Constitutional tolerance to heavy metals of a fiber crop, ramie (Boehmeria nivea), and its potential usage

Selenium increases antimony uptake in ramie (Boehmeria nivea L.) by enhancing the physiological, antioxidative, and ionomic mechanisms

Ramie (Boehmeria nivea L.) is a promising phytoremediation candidate due to its high tolerance and enrichment capacity for antimony (Sb). However, challenges arise as Sb accumulated mainly in roots, complicating soil extraction. Under severe Sb contamination, the growth of ramie may be inhibited. Strategies are needed to enhance Sb accumulation in ramie's aboveground parts and improve tolerance to Sb stress. Considering the beneficial effects of selenium (Se) on plant growth and enhancing resistance to abiotic stresses, this study aimed to investigate the potential use of Se in enhancing Sb uptake by ramie. We investigated the effects of Se (0.5, 1, 2, 5, or 10 μM) on ramie growth, Sb uptake and speciation, antioxidant responses, and ionomic profiling in ramie under 10 mg/L of SbIII or antimonate (SbV) stresses. Results revealed that the addition of 0.5 μM Se significantly increased shoot biomass by 75.73% under SbIII stress but showed minimal effects on shoot and root length in both SbIII and SbV treatments. Under SbIII stress, 2 μM Se significantly enhanced Sb concentrations by 48.42% in roots and 62.88% in leaves. In the case of SbV exposure, 10 μM Se increased Sb content in roots by 42.57%, and 1 μM Se led to a 91.74% increase in leaves. The speciation analysis suggested that Se promoted the oxidation of SbIII to less toxic SbV to mitigate Sb toxicity. Additionally, Se addition effectively minimized the excess reactive oxygen species produced by Sb exposure, with the lowest malondialdehyde (MDA) content at 0.5 μM Se under SbIII and 2 μM Se under SbV, by activating antioxidant enzymes including superoxide dismutase, catalase, peroxidase, and glutathione peroxidase. Ionomic analysis revealed that Se helped in maintaining the homeostasis of certain nutrient elements, including magnesium, potassium (K), calcium (Ca), iron (Fe), and copper (Cu) in the SbIII-treated roots and K and manganese (Mg) in the SbV-treated roots. The results suggest that low concentrations of Se can be employed to enhance the phytoremediation of Sb-contaminated soils using ramie.

Study on remediation of cadmium contaminated paddy field by ramie (Boehmeria nivea L.) floating island and its supporting technology

Ramie (Boehmeria nivea L.) is an ideal crop for cadmium (Cd) pollution remediation due to its advantages of both remediating and utilizing, however, it is mainly carried out in dry land, whose restoration effect is relatively slow. Previously, we found that the ramie plants cultivated by hydroponics has several tens of times higher Cd absorption capacity than that planted in soil. However, the issue of how to use hydroponic ramie to remediate Cd contaminated paddy fields needs to be addressed. In this study, we innovatively developed the ramie floating island technology and studied its remediation model on simulated Cd contaminated paddy fields. Different ramie varieties were used to compare the remediation effects, and the results showed that there were differences in adaptability among different varieties on floating islands and the remediation ability of the tested ramie varieties was Z2 > Z1 > Z3. Different harvested times were set to analyze the effects of harvested model on remediation, and it was suggested that multiple harvests can be carried out according to the plant growth status of ramie floating island after 30 days of remediation to achieve better remediation effects. Low water level height (5 cm) of paddy field was beneficial for the accumulation of Cd in the roots, but considering the adaptability of various ramie varieties and the effect of long-term restoration, it was recommended that the water level height of 20 cm for the cultivation of ramie floating island was more suitable. Moreover, we found that low concentration of citric acid (≤2 g L-1) or polyaspartic acid (≤3 g L-1) can improve the remediation effects for ramie floating island. Our study opens up a novel approach for ramie to remediate heavy metal pollution and provides a technical reference for water body Cd remediation by plants.

Plant growth-promoting rhizobacteria: A good companion for heavy metal phytoremediation

Phytoremediation is an environment-friendly approach regarded as a potential candidate for remediating heavy metal (HM)-contaminated soils. However, the low efficacy of phytoremediation is a major limitation that hampers its large-scale application. Therefore, developing strategies to enhance phytoremediation efficacy for contaminated soils is crucial. Plant growth-promoting rhizobacteria (PGPR) considerably contribute to phytoremediation intensification. To improve the efficiency of plant-microbe symbiosis for remediation, the mechanisms underlying PGPR-stimulated HM accumulation and tolerance in plants should be comprehensively understood. This review focuses on hyperaccumulators, PGPR, and the mechanisms by which PGPR enhance phytoremediation from four aspects: providing nutrients to plants, secreting plant hormones and specific enzymes, inducing systemic resistance, and altering the bioavailability of HMs in soils. It also provides a theoretical and technical basis for future research on PGPR synergism in promoting the phytoextraction efficiency in HM-contaminated soils.

