Integrative analysis of the metabolome and transcriptome reveal the phosphate deficiency response pathways of alfalfa

Physiological and molecular responses in phosphorus-hyperaccumulating Polygonum species to high phosphorus exposure

Phosphorus (P)-hyperaccumulators for phytoextraction from P-polluted areas generally show rapid growth and accumulate large amounts of P without any toxicity symptom, which depends on a range of physiological processes and gene expression patterns that have never been explored. We investigated growth, leaf element concentrations, P fractions, photosynthetic traits, and leaf metabolome and transcriptome response in amphibious P-hyperaccumulators, Polygonum hydropiper and P. lapathifolium, to high-P exposure (5 mmol L-1), with 0.05 mmol L-1 as the control. Under high-P exposure, both species demonstrated good growth, allocating more P to metabolite P and inorganic P (Pi) accompanied by high potassium and calcium. The expression of a cluster of unigenes associated with photosynthesis was maintained or increased in P. lapathifolium, explaining the increase in net photosynthetic rate and the rapid growth under high-P exposure. Metabolites of trehalose metabolism, including trehalose 6-phosphate and trehalose, were sharply increased in both species by the high-P exposure, in line with the enhanced expression of associated unigenes, indicating that trehalose metabolic pathway was closely related to high-P tolerance. These findings elucidated the physiological and molecular responses involved in the photosynthesis and trehalose metabolism in P-hyperaccumulators to high-P exposure, and provides potential regulatory pathways to improve the P-phytoextraction capability.

Effects of phosphorus stress on the growth and secondary metabolism of Artemisia argyi

Phosphorus is essential in critical plant processes such as signaling, photosynthesis, energy metabolism, and enzyme activity during respiration. Phosphorus stress therefore has a significant impact on plant growth and metabolism. Here, we characterized the biochemical responses of Artemisia argyi Level. et Vant to low phosphorus (LP) and high phosphorus (HP) stress. Plants were treated with 0 g (LP), 1.5 g (control), or 3 g (HP) P per 10 kg of soil. The results demonstrated that CK encouraged the most plant growth, as quantified by leaf size and plant biomass. We also found that the total amounts of phenolic and flavonoid compounds (such as chlorogenic acid, isochlorogenic acid A, isochlorogenic acid B, isochlorogenic acid C, cryptochlorogenic acid, neochlorogenic acid, hispidulin, jaceosidin, eupatilin, and casticin) were increased in the leaves of A. argyi plants exposed to LP stress compared to those raised under CK conditions. The levels of these compounds were inversely related to the amount of phosphorus added, and therefore peaked in plants treated with LP stress. Levels of terpenoids were also found to fluctuate under LP and HP stress compared to CK conditions. Furthermore, transcriptomic analyses showed up-regulation of several genes encoding key enzymes in the flavonoid and phenolic acid metabolic pathways under LP stress. There were also alterations in the expression levels of genes in the methylerythritol 4-phosphate and mevalonate pathways of terpene synthesis. This study contributes to a deeper understanding of the physiological and molecular mechanisms underlying phosphorus stress responses and their impacts on the growth and quality of the economically important species A. argyi.

Transcriptome and Metabolome Analysis of Selenium Treated Alfalfa Reveals Influence on Phenylpropanoid Biosynthesis to Enhance Growth

