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Summary: Harnessing the plant microbiome through plant genetics is of increasing interest to those seeking to improve plant nutrition and health. While genome‐wide association studies (GWAS) have been conducted to identify plant genes driving the plant microbiome, more multidisciplinary studies are required to assess the relationships among plant genetics, plant microbiome and plant fitness.Using a metabarcoding approach, we characterized the rhizosphere bacterial communities of a core collection of 155 Medicago truncatula genotypes along with the plant phenotype and investigated the plant genetic effects through GWAS.The different genotypes within the M. truncatula core collection showed contrasting growth and nutritional strategies but few loci were associated with these ecophysiological traits. To go further, we described its associated rhizosphere bacterial communities, dominated by Proteobacteria, Actinobacteria and Bacteroidetes, and defined a core rhizosphere bacterial community. Next, the occurrences of bacterial candidates predicting plant ecophysiological traits of interest were identified using random forest analyses. Some of them were heritable and plant loci were identified, pinpointing genes related to response to hormone stimulus, systemic acquired resistance, response to stress, nutrient starvation or transport, and root development.Together, these results suggest that plant genetics can affect plant growth and nutritional strategies by harnessing keystone bacteria in a well‐connected interaction network. [ABSTRACT FROM AUTHOR]

Given the difficulties in accessing plant roots in situ , high-throughput root phenotyping (HTRP) platforms under controlled conditions have been developed to meet the growing demand for characterizing root system architecture (RSA) for genetic analyses. However, a proper evaluation of their capacity to provide the same estimates for strictly identical root traits across platforms has never been achieved. In this study, we performed such an evaluation based on six major parameters of the RSA model ArchiSimple, using a diversity panel of 14 bread wheat cultivars in two HTRP platforms that had different growth media and non-destructive imaging systems together with a conventional set-up that had a solid growth medium and destructive sampling. Significant effects of the experimental set-up were found for all the parameters and no significant correlations across the diversity panel among the three set-ups could be detected. Differences in temperature, irradiance, and/or the medium in which the plants were growing might partly explain both the differences in the parameter values across the experiments as well as the genotype × set-up interactions. Furthermore, the values and the rankings across genotypes of only a subset of parameters were conserved between contrasting growth stages. As the parameters chosen for our analysis are root traits that have strong impacts on RSA and are close to parameters used in a majority of RSA models, our results highlight the need to carefully consider both developmental and environmental drivers in root phenomics studies. [ABSTRACT FROM AUTHOR]

Soybean [Glycine max (L.) Merr] is the legume with the largest cultivated area worldwide and its yield depends largely on symbiotic nitrogen fixation and root architecture. This study aimed to explore the genetic variability of root architectural traits and di-nitrogen fixing activity in a small collection of nine European cultivars belonging to the same maturity group during their early stages. New image analysis approaches were implemented to characterise root architecture at high throughput. Significant genetic variability was identified for the width of the root system, root density, and for nitrogen fixation. This study allowed us to highlight trade-offs among root and nodule traits, and structural and functional traits. Finally, both the image analysis approach and the results could be used for breeding programs of soybean, that could take into account the root system architecture, when the plant interacts in symbiosis with N2-fixing bacteria.

Introduction: Peas, as legume crops, could play a major role in the future of food security in the context of worldwide human nutrient deficiencies coupled with the growing need to reduce consumption of animal products. However, pea yields, in terms of quantity and quality (i.e. grain content), are both susceptible to climate change, and more specifically to water deficits, which nowadays occur more frequently during crop growth cycles and tend to last longer. The impact of soil water stress on plant development and plant growth is complex, as its impact varies depending on soil water availability (through the modulation of elements available in the soil), and by the plant’s ability to acclimate to continuous stress or to memorize previous stress events. Method: To identify the strategies underlying these plant responses to water stress events, pea plants were grown in controlled conditions under optimal water treatment and different types of water stress; transient (during vegetative or reproductive periods), recurrent, and continuous (throughout the plant growth cycle). Traits related to water, carbon, and ionome uptake and uses were measured and allowed the identification typical plant strategies to cope with water stress. Conclusion: Our results highlighted (i) the common responses to the three types of water stress in shoots, involving manganese (Mn) in particular, (ii) the potential implications of boron (B) for root architecture modification under continuous stress, and (iii) the establishment of an “ecophysiological imprint” in the root system via an increase in nodule numbers during the recovery period. [ABSTRACT FROM AUTHOR]