Comparative biochemical and transcriptomic analysis reveals the phosphate-starving tolerance of two ramie varieties

Ramie (Boehmeria nivea L.) is a highly valued fiber crop. Its yield is often limited by lack of available phosphate (Pi) in the soil, but the underlying molecular mechanisms of ramie's response to Pi deficiency remain largely unknown. To investigate how ramie adapts to low Pi stress, we selected a low Pi-tolerant variety (H-5) and a low Pi-sensitive variety (XYL), and conducted a biochemical and transcriptomic analysis on roots and leaves of both varieties. After subjecting the plants to Pi-deficient and Pi-sufficient conditions for 15 days, we found that H-5 exhibited higher dry weight, longer root systems, and higher levels of Pi, galactolipids, and organic acids when subjected to Pi deprivation, compared to XYL. Transcriptomic analysis further revealed that Pi-responsive genes involved in lipid metabolism, Pi transport, organic acid synthesis, and acid phosphatase activities were more induced in the tolerant variety H-5. Furthermore, weighted gene co-expression network analysis (WGCNA) identified five hub genes, including phosphate transporter, SPX domain-containing protein and sulfoquinovosyl transferase, which played key roles in low Pi tolerance in ramie. The present study will broaden our comprehension of the differences and molecular mechanisms of different ramie cultivars in response to Pi starvation, and lay a foundation for future agronomic improvements in ramie and other fiber crops.

A comparative study of different methods for the determination of cadmium in various tissues of ramie (Boehmeria nivea L.)

Remediation of cadmium (Cd) pollution is one of the priorities of global environmental governance and accurate detection of Cd content is a key link in remediation of Cd pollution. This study aimed to compare three methods (inductively coupled plasma optical emission spectrometry (ICP-OES), inductively coupled plasma mass spectrometry (ICP-MS), and graphite furnace-atomic absorption spectrometry (GF-AAS)) for the determination of Cd with different tissues of various ramie varieties, and distinguish the advantage and disadvantage of each method. In total, 162 samples of ramie (Boehmeria nivea L.), which is an ideal plant for heavy metal remediation, were detected and the results showed that the three methods were all suitable for the de-termination of Cd content in ramie. ICP-OES and ICP-MS were simpler, faster, and more sensitive than GF-AAS. ICP-MS could be recommended for the determination of samples with various concentrations of Cd. ICP-OES could be used for measurement of samples with > 100 mg/kg Cd content, while GF-AAS was suitable for the detection of samples with very high (> 550 mg/kg) or very low (< 10 mg/kg) Cd content. Overall, considering the accuracy, stability, and the cost of measurement, ICP-MS was the most suitable method for determination of Cd content. This study provides significant reference information for the research in the field of Cd pollution remediation.

The Impact of Heavy Metal Accumulation on Some Physiological Parameters in Silphium perfoliatum L. Plants Grown in Hydroponic Systems

Heavy metals like cadmium (Cd), copper (Cu), lead (Pb), and zinc (Zn), resulting from anthropogenic activities, are elements with high persistence in nature, being able to accumulate in soils, water, and plants with significant impact to human and animal health. This study investigates the phytoremediation capacity of Silphium perfoliatum L. as a specific heavy metal hyperaccumulator and the effects of Cu, Zn, Cd, and Pb on some physiological and biochemical indices by growing plants under floating hydroponic systems in nutrient solutions under the presence of heavy metals. One-year-old plants of S. perfoliatum grown for 20 days in Hoagland solution with the addition of (ppm) Cu-400, Zn-1200, Cd-20, Pb-400, and Cu+Zn+Cd+Pb (400/1200/20/400) were investigated with respect to the control. The level of phytoremediation, manifested by the ability of heavy metal absorption and accumulation, was assessed. In addition, the impact of stress on the proline content, photosynthetic pigments, and enzymatic activity, as being key components of metabolism, was determined. The obtained results revealed a good absorption and selective accumulation capacity of S. perfoliatum plants for the studied heavy metals. Therefore, Cu and Zn mainly accumulate in the stems, Cd in the roots and stems, while Pb mainly accumulates in the roots. The proline tended to increase under stress conditions, depending on the pollutant and its concentration, with higher values in leaves and stems under the associated stress of the four metals and individually for Pb and Cd. In addition, the enzymatic activity recorded different values depending on the plant organ, its type, and the metal concentration on its substrate. The obtained results indicate a strong correlation between the metal type, concentration, and the mechanisms of absorption/accumulation of S. perfoliatum species, as well as the specific reactions of metabolic response.

