Roots are generally the critical drought sensors, but little is known about their molecular response to drought stress. We used the drought-tolerant soybean variety ‘Jiyu 47’ to investigate the differentially expressed proteins (DEPs) in soybean roots during the seedling stage based on the tandem mass tag (TMT) proteomics analysis. Various expression patterns were observed in a total of six physiological parameters. A total of 468 DEPs (144 up-regulated and 324 down-regulated) among a total of 8687 proteins were identified in response to drought stress in 24 h. The expression of DEPs was further validated based on quantitative real-time PCR of a total of five genes (i.e., GmGSH, GmGST1, GmGST2 k GmCAT, and Gm6PGD) involved in the glutathione biosynthesis. Results of enrichment analyses revealed a coordinated expression pattern of proteins involved in various cellular metabolisms responding to drought stress in soybean roots. Our results showed that drought stress caused significant alterations in the expression of proteins involved in several metabolic pathways in soybean roots, including carbohydrate metabolism, metabolism of the osmotic regulation substances, and antioxidant defense system (i.e., the glutathione metabolism). Increased production of reduced glutathione (GSH) enhanced the prevention of the damage caused by reactive oxygen species and the tolerance of the abiotic stress. The glutathione metabolism played a key role in modifying the antioxidant defense system in response to drought stress in soybean roots. Our proteomic study suggested that the soybean plants responded to drought stress by coordinating their protein expression during the vegetative stage, providing novel insights into the molecular mechanisms regulating the response to abiotic stress in plants.

Two saline-alkali-tolerant bacterial strains, Priestia aryabhattai JL-5 and Staphylococcus pseudoxylosus XW-4, were isolated, with high capabilities of hydrolyzing phosphate and producing cellulase, respectively. The molecular mechanisms regulating the saline-alkali tolerance in the strain JL-5 were further investigated using transcriptome analysis. The contents of lactic acid and proline and the enzymatic activity of glutamine synthetase in the strain JL-5 were significantly increased. The properties of saline-alkali soils were significantly improved by the enhanced growth of the indicator plant Leymus chinensis under the combined applications of the strains JL-5 and XW-4 mixed with corn straw. The contents of catalase, peroxidase, superoxide dismutase and proline of L. chinensis were significantly increased, and the content of malondialdehyde was significantly decreased in the combined treatment of both bacterial strains. The contents of available nitrogen, phosphorus and potassium and organic matters in the soil treated with both strains were significantly increased, as well as the diversity and abundance of the soil microbiota. Our study evidently demonstrated the synergistic effects of the strains JL-5 and XW-4, indicator plants and the local microbiota in terms of improving the saline-alkali soil properties, providing strong experimental evidence to support the commercial development of the combined application of both strains to improve the properties of saline-alkali soils.

NAC transcription factors are commonly involved in the plant response to drought stress. A transcriptome analysis of root samples of the soybean variety ‘Jiyu47’ under drought stress revealed the evidently up-regulated expression of GmNAC19, consistent with the expression pattern revealed by quantitative real-time PCR analysis. The overexpression of GmNAC19 enhanced drought tolerance in Saccharomyces cerevisiae INVSc1. The seed germination percentage and root growth of transgenic Arabidopsis thaliana were improved in comparison with those of the wild type, while the transgenic soybean composite line showed improved chlorophyll content. The altered contents of physiological and biochemical indices (i.e., soluble protein, soluble sugar, proline, and malondialdehyde) related to drought stress and the activities of three antioxidant enzymes (i.e., superoxide dismutase, peroxidase, and catalase) revealed enhanced drought tolerance in both transgenic Arabidopsis and soybean. The expressions of three genes (i.e., P5CS, OAT, and P5CR) involved in proline synthesis were decreased in the transgenic soybean hairy roots, while the expression of ProDH involved in the breakdown of proline was increased. This study revealed the molecular mechanisms underlying drought tolerance enhanced by GmNAC19 via regulation of the contents of soluble protein and soluble sugar and the activities of antioxidant enzymes, providing a candidate gene for the molecular breeding of drought-tolerant crop plants.

