Transcriptome analysis provides molecular evidences for growth and adaptation of plant roots in cadimium-contaminated environments

Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety 'Jingu 21' (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).

Conjoint analysis of physio-biochemical, transcriptomic, and metabolomic reveals the response characteristics of solanum nigrum L. to cadmium stress

Cadmium (Cd) is a nonessential element in plants and has adverse effects on the growth and development of plants. However, the molecular mechanisms of Cd phytotoxicity, tolerance and accumulation in hyperaccumulators Solanum nigrum L. has not been well understood. Here, physiology, transcriptome, and metabolome analyses were conducted to investigate the influence on the S. nigrum under 0, 25, 50, 75 and 100 µM Cd concentrations for 7 days. Pot experiments demonstrated that compared with the control, Cd treatment significantly inhibited the biomass, promoted the Cd accumulation and translocation, and disturbed the balance of mineral nutrient metabolism in S. nigrum, particularly at 100 µM Cd level. Moreover, the photosynthetic pigments contents were severely decreased, while the content of total protein, proline, malondialdehyde (MDA), H2O2, and antioxidant enzyme activities generally increased first and then slightly declined with increasing Cd concentrations, in both leaves and roots. Furthermore, combined with the previous transcriptomic data, numerous crucial coding-genes related to mineral nutrients and Cd ion transport, and the antioxidant enzymes biosynthesis were identified, and their expression pattern was regulated under different Cd stress. Simultaneously, metabolomic analyses revealed that Cd treatment significantly changed the expression level of many metabolites related to amino acid, lipid, carbohydrate, and nucleotide metabolism. Metabolic pathway analysis also showed that S. nigrum roots activated some differentially expressed metabolites (DEMs) involved in energy metabolism, which may enhance the energy supply for detoxification. Importantly, central common metabolism pathways of DEGs and DEMs, including the "TCA cycle", "glutathione metabolic pathway" and "glyoxylate and dicarboxylate metabolism" were screened using conjoint transcriptomics and metabolomics analysis. Our results provide some novel evidences on the physiological and molecular mechanisms of Cd tolerance in hyperaccumulator S. nigrum plants.

Research progress of the detection and analysis methods of heavy metals in plants

Heavy metal (HM)-induced stress can lead to the enrichment of HMs in plants thereby threatening people's lives and health via the food chain. For this reason, there is an urgent need for some reliable and practical techniques to detect and analyze the absorption, distribution, accumulation, chemical form, and transport of HMs in plants for reducing or regulating HM content. Not only does it help to explore the mechanism of plant HM response, but it also holds significant importance for cultivating plants with low levels of HMs. Even though this field has garnered significant attention recently, only minority researchers have systematically summarized the different methods of analysis. This paper outlines the detection and analysis techniques applied in recent years for determining HM concentration in plants, such as inductively coupled plasma mass spectrometry (ICP-MS), atomic absorption spectrometry (AAS), atomic fluorescence spectrometry (AFS), X-ray absorption spectroscopy (XAS), X-ray fluorescence spectrometry (XRF), laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), non-invasive micro-test technology (NMT) and omics and molecular biology approaches. They can detect the chemical forms, spatial distribution, uptake and transport of HMs in plants. For this paper, the principles behind these techniques are clarified, their advantages and disadvantages are highlighted, their applications are explored, and guidance for selecting the appropriate methods to study HMs in plants is provided for later research. It is also expected to promote the innovation and development of HM-detection technologies and offer ideas for future research concerning HM accumulation in plants.

Combined application of biochar and sulfur alleviates cadmium toxicity in rice by affecting root gene expression and iron plaque accumulation

Biochar and sulfur are considered useful amendments for soil cadmium (Cd) contamination remediation. However, there is still a gap in the understanding of how combined biochar and sulfur application affects Cd resistance in rice, and the role of the accumulation of iron plaque and the expression of Cd efflux transporter-related genes are still unclear in this type of treatment. In this study, we screened an effective combination of biochar and sulfur (0.75 % biochar, 60 mg/kg sulfur) that significantly reduced the Cd content of rice roots (32.9 %) and shoots (12.3 %); significantly reduced the accumulation of amino acids and their derivatives, organic acids and their derivatives and flavonoids in rice roots; and altered secondary metabolite production and release. This combined biochar and sulfur application alleviated the toxicity of Cd to rice, in which the enhancement of iron plaque (24.8 %) formation and upregulated expression of heavy metal effector genes (NRAMP3, MTP3, ZIP1) were important factors. These findings show that iron plaque and heavy metal transport genes are involved in the detoxification of rice under the combined application of biochar and sulfur, which provides useful information for the combined treatment of soil Cd pollution.

