Integrated Proteomics and Metabolomics Analysis of Nitrogen System Regulation on Soybean Plant Nodulation and Nitrogen Fixation

Multi-omics analysis reveals differential molecular responses to cadmium toxicity in rice root tip and mature zone

Cadmium (Cd) is a highly toxic heavy metal that can be readily absorbed by plants and enriched in human body. Rice (Oryza sativa L.) yield and grain quality are affected by excessive Cd in the soil. Therefore, understanding the mechanisms of Cd absorption, accumulation and detoxification in the root apex is crucial for developing low-Cd rice cultivars. After Cd treatment, Cd concentration in rice root tips (RT) was 1.4 times higher than that in basal roots (BR). To uncover the distinct molecular responses to Cd toxicity, we conducted transcriptomic, proteomic, and metabolomic analyses on the two root sections. The results revealed that the RT exhibited 1.2-2.0 fold higher transcript or protein abundance of several Cd-related transporters than the BR, including Nramp1, Nramp5, IRT1, and HMA3, thereby contributing to more Cd accumulation in the RT. Furthermore, multi-omics analysis unveiled that the RT had enhanced activity in 'phenylpropanoid metabolism', 'AsA-GSH cycle' and 'tryptophan metabolism', conferring the stronger antioxidant system. While the BR showed higher activation in 'cell wall remodeling' and 'terpenoid biosynthesis'. This comprehensive study provides insights into the regulatory network of genes, proteins and metabolites involved in the differential responses to Cd toxicity between rice root tips and mature zones.

Transcriptome and Metabolome Analyses Reveal Mechanisms Underlying the Response of Quinoa Seedlings to Nitrogen Fertilizers

Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual amaranth herb that belongs to the family Chenopodiaceae. Quinoa can be cultivated across a wide range of climatic conditions. With regard to its cultivation, nitrogen-based fertilizers have a demonstrable effect on the growth and development of quinoa. How crops respond to the application of nitrogen affects grain quality and yield. Therefore, to explore the regulatory mechanisms that underlie the responses of quinoa seedlings to the application of nitrogen, we selected two varieties (i.e., Dianli-1299 and Dianli-71) of quinoa seedlings and analyzed them using metabolomic and transcriptomic techniques. Specifically, we studied the mechanisms underlying the responses of quinoa seedlings to varying concentrations of nitrogen by analyzing the dynamics of metabolites and genes involved in arginine biosynthesis; carbon fixation; and alanine, aspartate, and glutamate biosynthetic pathways. Overall, we found that differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) of quinoa are affected by the concentration of nitrogen. We detected 1057 metabolites, and 29,012 genes were annotated for the KEGG. We also found that 15 DEMs and 8 DEGs were key determinants of the differences observed in quinoa seedlings under different nitrogen concentrations. These contribute toward a deeper understanding of the metabolic processes of plants under different nitrogen treatments and provide a theoretical basis for improving the nitrogen use efficiency (NUE) of quinoa.

Fungi That Promote Plant Growth in the Rhizosphere Boost Crop Growth

The fungi species dwelling in the rhizosphere of crop plants, revealing functions that endeavor sustainability of the plants, are commonly referred to as 'plant-growth-promoting fungi' (PGPF). They are biotic inducers that provide benefits and carry out important functions in agricultural sustainability. The problem encountered in the agricultural system nowadays is how to meet population demand based on crop yield and protection without putting the environment and human and animal health at risk based on crop production. PGPF including Trichoderma spp., Gliocladium virens, Penicillium digitatum, Aspergillus flavus, Actinomucor elegans, Podospora bulbillosa, Arbuscular mycorrhizal fungi, etc., have proven their ecofriendly nature to ameliorate the production of crops by improving the growth of the shoots and roots of crop plants, the germination of seeds, the production of chlorophyll for photosynthesis, and the abundant production of crops. PGPF's potential mode of action is as follows: the mineralization of the major and minor elements required to support plants' growth and productivity. In addition, PGPF produce phytohormones, induced resistance, and defense-related enzymes to inhibit or eradicate the invasion of pathogenic microbes, in other words, to help the plants while encountering stress. This review portrays the potential of PGPF as an effective bioagent to facilitate and promote crop production, plant growth, resistance to disease invasion, and various abiotic stresses.