Plant roots play crucial roles in their response to drought conditions. However, the molecular responses in soybean roots to drought stress remain unclear. We investigated the alterations in the protein expression in the roots of a drought-resistant soybean cultivar ‘Jiyu 47’ during the seedling phase based on tandem mass tag (TMT) proteomics analysis. The results revealed significant variations in the expression of the proteins involved in several metabolic pathways in soybean roots, including sucrose metabolism, abscisic acid (ABA) metabolism, and the ATP-binding cassette (ABC) transporter pathway. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed a coordinated expression pattern of the proteins involved in the various cellular pathways responding to drought stress in soybean. The increased production of sucrose and betaine enhanced the inhibition of the damage caused by reactive oxygen species (ROS) and the tolerance of drought stress. The results of the physiological variations showed that sucrose metabolism, ABA metabolic mechanism, and the ABC transporter pathways played an important role in the antioxidant defense system in response to drought stress in soybean roots. The results of quantitative real-time PCR revealed the up-regulated expression of three genes (i.e., GmPYR1, GmHO-1, and GmSOD) involved in ABA biosynthesis and the signaling pathway. This study provides novel insights into the comprehension of the molecular pathways regulating the soybean root response to drought stress.

Identifying plant-growth-promoting rhizobacteria tolerant to saline–alkali conditions is critical for developing effective microbial agents and multi-strategy approaches to remediate saline–alkali soil. Two salt–alkali-tolerant bacterial strains—phosphorus-solubilizing Bacillus pumilus JL-C and cellulose-decomposing B. halotolerans XW-3—were isolated from saline–alkali soil, with both exhibiting multiple plant-growth-promoting properties, including nitrogen fixation and the generation of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylate deaminase. Alfalfa pot experiments were conducted under four treatments: a control, the strain JL-C treatment, the strain XW-3 treatment, and a co-inoculation treatment (JL-C/XW-3), all mixed with corn straw and applied to the saline–alkali soil. The results demonstrated that the co-inoculation treatment yielded the most significant growth-promoting effects on alfalfa, showing enhanced antioxidant enzyme activities; increased contents of proline, soluble sugar, and protein; reduced malondialdehyde content; lowered pH and electrical conductivity; elevated activities of key enzymes; and increased levels of available nitrogen, phosphorus, potassium, and organic matter content in the soil. The pot experiments were confirmed by field experiments. The results of 16S rRNA high-throughput sequencing revealed changes in the bacterial community composition in the alfalfa rhizosphere, showing shifts in the relative abundance of several bacterial taxa often reported as plant-associated or potentially beneficial. This study establishes a combined remediation strategy for saline–alkali soil utilizing complex microbial agents and corn straw.

The soybean GmPEAMT1/GmPLMT double-knockout mutant (Dko) was constructed to investigate how the disruption of phospholipid-related genes affects reproductive traits, seed nutrient composition, and associated molecular responses under experimental conditions. Dko plants showed coordinated changes in photosynthetic parameters and reproductive structures: the number of pollen grains and ovules was reduced, whereas pollen and ovule size-related traits were increased, while mature seed number and 100-seed weight were maintained. Developing Dko seeds showed higher protein content and increased levels of 12 out of 18 measured amino acids, particularly alanine and cysteine. Transcriptomic and qRT-PCR analyses further indicated coordinated changes in amino acid, pantothenate, coenzyme A, glycerolipid, and glycerophospholipid-related pathways. Lipidomics provided complementary evidence of changes in phospholipid-associated and other lipid molecular features, whereas total seed lipid content showed no significant difference from the control. Together, these results suggest that GmPEAMT1/GmPLMT disruption was associated with variations in reproductive traits at the developmental stages examined and seed nutrient allocation, with lipid-feature changes representing one component of a broader multi-omic response. The proposed lipid and amino acid metabolic remodeling in GmPEAMT1/GmPLMT double-knockout soybean seeds should be regarded as a working hypothesis because direct metabolic flux, protein abundance, and enzyme activity are not measured.