Selenium (Se) plays an important role in the growth of plants. Alfalfa (Medicago sativa L.) is a perennial legume forage crop with high nutritional value and Se-rich functions. Many studies have shown that selenium can promote alfalfa growth, but few have explored the molecular biology mechanisms behind this effect. In this study, alfalfa was divided into two groups. One group was sprayed with sodium selenite (Na2SeO3) and the other group was sprayed with distilled water as a control. This study determined the growth, reproductive traits, physiological changes, transcriptome and metabolome of both groups of alfalfa. We found that foliar spraying of 100 mg/L Na2SeO3 could significantly increase the growth rate, dry weight, total Se content, amount of pollen per flower, pollen viability, pod spirals, and seed number per pod of alfalfa plants. The level of chlorophyll, soluble protein, proline, and glutathione also increased dramatically in Na2SeO3-sprayed alfalfa seedlings. After transcriptome and metabolome analysis, a total of 614 differentially expressed genes (DEGs) and 1500 differentially expressed metabolites (DEMs), including 26 secondary differentially metabolites were identified. The DEGs were mainly enriched in MAPK signaling pathway, phenylpropanoid biosynthesis, isoflavonoid biosynthesis, cutin, suberine, and wax biosynthesis, and glycerolipid metabolism. The DEMs were mainly enriched in flavone and flavonol biosynthesis, carbon metabolism, glyoxylate and dicarboxylate metabolism, nitrogen metabolism, and phenylpropanoid biosynthesis. Integrative analysis of transcriptome and metabolome showed that the foliar spraying of Na2SeO3 mainly affects phenylpropanoid biosynthesis to promote alfalfa growth.

Metabolic footprints in phosphate-starved plants

Plants' requirement of Phosphorus (P) as an essential macronutrient is obligatory for their normal growth and metabolism. Besides restricting plants' primary growth, P depletion affects both primary and secondary metabolism and leads to altered levels of sugars, metabolites, amino acids, and other secondary compounds. Such metabolic shifts help plants optimize their metabolism and growth under P limited conditions. Under P deprivation, both sugar levels and their mobilization change that influences the expression of Pi starvation-inducible genes. Increased sugar repartitioning from shoot to root help root growth and organic acids secretion that in turn promotes phosphate (Pi) uptake from the soil. Other metabolic changes such as lipid remodeling or P reallocation from older to younger leaves release the P from its bound forms in the cell. In this review, we summarize the metabolic footprinting of Pi-starved plants with respect to the benefits offered by such metabolic changes to intracellular Pi homeostasis.

Comparative proteome analysis of phosphorus-responsive genotypes reveals the proteins differentially expressed under phosphorous starvation stress in rice

Phosphorus (P)-deficiency is one of the major nutrient constraints for global rice production. P-deficiency tolerance in rice involves complex regulatory mechanisms. To gain insights into the proteins involved in phosphorus acquisition and use efficiency in rice, proteome analysis of a high-yielding rice cultivar Pusa-44 and its near-isogenic line (NIL)-23 harboring a major phosphorous uptake (Pup1) QTL, grown under control and P-starvation stress, was performed. Comparative proteome profiling of shoot and root tissues from the plants grown hydroponically with P (16 ppm, +P) or without P (0 ppm, -P) resulted in the identification of 681 and 567 differentially expressed proteins (DEPs) in shoot of Pusa-44 and NIL-23, respectively. Similarly, 66 and 93 DEPs were identified in root of Pusa-44 and NIL-23, respectively. These P-starvation responsive DEPs were annotated to be involved in metabolic processes like photosynthesis, starch-, sucrose-, energy-metabolism, transcription factors (mainly ARF, ZFP, HD-ZIP, MYB), and phytohormone signaling. Comparative analysis of the expression patterns observed by proteome analysis with that reported at the transcriptome level indicated the Pup1 QTL-mediated post-transcriptional regulation plays an important role under -P stress. Thus, the present study describes the molecular aspect of the regulatory functions of Pup1 QTL under P-starvation stress in rice, which might help develop an efficient rice cultivar with enhanced P acquisition and assimilation for better performance in P-deficient soil.

Plant Metabolomics: An Overview of the Role of Primary and Secondary Metabolites against Different Environmental Stress Factors

