Metabolic reprogramming in nodules, roots, and leaves of symbiotic soybean in response to iron deficiency

Plant response to heavy metal stress toxicity: the role of metabolomics and other omics tools

Metabolomic investigations offers a significant foundation for improved comprehension of the adaptability of plants to reconfigure the key metabolic pathways and their response to changing climatic conditions. Their application to ecophysiology and ecotoxicology help to assess potential risks caused by the contaminants, their modes of action and the elucidation of metabolic pathways associated with stress responses. Heavy metal stress is one of the most significant environmental hazards affecting the physiological and biochemical processes in plants. Metabolomic tools have been widely utilised in the massive characterisation of the molecular structure of plants at various stages for understanding the diverse aspects of the cellular functioning underlying heavy metal stress-responsive mechanisms. This review emphasises on the recent progressions in metabolomics in plants subjected to heavy metal stresses. Also, it discusses the possibility of facilitating effective management strategies concerning metabolites for mitigating the negative impacts of heavy metal contaminants on the growth and productivity of plants.

Interaction of ammonium nutrition with essential mineral cations

Plant growth and development depend on sufficient nutrient availability in soils. Agricultural soils are generally nitrogen (N) deficient, and thus soils need to be supplemented with fertilizers. Ammonium (NH4+) is a major inorganic N source. However, at high concentrations, NH4+ becomes a stressor that inhibits plant growth. The cause of NH4+ stress or toxicity is multifactorial, but the interaction of NH4+ with other nutrients is among the main determinants of plants' sensitivity towards high NH4+ supply. In addition, NH4+ uptake and assimilation provoke the acidification of the cell external medium (apoplast/rhizosphere), which has a clear impact on nutrient availability. This review summarizes current knowledge, at both the physiological and the molecular level, of the interaction of NH4+ nutrition with essential mineral elements that are absorbed as cations, both macronutrients (K+, Ca2+, Mg2+) and micronutrients (Fe2+/3+, Mn2+, Cu+/2+, Zn2+, Ni2+). We hypothesize that considering these nutritional interactions, and soil pH, when formulating fertilizers may be key in order to boost the use of NH4+-based fertilizers, which have less environmental impact compared with nitrate-based ones. In addition, we are convinced that better understanding of these interactions will help to identify novel targets with the potential to improve crop productivity.

Iron in the Symbiosis of Plants and Microorganisms

Iron is an essential element for most organisms. Both plants and microorganisms have developed different mechanisms for iron uptake, transport and storage. In the symbiosis systems, such as rhizobia-legume symbiosis and arbuscular mycorrhizal (AM) symbiosis, maintaining iron homeostasis to meet the requirements for the interaction between the host plants and the symbiotic microbes is a new challenge. This intriguing topic has drawn the attention of many botanists and microbiologists, and many discoveries have been achieved so far. In this review, we discuss the current progress on iron uptake and transport in the nodules and iron homeostasis in rhizobia-legume symbiosis. The discoveries with regard to iron uptake in AM fungi, iron uptake regulation in AM plants and interactions between iron and other nutrient elements during AM symbiosis are also summarized. At the end of this review, we propose prospects for future studies in this fascinating research area.

Comparative transcriptomic and metabolite profiling reveals genotype-specific responses to Fe starvation in chickpea

