Integrated Transcriptomic and Metabolomic Analysis Reveals the Molecular Regulatory Mechanism of Flavonoid Biosynthesis in Maize Roots under Lead Stress.

Flavonoids are secondary metabolites that play important roles in the resistance of plants to abiotic stress. Despite the widely reported adverse effects of lead (Pb) contamination on maize, the effects of Pb on the biosynthetic processes of flavonoids in maize roots are still unknown. In the present work, we employed a combination of multi-omics and conventional assay methods to investigate the effects of two concentrations of Pb (40 and 250 mg/kg) on flavonoid biosynthesis in maize roots and the associated molecular regulatory mechanisms. Analysis using conventional assays revealed that 40 and 250 mg/kg Pb exposure increased the lead content of maize root to 0.67 ± 0.18 mg/kg and 3.09 ± 0.02 mg/kg, respectively, but they did not result in significant changes in maize root length. The multi-omics results suggested that exposure to 40 mg/kg of Pb caused differential expression of 33 genes and 34 metabolites related to flavonoids in the maize root system, while 250 mg/kg of Pb caused differential expression of 34 genes and 31 metabolites. Not only did these differentially expressed genes and metabolites participate in transferase activity, anthocyanin-containing compound biosynthetic processes, metal ion binding, hydroxyl group binding, cinnamoyl transferase activity, hydroxycinnamoyl transferase activity, and flavanone 4-reductase activity but they were also significantly enriched in the flavonoid, isoflavonoid, flavone, and flavonol biosynthesis pathways. These results show that Pb is involved in the regulation of maize root growth by interfering with the biosynthesis of flavonoids in the maize root system. The results of this study will enable the elucidation of the mechanisms of the effects of lead on maize root systems.

Changes in soil microbe-mediated carbon, nitrogen and phosphorus cycling during spontaneous succession in abandoned PbZn mining areas.

The mechanism through which soil microorganisms mediate carbon and nutrient cycling during mine wasteland restoration remained unknown. Using soil metagenome sequencing, we investigated the dynamic changes in soil microbial potential metabolic functions during the transition from biological soil crusts (BSC) to mixed broad-conifer forest (MBF) in a typical PbZn mine. The results showed soil microorganisms favored carbon sequestration through anaerobic and microaerobic pathways, predominantly using efficient, low-energy pathways during succession. Genes governing carbon degradation and aerobic respiration increased by 19.56 % and 24.79 %, respectively, reflecting change toward more efficient and intensive soil carbon utilization in late succession. Nitrogen-cycling genes mediated by soil microorganisms met their maximum influence during early succession (sparse grassland, SGL), leading to a respective increase of 75.29 % and 76.81 % in the net potential nitrification rate and total nitrogen content. Mantel and correlation analyses indicated that TOC, TN, Zn and Cd contents were the main factors affecting the soil carbon and phosphorus cycles. Soil AP content emerged as the primary influencer of genes associated with the nitrogen cycle. These results shed light on the dynamic shifts in microbial metabolic activities during succession, providing a genetic insight into biogeochemical cycling mechanisms and underscoring crucial factors influencing soil biogeochemical processes in mining regions.

Drivers and mechanisms of spontaneous plant community succession in abandoned PbZn mining areas in Yunnan, China.

The drivers and mechanisms underlying succession and the spontaneous formation of plant communities in mining wasteland remain largely unknown. This study investigated the use of nature-based restoration to facilitate the recovery of viable plant communities in mining wasteland. It was found that scientific analyses of spontaneously formed plant communities in abandoned mining areas can provide insights for nature-based restoration. A chronosequence ("space for time") approach was used to establish sites representing three successional periods with six successional stages, and 90 quadrats were constructed to investigate changes in plant species and functional diversity during succession in abandoned PbZn mining areas. A total of 140 soil samples were collected to identify changes in soil properties, including plant nutrient and heavy metal concentrations. Then, this paper used structural equation models to analyze the mechanisms that drive succession. It was found that the functional diversity of plant communities fluctuated substantially during succession. Species had similar functional traits in early and mid-succession, but traits tended to diverge during late succession. Soil bulk density and soil organic matter gradually increased during succession. Total nitrogen (N), pH, and soil Zn concentrations first increased and then decreased during succession. Concentrations of Mn and Cd gradually decreased during succession. During early succession, soil organic matter was the key factor driving plant colonization and succession. During mid-succession, soil Zn functioned as an environmental filter factor limiting the rates of succession in mining wasteland communities. During late succession, soil bulk density and competition for nutrient resources contributed to more balanced differentiation among plant species. This thesis proposed that a nature-based strategy for the stabilization of abandoned mining lands could facilitate effective plant community restoration that promotes ecosystem services and functioning.

Effects of Heavy Metals on Stomata in Plants: A Review.

