Transcriptome expression analysis of the gene regulation mechanism of bacterial mineralization tolerance to high concentrations of Cd2

Integrated analyses of characterization and transcriptome reveal the adaptive response mechanism of Bacillus cereus FCHN 7-1 in cadmium adsorption

Cadmium (Cd2+) pollution is a pressing environmental issue that seriously threatens human health. In recent years, microbial extracellular polymeric substances (EPS) have been developed as an eco-friendly and effective solution for heavy metal bioremediation. In this study, Bacillus cereus FCHN 7-1, which was isolated from highly Cd-polluted soils in Hunan Province, China, has strong resistance to Cd2+ and excellent Cd2+ adsorptive capacity. Microscopic analyses showed that B. cereus FCHN 7-1 mainly adsorbed Cd2+ on the surface of EPS via the formation of granule deposits. The Freundlich isotherm was proven to better describe the sorption data with a higher R2 of 0.958, and the pseudo-second-order model fitted the sorption kinetic processes well, with an adsorption capacity of 66.128 mg/g. The variations in zeta potential indicated the occurrence of electrostatic attraction during the Cd2+ adsorption process. XRD, FTIR, 3D-EEM, and XPS analyses revealed that the functional groups of the EPS involved in Cd2+ adsorption were mainly CO, N-H, and COO- groups of proteins in the EPS, which greatly facilitated the adsorption of Cd2+ by forming EPS-metal complexes. Transcriptome sequencing analysis showed that an adaptive response to Cd2+ increased the expression of genes involved in amino acid biosynthesis and metabolism (asnB, alsS, ablA), and ABC transporter pathways (brnQ, abc-f, U2I57_RS23145), which promoted the synthesis of proteins and secretion of abundant EPS. This study provides new insights into the biosorption of Cd2+ for future applications.

A cooperation mechanism between Bacillus thuringiensis and Citrobacter freundii that enhances cadmium biomineralization

The viability and tolerance of individual ureolytic bacteria are a bottleneck in the remediation of cadmium (Cd) by microbially induced carbonate precipitation (MICP) technology. To solve this issue, strains of Bacillus thuringiensis (B. thuringiensis, BT) and Citrobacter freundii (C. freundii, CF) were isolated from soil and studied for their growth characteristics and metabolism. A cooperation system (BT+CF, 1:1, v/v) was constructed and exposed to 20 mg/kg Cd2 + for 7 days, compared with individual bacteria. The synergistic mechanism of strains that immobilize Cd2+ was explored using characterization techniques. Results showed that the main metabolic pathways leading to urea up-regulation were pyrimidine metabolism, urea cycle, and lysine degradation by metabolomic analysis. The cooperation system can effectively remove Cd2+ with an efficiency of 97.68 %, which is higher than BT (66.66 %) and CF (88.61 %). The SEM-EDS, TEM, and XPS results revealed that the calcium carbonate polycrystals (vaterite and calcite) were formed during the MICP process, and the XRD and FTIR confirmed that the BT+CF produces more stable carbonate crystals. The BT+CF cooperation system was efficient at immobilizing Cd2+ by synergizing the molecular mechanisms of ureolytic bacteria. These results provide a novel perspective for the application of MICP.

Unravelling the mechanism of arsenic resistance and bioremediation in Stenotrophomonas maltophilia: A molecular approach

The mechanism of arsenic resistance in bacteria is under studied and still lacks a clear understanding despite of wide research work. The advanced technologies can help in analysing the arsenic bioremediating bacteria at a molecular level. With this line of idea, highly efficient arsenic bioremediating S. maltophilia was subjected to extensive analysis to understand the mechanism of arsenic resistance and bioremediation. The cell surface analysis revealed that S. maltophilia induces only slight changes in cell surface in the presence of arsenic. Whereas, TEM analysis has indicated the bioaccumulation of arsenic in S. maltophilia. Also, arsenic was found to generate ROS in a concentration dependant manner, and in response, S. maltophilia activated SOD, catalase, thioredoxin reductase etc. to manage oxidative stress which is very much crucial in managing arsenic toxicity. S. maltophilia was found to possess genes such as arsC, aoxB, aoxC and aioA. These genes are involved in arsenic reduction and oxidation. Transcriptomics and proteomics analysis have shown that S. maltophilia detoxifies arsenic by upregulating ars operon, arsH, BetB etc. which are responsible for arsenic reduction, efflux methylation, oxidation etc. A detailed molecular mechanism of arsenic bioremediation in S. maltophilia was put forth.

