Exploring the Cr(VI) removal mechanism of Sporosarcina saromensis M52 from a genomic perspective

Molecular and geochemical basis of microbially induced carbonate precipitation for treating acid mine drainage: The case of a novel Sporosarcina genomospecies from mine tailings

Microbially induced carbonate precipitation (MICP) immobilizes toxic metals and reduces their bioavailability in aqueous systems. However, its application in the treatment of acid mine drainage (AMD) is poorly understood. In this study, the genomes of Sporosarcina sp. UB5 and UB10 were sequenced. Urease, carbonic anhydrases, and metal resistance genes were identified and enzymatic assays were performed for their validation. The geochemical mechanism of precipitation in AMD was elucidated through geo-mineralogical analysis. Sporosarcina sp. UB5 was shown to be a new genomospecies, with an average nucleotide identity < 95 % (ANI) and DNA-DNA hybridization < 70 % (DDH) whereas UB10 is close to S. pasteurii. UB5 contained two urease operons, whereas only one was identified in UB10. The ureolytic activities of UB5 and UB10 were 122.67 ± 15.74 and 131.70 ± 14.35 mM NH4+ min-1, respectively. Both strains feature several carbonic anhydrases of the α, β, or γ families, which catalyzed the precipitation of CaCO3. Only Sporosarcina sp. UB5 was able to immobilize metals and neutralize AMD. Geo-mineralogical analyses revealed that UB5 directly immobilized Fe (1-23 %), Mn (0.65-1.33 %) and Zn (0.8-3 %) in AMD via MICP and indirectly through adsorption to calcite and binding to bacterial cell walls. The MICP-treated AMD exhibited high removal rates (>67 %) for Ag, Al, As, Ca, Cd, Co, Cu, Fe, Mn, Pb, and Zn, and a removal rate of 15 % for Mg. This study provides new insights into the MICP process and its applications to AMD treatment using autochthonous strains.

Cr(VI) removal performance from wastewater by microflora isolated from tannery effluents in a semi-arid environment: a SEM, EDX, FTIR and zeta potential study

Hexavalent chromium removal from the environment remains a crucial worldwide challenge. To address this issue, microbiological approaches are amongst the straightforward strategies that rely mainly on the bacteria's and fungi's survival mechanisms upon exposure to toxic metals, such as reduction, efflux system, uptake, and biosorption. In this work, scanning electron microscopy, energy-dispersive X-ray spectrophotometry, Fourier transform infrared spectroscopy, and zeta potential measurements were used to investigate the ability of chromium adsorption by Bacillus licheniformis, Bacillus megaterium, Byssochlamys sp., and Candida maltosa strains isolated from tannery wastewater. Scanning electron microscopy combined with energy dispersive X-ray spectroscopy revealed alterations in the cells treated with hexavalent chromium. When exposed to 50 mg/L Cr6+, Bacillus licheniformis and Candida maltosa cells become rough, extracellular secretions are reduced in Bacillus megaterium, and Byssochlamys sp. cells are tightly bound and exhibit the greatest Cr weight percentage. In-depth analysis of Fourier transform infrared spectra of control and Cr-treated cells unveiled Cr-microbial interactions involving proteins, lipids, amino acids, and carbohydrates. These findings were supported by zeta potential measurements highlighting significant variations in charge after treatment with Cr(VI) with an adsorption limit of 100 mg/L Cr6+ for all the strains. Byssochlamys sp. showed the best performance in Cr adsorption, making it the most promising candidate for treating Cr-laden wastewater.

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.

Exploration of risk analysis and elimination methods for a Cr(VI)-removal recombinant strain through a biosafety assessment in mice

Though recombinant strains are increasingly recognized for their potential in heavy metal remediation, few studies have evaluated their safety. Moreover, biosafety assessments of fecal-oral pathway exposure at country as well as global level have seldom analyzed the health risks of exposure to microorganisms from a microscopic perspective. The present study aimed to predict the long-term toxic effects of recombinant strains by conducting a subacute toxicity test on the chromium-removal recombinant strain 3458 and analyzing the gut microbiome. The available disinfection methods were also evaluated. The results showed that strain 3458 induced liver damage and affected renal function and lipid metabolism at 1.0 × 1011 CFU/mL, which may be induced by its carrier strain, pET-28a. Strain 3458 poses the risk of increasing the number of pathogenic bacteria under prolonged exposure. When 500 mg L-1 chlorine-containing disinfectant or 250 mg L-1 chlorine dioxide disinfectant was added for 30 min, the sterilization rate exceeded 99.9 %. These findings suggest that existing wastewater disinfection methods can effectively sterilize strain 3458, ensuring its application value. The present study can serve a reference for the biosafety evaluation of the recombinant strain through exposure to the digestive tract and its feasibility for application in environmental pollution remediation.

