Simple whole-cell biodetection and bioremediation of heavy metals based on an engineered lead-specific operon

Molecular and eco-physiological responses of soil-borne lead (Pb2+)-resistant bacteria for bioremediation and plant growth promotion under lead stress

Lead (Pb) is the 2nd known portentous hazardous substance after arsenic (As). Being highly noxious, widespread, non-biodegradable, prolonged environmental presence, and increasing accumulation, particularly in arable land, Pb pollution has become a serious global health concern requiring urgent remediation. Soil-borne, indigenous microbes from Pb-polluted sites have evolved diverse resistance strategies, involving biosorption, bioprecipitation, biomineralization, biotransformation, and efflux mechanisms, under continuous exposure to Pb in human-impacted surroundings. These strategies employ a wide range of functional bioligands to capture Pb and render it inaccessible for leaching. Recent breakthroughs in molecular technology and understanding of lead resistance mechanisms offer the potential for utilizing microbes as biological tools in environmental risk assessment. Leveraging the specific affinity and sensitivity of bacterial regulators to Pb2+ ions, numerous lead biosensors have been designed and deployed worldwide to monitor Pb bioavailability in contaminated sites, even at trace levels. Besides, the ongoing degradation of croplands due to Pb pollution poses a significant challenge to meet the escalating global food demands. The accumulation of Pb in plant tissues jeopardizes both food safety and security while severely impacting plant growth. Exploring Pb-resistant plant growth-promoting rhizobacteria (PGPR) presents a promising sustainable approach to agricultural practices. The active associations of PGPR with host plants have shown enhancements in plant biomass and stress alleviation under Pb influence. They thus serve a dual purpose for plants grown in Pb-contaminated areas. This review aims to offer a comprehensive understanding of the role played by Pb-resistant soil-borne indigenous bacteria in expediting bioremediation and improving the growth of Pb-challenged plants essential for potential field application, thus broadening prospects for future research and development.

Microbial strategies for lead remediation in agricultural soils and wastewater: mechanisms, applications, and future directions

High lead (Pb) levels in agricultural soil and wastewater threaten ecosystems and organism health. Microbial remediation is a cost-effective, efficient, and eco-friendly alternative to traditional physical or chemical methods for Pb remediation. Previous research indicates that micro-organisms employ various strategies to combat Pb pollution, including biosorption, bioprecipitation, biomineralization, and bioaccumulation. This study delves into recent advancements in Pb-remediation techniques utilizing bacteria, fungi, and microalgae, elucidating their detoxification pathways and the factors that influence Pb removal through specific case studies. It investigates how bacteria immobilize Pb by generating nanoparticles that convert dissolved lead (Pb-II) into less harmful forms to mitigate its adverse impacts. Furthermore, the current review explores the molecular-level mechanisms and genetic engineering techniques through which microbes develop resistance to Pb. We outline the challenges and potential avenues for research in microbial remediation of Pb-polluted habitats, exploring the interplay between Pb and micro-organisms and their potential in Pb removal.

A biocompatible surface display approach in Shewanella promotes current output efficiency

The biology-material hybrid method for chemical-electricity conversion via microbial fuel cells (MFCs) has garnered significant attention in addressing global energy and environmental challenges. However, the efficiency of these systems remains unsatisfactory due to the complex manufacturing process and limited biocompatibility. To overcome these challenges, here, we developed a simple bio-inorganic hybrid system for bioelectricity generation in Shewanella oneidensis (S. oneidensis) MR-1. A biocompatible surface display approach was designed, and silver-binding peptide AgBP2 was expressed on the cell surface. Notably, the engineered Shewanella showed a higher electrochemical sensitivity to Ag+, and a 60 % increase in power density was achieved even at a low concentration of 10 μM Ag+. Further analysis revealed significant upregulations of cell surface negative charge intensity, ATP metabolism, and reducing equivalent (NADH/NAD+) ratio in the engineered S. oneidensis-Ag nanoparticles biohybrid. This work not only provides a novel insight for electrochemical biosensors to detect metal ions, but also offers an alternative biocompatible surface display approach by combining compatible biomaterials with electricity-converting bacteria for advancements in biohybrid MFCs.