Site-specific ecological effect assessment at community level for polymetallic contaminated soil

Current ecological risk assessment (ERA) is based more on book-keeping than on science especially for terrestrial ecosystems due to the lack of relevance to real field. Accordingly, site-specific ecological effect assessment is critical for ERA, especially at high tiers. This study developed procedures to assess ecological effect at community level based on field data. As a case study, we assessed ecological effect of polymetallic contamination in soil in the surrounding of an abandoned mining and smelting site in Hunan, China. Firstly, Zn was identified as the dominant contaminant in soil and slope gradient (SG) and pH as environmental impact factors using distance-based redundancy analysis(db-RDA). Secondly, sensitive endpoints were screened using correlation analysis between Zn and parameters of plant community composition and functional traits. Thirdly, exposure-effect curves between Zn and screened endpoints were developed by taking SG and pH as covariates using Bayesian kernel machine regression analysis (BKMR), based on which half-effect concentrations (EC₅₀s) and 10 %-effect concentrations (EC₁₀s) of soil Zn for each endpoint were calculated. Finally, site-specific hazardous concentrations (HC₅₀s) of Zn were estimated. It was revealed site-specific EC₅₀s and EC₁₀s for soil Zn ranged 80.5-201 mg kg^-1 and 342-893 mgkg^-1, respectively, and HC₅₀s based on EC₁₀s and EC₅₀s ranged 104-110 mg kg^-1 and 595-612 mg kg^-1, respectively, which are more specific and inclusive than those obtained based on crop and vegetable seed germination and seedling growth toxicity experiments.

Effect of different ramie (Boehmeria nivea L. Gaud) cultivars on the adsorption of heavy metal ions cadmium and lead in the remediation of contaminated farmland soils

Heavy metal ions, including cadmium (Cd) and lead (Pb), are serious pollutants in farmland soils. The effective removal of heavy metals is an important task in soil remediation. This study aimed to evaluate the ability of seven ramie (Boehmeria nivea L. Gaud) cultivars to remove heavy metals. Results showed that the seven ramie varieties grew well in Cd and Pb polluted soils. The aboveground biological tissues and raw fiber yield of “Zhongzhu1” were 20.71 and 24.61 Mg ha−1 per year, respectively, which were significantly higher than those of the six other varieties. Cd levels in each ramie part can be arranged as husks > root > stem bone > leaf > raw fiber, while Pb levels in each ramie part can be arranged as root > leaf > husks > stem bone > raw fiber. The Cd content in the shoots of “Zhongzhu1” was 19.89 mg kg−1, and the Pb content of the aboveground shoots of “Shiqianzhugenma” was 9.41 mg kg−1. The extraction efficiency of Cd in “Zhongzhu1” was greatly higher than those of the six other varieties. The extraction efficiency of Pb was similar in all varieties. Our observations suggest that ramie can be used to remove toxic ions (Cd and Pb). This study provides a new understanding of planting ramie for heavy metal removal from contaminated soils.

Biogeochemical cycles of nutrients, rare earth elements (REEs) and Al in soil-plant system in ion-adsorption REE mine tailings remediated with amendment and ramie (Boehmeria nivea L.)

The exploitation of ion-adsorption rare earth element (REE) deposits in South China has left large areas of mine tailings. However, limited remediation practices on these tailings have been reported, and how the remediation strategies and economic plants cultivation affect the biogeochemical cycles of nutrients, REEs and Al remains unclear. The aim of the present study was to investigate the effects of the combination of the addition of soil amendment and the root development and activity of a fiber plant ramie (Boehmeria nivea L.) on the availability and distribution of nutrients, as well as of REEs and other potentially toxic elements (e.g. Al) in the soil-plant system. The results showed that the application of organic amendment and ramie planting induced a significant increase in soil pH, total carbon (C), nitrogen (N), and other nutrient (e.g. P and Ca) concentrations, while led to a decrease of 80-90% and 60-90% in soil extractable REE and Al concentrations respectively. Matrices of correlation showed that soil pH, total C, N, and P concentrations were among the most important factors controlling the availability of soil REEs and Al, and root characteristics (e.g. fine root length). The total C, N, P and extractable nutrient concentrations, and electrical conductivity were higher in the rhizosphere soils of ramie than those in the bulk soils. Moreover, more than 60% of the quantity of REE and Al in the whole ramie plant was stored within the thick roots. These results showed that, in addition to amendment, the effects induced by the roots of ramie could further improve soil properties through C input, nutrient mobilization and toxic element stabilization. Our study concludes that ramie planting with organic amendment is a promising phytostabilization strategy for the remediation of REE mine tailings in South China.

Assessment of the potential for phytoremediation of cadmium polluted soils by various crop rotation patterns based on the annual input and output fluxes

Phytoremediation potential of two oil crop rotations (oilseed sunflower-rape (O+Ra) and peanut-oilseed rape (P+Ra)) was compared with three conventional cropping patterns (rice-rape (R+Ra), rice-rice (R+R), single cropped rice (SR)) in experimental plots with cadmium (Cd)-contaminated soil. A new approach was used to evaluate phytoremediation potential based on the balance between annual input and output fluxes of Cd in farmland soil. In O+Ra and P+Ra rotations, 77.24 and 62.09 g/ha Cd were removed, respectively, whereas in R+Ra, R+R, and SR patterns, 41.79, 46.46, and 23.85 g/ha Cd were removed, respectively. The balance between inputs and outputs of Cd was - 40.72 and - 25.76 g/ha under O+Ra and P+Ra rotations, respectively. Available Cd content in topsoil was reduced by 5.58% and 3.91% under O+Ra and P+Ra rotations, respectively. Based on the balance between Cd inputs and outputs, phytoremediation efficiencies of O+Ra (1.23%) and P+Ra (0.78%) rotations were higher than those of R+R (0.29%), R+Ra (0.13%), and SR (-0.38%) systems. Because crop removal is the main Cd output pathway, selection of a suitable crop is particularly important in remediation of Cd-contaminated farmland.

