Phosphorus homeostasis in legume nodules as an adaptive strategy to phosphorus deficiency

Chickpea (Cicer arietinum) PHO1 family members function redundantly in Pi transport and root nodulation

Phosphorus (P), a macronutrient, plays key roles in plant growth, development, and yield. Phosphate (Pi) transporters (PHTs) and PHOSPHATE1 (PHO1) are central to Pi acquisition and distribution. Potentially, PHO1 is also involved in signal transduction under low P. The current study was designed to identify and functionally characterize the PHO1 gene family in chickpea (CaPHO1s). Five CaPHO1 genes were identified through a comprehensive genome-wide search. Phylogenetically, CaPHO1s formed two clades, and protein sequence analyses confirmed the presence of conserved domains. CaPHO1s are expressed in different plant organs including root nodules and are induced by Pi-limiting conditions. Functional complementation of atpho1 mutant with three CaPHO1 members, CaPHO1, CaPHO1;like, and CaPHO1;H1, independently demonstrated their role in root to shoot Pi transport, and their redundant functions. To further validate this, we raised independent RNA-interference (RNAi) lines of CaPHO1, CaPHO1;like, and CaPHO1;H1 along with triple mutant line in chickpea. While single gene RNAi lines behaved just like WT, triple knock-down RNAi lines (capho1/like/h1) showed reduced shoot growth and shoot Pi content. Lastly, we showed that CaPHO1s are involved in root nodule development and Pi content. Our findings suggest that CaPHO1 members function redundantly in root to shoot Pi export and root nodule development in chickpea.

Soil microbial functional profiles of P-cycling reveal drought-induced constraints on P-transformation in a hyper-arid desert ecosystem

Soil water conditions are known to influence soil nutrient availability, but the specific impact of different conditions on soil phosphorus (P) availability through the modulation of P-cycling functional microbial communities in hyper-arid desert ecosystems remains largely unexplored. To address this knowledge gap, we conducted a 3-year pot experiment using a typical desert plant species (Alhagi sparsifolia Shap.) subjected to two water supply levels (25 %-35 % and 65 %-75 % of maximum field capacity, MFC) and four P-supply levels (0, 1, 3, and 5 g P m-2 y-1). Our investigation focused on the soil Hedley-P pool and the four major microbial groups involved in the critical phases of soil microbial P-cycling. The results revealed that the drought (25 %-35 % MFC) and no P-supply treatments reduced soil resin-P and NaHCO3-Pi concentrations by 87.03 % and 93.22 %, respectively, compared to the well-watered (65 %-75 % MFC) and high P-supply (5 g P m-2 y-1) treatments. However, the P-supply treatment resulted in a 12 %-22 % decrease in the soil NH4+-N concentration preferred by microbes compared to the no P-supply treatment. Moreover, the abundance of genes engaged in microbial P-cycling (e.g. gcd and phoD) increased under the drought and no P-supply treatments (p < 0.05), suggesting that increased NH4+-N accumulation under these conditions may stimulate P-solubilizing microbes, thereby promoting the microbial community's investment in resources to enhance the P-cycling potential. Furthermore, the communities of Steroidobacter cummioxidans, Mesorhizobium alhagi, Devosia geojensis, and Ensifer sojae, associated with the major P-cycling genes, were enriched in drought and no or low-P soils. Overall, the drought and no or low-P treatments stimulated microbial communities and gene abundances involved in P-cycling. However, this increase was insufficient to maintain soil P-bioavailability. These findings shed light on the responses and feedback of microbial-mediated P-cycling behaviors in desert ecosystems under three-year drought and soil P-deficiency.

Nitrogen-fixing and non-nitrogen-fixing legume plants differ in leaf nutrient concentrations and relationships between photosynthetic and hydraulic traits

Legumes account for a significant proportion of plants in the terrestrial ecosystems. Nitrogen (N)-fixing capability of certain legumes is a pivotal trait that contributes to their ecological dominance. Yet, the functional traits and trait relationships between N-fixer and non-N-fixer legumes are poorly understood. Here, we investigated 27 functional traits associated with morphology, nutrients, hydraulic conductance and photosynthesis in 42 woody legumes (19 N-fixers and 23 non-N-fixers) in a common garden. Our results showed that N-fixers had higher specific leaf area, photosynthetic phosphorus (P)-use efficiency, leaf N, and iron concentrations on both area and mass basis, N/P ratio, and carbon (C) to P ratio, but lower wood density, area-based maximum photosynthetic rate (Aa), photosynthetic N-use efficiency, leaf mass- and area-based P and molybdenum and area-based boron concentrations, and C/N ratio, compared with non-N-fixers. The mass-based maximum photosynthetic rate (Am), stomatal conductance (gs), intrinsic water-use efficiency (WUEi), mass- and area-based leaf potassium and mass-based boron concentrations, leaf hydraulic conductance (Kleaf), and whole-shoot hydraulic conductance (Kshoot) showed no difference between N-fixers and non-N-fixers. Significant positive associations between all hydraulic and photosynthetic trait pairs were found in N-fixers, but only one pair (Kshoot-Aa) in non-N-fixers, suggesting that hydraulic conductance plays a more important role in mediating photosynthetic capacity in N-fixers compared with non-N-fixers. Higher mass-based leaf N was linked to lower time-integrated gs and higher WUEi among non-N-fixer legumes or all legumes pooled after phylogeny was considered. Moreover, mass-based P concentration was positively related to Am and gs in N-fixers, but not in non-N-fixers, indicating that the photosynthetic capacity and stomatal conductance in N-fixers were more dependent on leaf P status than in non-N-fixers. These findings expand our understanding of the trait-based ecology within and across N-fixer and non-N-fixer legumes in tropics.

Overexpression of GmPAP4 Enhances Symbiotic Nitrogen Fixation and Seed Yield in Soybean under Phosphorus-Deficient Condition

Legume crops establish symbiosis with nitrogen-fixing rhizobia for biological nitrogen fixation (BNF), a process that provides a prominent natural nitrogen source in agroecosystems; and efficient nodulation and nitrogen fixation processes require a large amount of phosphorus (P). Here, a role of GmPAP4, a nodule-localized purple acid phosphatase, in BNF and seed yield was functionally characterized in whole transgenic soybean (Glycine max) plants under a P-limited condition. GmPAP4 was specifically expressed in the infection zones of soybean nodules and its expression was greatly induced in low P stress. Altered expression of GmPAP4 significantly affected soybean nodulation, BNF, and yield under the P-deficient condition. Nodule number, nodule fresh weight, nodule nitrogenase, APase activities, and nodule total P content were significantly increased in GmPAP4 overexpression (OE) lines. Structural characteristics revealed by toluidine blue staining showed that overexpression of GmPAP4 resulted in a larger infection area than wild-type (WT) control. Moreover, the plant biomass and N and P content of shoot and root in GmPAP4 OE lines were also greatly improved, resulting in increased soybean yield in the P-deficient condition. Taken together, our results demonstrated that GmPAP4, a purple acid phosphatase, increased P utilization efficiency in nodules under a P-deficient condition and, subsequently, enhanced symbiotic BNF and seed yield of soybean.

Unregulated GmAGL82 due to Phosphorus Deficiency Positively Regulates Root Nodule Growth in Soybean

Nitrogen fixation, occurring through the symbiotic relationship between legumes and rhizobia in root nodules, is crucial in sustainable agriculture. Nodulation and soybean production are influenced by low levels of phosphorus stress. In this study, we discovered a MADS transcription factor, GmAGL82, which is preferentially expressed in nodules and displays significantly increased expression under conditions of phosphate (Pi) deficiency. The overexpression of GmAGL82 in composite transgenic plants resulted in an increased number of nodules, higher fresh weight, and enhanced soluble Pi concentration, which subsequently increased the nitrogen content, phosphorus content, and overall growth of soybean plants. Additionally, transcriptome analysis revealed that the overexpression of GmAGL82 significantly upregulated the expression of genes associated with nodule growth, such as GmENOD100, GmHSP17.1, GmHSP17.9, GmSPX5, and GmPIN9d. Based on these findings, we concluded that GmAGL82 likely participates in the phosphorus signaling pathway and positively regulates nodulation in soybeans. The findings of this research may lay the theoretical groundwork for further studies and candidate gene resources for the genetic improvement of nutrient-efficient soybean varieties in acidic soils.