Biosynthesis of Indigo Dyes and Their Application in Green Chemical and Visual Biosensing for Heavy Metals

Fermentative production of natural colorants using microbial strains has emerged as a cost-effective and sustainable alternative to chemical synthesis. Visual pigments are used as signal outputs in colorimetric bacterial biosensors, a promising method for monitoring environmental pollutants. In this study, we engineered four self-sufficient indigo-forming enzymes, including HbpAv, bFMO, cFMO, and rFPMO, in a model bacterium E. coli. TrxA-bFMO was chosen for its strong ability to produce indigo under T7 lac and mer promoters' regulation. The choice of bacterial hosts, the supplementation of substrate l-tryptophan, and ventilation were crucial factors affecting indigo production. The indigo reporter validated the biosensors for Hg(II), Pb(II), As(III), and Cd(II). The biosensors reported Hg(II) as low as 14.1 nM, Pb(II) as low as 1.5 nM, and As(III) as low as 4.5 nM but increased to 25 μM for Cd(II). The detection ranges for Hg(II), Pb(II), As(III), and Cd(II) were quantified from 14.1 to 225 nM, 1.5 to 24.4 nM, 4.5 to 73.2 nM, and 25 to 200 μM, respectively. The sensitivity, responsive concentration range, and selectivity are comparable to β-galactosidase and luciferase reporter enzymes. This study suggests that engineered enzymes for indigo production have great potential for green chemical synthesis. Additionally, heterologous biosynthesis of indigo production can lead to the development of novel, low-cost, and mini-equipment bacterial biosensors with zero background noise for visual monitoring of pollutant heavy metals.

Engineered Cyanobacteria-Based Living Materials for Bioremediation of Heavy Metals Both In Vitro and In Vivo

The pollution caused by heavy metals (HMs) represents a global concern due to their serious environmental threat. Photosynthetic cyanobacteria have a natural niche and the ability to remediate HMs such as cadmium. However, their practical application is hindered by a low tolerance to HMs and issues related to recycling. In response to these challenges, this study focuses on the development and evaluation of engineered cyanobacteria-based living materials for HMs bioremediation. Genes encoding phytochelatins (PCSs) and metallothioneins (MTs) were introduced into the model cyanobacterium Synechocystis sp. PCC 6803, creating PM/6803. The strain exhibited improved tolerance to multiple HMs and effectively removed a combination of Cd2+, Zn2+, and Cu2+. Using Cd2+ as a representative, PM/6803 achieved a bioremediation rate of approximately 21 μg of Cd2+/OD750 under the given test conditions. To facilitate its controllable application, PM/6803 was encapsulated using sodium alginate-based hydrogels (PM/6803@SA) to create "living materials" with different shapes. This system was feasible, biocompatible, and effective for removing Cd2+ under simulated conditions of zebrafish and mice models. Briefly, in vitro application of PM/6803@SA efficiently rescued zebrafish from polluted water containing Cd2+, while in vivo use of PM/6803@SA significantly decreased the Cd2+ content in mice bodies and restored their active behavior. The study offers feasible strategies for HMs bioremediation using the interesting biomaterials of engineered cyanobacteria both in vitro and in vivo.

Surface displayed MerR increases mercury accumulation by green microalga Chlamydomonas reinhardtii

Mercury is a highly toxic trace metal that can accumulate in aquatic ecosystems and when resent at high concentrations can pose risks to both aquatic life and humans consuming contaminated fish. This research explores the use of the metalloregulatory protein MerR, known for its high affinity and selectivity toward mercury, in a novel application. Through a cell surface engineering approach, MerR was displayed on cells of green alga Chlamydomonas reinhardtii. A hydroxyproline-rich GP1 protein was used as an anchor to construct the engineered strains GP1-MerR that expresses the fluorescent protein mVenus. The surface engineered GP1-MerR strain led up to five folds higher Hg2+ accumulation compared to the WT strain at concentration range from 10-9 to 10-7 M Hg2+. The binding of Hg2+ via MerR was specific and did not get significantly affected by major freshwater water quality variables such as Ca2+ and dissolved organic matter. The presence of other trace metals (Zn2+, Cu2+, Ni2+, Pb2+, Cd2+) in a same concentration range even resulted in 30-40 % increase in the accumulated Hg. Further, the engineered cells also demonstrated the ability to accumulate Hg2+ from the water extracts of the Hg-contaminated sediment samples. These results demonstrate a novel approach utilizing the cell surface display system in C. reinhardtii for its potential application in bioremediation.

