Microbial Cd(II) and Cr(VI) resistance mechanisms and application in bioremediation

Genomic and transcriptomic analyses reveal insights into cadmium resistance mechanisms of Cupriavidus nantongensis strain E324

The cadmium-resistant Cupriavidus sp. strain E324 has been previously shown to have a high potential for use in cadmium (Cd) remediation, due to its high capacity for cadmium bioaccumulation. According to the comparative genomic analysis, the strain E324 was most closely related to C. nantongensis X1T, indicating that the strain E324 should be re-identified as C. nantongensis. To unravel the Cd tolerance mechanisms of C. nantongensis strain E324, the transcriptional response of this strain to acute Cd exposure was assessed using RNA-seq-based transcriptome analysis, followed by validation through qRT-PCR. The results showed that the upregulated Differentially Expressed Genes (DEGs) were significantly enriched in categories related to metal binding and transport, phosphate transport, and oxidative stress response. Consistently, we observed significant increases in both the cell wall and intracellular contents of certain essential metals (Cu, Fe, Mn, and Zn) upon Cd exposure. Among these, only the Zn pretreatment resulting in high Zn accumulation in the cell walls could enhance bacterial growth under Cd stress conditions through its role in inhibiting Cd accumulation. Additionally, the promotion of catalase activity and glutathione metabolism upon Cd exposure to cope with Cd-induced oxidative stress was demonstrated. Meanwhile, the upregulation of phosphate transport-related genes upon Cd treatment seems to be the bacterial response to Cd-induced phosphate depletion. Altogether, our findings suggest that these adaptive responses are critical mechanisms contributing to increased Cd tolerance in C. nantongensis strain E324 via the enhancement of metal-chelating and antioxidant capacities of the cells.

Hexavalent chromium uptake in rice (Oryza sativa L.) mediated by sulfate and phosphate transporters OsSultr1;2 and OsPht1;1

Chromium (Cr) soil contamination is a critical global environmental concern, with hexavalent chromium (Cr[VI]) being especially perilous due to its high mobility, bioavailability, and phytotoxicity. This poses a significant threat to the cultivation of crops, particularly rice, where the mechanisms of Cr(VI) absorption remain largely unexplored. This study uncovered a competitive interaction between Cr(VI) and essential nutrients-sulfate and phosphate during the uptake process. Notably, deficiencies in sulfate and phosphate were associated with a marked increase in Cr(VI) accumulation in rice, reaching up to 76.5 % and 77.7 %, respectively. Employing q-PCR, this study identified significant up-regulation of the sulfate transporter gene, OsSultr1;2, and the phosphate transporter gene, OsPht1;1, in response to Cr(VI) stress. Genetic knockout studies have confirmed the crucial role of OsSultr1;2 in Cr(VI) uptake, with its deletion leading to a 36.1 % to 69.6 % decrease in Cr uptake by rice roots. Similarly, the knockout of OsPht1;1 resulted in an 18.1 % to 25.7 % decrease in root Cr accumulation. These findings highlight the key role of the sulfate transporter OsSultr1;2 in Cr(VI) uptake, with phosphate transporters also contributing significantly to the process. These insights are valuable for developing rice varieties with reduced Cr(VI) accumulation, ensuring the safety of rice grain production.

Strengthening bioremediation potential: Enterobacter ludwigii ES2 for combined nicosulfuron and Cd contamination through whole genome and microbial diversity community analysis

Nicosulfuron and Cd are common pollutants that pose significant threats to the environment and human health, particularly under combined stress. This study is the first to remediate environmental nicosulfuron and Cd under combined stress using microbiological techniques. Enterobacter ludwigii ES2 was isolated, characterized, and demonstrated to degrade 93.80 % of nicosulfuron and remove 59.64 % of Cd within 4 d. Potential functional genes, including nicosulfuron degradation genes gstA, gstB, glnQ, glnP, mreB, and sixA, and Cd tolerance/removal-related genes mntA, mntB, mntH, dnaK, znuA, and zupt, were predicted by sequencing the whole genome of strain ES2, and their expression was verified by qRT-PCR. Strain ES2 managed oxidative stress induced by Cd through superoxide dismutase, glutathione, catalase, peroxidase, and malondialdehyde. Furthermore, to repair compound stress, up to 90.48 % of nicosulfuron and 67.74 % of Cd were removed. The community structure analysis indicated that Enterobacteriaceae, Sphingomonadaceae, and Gemmatimonadaceae were dominant populations, with ES2 stably colonizing and becoming the dominant bacterium. In summary, ES2 demonstrated significant potential in remediating nicosulfuron and Cd pollution from various perspectives, providing a solid theoretical foundation.

DNA-stable isotope probing and metagenomics reveal Fe(II) oxidation by core microflora in microoxic rhizospheric habitats to mitigate the accumulation of cadmium and phenanthrene in rice

Rice rhizosphere soil-porewater microdomains exist within an iron (Fe)-rich microoxic habitat during paddy soil flooding. However, the response mechanisms of core microflora in this habitat to Fe(II)-oxidation-mediated cadmium (Cd) and phenanthrene (Phen) remain unclear. Using gel-stabilized gradient systems to replicate the microoxic conditions in the rice rhizosphere porewater, we found that microaerophilic rhizobacteria drove Fe(II) oxidation to yield iron oxides, thereby reducing the Cd and Phen contents in the rhizosphere porewater and rice (Cd and Phen decreased by 15.9%-78.0% and 10.1%-37.4%, respectively). However, co-exposure to Cd and Phen resulted in a greater reduction in the Cd uptake and a greater increase in the Phen uptake in rice as compared to those in the Cd or Phen treatments, possibly attributing to the cation-π interactions between Cd and Phen, as well as competition between the adsorption sites on the roots. The elevation of Cd-tolerant genes and Phen-degradation genes in biogenic cell-mineral aggregates unveiled the survival strategies of rhizobacteria with respect to Cd and Phen in the microoxic habitat. Potential Cd-tolerant rhizobacteria (e.g., Pandoraea and Comamonas) and Phen-degradation rhizobacteria (e.g., Pseudoxanthobacter) were identified through the DNA-SIP and 16S rRNA gene amplicon sequencing. Metagenomic analysis further confirmed that these core microbes harbor Cd-tolerant, Phen-degradation, and Fe(II) oxidation genes, supporting their metabolic potential for Cd and/or Phen in the microoxic habitat of the rice rhizosphere. These findings suggest the potential mechanism and ecological significance of core rhizospheric microbial-driven Fe(II) oxidation in mitigating the bioavailability of Cd and Phen in paddy soil during flooding.

Interplay of humic acid and Cr(VI) on green microalgae: Metabolic responses and chromium enrichment

Dissolved organic matter (DOM) present in aquatic environments can significantly influence microalgal metabolism and the enrichment of heavy metals. However, the specific mechanism through which typical DOM affects the enrichment of the heavy metal chromium (Cr) in green algae remains unclear. This study investigates the impacts of varying concentrations of humic acid (HA), selected as a representative DOM in water, on the growth, metabolism, and Cr enrichment in Chlorella vulgaris, a typical green alga. The results indicated that low concentrations of HA were capable of enhancing Cr enrichment in C. vulgaris, with the highest Cr enrichment rate recorded at 41.50 % at TOC = 10 mg/L. The enrichment of Cr in algal cells primarily occurred through cell proliferation and complexation reduction of extracellular polymeric substances (EPS). In the presence of HA, C. vulgaris predominantly removed Cr through extracellular adsorption, accounting for 79.76-85.88 % of the total Cr removal. Furthermore, carboxyl complexation and hydroxyl reduction within EPS facilitated both the enrichment of Cr (18.72-21.49 %) and the reduction of Cr(VI) (63.93-74.10 %). These findings provide valuable insights into strategies for mitigating heavy metal pollution and managing associated risks in aquatic environments.

CDR1, a DUF946 domain containing protein, positively regulates cadmium tolerance in Arabidopsis thaliana by maintaining the stability of OPT3 protein

Industrial and agricultural production processes lead to the accumulation of cadmium (Cd) in soil, resulting in crops absorb Cd from contaminated soil and then transfer it to human body through the food chain, posing a serious threat to human health. Thus, it is necessary to explore novel genes and mechanisms involved in regulating Cd tolerance and detoxification in plants. Here, we found that CDR1, a DUF946 domain containing protein, localizes to the plasma membrane and positively regulates Cd stress tolerance. The cdr1 mutants exhibited Cd sensitivity, accumulated excessive Cd in the seeds and roots, but decreased in leaves. However, CDR1-OE transgenic plants not only showed Cd tolerance but also significantly reduced Cd in seeds and roots. Additionally, both in vitro and in vivo assays demonstrated an interaction between CDR1 and OPT3. Cell free protein degradation and OPT3 protein level determination assays indicated that CDR1 could maintain the stability of OPT3 protein. Moreover, genetic phenotype analysis and Cd content determination showed that CDR1 regulates Cd stress tolerance and affect the distribution of Cd in plants by maintaining the stability of OPT3 protein. Our discoveries provide a key candidate gene for directional breeding to reduce Cd accumulation in edible seeds of crops.

