Heavy metal ATPase genes (HMAs) expression induced by endophytic bacteria, "AI001, and AI002" mediate cadmium translocation and phytoremediation

Two birds with one stone: Alleviating copper toxicity and inhibiting its upward transport in non-host rice (Oryza sativa L.) by inoculation of Cu-resistant endophytes from the hyperaccumulator Commelina communis

Endophytic bacteria derived from metal hyperaccumulators have demonstrated potential for improving copper (Cu) remediation in host plants; however, their potential application in non-host crops remains unclear. In this study, endophytic bacteria isolated from Commelina communis growing in mining areas and their mitigation effects on Cu toxicity in non-host rice were comprehensively evaluated. Among the isolated endophytes, Bacillus sp. D2 exhibited the highest Cu resistance, producing indole-3-acetic acid (IAA) at a concentration of 0.93 mg/L and exhibiting ACC deaminase activity of 13.88 μmol/mg·h under 200 mg/L Cu stress. Pot-experiment results revealed that Bacillus sp. D2 addition significantly increased the biomass and lengths of shoots under Cu stress conditions by 47.6% and 14.2%, respectively. Furthermore, Bacillus sp. D2 inoculation significantly reduced oxidative damage, enhanced antioxidant responses, and modulated plant hormone levels in Cu-exposed rice. Notably, Bacillus sp. D2 inoculation substantially decreased the upward translocation of Cu from underground roots to aboveground tissues. Moreover, Bacillus sp. D2 effectively alleviated Cu toxicity in rice plants by regulating the expression levels of genes involved in antioxidant systems (tAPx, Csd2, and FeSOD1), Cu transporters (AtPDR8 and HMA3), as well as metallothionein (MT2c). These results highlight the value of Bacillus sp. D2 as a bioinoculant for improving crop growth while reducing the risks associated with copper contamination in naturally Cu-contaminated soils.

Exploring the significance of different amendments to improve phytoremediation efficiency: focus on soil ecosystem services

Phytoremediation is recognized as an environmentally, economically and socially efficient phytotechnology for the reclamation of polluted soils. To improve its efficiency, several strategies can be used including the optimization of agronomic practices, selection of high-performance plant species but also the application of amendments. Despite evidences of the benefits provided by different types of amendments on pollution control through several phytoremediation pathways, their contribution to other soil ecosystem functions supporting different ecosystem services remains sparsely documented. This current review aims at (i) updating the state of the art about the contribution of organic, mineral and microbial amendments in improving phytostabilization, phytoextraction of inorganic and phytodegradation of organic pollutants and (ii) reviewing their potential beneficial effects on soil microbiota, nutrient cycling, plant growth and carbon sequestration. We found that the benefits of amendment application during phytoremediation go beyond limiting the dispersion of pollutants as they enable a more rapid recovery of soil functions leading to wider environmental, social and economic gains. Effects of amendments on plant growth are amendment-specific, and their effect on carbon balance needs more investigation. We also pointed out some research questions that should be investigated to improve amendment-assisted phytoremediation strategies and discussed some perspectives to help phytomanagement projects to improve their economic sustainability.

Microbial Contributions to Heavy Metal Phytoremediation in Agricultural Soils: A Review

Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with heavy metals such As, Pb, Cd, Hg, and Cr, plants can sequester, degrade, or stabilize contaminants more efficiently. Remarkably, some plant species are known for their hyper-accumulative traits in synergy with their microbial partners and can successfully mitigate heavy metal pollutants. This sustainable biotechnology based on plant-microbe associations not only aids in environmental cleanup but also enhances biodiversity, improves soil structure, and promotes plant growth and health, making it a promising solution for addressing agro-pollution challenges worldwide. The current review article emphasizes the potential of synergistic plant-microbe interactions in developing practical and sustainable solutions for heavy metal remediation in agricultural systems, which are essential for food security.