Medium nitrogen optimized Boehmeria nivea L. growth in copper contaminated soil

Copper (Cu) pollution in agricultural soils is considered as a serious health risk due to its accumulation in plants. Thus, there is an urgent need to optimize nutrient application for higher yield with lower Cu uptake to ensure food security. A pot experiment was conducted to investigate the effectiveness of nitrogen fertilizer (N) on Boehmeria nivea growth, gas exchange characteristics, antioxidant capacity and uptake of Cu in contaminated soil. Therefore, combinations of Cu levels (0, 100, 300 mg kg^-1) and N levels (0, 140, 280, 420 kg ha^-1) were applied. The results showed that N at 280 kg ha^-1 significantly (≤0.05) increased plant growth in terms of fresh biomass, plant height, stem diameter and number of leaves per plant up to100 mg kg^-1 Cu in soil for all harvests (H₁, H₂, H₃ and H₄). However, the interactive effect of Cu and N on Cu uptake by plant varied among N levels. Furthermore, N at 280 kg ha^-1 also improved the gas exchange characteristics viz., net photosynthesis (Pn), transpiration rate (Tr) and stomatal conductance (gs), while decreased oxidative stress in B. nivea up to 100 mg kg^-1 Cu in soil, relative to control. Thus N at 280 kg ha^-1 can be considered as an effective dose for high fresh biomass with lower Cu uptake by B. nivea grown as fodder in Cu contaminated soils (≤100 mg kg^-1). Overall, present research highlighted the necessity of balanced or optimum N application for sustainable B. nivea forage production in Cu contaminated agricultural lands.

A MYB transcription factor, BnMYB2, cloned from ramie (Boehmeria nivea) is involved in cadmium tolerance and accumulation

MYB-related transcription factors play important roles in plant development and response to various environmental stresses. In the present study, a novel MYB gene, designated as BnMYB2 (GenBank accession number: MF741319.1), was isolated from Boehmeria nivea using rapid amplification of cDNA ends (RACE) and RT-PCR on a sequence fragment from a ramie transcriptome. BnMYB2 has a 945 bp open reading frame encoding a 314 amino acid protein that contains a DNA-binding domain and shares high sequence identity with MYB proteins from other plant species. The BnMYB2 promoter contains several putative cis-acting elements involved in stress or phytohormone responses. A translational fusion of BnMYB2 with enhanced green fluorescent protein (eGFP) showed nuclear and cytosolic subcellular localization. Real-time PCR results indicated that BnMYB2 expression was induced by Cadmium (Cd) stress. Overexpression of BnMYB2 in Arabidopsis thaliana resulted in a significant increase of Cd tolerance and accumulation. Thus, BnMYB2 positively regulated Cd tolerance and accumulation in Arabidopsis, and could be used to enhance the efficiency of Cd removal with plants.

Phytostabilization of Cd and Pb in Highly Polluted Farmland Soils Using Ramie and Amendments

In-situ remediation of heavy-metal-contaminated soil in farmland using phytostabilization combined with soil amendments is a low-cost and effective technology for soil pollution remediation. In this study, coconut shell biochar (CB, 0.1% and 0.5%), organic fertilizer (OF, 3.0%), and Fe-Si-Ca material (IS, 3.0%) were used to enhance the phytostabilization effect of ramie (Boehmeria nivea L.) on Cd and Pb in highly polluted soils collected at Dabaoshan (DB) and Yangshuo (YS) mine sites. Results showed that simultaneous application of CB, OF, and IS amendments (0.1% CB + 3.0% OF + 3.0% IS and 0.5% CB + 3.0% OF + 3.0% IS, DB-T5 and DB-T6) could significantly increase soil pH, reduce the concentrations of CaCl₂-extractable Cd and Pb, and increase the contents of Ca, P, S, and Si in DB soil. Under these two treatments, the growth of ramie was significantly improved, its photosynthesis was enhanced, and its levels of Cd and Pb were reduced, in comparison with the control (DB-CK). After applying DB-T5 and DB-T6, the concentrations of Cd and Pb in roots were decreased by 97.7–100% and 64.6–77.9%, while in shoots they were decreased by up to 100% and 92.9–100%, respectively. In YS-T4 (0.5% CB + 3.0% OF), the concentrations of Cd and Pb in roots were decreased by 39.5% and 46.0%, and in shoots they were decreased by 44.7% and 88.3%. We posit that phytostabilization using ramie and amendments could reduce the Cd and Pb bioavailability in the soil mainly through rhizosphere immobilization and plant absorption. In summary, this study suggests that the use of tolerant plant ramie and simultaneous application of coconut shell biochar, organic fertilizer, and Fe-Si-Ca materials is an effective stabilization strategy that can reduce Cd and Pb availabilities in soil. Ultimately, this strategy may reduce the exposure risk of crops to heavy metal pollution in farmland.