Plant endophyte immobilization technology: A promising approach for chromium-contaminated water and soil remediation

Microbial immobilization technology is considered an efficient bioremediation method for chromium (Cr) pollution. However, it is currently unclear which strain is more beneficial for the remediation of Cr-contaminated water and soil. Therefore, corn straw biochar was used as a carrier to prepare materials for fixing the endophytes Serratia sp. Y-13 (BSR1), Serratia nematodiphila (BSR2), Lysinibacillus sp. strain SePC-36 (BLB1), Lysinibacillus mangiferihumi strain WK63 (BLB2) and the commercial bacteria Shewanella oneidensis MR-1 (BSW). The results demonstrated that, compared with BSW, endophyte-loaded biochar (especially BSR1) was more effective at remediating Cr pollution in water and soil. Endophyte-loaded biochar reduced the abundance of soil pathogenic bacteria, enhanced the number of beneficial plant endophytes, reduced the soil Cr(VI) concentration, improved soil fertility, reduced the plant Cr concentration and improved the yield of lettuce. Redundancy analysis (RDA) and structural equation modelling (PLS-PM) suggested that soil microbes are closely related to soil Cr(VI), plant fresh weight and soil organic matter, whereas endophyte-loaded biochar directly influences plant cell motility pathways by altering plant microbes. This study represents a pioneering investigation into the efficacy of endophyte-loaded biochar as a remediation strategy for Cr pollution.

Groundwater chromate removal by autotrophic sulfur disproportionation

Chromate [Cr(VI)] contamination in groundwater is a global environmental challenge. Traditional elemental sulfur-based biotechnologies for Cr(VI) removal depend heavily on the synthesis of dissolved organic carbon to fuel heterotrophic Cr(VI) reduction, a bottleneck in the remediation process. Here we show an alternative approach by leveraging sulfur-disproportionating bacteria (SDB) inherent to groundwater ecosystems, offering a novel and efficient Cr(VI) removal strategy. We implemented SDB within a sulfur-packed bed reactor for treating Cr(VI)-contaminated groundwater, achieving a notable removal rate of 6.19 mg L-1 h-1 under oligotrophic conditions. We identified the chemical reduction of Cr(VI) via sulfide, produced through sulfur disproportionation, as a key mechanism, alongside microbial Cr(VI) reduction within the sulfur-based biosystem. Genome-centric metagenomic analysis revealed a symbiotic relationship among SDB, sulfur-oxidizing, and chromate-reducing bacteria within the reactor, suggesting that Cr(VI) detoxification by these microbial communities enhances the sulfur-disproportionation process. This research highlights the significance of sulfur disproportionation in the cryptic sulfur cycle in Cr(VI)-contaminated groundwater and proposes its practical application in groundwater remediation efforts.

Cross-protection and cross-feeding between Enterobacter and Comamonas promoting their coexistence and cadmium tolerance in Oryza sativa L

Metabolic cross-feeding is a pervasive interaction between bacteria to acquire novel phenotypes. However, our current understanding of the survival mechanism for cross-feeding in cocultured bacterial biofilms under heavy-metal conditions remains limited. Herein, we found that Comamonas sp. A23 produces L-phenylalanine to activate the L-phenylalanine degradation pathway in Enterobacter sp. A11, enhancing biofilm formation and cadmium [Cd(II)] immobilization in A11. The genes responsible for L-phenylalanine-degradation (paaK) and cell attachment and aggregation (csgAD) are essential for biofilm formation and Cd(II) immobilization in A11 induced by L-phenylalanine. The augmentation of A11 biofilms, in turn, protects A23 under Cd(II) and H2O2 stresses. The plant-based experiments demonstrate that the induction of two rice Cd(II) transporters, OsCOPT4 and OsBCP1, by A11 and A23 enhances rice resistance against Cd(II) and H2O2 stresses. Overall, our findings unveil the mutual dependence between bacteria and rice on L-phenylalanine cross-feeding for survival under abiotic stress.

Fe Crystalline Phases in Fe/C Composites Modulated the Selective Adsorption of Pb(II) from Industrial Wastewater with Cd(II): An Electronic-Scale Perspective

Fe oxide or Fe0-based materials display weak removal capacity for Pb(II), especially in the presence of Cd(II), and the electronic-scale mechanisms are not reported. In this study, Fe3C(220) modified black carbon (BC) [Fe3C(220)@BC] with high adsorption and selectivity for Pb(II) from industrial wastewater with Cd(II) was developed. The quantitative experiment suggested that Fe species accounted for 80.5-100 and 18.4-33.8% of Pb(II) and Cd(II) removal, respectively. Based on X-ray absorption near-edge structure analysis, 57.3% of adsorbed Pb2+ was reduced to Pb0; however, 61.6% of Cd2+ existed on Fe3C@BC. Density functional theory simulation unraveled that Cd(II) adsorption was attributed to the cation-π interaction with BC, whereas that of Pb(II) was ascribed to the stronger interactions with different Fe phases following the order: Fe3C(220) > Fe0(110) > Fe3O4(311). Crystal orbital bond index and Hamilton population analyses were innovatively applied in the adsorption system and displayed a unique discovery: the stronger Pb(II) adsorption on Fe phases was mediated by a combination of covalent and ionic bonding, whereas ionic bonding was mainly accounted for Cd(II) adsorption. These findings open a new chapter in understanding the functions of different Fe phases in mediating the fate and transport of heavy metals in both natural and engineered systems.

A kinetic modelling approach to explore mechanism of Cr(VI) detoxification by a novel strain Pseudochrobactrum saccharolyticum NBRI-CRB 13 using response surface methodology

A novel Pseudochrobactrum saccharolyticum strain NBRI-CRB 13, isolated from tannery sludge, was studied to grow up to 500 mgL-1 of Cr(VI) and showed Cr(VI) detoxification by reducing > 90% of Cr(VI) at different concentrations 25, 50 and 100 mgL-1. Kinetic studies showed that first-order models were fitted (R2 = 0.998) to the time-dependent Cr(VI) reduction with degradation rate constant (k) (1.03-0.429 h-1). Cr(VI) detoxification was primarily related to the extracellular fraction of microbial cells, which showed a maximum extracellular reductase enzyme activity led to 94.6% reduction of Cr(VI). Moreover, the strain showed maximum extracellular polymeric substances (EPS) production at 100 mgL-1 Cr(VI), which is presumably the reason for Cr(VI) removal as EPS serves as the metal binding site for Cr(VI) ions. Further, an optimization study using Box-Behnken design was conducted considering parameters viz., pH, temperature, and initial concentration of Cr(VI). The maximum percent reduction of Cr(VI) was obtained at pH 6.5, temperature 30 °C with 62.5 mgL-1Cr(VI) concentration. Further, the Cr(VI) reduction and adsorption ability of strain P. saccharolyticum NBRI-CRB13 were confirmed by SEM-EDS, FTIR, and XRD analyses. FTIR analysis confirmed the presence of functional groups (-OH, -COOH, -PO4) on bacterial cell walls, which were more likely to interact with positively charged chromium ions. The study elucidated the reduction of Cr(VI) by the novel bacterium within 24 h using the response surface methodology approach and advocated its application in real-time situations.

Mercapto-functionalized palygorskite modified the growth of Ligusticum Chuanxiong and restrained the Cd migration in the soil-plant system

Ligusticum Chuanxiong is an essential medicinal and edible plant, but it is highly susceptible to the enrichment of soil Cadmium (Cd), which seriously affects its medical safety. However, the control of Cd uptake by Ligusticum Chuanxiong is little reported. In this study, we reported that a green Mercapto-functionalized palygorskite (MPAL) effectively promoted Ligusticum Chuanxiong growth, and restrained the Cd uptake by Ligusticum Chuanxiong both in the mildly contaminated soil (M-Soil) and severely contaminated soil (S-Soil). The experimental results demonstrated that the application of MPAL significantly increased the biomass and antioxidant enzyme activity of Ligusticum Chuanxiong. In the M-Soil, the Cd content in the roots, stems, and leaves of Ligusticum Chuanxiong decreased markedly by 82.46-86.66%, 64.17-71.73%, and 64.94-76.66%, respectively, after the MPAL treatment. In the S-Soil, MPAL application decreased the Cd content in roots, stems, and leaves by 89.43-98.92%, 24.19-86.22%, and 67.14-77.90%, respectively. Based on Diethylenetriamine Pentaacetic Acid (DTPA) extraction, the immobilization efficiency of MPAL for Cd in soils ranged from 22.01% to 77.04%. Additionally, the HOAc extractable Cd was transformed into reducible and oxidizable fractions. Furthermore, MPAL enhanced the activities of soil alkaline phosphatase, and urease, but decreased sucrase activity. Environmental toxicological analysis indicated that MPAL reduced the potential ecological risk of Cd in the soil. These findings revealed that MPAL can effectively reduce Cd accumulation in Ligusticum Chuanxiong and promote plant growth, suggesting its potential as a viable amendment for remediating Cd-contaminated soils.

