants provided with ammonium in comparison to nitrate but increased under P deficiency. Exudate phytase activity and pH varied with legume species, whereas citrate efflux, specific root length, and root diameter lengths were more variable among barley cultivars. Three legume species and four barley cultivars were identified as the most responsive to P deficiency and the most contrasting of the cultivars and species tested. Phenotypic response to nutrient availability may be a promising approach for the selection of plant combinations for minimal input cropping systems.

Impact of axial root growth angles on nitrogen acquisition in maize depends on environmental conditions

BACKGROUNDS AND AIMS

Crops with reduced requirement for nitrogen (N) fertilizer would have substantial benefits in developed nations, while improving food security in developing nations. This study employs the functional structural plant model SimRoot to test the hypothesis that variation in the growth angles of axial roots of maize (Zea mays L.) is an important determinant of N capture.

METHODS

Six phenotypes contrasting in axial root growth angles were modelled for 42 d at seven soil nitrate levels from 10 to 250 kg ha(-1) in a sand and a silt loam, and five precipitation regimes ranging from 0·5× to 1·5× of an ambient rainfall pattern. Model results were compared with soil N measurements of field sites with silt loam and loamy sand textures.

KEY RESULTS

For optimal nitrate uptake, root foraging must coincide with nitrate availability in the soil profile, which depends on soil type and precipitation regime. The benefit of specific root architectures for efficient N uptake increases with decreasing soil N content, while the effect of soil type increases with increasing soil N level. Extreme root architectures are beneficial under extreme environmental conditions. Extremely shallow root systems perform well under reduced precipitation, but perform poorly with ambient and greater precipitation. Dimorphic phenotypes with normal or shallow seminal and very steep nodal roots performed well in all scenarios, and consistently outperformed the steep phenotypes. Nitrate uptake increased under reduced leaching conditions in the silt loam and with low precipitation.

CONCLUSIONS

Results support the hypothesis that root growth angles are primary determinants of N acquisition in maize. With decreasing soil N status, optimal angles resulted in 15-50 % greater N acquisition over 42 d. Optimal root phenotypes for N capture varied with soil and precipitation regimes, suggesting that genetic selection for root phenotypes could be tailored to specific environments.

Reduced crown root number improves water acquisition under water deficit stress in maize (Zea mays L.)

In this study we test the hypothesis that maize genotypes with reduced crown root number (CN) will have greater root depth and improved water acquisition from drying soil. Maize recombinant inbred lines with contrasting CN were evaluated under water stress in greenhouse mesocosms and field rainout shelters. CN varied from 25 to 62 among genotypes. Under water stress in the mesocosms, genotypes with low CN had 31% fewer crown roots, 30% deeper rooting, 56% greater stomatal conductance, 45% greater leaf CO2 assimilation, 61% net canopy CO2 assimilation, and 55% greater shoot biomass than genotypes with high CN at 35 days after planting. Under water stress in the field, genotypes with low CN had 21% fewer crown roots, 41% deeper rooting, 48% lighter stem water oxygen isotope enrichment (δ(18)O) signature signifying deeper water capture, 13% greater leaf relative water content, 33% greater shoot biomass at anthesis, and 57% greater yield than genotypes with high CN. These results support the hypothesis that low CN improves drought tolerance by increasing rooting depth and water acquisition from the subsoil.

Spatiotemporal variation of nitrate uptake kinetics within the maize (Zea mays L.) root system is associated with greater nitrate uptake and interactions with architectural phenes

Increasing maize nitrogen acquisition efficiency is a major goal for the 21st century. Nitrate uptake kinetics (NUK) are defined by I max and K m, which denote the maximum uptake rate and the affinity of transporters, respectively. Because NUK have been studied predominantly at the molecular and whole-root system levels, little is known about the functional importance of NUK variation within root systems. A novel method was created to measure NUK of root segments that demonstrated variation in NUK among root classes (seminal, lateral, crown, and brace). I max varied among root class, plant age, and nitrate deprivation combinations, but was most affected by plant age, which increased I max, and nitrate deprivation time, which decreased I max K m was greatest for crown roots. The functional-structural simulation SimRoot was used for sensitivity analysis of plant growth to root segment I max and K m, as well as to test interactions of I max with root system architectural phenes. Simulated plant growth was more sensitive to I max than K m, and reached an asymptote near the maximum I max observed in the empirical studies. Increasing the I max of lateral roots had the largest effect on shoot growth. Additive effects of I max and architectural phenes on nitrate uptake were observed. Empirically, only lateral root tips aged 20 d operated at the maximum I max, and simulations demonstrated that increasing all seminal and lateral classes to this maximum rate could increase plant growth by as much as 26%. Therefore, optimizing I max for all maize root classes merits attention as a promising breeding goal.

Crop acquisition of phosphorus, iron and zinc from soil in cereal/legume intercropping systems: a critical review

BACKGROUND

Phosphorus (P), iron (Fe) and zinc (Zn) are essential elements for plant growth and development, but their availability in soil is often limited. Intercropping contributes to increased P, Fe and Zn uptake and thereby increases yield and improves grain nutritional quality and ultimately human health. A better understanding of how intercropping leads to increased plant P, Fe and Zn availability will help to improve P-fertilizer-use efficiency and agronomic Fe and Zn biofortification.