Earthworm gut bacteria facilitate cadmium immobilization through the formation of CdS nanoparticles

Gut bacteria of earthworm Amynthas hupeiensis exhibit significant potential for the in-situ remediation of cadmium (Cd)-contaminated soil. However, the mechanisms by which these gut bacteria immobilize and tolerate Cd remain elusive. The composition of the gut bacterial community was characterized by high-throughput sequencing. Cd-tolerant bacteria were isolated from the gut, and their roles in Cd immobilization, as well as their tolerance mechanisms, were explored through chemical characterization and transcriptome analysis. The predominant taxa in the gut bacterial community included unclassified Enterobacteriaceae, Citrobacter, and Bacillus, which were distinctly different from those in the surrounding soil. Notably, the most Cd-tolerant gut bacterium, Citrobacter freundii DS strain, immobilized 63.61% of Cd2+ within 96 h through extracellular biosorption and intracellular bioaccumulation of biosynthetic CdS nanoparticles, and modulation of solution pH and NH4+ concentration. Moreover, the characteristic signals of CdS were also observed in the gut content of A. hupeiensis when the sterilized Cd-contaminated soil was inoculated with C. freundii. The primary pathways involved in the response of C. freundii to Cd stress included the regulation of ABC transporters, bacterial chemotaxis, cell motility, oxidative phosphorylation, and two-component system. In conclusion, C. freundii facilitates Cd immobilization both in vitro and in vivo, thereby enhancing the host earthworm's adaptation to Cd-contaminated soil.

The Cd resistant mechanism of Proteus mirabilis Ch8 through immobilizing and detoxifying

Cadmium (Cd) pollution is a serious global environmental problem, which requires a global concern and practical solutions. Microbial remediation has received widespread attention owing to advantages, such as environmental friendliness and soil amelioration. However, Cd toxicity also severely deteriorates the remediation performance of functional microorganisms. Analyzing the mechanism of bacterial resistance to Cd stress will be beneficial for the application of Cd remediation. In this study, the bacteria strain, up to 1400 mg/L Cd resistance, was employed and identified as Proteus mirabilis Ch8 (Ch8) through whole genome sequence analyses. The results indicated that the multiple pathways of immobilizing and detoxifying Cd maintained the growth of Ch8 under Cd stress, which also possessed high Cd extracellular adsorption. Firstly, the changes in surface morphology and functional groups of Ch8 cells were observed under different Cd conditions through SEM-EDS and FTIR analyses. Under 100 mg/L Cd, Ch8 cells exhibited aggregation and less flagella; the Cd biosorption of Ch8 was predominately by secreting exopolysaccharides (EPS) and no significant change of functional groups. Under 500 mg/L Cd, Ch8 were present irregular polymers on the cell surface, some cells with wrapping around; the Cd biosorption capacity exhibited outstanding effects (38.80 mg/g), which was mainly immobilizing Cd by secreting and interacting with EPS. Then, Ch8 also significantly enhanced the antioxidant enzyme activity and the antioxidant substance content under different Cd conditions. The activities of SOD and CAT, GSH content of Ch8 under 500 mg/L Cd were significantly increased by 245.47%, 179.52%, and 241.81%, compared to normal condition. Additionally, Ch8 significantly induced the expression of Acr A and Tol C (the resistance-nodulation-division (RND) efflux pump), and some antioxidant genes (SodB, SodC, and Tpx) to reduce Cd damage. In particular, the markedly higher expression levels of SodB under Cd stress. The mechanism of Ch8 lays a foundation for its application in solving soil remediation.