Using soil nitrogen amendments in mitigating ozone stress in agricultural crops: a case study of cluster beans

The climate change scenario in the coming years is liable to have serious negative consequences on agricultural productivity. Increasing tropospheric ozone concentration is an important aspect of climate change, which, due to its oxidative nature, is injurious to the plants. Due to the multifarious nature and continuously increasing concentration of tropospheric ozone, it is prerequisite to develop strategies to manage ozone stress in plants. Present study not only evaluates the potential of soil nitrogen amendments in ameliorating ozone stress in plants, but also focuses upon the mechanistic approaches adopted by the different plant cultivars to combat ozone stress. Three doses of nitrogen amendments, recommended (N1), 1.5× recommended (N2) and 2× recommended (N3), were given to two cultivars (S-151 and PUSA-N) of Cymopsis tetragonoloba exposed to ambient ozone stress. Control plants were also maintained in which no nitrogen treatment was given. Nitrogen supplementation reduced the root nodulation frequency and leghaemoglobin content, which subsequently increased the cellular nitrogen metabolism as evident through increase in the activities of nitrate reductase and nitrite reductase in both the test cultivars. The positive effects of nitrogen amendments are clearly evident in the 1D protein profile studies which showed a greater accumulation of larger sub-units of RuBisCO in nitrogen amended plants. The results clearly indicate that N2 treatment effectively enhanced the yield of both the cultivars (84.8% and 76.37%, in S-151 and PUSA-N, respectively); however, the mechanistic approach adopted by the two cultivars was different. Whereas the yield quantity showed higher increments in S-151, the yield quality parameters (carbohydrates and nitrogen contents) responded more positively in PUSA-N.

Mineral and Carbon Metabolic Adjustments in Nodules of Symbiotically Grown Faba Bean (Vicia faba L.) Varieties in Response to Organic Phosphorus Supplementation

Phosphorus (P) is a major limiting factor for legume and symbiotic nitrogen fixation (SNF). Although overall adaptations of legumes to P supplementation have been extensively studied in connection with inorganic P, little information is currently available regarding nodulation or SNF responses to organic P (Po) in hydroponics. We investigated the mineral and carbon metabolism of Po-induced nodules of two contrasting faba bean varieties grown hydroponically under inorganic P (Pi), viz., in P-deficient (2 µM KH2PO4, -Pi), sufficient-P (200 µM KH2PO4, +Pi), and phytic acid (200 µM, Po) conditions, and were inoculated with Rhizobium leguminosarum bv. viciae 3841 and grown for 30 days. The results consistently reveal similar growth and biomass partitioning patterns between +Pi and Po, with both varying substantially from -Pi. In comparison, +Pi and Po observed equivalent accumulations of overall elemental P concentrations, with both increasing by 114 and 119%, respectively, relative to -Pi. A principal component analysis on metabolites showed a clear separation of the -Pi treatment from the others, with +Pi and Po correlating closely together, highlighting the nonsignificant differences between them. Additionally, the δ15N abundance of shoots, roots, and nodules was not significantly different between treatments and varieties and exhibited negative δ15N signatures for all tissues. Our study provides a novel perspective on mineral and carbon metabolism and their regulation of the growth, functioning, and reprogramming of nodules upon phytate supply.

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems

Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.

VPT-like genes modulate Rhizobium-legume symbiosis and phosphorus adaptation

Although vacuolar phosphate transporters (VPTs) are essential for plant phosphorus adaptation, their role in Rhizobium-legume symbiosis is unclear. In this study, homologous genes of VPT1 (MtVPTs) were identified in Medicago truncatula to assess their roles in Rhizobium-legume symbiosis and phosphorus adaptation. MtVPT2 and MtVPT3 mainly positively responded to low and high phosphate, respectively. However, both mtvpt2 and mtvpt3 mutants displayed shoot phenotypes with high phosphate sensitivity and low phosphate tolerance. The root-to-shoot phosphate transfer efficiency was significantly enhanced in mtvpt3 but weakened in mtvpt2, accompanied by lower and higher root cytosolic inorganic phosphate (Pi) concentration, respectively. Low phosphate induced MtVPT2 and MtVPT3 expressions in nodules. MtVPT2 and MtVPT3 mutations markedly reduced the nodule number and nitrogenase activity under different phosphate conditions. Cytosolic Pi concentration in nodules was significantly lower in mtvpt2 and mtvpt3 than in the wildtype, especially in tissues near the base of nodules, probably due to inhibition of long-distance Pi transport and cytosolic Pi supply. Also, mtvpt2 and mtvpt3 could not maintain a stable cytosolic Pi level in the nodule fixation zone as the wildtype under low phosphate stress. These findings show that MtVPT2 and MtVPT3 modulate phosphorus adaptation and rhizobia-legume symbiosis, possibly by regulating long-distance Pi transport.

The Global Dilemma of Soil Legacy Phosphorus and Its Improvement Strategies under Recent Changes in Agro-Ecosystem Sustainability

Phosphorus (P) is one of the six key elements in plant nutrition and effectively plays a vital role in all major metabolic activities. It is an essential nutrient for plants linked to human food production. Although abundantly present in both organic and inorganic forms in soil, more than 40% of cultivated soils are commonly deficient in P concentration. Then, the P inadequacy is a challenge to a sustainable farming system to improve the food production for an increasing population. It is expected that the whole world population will rise to 9 billion by 2050 and, therefore, it is necessary at the same time for agricultural strategies broadly to expand food production up to 80% to 90% by handling the global dilemma which has affected the environment by climatic changes. Furthermore, the phosphate rock annually produced about 5 million metric tons of phosphate fertilizers per year. About 9.5 Mt of phosphorus enters human food through crops and animals such as milk, egg, meat, and fish and is then utilized, and 3.5 Mt P is physically consumed by the human population. Various new techniques and current agricultural practices are said to be improving P-deficient environments, which might help meet the food requirements of an increasing population. However, 4.4% and 3.4% of the dry biomass of wheat and chickpea, respectively, were increased under intercropping practices, which was higher than that in the monocropping system. A wide range of studies showed that green manure crops, especially legumes, improve the soil-available P content of the soil. It is noted that inoculation of arbuscular mycorrhizal fungi could decrease the recommended phosphate fertilizer rate nearly 80%. Agricultural management techniques to improve soil legacy P use by crops include maintaining soil pH by liming, crop rotation, intercropping, planting cover crops, and the consumption of modern fertilizers, in addition to the use of more efficient crop varieties and inoculation with P-solubilizing microorganisms. Therefore, exploring the residual phosphorus in the soil is imperative to reduce the demand for industrial fertilizers while promoting long-term sustainability on a global scale.

Medicago truncatula PHO2 genes have distinct roles in phosphorus homeostasis and symbiotic nitrogen fixation

Three PHO2-like genes encoding putative ubiquitin-conjugating E2 enzymes of Medicago truncatula were characterized for potential roles in phosphorous (P) homeostasis and symbiotic nitrogen fixation (SNF). All three genes, MtPHO2A, B and C, contain miR399-binding sites characteristic of PHO2 genes in other plant species. Distinct spatiotemporal expression patterns and responsiveness of gene expression to P- and N-deprivation in roots and shoots indicated potential roles, especially for MtPHO2B, in P and N homeostasis. Phenotypic analysis of pho2 mutants revealed that MtPHO2B is integral to Pi homeostasis, affecting Pi allocation during plant growth under nutrient-replete conditions, while MtPHO2C had a limited role in controlling Pi homeostasis. Genetic analysis also revealed a connection between Pi allocation, plant growth and SNF performance. Under N-limited, SNF conditions, Pi allocation to different organs was dependent on MtPHO2B and, to a lesser extent, MtPHO2C and MtPHO2A. MtPHO2A also affected Pi homeostasis associated with nodule formation. Thus, MtPHO2 genes play roles in systemic and localized, i.e., nodule, P homeostasis affecting SNF.

Stoichiometric homeostasis of N:P ratio drives species-specific symbiotic N fixation inhibition under N addition

Introduction

Symbiotic N fixation inhibition induced by N supply to legumes is potentially regulated by the relative N and P availability in soil. However, the specific responses of different legume species to changes in N:P availability remain unclear, and must be better understood to optimize symbiotic N fixation inputs under N enrichment. This study investigated mechanisms by which soil N and P supply influence the symbiotic N fixation of eight legume species, to quantify the inter-specific differences, and to demonstrate how these differences can be determined by the stoichiometric homeostasis in N:P ratios (HN:P).

Methods

Eight herbaceous legume species were grown separately in outdoor pots and treated with either no fertilizer (control), N fertilizer (14 g N m-2), P fertilizer (3.5 g P m-2) or both N and P fertilizer. Plant nutrients, stoichiometric characteristics, root biomass, non-structural carbohydrates (NSC), rhizosphere chemistry, P mobilization, root nodulation and symbiotic N fixation were measured.