The dominant role of extracellular polymeric substances produced by Achromobacter xylosoxidans BP1 in Cr(VI) microbial reduction

Extracellular polymeric substances (EPS) have demonstrated significant benefits for reducing multivalent metal contamination. Using Achromobacter xylosoxidans BP1 isolated from a coal chemical site in China, this study elucidated the contribution of EPS production to Cr (VI) reduction and revealed its biological removal mechanism. BP1 grew at an optimum pH of 8 and the lowest inhibitory concentration of Cr(VI) was 300 mg/L. The spent medium completely removed Cr(VI), whereas resting cells were only able to remove 10.47 % and inactivated cells were nearly incapable of Cr(VI) removal. S-EPS and B-EPS reduced Cr(VI) by 98.59 % and 11.64 %, respectively. SEM-EDS analysis showed that the BP1 cells were stimulated to produce EPS under Cr stress. The XPS results showed that 29.63 % of Cr(VI) was enriched by intracellular bioaccumulation or biosorption and 70.37 % of Cr(VI) was reduced by extracellular enzymes to produce Cr(OH)3 and organic Cr(III) complexes. According to FTIR, EPS with -OH, COO-, and amide groups supplied binding sites and electrons for the reductive adsorption of Cr(VI). Genomic studies showed that BP1 primarily produces extracellular polysaccharides, metabolises sulphur and nitrogen, and reduces reactive oxygen species damage as a result of DNA repair proteases.

m6A-methylated Lonp1 drives mitochondrial proteostasis stress to induce testicular pyroptosis upon environmental cadmium exposure

Cadmium (Cd) is a widely distributed typical environmental pollutant and one of the most toxic heavy metals. It is well-known that environmental Cd causes testicular damage by inducing classic types of cell death such as cell apoptosis and necrosis. However, as a new type of cell death, the role and mechanism of pyroptosis in Cd-induced testicular injury remain unclear. In the current study, we used environmental Cd to generate a murine model with testicular injury and AIM2-dependent pyroptosis. Based on the model, we found that increased cytoplasmic mitochondrial DNA (mtDNA), activated mitochondrial proteostasis stress occurred in Cd-exposed testes. We used ethidium bromide to generate mtDNA-deficient testicular germ cells and further confirmed that increased cytoplasmic mtDNA promoted AIM2-dependent pyroptosis in Cd-exposed cells. Uracil-DNA glycosylase UNG1 overexpression indicated that environmental Cd blocked UNG-dependent repairment of damaged mtDNA to drive the process in which mtDNA releases to cytoplasm in the cells. Interestingly, we found that environmental Cd activated mitochondrial proteostasis stress by up-regulating protein expression of LONP1 in testes. Testicular specific LONP1-knockdown significantly reversed Cd-induced UNG1 protein degradation and AIM2-dependent pyroptosis in mouse testes. In addition, environmental Cd significantly enhanced the m6A modification of Lonp1 mRNA and its stability in testicular germ cells. Knockdown of IGF2BP1, a reader of m6A modification, reversed Cd-induced upregulation of LONP1 protein expression and pyroptosis activation in testicular germ cells. Collectively, environmental Cd induces m6A modification of Lonp1 mRNA to activate mitochondrial proteostasis stress, increase cytoplasmic mtDNA content, and trigger AIM2-dependent pyroptosis in mouse testes. These findings suggest that mitochondrial proteostasis stress is a potential target for the prevention of testicular injury.

Cadmium phytoremediation potential of Houttuynia cordata: Insights from growth, uptake, and rhizosphere mechanisms

Cadmium (Cd) pollutes 7.0 % of China's land area. This study examined the potential of Houttuynia cordata for Cd phytoremediation because of its ability to accumulate Cd in its growth matrix. H. cordata were planted in plastic pots filled with paddy field soils having low (LCd), medium (MCd), and high (HCd) Cd levels of 0.19, 0.69, and 2.91 mg/kg, respectively. After six months of growth, harvested plant parts were evaluated for Cd uptake and tolerance mechanisms. Metabolomics and metagenomics approaches were employed to investigate the soil rhizosphere mechanism. Results showed that the average plant biomass increased as soil Cd increased. The biomass Cd contents surpassed the allowable Cd limits for food (≤ 0.2 mg/kg) and medicinal uses (≤ 0.3 mg/kg). Cd contents were higher in H. cordata roots (30.59-86.27 mg/kg) than in other plant parts (0.63-2.90 mg/kg), with significantly increasing values as Cd soil level increased. Phenolic acids, lipids, amino acids and derivatives, organic acids, and alkaloids comprised the majority (69 in MCd vs HCd and 73 % in LCd vs HCd) of the shared upregulated metabolites. In addition, 13 metabolites specific to H. cordata root exudates were significantly increased. The top two principal metabolic pathways were arginine and proline metabolism, and beta-alanine metabolism. H. cordata increased the abundance of Firmicutes and Glomeromycota across all three Cd levels, and also stimulated the growth of Patescibacteria, Rozellomycota, and Claroideoglomus in HCd. Accordingly, H. cordata demonstrated potential for remediation of Cd-contaminated soils, and safety measures for its production and food use must be highly considered.

Cysteine and thiosulfate promoted cadmium immobilization in strain G303 by the formation of extracellular CdS

Bacteria have evolved a variety of strategies to defend themselves against cadmium toxicity, however, the specific mechanisms involved in the enhancement of bacterial cadmium resistance by sulfur sources are unclear. In this study, a novel cadmium (Cd)-tolerant bacterium, Stenotrophomonas geniculata G303, was isolated from activated sludge. The growth of strain G303 under diverse Cd concentrations was investigated, and the minimum inhibitory concentration of Cd was found to be 1 mM. Strain G303 effectively remove 94.7 % of Cd after 96 h of culture. Extracellular CdS was detected using multiple methods, with the CdS formed being aggregated in the biofilm. The addition of cysteine and thiosulfate to the medium significantly enhanced the Cd resistance and removal capacity of strain G303. Integrated genomic and proteomic analyses revealed that heavy metal transporters cooperate to resist Cd stress. Cysteine and thiosulfate improved Cd tolerance in strain G303 by upregulating nitrogen and energy metabolism. Proteins associated with nitrate reduction likely played a pivotal role in cysteine and thiosulfate metabolism. Notably, cysteine synthase and the SUF system played crucial roles in CdS formation. This study systematically explored the impact of cysteine and thiosulfate on the Cd resistance of strain G303, deepening our understanding of the microbial response mechanism to heavy metals.

A PadR family transcriptional repressor regulates the transcription of chromate efflux transporter in Enterobacter sp. Z1

Chromium is a prevalent toxic heavy metal, and chromate [Cr(VI)] exhibits high mutagenicity and carcinogenicity. The presence of the Cr(VI) efflux protein ChrA has been identified in strains exhibiting resistance to Cr(VI). Nevertheless, certain strains of bacteria that are resistant to Cr(VI) lack the presence of ChrB, a known regulatory factor. Here, a PadR family transcriptional repressor, ChrN, has been identified as a regulator in the response of Enterobacter sp. Z1(CCTCC NO: M 2019147) to Cr(VI). The chrN gene is cotranscribed with the chrA gene, and the transcriptional expression of this operon is induced by Cr(VI). The binding capacity of the ChrN protein to Cr(VI) was demonstrated by both the tryptophan fluorescence assay and Ni-NTA purification assay. The interaction between ChrN and the chrAN operon promoter was validated by reporter gene assay and electrophoretic mobility shift assay. Mutation of the conserved histidine residues His14 and His50 resulted in loss of ChrN binding with the promoter of the chrAN operon. This observation implies that these residues are crucial for establishing a DNA-binding site. These findings demonstrate that ChrN functions as a transcriptional repressor, modulating the cellular response of strain Z1 to Cr(VI) exposure.

Impact of meteorological factors on Cd availability and average concentration prediction in rice growth cycle

During the rice growth cycle, the average available cadmium concentration (CA-Cd) in the soil determines the Cd content in rice plant. Given defined soil properties and rice varieties, the meteorological factors play a crucial role in soil's available cadmium concentration (CCd) during the rice growth cycle. Thus, it is significant to investigate the influence of meteorological factors in CCd during the rice growth cycle and develop a predictive model for CA-Cd. The rice was cultivated under seven different sowing dates in Cd and As-contaminated soil in Hunan Province. Studied the impact of meteorological factors on paddy soil. The results showed that accumulated temperature (AT) and total precipitation (TP) were key factors affecting the soil CCd. The correlation coefficients between AT and TP with soil CA-Cd were 0.98 and -0.94 (p < 0.01), respectively. However, there was no significant correlation with CAs. AT mainly influenced the CCd during the grouting and maturity stages. A straightforward empirical prediction model was developed, capable of accurately forecasting CA-Cd during the rice growth cycle by considering meteorological factors and the initial soil CCd. This study supported a novel foundation for the precise prediction of Cd content in rice.