Iron deficiency is a major nutritional stress that severely impacts crop productivity worldwide. However, molecular intricacies and subsequent physiological and metabolic changes in response to Fe starvation, especially in leguminous crops like chickpea, remain elusive. In the present study, we investigated physiological, transcriptional, and metabolic reprogramming in two chickpea genotypes (H6013 and L4958) with contrasting seed iron concentrations upon Fe deficiency. Our findings revealed that iron starvation affected growth and physiological parameters of both chickpea genotypes. Comparative transcriptome analysis led to the identification of differentially expressed genes between the genotypes related to strategy I uptake, metal ions transporters, reactive oxygen species-associated genes, transcription factors, and protein kinases that could mitigate Fe deficiency. Our gene correlation network discovered several putative candidate genes like CIPK25, CKX3, WRKY50, NAC29, MYB4, and PAP18, which could facilitate the investigation of the molecular rationale underlying Fe tolerance in chickpea. Furthermore, the metabolite analysis also illustrated the differential accumulation of organic acids, amino acids and other metabolites associated with Fe mobilization in chickpea genotypes. Overall, our study demonstrated the comparative transcriptional dynamics upon Fe starvation. The outcomes of the current endeavor will enable the development of Fe deficiency tolerant chickpea cultivars.

Combined morpho-physiological, ionomic and transcriptomic analyses reveal adaptive responses of allohexaploid wheat (Triticum aestivum L.) to iron deficiency

BACKGROUND

Plants worldwide are often stressed by low Fe availability around the world, especially in aerobic soils. Therefore, the plant growth, seed yield, and quality of crop species are severely inhibited under Fe deficiency. Fe metabolism in plants is controlled by a series of complex transport, storage, and regulatory mechanisms in cells. Allohexaploid wheat (Triticum aestivum L.) is a staple upland crop species that is highly sensitive to low Fe stresses. Although some studies have been previously conducted on the responses of wheat plants to Fe deficiency, the key mechanisms underlying adaptive responses are still unclear in wheat due to its large and complex genome.

RESULTS

Transmission electron microscopy showed that the chloroplast structure was severely damaged under Fe deficiency. Paraffin sectioning revealed that the division rates of meristematic cells were reduced, and the sizes of elongated cells were diminished. ICP-MS-assisted ionmics analysis showed that low-Fe stress significantly limited the absorption of nutrients, including N, P, K, Ca, Mg, Fe, Mn, Cu, Zn, and B nutrients. High-throughput transcriptome sequencing identified 378 and 2,619 genome-wide differentially expressed genes (DEGs) were identified in the shoots and roots between high-Fe and low-Fe conditions, respectively. These DEGs were mainly involved in the Fe chelator biosynthesis, ion transport, photosynthesis, amino acid metabolism, and protein synthesis. Gene coexpression network diagrams indicated that TaIRT1b-4A, TaNAS2-6D, TaNAS1a-6A, TaNAS1-6B, and TaNAAT1b-1D might function as key regulators in the adaptive responses of wheat plants to Fe deficiency.

CONCLUSIONS

These results might help us fully understand the morpho-physiological and molecular responses of wheat plants to low-Fe stress, and provide elite genetic resources for the genetic modification of efficient Fe use.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Integration of the Metabolomic and Transcriptome Analysis Reveals the Remarkable Compounds of G. bicolor Young and Mature Leaves under Different Iron Nutrient Conditions

Gynura bicolor (Roxb. ex Willd.) DC. (G. bicolor) is a functional vegetable rich in iron (Fe) and widely grown in Asia (e.g., Japan and China). Because most Fe in the soil exists in the form of insoluble oxides or hydroxides, it is difficult for plants to obtain Fe from the soil. A comparative metabolomic and transcriptome study was carried out to investigate the effect of Fe deficiency on metabolite synthesis and gene expression in young and mature leaves of G. bicolor. Fe deficiency caused chlorosis and decreased the chlorophyll content in young leaves. The metabolomic results for young leaves showed that l-glutamate and 4-hydroxybutanoic acid lactone significantly increased and decreased, respectively. The transcriptome results showed that the expression levels of genes involved in ferric reduction oxidase 7 and 14-kDa proline-rich protein DC2.15-like were significantly upregulated and downregulated, respectively. However, Fe deficiency had little effect on mature leaves.

Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

Nodulating white lupins take advantage of the reciprocal interplay between N and P nutritional responses

The low bioavailability of nutrients, especially nitrogen (N) and phosphorus (P), is one of the most limiting factors for crop production. In this study, under N- and P-free nutrient solution (-N-P), nodulating white lupin plants developed some nodules and analogous cluster root structures characterized by different morphological, physiological, and molecular responses than those observed upon single nutrient deficiency (strong acidification of external media, a better nutritional status than -N+P and +N-P plants). The multi-elemental analysis highlighted that the concentrations of nutrients in white lupin plants were mainly affected by P availability. Gene-expression analyses provided evidence of interconnections between N and P nutritional pathways that are active to promote N and P balance in plants. The root exudome was mainly characterized by N availability in nutrient solution, and, in particular, the absence of N and P in the nutrient solution triggered a high release of phenolic compounds, nucleosides monophosphate and saponines by roots. These morphological, physiological, and molecular responses result from a close interplay between N and P nutritional pathways. They contribute to the good development of nodulating white lupin plants when grown on N- and P-free media. This study provides evidence that limited N and P availability in the nutrient solution can promote white lupin-Bradyrhizobium symbiosis, which is favourable for the sustainability of legume production.

Co-application of biogas slurry and hydrothermal carbonization aqueous phase substitutes urea as the nitrogen fertilizer and mitigates ammonia volatilization from paddy soil

Biogas slurry (BS) and bio-waste hydrothermal carbonization aqueous phase (HP) are nutrient-rich wastewater. To prevent environment contamination, transforming BS and HP into synthetic fertilizers in the agricultural field can potentially realize resource utilization. We hypothesized that acidic HP could neutralize alkaline BS, adjusting floodwater pH from 6.88 to 8.00 and mitigating ammonia (NH₃) volatilization from the paddy soil. In this soil column study, the mixture of BS and HP was applied to paddy soil to substitute 50%, 75%, and 100% to urea. With a low (L) or high (H) ratio of HP, treatments were labeled as BCL50, BCL75, BCL100, BCH50, BCH75, and BCH100. Results showed that microbial byproduct- and fulvic acid-like substance were the main components in BS and HP using 3D-EEM analysis, respectively. Co-application of BS and HP mitigated the NH₃ volatilization by 4.2%-65.5% compared with CKU. BCL100 and BCH100 treatments significantly (P < 0.05) mitigated NH₃ volatilization by 65.5% and 56.8%, which also significantly (P < 0.05) mitigated the yield-scale NH₃ volatilization by 49.6% and 42.3%, compared with CKU. The low NH₄⁺-N concentration and pH value in floodwater were the main reason explained the NH₃ mitigation. Therefore, this study demonstrated that BS and HP co-application can substitute the urea as a valuable N fertilizer in a rational rate and meanwhile mitigate the NH₃ volatilization. This study will provide new ideas for the utilization of BS and HP resources in the context of ammonia mitigation.

Iron Deficiency Leads to Chlorosis Through Impacting Chlorophyll Synthesis and Nitrogen Metabolism in Areca catechu L

Deficiency of certain elements can cause leaf chlorosis in Areca catechu L. trees, which causes considerable production loss. The linkage between nutrient deficiency and chlorosis phenomenon and physiological defect in A. catechu remains unclear. Here, we found that low iron supply is a determinant for chlorosis of A. catechu seedling, and excessive iron supply resulted in dark green leaves. We also observed morphological characters of A. catechu seedlings under different iron levels and compared their fresh weight, chlorophyll contents, chloroplast structures and photosynthetic activities. Results showed that iron deficiency directly caused chloroplast degeneration and reduced chlorophyll synthesis in chlorosis leaves, while excessive iron treatment can increase chlorophyll contents, chloroplasts sizes, and inflated starch granules. However, both excessive and deficient of iron decreases fresh weight and photosynthetic rate in A. catechu seedlings. Therefore, we applied transcriptomic and metabolomic approaches to understand the effect of different iron supply to A. catechu seedlings. The genes involved in nitrogen assimilation pathway, such as NR (nitrate reductase) and GOGAT (glutamate synthase), were significantly down-regulated under both iron deficiency and excessive iron. Moreover, the accumulation of organic acids and flavonoids indicated a potential way for A. catechu to endure iron deficiency. On the other hand, the up-regulation of POD-related genes was assumed to be a defense strategy against the excessive iron toxicity. Our data demonstrated that A. catechu is an iron-sensitive species, therefore the precise control of iron level is believed to be the key point for A. catechu cultivation.