Results

N addition enhanced rhizosphere P mobilization but drove a loss of root biomass and root NSC via exudation of P mobilization compound (organic acid), especially so in treatments without P addition. N addition also induced a 2-14% or 14-36% decline in symbiotic N fixation per plant biomass by legumes in treatments with or without P addition, as a result of decreasing root biomass and root NSC. The changes in symbiotic N fixation were positively correlated with stoichiometric homeostasis of N:P ratios in intact plants without root nodules, regardless of P additions.

Discussion

This study indicates that N addition can induce relative P limitations for growth, which can stimulate rhizosphere P mobilization at the expense of root biomass and carbohydrate concentrations, reducing symbiotic N fixation in legumes. Legume species that had less changes in plant N:P ratio, such as Lespedeza daurica and Medicago varia maintained symbiotic N fixation to a greater extent under N addition.

Allelic Variation in GmPAP14 Alters Gene Expression to Affect Acid Phosphatase Activity in Soybean

Improvement in acid phosphatase (APase) activity is considered as an important approach to enhance phosphorus (P) utilization in crops. Here, GmPAP14 was significantly induced by low P (LP), and its transcription level in ZH15 (P efficient soybean) was higher than in NMH (P inefficient soybean) under LP conditions. Further analyses demonstrated that there were several variations in gDNA (G-GmPAP14Z and G-GmPAP14N) and the promoters (P-GmPAP14Z and P-GmPAP14N) of GmPAP14, which might bring about differential transcriptional levels of GmPAP14 in ZH15 and NMH. Histochemical staining measurements revealed that a stronger GUS signal was present in transgenic Arabidopsis with P-GmPAP14Z under LP and normal P (NP) conditions compared with the P-GmPAP14N plant. Functional research demonstrated that transgenic Arabidopsis with G-GmPAP14Z had a higher level of GmPAP14 expression than the G-GmPAP14N plant. Meanwhile, higher APase activity was also observed in the G-GmPAP14Z plant, which led to increases in shoot weight and P content. Additionally, validation of variation in 68 soybean accessions showed that varieties with Del36 displayed higher APase activities than the del36 plant. Thus, these results uncovered that allelic variation in GmPAP14 predominantly altered gene expression to influence APase activity, which provided a possible direction for research of this gene in plants.

Improving phosphorus acquisition efficiency through modification of root growth responses to phosphate starvation in legumes

Phosphorus (P) is one of the essential macronutrients for plant growth and development, and it is an integral part of the major organic components, including nucleic acids, proteins and phospholipids. Although total P is abundant in most soils, a large amount of P is not easily absorbed by plants. Inorganic phosphate (Pi) is the plant-available P, which is generally immobile and of low availability in soils. Hence, Pi starvation is a major constraint limiting plant growth and productivity. Enhancing plant P efficiency can be achieved by improving P acquisition efficiency (PAE) through modification of morpho-physiological and biochemical alteration in root traits that enable greater acquisition of external Pi from soils. Major advances have been made to dissect the mechanisms underlying plant adaptation to P deficiency, especially for legumes, which are considered important dietary sources for humans and livestock. This review aims to describe how legume root growth responds to Pi starvation, such as changes in the growth of primary root, lateral roots, root hairs and cluster roots. In particular, it summarizes the various strategies of legumes to confront P deficiency by regulating root traits that contribute towards improving PAE. Within these complex responses, a large number of Pi starvation-induced (PSI) genes and regulators involved in the developmental and biochemical alteration of root traits are highlighted. The involvement of key functional genes and regulators in remodeling root traits provides new opportunities for developing legume varieties with maximum PAE needed for regenerative agriculture.

Cooperative interactions between nitrogen fixation and phosphorus nutrition in legumes

Legumes such as soybean are considered important crops as they provide proteins and oils for humans and livestock around the world. Different from other crops, leguminous crops accumulate nitrogen (N) for plant growth through symbiotic nitrogen fixation (SNF) in coordination with rhizobia. A number of studies have shown that efficient SNF requires the cooperation of other nutrients, especially phosphorus (P), a nutrient deficient in most soils. During the last decades, great progress has been made in understanding the molecular mechanisms underlying the interactions between SNF and P nutrition, specifically through the identification of transporters involved in P transport to nodules and bacteroids, signal transduction, and regulation of P homeostasis in nodules. These studies revealed a distinct N-P interaction in leguminous crops, which is characterized by specific signaling cross talk between P and SNF. This review aimed to present an updated picture of the cross talk between N fixation and P nutrition in legumes, focusing on soybean as a model crop, and Medicago truncatula and Lotus japonicus as model plants. We also discuss the possibilities for enhancing SNF through improving P nutrition, which are important for high and sustainable production of leguminous crops.

Integration of transcriptomic and metabolomic analyses provides insights into response mechanisms to nitrogen and phosphorus deficiencies in soybean

Nitrogen (N) and phosphorus (P) are two essential plant macronutrients that can limit plant growth by different mechanisms. We aimed to shed light on how soybean respond to low nitrogen (LN), low phosphorus (LP) and their combined deficiency (LNP). Generally, these conditions triggered changes in gene expression of the same processes, including cell wall organization, defense response, response to oxidative stress, and photosynthesis, however, response was different in each condition. A typical primary response to LN and LP was detected also in soybean, i.e., the enhanced uptake of N and P, respectively, by upregulation of genes for the corresponding transporters. The regulation of genes involved in cell wall organization showed that in LP roots tended to produce more casparian strip, in LN more secondary wall biosynthesis occurred, and in LNP reduction in expression of genes involved in secondary wall production accompanied by cell wall loosening was observed. Flavonoid biosynthesis also showed distinct pattern of regulation in different conditions: more anthocyanin production in LP, and more isoflavonoid production in LN and LNP, which we confirmed also on the metabolite level. Interestingly, in soybean the nutrient deficiencies reduced defense response by lowering expression of genes involved in defense response, suggesting a role of N and P nutrition in plant disease resistance. In conclusion, we provide detailed information on how LN, LP, and LNP affect different processes in soybean roots on the molecular and physiological levels.

Soil Acidification in Nutrient-Enriched Soils Reduces the Growth, Nutrient Concentrations, and Nitrogen-Use Efficiencies of Vachellia sieberiana (DC.) Kyal. & Boatwr Saplings

Nitrogen (N) and phosphorus (P) nutrient enrichment is important for grasslands. This study aimed to determine how soils enriched with N and P influenced soil concentration correlations and affected the growth kinetics, mineral nutrition, and nitrogen-use efficiencies of Vachellia sieberiana grown in a greenhouse experiment. The soils used as the growth substrate were analysed and showed extreme acidity (low soil pH, 3.9). Nitrogen-enriched soils were more acidic than P-enriched soils. Exchangeable acidity was strongly negatively correlated with an increase in soil pH, with soil pH between 3.9 and 4.1 units showing the strongest decline. Plant saplings showed increased root biomass, shoot biomass, total biomass, and plant N and P concentrations when grown in soils with high soil P concentrations. Extreme soil acidification in N-enriched soil was one of the main factors causing P unavailability, decreasing sapling growth. Extreme soil acidification increased concentrations of toxic heavy metals, such as Al which may be alleviated by adding lime to the extremely acidic soils. Research implications suggest that soil pH is an important chemical property of the soil and plays a significant role in legume plant growth. Legume species that are unable to tolerate acidic soils may acquire different strategies for growth and functioning.

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

Alien invasive Leucaena leucocephala successfully acquires nutrients by investing in below-ground biomass compared to native Vachellia nilotica in nutrient-amended soils in South Africa

Soils in grasslands and savannas of southern Africa are acidic and nutrient-poor. Legume plants, such as Vachellia nilotica and alien invasive Leucaena leucocephala, are a major component of the vegetation there. Vachellia nilotica can establish in drought-prone environments, and is invasive in high rainfall areas. Leucaena leucocephala is an emerging invasive in South Africa and is ranked among the world's 100 most invasive alien species. Alien plants can invade native habitats through their adaptability to low-resource soils, and thus can out-compete and displace native vegetation. We investigated the effects of phosphorus (P) deficiency and soil acidity on legume-microbe symbiosis, nitrogen (N) nutrition and carbon (C) growth costs of these two legumes in grassland soils. We used as inoculum and growth substrate soils collected from a long-term (>65 years) nutrient and lime-addition trial, the Veld Fertilizer Trial (VFT), located at Ukulinga Research Farm near Pietermaritzburg in South Africa. We used soils from three VFT treatments: soils fertilized with superphosphate (336 kg ha^-1) applied once per year (+P), soils fertilized with superphosphate (336 kg ha^-1) applied once per year with dolomitic lime (2250 kg ha^-1) applied once every 5 years (P+L) and soils with no superphosphate and no dolomitic lime applications (Control). Seeds of V. nilotica and L. leucocephala were germinated and grown independently in these soils in green house conditions and harvested after 125 days for measurement of growth, legume-microbe symbiosis, N nutrition and C growth costs. Results showed that the two legumes had different growth adaptations. Vachellia nilotica grown in control soils and +P soils nodulated with various Burkholderia spp., while L. leucocephala did not nodulate in all soil treatments. Both legumes utilized for growth both atmospheric- and soil-derived N across all treatments thereby decreasing C growth costs. Vachellia nilotica grown in +P soils accumulated the most biomass and N nutrition. Leucaena leucocephala maximized specific N assimilation rates by investing in below-ground biomass accumulation in control soils. This shows that L. leucocephala possesses traits that are successful in acquiring nutrients by investing in below-ground biomass and relying on utilization of N from both the soil and the atmosphere.