Selection of Reference Genes for qPCR Analyses of Gene Expression in Ramie Leaves and Roots across Eleven Abiotic/Biotic Treatments

Quantitative real-time PCR (qPCR) is commonly used for deciphering gene functions. For effective qPCR analyses, suitable reference genes are needed for normalization. The objective of this study is to identify the appropriate reference gene(s) for qPCR analyses of the leaves and roots of ramie (Boehmeria nivea L.), an important natural fiber crop. To accomplish this goal, we investigated the expression patterns of eight common plant qPCR reference genes in ramie leaves and roots under five abiotic stresses, five hormonal treatments, and one biotic stress. The relative expression stabilities of the eight genes were evaluated using four common but different approaches: geNorm, NormFinder, BestKeeper, and RefFinder. Across the 11 tested conditions, ACT1 was the most stably expressed among the eight genes while GAPDH displayed the biggest variation. Overall, while variations in the suggested reference genes were found for different tissue x treatment combinations, our analyses revealed that together, genes ACT1, CYP2, and UBQ can provide robust references for gene expression studies of ramie leaves under most conditions, while genes EF-1α, TUB, and ACT1 can be used for similar studies of ramie roots. Our results should help future functional studies of the genes in ramie genome across tissues and environmental conditions.

Potential of indigenous plant species for phytoremediation of metal(loid)-contaminated soil in the Baoshan mining area, China

A field survey was conducted to investigate metal(loid) concentration in soils and native plants in the Baoshan mining area for potential application in phytoremediation. Total concentrations of arsenic (As), cadmium (Cd), lead (Pb), and zinc (Zn) in soil varied from 125 to 6656, 5.10 to 1061, 568 to 49294, and 241 to 17296 mg kg^-1, respectively, showing severe contamination. Among 20 species native to this area, Pteris ensiformis accumulated 1091 mg kg^-1 As in the shoot, and its translocation factor (TF) was greater than 1, suggesting potential capacity for As phytoextraction. Boehmeria nivea, Aster prorerus, and Hydrocotyle sibthorpioides showed potential for phytoextraction of Cd due to their high accumulation of Cd in shoots (490.3, 175.4, and 128.5 mg kg^-1, respectively) and high TFs (92.0, 22.1, and 6.7, respectively). Eleusine indica and P. ensiformis were found to contain high concentrations of Pb (7474 mg kg^-1) and Zn (1662 mg kg^-1) in roots, but with low TFs for Pb (0.4) and Zn (0.2), suggesting potential capability for phytostabilization. There was a positive correlation (p < 0.01, N = 25) of TFs between the metal(loid)s, indicating a synergic interaction in the uptake of metal(loid)s by these plants. According to metal(loid) concentrations in shoots, bioconcentration factors (BFs), and TFs, as well as the botanical features such as wide occurrence, high biomass yield, and rapid growth of the plants, the five native species identified above have the potential for phytoremediation in the Baoshan mining area.

Copper environmental toxicology, recent advances, and future outlook: a review

Copper (Cu) is one of the micronutrients needed by living organisms. In plants, Cu plays key roles in chlorophyll formation, photosynthesis, respiratory electron transport chains, oxidative stress protection as well as protein, carbohydrate, and cell wall metabolism. Therefore, deficiency of Cu can alter various functions of plant metabolism. However, Cu-based agrochemicals have traditionally been used in agriculture and being excessively released into the environment by anthropogenic activities. Continuous and extensive release of Cu is an imperative issue with various documented cases of phytotoxicity by the overproduction of reactive oxygen species (ROS) and damage to carbohydrates, lipids, proteins, and DNA. The mobility of Cu from soil to plant tissues has several concerns including its adverse effects on humans. In this review, we have described about importance and occurrence of Cu in environment, Cu homeostasis and toxicity in plants as well as remediation and progress in research so far done worldwide in the light of previous findings. Furthermore, present review provides a comprehensive ecological risk assessment on Cu in soils and thus provides insights for agricultural soil management and protection.

Morpho-physiological traits, antioxidant capacity and phytoextraction of copper by ramie (Boehmeria nivea L.) grown as fodder in copper-contaminated soil

Ramie (Boehmeria nivea L.), the oldest fiber crop in China, can also be grown as fodder crop because of its huge biomass production. Moreover, it has the potential to colonize heavy metal-contaminated soils which showed the possibilities of phytoremediation using B. nivea. Therefore, the present study was conducted to investigate the potential of B. nivea for phytoextraction of copper (Cu)-contaminated soil. Moreover, the impact of different concentrations of Cu on growth and antioxidant enzymatic activity by B. nivea were also studied. For this purpose, a pot experiment was conducted to examine the growth, antioxidative response, and localization (distribution) of Cu in B. nivea plant under different Cu concentrations (0, 50, 100, 200, 300, and 400 mg kg^-1 soil). Results revealed that B. nivea tolerated up to 100 mg kg^-1 Cu concentration without a significant decrease in biomass, but further increase in Cu concentration from 200 to 400 mg kg^-1 exhibited a significant reduction in chlorophyll content, fresh and dry biomass, plant height, and number of leaves. It was further observed that B. nivea accumulated more Cu in roots (26 to 53 mg kg^-1), followed by the leaves (23 to 28 mg kg^-1) and stems (14 to 21 mg kg^-1), while the values for both bioaccumulation factor (BAF) and translocation factor (TF) at all treatments were less than 1. Moreover, activities of antioxidative enzymes (superoxide dismutase and peroxidase) were initially increased with the exposure of 50, 100, and 200 mg kg^-1 Cu, but decreased by further increasing the Cu concentration to 300 and 400 mg kg^-1 indicating the oxidative stress which is manifested by high malondialdehyde (MDA) and proline contents also. Thus, based on results, it can be concluded that B. nivea accumulated relatively low Cu contents in aboveground parts and could be grown as fodder crop for phytoremediation of Cu-contaminated sites.