Comparative transcriptomics revealed the mechanism of Stenotrophomonas rhizophila JC1 response and biosorption to Pb2

Nowadays, there is limited research focusing on the biosorption of Pb2+ through microbial process, particularly at the level of gene expression. To overcome this knowledge gap, we studied the adsorption capacity of Stenotrophomonas rhizophila JC1 to Pb2+, and investigated the physiological mechanism by means of SEM, EDS, FTIR, membrane permeability detection, and investigated the molecular mechanism through comparative transcriptomics. The results showed that after 16 h of cultivation, the biosorption capacity of JC1 for 100 mg/L of Pb2+ reached at 79.8%. The main mechanism of JC1 adsorb Pb2+ is via intracellular accumulation, accounting for more than 90% of the total adsorption. At the physiological level, Pb2+ can precipitate with anion functional groups (e.g., -OH, -NH) on the bacterial cell wall or undergo replacement reaction with cell component elements (e.g., Si, Ca) to adsorb Pb2+ outside of the cell wall, thus accomplishing extracellular adsorption of Pb2+ by strains. Furthermore, the cell membrane acts as a "switch" that inhibits the entry of metal ions into the cell from the plasma membrane. At the molecular level, the gene pbt specificity is responsible for the adsorption of Pb2+ by JC1. In addition, phosphate permease is a major member of the ABC transporter family involved in Pb2+, and czcA/cusA or Co2+/Mg2+ efflux protein plays an important role in the efflux of Pb2+ in JC1. Further, cellular macromolecule biosynthesis, inorganic cation transmembrane transport, citrate cycle (TCA) and carbon metabolism pathways all play crucial roles in the response of strain JC1 to Pb2+ stress.

Engineered Bacillus subtilis Biofilm@Biochar living materials for in-situ sensing and bioremediation of heavy metal ions pollution

The simultaneous sensing and remediation of multiple heavy metal ions in wastewater or soil with microorganisms is currently a significant challenge. In this study, the microorganism Bacillus subtilis was used as a chassis organism to construct two genetic circuits for sensing and adsorbing heavy-metal ions. The engineered biosensor can sense three heavy metal ions (0.1-75 μM of Pb2+ and Cu2+, 0.01-3.5 μM of Hg2+) in situ real-time with high sensitivity. The engineered B. subtilis TasA-metallothionein (TasA-MT) biofilm can specifically adsorb metal ions from the environment, exhibiting remarkable removal efficiencies of 99.5% for Pb2+, 99.9% for Hg2+and 99.5% for Cu2+ in water. Furthermore, this engineered strain (as a biosensor and absorber of Pb2+, Cu2+, and Hg2+) was incubated with biochar to form a hybrid biofilm@biochar (BBC) material that could be applied in the bioremediation of heavy metal ions. The results showed that BBC material not only significantly reduced exchangeable Pb2+ in the soil but also reduced Pb2+ accumulation in maize plants. In addition, it enhanced maize growth and biomass. In conclusion, this study examined the potential applications of biosensors and hybrid living materials constructed using sensing and adsorption circuits in B. subtilis, providing rapid and cost-effective tools for sensing and remediating multiple heavy metal ions (Pb2+, Hg2+, and Cu2+).

A novel antimony metallochaperone AntC in Comamonas testosteroni JL40 and its application in antimony immobilization

The microbial metabolism of toxic antimony (Sb) and the bioremediation of Sb-contaminated environments have attracted significant attention recently. This study identified an Sb(III) metallochaperone AntC in the Sb(III) efflux operon antRCA of Comamonas testosteroni JL40. The deletion of AntC significantly increased the intracellular Sb content in strain JL40 and concomitantly diminished resistance to Sb(III). By contrast, the complementary expression of AntC in the knockout strain resulted in a substantial recovery of Sb(III) resistance. The site-directed mutagenesis assay demonstrated the three conserved cysteine (Cys) residues (Cys30, Cys34, and Cys36) play an essential role in the binding of Sb(III) to AntC and its transfer. The function of the metallochaperone AntC was further investigated in an Sb(III) sensitive bacterium Escherichia coli AW3110 (Δars). The co-expression of AntC and AntA in AW3110 cells resulted in a four-fold increase in minimum inhibitory concentrations (MICs) toward Sb(III), while the intracellular Sb content decreased five-fold compared to cells expressing AntA alone. In addition, a genetically modified E. coli strain was engineered to co-express AntC and the Sb uptake protein GlpF, showing an eight-fold increase in Sb absorption and achieving a remarkable 90% removal of Sb from the solution. This engineered strain was also applied in a hydroponic experiment, displaying a significant 80% reduction in Sb uptake by rice seedlings. This finding provides new insights into the mechanisms of bacterial Sb detoxification and a potential bioremediation strategy for Sb pollution.