Metabolite shift in Medicago truncatula occurs in phosphorus deprivation

Symbiotic nitrogen (N) fixation entails successful interaction between legume hosts and rhizobia that occur in specialized organs called nodules. N-fixing legumes have a higher demand for phosphorus (P) than legumes grown on mineral N. Medicago truncatula is an important model plant for characterization of effects of P deficiency at the molecular level. Hence, a study was carried out to address the alteration in metabolite levels of M. truncatula grown aeroponically and subjected to 4 weeks of P stress. First, GC-MS-based untargeted metabolomics initially revealed changes in the metabolic profile of nodules, with increased levels of amino acids and sugars and a decline in amounts of organic acids. Subsequently, LC-MS/MS was used to quantify these compounds including phosphorylated metabolites in the whole plant. Our results showed a drastic reduction in levels of organic acids and phosphorylated compounds in -P leaves, with a moderate reduction in -P roots and nodules. Additionally, sugars and amino acids were elevated in the whole plant under P deprivation. These findings provide evidence that N fixation in M. truncatula is mediated through a N feedback mechanism that in parallel is related to carbon and P metabolism.

Metabolite Profiles Provide Insights into Underlying Mechanism in Bupleurum (Apiaceae) in Response to Three Levels of Phosphorus Fertilization

Phosphorus (P) deficiency affects plant yield and quality, yet at the same time, excessive phosphorus application does not necessarily promote the growth of plants. How to maintain a balance between biomass accumulation and phosphorus application is a problem. Therefore, the purpose of this research was to explore the relationship between yield and quality of Bupleurum and phosphorus fertilization, based on three phosphorus fertilization levels (20 kg∙ha^-1; 10 kg∙ha^-1; and 0 kg∙ha^-1). We adopted gas chromatography-mass spectrometry to assess the response of primary metabolites of different plant tissues (flowers, main shoots, lateral shoots and roots) to phosphorus fertilization. At the same time, high-performance liquid chromatography was used to quantify saikosaponin A and saikosaponin D, the main active ingredients of Bupleurum. Our research showed that low phosphorus level application has a positive impact on the yield and quality of Bupleurum, especially the above-ground parts increasing the fresh weight of flowers and lateral shoots and the length of main shoots, and moreover, increasing the saikosaponins content in all above-ground parts while decreasing the content in roots which show no significance increase in fresh weight and length. However, high phosphorus level showed a negative impact as it decreases the saikosaponins content significantly in flowers and roots. Furthermore, phosphorus application changed the proportion of saikosaponins, promoting the content of saikosaponin A and inhibiting the content of saikosaponin D in most organs of Bupleurum. Therefore, we can say that high phosphorus application is not preferable to the yield and quality of Bupleurum. To identify the metabolic pathways and special key metabolites, a total of 73 metabolites were discovered, and four differential metabolites-ether, glycerol, chlorogenic and L-rhamnose-were considered to be the key metabolites of Bupleurum's response to phosphorus fertilization. Furthermore, Bupleurum's response to phosphorus fertilization was mainly related to metabolic pathways, such as starch and sucrose metabolism and galactose metabolism. Under the phosphorus level, the content of sugars, organic acids and their derivatives, polyols and their derivatives and alkyl were upregulated in flowers. Furthermore, the contents of compounds in the main shoot and lateral shoots showed the same upward trend, except glycosides and polyols and their derivatives.

Increased nodular P level induced by intercropping stimulated nodulation in soybean under phosphorus deficiency

Low P availability is a vital constraint for nodulation and efficient N2 fixation of legume, including soybean. To elucidate the mechanisms involved in nodule adaption to low P availability under legume/cereal intercropping systems, two experiments consisting of three cropping patterns (monocropped soybean, monocropped maize, soybean/maize intercropping) were studied under both sufficient- and deficient-P levels. Our results demonstrated that intercropped soybean with maize showed a higher nodulation and N2 fixation efficiency under low P availability than monocropped soybean as evidenced by improvement in the number, dry weight and nitrogenase activity of nodules. These differences might be attributed to increase in P level in intercropping-induced nodules under low P supply, which was caused by the elevated activities of phytase and acid phosphatases in intercropping-induced nodules. Additionally, the enhanced expression of phytase gene in nodules supplied with deficient P level coincided with an increase in phytase and acid phosphatase activities. Our results revealed a mechanism for how intercropped maize stimulated nodulation and N2 fixation of soybean under P deficient environments, where enhanced synthesis of phytase and acid phosphatases in intercropping-induced nodules, and stimulated nodulation and N2 fixation.

Grain Legume Yield Responses to Rhizobia Inoculants and Phosphorus Supplementation Under Ghana Soils: A Meta-Synthesis

A discrete number of studies have been conducted on the effects of rhizobia (Rhz) inoculants, phosphorus (P) management, and combined application of Rhz and P fertilizer on the enhancement of grain legume yield across soils of Ghana and elsewhere. However, the extent to which the various inoculated Rhz strains, P application, and combined application of Rhz + P studies contribute to improving yield, performed on a comprehensive analysis approach, and profit farmers are yet to be understood. This study reviewed different experimental studies conducted on soybean (Glycine max (L.) Merr.), cowpea (Vigna unguiculata [L.] Walp), and groundnut (Arachis hypogaea [L.]) to which Rhz inoculants, P supplements, or Rhz + P combination were applied to improve the yield in Ghana. Multiple-step search combinations of published articles and multivariate analysis computing approaches were used to assess the effects of Rhz inoculation, P application, or both application of Rhz and P on yield variation. The random forest (RF) regression model was further employed to quantify the relative importance of various predictor variables on yield. The meta-analysis results showed that cowpea exhibited the highest (61.7%) and groundnut (19.8%) the lowest average yield change. The RF regression model revealed that the combined application of Rhz and P fertilizer (10.5%) and Rhz inoculation alone (7.8%) were the highest explanatory variables to predict yield variation in soybean. The Rhz + P combination, Rhz inoculation, and genotype wang-Kae explained 11.6, 10.02, and 8.04% of yield variability for cowpea, respectively. The yield in the inoculated plants increased by 1.48-, 1.26-, and 1.16-fold when compared to that in the non-inoculated cowpea plants following inoculation with BR 3299, KNUST 1002, and KNUST 1006 strains, respectively. KNUST 1006 strain exhibited the highest yield increase ratio (1.3-fold) in groundnut plants. Inoculants formulation with a viable concentration of 10⁹ cells g^-1 and a minimum inoculum rate of 1.0 × 10⁶ cells seed^-1 achieved the highest average yield change for soybean but not for cowpea and groundnut. The meta-analysis calls for prospective studies to investigate the minimum rate of bacterial cells required for optimum inoculation responses in cowpea and groundnut.

