Functional components of the bacterial CzcCBA efflux system reduce cadmium uptake and accumulation in transgenic tobacco plants

Emerging antibiotic and heavy metal resistance in spore-forming bacteria from pig manure, manure slurry and fertilized soil

Spore-forming bacteria (SFB), like Bacillus, are the gram-positive bacteria with broad-spectrum activity that is one of the commonly used strains of probiotics. However, these bacteria also have significant resistance. In this study, we systematically investigated pig manure, manure slurry and soil by 16S rRNA high-throughput sequencing and traditional culture techniques. We found the SFB was widespread in manure, manure slurry and soil, Firmicutes was one of the main dominant phyla in pig manure, manure slurry and soil, the relative abundance of Bacillus were 0.98%, 0.01%, and 2.57%, respectively, and metals such as copper have complex relationships with bacteria. We isolated 504 SFB from 369 samples, with the highest number identified as Bacillus subtilis. SFB strains showed varying degrees of antibiotic resistance; the greatest against erythromycin, followed by imipenem. The MICs of SFB varied greatly against different heavy metals; with high (est) resistance against Zn2+, followed by Cu2+. Second-generation whole genome sequencing (WGS) revealed that nine Bacillus strains carried different subtypes of vancomycin resistance genes, among which vanRM had the highest frequency. The strain W129 included the vanRA-vanRM-vanSA-vanZF cluster. The nine Bacillus strains also contained antibiotic genes such as aminoglycoside (ant(9)-Ia), β-lactam (bcII), and macrolide (msrE). Twenty-six Bacillus isolates carried copper resistance clusters, including csoR-copZ, copA-copZ-csoR, and copZ-copA. WGS showed that strain W166 carried 11 vancomycin resistance genes and 11 copper resistance genes. There were 4 vancomycin resistance genes and 14 copper resistance genes on the W129 chromosome. Strain W129 also harbors the plasmid pLKYM01 that contains an intact transposon consisting of insertion sequence and vancomycin resistance genes vanYF and vanRA. This study explores the potential risks of using pig manure and fertilized soil to inform safe and effective use of probiotics in agriculture. It highlights scientific evidence for concern over the safe utilization and control of animal waste products.

Mitigating heavy metal accumulation in tobacco: Strategies, mechanisms, and global initiatives

The threat of heavy metal (HM) pollution looms large over plant growth and human health, with tobacco emerging as a highly vulnerable plant due to its exceptional absorption capacity. The widespread cultivation of tobacco intensifies these concerns, posing increased risks to human health as HMs become more pervasive in tobacco-growing soils globally. The absorption of these metals not only impedes tobacco growth and quality but also amplifies health hazards through smoking. Implementing proactive strategies to minimize HM absorption in tobacco is of paramount importance. Various approaches, encompassing chemical immobilization, transgenic modification, agronomic adjustments, and microbial interventions, have proven effective in curbing HM accumulation and mitigating associated adverse effects. However, a comprehensive review elucidating these control strategies and their mechanisms remains notably absent. This paper seeks to fill this void by examining the deleterious effects of HM exposure on tobacco plants and human health through tobacco consumption. Additionally, it provides a thorough exploration of the mechanisms responsible for reducing HM content in tobacco. The review consolidates and synthesizes recent domestic and international initiatives aimed at mitigating HM content in tobacco, delivering a comprehensive overview of their current status, benefits, and limitations.