Analysis of the Cadmium Removal Mechanism of Human Gut Bacteria Enterococcus faecalis Strain ATCC19433 from a Genomic Perspective

Cadmium (Cd) is one of the most well-known toxic metals capable of entering the human body via the food chain, leading to serious health problems. Human gut microbes play a pivotal role in controlling Cd bioavailability and toxicity within the human gastrointestinal tract, primarily due to their capacity for Cd adsorption and metabolism. In this work, a Cd-resistant bacterial strain, Enterococcus faecalis strain ATCC19433 was isolated from human gut microbiota. Cd binding assays and comprehensive characterization analyses were performed, revealing the ability of strain ATCC19433 to remove Cd from the solution. Cd adsorption primarily occurred on the bacterial cell walls, which was ascribed to the exciting of functional groups on the bacterial surfaces, containing alkyl, amide II, and phosphate groups; meanwhile, Cd could enter cells, probably through transport channels or via diffusion. These results indicated that Cd removal by the strain was predominantly dependent on biosorption and bioaccumulation. Whole-genome sequencing analyses further suggested the probable mechanisms of biosorption and bioaccumulation, including Cd transport by transporter proteins, active efflux of Cd by cadmium efflux pumps, and mitigating oxidative stress-induced cell damage by DNA repair proteases. This study evaluated the Cd removal capability and mechanism of Enterococcus faecalis strain ATCC19433 while annotating the genetic functions related to Cd removal, which may facilitate the development of potential human gut strains for the removal of Cd.

Field-scale assessment of soil, water, plant, and soil microbiome in and around Rania-Khan Chandpur Chromium contaminated site, India

Rania-Khan Chandpur site, (Kanpur Dehat, Uttar Pradesh, India), one of the highly Chromium (Cr) contaminated sites in India due to Chromite Ore Processing Residue (COPR), has been investigated at the field-scale. We found that the area around the COPR dumps was hazardously contaminated with the Cr where its concentrations in the surface water and groundwater were > 40 mgL-1, its maximum contents in the COPRs and in the soils of the adjoining lands were 9.6 wt% and 3.83 wt%, respectively. By exploring the vegetation and microbial distribution across the site, we advocate the appropriateness of Cynodon dactylon, Chrysopogon zizanioides, Cyperus sp., and Typha angustifolia as the most suitable phytoremediation agent because their association with Cr remediating bacterial species (Pseudomonas sp., Clostridium sp. and Bacillus sp.) was strong. Using this remarkable information for the bioremediation projects, this site can be re-vegetated and bioaugmented to remediate Cr in soils, waterlogged ditches, surface water, and in groundwater systems.

Effect of soil organic matter-mediated electron transfer on heavy metal remediation: Current status and perspectives

Soil contamination by heavy metals poses major risks to human health and the environment. Given the current status of heavy metal pollution, many remediation techniques have been tested at laboratory and contaminated sites. The effects of soil organic matter-mediated electron transfer on heavy metal remediation have not been adequately studied, and the key mechanisms underlying this process have not yet been elucidated. In this review, microbial extracellular electron transfer pathways, organic matter electron transfer for heavy metal reduction, and the factors affecting these processes were discussed to enhance our understanding of heavy metal pollution. It was found that microbial extracellular electrons delivered by electron shuttles have the longest distance among the three electron transfer pathways, and the application of exogenous electron shuttles lays the foundation for efficient and persistent remediation of heavy metals. The organic matter-mediated electron transfer process, wherein organic matter acts as an electron shuttle, promotes the conversion of high valence state metal ions, such as Cr(VI), Hg(II), and U(VI), into less toxic and morphologically stable forms, which inhibits their mobility and bioavailability. Soil type, organic matter structural and content, heavy metal concentrations, and environmental factors (e.g., pH, redox potential, oxygen conditions, and temperature) all influence organic matter-mediated electron transfer processes and bioremediation of heavy metals. Organic matter can more effectively mediate electron transfer for heavy metal remediation under anaerobic conditions, as well as when the heavy metal content is low and the redox potential is suitable under fluvo-aquic/paddy soil conditions. Organic matter with high aromaticity, quinone groups, and phenol groups has a stronger electron transfer ability. This review provides new insights into the control and management of soil contamination and heavy metal remediation technologies.

DIET-like and MIET-like mutualism of S. oneidensis MR-1 and metal-reducing function microflora boosts Cr(VI) reduction

Microbial treatment of Cr(VI) is an environmentally friendly and low-cost approach. However, the mechanism of mutualism and the role of interspecies electron transfer in Cr(VI) reducing microflora are unclear. Herein, we constructed an intersymbiotic microbial association flora to augment interspecies electron transfer via functionalizing electroactive Shewanella oneidensis MR-1 with metal-reducing microflora, and thus the efficiency of Cr(VI) reduction. The findings suggest that the metal-reducing active microflora could converts glucose into lactic acid and riboflavin for S. oneidensis MR-1 to act as a carbon source and electron mediator. Thus, when adding initial 25 mg/L Cr (VI), this microflora exhibited an outstanding Cr (VI) removal efficiency (100%) at 12 h and elevated Cr (III) immobilization efficiency (80%) at 60 h with the assistance of 25 mg/L Cu(II). A series of electrochemical experiments proved this remarkable removal efficiency were ascribed to the improved interspecies electron transfer efficiency through direct interspecies electron transfer and riboflavin through mediated interspecies electron transfer. Furthermore, the metagenomic analysis revealed the expression level of the electron transport pathway was promoted. Intriguing high abundance of genes participating in the bio-reduction and biotransformation of Cr(VI) was also observed in functional microflora. These outcomes give a novel strategy for enhancing the reduction and fixation of harmful heavy metals by coculturing function microflora with electrogenic microorganisms.

Responses of a polycyclic aromatic hydrocarbon-degrading bacterium, Paraburkholderia fungorum JT-M8, to Cd (II) under P-limited oligotrophic conditions

For the bioremediation of mixed-contamination sites, studies on polycyclic aromatic hydrocarbon (PAH) degradation or Cd (II) tolerance in bacteria are commonly implemented in nutrient-rich media. In contrast, in the field, inocula usually encounter harsh oligotrophic habitats. In this study, the environmental strain Paraburkholderia fungorum JT-M8 was used to explore the overlooked Cd (II) defense mechanism during PAH dissipation under P-limited oligotrophic condition. The results showed that the growth and PAH degradation ability of JT-M8 under Cd (II) stress were correlated with phosphate contents and exhibited self-regulating properties. Phosphates mainly affected the Cd (II) content in solution, while the cellular distribution of Cd (II) depended on Cd (II) levels; Cd (II) was mainly located in the cytoplasm when exposed to less Cd (II), and vice versa. The unique Cd (II) detoxification pathways could be classified into three aspects: (i) Cd (II) ionic equilibrium and dose-response effects regulated by environmental matrices (phosphate contents); (ii) bacterial physiological self-regulation, e.g., cell surface-binding, protein secretion and active transport systems; and (iii) specific adaptive responses (flagellum aggregation). This study emphasizes the importance of considering culture conditions when assessing the metal tolerance and provides new insight into the bacterial detoxification process of complex PAH-Cd (II) pollutants.

Impact of iron and sulfur cycling on the bioavailability of cadmium and arsenic in co-contaminated paddy soil

The biogeochemical cycling of iron (Fe) or sulfur (S) in paddy soil influences the cadmium (Cd) and arsenic (As) migration. However, the influence of coupled reduction effects and reaction precedence of Fe and S on the bioavailability of Cd and As is still not fully understood. This study aimed to reveal the influence of Fe and S reduction on soil Cd and As mobility under various pe + pH conditions and to elucidate the related mechanism in subtropical China. According to the findings, higher adsorption from Fe reduction caused high-crystalline goethite (pe + pH > 2.80) to become amorphous ferrihydrite, which in turn caused water-soluble Cd (62.0%) to first decrease. Cd was further decreased by 72.7% as a result of the transformation of SO42- to HS-/S2- via sulfate reduction and the formation of CdS and FeS. As release (an increase of 8.1 times) was consequently caused by the initial reduction and dissolution of iron oxide (pe + pH > 2.80). FeS had a lesser impact on the immobilization of As than sulfate-mediated As (V) reduction in the latter stages of the reduction process (pe + pH < 2.80). pe + pH values between 3 and 3.5 should be maintained to minimize the bioavailability of As and Cd in moderate to mildly polluted soil without adding iron oxides and sulfate amendments. The practical remediation of severely co-contaminated paddy soil can be effectively achieved by using Fe and S additions at different pe + pH conditions. This technique shows promise in reducing the bioavailability of Cd and As.