Mechanistic understanding of interspecific interaction between a C4 grass and a C3 legume via arbuscular mycorrhizal fungi, as influenced by soil phosphorus availability using a 13 C and 15 N dual-labelled organic patch

Arbuscular mycorrhizal fungi (AMF) can improve plant nutrient acquisition, either by directly supplying nutrients to plants or by promoting soil organic matter mineralization, thereby affecting interspecific plant relationships in natural communities. We examined the mechanism by which the addition of P affects interspecific interactions between a C4 grass (Bothriochloa ischaemum, a dominant species in natural grasslands) and a C3 legume (Lespedeza davurica, a subordinate species in natural grasslands) via AMF and plant growth, by continuous ¹³ C and ¹⁵ N labelling, combined with soil enzyme analyses. The results of ¹⁵ N labelling revealed that P addition affected the shoot uptake of N via AMF by B. ischaemum and L. davurica differently. Specifically, the addition of P significantly increased the shoot uptake of N via AMF by B. ischaemum but significantly decreased that by L. davurica. Interspecific plant interactions via AMF significantly facilitated the plant N uptake via AMF by B. ischaemum but significantly inhibited that by L. davurica under P-limited soil conditions, whereas the opposite effect was observed in the case of excess P. This was consistent with the impact of interspecific plant interaction via AMF on arbuscular mycorrhizal (AM) benefit for plant growth. Our data indicate that the capability of plant N uptake via AMF is an important mechanism that influences interspecific relationships between C4 grasses and C3 legumes. Moreover, the effect of AMF on the activities of the soil enzymes responsible for N and P mineralization substantially contributed to the consequence of interspecific plant interaction via AMF for plant growth.

Comparative transcriptomic and metabolomic analyses reveal the protective effects of silicon against low phosphorus stress in tomato plants

Phosphorus (P) is an essential nutrient controlling plant growth and development through the regulation of basic metabolic processes. Soil P deficiency is one of the major limiting factors for sustainable crop production worldwide. Previous studies have demonstrated that silicon (Si), as a beneficial element, promotes plant nutrition, growth, development, and responses to low P (LP) stress; however, the molecular mechanisms underlying Si-mediated LP tolerance remain largely unclear. Here, we found that LP + Si treatment increased the net photosynthetic rate and shoot fresh weight by 34.3%, and 121.3%, respectively compared with LP alone. RNA-sequencing and metabolomic analyses were subsequently performed with tomato plants grown under control and P depleted conditions with or without Si amendment. RNA-sequencing showed that Si supply alters not only the expression of genes involved in the metabolism of carbon (C), nitrogen (N), and P but also phosphorylation processes and metabolism of glutathione and reactive active oxygen in tomato roots. Si also affected the expression of genes encoding major transcription factors such as WRKY and MYB under LP stress. Moreover, a set of genes encoding the enzymes or regulators of organic acid (OA) metabolism or secretion were differentially expressed in Si-treated P deficient roots compared with those in LP stress alone. Furthermore, the metabolomic analysis showed that the levels of several OAs were significantly elevated in Si-treated P deficient roots. Taken together, these results indicate that exogenous Si increases the secretion of OAs by modulating C/N metabolism in LP-treated tomato roots and thereby improving plant growth under LP stress.

Altering Nitrogen Sources Affects Growth Carbon Costs in Vachellia nilotica Growing in Nutrient-Deficient Grassland Soils

Vachellianilotica (L.) Willd. Ex Del. is a multipurpose leguminous tree that is common in grassland and savanna ecosystems in southern and eastern Africa. These ecosystem soils are reported to be acidic and nutrient-limited, specifically with regards to nitrogen (N) and phosphorus (P). The presence of this plant in these terrestrial ecosystems improves soil fertility benefiting the surrounding vegetation due to its ability to fix atmospheric N. This study seeks to understand the N-fixing bacteria symbiosis and physiological adaptations of V. nilotica in these acidic and nutrient-deficient KwaZulu-Natal soils. The soils used for this study were collected from the Ukulinga Grassland Nutrient Experiment located at the Ukulinga research farm of the University of KwaZulu-Natal, Pietermaritzburg, South Africa. Due to long-term soil nutrient addition treatments, these soils offered a diverse nutrient variation for better understanding the effects of acidity and nutrient variation on microbial symbiosis, plant nutrition, and biomass accumulation of V. nilotica. V. nilotica was able to maintain growth by relying on both atmospheric and soil-derived N across all treatments decreasing carbon (C) growth costs. There was an increased reliance on atmospheric-derived N of un-nodulated high N-treated plants. The plants grown in high N + P soils were able to nodulate with various species from the Mesorhizobium genus, which resulted in increased biomass compared to other plants. The results of this study show that V. nilotica can alter N sources to reduce C growth costs. In addition, both nodulating and free-living soil N₂ fixing bacteria such as Caulobacter rhizosphaerae, Sphingomonas sp. and Burkholderia contaminans identified in the experimental soils may play an important role under P-deficient conditions.

The soybean β-expansin gene GmINS1 contributes to nodule development in response to phosphate starvation

Legume biological nitrogen fixation (BNF) is the most important N source in agricultural ecosystems. Nodule organogenesis from the primordia to the development of mature nodules with the ability to fix N2 largely determines BNF capacity. However, nodule growth is often limited by low phosphorus (P) availability, while the mechanisms underlying nodule development responses to P deficiency remain largely unknown. In this study, we found that nodule enlargement is severely inhibited by P deficiency, as reflected by the smaller individual nodule size from a soybean core collection in the field. Wide-ranging natural diversity in nodule size was further identified in soybeans reared in low P soils, with the FC-1 genotype outperforming FC-2 in assessments of nodulation under low P conditions. Among β-expansin members, GmINS1 expression is most abundantly enhanced by P deficiency in FC-1 nodules, and its transcript level is further displayed to be tightly associated with nodule enlargement. Four single nucleotide polymorphisms discovered in the GmINS1 promoter distinguished the FC-1 and FC-2 genotypes and accounted for the differential expression levels of GmINS1 responses to P deficiency. GmINS1 overexpression led to increases in nodule size, infected cell abundance, and N2 fixation capacity and subsequently promoted increases in N and P content, soybean biomass, and yield. Our findings provide a candidate gene for optimizing BNF capacity responses to low P stress in soybean molecular breeding programs.

Differentially expressed microRNAs that target functional genes in mature soybean nodules

MicroRNAs (miRNAs) are important regulators of biological functions in plants. To find out what roles miRNAs play in regulating symbiotic nitrogen fixation (SNF) in soybean [Glycine max (L.) Merr.], we identified high-confidence differentially expressed (DE) miRNAs from uninoculated roots (UR), rhizobium-inoculated roots (IR), and nodules (NODs) of soybean by robust small RNA sequencing (sRNA-seq). Based on their predicted target messenger RNAs (mRNAs), the expression profiles of some of these DE miRNAs could be linked to nodule functions. In particular, several miRNAs associated with nutrient transportation genes were differentially expressed in IRs and mature NODs. MiR399b, specifically, was highly induced in IRs and NODs, as well as by inorganic phosphate (Pi) starvation. In composite soybean plants overexpressing miR399b, PHOSPHATE2 (PHO2), a known target of miR399b that inhibits the activities of high-affinity Pi transporters, was strongly repressed. In addition, the overexpression of miR399b in the roots of transgenic composite plants significantly improved whole-plant Pi and ureide concentrations and the overall growth in terms of leaf node numbers and whole-plant dry weight. Our findings suggest that the induction of miR399b in NODs could enhance nitrogen fixation and soybean growth, possibly via improving Pi uptake to achieve a better Pi-nitrogen balance to promote SNF in nodules.

Application of Nitrate, Ammonium, or Urea Changes the Concentrations of Ureides, Urea, Amino Acids and Other Metabolites in Xylem Sap and in the Organs of Soybean Plants (Glycine max (L.) Merr.)

Soybean (Glycine max (L.) Merr.) plants form root nodules and fix atmospheric dinitrogen, while also utilizing the combined nitrogen absorbed from roots. In this study, nodulated soybean plants were supplied with 5 mM N nitrate, ammonium, or urea for 3 days, and the changes in metabolite concentrations in the xylem sap and each organ were analyzed. The ureide concentration in the xylem sap was the highest in the control plants that were supplied with an N-free nutrient solution, but nitrate and asparagine were the principal compounds in the xylem sap with nitrate treatment. The metabolite concentrations in both the xylem sap and each organ were similar between the ammonium and urea treatments. Considerable amounts of urea were present in the xylem sap and all the organs among all the treatments. Positive correlations were observed between the ureides and urea concentrations in the xylem sap as well as in the roots and leaves, although no correlations were observed between the urea and arginine concentrations, suggesting that urea may have originated from ureide degradation in soybean plants, possibly in the roots. This is the first finding of the possibility of ureide degradation to urea in the underground organs of soybean plants.