Several environmental stresses, including biotic and abiotic factors, adversely affect the growth and development of crops, thereby lowering their yield. However, abiotic factors, e.g., drought, salinity, cold, heat, ultraviolet radiations (UVr), reactive oxygen species (ROS), trace metals (TM), and soil pH, are extremely destructive and decrease crop yield worldwide. It is expected that more than 50% of crop production losses are due to abiotic stresses. Moreover, these factors are responsible for physiological and biochemical changes in plants. The response of different plant species to such stresses is a complex phenomenon with individual features for several species. In addition, it has been shown that abiotic factors stimulate multi-gene responses by making modifications in the accumulation of the primary and secondary metabolites. Metabolomics is a promising way to interpret biotic and abiotic stress tolerance in plants. The study of metabolic profiling revealed different types of metabolites, e.g., amino acids, carbohydrates, phenols, polyamines, terpenes, etc, which are accumulated in plants. Among all, primary metabolites, such as amino acids, carbohydrates, lipids polyamines, and glycine betaine, are considered the major contributing factors that work as osmolytes and osmoprotectants for plants from various environmental stress factors. In contrast, plant-derived secondary metabolites, e.g., phenolics, terpenoids, and nitrogen-containing compounds (alkaloids), have no direct role in the growth and development of plants. Nevertheless, such metabolites could play a significant role as a defense by protecting plants from biotic factors such as herbivores, insects, and pathogens. In addition, they can enhance the resistance against abiotic factors. Therefore, metabolomics practices are becoming essential and influential in plants by identifying different phytochemicals that are part of the acclimation responses to various stimuli. Hence, an accurate metabolome analysis is important to understand the basics of stress physiology and biochemistry. This review provides insight into the current information related to the impact of biotic and abiotic factors on variations of various sets of metabolite levels and explores how primary and secondary metabolites help plants in response to these stresses.

Integrated Omics Approach to Discover Differences in the Metabolism of a New Tibetan Desmodesmus sp. in Two Types of Sewage Treatments

Microalgae are now widely applied in municipal (YH_3) and industrial sewage (YH_4) treatments. Through integrated omics analysis, we studied the similarities and differences at the molecular level between the two different types of sewage treatment processes. The most significantly enriched gene ontology (GO) terms in both types of sewage treatments were the ribosome, photosynthesis, and proteasome pathways. The results show that the pathways of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were enriched for photosynthesis, glyoxylate and dicarboxylate metabolism, and carbon fixation in photosynthetic organisms. Considering YH_3 vs. YH_4, the metabolism of citrate, sedoheptulose-7P, and succinate was significantly upregulated. In addition, the results showed that the pathways of DEGs and DAMs were enriched in terms of amino acid metabolism and carotenoid biosynthesis in YH_4 vs. YH_3. The metabolism of S-Adenosyl-L-homocysteine was significantly downregulated, 2-oxobutanoate was significantly upregulated and downregulated, and the metabolism of abscisic acid glucose ester (ABA-GE) was also significantly upregulated. Overall, the results of this paper will help to improve the basic knowledge of the molecular response of microalgae to sewage treatments, and help design a response strategy based on microalgae for complex, mixed sewage treatments.

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.

Characterization of phosphate transporter genes and the function of SgPT1 involved in phosphate uptake in Stylosanthes guianensis

Phosphorus (P) is one of the principal macronutrients for plant growth and productivity. Although the phosphate (Pi) transporter (PT) of the PHT1 family has been functionally characterized as participating in Pi uptake and transport in plants, information about PT genes in stylo (Stylosanthes guianensis), an important tropical forage legume that exhibits good adaptability to low-P acid soils, is limited. In this study, stylo root growth was found to be stimulated under P deficiency. The responses of PT genes to nutrient deficiencies and their roles in Pi uptake were further investigated in stylo. Four novel PT genes were identified in stylo and designated SgPT2 to SgPT5. Like SgPT1, which had been previously identified, all five SgPT proteins harboured the major facilitator superfamily (MFS) domain. Variations in tissue-specific expression were observed among the SgPT genes, which displayed diverse responses to deficiencies in nitrogen (N), P and potassium (K) in stylo roots. Four of the five SgPTs exhibited high levels of transcriptional responsiveness to P deficiency in roots. Furthermore, SgPT1, a Pi-starvation-induced gene closely related to legume PT homologues that participate in Pi transport, was selected for functional analysis. SgPT1 was localized to the plasma membrane. Analysis of transgenic Arabidopsis showed that overexpression of SgPT1 led to increased Pi accumulation and promoted root growth in Arabidopsis plants. Taken together, the results of this study suggest the involvement of SgPTs in the stylo response to nutrient deprivation. SgPT1 might mediate Pi uptake in stylo, which is beneficial for root growth during P deficiency.