Post-anthesis phosphorus (P) uptake and the remobilization of the previously acquired P are the principal sources of grain P nutrition in wheat. However, how the acquired P reaches the grains and its partitioning at the whole plant level remain poorly understood. Here, the temporal dynamics of the newly acquired P in durum wheat organs and its allocation to grain were examined using pulse-chase 32 P-labeling experiments at 5 and 14 days after anthesis. Durum wheat plants were grown hydroponically under high and low P supplies. Each labeling experiment lasted for 24 h. Plants were harvested 24, 48, and 96 h after labeling. Low and high P treatments significantly affected the allocation of the newly acquired P at the whole plant level. Three days (96 h) after the first 32 P-labeling, 8% and 4% of the newly acquired P from exogenous solution were allocated to grains, 73% and 55% to the remainder aboveground organs, and 19% and 41% to the roots at low and high P supplies, respectively. Three days after the second labeling, the corresponding values were 48% and 20% in grains, 44% and 53% in the remainder aboveground organs, and 8% and 27% in roots at low and high P supplies, respectively. These results reveal that the dynamics of P allocation to grain was faster in plants grown under low P supply than under high supply. However, the obtained results also indicate that the origin of P accumulated in durum wheat grains was mainly from P remobilization with little contribution from post-anthesis P uptake. The present study emphasizes the role of vegetative organs as temporary storage of P taken up during the grain filling period before its final allocation to grains. [ABSTRACT FROM AUTHOR]

Roots are essential for water and nutrient uptake but are rarely the direct target of breeding efforts. To characterize the genetic variability of wheat root architecture, the root and shoot traits of 200 durum and 715 bread wheat varieties were measured at a young stage on a high-throughput phenotyping platform. Heritability of platform traits ranged from 0.40 for root biomass in durum wheat to 0.82 for the number of tillers. Field phenotyping data for yield components and SNP genotyping were already available for all the genotypes. Taking differences in earliness into account, several significant correlations between root traits and field agronomic performances were found, suggesting that plants investing more resources in roots in some stressed environments favored water and nutrient uptake, with improved wheat yield. We identified 100 quantitative trait locus (QTLs) of root traits in the bread wheat panels and 34 in the durum wheat panel. Most colocalized with QTLs of traits measured in field conditions, including yield components and earliness for bread wheat, but only in a few environments. Stress and climatic indicators explained the differential effect of some platform QTLs on yield, which was positive, null, or negative depending on the environmental conditions. Modern breeding has led to deeper rooting but fewer seminal roots in bread wheat. The number of tillers has been increased in bread wheat, but decreased in durum wheat, and while the root-shoot ratio for bread wheat has remained stable, for durum wheat it has been increased. Breeding for root traits or designing ideotypes might help to maintain current yield while adapting to specific drought scenarios. [ABSTRACT FROM AUTHOR]

Artificial selection of microbiota opens new avenues for improving plants. However, reported results lack consistency. We hypothesised that the success in artificial selection of microbiota depends on the stabilisation of community structure. In a ten‐generation experiment involving 1,800 plants, we selected rhizosphere microbiota of Brachypodium distachyon associated with high or low leaf greenness, a proxy of plant performance. The microbiota structure showed strong fluctuations during an initial transitory phase, with no detectable leaf greenness heritability. After five generations, the microbiota structure stabilised, concomitantly with heritability in leaf greenness. Selection, initially ineffective, did successfully alter the selected property as intended, especially for high selection. We show a remarkable correlation between the variability in plant traits and selected microbiota structures, revealing two distinct sub‐communities associated with high or low leaf greenness, whose abundance was significantly steered by directional selection. Understanding microbiota structure stabilisation will improve the reliability of artificial microbiota selection. [ABSTRACT FROM AUTHOR]

Legume plants, such as peas, are of significant nutritional interest for both humans and animals. However, plant nutrition and thus, seed composition, depends on soil mineral nutrient availability. Understanding the impact of their deprivation on the plant mineral nutrient content, net uptake, and remobilization is of key importance but remains complex as the elements of the plant ionome are linked in intricate networks, one element deprivation impacting uptake and remobilization of other nutrients. To get a better insight into pea mineral nutrition, the transitory deprivations of 13 mineral nutrients were imposed during the vegetative growth phase. Thereafter, plants were grown under optimal mineral conditions until physiological maturity. Plant nutritional status and seed quality impacts caused by the deprivations were characterized using measurement of mineral nutrient concentration and plant biomass allocation. Our results highlight: (i) the preferential allocation of dry weight and elements to shoots at the expense of the roots under non-limiting conditions, and more particularly to the tendrils in comparison to the other shoot organs, (ii) the positive and/or negative impact of one mineral nutrient deprivation on other elements of the ionome, (iii) four different remobilization strategies for eight mineral nutrients, and (iv) possible strategies to improve seed quality via fine control of fertilization during a period of mineral nutrient deficiency. [ABSTRACT FROM AUTHOR]