The toxic mechanism of tetracycline on root tips in hulless barley (Hordeum vulgare L. var. nudum)

Tetracycline (TC) is a commonly used antibiotic that affects various physiological processes in plants. However, its negative effects on plants remain poorly understood at the molecular level. To ascertain the TC toxicity in the roots, transcriptomic, cytological, and physiological analyses were performed to explore the molecular mechanisms of TC influencing the growth of hulless barley root. At a low concentration (1 mg/L), TC promoted root growth by upregulating the genes related to the flavonoid pathway. At high concentrations (10, 100, and 200 mg/L), TC downregulated genes related to homologous recombination in the root meristem zone and inhibited the mitosis index by 16.4%. Disruption of the DNA repair process can lead to chromosomal aberrations, resulting in a 6.8% C-mitosis rate in the most severe cases. Finally, root growth was inhibited by TC, as evidenced by a reduction in root viability, an increase in reactive oxygen species content, and an inhibition of root length. Cross-comparison of physiological and cytological characterizations and transcriptomic information revealed changes in genetic processes under TC stress. Overall, we present an early genetic strategy to study the significant influence of TC stress on roots.

Integration of Physiological, Transcriptomic and Metabolomic Reveals Molecular Mechanism of Paraisaria dubia Response to Zn2+ Stress

Utilizing mycoremediation is an important direction for managing heavy metal pollution. Zn²⁺ pollution has gradually become apparent, but there are few reports about its pollution remediation. Here, the Zn²⁺ remediation potential of Paraisaria dubia, an anamorph of the entomopathogenic fungus Ophiocordyceps gracilis, was explored. There was 60% Zn²⁺ removed by Paraisaria dubia mycelia from a Zn²⁺-contaminated medium. To reveal the Zn²⁺ tolerance mechanism of Paraisaria dubia, transcriptomic and metabolomic were executed. Results showed that Zn²⁺ caused a series of stress responses, such as energy metabolism inhibition, oxidative stress, antioxidant defense system disruption, autophagy obstruction, and DNA damage. Moreover, metabolomic analyses showed that the biosynthesis of some metabolites was affected against Zn²⁺ stress. In order to improve the tolerance to Zn²⁺ stress, the metabolic mechanism of metal ion transport, extracellular polysaccharides (EPS) synthesis, and microcycle conidiation were activated in P. dubia. Remarkably, the formation of microcycle conidiation may be triggered by reactive oxygen species (ROS) and mitogen-activated protein kinase (MAPK) signaling pathways. This study supplemented the gap of the Zn²⁺ resistance mechanism of Paraisaria dubia and provided a reference for the application of Paraisaria dubia in the bioremediation of heavy metals pollution.

Integrated transcriptomics and metabolomics reveal key metabolic pathway responses in Pistia stratiotes under Cd stress

Cadmium (Cd) can interfere with plant gene expression, change the content of metabolites and affect plant growth. In this study, untargeted metabolomics (LC-MS) and RNA-Seq sequencing were performed on root tissues of Pistia stratiotes exposed to Cd stress. The results showed that cadmium stress affected the accumulation and transport of cadmium in plants and increased the content of soluble sugar, the activities of ascorbate peroxidase (APX), and peroxidase (POD) by 34.89%, 41.45%, and 6.71% on average, and decreased the activity of superoxide dismutase (SOD) by 51.51% on average. At the same time, the contents of carotenoid, chlorophyll a, and chlorophyll b decreased by 29.52%, 20.11%, and 13.14%, respectively, Thus affecting the growth and development of plants. Metabolomic analysis showed that Cd stress affected eight metabolic pathways, involving 27 differentially expressed metabolites, mainly including unsaturated fatty acids, amino acids (phenylalanine), nucleotides, sulfur compounds, and flavonoids. By transcriptome analysis, a total of 3107 differentially expressed genes (DEGs, 2666 up-regulated genes, and 441 down-regulated genes) were identified, which were mainly involved in four pathways, among which glutathione metabolism and lignin biosynthesis were the key metabolic pathways. In conclusion, this study reveals the metabolic and transcriptional response mechanisms of P. stratiotes to Cd stress through multi-omics, providing the theoretical basis for the phytoremediation of water contaminated by Cd.

Physiological and transcriptional mechanisms associated with cadmium stress tolerance in Hibiscus syriacus L

BACKGROUND

Cadmium (Cd) pollution of soils is a global concern because its accumulation in plants generates severe growth retardation and health problems. Hibiscus syriacus is an ornamental plant that can tolerate various abiotic stresses, including Cd stress. Therefore, it is proposed as a plant material in Cd-polluted areas. However, the molecular mechanisms of H. syriacus tolerance to Cd are not yet understood.