Copper-dependent control of uptake, translocation and accumulation of cadmium in hyperaccumlator Sedum alfredii

Cadmium (Cd) is detrimental to plant growth and threatens human health. Here, we investigated the potential for remediation of Cd-contaminated soil with high copper (Cu) background using Cd hyperaccumulator ecotype (HE) Sedum alfredii. We assessed effects of Cu on Cd accumulation, compartmentation and translocation in HE S. alfredii, and compared with those in a related non-accumulator ecotype (NHE). We found that Cu supply significantly induced Cd accumulation in roots and shoots of long-term soil-cultivated HE S. alfredii. A large fraction of root Cd was accumulated in the organelles, but a small fraction was stored in the cell wall. Importantly, Cu addition reduced Cd accumulation in the cell wall and the organelles in root cells. Furthermore, leaf cell capacity to sequestrate Cd in the organelles was greatly improved upon Cu exposure. We also found that genes involving metal transport and cell wall remodeling were distinctly regulated to mediate Cd accumulation in HE S. alfredii. These findings indicate that Cu-dependent decrease of root cell-wall-bound Cd, and stimulation of efflux/influx of organelle Cd transport in root and leaf cells plays a role in the dramatic Cd hyperaccumulation expressed in naturally survived HE S. alfredii.

A potential heavy metals detoxification system in composting: Biotic and abiotic synergy mediated by shell powder

Regulating heavy metal resistance genes (HMRGs) was an effective method for heavy metal resistant bacteria (HMRB) to cope with heavy metal stress during dairy manure composting. This research aimed to investigate heavy metal detoxification mediated by shell powder (SP) in composting and the response of HMRB and HMRGs to changes in heavy metal bioavailability during composting. Research showed that SP additive reduced the bioavailability of Zu, Cu, and Mn by 10.64%, 13.90% and 14.14%, respectively. SP increased the composition percentage of humic acid (HA) in humus (HS) by 8%. SP enhanced the resistance of Actinobacteria to heavy metals and improved the regulation of HMRGs. Correlation analysis demonstrated that the bioavailability of heavy metals was positively correlated with most HMRGs. HA was significantly negatively correlated with the bioavailability of Zn, Cu and Mn. Therefore, SP additive could be a novel strategy for heavy metals detoxification during composting.

Cd-induced cytosolic proteome changes in the cyanobacterium Anabaena sp. PCC7120 are mediated by LexA as one of the regulatory proteins

LexA, a well-characterized transcriptional repressor of SOS genes in heterotrophic bacteria, has been shown to regulate diverse genes in cyanobacteria. An earlier study showed that LexA overexpression in a cyanobacterium, Anabaena sp. PCC7120 reduces its tolerance to Cd stress. This was later shown to be due to modulation of photosynthetic redox poising by LexA under Cd stress. However, due to the global regulatory nature of LexA and the prior prediction of AnLexA-box in a few heavy metal-responsive genes, we speculated that LexA has a broad role in Cd tolerance, with regulation over a variety of Cd stress-responsive genes in addition to photosynthetic genes. Thus, to further expand the knowledge on the regulatory role of LexA in Cd stress tolerance, a cytosolic proteome profiling of Anabaena constitutively overexpressing LexA upon Cd stress was performed. The proteomic study revealed 25 differentially accumulated proteins (DAPs) in response to the combined effect of LexA overexpression and Cd stress, and the other 11 DAPs exclusively in response to either LexA overexpression or Cd stress. The 36 identified proteins were related with a variety of functions, including photosynthesis, C-metabolism, antioxidants, protein turnover, post-transcriptional modifications, and a few unknown and hypothetical proteins. The regulation of LexA on corresponding genes, and six previously reported Cd efflux transporters, was further validated by the presence of AnLexA-boxes, transcript, and/or promoter analyses. In a nutshell, this study identifies the regulation of Anabaena LexA on several Cd stress-responsive genes of various functions, hence expanding the regulatory role of LexA under Cd stress.