Exploring the synergistic interplay of sulfur metabolism and electron transfer in Cr(VI) and Cd(II) removal by Clostridium thiosulfatireducens: Genomic and mechanistic insights

In this study, a sulfate-reducing bacterium, Clostridium thiosulfatireducens (CT) was reported and the performance and removal mechanism of Cr(VI) and Cd(II) removal were investigated. It is noteworthy that the dsrAB gene is absent in this strain, but the strain is capable of producing sulfide. The conversion rate of Cr(VI) by CT was 84.24 % at a concentration of 25 mg/L, and the conversion rate of Cd(II) was 94.19 % at a concentration of 28 mg/L. The complete genome is 6,106,624 bp and the genome consisted of a single chromosome. The GC content of the chromosomes was 29.65 %. The mechanism of heavy metal removal by CT bacteria mainly includes biosorption, electron transfer and redox, with reduction combined with S2- precipitation as the main pathway. The product characterization results showed that the formation of mainly ionic crystals and precipitates (CdS, Cd(OH)2, Cr(OH)3, Cr2O3) after adsorption. Genome-wide techniques have shown that the clearance of Cr(VI) and Cd(II) by CT is largely dependent on sulfate transport, sulfur metabolism, and energy metabolism to some extent. In addition, genes related to ATP binding, electron carrier activity, transporter protein genes, and DNA repair are also important factors to improve the heavy metal resistance and transformation ability of CT strains. Both the Fe-S cycle and the ROS-resistant system can enhance the electron transfer activity and thus slow down the damage of heavy metals to microorganisms. This study fills the gap in the understanding of the basic properties and heavy metal transformation mechanism of CT.

Inhibition of high sulfur on functional microorganisms and genes in slightly contaminated soil by cadmium and chromium

It is generally accepted that sulfur can passivate the bioavailability of heavy metals in soil, but it is not clear whether high sulfur in cadmium (Cd) and chromium (Cr) contaminated soil has negative effect on soil microbial community and ecological function. In this study, total sulfur (TS) inhibited the Chao 1, Shannon, Phylogenetic diversity (Pd) of bacterial and Pd of fungi in slightly contaminated soil by Cd and Cr around pyrite. TS, total potassium, pH, total chromium, total cadmium, total nitrogen, soil organic matter were the predominant factors for soil microbial community; the contribution of TS in shaping bacterial and fungal communities ranked at first and fifth, respectively. Compared with the low sulfur group, the abundance of sulfur sensitive microorganisms Gemmatimonas, Pseudolabrys, MND1, and Schizothecium were decreased by 68.79-97.22% (p < 0.01) at high sulfur one; the carbon fixation, nitrogen cycling, phosphorus cycling and resistance genes abundance were significantly lower (p < 0.01) at the latter. Such variations were strongly and closely correlated to the suppression of energy metabolism (M00009, M00011, M00086) and carbon fixation (M00173, M00376) functional module genes abundance in the high sulfur group. Collectively, high sulfur significantly suppressed the abundances of functional microorganisms and functional genes in slightly contaminated soil with Cd and Cr, possibly through inhibition of energy metabolism and carbon fixation of functional microorganisms. This study provided new insights into the environmental behavior of sulfur in slightly contaminated soil with Cd and Cr.

Contributions of selenium-oxidizing bacteria to selenium biofortification and cadmium bioremediation in a native seleniferous Cd-polluted sandy loam soil

Selenium (Se) is a trace element that is essential for human health. Daily dietary Se intake is governed by the food chain through soil-plant systems. However, the cadmium (Cd) content tends to be excessive in seleniferous soil, in which Se and Cd have complex interactions. Therefore, it is a great challenge to grow crops containing appreciable amounts of Se but low amounts of Cd. We compared the effects of five Se-transforming bacteria on Se and Cd uptake by Brassica rapa L. in a native seleniferous Cd-polluted soil. The results showed that three Se-oxidizing bacteria (LX-1, LX-100, and T3F4) increased the Se content of the aboveground part of the plant by 330.8%, 309.5%, and 724.3%, respectively, compared to the control (p < 0.05). The three bacteria also reduced the aboveground Cd content by 15.1%, 40.4%, and 16.4%, respectively (p < 0.05). In contrast, the Se(IV)-reducing bacterium ES2-45 and weakly Se-transforming bacterium LX-4 had no effect on plant Se uptake, although they did decrease the aboveground Cd content. In addition, the three Se-oxidizing bacteria increased the Se available in the soil by 38.4%, 20.4%, and 24.0%, respectively, compared to the control (p < 0.05). The study results confirm the feasibility of using Se-oxidizing bacteria to simultaneously enhance plant Se content and reduce plant Cd content in seleniferous Cd-polluted soil.

Heavy metal contamination impacts the structure and co-occurrence patterns of bacterial communities in agricultural soils

Heavy metal (HM) contamination caused by mining and smelting activities can be harmful to soil microbiota, which are highly sensitive to HM stress. Here, we explore the effects of HM contamination on the taxonomic composition, predicted function, and co-occurrence patterns of soil bacterial communities in two agricultural fields with contrasting levels of soil HMs (i.e., contaminated and uncontaminated natural areas). Our results indicate that HM contamination does not significantly influence soil bacterial α diversity but changes the bacterial community composition by enriching the phyla Gemmatimonadetes, Planctomycetes, and Parcubacteria and reducing the relative abundance of Actinobacteria. Our results further demonstrate that HM contamination can strengthen the complexity and modularity of the bacterial co-occurrence network but weaken positive interactions between keystone taxa, leading to the gradual disappearance of some taxa that originally played an important role in healthy soil, thereby possibly reducing the resistance of bacterial communities to HM toxicity. The predicted functions of bacterial communities are related to membrane transport, amino acid metabolism, energy metabolism, and carbohydrate metabolism. Among these, functions related to HM detoxification and antioxidation are enriched in uncontaminated soils, while HM contamination enriches functions related to metal resistance. This study demonstrated that microorganisms adapt to the stress of HM pollution by adjusting their composition and enhancing their network complexity and potential ecological functions.

Metabolic mechanism of Cr(VI) pollution remediation by Alicycliphilus denitrificans Ylb10

Cr(VI) is a well-known toxic pollutant and its remediation has attracted great attention. It is important to continuously discover and explore new high-efficiency Cr(VI) reducing bacteria to further improve the efficiency of Cr(VI) pollution remediation. In this paper, metabolic mechanism of Cr(VI) reduction in a new highly efficient Cr(VI) reducing bacterium, Alicycliphilus denitrificans Ylb10, was investigated. The results showed that Ylb10 could tolerate and completely reduce 450 mg/L Cr(VI). Cr(VI) can be reduced in the intracellular compartment, membrane and the extracellular compartment, with the plasma membrane being the main active site for Cr(VI) reduction. With the addition of NADH, the reduction efficiency of cell membrane components for Cr(VI) increased 2.3-fold. The omics data analysis showed that sulfite reductase CysJ, thiosulfate dehydrogenase TsdA, nitrite reductase NrfA, nitric oxide reductase NorB, and quinone oxidoreductase ChrR play important roles in the reduction of Cr(VI), in the intracellular, and the extracellular compartment, and the membrane of Ylb10, and therefore Cr(VI) was reduced by the combined action of several reductases at these three locations.

Chromate-induced methylglyoxal detoxification system drives cadmium and chromate immobilization by Cupriavidus sp. MP-37

The detoxification of cadmium (Cd) or chromium (Cr) by microorganisms plays a vital role in bacterial survival and restoration of the polluted environment, but how microorganisms detoxify Cd and Cr simultaneously is largely unknown. Here, we isolated a bacterium, Cupriavidus sp. MP-37, which immobilized Cd(II) and reduced Cr(VI) simultaneously. Notably, strain MP-37 exhibited variable Cd(II) immobilization phenotypes, namely, cell adsorption and extracellular immobilization in the co-presence of Cd(II) and Cr(VI), while cell adsorption in the presence of Cd(II) alone. To unravel Cr(VI)-induced extracellular Cd(II) immobilization, proteomic analysis was performed, and methylglyoxal-scavenging protein (glyoxalase I, GlyI) and a regulator (YafY) showed the highest upregulation in the co-presence of Cd(II) and Cr(VI). GlyI overexpression reduced the intracellular methylglyoxal content and increased the immobilized Cd(II) content in extracellular secreta. The addition of lactate produced by GlyI protein with methylglyoxal as substrate increased the Cd(II) content in extracellular secreta. Reporter gene assay, electrophoretic mobility shift assay, and fluorescence quenching assay demonstrated that glyI expression was induced by Cr(VI) but not by Cd(II), and that YafY positively regulated glyI expression by binding Cr(VI). In the pot experiment, inoculation with the MP-37 strain reduced the Cd content of Oryza sativa L., and their secreted lactate reduced the Cr accumulation in Oryza sativa L. This study reveals that Cr(VI)-induced detoxification system drives methylglyoxal scavenging and Cd(II) extracellular detoxification in Cd(II) and Cr(VI) co-existence environment.

Ultrafast removal of toxic Cr(VI) by the marine bacterium Vibrio natriegens

The fastest-growing microbe Vibrio natriegens is an excellent platform for bioproduction processes. Until now, this marine bacterium has not been examined for bioremediation applications, where the production of substantial amounts of biomass would be beneficial. V. natriegens can perform extracellular electron transfer (EET) to Fe(III) via a single porin-cytochrome circuit conserved in Vibrionaceae. Electroactive microbes capable of EET to Fe(III) usually also reduce toxic metals such as carcinogenic Cr(VI), which is converted to Cr(III), thus decreasing its toxicity and mobility. Here, the performance of V. natriegens was explored for the bioremediation of Cr(VI). At a density of 100 mg/mL, V. natriegens removed 5-20 mg/L Cr(VI) within 30 s and 100 mg/L Cr(VI) within 10 min. In comparison, the model bacterium Escherichia coli grown to a comparable cell density removed Cr(VI) 36 times slower. To eliminate Cr(VI), V. natriegens had to be metabolically active, and functional outer-membrane c-type cytochromes were required. At the end of the Cr(VI) removal process, V. natriegens had reduced all of it into Cr(III) while adsorbing more than half of the metallic ions. These results demonstrate that V. natriegens, with its fast metabolism, is a viable option for the rapid treatment of aqueous pollution with Cr.