RESULTS

This study investigated the physiological and transcriptional response of "Hongxing", a Cd²⁺-tolerant H. syriacus variety, grown on a substrate containing higher concentration of Cd (400 mg/kg). The Cd treatment induced only 28% of plant mortality, but a significant decrease in the chlorophyll content was observed. Malondialdehyde content and activity of the antioxidant enzymes catalase, peroxidase, and superoxide dismutase were significantly increased under Cd stress. Transcriptome analysis identified 29,921 differentially expressed genes (DEGs), including 16,729 down-regulated and 13,192 up-regulated genes, under Cd stress. Functional enrichment analyses assigned the DEGs mainly to plant hormone signal transduction, transport, nucleosome and DNA processes, mitogen-activated protein kinase signaling pathway, antioxidant process, fatty acid metabolism, and biosynthesis of secondary metabolites. Many MYB, EP2/ERF, NAC, WRKY family genes, and genes containing metal binding domains were up-regulated, implying that they are essential for the Cd-stress response in H. syriacus. The most induced genes were filtered out, providing valuable resources for future studies.

CONCLUSIONS

Our findings provide insights into the molecular responses to Cd stress in H. syriacus. Moreover, this study offers comprehensive and important resources for future studies toward improving the plant Cd tolerance and its valorization in phytoremediation.

Arbuscular mycorrhizal fungi influence the uptake of cadmium in industrial hemp (Cannabis sativa L.)

Phytoremediation is currently a more environmentally friendly and economical measure for the remediation of cadmium (Cd) contaminated soil. Heavy metal-resistant plant species, Cannabis sativa L. was inoculated with Rhizophagus irregularis to investigate the mechanisms of mycorrhizal in improving the Cd remediation ability of C. sativa. The results showed that after inoculation with R. irregularis, C. sativa root Cd contents increased significantly, and leaf Cd enrichment decreased significantly. At the transcriptional level, R. irregularis down-regulated the expression of the ABC transporter family but up-regulated differentially expressed genes regulating low molecular weight organic acids. The levels of malic acid, citric acid, and lactic acid were significantly increased in the rhizosphere soil, and they were significantly and strongly related to oxidizable Cd concentrations. Then citric acid levels were considerably and positively connected to exchangeable Cd concentrations. Our findings revealed that through regulating the movement of root molecules, arbuscular mycorrhizal fungus enhanced the heavy metal tolerance of C. sativa even more, meanwhile, they changed the Cd chemical forms by altering the composition of low molecular weight organic acids, which in turn affected soil Cd bioavailability.

Comparative transcriptomic analysis reveals the important process in two rice cultivars with differences in cadmium accumulation

To date, Cd remains a major contaminant in rice production. An in-depth exploration of the mechanism that causes genotypic differences in Cd enrichment in rice is necessary to develop strategies to regulate Cd enrichment in rice. Here, two rice cultivars (low grain Cd, ZZ143; and high grain Cd, YX409) displayed different transcriptomic profile patterns when subjected to 100μmol/L Cd stress. In fact, 18,721(9833 upregulated and 8888 downregulated) and 16,403 (8366 upregulated and 8037 downregulated) differentially expressed genes (DEGs) were found in ZZ143 and YX409, respectively. Gene ontology (GO) classification revealed 28 and 26 terms enriched in ZZ143 and YX409, respectively. ZZ143 had more enriched DEGs than YX409, primarily in cellular processes, metabolic processes, binding terms, catalytic activity, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 21 and 24 pathways were significantly enriched in ZZ143 and YX409, respectively. Based on the DEGs, ZZ143 had a stronger ability for sulfur assimilation and Cys synthesis, whereas YX409 had a stronger ability to maintain cell wall stability. A series of DEGs involved in metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction pathways, and mitogen-activated protein kinase signaling pathways were identified, which maybe closely related to Cd resistance and the different Cd concentrations between cultivars. The above pathways and the greater number of identified DEGs in more than half of the GO terms and KEGG pathways suggest a higher absorption and stronger tolerance of the roots of ZZ143 than YX409 to Cd.

Integration of transcriptome and metabolome analyses reveals sorghum roots responding to cadmium stress through regulation of the flavonoid biosynthesis pathway

Cadmium (Cd) pollution is a serious threat to plant growth and human health. Although the mechanisms controlling the Cd response have been elucidated in other species, they remain unknown in Sorghum (Sorghum bicolor (L.) Moench), an important C₄ cereal crop. Here, one-week-old sorghum seedlings were exposed to different concentrations (0, 10, 20, 50, 100, and 150 μM) of CdCl₂ and the effects of these different concentrations on morphological responses were evaluated. Cd stress significantly decreased the activities of the enzymes peroxidase (POD), superoxide dismutase (SOD), glutathione S-transferase (GST) and catalase (CAT), and increased malondialdehyde (MDA) levels, leading to inhibition of plant height, decreases in lateral root density and plant biomass production. Based on these results, 10 μM Cd concentration was chosen for further transcription and metabolic analyses. A total of 2683 genes and 160 metabolites were found to have significant differential abundances between the control and Cd-treated groups. Multi-omics integrative analysis revealed that the flavonoid biosynthesis pathway plays a critical role in regulating Cd stress responses in sorghum. These results provide new insights into the mechanism underlying the response of sorghum to Cd.