Bacterial tolerance and detoxification of cyanide, arsenic and heavy metals: Holistic approaches applied to bioremediation of industrial complex wastes

Cyanide is a highly toxic compound that is found in wastewaters generated from different industrial activities, such as mining or jewellery. These residues usually contain high concentrations of other toxic pollutants like arsenic and heavy metals that may form different complexes with cyanide. To develop bioremediation strategies, it is necessary to know the metabolic processes involved in the tolerance and detoxification of these pollutants, but most of the current studies are focused on the characterization of the microbial responses to each one of these environmental hazards individually, and the effect of co-contaminated wastes on microbial metabolism has been hardly addressed. This work summarizes the main strategies developed by bacteria to alleviate the effects of cyanide, arsenic and heavy metals, analysing interactions among these toxic chemicals. Additionally, it is discussed the role of systems biology and synthetic biology as tools for the development of bioremediation strategies of complex industrial wastes and co-contaminated sites, emphasizing the importance and progress derived from meta-omic studies.

Pollution status and ecological risks of metals in surface water of a coastal estuary and health risk assessment for recreational users

Since the areas close to the Sundarbans mangrove estuary, which is one of the most dynamic and productive ecosystems in the world, are very suitable for urban and industrial activities, the coastal areas of this ecosystem are constantly exposed to metal contamination. In this study, we analyzed the levels, spatial distributions, sources, pollution status, ecological risks, and health risks for recreational users of 16 metals in surface water collected from 18 sampling sites in the Sundarbans estuary. Considering the mean values of metals, Sr (2523 μg/L), Al (1731 μg/L), B (1692 μg/L) and Fe (1321 μg/L) were the most abundant metals in the coastal waters of the estuary, while Cd (0.977 μg/L), Ni (3.11 μg/L), Cu (5.98 μg/L) and Cr (9.77 μg/L) were the less abundant metals. All metals except Zr had the coefficient of variation (CV) values of over 35%, suggesting that other metals showed strong variation between sampling sites due to anthropogenic activities. Al, Fe and Pb levels of all sampling sites were above the limit values set for coastal and marine waters. Similarly, Pb levels of all sites exceeded the USEPA chronic criterion set for saltwater aquatic life. The results of pollution indices indicated that there was a serious metal pollution in almost all sampling sites. Low ecological risk (ER) at four sites, moderate ER at five sites and considerable ER at nine sites were recorded. Dual hierarchical clustering analysis grouped 16 metals into four clusters based on their potential sources and 18 sampling sites into three clusters based on their similar pollution characteristics. Health risk assessment results indicated that total hazard index (THI) values of all sites for recreational children were above the acceptable level of 1, indicating that water of all sites is not safe for health of children. However, THI values of all sites except ST8 (1.1) and ST11 (1.19) for recreational adults were below 1. Among the metals studied, Zr was found to be metal that contributes the most (75.89%) to total health risk in this coastal estuary. This finding reveals the necessity of monitoring of such less-studied metals such as Zr in the surface water of coastal estuaries. Carcinogenic risk values of As were within or below the acceptable range at all sites, indicating that carcinogenic risks would not be expected for recreational users.

Preparation of N-doped porous biochar with high specific surface area and its efficient adsorption for mercury ion from aqueous solution

Herein, a new type of super active nitrogen-doped biochar sheet (SNBC) was prepared by two-step pyrolysis and KOH chemical activation with melamine and cherry kernel powder as precursors of nitrogen and carbon source for removing Hg2+ from wastewater. The N2 adsorption/desorption and scanning electron microscope characterization revealed that the resulted SNBC under 600 °C calcination owned huge specific surface area of 2828 m2/g and plenty of well-developed micropores, and X-ray photoelectron spectroscopy and Fourier transform-infrared spectroscopy analysis testified the existence of functional groups containing N and O, which could provide adsorption sites for Hg2+. The SNBC-600 showed high adsorption capacity for Hg2+ even at low pH, and interfering cations had little effect on the adsorption. The adsorption process was rapid and dynamic data fit the pseudo-second-order dynamic model well. The maximum adsorption capacity of Hg2+ on SNBC-600 calculated by Langmuir model was 230 mg/g. After six times of reuse, the adsorption capacity still exceeded 200 mg/g, exhibiting good reusability. The designed microfiltration membrane device base on SNBC-600 could remove low concentration of Hg2+ effectively from solution. This study provided a simple and environment-friendly method for manufacturing nitrogen-doped biochar sheet, which was of great significance in the practical application of Hg2+ pollution treatment.