The miRNAome of ramie (Boehmeria nivea L.): identification, expression, and potential roles of novel microRNAs in regulation of cadmium stress response

BACKGROUND

MicroRNAs (miRNAs) regulate numerous crucial abiotic stress processes in plants. However, information is limited on their involvement in cadmium (Cd) stress response and tolerance mechanisms in plants, including ramie (Boehmeria nivea L.) that produces a number of economic valuable as an important natural fibre crop and an ideal crop for Cd pollution remediation.

RESULTS

Four small RNA libraries of Cd-stressed and non-stressed leaves and roots of ramie were constructed. Using small RNA-sequencing, 73 novel miRNAs were identified. Genome-wide expression analysis revealed that a set of miRNAs was differentially regulated in response to Cd stress. In silico target prediction identified 426 potential miRNA targets that include several uptake or transport factors for heavy metal ions. The reliability of small RNA sequencing and the relationship between the expression levels of miRNAs and their target genes were confirmed by quantitative PCR (q-PCR). We showed that the expression patterns of miRNAs obtained by q-PCR were consistent with those obtained from small RNA sequencing. Moreover, we demonstrated that the expression of six randomly selected target genes was inversely related to that of their corresponding miRNAs, indicating that the miRNAs regulate Cd stress response in ramie.

CONCLUSIONS

This study enriches the number of Cd-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in ramie during Cd stress.

Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

BACKGROUND

Ramie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known.

RESULTS

A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170-64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F₁ hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170-64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie.

CONCLUSIONS

The identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.

Uptake and accumulation of potentially toxic elements in colonized plant species around the world's largest antimony mine area, China

To provide information on reclamation of multi-heavy metal polluted soils with conception of phytostabilization, a field survey on the uptake and accumulation of potentially toxic elements such as antimony (Sb), arsenic (As), lead (Pb), cadmium (Cd), copper (Cu), and zinc (Zn) in colonized plant species around the world's largest antimony mine area, China, was conducted. Samples including leaves and shoots (including roots and stems) of colonized plants as well as rhizospheric soils were collected from eight sampling zones in the studied area. The results showed that the contents of Cu, Zn, and Pb in rhizospheric soils below plants were comparable to the corresponding background values of Hunan province, otherwise Sb, Cd, and As contents were extremely high (17-106, 17-87, and 3-7 times of the corresponding background values). The highest concentration of Sb was found in Aster subulatus (410 mg kg^-1); Cd, As, and Zn were in Herba bidentis bipinnatae (10.9, 264, and 265 mg kg^-1, respectively); and Cu was in Artemisia lavandulaefolia (27.1 mg kg^-1). It also exhibited that all the contents of As in leaves were several times of those in shoots of plants, Cd and other heavy metals showed in a similar pattern in several studied species, implying that the uptake route of these heavy metals via foliar might contribute to the accumulation. With high bioconcentration factors of heavy metals (more than 1, except for Zn), together with the growth abundance, Herba bidentis bipinnatae was considered as the most suitable colonized species for phytostabilization of the multi-heavy metal pollution in soils on this antimony mine area.

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae.

A Ramie bZIP Transcription Factor BnbZIP2 Is Involved in Drought, Salt, and Heavy Metal Stress Response

bZIP transcription factors play key roles in plant growth, development, and stress signaling. A bZIP gene BnbZIP2 (GenBank accession number: KP642148) was cloned from ramie. BnbZIP2 has a 1416 base pair open reading frame, encoding a 471 amino acid protein containing a characteristic bZIP domain and a leucine zipper. BnbZIP2 shares high sequence similarity with bZIP factors from other plants. The BnbZIP2 protein is localized to both nuclei and cytoplasm. Transcripts of BnbZIP2 were found in various tissues in ramie, with significantly higher levels in female and male flowers. Its expression was induced by drought, high salinity, and abscisic acid treatments. Analysis of the cis-elements in promoters of BnbZIP2 identified cis-acting elements involved in growth, developmental processes, and a variety of stress responses. Transgenic Arabidopsis plants' overexpression of BnbZIP2 exhibited more sensitivity to drought and heavy metal Cd stress during seed germination, whereas more tolerance to high-salinity stress than the wild type during both seed germination and plant development. Thus, BnbZIP2 may act as a positive regulator in plants' response to high-salinity stress and be an important candidate gene for molecular breeding of salt-tolerant plants.