Biotechnological approaches for enhancement of heavy metal phytoremediation capacity of plants

Heavy metals are extremely hazardous for human health due to their toxic effects. They are non-biodegradable in nature, thus remain in the environment and enter and accumulate in the human body through biomagnification; hence, there is a serious need of their remediation. Phytoremediation has emerged as a green, sustainable, and effective solution for heavy metal removal and many plant species could be employed for this purpose. Plants are able to sequester substantial quantity of heavy metals, in some cases thousands of ppm, due to their robust physiology enabling high metal tolerance and anatomy supporting metal ion accumulation. Identification and modification of potential target genes involved in heavy metal accumulation have led to improved phytoremediation capacity of plants at the molecular level. The introduction of foreign genes through genetic engineering approaches has further enhanced phytoremediation capacity manifolds. This review gives an insight towards improving the phytoremediation efficiency through a better understanding of molecular mechanisms involved, expression of different proteins, genetic engineering approaches for transgenic production, and genetic modifications. It also comprehends novel omics tools such as genomics, metabolomics, proteomics, transcriptomics, and genome editing technologies for improvement of phytoremediation ability of plants.

PGPR-Enabled bioremediation of pesticide and heavy metal-contaminated soil: A review of recent advances and emerging challenges

The excessive usage of agrochemicals, including pesticides, along with various reckless human actions, has ensued discriminating prevalence of pesticides and heavy metals (HMs) in crop plants and the environment. The enhanced exposure to these chemicals is a menace to living organisms. The pesticides may get bioaccumulated in the food chain, thereby leading to several deteriorative changes in the ecosystem health and a rise in the cases of some serious human ailments including cancer. Further, both HMs and pesticides cause some major metabolic disturbances in plants, which include oxidative burst, osmotic alterations and reduced levels of photosynthesis, leading to a decline in plant productivity. Moreover, the synergistic interaction between pesticides and HMs has a more serious impact on human and ecosystem health. Various attempts have been made to explore eco-friendly and environmentally sustainable methods of improving plant health under HMs and/or pesticide stress. Among these methods, the employment of PGPR can be a suitable and effective strategy for managing these contaminants and providing a long-term remedy. Although, the application of PGPR alone can alleviate HM-induced phytotoxicities; however, several recent reports advocate using PGPR with other micro- and macro-organisms, biochar, chelating agents, organic acids, plant growth regulators, etc., to further improve their stress ameliorative potential. Further, some PGPR are also capable of assisting in the degradation of pesticides or their sequestration, reducing their harmful effects on plants and the environment. This present review attempts to present the current status of our understanding of PGPR's potential in the remediation of pesticides and HMs-contaminated soil for the researchers working in the area.

Synergistic interactions of assorted ameliorating agents to enhance the potential of heavy metal phytoremediation

Pollution by toxic heavy metals creates a significant impact on the biotic community of the ecosystem. Nowadays, a solution to this problem is an eco-friendly approach like phytoremediation, in which plants are used to ameliorate heavy metals. In addition, various amendments are used to enhance the potential of heavy metal phytoremediation. Symbiotic microorganisms such as phosphate-solubilizing bacteria (PSB), endophytes, mycorrhiza and plant growth-promoting rhizobacteria (PGPR) play a significant role in the improvement of heavy metal phytoremediation potential along with promoting the growth of plants that are grown in contaminated environments. Various chemical chelators (Indole 3-acetic acid, ethylene diamine tetra acetic acid, ethylene glycol tetra acetic acid, ethylenediamine-N, N-disuccinic acid and nitrilotri-acetic acid) and their combined action with other agents also contribute to heavy metal phytoremediation enhancement. With modern techniques, transgenic plants and microorganisms are developed to open up an alternative strategy for phytoremediation. Genomics, proteomics, transcriptomics and metabolomics are widely used novel approaches to develop competent phytoremediators. This review accounts for the synergistic interactions of the ameliorating agent's role in enhancing heavy metal phytoremediation, intending to highlight the importance of these various approaches in reducing heavy metal pollution.