Phosphorus deprivation affects composition and spatial distribution of membrane lipids in legume nodules

In legumes, symbiotic nitrogen (N) fixation (SNF) occurs in specialized organs called nodules after successful interactions between legume hosts and rhizobia. In a nodule, N-fixing rhizobia are surrounded by symbiosome membranes, through which the exchange of nutrients and ammonium occurs between bacteria and the host legume. Phosphorus (P) is an essential macronutrient, and N2-fixing legumes have a higher requirement for P than legumes grown on mineral N. As in the previous studies, in P deficiency, barrel medic (Medicago truncatula) plants had impaired SNF activity, reduced growth, and accumulated less phosphate in leaves, roots, and nodules compared with the plants grown in P sufficient conditions. Membrane lipids in M. truncatula tissues were assessed using electrospray ionization-mass spectrometry. Galactolipids were found to increase in P deficiency, with declines in phospholipids (PL), especially in leaves. Lower PL losses were found in roots and nodules. Subsequently, matrix-assisted laser desorption/ionization-mass spectrometry imaging was used to spatially map the distribution of the positively charged phosphatidylcholine (PC) species in nodules in both P-replete and P-deficient conditions. Our results reveal heterogeneous distribution of several PC species in nodules, with homogeneous distribution of other PC classes. In P poor conditions, some PC species distributions were observed to change. The results suggest that specific PC species may be differentially important in diverse nodule zones and cell types, and that membrane lipid remodeling during P stress is not uniform across the nodule.

Title: Hypermethylation of miRNA Genes During Nodule Development

DNA methylation has recently emerged as a powerful regulatory mechanism controlling the expression of key regulators of various developmental processes, including nodulation. However, the functional role of DNA methylation in regulating the expression of microRNA (miRNA) genes during the formation and development of nitrogen-fixing nodules remains largely unknown. In this study, we profiled DNA methylation patterns of miRNA genes during nodule formation, development, and early senescence stages in soybean (Glycine max) through the analysis of methylC-seq data. Absolute DNA methylation levels in the CG, CHH, and CHH sequence contexts over the promoter and primary transcript regions of miRNA genes were significantly higher in the nodules compared with the corresponding root tissues at these three distinct nodule developmental stages. We identified a total of 82 differentially methylated miRNAs in the nodules compared with roots. Differential DNA methylation of these 82 miRNAs was detected only in the promoter (69), primary transcript region (3), and both in the promoter and primary transcript regions (10). The large majority of these differentially methylated miRNAs were hypermethylated in nodules compared with the corresponding root tissues and were found mainly in the CHH context and showed stage-specific methylation patterns. Differentially methylated regions in the promoters of 25 miRNAs overlapped with transposable elements, a finding that may explain the vulnerability of miRNAs to DNA methylation changes during nodule development. Gene expression analysis of a set of promoter-differentially methylated miRNAs pointed to a negative association between DNA methylation and miRNA expression. Gene Ontology and pathways analyses indicate that changes in DNA methylation of miRNA genes are reprogrammed and contribute to nodule development through indirect regulation of genes involved in cellular processes and pathways with well-established roles in nodulation.

The cross-kingdom roles of mineral nutrient transporters in plant-microbe relations

The regulation of plant physiology by plant mineral nutrient transporter (MNT) is well understood. Recently, the extensive characterization of beneficial and pathogenic plant-microbe interactions has defined the roles for MNTs in such relationships. In this review, we summarize the roles of diverse nutrient transporters in the symbiotic or pathogenic relationships between plants and microorganisms. In doing so, we highlight how MNTs of plants and microbes can act in a coordinated manner. In symbiotic relationships, MNTs play key roles in the establishment of the interaction between the host plant and rhizobium or mycorrhizae as well in the subsequent coordinated transport of nutrients. Additionally, MNTs may also regulate the colonization or degeneration of symbiotic microorganisms by reflecting the nutrient status of the plant and soil. This allows the host plant obtain nutrients from the soil in the most optimal manner. With pathogenic-interactions, MNTs influence pathogen proliferation, the efficacy of the host's biochemical defense and related signal transduction mechanisms. We classify the MNT effects in plant-pathogen interactions as either indirect by influencing the nutrient status and fitness of the pathogen, or direct by initiating host defense mechanisms. While such observations indicate the fundamental importance of MNTs in governing the interactions with a range of microorganisms, further work is needed to develop an integrative understanding of their functions.

Co-Inoculation of Mesorhizobium ciceri with Either Bacillus sp. or Enterobacter aerogenes on Chickpea Improves Growth and Productivity in Phosphate-Deficient Soils in Dry Areas of a Mediterranean Region

Biological nitrogen fixation requires a large amount of phosphorus (P). However, most of the soils are P-deficient and the extensive use of P- chemical fertilizers constitute a serious threat to the environment. In this context, two field experiments were carried out to investigate the effect of co-inoculation of Mesorhizobium ciceri with phosphate solubilizing bacteria (PSB), Bacillus sp., and Enterobacter aerogenes, on chickpea as an alternative to chemical nitrogen (N) and phosphorous fertilizers in P-deficient soils in dry areas of Morocco. The results revealed that combined inoculation of chickpea with rhizobia and PSB showed a significant enhancement of chickpea nodulation, biomass production, yields and N, P, and protein content in grains as compared to single inoculation or single application of N or P. A significantly higher increase was obtained by inoculating chickpea with Mesorhizobium sp. MA72 combined with E. aerogenes P1S6. This combination allowed an enhancement of more than 270% in nodulation, 192% in shoot dry weight and 242% in grain yield. The effect of this combination was equivalent to the effect of combined application of N and P fertilizers. Formulation of biofertilizers based on tasted strains could be used for chickpea co-inoculation in P-deficient soils for an eco-friendly sustainable production of chickpea.

Nitrogen and Phosphorus Interplay in Lupin Root Nodules and Cluster Roots

Nitrogen (N) and phosphorus (P) are two major plant nutrients, and their deficiencies often limit plant growth and crop yield. The uptakes of N or P affect each other, and consequently, understanding N-P interactions is fundamental. Their signaling mechanisms have been studied mostly separately, and integrating N-P interactive regulation is becoming the aim of some recent works. Lupins are singular plants, as, under N and P deficiencies, they are capable to develop new organs, the N2-fixing symbiotic nodules, and some species can also transform their root architecture to form cluster roots, hundreds of short rootlets that alter their metabolism to induce a high-affinity P transport system and enhance synthesis and secretion of organic acids, flavonoids, proteases, acid phosphatases, and proton efflux. These modifications lead to mobilization in the soil of, otherwise unavailable, P. White lupin (Lupinus albus) represents a model plant to study cluster roots and for understanding plant acclimation to nutrient deficiency. It tolerates simultaneous P and N deficiencies and also enhances uptake of additional nutrients. Here, we present the structural and functional modifications that occur in conditions of P and N deficiencies and lead to the organogenesis and altered metabolism of nodules and cluster roots. Some known N and P signaling mechanisms include different factors, including phytohormones and miRNAs. The combination of the individual N and P mechanisms uncovers interactive regulation pathways that concur in nodules and cluster roots. L. albus interlinks N and P recycling processes both in the plant itself and in nature.

PHO1 family members transport phosphate from infected nodule cells to bacteroids in Medicago truncatula

Legumes play an important role in the soil nitrogen availability via symbiotic nitrogen fixation (SNF). Phosphate (Pi) deficiency severely impacts SNF because of the high Pi requirement of symbiosis. Whereas PHT1 transporters are involved in Pi uptake into nodules, it is unknown how Pi is transferred from the plant infected cells to nitrogen-fixing bacteroids. We hypothesized that Medicago truncatula genes homologous to Arabidopsis PHO1, encoding a vascular apoplastic Pi exporter, are involved in Pi transfer to bacteroids. Among the seven MtPHO1 genes present in M. truncatula, we found that two genes, namely MtPHO1.1 and MtPHO1.2, were broadly expressed across the various nodule zones in addition to the root vascular system. Expressions of MtPHO1.1 and MtPHO1.2 in Nicotiana benthamiana mediated specific Pi export. Plants with nodule-specific downregulation of both MtPHO1.1 and MtPHO1.2 were generated by RNA interference (RNAi) to examine their roles in nodule Pi homeostasis. Nodules of RNAi plants had lower Pi content and a three-fold reduction in SNF, resulting in reduced shoot growth. Whereas the rate of 33Pi uptake into nodules of RNAi plants was similar to control, transfer of 33Pi from nodule cells into bacteroids was reduced and bacteroids activated their Pi-deficiency response. Our results implicate plant MtPHO1 genes in bacteroid Pi homeostasis and SNF via the transfer of Pi from nodule infected cells to bacteroids.