Multi-omics analysis of the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots

The regulatory effects of uneven phosphorus supplies on phosphorus transport in soybean roots are still unclear. To further analyze the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots and the effects of uneven phosphorus application on the physiological mechanism of phosphorus transport in soybean roots, dual-root soybean plants were prepared via grafting, and a sand culture experiment was performed. From the unfolded cotyledon stage to the initial flowering stage, one side of each dual-root soybean system was irrigated with a low-phosphorus-concentration solution (phosphorus-application [P+] side), and the other side was irrigated with a phosphorus-free nutrient solution (phosphorus-free [P-] side); this setup allowed the study of the effects of different phosphorus supply levels on the expression of genes and proteins and the accumulation of metabolites in soybean roots on the P- side to clarify the method through which phosphorus transport is regulated in soybean roots and to provide a theoretical basis for improving the use rate of phosphorus fertilizer. The results revealed that the unilateral supply of low-concentration phosphorus promoted the uptake of phosphorus by soybean roots and the transport of phosphorus from the P+ side to the P- side. Compared with the normal concentration of phosphorus supply and the phosphorus-free supply, the low concentration phosphorus supply affected the regulation of the metabolic pathways involved in starch and sucrose metabolism, glycolysis, fructose, and mannose metabolism, etc., thereby affecting soybean root phosphorus transport. The low-phosphorus stress inhibited fructose synthesis and sucrose synthase synthesis in the soybean roots and the synthesis of hexokinase (HK) and fructose kinase, which catalyzes the conversion of fructose to fructose-6-phosphate. Low-phosphorus stress promoted the synthesis of sucrose invertase and the conversion of sucrose into maltose by the activity of starch synthase (StS) and stimulated the synthesis of UDPG pyrophosphorylase (UGP) and phosphoglucose isomerase (GP1), which is involved in the conversion of UDP-glucose to glucose-6-phosphate. The phosphorus transport pathway of soybean roots was then affected, which promoted phosphorus allocation to UTP and glucose-6-phosphate. Additionally, low-phosphorus stress hastened glycolysis in the soybean roots and inhibited the synthesis of malic acid, thereby promoting the transport of phosphorus in the roots. In addition, low-phosphorus stress inhibited the synthesis of fructose, mannose, and mannose-1-phosphate and the synthesis of other enzymes involved in phosphorus transport as well as invertase, thereby inhibiting the transport and synthesis of several organic phosphorus-containing compounds.

Systemic regulation of soybean nodulation and nitrogen fixation by nitrogen via isoflavones

Nitrogen (N) inhibits soybean (Glycine max L.) nodulation and N₂ fixation. Isoflavones secreted by soybean roots can stimulate signal transduction for symbiotic nodules, thus playing a key role in root nodule development and N₂ fixation. The relationship between the inhibition of soybean nodulation, N₂ fixation and isoflavones by N is still unclear. In this study, dual-root soybean plants were prepared by grafting, and N or isoflavones were supplied to unilateral roots. The number and dry weight of the soybean nodules, nitrogenase activity, isoflavone concentrations and relative changes in the level of expression of nodulation-related genes were measured to study the response relationship between the N systemic regulation the soybean nodule N₂ fixation and changes in the concentrations of isoflavones in its roots. The results showed that N supply to one side of the dual-root soybeans systematically affected the N₂ fixation of root nodules on both sides, and this effect began in the early stage of nodulation. Moreover, a unilateral supply of N systematically affected the concentrations of daidzein and genistein on both sides of the roots. The concentrations of isoflavones were consistent with the change trend of soybean root nodule and nodulation-related gene expression level. Treatment with unilateral N or isoflavones affected the soybean nodule N₂ fixation and its nodulation-related genes, which had the same response to the changes in concentrations of root isoflavones. N regulates soybean nodulation and N₂ fixation by systematically affecting the concentrations of isoflavones in the roots.