The Effect of Cadmium Tolerant Plant Growth Promoting Rhizobacteria on Plant Growth Promotion and Phytoremediation: A Review

Cadmium (Cd) is a heavy metal of considerable toxicity with destructive impacts on plants, microbes and environments. Its toxicity is due to mishandling and manual hazards in plants and is primarily observed within the soil to cause decline of plants and microbial activity inside the rhizosphere. Cadmium accumulation in crops and the probability of Cd entering the food chain are grave for public health in the worldwide. Cadmium toxicity leads to depletion in seed germination, initial seedling growth, plant biomass, chlorosis, necrosis, hindrance of photosynthetic machinery and other physiological and biological activities in plants. Cadmium triggers the reactive oxygen species (ROS) that influences gene mutation and DNA damage that affects the cell cycle and cell division. Cd toxicity altered the levels of phenolic compounds, carbohydrates, glycine betaine, proline and organic acids in crops. Under stress conditions, the plant growth promoting rhizobacteria (PGPR) have various properties such as enzymatic activities, plant growth hormones production, phosphate solubilization, siderophores production and chelating agents that help the plants tolerate against Cd stress and also increase phenolic compound levels and osmolytes. Hence, this review highlights the crucial role of cadmium tolerant PGPR for crop production, declining metal phytoavailability and enhancing morphological and physiological boundaries of plants under stress conditions. It could be an environment friendly and cost effective technology under sustainable crop production.

Duckweed: a potential phytosensor for heavy metals

Globally, heavy metal (HM) contamination is one of the primary causes of environmental pollution leading to decreased quality of life for those affected. In particular, HM contamination in groundwater poses a serious risk to human health and the potential for destabilization of aquatic ecosystems. At present, strategies to remove HM contamination from wastewater are inefficient, costly, laborious, and often the removal poses as much risk to the environment as the initial contamination. Phytoremediation, plant-based removal of contaminants from soil or water, has long been viewed as an economical and sustainable solution to remove toxic metals from the environment. However, to date, phytoremediation has demonstrated limited successes despite a large volume of literature supporting its potential. A key aspect for achieving robust and meaningful phytoremediation is the selection of a plant species that is well suited to the task. For the removal of pollutants from wastewater, hydrophytes, like duckweed, exhibit significant potential due to their rapid growth on nutrient-rich water, ease of collection, and ability to survive in various ecosystems. As a model for ecotoxicity studies, duckweed is an ideal candidate, as it is easy to cultivate under controlled and even sterile conditions, and the rapid growth enables multi-generational studies. Similarly, recent advances in the genetic engineering and genome-editing of duckweed will enable the transition from fundamental ecotoxicity studies to engineered solutions for phytoremediation of HMs. This review will provide insight into the suitability of duckweeds for phytoremediation of HMs and strategies for engineering next-generation duckweed to provide real-world environmental solutions.

Resistance properties and adaptation mechanism of cadmium in an enriched strain, Cupriavidus nantongensis X1T

Bacterial adaption to heavy metal stress is a complex and comprehensive process of multi-response regulation. However, the mechanism is largely unexplored. In this study, cadmium (Cd) resistance and adaptation mechanism in Cupriavidus nantongensis X1^T were investigated. Strain X1^T could resist the stress of 307 mg/L Cd²⁺ and remove 70% Cd²⁺ in 48 h. Spectroscopic analyses suggested interactions between Cd²⁺ with C-N, -COOH, and -NH ligands of extracellular polymeric substances. Whole-genome sequencing found that the resistance of Cd²⁺ in strain X1^T was caused by the joint action of Czc and Cad systems. Cd²⁺ at 20 mg/L elicited differential expression of 1157 genes in strain X1^T. In addition to the reported effects of uptake, adsorption, effluxion, and accumulation system, the oxidative stress system, Type-VI secretory protein system, Fe-S protein synthesis, and cysteine synthesis system in strain X1^T were involved in the Cd²⁺ resistance and accumulation. The intracellular accumulation content of Cd²⁺ in strain X1^T was higher than the extracellular adsorption content made strain X1^T to be an important resource strain in the bioremediation of Cd-contaminated sewage. The results provide a theoretical network for understanding the complex regulatory system of bacterial resistance and adaptation of Cd against stressful environments.

Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria

Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.