Growth, photosynthesis, and defense mechanism of antimony (Sb)-contaminated Boehmeria nivea L

Ramie (Boehmeria nivea L.) is the oldest cash fiber crop in China and is widely grown in antimony (Sb) mining areas. To evaluate the extent of Sb resistance and tolerance, the growth, tolerance index (TI), Sb content in plant parts and in Hoagland solution, bioaccumulation factor (BF), photosynthesis, and physiological changes in Sb-contaminated B. nivea (20, 40, 80, and 200 mg L(-1) Sb) grown hydroponically were investigated. The Sb tolerance and resistance of ramie were clearly revealed by growth inhibition, a TI between 13 and 99 %, non-significant changes in the maximum quantum efficiency of photosystem (F v /F m ), energy-harvesting efficiency (photosystem II (PSII)) and single-photon avalanche diode (SPAD) value, a significant increase in Sb in plant parts, BF >1, and an increase in catalase (CAT) and malondialdehyde (MDA) at 200 mg L(-1) Sb. Under increasing Sb stress, nearly the same non-significant decline in the maximum quantum efficiency of photosystem (F v /F m ), energy-harvesting efficiency (PSII), relative quantum yield of photosystem II (φPSII), and photochemical quenching (qP), except for F v /F m at 20 mg L(-1) Sb, were recorded. SPAD values for chlorophyll under Sb stress showed an increasing trend, except for a slight decrease, i.e., <2 %, than the control SPAD value at 200 mg L(-1) Sb. With a continuous increase in MDA, superoxide dismutase (SOD), peroxidase (POD), and CAT activities were suppressed under Sb addition up to 40 mg L(-1) Sb and the addition of Sb enhanced enzyme production at 80 and 200 mg L(-1) Sb. A continuous decrease in SOD, POD, and CAT up to 40 mg L(-1) Sb and enhancements at ≥80 mg L(-1), along with the continuous enhancement of MDA activity and inhibited biomass production, clearly reveal the roles of these enzymes in detoxifying Sb stress and the defense mechanism of ramie at 80 mg L(-1) Sb. Thus, B. nivea constitutes a promising candidate for Sb phytoremediation at mining sites.

Biochemical and Metabolic Changes in Arsenic Contaminated Boehmeria nivea L

Arsenic (As) is identified by the EPA as the third highest toxic inorganic contaminant. Almost every 9th or 10th human in more than 70 countries including mainland China is affected by As. Arsenic along with other toxins not only affects human life but also creates alarming situations such as the deterioration of farm lands and desertion of industrial/mining lands. Researchers and administrators have agreed to opt for phytoremediation of As over costly cleanups. Boehmeria nivea L. can soak up various heavy metals, such as Sb, Cd, Pb, and Zn. But the effect of As pollution on the biology and metabolism of B. nivea has been somewhat overlooked. This study attempts to evaluate the extent of As resistance, chlorophyll content, and metabolic changes in As-polluted (5, 10, 15, and 20 mg L(-1) As) B. nivea in hydroponics. Toxic effects of As in the form of inhibited growth were apparent at the highest level of added As. The significant changes in the chlorophyll, electrolyte leakage, and H2O2, significant increases in As in plant parts, catalase (CAT), and malondialdehyde (MDA), with applied As revealed the potential of B. nivea for As decontamination. By employing the metabolic machinery of B. nivea, As was sustainably removed from the contaminated areas.

Variability of cadmium, lead, and zinc tolerance and accumulation among and between germplasms of the fiber crop Boehmeria nivea with different root-types

Crop germplasms substantially vary in their tolerance for and accumulation of heavy metals, and assessment of this variability plays a significant role in selecting species to use in phytoremediation projects. Here, we examined germplasm-variations in cadmium (Cd), lead (Pb), and zinc (Zn) tolerance and accumulation in ramie (Boehmeria nivea), a fiber crop native to China, which has received little attention. In an 8-week greenhouse test, fourteen germplasms of ramie, among and within deep, middle, and shallow rooted-types, were compared for growth and metal accumulation traits. Results showed that both tolerance and accumulation traits varied across germplasms and rooted-types. The deep rooted-type germplasms produced more biomass and had higher tolerance to metals than the two others. In addition, considerable variations in metal accumulation were observed among plant organs (root, stem, and leaf), rooted-types, germplasms, and metal supply. However, the observed variations in metal tolerance and accumulation among both germplasms and rooted-types were not significant in most cases. In addition to supporting the idea of a certain degree of constitutional metal tolerance for ramie, our results also contribute to deep-rooted germplasms of ramie as a good candidate, rather than middle-/shallow- ones as a least-bad option, for the remediation of multi metal-contaminated soils.