Stomata are one of the important structures for plants to alleviate metal stress and improve plant resistance. Therefore, a study on the effects and mechanisms of heavy metal toxicity to stomata is indispensable in clarifying the adaptation mechanism of plants to heavy metals. With the rapid pace of industrialization and urbanization, heavy metal pollution has been an environmental issue of global concern. Stomata, a special physiological structure of plants, play an important role in maintaining plant physiological and ecological functions. Recent studies have shown that heavy metals can affect the structure and function of stomata, leading to changes in plant physiology and ecology. However, although the scientific community has accumulated some data on the effects of heavy metals on plant stomata, the systematic understanding of the effects of heavy metals on plant stomata remains limited. Therefore, in this review, we present the sources and migration pathways of heavy metals in plant stomata, analyze systematically the physiological and ecological responses of stomata on heavy metal exposure, and summarize the current mechanisms of heavy metal toxicity on stomata. Finally, the future research perspectives of the effects of heavy metals on plant stomata are identified. This paper can serve as a reference for the ecological assessment of heavy metals and the protection of plant resources.

Community assembly during vegetation succession after metal mining is driven by multiple processes with temporal variation.

The mechanisms governing community assembly is fundamental to ecological restoration and clarification of the assembly processes associated with severe disturbances (characterized by no biological legacy and serious environmental problems) is essential. However, a systematic understanding of community assembly in the context of severe anthropogenic disturbance remains lacking. Here, we explored community assembly processes after metal mining, which is considered to be a highly destructive activity to provide insight into the assembly rules associated with severe anthropogenic disturbance. Using a chronosequence approach, we selected vegetation patches representing different successional stages and collected data on eight plant functional traits from each stage. The traits were classified as establishment and regenerative traits. Based on these traits, null models were constructed to identify the processes driving assembly at various successional stages. Comparison of our observations with the null models indicated that establishment and regenerative traits converged in the primary stage of succession. As succession progressed, establishment traits shifted to neutral assembly, whereas regeneration traits alternately converged and diverged. The observed establishment traits were equal to expected values, whereas regenerative traits diverged significantly after more than 20 years of succession. Furthermore, the available Cr content was linked strongly to species' ecological strategies. In the initial stages of vegetation succession in an abandoned metal mine, the plant community was mainly affected by the available metal content and dispersal limitation. It was probably further affected by strong interspecific interaction after the environmental conditions had improved, and stochastic processes became dominant during the stage with a successional age of more than 20 years.

Genome-Wide Analysis of the ATP-Binding Cassette (ABC) Transporter Family in Zea mays L. and Its Response to Heavy Metal Stresses.

The ATP-binding cassette (ABC) transporter family is one of the largest eukaryotic protein families. Its members play roles in numerous metabolic processes in plants by releasing energy for substrate transport across membranes through hydrolysis of ATP. Maize belongs to the monocotyledonous plant family, Gramineae, and is one of the most important food crops in the world. We constructed a phylogenetic tree with individual ABC genes from maize, rice, sorghum, Arabidopsis, and poplar. This revealed eight families, each containing ABC genes from both monocotyledonous and dicotyledonous plants, indicating that the amplification events of ABC gene families predate the divergence of plant monocotyledons. To further understand the functions of ABC genes in maize growth and development, we analyzed the expression patterns of maize ABC family genes in eight tissues and organs based on the transcriptome database on the Genevestigator website. We identified 133 ABC genes expressed in most of the eight tissues and organs examined, especially during root and leaf development. Furthermore, transcriptome analysis of ZmABC genes showed that exposure to metallic lead induced differential expression of many maize ABC genes, mainly including ZmABC 012, 013, 015, 031, 040, 043, 065, 078, 080, 085, 088, 102, 107, 111, 130 and 131 genes, etc. These results indicated that ZmABC genes play an important role in the response to heavy metal stress. The comprehensive analysis of this study provides a foundation for further studies into the roles of ABC genes in maize.

The Arabidopsis transcription factor LBD15 mediates ABA signaling and tolerance of water-deficit stress by regulating ABI4 expression.

To survive, sessile plants must adapt to grow and develop when facing water-deficit stress. However, the molecular mechanisms underlying fine-tuning of the antagonistic action between stress response and growth remain to be determined. Here, plants overexpressing Lateral Organ Boundaries Domain 15 (LBD15) showed abscisic acid (ABA) hypersensitivity and tolerance of water-deficit stress, whereas the loss-of-function mutant lbd15 presented decreased sensitivity to ABA and increased sensitivity to water-deficit stress. Further analysis revealed that LBD15 directly binds to the promoter of the ABA signaling pathway gene ABSCISIC ACID INSENSITIVE4 (ABI4) to activate its expression, thereby forming an LBD15-ABI4 cascade to optimally regulate ABA signaling-mediated plant growth and tolerance of water-deficit stress. In addition, drought stress-induced ABA signaling promoted LBD15 expression, which directly activates expression of ABI4 to close stomata. As a result, water loss is reduced, and then water-deficit stress tolerance is increased. The results of this study reveal a molecular mechanism by which LBD15 coordinates and balances plant growth and resistance to water-deficit stress.