The root system plays an essential role in the development and physiology of the plant, as well as in its response to various stresses. However, it is often insufficiently studied, mainly because it is difficult to visualize. For grapevine, a plant of major economic interest, there is a growing need to study the root system, in particular to assess its resistance to biotic and abiotic stresses, understand the decline that may affect it, and identify new ecofriendly production systems. In this context, we have evaluated and compared three distinct growing methods (hydroponics, plane, and cylindric rhizotrons) in order to describe relevant architectural root traits of grapevine cuttings (mode of grapevine propagation), and also two 2D- (hydroponics and rhizotron) and one 3D- (neutron tomography) imaging techniques for visualization and quantification of roots. We observed that hydroponics tubes are a system easy to implement but do not allow the direct quantification of root traits over time, conversely to 2D imaging in rhizotron. We demonstrated that neutron tomography is relevant to quantify the root volume. We have also produced a new automated analysis method of digital photographs, adapted for identifying adventitious roots as a feature of root architecture in rhizotrons. This method integrates image segmentation, skeletonization, detection of adventitious root skeleton, and adventitious root reconstruction. Although this study was targeted to grapevine, most of the results obtained could be extended to other plants propagated by cuttings. Image analysis methods could also be adapted to characterization of the root system from seedlings. [ABSTRACT FROM AUTHOR]

Including more grain legumes in cropping systems is important for the development of agroecological practices and the diversification of protein sources for human and animal consumption. Grain legume yield and quality is impacted by abiotic stresses resulting from fluctuating availabilities in essential nutrients such as iron deficiency chlorosis (IDC). Promoting plant iron nutrition could mitigate IDC that currently impedes legume cultivation in calcareous soils, and increase the iron content of legume seeds and its bioavailability. There is growing evidence that plant microbiota contribute to plant iron nutrition and might account for variations in the sensitivity of pea cultivars to iron deficiency and in fine to seed nutritional quality. Pyoverdine (pvd) siderophores synthesized by pseudomonads have been shown to promote iron nutrition in various plant species (Arabidopsis , clover and grasses). This study aimed to investigate the impact of three distinct ferripyoverdines (Fe-pvds) on iron status and the ionome of two pea cultivars (cv.) differing in their tolerance to IDC, (cv. S) being susceptible and (cv. T) tolerant. One pvd came from a pseudomonad strain isolated from the rhizosphere of cv. T (pvd1T), one from cv. S (pvd2S), and the third from a reference strain C7R12 (pvdC7R12). The results indicated that Fe-pvds differently impacted pea iron status and ionome, and that this impact varied both according to the pvd and the cultivar. Plant iron concentration was more increased by Fe-pvds in cv. T than in cv. S. Iron allocation within the plant was impacted by Fe-pvds in cv. T. Furthermore, Fe-pvds had the greatest favorable impact on iron nutrition in the cultivar from which the producing strain originated. This study evidences the impact of bacterial siderophores on pea iron status and pea ionome composition, and shows that this impact varies with the siderophore and host-plant cultivar, thereby emphasizing the specificity of these plant-microorganisms interactions. Our results support the possible contribution of pyoverdine-producing pseudomonads to differences in tolerance to IDC between pea cultivars. Indeed, the tolerant cv. T, as compared to the susceptible cv. S, benefited from bacterial siderophores for its iron nutrition to a greater extent. [ABSTRACT FROM AUTHOR]

The cultivation of legumes shows promise for the development of sustainable agriculture, but yield instability remains one of the main obstacles for its adoption. Here, we tested whether the yield stability (i.e., resistance and resilience) of pea plants subjected to drought could be enhanced by soil microbial diversity. We used a dilution approach to manipulate the microbial diversity, with a genotype approach to distinguish the effect of symbionts from that of microbial diversity as a whole. We investigated the physiology of plants in response to drought when grown on a soil containing high or low level of microbial diversity. Plants grown under high microbial diversity displayed higher productivity and greater resilience after drought. Yield losses were mitigated by 15% on average in the presence of high soil microbial diversity at sowing. Our study provides proof of concept that the soil microbial community as a whole plays a key role for yield stability after drought even in plant species living in relationships with microbial symbionts. These results emphasize the need to restore soil biodiversity for sustainable crop management and climate change adaptation. Plants grown under high microbial diversity display higher productivity and better resilience after drought. We provide proof of concept that the soil microbial community as a whole plays a key role in plant stability under drought even in plant species supporting microbial symbiotic relationships. [ABSTRACT FROM AUTHOR]