Designed bacteria based on natural pbr operons for detecting and detoxifying environmental lead: A mini-review

Lead (Pb), a naturally occurring element, is redistributed in the environment mainly due to anthropogenic activities. Pb pollution is a crucial public health problem worldwide due to its adverse effects. Environmental bacteria have evolved various protective mechanisms against high levels of Pb. The pbr operon, first identified in Cupriavidus metallidurans CH34, encodes a unique Pb(II) resistance mechanism involving transport, efflux, sequestration, biomineralization, and precipitation. Similar pbr operons are gradually found in diverse bacterial strains. This review focuses on the pbr-encoded Pb(II) resistance system. It summarizes various whole-cell biosensors harboring artificially designed pbr operons for Pb(II) biomonitoring with fluorescent, luminescent, and colorimetric signal output. Optimization of genetic circuits, employment of pigment-based reporters, and screening of host cells are promising in improving the sensitivity, selectivity, and response range of whole-cell biosensors. Engineered bacteria displaying Pb(II) binding and sequestration proteins, including PbrR and its derivatives, PbrR2 and PbrD, for adsorption are involved. Although synthetic bacteria show great potential in determining and removing Pb at the nanomolar level for environmental protection and food safety, some challenges must be addressed to meet demanding application requirements.

Making the connections: physical and electric interactions in biohybrid photosynthetic systems

Biohybrid photosynthesis systems, which combine biological and non-biological materials, have attracted recent interest in solar-to-chemical energy conversion. However, the solar efficiencies of such systems remain low, despite advances in both artificial photosynthesis and synthetic biology. Here we discuss the potential of conjugated organic materials as photosensitisers for biological hybrid systems compared to traditional inorganic semiconductors. Organic materials offer the ability to tune both photophysical properties and the specific physicochemical interactions between the photosensitiser and biological cells, thus improving stability and charge transfer. We highlight the state-of-the-art and opportunities for new approaches in designing new biohybrid systems. This perspective also summarises the current understanding of the underlying electron transport process and highlights the research areas that need to be pursued to underpin the development of hybrid photosynthesis systems.

Pb(II)-inducible proviolacein biosynthesis enables a dual-color biosensor toward environmental lead

With the rapid development of synthetic biology, various whole-cell biosensors have been designed as valuable biological devices for the selective and sensitive detection of toxic heavy metals in environmental water. However, most proposed biosensors are based on fluorescent and bioluminescent signals invisible to the naked eye. The development of visible pigment-based biosensors can address this issue. The pbr operon from Klebsiella pneumoniae is selectively induced by bioavailable Pb(II). In the present study, the proviolacein biosynthetic gene cluster was transcriptionally fused to the pbr Pb(II) responsive element and introduced into Escherichia coli. The resultant biosensor responded to Pb(II) in a time- and dose-dependent manner. After a 5-h incubation with Pb(II), the brown pigment was produced, which could be extracted into n-butanol. Extra hydrogen peroxide treatment during n-butanol extract resulted in the generation of a stable green pigment. An increased brown signal was observed upon exposure to lead concentrations above 2.93 nM, and a linear regression was fitted from 2.93 to 3,000 nM. Extra oxidation significantly decreased the difference between parallel groups. The green signal responded to as low as 0.183 nM Pb(II), and a non-linear regression was fitted in a wide concentration range from 0.183 to 3,000 nM. The specific response toward Pb(II) was not interfered with by various metals except for Cd(II) and Hg(II). The PV-based biosensor was validated in monitoring bioaccessible Pb(II) spiked into environmental water. The complex matrices did not influence the regression relationship between spiked Pb(II) and the dual-color signals. Direct reading with the naked eye and colorimetric quantification enable the PV-based biosensor to be a dual-color and low-cost bioindicator for pollutant heavy metal.

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.