Docking assisted mechanistic elucidation of bio conversion of hexavalent chromium by Serratia marcescens AJRR-22 that is effective yet long term sustainable in bio-geosphere

Environmental accumulation of hexavalent chromium [Cr(VI)] in the food chain can induce detrimental effects on plants and animals, which calls for effective remediation strategies using biological entities. The bacterium isolated from an iron mine in Odisha, India, is identified asSerratia marcescensAJRR-22. This multi-metal tolerant strain is capable of bio-converting up to 350 mg/L Cr(VI) within 72 h of incubation. Observable electron dense precipitates in transmission electron microscopic images, data patterns in fluorescence microscopy and flow cytometry clearly reveal the chromate reduction ability of the strain. The molecular study is depicted by X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopic analyses. Furthermore, a simulation study to estimate the interactions of chromium bound flavin reductasewith predicted docked complexes suggests significant negative Gibbs free energy and a low inhibition constant (Ki), signifying strong spontaneous binding of Cr(VI) to the enzyme, which makes the strain an efficient candidate for chromium bioremediation.

Investigation on Cr(VI)-bioreduction mechanism and reduction products by a novel Microbacterium sp. strain NEAU-W11

Cr(VI) widely exists in the environment and has highly toxic, carcinogenic and mutagenic effects on all organisms. Physical/chemical methods to remove chromium pollution are economically expensive and have disadvantages like high reagent consumption, energy requirements and so on, while bioremediation is an eco-friendly, simple and cost-effective way. In this study, a novel Cr(VI)-reducing strain, Microbacterium sp. NEAU-W11, was reported, and its reduction mechanism was investigated. Microbacterium sp. NEAU-W11 could effectively degrade Cr(VI) under the conditions of pH 7-10, 15-35 °C, and the coexistence of metal pollutants such as Pb and Ni, etc. In addition, both Fe3+ and Cu2+ could improve the reducing ability of strain NEAU-W11, and glucose and lactose as electron donors also had promoting effect. Heat treatment of resting cells confirmed that chromium removal was not biological sorption but biological reduction. The active reductase of strain NEAU-W11 to chromium(VI) mainly existed in the cell cytoplasm, which is the first report in the genus Microbacterium. Micro-characterization of strain NEAU-W11 and the reduction products identified the reduction products as Cr(III)-ligand complexes bound to extracellular polymeric substances (EPS). Collectively, this study systematically investigated the degradation mechanism of Microbacterium sp. NEAU-W11 and the distribution of degradation product Cr(III), providing a new reduction mechanism for the genus Microbacterium, providing a new perspective for a comprehensive understanding of the degradation and transport of chromium by bacteria, and providing theoretical reference for the migration of metal ions in environmental governance.

Biosorption of U(VI) and mechanisms by live and dead cells of Sphingopyxis sp. YF1