Nitrogen and Phosphorus Signaling and Transport During Legume-Rhizobium Symbiosis

Nitrogen (N) and phosphorus (P) are the two predominant mineral elements, which are not only essential for plant growth and development in general but also play a key role in symbiotic N fixation in legumes. Legume plants have evolved complex signaling networks to respond to both external and internal levels of these macronutrients to optimize symbiotic N fixation in nodules. Inorganic phosphate (Pi) and nitrate (NO₃ ^-) are the two major forms of P and N elements utilized by plants, respectively. Pi starvation and NO₃ ^- application both reduce symbiotic N fixation via similar changes in the nodule gene expression and invoke local and long-distance, systemic responses, of which N-compound feedback regulation of rhizobial nitrogenase activity appears to operate under both conditions. Most of the N and P signaling and transport processes have been investigated in model organisms, such as Medicago truncatula, Lotus japonicus, Glycine max, Phaseolus vulgaris, Arabidopsis thaliana, Oryza sativa, etc. We attempted to discuss some of these processes wherever appropriate, to serve as references for a better understanding of the N and P signaling and transport during symbiosis.

Formulation of Biochar-Based Phosphorus Fertilizer and Its Impact on Both Soil Properties and Chickpea Growth Performance

There is no alternative to phosphorus (P) in agriculture as it is second most important plant nutrient after nitrogen. Mineral P fertilizers are derived from rock phosphate (RP) which is finite, non-renewable and geographically restricted to a few countries, thus its shortage likely affects agriculture in near future as the world population is growing at a greater pace. This could increase P inputs in agriculture in order to meet rising food demands which may result in the depletion of RP reserves. Furthermore, P losses from farmlands in case of mineral P fertilizers also demands the sustainable use of P not only because of its finite resources but also the environmental concerns associated with P fertilization such as eutrophication. The present study was designed to formulate biochar-based P fertilizer that would help in the sustainable use of P fertilizer. Biochar(s) were prepared using wheat straw at 350–400 °C pyrolytic temperature followed by enrichment with Di-ammonium phosphate (DAP) taking into account all possible combination of DAP to biochar on the w/w basis (0:100, 25:75, 50:50, 75:25 and 100:0). Enrichment was carried out using two different methods i.e., phosphorus enriched biochar (PEB1) by hot method and cold method (PEB2). An incubation experiment was performed to assess the impact of each biochar on selected properties of soil. The treatments were organized in factorial arrangement under complete randomized design (CRD) with three replications. Both the amendments were applied at rate of 1% of dry soil on a w/w basis. A significant increase in soil extractable P and total nitrogen (N) was recorded for the ratio 50:50 as compared to control as well of rest of treatments. Similarly, high organic contents were found for both PEB1 and PEB2 at the ratio 50:50. An incubation experiment was followed by pot trial using 50:50 for both PEB1 and PEB2 and split doses of recommended P were applied (0%, 25%, 50% and 100%) with a control under CRD with three replications using chickpea as test crop. Both PEB1 and PEB2 with 50% P have significantly improved crop growth, yield, nodulation, and plant physiological and chemical parameters as compared to a recommended dose of P alone. The result may imply that the integration of P-enriched biochar and chemical fertilizer could be an effective approach to improve chickpea production and soil properties.

Field pea (Pisum sativum L.) shows genetic variation in phosphorus use efficiency in different P environments

Field pea is important to agriculture as a nutritionally dense legume, able to fix nitrogen from the atmosphere and supply it back to the soil. However, field pea requires more phosphorus (P) than other crops. Identifying field pea cultivars with high phosphorus use efficiency (PUE) is highly desirable for organic pulse crop biofortification. This study identified field pea accessions with high PUE by determining (1) the variation in P remobilization rate, (2) correlations between P and phytic acid (PA), and (3) broad-sense heritability estimates of P concentrations. Fifty field pea accessions were grown in a completely randomized design in a greenhouse with two replicates under normal (7551 ppm) and reduced (4459 ppm) P fertilizer conditions and harvested at two time points (mid-pod and full-pod). P concentrations ranged from 332 to 9520 ppm under normal P and from 83 to 8473 ppm under reduced P conditions across all tissues and both time points. Field pea accessions showed variation in remobilization rates, with PI 125840 and PI 137119 increasing remobilization of P under normal P conditions. Field pea accessions PI 411142 and PI 413683 increased P remobilization under the reduced P treatment. No correlation was evident between tissue P concentration and seed PA concentration (8-61 ppm). Finally, seed P concentration under limited P conditions was highly heritable (H2 = 0.85), as was mid-pod lower leaf P concentrations under normal P conditions (H2 = 0.81). In conclusion, breeding for PUE in field pea is possible by selecting for higher P remobilization accessions in low P soils with genetic and location sourcing.

The histone modification H3K4me3 marks functional genes in soybean nodules

Nitrogen fixation in legumes requires the development of specialized organs called root nodules. Here we characterized the high-confidence transcriptome and genome-wide patterns of H3K4me3 marks in soybean roots and mature nodules symbiotic with Sinorhizobium fredii. Changes in H3K4me3 levels were positively associated with the transcription levels of functional genes in the nodules. The up-regulation of H3K4me3 levels was not only present in leghaemoglobin and nodulin-related genes, but also in genes involved in nitrogen and carbon metabolic pathways. In addition, genes regulating the transmembrane transport of metal ions, phosphates, sulphates, peptides, and sugars were differentially modified. On the contrary, a loss of H3K4me3 marks was found in several key transcription factor genes and was correlated with the down-regulation of the defense-related network in nodules, which could contribute to nodule maintenance. All these findings demonstrate massive reprogramming of gene expressions via alterations in H3K4me3 levels in the genes in mature soybean nodules.

miR168 targets Argonaute1A mediated miRNAs regulation pathways in response to potassium deficiency stress in tomato

BACKGROUND

Potassium (K⁺) is an essential ion for most plants, as it is involved in the regulation of growth and development. K⁺ homeostasis in plant cells has evolved to facilitate plant adaptation to K⁺-deficiency stress. Argonaute1 (AGO1) is regulated by miR168 to modulate the small RNA regulatory pathway by RNA silencing complex (RISC) in tomatoes. However, the role of miR168-mediated regulation of AGO1 in the context of K⁺ deficiency stress in tomatoes has not been elucidated yet.

RESULTS

SlmiR168 and its target gene SlAGO1A were differentially expressed among low-K⁺-tolerant JZ34 and low-K⁺-sensitive JZ18 tomato plants. Transgenic tomato plants constitutively expressing pri-SlmiR168a showed stronger root system growth, better leaves development, and higher K⁺ contents in roots under K⁺-deficiency stress than those of the transgenic tomato lines expressing rSlAGO1A (SlmiR168-resistant) and the wild type (WT). Deep sequencing analysis showed that 62 known microRNAs (miRNAs) were up-regulated in 35S:rSlAGO1 compared with WT tomatoes. The same miRNAs were down-regulated in 35S:SlmiR168a compared with WT plants. The integrated analysis found 12 miRNA/mRNA pairs from the 62 miRNAs, including the root growth and cytokinin (CTK)/abscisic acid (ABA) pathways.

CONCLUSIONS

The regulation mediated by SlmiR168 of SlAGO1A contributes to the plant development under low-K⁺ stress. Moreover, this regulation mechanism may influence downstream miRNA pathways in response to low-K⁺ stress through the CTK/ABA and root growth modulation pathways.

In Vivo Metabolic Regulation of Alternative Oxidase under Nutrient Deficiency-Interaction with Arbuscular Mycorrhizal Fungi and Rhizobium Bacteria

The interaction of the alternative oxidase (AOX) pathway with nutrient metabolism is important for understanding how respiration modulates ATP synthesis and carbon economy in plants under nutrient deficiency. Although AOX activity reduces the energy yield of respiration, this enzymatic activity is upregulated under stress conditions to maintain the functioning of primary metabolism. The in vivo metabolic regulation of AOX activity by phosphorus (P) and nitrogen (N) and during plant symbioses with Arbuscular mycorrhizal fungi (AMF) and Rhizobium bacteria is still not fully understood. We highlight several findings and open questions concerning the in vivo regulation of AOX activity and its impact on plant metabolism during P deficiency and symbiosis with AMF. We also highlight the need for the identification of which metabolic regulatory factors of AOX activity are related to N availability and nitrogen-fixing legume-rhizobia symbiosis in order to improve our understanding of N assimilation and biological nitrogen fixation.