Metabolic profiling reveals local and systemic responses of kiwifruit to Pseudomonas syringae pv. actinidiae

Pseudomonas syringae pv. actinidiae (Psa), a bacterial pathogen, causes bacterial canker disease in kiwifruit. To elucidate the local and systemic influences of Psa infection on kiwifruit, comprehensive analyses were conducted by combining metabolomic and physiological approach under Psa-infected treatment and mock-inoculated control in leaves, stems, and bleeding saps. Our results show that Psa infection stimulated kiwifruit metabolic reprogramming. Levels of many sugars, fumarate, and malic acid were decreased in Psa-infected leaves and stems, accompanied by the increased level of amino acids (AAs), which implies the anaplerotic reaction to replenish the TCA cycle generating energy and intermediates for defense-related metabolic pathways, such as phenylpropanoid metabolism. The inconsistent results were observed in bleeding saps, which may be attributed to the induced phloem transport of carbon (C) out of leaves and such a transport benefits bacterium movement. Arg, Gln, and pyroglutamic acid systematically were accumulated in long-distance leaves, which probably confers to systemic acquired resistance (SAR) and Psa inoculation accelerated the nitrogen (N) cycling in kiwifruit. Moreover, Psa infection specifically affected the content of phenolic compounds and lignin. Phenolic compounds were negatively and lignin was positively related to kiwifruit Psa resistance, respectively. Our results first reveal that Psa enhances infection by manipulating C/N metabolism and sweet immunity, and that host lignin synthesis is a major physical barrier for restricting bacterial infection. This study provides an insight into the complex remodeling of plant metabolic response to Psa stress.

Minerals loaded with oxygen nanobubbles mitigate arsenic translocation from paddy soils to rice

Inhibiting reductive transformation of arsenic (As) in flooded paddy soils is fundamentally important for mitigating As transfer into the food chain. In this study, oxygen-nanobubble-loaded-zeolites (ZON) and -vermiculites (VON) were tested as a novel approach for supplying oxygen to paddy soils to inhibit As influx into rice. The dynamic physio- and bio-chemical variations in the rhizosphere and bulk soil were profiled in a rhizobox experiment. Upon adding ZON and VON, the redox potential and dissolved oxygen consistently increased throughout the cultivation period. The improved redox environment inhibited As(III) release into porewater and increased As(V) adsorbed on crystalline Fe (hydr)oxides, following the reduction of arsC and arrA gene abundances and enhancement of the aioA gene. Moreover, adding ZON and VON promoted root iron plaque formation, which increased As retention on iron plaque. Both ZON and VON treatments mitigated As translocation from soil to rice, meanwhile increasing root and shoot biomass. ZON was superior to VON in repressing As transfer and promoting rice growth due to its higher oxygen loading capacity. This study provides a novel and environment-friendly material to both mitigate the As translocation from paddy soil to rice and improve rice growth.