Dissection of the response mechanism of alfalfa under phosphite stress based on metabolomic and transcriptomic data

Phosphite, a reduced form of phosphate, inhibits the growth and even has toxic effect on plants. To learn more about the mechanism of alfalfa responses to phosphite, the morphological and physiological characteristics, and the metabolites and transcript levels were comprehensively analyzed following the exposure of alfalfa seedlings to phosphite and phosphate under greenhouse conditions. The results showed that phosphite inhibited seedling growth and photosynthesis. However, the absorption efficiency of phosphite was higher than that of phosphate in roots, which was supported by increased total phosphorus concentration of 16.29% and 52.30% on days 8 and 12. Moreover, phosphite stress affected the synthesis of lipids and carbohydrates, which were reflected in enhanced glycolipid and sulfolipid in roots and amylose in shoots. Phosphite stress resulted in a decrease in indole acetic acid (IAA) in the whole plant and zeatin in the shoots, which could enable alfalfa to adapt to the phosphite environment. Some genes involved in phosphate starvation response included SPX, phosphate response regulator2, and inorganic phosphate transporter 1-4 (PHT1;4) in roots were affected by phosphite stress. In addition, some genes that are involved in stress responses and DNA repair were induced by phosphite stress. These observations together suggest that alfalfa responds to phosphite stress by inhibiting growth, regulating the genes induced by phosphate starvation, improving oxidative protection, promoting DNA repair, and adjusting the IAA and zeatin signaling transductions. Our findings provide novel insights into the molecular response to phosphite stress in alfalfa.

Transcriptional profiling of long non-coding RNAs regulating fruit cracking in Punica granatum L. under bagging

Fruit cracking tremendously damages the appearance of fruit, easily leads to pathogen invasion, greatly reduces the marketability and causes immense economic losses. The pivotal role of long non-coding RNAs (lncRNAs) in diverse biological processes has been confirmed, while the roles of lncRNAs underlying fruit cracking remain poorly understood. In this study, the incidence of fruit cracking was 7.26% under the bagging treatment, the control group was 38.11%, indicating that bagging considerably diminished the fruit cracking rate. LncRNA libraries for fruit cracking (FC), fruit non-cracking (FNC) and fruit non-cracking under bagging (FB) in pomegranate (Punica granatum L.) were performed and analysed via high-throughput transcriptome sequencing. A total of 3194 lncRNAs were obtained with a total length of 4898846 nt and an average length of 1533.77 nt in pomegranate. We identified 42 differentially expressed lncRNAs (DELs) and 137 differentially expressed mRNAs (DEGs) in FC vs FNC and 35 DELs and 160 DEGs in FB vs FC that formed co-expression networks respectively, suggesting that there are involved in phytohormone signaling pathway, lignin catabolic process, lipid transport/binding, cutin biosynthetic process and cell wall organization. We also found that 18 cis-acting DELs regulated 18 target genes, and 10 trans-acting DELs regulated 24 target genes in FC vs FNC, 23 DELs regulate 23 target genes for the cis-acting lncRNAs and 12 DELs regulated 36 target genes in FB vs FC, which provides an understanding for the regulation of the fruit cracking. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results demonstrated that DELs participated in calcium ion binding, glycerophospholipid metabolism, flavonoid biosynthetic process, cell wall biogenesis, xyloglucan metabolic process, hormone signal transduction and starch and sucrose metabolism. Our findings provide new insights into the roles of lncRNAs in regulating the fruit cracking and lay the foundation for further improvement of pomegranate quality.

Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa

The deficiency of available phosphate significantly limits plant growth and development. This study sought to investigate how alfalfa (Medicago sativa), a high-yielding and high-quality forage widely cultivated worldwide, responds to phosphate deficiency stress by integrating transcriptional and post-transcriptional data. In this study, 6,041 differentially expressed genes (DEGs) were identified in alfalfa roots under phosphate deficiency conditions. Furthermore, psRNATarget, RNAhybrid, and TargetFinder were used to predict the target genes of 137 differentially expressed miRNAs (DEMs) in the root. In total, 3,912 DEGs were predicted as target genes. Pearson correlation analysis revealed 423 pairs of miRNA-mRNA regulatory relationships. MiRNA negatively regulates mRNA involved in regulatory pathways of phosphate deficiency responses in alfalfa. miR156e targeted squamosa promoter-binding-like protein 13A (SPL13), miR160c targeted auxin response factor 18 (ARF18), and miR2587a controlled glycolysis and citrate cycle via Phosphoenolpyruvate carboxykinase (ATP) (PCKA). Novel-miR27 regulated SPX domain-containing protein that controls phosphate transport in alfalfa root, novel-miR3-targeted sulfoquinovosyl transferase SQD2 controlled sulfolipid synthesis and glutathione S-transferase (GST; mediated by miR169j/k and novel-miR159) regulated glutathione metabolism. miR399l regulated auxin-responsive protein SAUR72 involved in IAA signal transduction, while abscisic acid receptor PYL4 (regulated by novel-miR205 and novel-miR83) participated in ABA signal transduction. Combined miRNA-mRNA enrichment analysis showed that most miRNAs regulate the phosphate starvation response of alfalfa by modulating target genes involved in carbohydrate metabolism, sulfolipid metabolism, glutathione metabolism, and hormone signal transduction. Therefore, this study provides new insights into the post-transcriptional regulation mechanism of phosphate deficiency responses and new perspectives on phosphate assimilation pathways in alfalfa and other legumes.

Phytoremediation of potentially toxic elements (PTEs) contaminated soils using alfalfa (Medicago sativa L.): A comprehensive review

Soil contamination with potentially toxic elements (PTEs) is an increasing environmental problem, posing serious threats to the living organisms. Phytoremediation is a sustainable and highly accepted technology for remediation of PTE-contaminated soils. Alfalfa has been widely adopted for the phytoremediation of PTE-contaminated soils due to its large biomass productivity, high PTE tolerance, and strong capacity to take up PTEs. However, there are still no literature reviews systematically summarized the potential of alfalfa in the phytoremediation. Therefore, we review the available literatures that present its PTE uptake, phytotoxicity, tolerance mechanisms, and aided techniques improving the phytoremediation efficiency. In this review, alfalfa shows high amounts of PTEs accumulation, especially in their root tissue. Meanwhile, the inner mechanisms of PTE tolerance and accumulation in alfalfa are discussed including: (i) the activation of antioxidant enzyme system, (ii) subcellular localization, (iii) production of glutathione, phytochelatins, and proline, and (iv) regulation of gene expression. Indeed, excessive PTE can overcome the defense system, which causes oxidative damage in alfalfa plants, thereby inhibiting growth and physiological processes and weakening the ability of PTE uptake. Till now, several approaches have been developed to improve the tolerance and/or accumulation of PTE in alfalfa plants as follows: (i) selection of PTE tolerant cultivars, (ii) applying plant growth regulators, (iii) addition of chelating agents, fertilizer, and biochar materials, and (iv) inoculation of soil microbes. Finally, we indicate that the selection of PTE-tolerant cultivars along with inoculation of soil microbes may be an efficient and eco-friendly strategy of the soil PTE phytoremediation.