Metagenomic and proteomic insights into the self-adaptive cell surface hydrophobicity of Sphingomonas sp. strain PAH02 reducing the migration of cadmium-phenanthrene co-pollutant in rice

Cell surface hydrophobicity (CSH) dominates the interactions between rhizobacteria and pollutants at the soil-water interface, which is critical for understanding the dissipation of pollutants in the rhizosphere microzone of rice. Herein, we explored the effects of self-adaptive CSH of Sphingomonas sp. strain PAH02 on the translocation and biotransformation behaviour of cadmium-phenanthrene (Cd-Phe) co-pollutant in rice and rhizosphere microbiome. We evidenced that strain PAH02 reduced the adsorption of Cd-Phe co-pollutant on the rice root surface while enhancing the degradation of Phe and adsorption of Cd via its self-adaptive CSH in the hydroponic experiment. The significant upregulation of key protein expression levels such as MerR, ARHDs and enoyl-CoA hydratase/isomerase, ensures self-adaptive CSH to cope with the stress of Cd-Phe co-pollutant. Consistently, the bioaugmentation of strain PAH02 promoted the formation of core microbiota in the rhizosphere soil of rice (Oryza sativa L.), such as Bradyrhizobium and Streptomyces and induced gene enrichment of CusA and PobA that are strongly associated with pollutant transformation. Consequently, the contents of Cd and Phe in rice grains at maturity decreased by 17.2% ± 0.2% and 65.7% ± 0.3%, respectively, after the bioaugmentation of strain PAH02. These findings present new opportunities for the implementation of rhizosphere bioremediation strategies of co-contaminants in paddy fields.

Bacteria-loaded biochar for the immobilization of cadmium in an alkaline-polluted soil

The combination of biochar and bacteria is a promising strategy for the remediation of Cd-polluted soils. However, the synergistic mechanisms of biochar and bacteria for Cd immobilization remain unclear. In this study, the experiments were conducted to evaluate the effects of the combination of biochar and Pseudomonas sp. AN-B15, on Cd immobilization, soil enzyme activity, and soil microbiome. The results showed that biochar could directly reduce the motility of Cd through adsorption and formation of CdCO3 precipitates, thereby protecting bacteria from Cd toxicity in the solution. In addition, bacterial growth further induces the formation of CdCO3 and CdS and enhances Cd adsorption by bacterial cells, resulting in a higher Cd removal rate. Thus, bacterial inoculation significantly enhances Cd removal in the presence of biochar in the solution. Moreover, soil incubation experiments showed that bacteria-loaded biochar significantly reduced soil exchangeable Cd in comparison with other treatments by impacting soil microbiome. In particular, bacteria-loaded biochar increased the relative abundance of Bacillus, Lysobacter, and Pontibacter, causing an increase in pH, urease, and arylsulfatase, thereby passivating soil exchangeable Cd and improving soil environmental quality in the natural alkaline Cd-contaminated soil. Overall, this study provides a systematic understanding of the synergistic mechanisms of biochar and bacteria for Cd immobilization in soil and new insights into the selection of functional strain for the efficient remediation of the contaminated environments by bacterial biochar composite.

Cadmium-tolerant Bacillus cereus 2-7 alleviates the phytotoxicity of cadmium exposure in banana plantlets

Bananas are the world's important fruit and staple crop in the developing countries. Cadmium (Cd) contamination in soils results in the decrease of crop yield and food safety. Bioremediation is an environmental-friendly and effective measure using Cd-tolerant plant growth promoting rhizobacteria (PGPR). In our study, a Cd-resistant PGPR Bacillus cereus 2-7 was isolated and identified from a discarded gold mine. It could produce multiple plant growth promoting biomolecules such as siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC)-deaminase and phosphatase. The extracellular accumulation was a main manner of Cd removal. Surplus Cd induced the expression of Cd resistance/transport genes of B. cereus 2-7 to maintain the intracellular Cd homeostasis. The pot experiment showed that Cd contents decreased by 50.31 % in soil, 45.43 % in roots, 56.42 % in stems and 79.69 % in leaves after the strain 2-7 inoculation for 40 d. Bacterial inoculation alleviated the Cd-induced oxidative stress to banana plantlets, supporting by the increase of chlorophyll contents, plant height and total protein contents. The Cd remediation mechanism revealed that B. cereus 2-7 could remodel the rhizosphere bacterial community structure and improve soil enzyme activities to enhance the immobilization of Cd. Our study provides a Cd-bioremediation strategy using Cd-resistant PGPR in tropical and subtropical area.

Plant growth-promoting rhizobacteria: a potential bio-asset for restoration of degraded soil and crop productivity with sustainable emerging techniques

The rapid expansion of degraded soil puts pressure on agricultural crop yield while also increasing the likelihood of food scarcity in the near future at the global level. The degraded soil does not suit plants growth owing to the alteration in biogeochemical cycles of nutrients, soil microbial diversity, soil organic matter, and increasing concentration of heavy metals and organic chemicals. Therefore, it is imperative that a solution should be found for such emerging issues in order to establish a sustainable future. In this context, the importance of plant growth-promoting rhizobacteria (PGPR) for their ability to reduce plant stress has been recognized. A direct and indirect mechanism in plant growth promotion is facilitated by PGPR via phytostimulation, biofertilizers, and biocontrol activities. However, plant stress mediated by deteriorated soil at the field level is not entirely addressed by the implementation of PGPR at the field level. Thus, emerging methods such as CRISPR and nanotechnological approaches along with PGPR could manage degraded soil effectively. In the pursuit of the critical gaps in this respect, the present review discusses the recent advancement in PGPR action when used along with nanomaterials and CRISPR, impacting plant growth under degraded soil, thereby opening a new horizon for researchers in this field to mitigate the challenges of degraded soil.

Mechanisms involved in the sequestration and resistance of cadmium for a plant-associated Pseudomonas strain

Understanding Cd-resistant bacterial cadmium (Cd) resistance systems is crucial for improving microremediation in Cd-contaminated environments. However, these mechanisms are not fully understood in plant-associated bacteria. In the present study, we investigated the mechanisms underlying Cd sequestration and resistance in the strain AN-B15. These results showed that extracellular Cd sequestration by complexation in strain AN-B15 was primarily responsible for the removal of Cd from the solution. Transcriptome analyses have shown that the mechanisms of Cd resistance at the transcriptional level involve collaborative processes involving multiple metabolic pathways. The AN-B15 strain upregulated the expression of genes related to exopolymeric substance synthesis, metal transport, Fe-S cluster biogenesis, iron recruitment, reactive oxygen species oxidative stress defense, and DNA and protein repair to resist Cd-induced stress. Furthermore, inoculation with AN-B15 alleviated Cd-induced toxicity and reduced Cd uptake in the shoots of wheat seedlings, indicating its potential for remediation. Overall, the results improve our understanding of the mechanisms involved in Cd resistance in bacteria and thus have important implications for improving microremediation.

Soil microbial community compositions and metabolite profiles of Achnatherum inebrians affect phytoremediation potential in Cd contaminated soil

Cadmium (Cd) contamination poses serious risks to soil ecosystems and human health. Herein, the effect of two drunken horse grasses (Achnatherum inebrians) including endophytes Epichloë gansuensis infected (E+ ) and uninfected (E-) on the phytoremediation of Cd-contaminated soils were analyzed by coupling high-throughput sequencing and soil metabolomics. The results showed that the high-risk soil Cd decreased and the medium- and low-risk Cd fraction increased to varying degrees after planting E+ and E- plants in the soil. Meanwhile, total Cd content decreased by 19.7 % and 35.1 % in E+ and E- A. inebrians-planted soils, respectively. Principal coordinate analysis revealed a significant impact of E+ and E- plants on the soil microbial community. Most stress-tolerant and gram-positive functional bacterial taxa were enriched to stabilize Cd(II) in E+ planted soil. Several beneficial fungal groups related to saprotroph and symbiotroph were enriched to absorb Cd(II) in E- soil. Soil metabolomic analysis showed that the introduction of A. inebrians could weaken the threat of CdCl2 to soil microbe metabolism and improve soil quality, which in turn promoted plant growth and improved phytoremediation efficiency in Cd-contaminated soil. In conclusion, A. inebrians plants alleviate soil Cd pollution by regulating soil microbial metabolism and microbial community structure. These results provide valuable information for an in-depth understanding of the phytoremediation mechanisms of A. inebrians.