Proteomics-based analysis on the stress response mechanism of Bidens pilosa L. under cadmium exposure

Bidens pilosa L. (B. pilosa) has great potential for the phytoremediation of cadmium (Cd)-contaminated soils. However, the molecular mechanism underlying Cd tolerance and detoxification in B. pilosa is still unclear. In the present study, a 4D label-free quantification technique combined with liquid chromatography-parallel reaction monitoring mass spectrometry was used to explore the stress response mechanism of B. pilosa. Proteomic analysis revealed 213 and 319 differentially expressed proteins (DEPs) in the roots and leaves of B. pilosa, respectively, and 12 target proteins were selected for further analysis. SWISS-MODEL was used to predict the 3D structures of the target proteins. The cation-ATPase-N structural domain and an ATPase-E1-E2 motif, which help to regulate ATPase function, were detected in the TR10519_c0_g1_ORF protein. In addition, the TR6620_c0_g1_ORF_1 and TR611_c1_g1_ORF proteins contained peroxidase-1 and peroxidase-2 motifs. The TR11239_c0_g1_ORF protein was found to belong to the Fe-SOD family, to have a dimeric structure and to contain a relatively high proportion of α-helices but few β-sheets, which play important roles in reactive oxygen intermediate scavenging. Thus, the current study provides an overview of the proteomic response of B. pilosa in scavenging of Cd-induced reactive oxygen intermediates and reveals key proteins involved in the stress response of B. pilosa under Cd exposure.

Root Exposure of Graphitic Carbon Nitride (g-C3N4) Modulates Metabolite Profile and Endophytic Bacterial Community to Alleviate Cadmium- and Arsenate-Induced Phytotoxicity to Rice (Oryza sativa L.)

To investigate the mechanisms by which g-C3N4 alleviates metal(loid)-induced phytotoxicity, rice seedlings were exposed to 100 and 250 mg/kg graphitic carbon nitride (g-C3N4) with or without coexposure to 10 mg/kg Cd and 50 mg/kg As for 30 days. Treatment with 250 mg/kg g-C3N4 significantly increased shoot and root fresh weight by 22.4-29.9%, reduced Cd and As accumulations in rice tissues by 20.6-26.6%, and elevated the content of essential nutrients (e.g., K, S, Mg, Cu, and Zn) compared to untreated controls. High-throughput sequencing showed that g-C3N4 treatment increased the proportion of plant-growth-promoting endophytic bacteria, including Streptomyces, Saccharimonadales, and Thermosporothrix, by 0.5-3.30-fold; these groups are known to be important to plant nutrient assimilation, as well as metal(loid) resistance and bioremediation. In addition, the population of Deinococcus was decreased by 72.3%; this genus is known to induce biotransformation As(V) to As(III). Metabolomics analyses highlighted differentially expressed metabolites (DEMs) involved in the metabolism of tyrosine metabolism, pyrimidines, and purines, as well as phenylpropanoid biosynthesis related to Cd/As-induced phytotoxicity. In the phenylpropanoid biosynthesis pathway, the increased expression of 4-coumarate (1.13-fold) and sinapyl alcohol (1.26-fold) triggered by g-C3N4 coexposure with Cd or As played a critical role in promoting plant growth and enhancing rice resistance against metal(loid) stresses. Our findings demonstrate the potential of g-C3N4 to enhance plant growth and minimize the Cd/As-induced toxicity in rice and provide a promising nanoenabled strategy for remediating heavy metal(loid)-contaminated soil.

CaHMA1 promotes Cd accumulation in pepper fruit

The main planting areas for pepper (Capsicum sp.) are high in cadmium (Cd), which is the most prevalent heavy metal pollutant worldwide. Breeding pepper cultivars with low Cd levels can promote sustainable agricultural production and ensure the safety of pepper products. To identify breeding targets for reducing Cd accumulation in pepper fruits, we performed a genome-wide association study on 186 accessions. Polymorphisms were associated with fruit Cd content in a genomic region containing a homolog of Arabidopsis (Arabidopsis thaliana) Heavy metal-transporting ATPase 1 (HMA1) encoding a P-type ATPase. In two cultivars with contrasting Cd accumulation, transcriptome analysis revealed differentially expressed genes enriched for carbohydrate metabolism and photosynthesis in fruits with high Cd accumulation, and a Cd2+/Zn2+-exporting ATPase gene (HMA). Heterologous expression of CaHMA1 in yeast increases Cd sensitivity. Overexpression of CaHMA1 conferred a severe increase in Cd content in Arabidopsis plants, whereas reduced CaHMA1 expression in pepper fruits decreased Cd content. We propose that CaHMA1 expression may be an important component of the high Cd accumulation in pepper plants.