As drought is increasingly frequent in the context of climate change it is a major constraint for crop growth and yield. The ability of plants to maintain their yield in response to drought depends not only on their ability to tolerate drought, but also on their capacity to subsequently recover. Post-stress recovery can indeed be decisive for drought resilience and yield stability. Pea (Pisum sativum), as a legume, has the capacity to fix atmospheric nitrogen through its symbiotic interaction with soil bacteria within root nodules. Biological nitrogen fixation is highly sensitive to drought which can impact plant nitrogen nutrition and growth. Our study aimed at dynamically evaluating whether the control of plant N status after drought could affect nodulated pea plant’s ability to recover. Two pea genotypes, Puget and Kayanne, displaying different drought resilience abilities were compared for their capacity to tolerate to, and to recover from, a 2-weeks water-deficit period applied before flowering. Physiological processes were studied in this time-series experiment using a conceptual structure–function analysis framework focusing on whole plant carbon, nitrogen, and water fluxes combined to two 13CO2 and 15N2 labeling experiments. While Puget showed a yield decrease compared to well-watered plants, Kayanne was able to maintain its yield. During the recovery period, genotype-dependent strategies were observed. The analysis of the synchronization of carbon, nitrogen, and water related traits dynamics during the recovery period and at the whole plant level, revealed that plant growth recovery was tightly linked to N nutrition. In Puget, the initiation of new nodules after water deficit was delayed compared to control plants, and additional nodules developed, while in Kayanne the formation of nodules was both rapidly and strictly re-adjusted to plant growth needs, allowing a full recovery. Our study suggested that a rapid re-launch of N acquisition, associated with a fine-tuning of nodule formation during the post-stress period is essential for efficient drought resilience in pea leading to yield stability. [ABSTRACT FROM AUTHOR]

Summary: To circumvent the paucity of nitrogen sources in the soil legume plants establish a symbiotic interaction with nitrogen‐fixing soil bacteria called rhizobia. During symbiosis, the plants form root organs called nodules, where bacteria are housed intracellularly and become active nitrogen fixers known as bacteroids. Depending on their host plant, bacteroids can adopt different morphotypes, being either unmodified (U), elongated (E) or spherical (S). E‐ and S‐type bacteroids undergo a terminal differentiation leading to irreversible morphological changes and DNA endoreduplication. Previous studies suggest that differentiated bacteroids display an increased symbiotic efficiency (E > U and S > U). In this study, we used a combination of Aeschynomene species inducing E‐ or S‐type bacteroids in symbiosis with Bradyrhizobium sp. ORS285 to show that S‐type bacteroids present a better symbiotic efficiency than E‐type bacteroids. We performed a transcriptomic analysis on E‐ and S‐type bacteroids formed by Aeschynomene afraspera and Aeschynomene indica nodules and identified the bacterial functions activated in bacteroids and specific to each bacteroid type. Extending the expression analysis in E‐ and S‐type bacteroids in other Aeschynomene species by qRT‐PCR on selected genes from the transcriptome analysis narrowed down the set of bacteroid morphotype‐specific genes. Functional analysis of a selected subset of 31 bacteroid‐induced or morphotype‐specific genes revealed no symbiotic phenotypes in the mutants. This highlights the robustness of the symbiotic program but could also indicate that the bacterial response to the plant environment is partially anticipatory or even maladaptive. Our analysis confirms the correlation between differentiation and efficiency of the bacteroids and provides a framework for the identification of bacterial functions that affect the efficiency of bacteroids.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd [ABSTRACT FROM AUTHOR]

Pea (Pisum sativum L.) is an important source of dietary proteins. Nutrient recycling from leaves contributes to the accumulation of seed proteins and is a pivotal determinant of protein yields in this grain legume. The aim of this study was to unveil the transcriptional regulations occurring in pea leaves before the sharp decrease in chlorophyll breakdown. As a prelude to this study, a time-series analysis of 15N translocation at the whole plant level was performed, which indicated that nitrogen recycling among organs was highly dynamic during this period and varied depending on nitrate availability. Leaves collected on vegetative and reproductive nodes were further analyzed by transcriptomics. The data revealed extensive transcriptome changes in leaves of reproductive nodes during early seed development (from flowering to 14 days after flowering), including an up-regulation of genes encoding transporters, and particularly of sulfate that might sustain sulfur metabolism in leaves of the reproductive part. This developmental period was also characterized by a down-regulation of cell wall-associated genes in leaves of both reproductive and vegetative nodes, reflecting a shift in cell wall structure. Later on, 27 days after flowering, genes potentially switching the metabolism of leaves toward senescence were pinpointed, some of which are related to ribosomal RNA processing, autophagy, or transport systems. Transcription factors differentially regulated in leaves between stages were identified and a gene co-expression network pointed out some of them as potential regulators of the above-mentioned biological processes. The same approach was conducted in Medicago truncatula to identify shared regulations with this wild legume species. Altogether the results give a global view of transcriptional events in leaves of legumes at early reproductive stages and provide a valuable resource of candidate genes that could be targeted by reverse genetics to improve nutrient remobilization and/or delay catabolic processes leading to senescence. [ABSTRACT FROM AUTHOR]