Chronic Exposure to Drinking Water As, Pb, and Cd at Provisional Guideline Values Reduces Weight Gain in Male Mice via Gut Microflora Alterations and Intestinal Inflammation

Few studies have investigated the long-term effect of exposure to arsenic (As), lead (Pb), and cadmium (Cd) via drinking water at the provisional guideline values on gut microflora. In this study, male and female mice were exposed to water As, Pb, or Cd at 10, 10, or 5 μg L-1 for 6 months. At the end of the exposure, the net weight gain of male mice exposed to As and Pb (9.91 ± 1.35 and 11.2 ± 1.50 g) was significantly (p < 0.05) lower compared to unexposed control mice (14.1 ± 3.24 g), while this was not observed for female mice. Relative abundance of Akkermansia, a protective gut bacterium against intestinal inflammation, was reduced from 29.7% to 3.20%, 4.83%, and 17.0% after As, Pb, and Cd exposure in male mice, which likely caused chronic intestinal inflammation, as suggested by 2.81- to 9.60-fold higher mRNA levels of pro-inflammatory factors in ileal enterocytes of male mice. These results indicate that long-term exposure to drinking water As, Pb, and Cd at concentrations equivalent to the China provisional guideline values can cause loss of protective bacteria and lead to chronic intestinal inflammation, thereby affecting body weight gain in male mice.

Recruitment and metabolomics between Canna indica and rhizosphere bacteria under Cr stress

It is of positive significance to explore the mechanism of antioxidant and metabolic response of Canna indica under Cr stress mediated by rhizosphere niche. However, the mechanisms of recruitment and interaction of rhizosphere microorganisms in plants still need to be fully understood. This study combined physiology, microbiology, and metabolomics, revealing the interaction between C. indica and rhizosphere microorganisms under Cr stress. The results showed that Cr stress increased the content of malondialdehyde (MDA) and oxygen-free radicals (ROS) in plants. At the same time, the activities of antioxidant enzymes (SOD, POD, and APX) and the contents of glutathione (GSH) and soluble sugar were increased. In addition, Cr stress decreased the α diversity index of C. indica rhizosphere bacterial community and changed its community structure. The dominant bacteria, namely, Actinobacteriota, Proteobacteria, and Chloroflexi accounted for 75.16% of the total sequence. At the same time, with the extension of stress time, the colonization amount of rhizosphere-dominant bacteria increased significantly, and the metabolites secreted by roots were associated with the formation characteristics of Proteobacteria, Actinobacteria, Bacteroidetes, and other specific bacteria. Five critical metabolic pathways were identified by metabolome analysis, involving 79 differentially expressed metabolites, which were divided into 15 categories, mainly including lipids, terpenoids, and flavonoids. In conclusion, this study revealed the recruitment and interaction response mechanism between C. indica and rhizosphere bacteria under Cr stress through multi-omics methods, providing the theoretical basis for the remediation of Cr-contaminated soil.

Cleanup of Cr(VI)-polluted groundwater using immobilized bacterial consortia via bioreduction mechanisms

Cr(VI) bioreduction has become a remedial alternative for Cr(VI)-polluted site cleanup. However, lack of appropriate Cr(VI)-bioreducing bacteria limit the field application of the in situ bioremediation process. In this study, two different immobilized Cr(VI)-bioreducing bacterial consortia using novel immobilization agents have been developed for Cr(VI)-polluted groundwater remediation: (1) granular activated carbon (GAC) + silica gel + Cr(VI)-bioreducing bacterial consortia (GSIB), and (2) GAC + sodium alginate (SA) + polyvinyl alcohol (PVA) + Cr(VI)-bioreducing bacterial consortia (GSPB). Moreover, two unique substrates [carbon-based agent (CBA) and emulsified polycolloid substrate (EPS)] were developed and used as the carbon sources for Cr(VI) bioreduction enhancement. The microbial diversity, dominant Cr-bioreducing bacteria, and changes of Cr(VI)-reducing genes (nsfA, yieF, and chrR) were analyzed to assess the effectiveness of Cr(VI) bioreduction. Approximately 99% of Cr(VI) could be bioreduced in microcosms with GSIB and CBA addition after 70 days of operation, which caused increased populations of total bacteria, nsfA, yieF, and chrR from 2.9 × 10⁸ to 2.1 × 10¹², 4.2 × 10⁴ to 6.3 × 10¹¹, 4.8 × 10⁴ to 2 × 10¹¹, and 6.9 × 10⁴ to 3.7 × 10⁷ gene copies/L. In microcosms with CBA and suspended bacteria addition (without bacterial immobilization), the Cr(VI) reduction efficiency dropped to 60.3%, indicating that immobilized Cr-bioreducing bacteria supplement could enhance Cr(VI) bioreduction. Supplement of GSPB led to a declined bacterial growth due to the cracking of the materials. The addition of GSIB and CBA could establish a reduced condition, which favored the growth of Cr(VI)-reducing bacteria. The Cr(VI) bioreduction efficiency could be significantly improved through adsorption and bioreduction mechanisms, and production of Cr(OH)₃ precipitates confirmed the occurrence of Cr(VI) reduction. The main Cr-bioreducing bacteria included Trichococcus, Escherichia-Shigella, and Lactobacillus. Results suggest that the developed GSIB bioremedial system could be applied to cleanup Cr(VI)-polluted groundwater effectively.

Cr(VI) Reduction and Fe(II) Regeneration by Penicillium oxalicum SL2-Enhanced Nanoscale Zero-Valent Iron

Nanoscale zero-valent iron (nZVI) faces significant challenges in Cr(VI) remediation through aggregation and passivation. This study identified a Cr(VI)-resistant filamentous fungus (Penicillium oxalicum SL2) for nZVI activation and elucidated the synergistic mechanism in chromium remediation. P. oxalicum SL2 and nZVI synergistically and effectively removed Cr(VI), mainly by extracellular nonenzymatic reduction (89.1%). P. oxalicum SL2 exhibited marked iron precipitate solubilization and Fe(II) regeneration capabilities. The existence of the Fe(II)-Cr(V)-oxalate complex (HCrFeC₄O₉) indicated that in addition to directly reducing Cr(VI), iron ions generated by nZVI stimulated Cr(VI) reduction by organic acids secreted by P. oxalicum SL2. RNA sequencing and bioinformatics analysis revealed that P. oxalicum SL2 inhibited phosphate transport channels to suppress Cr(VI) transport, facilitated iron and siderophore transport to store Fe, activated the glyoxylate cycle to survive harsh environments, and enhanced organic acid and riboflavin secretion to reduce Cr(VI). Cr(VI) exposure also stimulated the antioxidative system, promoting catalase activity and maintaining the intracellular thiol/disulfide balance. Cr(VI)/Fe(III) reductases played crucial roles in the intracellular reduction of chromium and iron, while nZVI decreased cellular oxidative stress and alleviated Cr(VI) toxicity to P. oxalicum SL2. Overall, the P. oxalicum SL2-nZVI synergistic system is a promising approach for regenerating Fe(II) while reducing Cr(VI).

Nitrate_dependent suberization regulates cadmium uptake and accumulation in maize

In this study, effect of nitrate-dependent suberization in maize root on cadmium (Cd) uptake and accumulation was investigated. Suberization in maize roots was significantly lower in plants grown with a high nitrate supply compared with low nitrate. This decrease was seen in the total amount of suberin, in which the aliphatic suberin amount was significantly decreased, whereas no difference in aromatic suberin content between different N-treatments. RNA-sequencing showed that suberin biosynthesis genes were upregulated in low nitrate treatment, which correlated well with the increased suberin content. Bioimaging and xylem sap analysis showed that reduced exodermal and endodermal suberization in roots of plants grown under high nitrate promoted radial Cd transport along the crown root. The enhanced suberization in crown roots of plants grown in low nitrate restricted the radial transport of Cd from epidermis to cortex via decreased accessibility to Cd related transporters at the plasmalemma. Also, under low nitrate supply, the Cd transport gene ZmNramp5 was upregulated in the crown root, which may enhance Cd uptake by root tip where exodermis and endodermis were not fully suberized. These results suggest that high nitrate supply enhances Cd uptake and radial transport in maize roots by reducing exodermal and endodermal suberization.

Selenium-mediated Cr(VI) reduction and SeNPs synthesis accelerated Bacillus cereus SES to remediate Cr contamination

Microbial biotransformation of Cr(VI) is a sustainable approach to reduce Cr(VI) toxicity and remediate Cr(VI) contamination. In this study, Bacillus cereus SES with the capability of reducing both Cr(VI) and Se(IV) was isolated, and the effect of Se supplementation on Cr(VI) reduction by Bacillus cereus SES was investigated. Se(IV) addition enabled 2.6-fold faster Cr(VI) reduction, while B. cereus SES reduced 96.96% Se(IV) and produced more selenium nanoparticles (SeNPs) in the presence of Cr(VI). Co-reduction products of B. cereus SES on Cr(VI) and Se(IV) were SeNPs adsorbed with Cr(III). The relevant mechanisms were further revealed by proteomics. Se(IV) supplementation mediated the synthesis of Cr(VI) reductants and stress-resistant substances, thus enhancing Cr(VI) resistance and promoting Cr(VI) reduction. Meanwhile, high Se(IV) reduction rate was associated with Cr(VI)-induced electron transport processes, and Cr(VI) mediated the up-regulation of flagellar assembly, protein export and ABC transporters pathways to synthesis and export more SeNPs. Furthermore, Se combined with B. cereus SES had the potential to reduce the toxicity of Cr(VI) via reducing the bioavailability of Cr and improving the bioavailability of Se in soil. Results suggested that Se could be an efficient strategy to enhance the remediation of B. cereus SES on Cr contamination.

