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Background Suboptimal water and nutrient availability are primary constraints in global agriculture. Root anatomy plays key roles in soil resource acquisition. In this article we summarize evidence that root anatomical phenotypes present opportunities for crop breeding. Scope Root anatomical phenotypes influence soil resource acquisition by regulating the metabolic cost of soil exploration, exploitation of the rhizosphere, the penetration of hard soil domains, the axial and radial transport of water, and interactions with soil biota including mycorrhizal fungi, pathogens, insects, and the rhizosphere microbiome. For each of these topics we provide examples of anatomical phenotypes which merit attention as selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of phenotypic plasticity, integrated phenotypes, C sequestration, in silico modeling, and novel methods to phenotype root anatomy including image analysis tools. Conclusions An array of anatomical phenes have substantial importance for the acquisition of water and nutrients. Substantial phenotypic variation exists in crop germplasm. New tools and methods are making it easier to phenotype root anatomy, determine its genetic control, and understand its utility for plant fitness. Root anatomical phenotypes are underutilized yet attractive breeding targets for the development of the efficient, resilient crops urgently needed in global agriculture.

Background Silicon (Si) is widely considered a non-essential but beneficial element for higher plants, providing broad protection against various environmental stresses (both biotic and abiotic), particularly in species that can readily absorb the element. Two plasma-membrane proteins are known to coordinate the radial transport of Si (in the form of Si(OH) 4 ) from soil to xylem within roots: the influx channel Lsi1 and the efflux transporter Lsi2. From a structural and mechanistic perspective, much more is known about Lsi1 (a member of the NIP-III subgroup of the Major Intrinsic Proteins) compared to Lsi2 (a putative Si(OH) 4 /H + antiporter, with some homology to bacterial anion transporters). Scope Here, we critically review the current state of understanding regarding the physiological role and molecular characteristics of Lsi2. We demonstrate that the structure–function relationship of Lsi2 is largely uncharted and that the standing transport model requires much better supportive evidence. We also provide (to our knowledge) the most current and extensive phylogenetic analysis of Lsi2 from all fully sequenced higher-plant genomes. We end by suggesting research directions and hypotheses to elucidate the properties of Lsi2. Conclusions Given that Lsi2 is proposed to mediate xylem Si loading and thus root-to-shoot translocation and biosilicification, it is imperative that the field of Si transport focus its efforts on a better understanding of this important topic. With this review, we aim to stimulate and advance research in the field of Si transport and thus better exploit Si to improve crop resilience and agricultural output.

Background Arsenic (As) and cadmium (Cd) are two toxic elements that have a relatively high risk of transfer from paddy soil to rice grain. Rice is a major dietary source of these two elements for populations consuming rice as a staple food. Reducing their accumulation in rice grain is important for food safety and human health. Scope We review recent progress in understanding the biogeochemical processes controlling As and Cd bioavailability in paddy soil, the mechanisms of their uptake, translocation and detoxification in rice plants, and strategies to reduce their accumulation in rice grain. Similarities and differences between the two elements are emphasized. Some knowledge gaps are also identified. Conclusions The concentrations of As and Cd in rice grain vary by three orders of magnitude, depending on the bioavailability of the two elements in soil, rice genotype and growing conditions. The redox potential in paddy soil has a profound but opposite effect on As and Cd bioavailability, whereas soil pH affects Cd bioavailability more than As bioavailability. A number of key genes involved in As and Cd uptake, translocation, sequestration, and detoxification in rice have been characterized. Allelic variations of several genes underlying the variations in Cd accumulation have been identified, but more remains to be elucidated, especially for As. Two types of strategies can be used to reduce As and Cd accumulation, reducing their bioavailability in soil or their uptake and translocation in rice. Reducing the accumulation of both As and Cd in rice simultaneously remains a great challenge.