The Cd immobilization mechanisms in paddy soil through ureolysis-based microbial induced carbonate precipitation: Emphasis on the coexisting cations and metatranscriptome analysis

Microbial induced carbonate precipitation (MICP) can immobilize metals and reduce their bioavailability. However, little is known about the immobilization mechanism of Cd in the presence of soil cations and the triggered gene expression and metabolic pathways in paddy soil. Thus, microcosmic experiments were conducted to study the fractionation transformation of Cd and metatranscriptome analysis. Results showed that bioavailable Cd decreased from 0.62 to 0.29 mg/kg after 330 d due to the MICP immobilization. This was ascribed to the increase in carbonate bound, Fe-Mn oxides bound, and residual Cd. The underlying immobilization mechanisms could be attributed to the formation of insoluble Cd-containing precipitates, the complexation and lattice substitution with carbonate and Fe, Mn and Al (hydr)oxides, and the adsorption on functional group on extracellular polymers of cell. During the MICP immobilization process, up-regulated differential expression urease genes were significantly enriched in the paddy soil, corresponding to the arginine biosynthesis, purine metabolism and atrazine degradation. The metabolic pathway of bacterial chemotaxis, flagellum assembly, and peptidoglycan biosynthesis and the expression of cadA gene related to Cd excretion enhanced Cd resistance of soil microbiome. Therefore, this study provided new insights into the immobilization mechanisms of Cd in paddy soils through ureolysis-based MICP process.

Transcriptome analysis reveals how cadmium promotes root development and accumulates in Apocynum venetum, a promising plant for greening cadmium-contaminated soil

Cadmium (Cd) contamination poses a substantial threat the environment, necessitating effective remediation strategies. Phytoremediation emerges as a cost-efficient and eco-friendly approach for reducing Cd levels in the soil. In this study, the suitability of A. venetum for ameliorating Cd-contaminated soils was evaluated. Mild Cd stress promoted seedling and root growth, with the root being identified as the primary tissue for Cd accumulation. The Cd content of roots ranged from 0.35 to 0.55 mg/g under treatment with 10-50 µM CdCl2·2.5 H2O, and the bioaccumulation factor ranged from 28.78 to 84.43. Transcriptome sequencing revealed 20,292 unigenes, and 7507 nonredundant differentially expressed genes (DEGs) were identified across five comparison groups. DEGs belonging to the "MAPK signaling pathway-plant," "monoterpenoid biosynthesis," and "flavonoid biosynthesis pathway" exhibited higher expression levels in roots compared to stems and leaves. In addition, cytokinin-related DEGs, ROS scavenger genes, such as P450, glutathione-S-transferase (GST), and superoxide dismutase (SOD), and the cell wall biosynthesis-related genes, CSLG and D-GRL, were also upregulated in the root tissue, suggesting that Cd promotes root development. Conversely, certain ABC transporter genes, (e.g, NRAMP5), and some vacuolar iron transporters, predominantly expressed in the roots, displayed a strong correlation with Cd content, revealing the mechanism underlying the compartmentalized storage of Cd in the roots. KEGG enrichment analysis of DEGs showed that the pathways associated with the biosynthesis of flavonoids, lignin, and some terpenoids were significantly enriched in the roots under Cd stress, underscoring the pivotal role of these pathways in Cd detoxification. Our study suggests A. venetum as a potential Cd-contaminated phytoremediation plant and provides insights into the molecular-level mechanisms of root development promotion and accumulation mechanism in response to Cd stress.

Potential use of two Serratia strains for cadmium remediation based on microbiologically induced carbonate precipitation and their cadmium resistance