Bacterial metal(loid) resistance genes (MRGs) and their variation and application in environment: A review

Toxic metal(loid)s are widespread and permanent in the biosphere, and bacteria have evolved a wide variety of metal(loid) resistance genes (MRGs) to resist the stress of excess metal(loid)s. Via active efflux, permeability barriers, extracellular/intracellular sequestration, enzymatic detoxification and reduction in metal(loid)s sensitivity of cellular targets, the key components of bacterial cells are protected from toxic metal(loid)s to maintain their normal physiological functions. Exploiting bacterial metal(loid) resistance mechanisms, MRGs have been applied in many environmental fields. Based on the specific binding ability of MRGs-encoded regulators to metal(loid)s, MRGs-dependent biosensors for monitoring environmental metal(loid)s are developed. MRGs-related biotechnologies have been applied to environmental remediation of metal(loid)s by using the metal(loid) tolerance, biotransformation, and biopassivation abilities of MRGs-carrying microorganisms. In this work, we review the historical evolution, resistance mechanisms, environmental variation, and environmental applications of bacterial MRGs. The potential hazards, unresolved problems, and future research directions are also discussed.

Selenium and Bacillus proteolyticus SES synergistically enhanced ryegrass to remediate Cu-Cd-Cr contaminated soil

Heavy metal compound contaminated soil is an ecological threat, and soil containing copper (Cu), cadmium (Cd) and chromium (Cr) simultaneously is widely distributed. The application of phytoremediation in heavy metal combined contamination is still limited. In this study, to explore whether and how exogenous selenium (Se) and Bacillus proteolyticus SES enhance the remediation of combined Cu-Cd-Cr contaminated soil by ryegrass, pot experiments were carried out. Se alone or in combination with B. proteolyticus SES treatment increased the removal rates of heavy metals in the rhizosphere soil by 17.38%-157.25% relative to the control, while Se + B. proteolyticus SES treatment played a greater role in improving the heavy metals tolerance of ryegrass and increasing the activity of soil acid phosphatase. Moreover, Se and B. proteolyticus SES favored the preferential recruitment of specific taxa with the capacity of plant growth promotion and heavy metals resistance to the rhizosphere. The rhizosphere soil of Se treatment was specifically enriched with Lysobacter, Rhodanobacter, Micrococcales, Paenarthrobacter, and Adhaeribacter, while from class Bacilli to genus Bacillus enriched extensively and specifically in the rhizosphere of B. proteolyticus SES + Se treatment. Furthermore, five functional beneficial rhizosphere microbes including: Microbacterium sp., Pseudomonas extremaustralis, Bacillus amyloliquefaciens, Priestia megaterium, and Bacillus subtilis were isolated from the two treatments with the best remediation effect and synthetic communities (SynComs) were constructed. SynComs inoculation experiment further demonstrated the role of specific beneficial microbes in regulating the bioavailability of heavy metals. Results revealed that Se supplementation efficiently facilitated the phytoextraction of combined Cu-Cd-Cr contaminated soil, and B. proteolyticus SES inoculation showed the synergistical enhancement effect in the presence of Se.

A novel N-arachidonoyl-l-alanine-catabolizing strain of Serratia marcescens for the bioremediation of Cd and Cr co-contamination

Cadmium (Cd) and chromium (Cr) are widespread contaminants with a high risk to the environment and humans. Herein we isolated a novel strain of Serratia marcescens, namely strain S27, from soil co-contaminated with Cd and Cr. This strain showed strong resistance to Cd as well as Cr. S27 cells demonstrated Cd adsorption rate of 45.8% and Cr reduction capacity of 84.4% under optimal growth conditions (i.e., 30 °C, 200 rpm, and pH 7.5). Microscopic characterization of S27 cells revealed the importance of the functional groups C-O-C, C-H-O, C-C, C-H, and -OH, and also indicated that Cr reduction occurred on bacterial cell membrane. Cd(II) and Cr(VI) bioaccumulation on S27 cell surface was mainly in the form of Cd(OH)₂ and Cr₂O₃, respectively. Further, metabolomic analyses revealed that N-arachidonoyl-l-alanine was the key metabolite that promoted Cd and Cr complexation by S27; it primarily promotes γ-linolenic acid (GLA) metabolism, producing siderophores and coordinating with organic acids to enhance metal bioavailability. To summarize, our results suggest that S27 is promising for the bioremediation of environments contaminated with Cd and Cr in tropical regions.

The relationships between heavy metals and bacterial communities in a coal gangue site

Coal is the main source of energy for China's economic development, but coal gangue dumps are a major source of heavy metal pollution. Bacterial communities have a major effect on the bioremediation of heavy metals in coal gangue dumps. The effects of different concentrations of heavy metals on the composition of bacterial communities in coal gangue sites remain unclear. Soil bacterial communities from four gangue sites that vary in natural heavy metal concentrations were investigated using high-throughput sequencing in this study. Correlations among bacterial communities, heavy metal concentrations, physicochemical properties of the soil, and the composition of dissolved organic matter of soil in coal gangue dumps were also analyzed. Our results indicated that Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota were the bacterial taxa most resistant to heavy metal stress at gangue sites. Heavy metal contamination may be the main cause of changes in bacterial communities. Heavy metal pollution can foster mutually beneficial symbioses between microbial species. Microbial-derived organic matter was the main source of soil organic matter in unvegetated mining areas, and this could affect the toxicity and transport of heavy metals in soil. Polar functional groups such as hydroxyl and ester groups (A_226-400) play an important role in the reaction of cadmium (Cd) and lead (Pb), and organic matter with low molecular weight (S_R) tends to bind more to mercury (Hg). In addition to heavy metals, the content of nitrogen (N), phosphorus (P), and total organic carbon (TOC) also affected the composition of the bacterial communities; TOC had the strongest effect, followed by N, SOM, and P. Our findings have implications for the microbial remediation of heavy metal-contaminated soils in coal gangue sites and sustainable development.

Transcriptomic Analysis of Differentially Expressed Genes in Arabidopsis thaliana Overexpressing BnMYB2 from Boehmeria nivea under Cadmium Stress

Boehmeria nivea (ramie) is an important fiber crop with strong tolerance to cadmium (Cd). In our previous study, a novel MYB transcription factor gene from ramie, BnMYB2, was found to positively regulate Cd tolerance and accumulation in the transgenic Arabidopsis thaliana lines. Herein, transcriptome sequencing was performed to identify the differentially expressed genes involved in cadmium response between the wild-type (WT) and BnMYB2 overexpressed lines; 1598 differentially expressed genes (DEGs) were detected in the shoot. GO and KEGG analysis indicated that the majority of DEGs belonged to the categories of transcription factors, plant hormone signal transduction and nitrogen metabolism. The expression level of the Ib subgroup bHLH genes (AtbHLH38, AtbHLH39, AtbHLH100 and AtbHLH101) and nitrogen assimilation-related genes (AtNIA1, AtNIA2, AtNIR1 and AtASN2) were significantly higher than that of WT, accompanied with the positive changes in iron (Fe) and total nitrogen content in the shoot of BnMYB2 overexpression lines. Several DEGs belonging to the bZIP transcription factor family or SAUR family were also found up-regulated in the transgenic plants. These results provide important clues for elucidating how the molecular mechanisms of BnMYB2 regulate plant response to Cd stress.

A contrast of Pb(II), Cd(II), and Cu(II) toxicities to Aspergillus niger through biochemical, morphological, and genetic investigations

The toxicity of metals to microorganisms is highly correlated with the type of metal used. However, the differences in the resistance mechanisms of filamentous fungi to multiple metals remain unclear. In this study, we investigated the responses of Aspergillus niger to three toxic metals, i.e., Pb²⁺, Cd²⁺, and Cu²⁺. Fungal growth and metabolism indices showed that A. niger had a higher tolerance to Pb²⁺ (>1000 mg L^-1) than to Cu²⁺ (300 mg L^-1) and Cd²⁺ (50 mg L^-1). An appropriate Pb²⁺ concentration (<500 mg L^-1) stimulated fungal growth and metabolic activity, whereas Cd²⁺ and Cu²⁺ stress showed continuously negative influences on fungal physiological parameters, such as biomass and secretion of oxalic acid. A. niger responded to Pb stress by constructing a new border layer around its cell wall. This pathway was also confirmed using RNA-seq analysis, i.e., the gene encoding cell wall α-1,3-glucan synthase was upregulated. This upregulation subsequently promoted the production of polysaccharides, which are the main components that support fungal cell walls. In contrast, the expression of genes encoding both AAA family ATPase and efflux pump antibiotic resistance proteins for Cd²⁺ and Cu²⁺ was significantly downregulated. Therefore, these findings elucidated the relatively complete fungal responses to different metal stresses.