Heavy metals (HMs) pollution in the aquatic environment: Role of probiotics and gut microbiota in HMs remediation

The presence of heavy metals (HMs) in aquatic ecosystems is a universal concern due to their tendency to accumulate in aquatic organisms. HMs accumulation has been found to cause toxic effects in aquatic organisms. The common HMs-induced toxicities are growth inhibition, reduced survival, oxidative stress, tissue damage, respiratory problems, and gut microbial dysbiosis. The application of dietary probiotics has been evolving as a potential approach to bind and remove HMs from the gut, which is called "Gut remediation". The toxic effects of HMs in fish, mice, and humans with the potential of probiotics in removing HMs have been discussed previously. However, the toxic effects of HMs and protective strategies of probiotics on the organisms of each trophic level have not been comprehensively reviewed yet. Thus, this review summarizes the toxic effects caused by HMs in the organisms (at each trophic level) of the aquatic food chain, with a special reference to gut microbiota. The potential of bacterial probiotics in toxicity alleviation and their protective strategies to prevent toxicities caused by HMs in them are also explained. The dietary probiotics are capable of removing HMs (50-90%) primarily from the gut of the organisms. Specifically, probiotics have been reported to reduce the absorption of HMs in the intestinal tract via the enhancement of intestinal HM sequestration, detoxification of HMs, changing the expression of metal transporter proteins, and maintaining the gut barrier function. The probiotic is recommended as a novel strategy to minimize aquaculture HMs toxicity and safe human health.

Synthetic bacteria for the detection and bioremediation of heavy metals

Toxic heavy metal accumulation is one of anthropogenic environmental pollutions, which poses risks to human health and ecological systems. Conventional heavy metal remediation approaches rely on expensive chemical and physical processes leading to the formation and release of other toxic waste products. Instead, microbial bioremediation has gained interest as a promising and cost-effective alternative to conventional methods, but the genetic complexity of microorganisms and the lack of appropriate genetic engineering technologies have impeded the development of bioremediating microorganisms. Recently, the emerging synthetic biology opened a new avenue for microbial bioremediation research and development by addressing the challenges and providing novel tools for constructing bacteria with enhanced capabilities: rapid detection and degradation of heavy metals while enhanced tolerance to toxic heavy metals. Moreover, synthetic biology also offers new technologies to meet biosafety regulations since genetically modified microorganisms may disrupt natural ecosystems. In this review, we introduce the use of microorganisms developed based on synthetic biology technologies for the detection and detoxification of heavy metals. Additionally, this review explores the technical strategies developed to overcome the biosafety requirements associated with the use of genetically modified microorganisms.

Heavy metal bioremediation using microbially induced carbonate precipitation: Key factors and enhancement strategies

With the development of economy, heavy metal (HM) contamination has become an issue of global concern, seriously threating animal and human health. Looking for appropriate methods that decrease their bioavailability in the environment is crucial. Microbially induced carbonate precipitation (MICP) has been proposed as a promising bioremediation method to immobilize contaminating metals in a sustainable, eco-friendly, and energy saving manner. However, its performance is always affected by many factors in practical application, both intrinsic and external. This paper mainly introduced ureolytic bacteria-induced carbonate precipitation and its implements in HM bioremediation. The mechanism of HM immobilization and in-situ application strategies (that is, biostimulation and bioaugmentation) of MICP are briefly discussed. The bacterial strains, culture media, as well as HMs characteristics, pH and temperature, etc. are all critical factors that control the success of MICP in HM bioremediation. The survivability and tolerance of ureolytic bacteria under harsh conditions, especially in HM contaminated areas, have been a bottleneck for an effective application of MICP in bioremediation. The effective strategies for enhancing tolerance of bacteria to HMs and improving the MICP performance were categorized to provide an in-depth overview of various biotechnological approaches. Finally, the technical barriers and future outlook are discussed. This review may provide insights into controlling MICP treatment technique for further field applications, in order to enable better control and performance in the complex and ever-changing environmental systems.