Background Soil organic matter (SOM) supports multiple soil ecosystem functions, underpinned by processes such as C sequestration, N mineralization, aggregation, promotion of plant health and compound retention. We know little about the relationship between these functions and SOM quality. Scope We aimed to develop “eco-functionality” as a framework to address questions on the relation between SOM properties and soil ecosystem functions. Conclusions Paradigm shifts in SOM research have not led to metrics for eco-functionality beyond decomposability and C:N ratio. Recalcitrant OM is under-researched despite its essential role in aggregation and C sequestration, especially in C-saturated soils. Most soil functions are dependent on SOM decomposition and require labile compounds. We conclude that eco-functionality is context-dependent and needs to take time scales into account. We plea for attempts to link operationally defined SOM fractions to functions in order to make SOM research more applicable.

Background The potential benefits of intercropping are manifold and have been repeatedly demonstrated. Intercropping has the potential to create more productive and resilient agroecosystems, by improving land utilisation, yield and yield stability, soil quality, and pest, disease and weed suppression. Despite these potential benefits, significant gaps remain in the understanding of ecological mechanisms that govern the outcomes when crop species are grown together. A major part of plant-plant interactions takes place belowground and these are often overlooked. Scope This review synthesises current evidence for belowground plant-plant interactions of competition, niche differentiation and facilitation, with the aim of identifying root traits that influence the processes contributing to enhanced performance of intercrops compared with monocultures. We identify a suite of potentially complementary root traits for maximising the benefits of intercropping. These traits underpin improved soil exploration, more efficient resource use, and suppression of soil-borne pathogens and pests in intercrops. Conclusion This review brings together understanding of the mechanisms underpinning interactions between intercropped roots, and how root traits and their plasticity can promote positive outcomes. Root trait ‘ideotypes’ for intercropped partners are identified that could be selected for crop improvement. We highlight the importance of examining belowground interactions and consider both spatial and temporal distribution of roots and rhizosphere mechanisms that aid complementarity through niche differentiation and facilitation. Breeding of crop ideotypes with specific beneficial root traits, combined with considerations for optimal spatio-temporal arrangement and ratios of component crops, are essential next steps to promote the adoption of intercropping as a sustainable farming practice.

Background Phosphorus (P) fertilizer is usually applied in excess of plant requirement and accumulates in soils due to its strong adsorption, rapid precipitation and immobilisation into unavailable forms including organic moieties. As soils are complex and diverse chemical, biochemical and biological systems, strategies to access recalcitrant soil P are often inefficient, case specific and inconsistently applicable in different soils. Finding a near-universal or at least widely applicable solution to the inefficiency in agricultural P use by plants is an important unsolved problem that has been under investigation for more than half a century. Scope In this paper we critically review the strategies proposed for the remobilization of recalcitrant soil phosphorus for crops and pastures worldwide. We have additionally performed a meta-analysis of available soil 31P–NMR data to establish the potential agronomic value of different stored P forms in agricultural soils. Conclusions Soil inorganic P stocks accounted on average for 1006 ± 115 kg ha−1 (57 ± 7%), while the monoester P pool accounted for 587 ± 32 kg ha−1 (33 ± 2%), indicating the huge potential for the future agronomic use of the soil legacy P. New impact driven research is needed in order to create solutions for the sustainable management of soil P stocks.

Background Global climate is changing more rapidly than ever, threatening plant growth and productivity while exerting considerable direct and indirect effects on the quality and quantity of plant nutrients. Scope This review focuses on the global impact of climate change on the nutritional value of plant foods. It showcases the existing evidence linking the effects of climate change factors on crop nutrition and the concentration of nutrients in edible plant parts. It focuses on the effect of elevated CO 2 (eCO 2 ), elevated temperature (eT), salinity, waterlogging and drought stresses, and what is known regarding their direct and indirect influence on nutrient availability. Furthermore, it provides possible strategies to preserve the nutritional composition of plant foods under changing climates. Conclusions Climate change has an impact on the accumulation of minerals and protein in crop plants, with eCO 2 being the underlying factor of most of the reported changes. The effects are clearly dependent on the type, intensity and duration of the imposed stress, plant genotype and developmental stage. Strong interactions (both positive and negative) can be found between individual climatic factors and soil availability of nitrogen (N), potassium (K), iron (Fe) and phosphorous (P). The development of future interventions to ensure that the world's population has access to plentiful, safe and nutritious food may need to rely on breeding for nutrients under the context of climate change, including legumes in cropping systems, better farm management practices and utilization of microbial inoculants that enhance nutrient availability.