GmPAP12 Is Required for Nodule Development and Nitrogen Fixation Under Phosphorus Starvation in Soybean

Nodulation process in legume plants is essential for biological nitrogen fixation during which process a large amount of phosphorus (P) is required. Under P deficiency, nodule formation is greatly affected, and induction of purple acid phosphatases (PAPs) is an adaptive strategy for nodules to acquire more P. However, regulation roles of PAPs in nodules remain largely understood. In this study, by transcriptome sequencing technology, five PAP genes were found to be differentially expressed, which led to the greatly increased acid phosphatase (APase) and phytase activities in soybean mature nodules under P starvation conditions; and among the five PAP genes, GmPAP12 had the highest transcript level, and RT-PCR indicated expression of GmPAP12 was gradually increasing during nodule development. GUS activity driven by GmPAP12 promoter was also significantly induced in low phosphorus conditions. Further functional analysis showed that under low phosphorus stress, overexpression of GmPAP12 resulted in higher nodule number, fresh weight, and nitrogenase activity as well as the APase activity than those of control plant nodules, whereas the growth performance and APase activity of nodules on hairy roots were greatly lower when GmPAP12 was suppressed, indicating that GmPAP12 may promote P utilization in soybean nodules under low P stress, which thus played an important role in nodulation and biological nitrogen fixation. Moreover, P1BS elements were found in the promoter of GmPAP12, and yeast one-hybrid experiment further proved the binding of P1BS by transcription factor GmPHR1 in the promoter of GmPAP12. At last, overexpression and suppression of GmPHR1 in nodules indeed caused highly increased and decreased expression of GmPAP12, respectively, indicating that GmPAP12 is regulated by GmPHR1 in soybean nodules. Taken together, these data suggested that GmPAP12 was a novel soybean PAP involved in the P utilization and metabolism in soybean root nodules and played an important role in the growth and development of root nodules and biological nitrogen fixation.

Biochemical and Molecular Characterization of PvNTD2, a Nucleotidase Highly Expressed in Nodules from Phaseolus vulgaris

Nucleotides are molecules of great importance in plant physiology. In addition to being elementary units of the genetic material, nucleotides are involved in bio-energetic processes, play a role as cofactors, and are also components of secondary metabolites and the hormone cytokinin. The common bean (Phaseolus vulgaris) is a legume that transports the nitrogen fixed in nodules as ureides, compounds synthetized from purine nucleotides. The first step in this pathway is the removal of the 5’-phosphate group by a phosphatase. In this study, a gene that codes for a putative nucleotidase (PvNTD2) has been identified in P. vulgaris. The predicted peptide contains the conserved domains for haloacid dehalogenase-like hydrolase superfamily. The protein has been overexpressed in Escherichia coli, and the purified protein showed molybdate-resistant phosphatase activity with nucleoside monophosphates as substrates, confirming that the identified gene codes for a nucleotidase. The optimum pH for the activity was 7–7.5. The recombinant enzyme did not show special affinity for any particular nucleotide, although the behaviour with AMP was different from that with the other nucleotides. The activity was inhibited by adenosine, and a regulatory role for this nucleoside was proposed. The expression pattern of PvNTD2 shows that it is ubiquitously expressed in all the tissues analysed, with higher expression in nodules of adult plants. The expression was maintained during leaf ontogeny, and it was induced during seedling development. Unlike PvNTD1, another NTD previously described in common bean, the high expression of PvNTD2 was maintained during nodule development, and its possible role in this organ is discussed.

Divergent metabolic adjustments in nodules are indispensable for efficient N2 fixation of soybean under phosphate stress

The main objective of the present study was to characterize the symbiotic N2 fixation (SNF) capacity and to elucidate the underlying mechanisms for low-Pi acclimation in soybean plants grown in association with two Bradyrhizobium diazoefficiens strains which differ in SNF capacity (USDA110 vs. CB1809). In comparison with the USDA110-soybean, the CB1809-soybean association revealed a greater SNF capacity in response to Pi starvation, as evidenced by relative higher plant growth and higher expression levels of the nifHDK genes. This enhanced Pi acclimation was partially related to the efficient utilization to the overall carbon (C) budget of symbiosis in the CB1809-induced nodules compared with that of the USDA110-induced nodules under low-Pi provision. In contrast, the USDA110-induced nodules favored other metabolic acclimation mechanisms that expend substantial C cost, and consequently cause negative implications on nodule C expenditure during low-Pi conditions. Fatty acids, phytosterols and secondary metabolites are characterized among the metabolic pathways involved in nodule acclimation under Pi starvation. While USDA110-soybean association performed better under Pi sufficiency, it is very likely that the CB1809-soybean association is better acclimatized to cope with Pi deficiency owing to the more effective functional plasticity and lower C cost associated with these nodular metabolic arrangements.

Checking Agriculture's Pulse: Field Pea (Pisum Sativum L.), Sustainability, and Phosphorus Use Efficiency

Investigations regarding the incorporation of better sustainable production strategies into current agricultural-food systems are necessary to grow crops that reduce negative impacts on the environment yet will meet the production and nutritional demand of 10 billion people by 2050. The introduction of organic, alternative staple food crops, such as nutrient-dense field pea (Pisum sativum L.), to the everyday diet, may alleviate micronutrient malnutrition and incorporate more sustainable agriculture practices globally. Varieties are grown in organic systems currently yield less than conventionally produced foods, with less bioavailable nutrients, due to poor soil nutrient content. One of the most limiting nutrients for field pea is phosphorus (P) because this legume crop requires significant inputs for nodule formation. Therefore, P use efficiency (PUE) should be a breeding target for sustainable agriculture and biofortification efforts; the important role of the soil microbiome in nutrient acquisition should also be examined. The objectives of this review are to highlight the benefits of field pea for organic agriculture and human health, and discuss nutritional breeding strategies to increase field pea production in organic systems. Field pea and other pulse crops are underrepresented in agricultural research, yet are important crops for a sustainable future and better food systems. Furthermore, because field pea is consumed globally by both developed and at-risk populations, research efforts could help increase global health overall and combat micronutrient malnutrition.

Silicon Compensates Phosphorus Deficit-Induced Growth Inhibition by Improving Photosynthetic Capacity, Antioxidant Potential, and Nutrient Homeostasis in Tomato

Phosphorus (P) deficiency in soils is a major problem for sustainable crop production worldwide. Silicon (Si) is a beneficial element that can promote plant growth, development and responses to stresses. However, the effect of Si on tomato (Solanum lycopersicum L.) growth, photosynthesis and mineral uptake under P deficit conditions and underlying mechanisms remain unclear. Here, we showed that low P (LP) supply inhibited tomato growth as revealed by significantly decreased fresh and dry weights of shoots and impaired root morphological traits. LP-induced growth inhibition was associated with decreased photosynthetic pigment content, net photosynthetic rate (Pn), stomatal conductance, transpiration rate and water use efficiency. However, exogenous Si application alleviated LP-induced decreases in growth and physiological parameters. In particular, Si increased Pn by 65.2%, leading to a significantly increased biomass accumulation. Biochemical quantification and in situ visualization of reactive oxygen species (ROS) showed increased ROS (O2−· and H2O2) accumulation under LP stress, which eventually elevated lipid peroxidation. Interestingly, exogenous Si decreased ROS and malondialdehyde levels by substantially increasing the activity of antioxidant enzymes, including superoxide dismutase, peroxidase, and catalase. In addition, Si increased concentrations of osmoregulatory substances, such as proline, soluble sugar, soluble proteins, free amino acids, and organic acids under LP stress. Analysis of major element concentrations revealed that exogenous Si application under LP stress not only increased Si uptake but also enhanced the concentrations of most essential elements (K, Na, Ca, Mg, Fe, and Mn) in different tissues (roots, leaves, and stems). These results reveal that Si mitigates LP stress by improving photosynthetic capacity, antioxidant potential, and nutrient homeostasis and that it can be used for agronomic management of vegetable crops in P-deficient soils.

Genetic variability of morpho-physiological response to phosphorus deficiency in Tunisian populations of Brachypodium hybridum

Brachypodium hybridum (Poaceae) is widely distributed in the dry environments in Mediterranean basin, due to its high tolerance to drought. Investigating the natural variation of B. hybridum in response to environmental stresses is crucial for unraveling the genetic network of its stress tolerance. 79 B. hybridum lines from eight Tunisian populations were screened for their performance to low P availability using morpho-physiological parameters. ANOVA showed that treatment and population*treatment factors were the most contributors in the explained variance for the majority of parameters. A considerable population differentiation was detected in control and under P level (Qst = 0.77 vs Qst = 0.62). This suggests that B. hybridum exhibit an adaptive differential response to P deficiency related environmental conditions. Results revealed that Raouad and Sejnen lines were the most tolerant to P deficiency followed by Haouaria and Enfidha lines. The remaining populations were classified as sensitive. This pattern suggests that coastal populations were more tolerant to P deficiency than the inland ones. A slightly higher heritability was evidenced under low P level for most of traits, indicating that the direct selection under P deficiency is more reliable than an indirect one under optimal P supply.