Expression profiling of cadmium response genes in ramie (Boehmeria nivea L.) root

Ramie (Boehmeria nivea), a perennial herb belongs to Urticaceae family, is a rapid growth and high biomass crop with highly tolerant and accumulative to heavy metals. However, the gene expression and regulation caused by cadmium (Cd) in ramie has not been well studied. In the present study, a gene expression database of ramie root in the absence (control) or presence of 100 μM Cd was established. Solexa high-throughput sequencing technology showed that 3,654,395 and 3,572,333 tags have been obtained from control and Cd treatment respectively. In total, 3887 genes were detected with significant differential expression levels, in which 2883 genes were up-regulated and 1004 genes were down-regulated. Gene ontology and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes. Fifteen genes were selected and their expression levels were confirmed by quantitative RT-PCR, and twelve of them showed consistent expression patterns with the digital gene expression data. Results on these expression profiling of genes lay the basis for biotechnological modification of new transgenic plants with improved phytoremediation capacity.

Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species

Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (G_ST = 0.27) and moderate gene flow (N_m = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement.

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Genetic diversity and population structure of ramie (Boehmeria nivea) were assessed by SCoT markers.

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SCoT markers revealed high polymorphism and resolving ability in Boehmeria nivea.

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The wild ramie showed moderate heterozygosity and gene flow with high genetic variation, suggesting unidirectional gene flow.

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The domesticated population exhibited highest heterozygosity and close association with introduced population.

Cadmium accumulation and apoplastic and symplastic transport in Boehmeria nivea (L.) Gaudich on cadmium-contaminated soil with the addition of EDTA or NTA

A Cd-tolerant plant species named Boehmeria nivea (L.) Gaudich (ramie) was applied to study its Cd accumulation and translocation mechanisms with the addition of ethylene diamine tetracetic acid (EDTA) or nitrilotriacetic acid (NTA).

Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress

Cadmium (Cd) contamination in agricultural soils has become a major environmental problem in China. Ramie, a fiber crop, has frequently been proposed for use as a phytoremediation crop for the restoration of Cd-contaminated farmlands. However, high levels of Cd can greatly inhibit stem growth in ramie, which reduces its economic value as a crop. To understand the potential mechanisms behind this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing on two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2). Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequence reads were generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, and de novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels in CO and CdS ramie revealed 155 differentially expressed genes (DEGs) between treatment and control conditions. Sixteen DEGs were further analyzed for expression differences by using real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase (a major enzyme for deactivating bioactive gibberellins [GAs]) showed markedly up-regulated expression in Cd stressed ramie. This might be responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that the cutin, suberine and wax biosynthesis pathway was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful in further understanding the mechanism of Cd-stress response and improving Cd stress tolerance in ramie.

Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of Ramie (Boehmeria nivea L. Gaud)

In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.

Evaluation of heavy metal and polycyclic aromatic hydrocarbons accumulation in plants from typical industrial sites: potential candidate in phytoremediation for co-contamination

The heavy metal and polycyclic aromatic hydrocarbons (PAHs) contents were evaluated in surface soil and plant samples of 18 wild species collected from 3 typical industrial sites in South Central China. The accumulative characteristics of the plant species for both heavy metal and PAHs were discussed. The simultaneous accumulation of heavy metal and PAHs in plant and soil was observed at all the investigated sites, although disparities in spatial distributions among sites occurred. Both plant and soil samples were characterized by high accumulation for heavy metal at smelting site, moderate enrichment at coke power and coal mining sites, whereas high level of PAHs (16 priority pollutants according to US Environmental Protection Agency) at coke power site, followed sequentially by coal mining and smelting sites. Based on the differences of heavy metal and PAH accumulation behaviors of the studied plant species, heavy metal and PAH accumulation strategies were suggested: Pteris vittata L. and Pteris cretica L. for As and PAHs, Boehmeria nivea (L.) Gaud for Pb, As, and PAHs, and Miscanthus floridulu (Labnll.) Warb for Cu and PAHs. These native plant species could be proposed as promising materials for heavy metal and PAHs combined pollution remediation.

Identification of 32 full-length NAC transcription factors in ramie (Boehmeria nivea L. Gaud) and characterization of the expression pattern of these genes

NAM, ATAF, and CUC (NAC) genes are plant-specific transcription factors (TFs) that play key roles in plant growth, development, and stress tolerance. To date, none of the ramie NAC (BnNAC) genes had been identified, even though ramie is one of the most important natural fiber crops. In order to mine the BnNAC TFs and identify their potential function, the search for BnNAC genes against two pools of unigenes de novo assembled from the RNA-seq in our two previous studies was performed, and a total of 32 full-length BnNAC genes were identified in this study. Forty-seven function-known NAC proteins published in other species, in concert with these 32 BnNAC proteins were subjected to phylogenetic analysis, and the result showed that all the 79 NAC proteins can be divided into eight groups (NAC-I-VIII). Among the 32 BnNAC genes, 24, 2, and 1 gene showed higher expression in stem xylem, leaf, and flower, respectively. Furthermore, the expression of 14, 11 and 4 BnNAC genes was regulated by drought, cadmium stress, and infection by root lesion nematode, respectively. Interestingly, there were five BnNAC TFs which showed high homology with the NAC TFs of other species involved in regulating the secondary wall synthesis, and their expressions were not regulated by drought and cadmium stress. These results suggested that the BnNAC family might have a functional diversity. The identification of these 32 full-length BnNAC genes and the characterization of their expression pattern provide a basis for future clarification of their functions in ramie growth and development.