Metagenomics combined with metabolomics reveals the effect of Enterobacter sp. inoculation on the rhizosphere microenvironment of Bidens pilosa L. in heavy metal contaminated soil

Metagenomics analysis was performed to determine the effects of Enterobacter sp. FM-1 (FM-1) on key genera as well as functional genes in the rhizosphere of Bidens pilosa L. (B. pilosa L.). Moreover, metabolomics was used to reveal the differences among rhizosphere metabolites after FM-1 inoculation. FM-1 inoculation significantly increased the activity of enzymes associated with the carbon cycle in soil; among them, invertase activity increased by 5.52 units compared to a control. Specifically, the relative abundance of beneficial genera increased significantly, such as Lysobacter (0.45-2.58 unit increase) in low-contamination soils (LC) and Pseudomonas (31.17-45.99 unit increase) in high-contamination soils (HC). Comparison of different transformation processes of the C cycle revealed that inoculation of FM-1 increased the abundance of functional genes related to the carbon cycle in LC soil. In contrast, the nitrogen cycling pathway was significantly elevated in both the LC and HC soils. FM-1 inoculation reduced HM resistance gene abundance in the rhizosphere soil of B. pilosa L. in the LC soil. Moreover, FM-1 and B. pilosa L. interactions promoted the secretion of rhizosphere metabolites, in which lipids and amino acids played important roles in the phytoremediation process. Overall, we explored the rhizosphere effects induced by plantmicrobe interactions, providing new insights into the functional microbes and rhizosphere metabolites involved in phytoremediation.

Endophytic Bacillus sp. AP10 harboured in Arabis paniculata mediates plant growth promotion and manganese detoxification

Phytoremediation of heavy metal-polluted soils assisted by plant-associated endophytes, is a suitable method for plant growth and manganese (Mn) removal in contaminated soils. This investigation was conducted to evaluate the Mn-resistant endophytic resources of the Mn hyperaccumulator Arabis paniculata and their functions in the phytoremediation of Mn²⁺ toxicity. This study isolated an endophytic bacterium with high Mn resistance and indole-3-acetic acid (IAA) production form A. paniculata and identified it as Bacillus sp. AP10 using 16 S rRNA gene sequencing analysis. The effects of Bacillus sp. AP10 on the alleviation of Mn²⁺ toxicity in Arabidopsis thaliana seedlings and the molecular mechanisms were further investigated using biochemical tests and RNA-seq analysis. Under Mn²⁺ stress, Bacillus sp. AP10 increased the biomass, chlorophyll content and the translocation factor (TF) values of Mn in the aerial parts, while decreased the malondialdehyde (MDA) content of A. thaliana seedlings compared with that of control plants. The differentially expressed genes (DEGs) and enrichment analysis showed that Bacillus sp. AP10 could significantly increase the expression of key genes involved in cell-wall loosening, which may improve plant growth under Mn stress. Superoxide dismutase (SOD)-encoding genes were detected as DEGs after AP10 treatment. Moreover, AP10 regulated the expression of genes responsible for phenylpropanoid pathway, which may promote antioxidant flavonoids accumulation for reactive oxygen species (ROS) scavenging to improve Mn tolerance. The activation of ATP-binding cassette (ABC) transporter gene expression especially ABCB1 after AP10 stimulation, explained the elevation of metal ion binding or transport related to enhanced Mn accumulation in plants. Futhermore, AP10 might alleviate Mn toxicity through enhancing abscisic acid (ABA) responsive gene expression and ABA biosynthesis. These findings provide new insights into the functions and regulatory mechanism of Bacillus sp. AP10 in promoting plant growth, and tolerance, improving Mn accumulation and alleviating Mn²⁺ toxicity in plants. The application of Bacillus sp. AP10 as potential phytoremediators may be a promising strategy in Mn²⁺ contaminated fields. AVAILABILITY OF DATA AND MATERIALS: The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