Heavy metal pollution seriously threatens the environment and human health. The biosorption of heavy metals has attracted worldwide attention due to its cost-effectiveness and environmental friendliness. It is significant to develop biosorbents with excellent adsorption performance. Sphingopyxis is widely used in the removal of various organic pollutants, but its potential application in heavy metal adsorption has been largely overlooked. This study investigates the biosorption of U(VI) onto live and dead cells of a Sphingopyxis strain YF1. The effects of pH, contact time and initial ion concentration on U(VI) adsorption investigated, and kinetic and isothermal models were used to fit the adsorption results. The results show that under pH 3-6, the adsorption of U(VI) by YF1 live cells increased with the increase of the pH. Both the pseudo-first order and pseudo-second order models can satisfactorily interpret the adsorption by live and dead cells. Three isothermal adsorption models (Langmuir, Freundlich, and Sips) were used to fit the adsorption process. The adsorption of uranium by live and dead cells was best fitted by the Sips model. The maximal adsorption capacities of U(VI) by live and dead cells were 140.7 mg g-1 and 205.7 mg g-1, respectively. The mechanisms of U(VI) adsorption by Sphingopyxis sp. YF1 were revealed. Scanning electron microscopy and energy dispersive spectroscopy (SEM-EDS) show that U(VI) was deposited on the surface of the bacterial cells. Fourier-transform infrared spectroscopy (FTIR) shows that amine, hydroxyl, alkyl, amide I, amide II, phosphate, carboxylates and carboxylic acids were the major functional groups that are involved in U(VI) adsorption by live and dead cells. X-ray photoelectron spectroscopy (XPS) suggests that the main functional groups of live cells involved in adsorption were O = C-O, C-OH/C-O-C and N-C = O. This study indicates Sphingopyxis sp. YF1 is a high-efficiency U(VI)-adsorbing strain, promising to remove U(VI) from aquatic environment.

Chromium Toxicity in Plants: Signaling, Mitigation, and Future Perspectives

Plants are very often confronted by different heavy metal (HM) stressors that adversely impair their growth and productivity. Among HMs, chromium (Cr) is one of the most prevalent toxic trace metals found in agricultural soils because of anthropogenic activities, lack of efficient treatment, and unregulated disposal. It has a huge detrimental impact on the physiological, biochemical, and molecular traits of crops, in addition to being carcinogenic to humans. In soil, Cr exists in different forms, including Cr (III) "trivalent" and Cr (VI) "hexavalent", but the most pervasive and severely hazardous form to the biota is Cr (VI). Despite extensive research on the effects of Cr stress, the exact molecular mechanisms of Cr sensing, uptake, translocation, phytotoxicity, transcript processing, translation, post-translational protein modifications, as well as plant defensive responses are still largely unknown. Even though plants lack a Cr transporter system, it is efficiently accumulated and transported by other essential ion transporters, hence posing a serious challenge to the development of Cr-tolerant cultivars. In this review, we discuss Cr toxicity in plants, signaling perception, and transduction. Further, we highlight various mitigation processes for Cr toxicity in plants, such as microbial, chemical, and nano-based priming. We also discuss the biotechnological advancements in mitigating Cr toxicity in plants using plant and microbiome engineering approaches. Additionally, we also highlight the role of molecular breeding in mitigating Cr toxicity in sustainable agriculture. Finally, some conclusions are drawn along with potential directions for future research in order to better comprehend Cr signaling pathways and its mitigation in sustainable agriculture.

Characterization of the simultaneous degradation of pyrene and removal of Cr(VI) by a bacteria consortium YH

Microorganisms that can simultaneously remediate organic pollutants and heavy metal contamination are great significance in bioremediation. Nevertheless, reports of such microorganisms are still scarce. Here, Pseudomonas sp. YH-1 and Rhodococcus sp. YH-3 were isolated and identified, and they showed greater tolerance to hexavalent (VI) (750 and 800 mg·L^-1). The constructed bacteria consortium YH (YH-1:YH-3 = 1:1) could simultaneously degrade 41.69% of pyrene (50 mg·L^-1) and remove 76.67% of Cr(VI) (30 mg·L^-1) within 5 days. The potential mechanism of Cr(VI) tolerance of YH was further explored by genomic and microscopic analysis. The results showed that YH responded to Cr(VI) stress mainly through efflux of Cr(VI) by chrA and copZ, chromate reduction, DNA-repaired proteases reduces ROS damage, and biosorption by carboxyl, hydroxyl, amino functional groups. Strains YH-1 and YH-3 also contained a variety of genes associated with resistance to other heavy metals, such as cadmium (czcBD), mercury (merAPTR), manganese (mntABC) and copper (copAC, cusABRF and pcoBD). Based on GC-MS and genomic analysis, pyrene was degraded via salicylic acid and phthalic acid pathways. Moreover, a great number of genes related to aromatic hydrocarbon catabolism were identified in the genomes of YH-1 and YH-3. These results confirmed the potential application of the bacteria consortium YH in the bioremediation of water and soil co-contaminated with PAHs-heavy metals.