Cadmium (Cd) presence and bioavailability in soils is a serious concern for cocoa producers. Cocoa plants can bioaccumulate Cd that can reach humans through the food chain, thus posing a threat to human health, as Cd is a highly toxic metal. Currently, microbiologically induced carbonate precipitation (MICP) by the ureolytic path has been proposed as an effective technique for Cd remediation. In this work, the Cd remediation potential and Cd resistance of two ureolytic bacteria, Serratia sp. strains 4.1a and 5b, were evaluated. The growth of both Serratia strains was inhibited at 4 mM Cd(II) in the culture medium, which is far higher than the Cd content that can be found in the soils targeted for remediation. Regarding removal efficiency, for an initial concentration of 0.15 mM Cd(II) in liquid medium, the maximum removal percentages for Serratia sp. 4.1.a and 5b were 99.3% and 99.57%, respectively. Their precipitates produced during Cd removal were identified as calcite by X-ray diffraction. Energy dispersive X-ray spectroscopy analysis showed that a portion of Cd was immobilized in this matrix. Finally, the presence of a partial gene from the czc operon, involved in Cd resistance, was observed in Serratia sp. 5b. The expression of this gene was found to be unaffected by the presence of Cd(II), and upregulated in the presence of urea. This work is one of the few to report the use of bacterial strains of the Serratia genus for Cd remediation by MICP, and apparently the first one to report differential expression of a Cd resistance gene due to the presence of urea.

Multiple mechanisms collectively mediate tungsten homeostasis and resistance in Citrobacter sp. Lzp2

Tungsten (W) is an emerging contaminant, and current knowledge on W resistance profiles of microorganisms remains scarce and fragmentary. This study aimed to explore the physiological responses of bacteria under W stress and to resolve genes and metabolic pathways involved in W resistance using a transcriptome expression profiling assay. The results showed that the bacterium Citrobacter sp. Lzp2, screened from W-contaminated soil, could tolerate hundreds of mM W(VI) with a 50% inhibiting concentration of ∼110 mM. To cope with W stress, Citrobacter sp. Lzp2 secreted large amounts of proteins through the type VI secretory system (T6SS) to chelate W oxoanions via carboxylic groups in extracellular polymeric substances (EPS), and could transport cytosolic W outside via the multidrug efflux pumps (mdtABC and acrD). Intracellular W is probably bound by chaperone proteins and metal-binding pterin (tungstopterin) through the sulfur relay system. We propose that tetrathionate respiration is a new metabolic pathway for cellular W detoxification likely producing thio-tungstate. We conclude that multiple mechanisms collectively mediate W homeostasis and resistance in Citrobacter sp. Lzp2. Our results have important implications not only for understanding the intricate regulatory network of W homeostasis in microbes but also for bio-recovery and bioremediation of W in contaminated environments.

Isolation of urease-producing bacteria from cocoa farms soils in Santander, Colombia, for cadmium remediation

Cadmium (Cd) is a toxic heavy metal that causes serious health problems and is present in agriculturally important soils in Colombia, such as the ones used for cocoa farming. Recently, the use of ureolytic bacteria by the Microbiologically Induced Carbonate Precipitation (MICP) activity has been proposed as an alternative to mitigate the availability of Cd in contaminated soils. In this study, 12 urease-positive bacteria able to grow in the presence of Cd(II) were isolated and identified. Three were selected based on urease activity, precipitates formation and growth, with two belonging to the genus Serratia (codes 4.1a and 5b) and one to Acinetobacter (code 6a). These isolates exhibited low urease activity levels (3.09, 1.34 and 0.31 μmol mL-1 h-1, respectively), but could raise the pH to values close to 9.0 and to produce carbonate precipitates. It was shown that the presence of Cd affects the growth of the selected isolates. However, urease activity was not negatively influenced. In addition, the three isolates were observed to efficiently remove Cd from solution. The two Serratia isolates presented maximum removals of 99.70% and 99.62%, with initial 0.05 mM Cd(II) in the culture medium (supplemented with urea and Ca(II)) at 30 °C and 144 h of incubation. For the Acinetobacter isolate, the maximum removal was 91.23% at the same conditions. Thus, this study evidences the potential use of these bacteria for bioremediation treatments in samples contaminated with Cd, and it is one of the few reports that shows the high cadmium removal capacity of bacteria from the genus Serratia.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03495-1.