Phosphorus homeostasis: acquisition, sensing, and long-distance signaling in plants

Phosphorus (P), an essential nutrient required by plants often becomes the limiting factor for plant growth and development. Plants employ various mechanisms to sense the continuously changing P content in the soil. Transcription factors, such as SHORT ROOT (SHR), AUXIN RESPONSE FACTOR19 (ARF19), and ETHYLENE-INSENSITIVE3 (EIN3) regulate the growth of primary roots, root hairs, and lateral roots under low P. Crop improvement strategies under low P depend either on improving P acquisition efficiency or increasing P utilization. The various phosphate transporters (PTs) are involved in the uptake and transport of P from the soil to various plant cellular organelles. A plethora of regulatory elements including transcription factors, microRNAs and several proteins play a critical role in the regulation of coordinated cellular P homeostasis. Among these, the well-established P starvation signaling pathway comprising of central transcriptional factor phosphate starvation response (PHR), microRNA399 (miR399) as a long-distance signal molecule, and PHOSPHATE 2 (PHO2), an E2 ubiquitin conjugase is crucial in the regulation of phosphorus starvation responsive genes. Under PHR control, several classes of PHTs, microRNAs, and proteins modulate root architecture, and metabolic processes to enable plants to adapt to low P. Even though sucrose and inositol phosphates are known to influence the phosphorus starvation response genes, the exact mechanism of regulation is still unclear. In this review, a basic understanding of P homeostasis under low P in plants and all the above aspects are discussed.

Uncovering Pathways Highly Correlated to NUE through a Combined Metabolomics and Transcriptomics Approach in Eggplant

Nitrogen (N) fertilization is one of the main inputs to increase crop yield and food production. However, crops utilize only 30–40% of N applied; the remainder is leached into the soil, causing environmental and health damage. In this scenario, the improvement of nitrogen-use efficiency (NUE) will be an essential strategy for sustainable agriculture. Here, we compared two pairs of NUE-contrasting eggplant (Solanum melongena L.) genotypes, employing GC-MS and UPLC-qTOF-MS-based technologies to determine the differential profiles of primary and secondary metabolites in root and shoot tissues, under N starvation as well as at short- and long-term N-limiting resupply. Firstly, differences in the primary metabolism pathways of shoots related to alanine, aspartate and glutamate; starch, sucrose and glycine; serine and threonine; and in secondary metabolites biosynthesis were detected. An integrated analysis between differentially accumulated metabolites and expressed transcripts highlighted a key role of glycine accumulation and the related glyA transcript in the N-use-efficient genotypes to cope with N-limiting stress. Interestingly, a correlation between both sucrose synthase (SUS)- and fructokinase (scrK)-transcript abundances, as well as D-glucose and D-fructose accumulation, appeared useful to distinguish the N-use-efficient genotypes. Furthermore, increased levels of L-aspartate and L-asparagine in the N-use-efficient genotypes at short-term low-N exposure were detected. Granule-bound starch synthase (WAXY) and endoglucanase (E3.2.1.4) downregulation at long-term N stress was observed. Therefore, genes and metabolites related to these pathways could be exploited to improve NUE in eggplant.

Stimulation of Hyphal Ramification and Sporulation in Funneliformis mosseae by Root Extracts Is Host Phosphorous Status-Dependent

A simulation of the environment inhabited by arbuscular mycorrhizal (AM) fungi could provide clues as to how to cultivate these obligate biotrophs axenically. Host intraradical and rhizospheric environments, root extracts and exudates in particular, would be crucial for AM fungi to complete their life cycles. In this study, we analyzed and compared the effects of root exudates (RE) and root extracts (RET) of white clover (Trifolium repens) on the asymbiotic growth of the AM fungus Funneliformis mosseae in vitro, and furtherly analyzed the chemical components of different RET with the LC-MS/MS technique in order to establish an asymbiotic cultivation system for this important and hardly domesticated AM fungus. RET is superior to RE in stimulating spore germination, hyphal elongation and branching, and secondary spore formation (p < 0.05). RET-induced effects were dependent on phosphate supplement levels, and the RET obtained following the treatment with low levels of phosphorus significantly promoted hyphal growth and sporulation (p < 0.05). A few newly formed secondary spores showed limited colonization of white clover roots. The low phosphorus-induced effects could be ascribed to the metabolic adjustment (mainly lipids and organic acids) of white clover roots under low phosphate conditions. Our findings demonstrate that the low phosphate-induced RET boosts the asymbiotic growth of AM fungus, and thus offers an alternative way to fulfill the life cycle of AM fungi asymbiotically.