Evaluating responses of nitrification and denitrification to the co-selective pressure of divalent zinc and tetracycline based on resistance genes changes

The responses of nitrification and denitrification to the divalent zinc (Zn(II)) and tetracycline (TC) co-selective pressure were evaluated in a sequencing batch reactor (SBR). The removal rates of organics and nitrogen, nitrifying and denitrifying enzymatic activity, and microbial diversity and richness at the Zn(II) and TC co-selective pressure were higher than those at the alone Zn(II) selective pressure, while were lower than those at the individual TC selective pressure. The Zn(II) and TC co-selective pressure induced the TC resistance genes abundance increase and the Zn(II) resistance genes levels decrease, and enhanced bacterial enzymatic modification resistance to TC and bacterial outer membrane resistance to Zn(II). The network analysis showed that the genera Nitrospira and Nitrosomonas of nitrifiers and the genera Ferruginibacter, Dechloromonas, Acidovorax, Rhodobacter, Thauera, Cloacibacterium, Zoogloea and Flavobacterium of denitrifiers were the potential hosts of antibiotics resistance genes (ARGs) and/or heavy metals resistance genes (HMRGs).

Molecular mechanisms in phytoremediation of environmental contaminants and prospects of engineered transgenic plants/microbes

Concerns about emerging environmental contaminants have been growing along with industrialization and urbanization around the globe. Among various options for remediating these contaminants, phytotechnology is suggested as a feasible option to maintain the environmental sustainability. The recent advances in phytoremediation, genetic/molecular/omics/metabolic engineering, and nanotechnology are opening new paths for efficient treatment of emerging organic/inorganic contaminants. In this respect, elucidation of molecular mechanisms and genetic engineering of hyperaccumulator plants is expected to enhance remediation of environmental contaminants. This review was organized to offer valuable insights into the molecular mechanisms of phytoremediation and the prospects of transgenic hyperaccumulators with enhanced stress tolerance to diverse contaminants such as heavy metals and metalloids, xenobiotics, explosives, poly aromatic hydrocarbons (PAHs), petroleum hydrocarbons, pesticides, and nanoparticles. The roles of genoremediation and nanoparticles in augmenting the phytoremediation technology are also described in an interrelated framework with biotechnological prospects (e.g., plant molecular nano-farming). Finally, political debate on the preferential use of crops versus non-crop hyperaccumulators in genoremediation, limitations of transgenics in phytotechnologies, and their public acceptance issues are discussed in the policy framework.

Diversity evolution of functional bacteria and resistance genes (CzcA) in aerobic activated sludge under Cd(II) stress

An activated sludge sequencing batch reactor (SBR) was used to treat divalent cadmium (Cd(II)) wastewater for 60 d to investigate the overall treatment performance, evolution of the bacterial community, and abundance of the Cd(II) resistance gene CzcA and shifts in its potential host bacteria. During stable operation with a Cd(II) concentration of 20 mg/L, the average removal efficiencies of Cd(II) and chemical oxygen demand (COD) were more than 85% and that of total phosphorus was greater than 70%, while the total nitrogen (TN) was only about 45%. The protein (PN) content in the extracellular polymeric substances (EPS) increased significantly after Cd(II) addition, while polysaccharides displayed a decreasing trend (p < 0.05), indicating that EPS prefer to release PN to adsorb Cd(II) and protect bacteria from damage. Three-dimensional fluorescence spectral analysis showed that fulvic acid-like substances were the most abundant chemical components of EPS. The addition of Cd(II) adversely affected most denitrifying bacteria (p < 0.05), which is consistent with the low TN removal. In addition, quantitative polymerase chain reaction analysis revealed that CzcA gene abundance decreased as the Cd(II) concentration increased, possibly because expression of the CzcA gene was inhibited by Cd(II) stress. The majority of CzcA gene sequences were carried by Pseudomonas, making it the dominant genus among Cd(II)-resistant bacteria.