Hydrogen sulfide alleviates oxidative damage under excess nitrate stress through MAPK/NO signaling in cucumber.

Hydrogen sulfide (H2S) is emerging as a potential messenger molecule involved in modulation of physiological processes in plants. Mitogen-activated protein kinase (MAPK) and nitric oxide (NO) are essential for abiotic stress signaling. This work investigated the effects of H2S and the crosstalk between H2S, MAPK and NO in cucumber roots under nitrate stress. The inhibitory effect of 140 mM nitrate on the growth of shoot and root was substantially alleviated by treatment with H2S donor sodium hydrosulfide (NaHS), especially 100 µM NaHS. Treatment with 100 µM NaHS reduced malondialdehyde (MDA) and H2O2 contents, ROS accumulation and increased the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and ascorbate peroxidase (APX). CsNMAPK transcript level was up-regulated by NaHS treatment, while significantly decreased by propargylglycine (PAG, specific inhibitor of H2S biosynthesis) and hypotaurine (HT, H2S scavenger) in cucumber roots under nitrate stress. NO accumulation was increased by NaHS treatment under nitrate stress, but reduced by HT, PAG and PD98059, indicating that NO might function downstream of MAPK and H2S. MAPK inhibitor PD98059 and NO scavenger (cPTIO) reversed the alleviating effect of H2S by increasing MDA and H2O2 contents, and decreasing antioxidant enzyme activities of SOD, CAT, POD, APX, and the endogenous H2S contents and LCD activities under nitrate stress. In conclusion, H2S played a protective role in cucumber seedlings under nitrate stress and MAPK/NO signaling were involved in the process by regulating antioxidant enzyme activities.

Gateway-compatible inducible vector set for the functional analysis of transcription factors in plants.

MAIN CONCLUSION: The inducible vectors pER8-Gateway-3Flag and pER8-Gateway-3Flag-SRDX have been subjected to considerable research in terms of the function of transcription factors (TFs) via transcription activity and repression, respectively. Approximately 1500 TFs have been identified in Arabidopsis thaliana genome. To identify their functions, loss-of-function and gain-of-function mutants were generated to analyze the phenotype. However, many loss-of-function mutants did not show any evident phenotype because of the functional redundancy within the TF family. The constitutive misexpression of some TFs may result in lethality or sterility. To overcome these problems, we produced a Gateway-compatible inducible binary vector system that facilitates fast and reliable DNA cloning and biological function identification. The vector can be used for the inducible expression of protein fusions to a polypeptide protein tag named 3xFLAG tag. This vector system can also be used to generate an inducible transcription inhibition of protein fusion to an Ethylene-Responsive Factor-associated amphiphilic repression (EAR) motif. The EAR motif makes it possible to get rid of redundancy within a TF family, thereby facilitating studies on loss of function. With these Gateway vectors, conventional subcloning technology that depends on restriction digestion and ligation is avoided. Thus, these Gateway vectors should be useful not only for the rapid analysis of the functions of redundant plant TFs, but also for the manipulation of TF overexpression, resulting in plant lethality or sterility, via an inducible promoter.

Physiological response and transcription profiling analysis reveals the role of H2S in alleviating excess nitrate stress tolerance in tomato roots.

Soil secondary salinization caused by excess nitrate addition is one of the major obstacles in greenhouse vegetable production. Excess nitrate inhibited the growth of tomato plants, while application of 100 µM H2S donor NaHS efficiently increased the plant height, fresh and dry weight of shoot and root, root length, endogenous H2S contents and L-cysteine desulfhydrases activities. NaHS altered the oxidative status of nitrate-stressed plants as inferred by changes in reactive oxygen species (ROS) accumulation and lipid peroxidation accompanied by regulation of the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX). Besides, NaHS increased the nitric oxide (NO) and total S-nitrosothiols (SNOs) contents, nitrate reductase (NR) activities and decreased the S-nitrosoglutathione reductase (GSNOR) activities under nitrate stress. Furthermore, microarray analysis using the Affymetrix Tomato GeneChip showed that 5349 transcripts were up-regulated and 5536 transcripts were down-regulated under NaHS and excess nitrate stress treatment, compared to the excess nitrate stress alone. The differentially expressed genes (log2 fold change >2 or <  -2) of up-regulated (213) and down-regulated (271) genes identified were functionally annotated and subsequently classified into 9 functional categories. These categories included metabolism, signal transduction, defence response, transcription factor, protein synthesis and protein fate, transporter, cell wall related, hormone response, cell death, energy and unknown proteins. Our study suggested exogenous NaHS might enhance excess nitrate stress tolerance of tomato plants by modulating ROS and reactive nitrogen species (RNS) signaling and downstream transcriptional adjustment, such as defence response, signal transduction and transcription factors.