The Role of the Plant-Soil Relationship in Agricultural Production-With Particular Regard to PGPB Application and Phytoremediation

Plant growth-promoting bacteria (PGPB) and other living organisms can help with the challenges of modern agriculture. PGPB offer ever-expanding possibilities for science and commerce, and the scientific results have been very advanced in recent years. In our current work, we collected the scientific results of recent years and the opinions of experts on the subject. Opinions and results on soil-plant relations, as well as the importance of PGPB and the latest related experiences, are important topics of our review work, which highlights the scientific results of the last 3-4 years. Overall, it can be concluded from all these observations that the bacteria that promote plant development are becoming more and more important in agriculture almost all over the world, thus, promoting more sustainable and environmentally conscious agricultural production and avoiding the use of artificial fertilizers and chemicals. Since many mechanisms of action, namely biochemical and operational processes, are still under investigation, a new emerging scientific direction is expected in the coming years with regard to PGPB, microbial, and other plant growth-stimulating substances, in which omics and microbial modulation also play a leading role.

Interactions among heavy metals and methane-metabolizing microorganisms and their effects on methane emissions in Dajiuhu peatland

Peatlands play a crucial role in mediating the emissions of methane through active biogeochemical cycling of accumulated carbon driven by methane-metabolizing microorganisms; meanwhile, they serve as vital archives of atmospheric heavy metal deposition. Despite many edaphic factors confirmed as determinants to modulate the structure of methanotrophic and methanogenic communities, recognition of interactions among them is limited. In this study, peat soils were collected from Dajiuhu peatland to assess the presence of heavy metals, and methanotrophs and methanogens were investigated via high-throughput sequencing for functional genes mcrA and pmoA. Further analyses of the correlations between methane-related functional groups were conducted. The results demonstrated that both methane-metabolizing microorganisms and heavy metals have prominent vertical heterogeneity upward and downward along the depth of 20 cm. Pb, Cd, and Hg strongly correlated with methanotrophs and methanogens across all seasons and depths, serving as forceful factors in structural variations of methanogenic and methanotrophic communities. Particularly, Pb, Cd, and Hg were identified as excessive elements in Dajiuhu peatland. Furthermore, seasonal variations of networks among methane-related functional groups and environmental factors significantly affected the changes of methane fluxes across different seasons. Concretely, the complicated interactions were detrimental to methane emissions in the Dajiuhu peatland, leading to the minimum methane emissions in winter. Our study identified the key heavy metals affecting the composition of methane-metabolizing microorganisms and linkages between seasonal variations of methane emissions and interaction among heavy metals and methane-metabolizing microorganisms, which provided much new reference and theoretical basis for integrated management of natural peatlands.

Plant growth-promoting bacteria in phytoremediation of metal-polluted soils: Current knowledge and future directions