Transcriptomic comparison reveals modifications in gene expression, photosynthesis, and cell wall in woody plant as responses to external pH changes

Soil acidification is one of the crucial global environmental problems, affecting sustainable land use, crop yield, and ecosystem stability. Previous research reported the tolerance of crops to acid soil stress. However, the molecular response of woody plant to acid conditions remains largely unclear. Rhododendron L. is a widely distributed woody plant genus and prefers to grow in acidic soils. Herein, weighted gene coexpression network analysis was performed on R. protistum var. giganteum seedlings subjected to five pH treatments (3.5, 4.5, 5.5, 6.0, 7.0), and their ecophysiological characteristics were determined for the identification of their molecular responses to acidic environments. Through pairwise comparison, 855 differentially expressed genes (DEGs) associated with photosynthesis, cell wall, and phenylpropanoid metabolism were identified. Most of the DEGs related to photosynthesis and cell wall were up-regulated after pH 4.5 treatment. Results implied that the species improves its photosynthetic abilities and changes its cell wall characteristics to adapt to acidic conditions. Weighted gene co-expression network analyses showed that most of the hub genes were annotated to the biosynthetic pathways of ribosomal proteins and photosynthesis. Expression pattern analysis showed that genes encoding subunit ribosomal proteins decreased at pH 7.0 treatment, suggesting that pH 7.0 treatment led to cell injury in the seedlings. The species regulates protein synthesis in response to high pH stress (pH 7.0). The present study revealed the molecular response mechanism of woody plant R. protistum var. giganteum to acid environments. These findings can be useful in enriching current knowledge of how woody species adapt to soil acidification under global environmental changes.

Speciation of essential nutrient trace elements in coconut water

Coconut water (Cocos Nucifera) is shown to be a source of essential elements present in the form of low-molecular weight stable complexes known for their bio-availability. The total element concentrations were in the range of 0.2-2.7, 0.3-1, 3-14 and 0.5-2 ppm for Fe, Cu, Mn, and Zn, respectively, and varied as a function of the origin of the nut and its maturity. Speciation was investigated by size-exclusion chromatography - inductively coupled plasma mass spectrometry (ICPMS), and hydrophilic interaction liquid chromatography (HILIC) - electrospray-OrbitrapMS. The metal species identified included: iron complexes with citrate and malate: Fe^III(Cit)₃(Mal), Fe^III(Cit)₂(Mal)₂, Fe^III(Mal)₂, glutamine: Fe^III(Glu)₂ and nicotianamine: Fe^II(NA); copper complexes with phenylanine: Cu^II(Phe)₂ and Cu^II(Phe)₃ and nicotianamine: Cu^II(NA); zinc complexes with citrate: Zn^II(Cit)₂ and nicotianamine Zn^II(NA) and manganese complex with asparagine Mn^II(Asp)₂. The contributions of the individual species to the total elements concentrations could be estimated by HILIC - ICP MS.

Microalgae-derived hydrochar application on rice paddy soil: Higher rice yield but increased gaseous nitrogen loss

Hydrothermal carbonization represents a promising technique for transforming microalgae into the hydrochar with abundant phytoavailable nutrients. However, the effects of microalgae-derived hydrochars on the gaseous nitrogen (N) loss from agricultural field are still unclear. Chlorella vulgaris powder (CVP) and two Chlorella vulgaris-derived hydrochars that employ water (CVHW) or citrate acid solution (CVHCA) as the reaction medium were applied to a soil column system grown with rice. The temporal variations of nitrous oxide (N₂O) emissions and ammonia (NH₃) volatilization were monitored during the whole rice-growing season. Results showed that CVHW and CVHCA addition significantly increased the grain yield (by 13.5-26.8% and 10.5-23.4%) compared with control and CVP group, while concomitantly increasing the ammonia volatilization (by 53.8% and 72.9%) as well as N₂O emissions (by 2.17- and 2.82-fold) from paddy soil compared to control. The microbial functional genes (AOA, AOB, nirk, nirS, nosZ) in soil indicated that CVHW and CVHCA treatment stimulated the nitrification and denitrification, and inhibited the N₂O oxidation in soil. Notably, CVHW was recommended in the view of improving yield and controlling NH₃ volatilization because no significant difference of the yield-scale NH₃ volatilization was detected between control and CVHW treatment. This study for the first time uncovered that Chlorella vulgaris-derived hydrochars have positive effects on rice N utilization and growth but negative effects on the atmospheric environment.