A review on global metal accumulators-mechanism, enhancement, commercial application, and research trend

The biosphere is polluted with metals due to burning of fossil fuels, pesticides, fertilizers, and mining. The metals interfere with soil conservations such as contaminating aqueous waste streams and groundwater, and the evidence of this has been recorded since 1900. Heavy metals also impact human health; therefore, the emancipation of the environment from these environmental pollutants is critical. Traditionally, techniques to remove these metals include soil washing, removal, and excavation. Metal-accumulating plants could be utilized to remove these metal pollutants which would be an alternative option that would simultaneously benefit commercially and at the same time clean the environment from these pollutants. Commercial application of pollutant metals includes biofortification, phytomining, phytoremediation, and intercropping. This review discusses about the metal-accumulating plants, mechanism of metal accumulation, enhancement of metal accumulation, potential commercial applications, research trends, and research progress to enhance the metal accumulation, benefits, and limitations of metal accumulators. The review identified that the metal accumulator plants only survive in low or medium polluted environments with heavy metals. Also, more research is required about metal accumulators in terms of genetics, breeding potential, agronomics, and the disease spectrum. Moreover, metal accumulators' ability to uptake metals need to be optimized by enhancing metal transportation, transformation, tolerance to toxicity, and volatilization in the plant. This review would benefit the industries and environment management authorities as it provides up-to-date research information about the metal accumulators, limitation of the technology, and what could be done to improve the metal enhancement in the future.

Metal resistant PGPR lowered Cd uptake and expression of metal transporter genes with improved growth and photosynthetic pigments in Lycopersicon esculentum under metal toxicity

Plant growth promoting rhizobacteria (PGPRs) are very effective in immobilization of heavy metals and reducing their translocation in plants via precipitation, complex formation and adsorption. The present study was therefore designed to understand the role of Pseudomonas aeruginosa and Burkholderia gladioli in mitigation of Cd stress (0.4 mM) in 10-days old L. esculentum seedlings. The present work investigated growth characteristics, photosynthetic pigments, metal tolerance index, metal uptake and the contents of metal chelating compounds (protein bound and non-protein bound thiols, total thiols) in microbes inoculated Cd treated L. esculentum seedlings. The gene expression profiling of different metal transporters was conducted in order to investigate the quantitative analysis. Our results revealed Cd generated toxicity in seedlings in terms of reduced growth (root length, shoot length and fresh weight) and photosynthetic pigments (chlorophyll, carotenoid and xanthophyll) which enhanced upon inoculations of P. aeruginosa and B. gladioli. Further, the metal uptake along with levels of protein and non-protein bound thiols was also enhanced in Cd-treated seedlings. Gene expression studies suggested enhanced expression in the metal transporter genes which were further declined in the microbe supplemented seedlings. Therefore, micro-organisms possess growth promoting traits that enable them to reduce metal toxicity in plants.

Metal resistant PGPR lowered Cd uptake and expression of metal transporter genes with improved growth and photosynthetic pigments in Lycopersicon esculentum under metal toxicity

Plant growth promoting rhizobacteria (PGPRs) are very effective in immobilization of heavy metals and reducing their translocation in plants via precipitation, complex formation and adsorption. The present study was therefore designed to understand the role of Pseudomonas aeruginosa and Burkholderia gladioli in mitigation of Cd stress (0.4 mM) in 10-days old L. esculentum seedlings. The present work investigated growth characteristics, photosynthetic pigments, metal tolerance index, metal uptake and the contents of metal chelating compounds (protein bound and non-protein bound thiols, total thiols) in microbes inoculated Cd treated L. esculentum seedlings. The gene expression profiling of different metal transporters was conducted in order to investigate the quantitative analysis. Our results revealed Cd generated toxicity in seedlings in terms of reduced growth (root length, shoot length and fresh weight) and photosynthetic pigments (chlorophyll, carotenoid and xanthophyll) which enhanced upon inoculations of P. aeruginosa and B. gladioli. Further, the metal uptake along with levels of protein and non-protein bound thiols was also enhanced in Cd-treated seedlings. Gene expression studies suggested enhanced expression in the metal transporter genes which were further declined in the microbe supplemented seedlings. Therefore, micro-organisms possess growth promoting traits that enable them to reduce metal toxicity in plants.