Microbial remediation mechanisms and applications for lead-contaminated environments

High concentrations of lead (Pb) in agricultural soil and wastewater represent a severe threat to the ecosystem and health of living organisms. Among available removal techniques, microbial remediation has attracted much attention due to its lower cost, higher efficiency, and less impact on the environment; hence, it is an effective alternative to conventional physical or chemical Pb-remediation technologies. In the present review, recent advances on the Pb-remediation mechanisms of bacteria, fungi and microalgae have been reported, as well as their detoxification pathways. Based on the previous researches, microorganisms have various remediation mechanisms to cope with Pb pollution, which are basically categorized into biosorption, bioprecipitation, biomineralization, and bioaccumulations. This paper summarizes microbial Pb-remediation mechanisms, factors affecting Pb removal, and examples of each case are described in detail. We emphatically discuss the mechanisms of microbial immobilization of Pb, which can resist toxicity by synthesizing nanoparticles to convert dissolved Pb(II) into less toxic forms. The tolerance mechanisms of microbes to Pb are discussed at the molecular level as well. Finally, we conclude the research challenges and development prospects regarding the microbial remediation of Pb-polluted environment. The current review provides insight of interaction between lead and microbes and their potential applications for Pb removal.

Metabolic engineering of the violacein biosynthetic pathway toward a low-cost, minimal-equipment lead biosensor

Metabolic engineered bacteria have been successfully employed to produce various natural colorants, which are expected to be used as the visually recognizable signals to develop mini-equipment biological devices for monitoring toxic heavy metals. The violacein biosynthetic pathway has been reconstructed in Escherichia coli (E. coli). Here the successful production of four violacein derivatives was achieved by integrating metabolic engineering and synthetic biology. Lead binding to the metalloregulator enables whole-cell colorimetric biosensors capable of assessing bioavailable lead. Deoxyviolacein-derived signal showed the most satisfied biosensing properties among prodeoxyviolacein (green), proviolacein (blue), deoxyviolacein (purple), and violacein (navy). The limit of detection (LOD) of pigment-based biosensors was 2.93 nM Pb(II), which is lower than that of graphite furnace atomic absorption spectrometry. Importantly, a good linear dose-response model in a wide dose range (2.93-6000 nM) was obtained in a non-cytotoxic deoxyviolacein-based biosensor, which was significantly better than cytotoxic violacein-based biosensor (2.93-750 nM). Among ten metal ions, only Cd(II) and Hg(II) exerted a slight influence on the response of the deoxyviolacein-based biosensor toward Pb(II). The deoxyviolacein-based biosensor was validated in detecting bioaccessible Pb(II) in environmental samples. Factors such as low cost and minimal-equipment requirement make this biosensor a suitable biological device for monitoring toxic lead in the environment.

Anthocyanin biosynthetic pathway switched by metalloregulator PbrR to enable a biosensor for the detection of lead toxicity

Environmental lead pollution mainly caused by previous anthropogenic activities continuously threatens human health. The determination of bioavailable lead is of great significance to predict its ecological risk. Bacterial biosensors using visual pigments as output signals have been demonstrated to have great potential in developing minimal-equipment biosensors for environmental pollutant detection. In this study, the biosynthesis pathway of anthocyanin was heterogeneously reconstructed under the control of the PbrR-based Pb(II) sensory element in Escherichia coli. The resultant metabolic engineered biosensor with colored anthocyanin derivatives as the visual signal selectively responded to concentrations as low as 0.012 μM Pb(II), which is lower than the detection limit of traditional fluorescent protein-based biosensors. A good linear dose–response pattern in a wide Pb(II) concentration range (0.012–3.125 μM) was observed. The color deepening of culture was recognized to the naked eye in Pb(II) concentrations ranging from 0 to 200 μM. Importantly, the response of metabolic engineered biosensors toward Pb(II) was not significantly interfered with by organic and inorganic ingredients in environmental water samples. Our findings show that the metabolic engineering of natural colorants has great potential in developing visual, sensitive, and low-cost bacterial biosensors for the detection and determination of pollutant heavy metals.

A cell-free paper-based biosensor dependent on allosteric transcription factors (aTFs) for on-site detection of harmful metals Hg2+ and Pb2+ in water

Water quality monitoring requires a reliable and practical on-site detection method for heavy metal ions. Combining an in vitro transcription (IVT) technology with allosteric transcription factors (aTFs), we developed a cell-free paper-based biosensor for on-site detection of Hg²⁺ and Pb²⁺ in water. Suitable aTFs screened using surface plasmon resonance (SPR) were employed for building biosensors. ATFs could disassociate from DNA due to their specific affinity to metal ions, and fluorescent RNA was transcribed as a signal. The developed biosensor could quantitatively detect Hg²⁺ in a linear dynamic range of 0.5-500 nM and Pb²⁺ in a 1-250 nM range in a 1 h period. The LOD of the biosensor was 0.5 nM for Hg²⁺ and 0.1 nM for Pb²⁺. The recoveries ranged from 91.09% to 123.24% for actual water samples detection. Furthermore, freeze-drying was used to create a paper-based biosensor that could detect Hg²⁺ and Pb²⁺ simultaneously on-site. This research presents a useful technique for various heavy metal ion detections.