Soil metal contamination is a major concern due to the ever-rising number of areas afflicted worldwide and the detrimental effects of metals to the environment and human health. Due to their non-biodegradability and toxicity, it is paramount to prevent further metal contamination and remediate the thousands of contaminated sites across the planet. Yet, conventional reclamation based on physical and chemical methods is often expensive, impractical, and triggers secondary pollution issues. Hence, microbe-aided phytoremediation has been gaining significant traction due to its environment-friendly character, cost-effectiveness, and the breakthroughs achieved during the past few decades. Microorganisms are an essential part of natural ecosystems and play a crucial role in their restoration. Indeed, plant-microbe associations in metal-polluted soils are pivotal for plants to tolerate metal toxicity and thrive in these harsh environments. Therefore, improving the understanding of this intricate relationship is invaluable for boosting phytoremediation. In this review, we focus on the potential of plant growth promoting bacteria (PGPB) for enhancing phytoremediation of metal-polluted soils. We discuss the mechanisms employed by microbes to promote plant growth and assist the removal or immobilization of metals in soil, thereby enhancing phytoextraction and phytostabilization, respectively. Microbe-mediated metal removal and detoxification through processes entailing adsorption, chelation, transformation, and precipitation, to list but a few, are also critically examined. Moreover, this work covers the direct and indirect mechanisms used by PGPB to facilitate plant acquisition of nutrients like nitrogen and phosphorus, supply and regulate phytohormones, and exert control over antagonistic microorganisms. Lastly, we provide an outlook on the future directions of microbe-aided phytoremediation and phytomining. Clearly, to fully validate and comprehend the potential of PGPB-aided phytoremediation, a considerable shift from bench-scale to field research is necessary. What's more, it is envisaged that recent advancements in genetic engineering may soon help furthering the efficiency of microbe-assisted phytoremediation.

Insight into soilless revegetation of oligotrophic and heavy metal contaminated gold tailing pond by metagenomic analysis

Soilless revegetation is an efficient way for gold tailing remediation, and micro-ecological environments in plant rhizosphere are important for vegetation establishment and pollution removal. In the present study, a field experiment of soilless revegetation has been carried out in a gold tailings pond, and the key genera and functional genes in the plant rhizosphere of gold mine tailings were revealed by metagenomics analysis. Soilless revegetation significantly decreased rhizosphere tailing pH from 8.54 to 7.43-7.87, reduced heavy metal (HM) concentration by 29.81-44.02% and enhanced the nutrient content by 50.30-169.50% averagely. Such improvements were strongly and closely correlated to microbial community and functional gene composition variation. The relative abundance of ecologically beneficial genus such as Actinobacteria (increased 9.7-18.8%) and functional genes involved in carbon, nitrogen and phosphorus cycling such as pyruvate metabolism (relatively increased 8.7-15.0%), assimilatory (increased to 1.44-2.08 times), phosphate ester mineralization (increased to 1.12-1.29 times) and phosphate transportation (increased to 1.28-1.85 times) were significantly increased. Moreover, the relative abundance of most As and Zn resistance genes were reduced, which may relate to the decrease of As and Zn concentration in the rhizosphere tailings. These results revealed the correlation among HM concentrations, microbial composition and functional genes, and provided clear strategies for improving gold mine tailing ecological restoration efficiency.

Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing

Panax notoginseng is a traditional Chinese medicinal herb with diverse properties that is cultivated in a narrow ecological range because of its sensitivity to high temperatures. Endophytic bacteria play a prominent role in plant response to climate warming. However, the endophytic bacterial structures in P. notoginseng at high temperatures are yet unclear. In the present study, the diversity and composition of the endophytic bacterial community, and their relationships with two P. notoginseng plants with different heat tolerance capacities were compared using the full-length 16S rRNA PacBio sequencing system. The results revealed that the diversity and richness of endophytic bacteria were negatively associated with the heat tolerance of P. notoginseng. Beneficial Cyanobacteria, Rhodanobacter and Sphingomonas may be recruited positively by heat-tolerant plants, while higher amounts of adverse Proteobacteria such as Cellvibrio fibrivorans derived from soil destructed the cellular protective barriers of heat-sensitive plants and caused influx of pathogenic bacteria Stenotrophomonas maltophilia. Harmonious and conflicting bacterial community was observed in heat-tolerant and heat-sensitive P. notoginseng, respectively, based on the co-occurrence network. Using functional gene prediction of metabolism, endophytic bacteria have been proposed to be symbiotic with host plants; the bacteria improved primary metabolic pathways and secondary metabolite production of plants, incorporated beneficial endophytes, and combated adverse endophytes to prompt the adaptation of P. notoginseng to a warming environment. These findings provided a new perspective on the function of endophytes in P. notoginseng adaptation to high temperatures, and could pave the way for expanding the cultivable range of P. notoginseng.