Killing Two Birds with One Stone: Biomineralized Bacteria Tolerate Adverse Environments and Absorb Hexavalent Chromium

Heavy metal ions in contaminated water, such as hexavalent chromium, are harmful to humans. Bacterial biosorption is an ideal method for the treatment of hexavalent chromium. However, hexavalent chromium in solution causes bacteria to produce reactive oxygen species, which leads to bacterial death and affects biosorption. We developed a microfluidics-based biomimetic mineralization method to encapsulate bacteria (e.g., Escherichia coli and Bacillus subtilis) with zeolitic imidazolate framework-8 (ZIF-8), thus allowing the bacteria to form a continuous and homogeneous shell. The artificial shells endowed bacteria with the ability to tolerate harsh environments, which was significant during the treatment of contaminated water. The adsorption of hexavalent chromium was a two-step process: first the fast physical adsorption of ZIF-8 and biosorption by bacteria (up to 30-50% adsorption in 1 day), followed by secondary biosorption after decomposition of the system. The maximum adsorption of hexavalent chromium by the encapsulated bacteria reached 90%. The microfluidic device developed in this study provides a simple method to encapsulate bacteria mildly and enable cell survival in extreme environments, offering the possibility of future microbial applications in environmental and other fields.

Sustainable and efficient technologies for removal and recovery of toxic and valuable metals from wastewater: Recent progress, challenges, and future perspectives

Due to their numerous effects on human health and the natural environment, water contamination with heavy metals and metalloids, caused by their extensive use in various technologies and industrial applications, continues to be a huge ecological issue that needs to be urgently tackled. Additionally, within the circular economy management framework, the recovery and recycling of metals-based waste as high value-added products (VAPs) is of great interest, owing to their high cost and the continuous depletion of their reserves and natural sources. This paper reviews the state-of-the-art technologies developed for the removal and recovery of metal pollutants from wastewater by providing an in-depth understanding of their remediation mechanisms, while analyzing and critically discussing the recent key advances regarding these treatment methods, their practical implementation and integration, as well as evaluating their advantages and remaining limitations. Herein, various treatment techniques are covered, including adsorption, reduction/oxidation, ion exchange, membrane separation technologies, solvents extraction, chemical precipitation/co-precipitation, coagulation-flocculation, flotation, and bioremediation. A particular emphasis is placed on full recovery of the captured metal pollutants in various reusable forms as metal-based VAPs, mainly as solid precipitates, which is a powerful tool that offers substantial enhancement of the remediation processes' sustainability and cost-effectiveness. At the end, we have identified some prospective research directions for future work on this topic, while presenting some recommendations that can promote sustainability and economic feasibility of the existing treatment technologies.

Cr(VI) Removal by Recombinant Escherichia coli Harboring the Main Functional Genes of Sporosarcina saromensis M52

Hexavalent chromium [Cr(VI)], a recognized heavy metal pollutant, has attracted much attention because of its negative impact on the ecological environment and human health. A chromium-resistant strain, Sporosarcina saromensis M52, was discovered, and the functional genes orf2987, orf3015, orf0415, and orf3237 were identified in the strain by genomics. With the advancement of DNA recombination and gene-splicing technology, genetic engineering technology was used to produce recombinant strains 2987, 3015, 0415, and 3237. The study revealed Cr(VI) tolerance in the order of M52 ≈ 2987 > 3015 ≈ 0415 > 3237 and reduction abilities in the order of M52 ≈ 2987 > 3015 > 0415 ≈ 3237. SEM-EDS, XRD, FT-IR and XPS were utilized to examine the surface structure of the recombinant strains and analyze the surface components and main functional groups. A comprehensive review of the recombinant strains’ capacity to tolerate and reduce Cr(VI) revealed that orf2987 and orf0415 were the main functional genes in Sporosarcina saromensis M52, which may play a key role in removing Cr(VI) and protecting the strain, respectively. The optimum pH for recombinant strains 2987 and 0415 was 7.5–8.5, and the optimum temperature was 37°C. Cu²⁺ had the greatest promotional effect when Cr(VI) was removed by them, while SDS had an inhibitory effect. This research provided the foundation for further study into the mechanism of Cr(VI) reduction in Sporosarcina saromensis M52, as well as a theoretical basis for the development of effective engineered strains to repair Cr(VI) contamination.