Remediation of chromium, zinc, arsenic, lead and antimony contaminated acidic mine soil based on Phanerochaete chrysosporium induced phosphate precipitation

Microbial induced phosphate precipitation (MIPP) is an advanced bioremediation technology to reduce the mobility and bioavailability of heavy metals (HMs), but the high level of HMs would inhibit the growth of phosphate solubilizing microbes. This study proposed a new combination system for the remediation of multiple HMs contaminated acidic mine soil, which included hydroxyapatite (HAP) and Phanerochaete chrysosporium (P. chrysosporium, PC) that had high phosphate solubilizing ability and HMs tolerance. Experimental data suggested that in HAP/PC treatment after 35 d of remediation, labile Cr, Zn and As could be transformed into the stable fraction with the maximum immobilization efficiencies increased by 53.01 %, 22.43 %, and 35.65 %, respectively. The secretion of organic acids by P. chrysosporium was proved to promote the dissolution of HAP. Besides, the pH value, available phosphorus (AP) and organic matter (OM) increased in treated soil than in original soil, which also indicated the related dissolution-precipitation mechanism of HMs immobilization. Additionally, characterization results revealed that adsorption and ion exchange also played an important role in the remediation process. The overall results suggested that applying P. chrysosporium coupled with HAP could be considered as an efficient strategy for the remediation of multiple HMs contaminated mine soil and laid a foundation for the future exploration of soil microenvironment response during the remediation process.

Lead oxalates in some Chinese leafy vegetable cultivation: their biomineralization and remediation by oxalate degrading Streptomyces sp

Heavy metal contamination is a global threat with far-reaching effects for both human health and the environment. Biological agents, such as plants and microorganisms, provide uncomplicated and eco-friendly ways of removing toxic metals; thus, they are regarded as successful and alternative tools. In this study, we evaluated the ability of Streptomyces NJ10 (SN10), an oxalotrophic bacterium with outstanding oxalate metabolizing potential, to convert toxic lead oxalate (PbOx) into lead carbonate (PbCO3). SN10 was therefore used to determine the reduction of toxicity of Chinese leafy vegetables grown in the presence of PbOx in the soil. When compared to control, SN10 treated pots showed improved plant growth characters, i.e. shoot length (5.85 ± 0.56 cm), average leaf area (5.5 ± 0.44 cm2) and root length (7.2 ± 0.45 cm), as established by the plant growth attributes and the results obtained are statistically significant (at P ≤ 0.05) (for a period of 30 days). Furthermore, X-ray diffraction (XRD) and Scanning Electronic Microscopy-Energy-Dispersive X-ray Spectroscopy (SEM-EDS) studies revealed that PbOx was successfully transformed into a less toxic, water-insoluble precipitate of Pb-bearing carbonate, Phosgenite. The results provided a new idea for the biotransformation and toxicity mitigation of Pb contamination in soil.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03353-6.

Construction of CdS-Tetrahymena thermophila hybrid system by efficient cadmium adsorption for dye removal under light irradiation

The water pollution caused by heavy metals and dyes emitted by industries has become a worldwide problem. These pollutants are difficult to be biodegraded. Even at low concentrations, they are toxic and at last threaten human health. Herein, while using Tetrahymena thermophila, a single-celled ciliate protozoa, to enrich and remove the heavy metal Cd²⁺ from water, CdS nanoparticle-Tetrahymena thermophila hybrid system (CdS-T. thermophila) for dye pollution remediation under light irradiation was developed. The conditions of Cd²⁺ enrichment and removal by T. thermophila, construction of efficient CdS-T. thermophila, and decolorization of Congo red using CdS-T. thermophila were investigated. In the presence of cysteine ethyl ester, the removal rate of Cd²⁺ by T. thermophila was 94% at low Cd²⁺ concentration of 1 mg L^-1. The adsorption capacity of T. thermophila to Cd²⁺ reached 43 mg g^-1 at Cd²⁺ concentration of 80 mg L^-1. Using 0.1 g L^-1 constructed CdS-T. thermophila, the decolorization rate of 50 mg L^-1 Congo red solution reached 95% in 60 min under light irradiation. This study provides a new insight to effective removing Cd²⁺ from water by T. thermophila to construct the CdS-T. thermophila and using it to remediate dye pollution in the environment.