SCOPE

This review synthesizes the literature on how intercropping of legumes with cereals increases acquisition of P, Fe and Zn from soil and recapitulates what is known about root-to-shoot nutrient translocation, plant-internal nutrient remobilization and allocation to grains.

CONCLUSIONS

Direct interspecific facilitation in intercropping involves below-ground processes in which cereals increase Fe and Zn bioavailability while companion legumes benefit. This has been demonstrated and verified using isotopic nutrient tracing and molecular analysis. The same methodological approaches and field studies should be used to explore direct interspecific P facilitation. Both niche complementarity and interspecific facilitation contribute to increased P acquisition in intercropping. Niche complementarity may also contribute to increased Fe and Zn acquisition, an aspect poorly understood. Interspecific mobilization and uptake facilitation of sparingly soluble P, Fe and Zn from soil, however, are not the only determinants of the concentrations of P, Fe and Zn in grains. Grain yield and nutrient translocation from roots to shoots further influence the concentrations of these nutrients in grains.

Root phenes that reduce the metabolic costs of soil exploration: opportunities for 21st century agriculture

Crop genotypes with reduced metabolic costs of soil exploration would have improved water and nutrient acquisition. Three strategies to achieve this goal are (1) production of the optimum number of axial roots; (2) greater biomass allocation to root classes that are less metabolically demanding; and (3) reduction of the respiratory requirement of root tissue. An example of strategy 1 is the case of reduced crown root number in maize, which is associated with greater rooting depth, N capture and yield in low N soil. An example of strategy 2 is the case of increased hypocotyl-borne rooting in bean, which decreases root cost and increases P capture from low P soil. Examples of strategy 3 are the cases of increased formation of root cortical aerenchyma, decreased cortical cell file number and increased cortical cell size in maize, which decrease specific root respiration, increase rooting depth and increase water capture and yield under water stress. Root cortical aerenchyma also increases N capture and yield under N stress. Root phenes that reduce the metabolic cost of soil exploration are promising, underexploited avenues to the climate-resilient, resource-efficient crops that are urgently needed in global agriculture.

Intensive field phenotyping of maize (Zea mays L.) root crowns identifies phenes and phene integration associated with plant growth and nitrogen acquisition

Root architecture is an important regulator of nitrogen (N) acquisition. Existing methods to phenotype the root architecture of cereal crops are generally limited to seedlings or to the outer roots of mature root crowns. The functional integration of root phenes is poorly understood. In this study, intensive phenotyping of mature root crowns of maize was conducted to discover phenes and phene modules related to N acquisition. Twelve maize genotypes were grown under replete and deficient N regimes in the field in South Africa and eight in the USA. An image was captured for every whorl of nodal roots in each crown. Custom software was used to measure root phenes including nodal occupancy, angle, diameter, distance to branching, lateral branching, and lateral length. Variation existed for all root phenes within maize root crowns. Size-related phenes such as diameter and number were substantially influenced by nodal position, while angle, lateral density, and distance to branching were not. Greater distance to branching, the length from the shoot to the emergence of laterals, is proposed to be a novel phene state that minimizes placing roots in already explored soil. Root phenes from both older and younger whorls of nodal roots contributed to variation in shoot mass and N uptake. The additive integration of root phenes accounted for 70% of the variation observed in shoot mass in low N soil. These results demonstrate the utility of intensive phenotyping of mature root systems, as well as the importance of phene integration in soil resource acquisition.

Evolution of US maize (Zea mays L.) root architectural and anatomical phenes over the past 100 years corresponds to increased tolerance of nitrogen stress

Increasing the nitrogen use efficiency of maize is an important goal for food security and agricultural sustainability. In the past 100 years, maize breeding has focused on yield and above-ground phenes. Over this period, maize cultivation has changed from low fertilizer inputs and low population densities to intensive fertilization and dense populations. The authors hypothesized that through indirect selection the maize root system has evolved phenotypes suited to more intense competition for nitrogen. Sixteen maize varieties representing commercially successful lines over the past century were planted at two nitrogen levels and three planting densities. Root systems of the most recent material were 7 º more shallow, had one less nodal root per whorl, had double the distance from nodal root emergence to lateral branching, and had 14% more metaxylem vessels, but total mextaxylem vessel area remained unchanged because individual metaxylem vessels had 12% less area. Plasticity was also observed in cortical phenes such as aerenchyma, which increased at greater population densities. Simulation modelling with SimRoot demonstrated that even these relatively small changes in root architecture and anatomy could increase maize shoot growth by 16% in a high density and high nitrogen environment. The authors concluded that evolution of maize root phenotypes over the past century is consistent with increasing nitrogen use efficiency. Introgression of more contrasting root phene states into the germplasm of elite maize and determination of the functional utility of these phene states in multiple agronomic conditions could contribute to future yield gains.