GmHMA3 sequesters Cd to the root endoplasmic reticulum to limit translocation to the stems in soybean

A single point-mutation in GmHMA3 (Glycine max heavy metal-associated ATPase; a wild type allele cloned from a low Cd-accumulated soybean) is closely associated with seed cadmium (Cd) concentration. It is linked to Cd transportation in yeast, and is primarily expressed in the roots of plants. We hypothesized that the function of GmHMA3w in soybean would be akin to that of OsHMA3 in rice, which expresses in the root tonoplast and sequestrates Cd into the root vacuole to reduce Cd translocation to the shoots and limit its accumulation in the seeds. In this study, the transient expression of the GmHMA3w-GFP fusion protein in rice mesophyll protoplasts indicated that the subcellular localization of GmHAM3w was in the endoplasmic reticulum (ER). Overexpression of GmHMA3w increased the Cd concentration in the roots, decreased the Cd concentration in the stems, and did not affect the Cd concentration in the leaves. Additionally, its overexpression did not alter the Cd concentration across the whole plant. These findings indicated that GmHMA3w does not influence the Cd uptake, but limits the translocation of Cd from the roots to the stems. GmHMA3w thus acts in metal transportation. Assessment of the subcellular distribution of Cd indicated that GmHMA3w facilitated transport of Cd from the cell wall fraction to the organelle fraction, and then sequestrated Cd into the root ER, thus limiting its translocation to the stems. Additionally, the results also suggested that the ER constitutes a site of particularly high Cd sensitively in plants.

Variation in Membrane Trafficking Linked to SNARE AtSYP51 Interaction With Aquaporin NIP1;1

SYP51 and 52 are the two members of the SYP5 Qc-SNARE gene family in Arabidopsis thaliana. These two proteins, besides their high level of sequence identity (85%), have shown to have differential functional specificity and possess a different interactome. Here we describe a unique and specific interaction of SYP51 with an ER aquaporin, AtNIP1;1 (also known as NLM1) indicated to be able to transport arsenite [As(III)] and previously localized on PM. In the present work we investigate in detail such localization in vivo and characterize the interaction with SYP51. We suggest that this interaction may reveal a new mechanism regulating tonoplast invagination and recycling. We propose this interaction to be part of a regulatory mechanism associated with direct membrane transport from ER to tonoplast and Golgi mediated vesicle trafficking. We also demonstrate that NIP1;1 is important for plant tolerance to arsenite but does not alter its uptake or translocation. To explain such phenomenon the hypothesis that SYP51/NIP1;1 interaction modifies ER and vacuole ability to accumulate arsenite is discussed.

Recent strategies of increasing metal tolerance and phytoremediation potential using genetic transformation of plants

Avoidance and reduction of soil contamination with heavy metals is one of the most serious global challenges. Nowadays, science offers us new opportunities of utilizing plants to extract toxic elements from the soil by means of phytoremediation. Plant abilities to uptake, translocate, and transform heavy metals, as well as to limit their toxicity, may be significantly enhanced via genetic engineering. This paper provides a comprehensive review of recent strategies aimed at the improvement of plant phytoremediation potential using plant transformation and employing current achievements in nuclear and cytoplasmic genome transformation. Strategies for obtaining plants suitable for effective soil clean-up and tolerant to excessive concentrations of heavy metals are critically assessed. Promising directions in genetic manipulations, such as gene silencing and cis- and intragenesis, are also discussed. Moreover, the ways of overcoming disadvantages of phytoremediation using genetic transformation approachare proposed. The knowledge gathered here could be useful for designing new research aimed at biotechnological improvement of phytoremediation efficiency.