Response mechanisms of bacterial communities and nitrogen cycle functional genes in millet rhizosphere soil to chromium stress

Introduction

A growing amount of heavy metal contamination in soil disturbs the ecosystem's equilibrium, in which microbial populations play a key role in the nutrient cycle of soils. However, given the different sensitivity of microbial communities to different spatial and temporal scales, microbial community structure and function also have varied response mechanisms to different heavy metal contaminated habitats.

Methods

In this study, samples were taken prior to Cr stress (CK) and 6 h and 6 days after Cr stress (Cr_6h, Cr_6d) in laboratory experiments. High-throughput sequencing revealed trends in the structure and diversity of the bacterial communities, and real-time fluorescence quantitative polymerase chain reaction (qPCR) was used to analyze trends in nitrogen cycle functional genes (AOA-amoA, AOB-amoA, narG, nirK, and nifH).

Results

The findings showed that (1) the composition structure of the soil bacterial community changed considerably in Cr-stressed soils; α-diversity showed significant phase transition characteristic from stress to stability (p < 0.05). (2) With an overall rising tendency, the abundance of the nitrogen cycle functional genes (AOA-amoA and AOB-amoA) decreased considerably before increasing, and α-diversity dramatically declined (p < 0.05). (3) The redundancy analysis (RDA) and permutational multivariate analysis of variance (PERMANOVA) tests results showed that the soil physicochemical parameters were significantly correlated with the nitrogen cycle functional genes (r: 0.4195, p < 0.01). Mantel analysis showed that available nitrogen (N), available potassium (K), and available phosphorus (P) were significantly correlated with nifH (p = 0.006, 0.008, 0.004), and pH was highly significantly correlated with nifH (p = 0.026). The PLS-ME (partial least squares path model) model further demonstrated a significant direct effect of the soil physicochemical parameters on the nitrogen cycling functional genes.

Discussion

As a result, the composition and diversity of the bacterial community and the nitrogen cycle functional genes in Cr-stressed agricultural soils changed considerably. However, the influence of the soil physicochemical parameters on the functional genes involved in the nitrogen cycle was greater than that of the bacterial community. and Cr stress affects the N cycling process in soil mainly by affecting nitrification. This research has significant practical ramifications for understanding the mechanisms of microbial community homeostasis maintenance, nitrogen cycle response mechanisms, and soil remediation in heavy metal-contaminated agricultural soils.

Integrated ionomic and transcriptomic dissection reveals the core transporter genes responsive to varying cadmium abundances in allotetraploid rapeseed

BACKGROUND

Oilseed rape (B. napus L.) has great potential for phytoremediation of cadmium (Cd)-polluted soils due to its large plant biomass production and strong metal accumulation. Soil properties and the presence of other soluble compounds or ions, cause a heterogeneous distribution of Cd.

RESULTS

The aim of our study was to reveal the differential responses of B. napus to different Cd abundances. Herein, we found that high Cd (50 μM) severely inhibited the growth of B. napus, which was not repressed by low Cd (0.50 μM) under hydroponic culture system. ICP-MS assays showed that the Cd2+ concentrations in both shoots and roots under 50 μM Cd were over 10 times higher than those under 0.50 μM Cd. Under low Cd, the concentrations of only shoot Ca2+/Mn2+ and root Mn2+ were obviously changed (both reduced); under high Cd, the concentrations of most cations assayed were significantly altered in both shoots and roots except root Ca2+ and Mg2+. High-throughput transcriptomic profiling revealed a total of 18,021 and 1408 differentially expressed genes under high Cd and low Cd conditions, respectively. The biological categories related to the biosynthesis of plant cell wall components and response to external stimulus were over-accumulated under low Cd, whereas the terms involving photosynthesis, nitrogen transport and response, and cellular metal ion homeostasis were highly enriched under high Cd. Differential expression of the transporters responsible for Cd uptake (NRAMPs), transport (IRTs and ZIPs), sequestration (HMAs, ABCs, and CAXs), and detoxification (MTPs, PCR, MTs, and PCSs), and some other essential nutrient transporters were investigated, and gene co-expression network analysis revealed the core members of these Cd transporters. Some Cd transporter genes, especially NRAMPs and IRTs, showed opposite responsive patterns between high Cd and low Cd conditions.

CONCLUSIONS

Our findings would enrich our understanding of the interaction between essential nutrients and Cd, and might also provide suitable gene resources and important implications for the genetic improvement of plant Cd accumulation and resistance through molecular engineering of these core genes under varying Cd abundances in soils.