Background Biochar-based fertilizer products (BCF) have been reported to increase both crop yield and N-use efficiency. Such positive effects are often assumed to result from the slow-release of N adsorbed on BCF structures. However, a careful review of the literature suggests that actual mechanisms remain uncertain, which hampers the development of efficient BCF products. Scope Here, we aim at reviewing BCF mechanisms responsible for enhanced N uptake by plants, and evaluate the potential for further improvement. We review the capacity of biochar structures to adsorb and release N forms, the biochar properties supporting this effect, and the methods that have been proposed to enhance this effect. Conclusions Current biochar products show insufficient sorption capacity for the retention of N forms to support the production of slow-release BCFs of high enough N concentration. Substantial slow-release effects appear to require conventional coating technology. Sorption capacity can be improved through activation and additives, but currently not to the extent needed for concentrated BCFs. Positive effects of commercial BCFs containing small amount of biochar appear to result from pyrolysis-derived biostimulants. Our review highlights three prospects for improving N retention: 1) sorption of NH3 gas on specifically activated biochar, 2) synergies between biochar and clay porosities, which might provide economical sorption enhancement, and 3) physical loading of solid N forms within biochar. Beyond proof of concept, quantitative nutrient studies are needed to ascertain that potential future BCFs deliver expected effects on both slow-release and N use efficiency.

Background Phosphorus (P) is a limiting nutrient in many agroecosystems and costly fertilizer inputs can cause negative environmental impacts. Cover crops constitute a promising management option for sustainable intensification of agriculture. However, their interactions with the soil microbial community, which is a key driver of P cycling, and their effects on the following crop, have not yet been systematically assessed. Scope We conducted a meta-analysis of published field studies on cover crops and P cycling, focusing on plant-microbe interactions. Conclusions We describe several distinct, simultaneous mechanisms of P benefits for the main crop. Decomposition dynamics, governed by P concentration, are critical for the transfer of P from cover crop residues to the main crop. Cover crops may enhance the soil microbial community by providing a legacy of increased mycorrhizal abundance, microbial biomass P, and phosphatase activity. Cover crops are generally most effective in systems low in available P, and may access ‘unavailable’ P pools. However, their effects on P availability are difficult to detect by standard soil P tests, except for increases after the use of Lupinus sp. Agricultural management (i.e. cover crop species selection, tillage, fertilization) can improve cover crop effects. In summary, cover cropping has the potential to tighten nutrient cycling in agricultural systems under different conditions, increasing crop P nutrition and yield.

Background For more than a century, crop N nutrition research has primarily focused on inorganic N (IN) dynamics, building the traditional model that agricultural plants predominantly take up N in the form of NO 3 − and NH 4 + . However, results reported in the ecological and agricultural literature suggest that the traditional model of plant N nutrition is oversimplified. Scope We examine the role of organic N (ON) in plant N nutrition, first by reviewing the historical discoveries by ecologists of plant ON uptake, then by discussing the advancements of key analytical techniques that have furthered the cause (stable isotope and microdialysis techniques). The current state of knowledge on soil ON dynamics is analyzed concurrently with recent developments that show ON uptake and assimilation by agricultural plant species. Lastly, we consider the relationship between ON uptake and nitrogen use efficiency (NUE) in an agricultural context. Conclusions We propose several mechanisms by which ON uptake and assimilation may increase crop NUE, such as by reducing N assimilation costs, promoting root biomass growth, shaping N cycling microbial communities, recapturing exuded N compounds, and aligning the root uptake capacity to the soil N supply in highly fertilized systems. These hypothetical mechanisms should direct future research on the topic. Although the quantitative role remains unknown, ON compounds should be considered as significant contributors to plant N nutrition.