Human mineral malnutrition or hidden hunger is considered a global challenge, affecting a large proportion of the world's population. The reduction in the mineral content of edible plant products is frequently found in cultivars bred for higher yields, and is probably increased by intensive agricultural practices. The filling of grain with macro and micronutrients is partly the result of a direct allocation from root uptake and remobilization from vegetative tissues. The aim of this bibliographic review is to focus on recent knowledge obtained from ionomic analysis of plant tissues in order to build a global appraisal of the potential remobilization of all macro and micronutrients, and especially those from leaves. Nitrogen is always remobilized from leaves of all plant species, although with different efficiencies, while nutrients such as K, S, P, Mg, Cu, Mo, Fe and Zn can be mobilized to a certain extent when plants are facing deficiencies. On the opposite, there is few evidence for leaf mobilization of Ca, Mn, Ni and B. Mechanisms related to the remobilization process (remobilization of mineral forms from vacuolar and organic compounds associated with senescence, respectively) are also discussed in the context of drought, an abiotic stress that is thought to increase and known to modulate the ionic composition of grain in crops. [ABSTRACT FROM AUTHOR]

Background: In order to maintain high yields while saving water and preserving non-renewable resources and thus limiting the use of chemical fertilizer, it is crucial to select plants with more efficient root systems. This could be achieved through an optimization of both root architecture and root uptake ability and/or through the improvement of positive plant interactions with microorganisms in the rhizosphere. The development of devices suitable for highthroughput phenotyping of root structures remains a major bottleneck. Results: Rhizotrons suitable for plant growth in controlled conditions and non-invasive image acquisition of plant shoot and root systems (RhizoTubes) are described. These RhizoTubes allow growing one to six plants simultaneously, having a maximum height of 1.1 m, up to 8 weeks, depending on plant species. Both shoot and root compartment can be imaged automatically and non-destructively throughout the experiment thanks to an imaging cabin (Rhizo- Cab). RhizoCab contains robots and imaging equipment for obtaining high-resolution pictures of plant roots. Using this versatile experimental setup, we illustrate how some morphometric root traits can be determined for various species including model (Medicago truncatula), crops (Pisum sativum, Brassica napus, Vitis vinifera, Triticum aestivum) and weed (Vulpia myuros) species grown under non-limiting conditions or submitted to various abiotic and biotic constraints. The measurement of the root phenotypic traits using this system was compared to that obtained using "classic" growth conditions in pots. Conclusions: This integrated system, to include 1200 Rhizotubes, will allow high-throughput phenotyping of plant shoots and roots under various abiotic and biotic environmental conditions. Our system allows an easy visualization or extraction of roots and measurement of root traits for high-throughput or kinetic analyses. The utility of this system for studying root system architecture will greatly facilitate the identification of genetic and environmental determinants of key root traits involved in crop responses to stresses, including interactions with soil microorganisms. [ABSTRACT FROM AUTHOR]

Plant and soil types are usually considered as the two main drivers of the rhizosphere microbial communities. The aim of this work was to study the effect of both N availability and plant genotype on the plant associated rhizosphere microbial communities, in relation to the nutritional strategies of the plant-microbe interactions, for six contrasted Medicago truncatula genotypes. The plants were provided with two different nutrient solutions varying in their nitrate concentrations (0 mM and 10 mM). First, the influence of both nitrogen availability and Medicago truncatula genotype on the genetic structure of the soil bacterial and fungal communities was determined by DNA fingerprint using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Secondly, the different nutritional strategies of the plant-microbe interactions were evaluated using an ecophysiological framework. We observed that nitrogen availability affected rhizosphere bacterial communities only in presence of the plant. Furthermore, we showed that the influence of nitrogen availability on rhizosphere bacterial communities was dependent on the different genotypes of Medicago truncatula. Finally, the nutritional strategies of the plant varied greatly in response to a modification of nitrogen availability. A new conceptual framework was thus developed to study plant-microbe interactions. This framework led to the identification of three contrasted structural and functional adaptive responses of plant-microbe interactions to nitrogen availability. [ABSTRACT FROM AUTHOR]