Insights into the spatiotemporal differences in tailings seepage pollution by assessing the diversity and metabolic functions of the soil microbial community

The formation of tailings ponds depends on the long-term accumulation of tailing and high terrain. Its seepage pollution characteristics may have gradient variations on spatiotemporal scales. Used three nearby metal tailings ponds with different service times, we aimed to reveal seepage pollution trends on spatiotemporal scales and the response of soil microbial community. The results showed that the degree of seepage pollution was negatively correlated with the distance from the tailings pond on the spatial scale, while the seepage pollution showed higher levels in tailings ponds with longer service times on the temporal scale (RI = 248.04-2109.85). The pollution effect of seepage persisted after the tailings pond was discontinued (RI = 226.72). Soil microbial diversity increased with spatial scale expansion. The proportion of Actinomyces gradually increased and Proteobacteria decreased. Cr (r = 0.21) and Fe (r = 0.22) contributed more to the microbial community changes. Functional predictions showed that pathways related to signal transduction and energy metabolism were more abundant in the tailings pond. In contaminated areas, the proportion of nitrate respiration and cellulolysis functional communities had decreased, and some potentially pathogenic human taxa had accumulated. These results emphasized that there was pollution accumulation on temporal scale and pollution dispersion on spatial scale around tailings ponds, and the response of the microbial community further illustrated these trends.

Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants

Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg²⁺, Zn²⁺, Pb²⁺, Au³⁺, Cd²⁺, As³⁺, Ni²⁺, Cu²⁺, and UO₂²⁺) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.

Design of Pb(II)-Specific E. coli-Based Biosensors by Engineering Regulatory Proteins and Host Cells

Bacterial cell-based biosensors have been widely developed for detecting environmental toxic materials. The znt-operon in Escherichia coli is a Zn(II)-responsive genetic system and is employed in Zn(II), Cd(II), and Hg(II)-sensing biosensors. In this study, point mutations were introduced in the regulatory protein ZntR to modulate its target selectivity, and metal ion-exporting genes, such as copA and zntA, in host cells were deleted to increase cellular metal ion levels and enhance specificity. Thus, the overall responses of the E. coli cell-based biosensors toward metal(loid) ions were increased, and their selectivity, which was originally for Cd(II) and Hg(II), was shifted to Pb(II). The gene encoding ZntA, known as the Zn(II)-translocating P-type ATPase, showed an impact on the ability of E. coli to export Pb(II), whereas copA deletion showed no significant impact. Noteworthily, the newly generated biosensors employing ZntR Cys115Ile showed the capacity to detect under 5 nM Pb(II) in solution, without response to other tested metal ions within 0–100 nM. To understand the marked effect of single point mutations on ZntR, computational modeling was employed. Although it did not provide clear answers, changes in the sequences of the metal-binding loops of ZntR modulated its transcriptional strength and target selectivity. In summary, the approaches proposed in this study can be valuable to generate new target-sensing biosensors with superior selectivity and specificity, which can in turn broaden the applicability of cell-based biosensors to monitor Pb(II) in environmental systems.

Differential Detection of Bioavailable Mercury and Cadmium Based on a Robust Dual-Sensing Bacterial Biosensor

Genetically programmed biosensors have been widely used to monitor bioavailable heavy metal pollutions in terms of their toxicity to living organisms. Most bacterial biosensors were initially designed to detect specific heavy metals such as mercury and cadmium. However, most available biosensors failed to distinguish cadmium from various heavy metals, especially mercury. Integrating diverse sensing elements into a single genetic construct or a single host strain has been demonstrated to quantify several heavy metals simultaneously. In this study, a dual-sensing construct was assembled by employing mercury-responsive regulator (MerR) and cadmium-responsive regulator (CadR) as the separate sensory elements and enhanced fluorescent protein (eGFP) and mCherry red fluorescent protein (mCherry) as the separate reporters. Compared with two corresponding single-sensing bacterial sensors, the dual-sensing bacterial sensor emitted differential double-color fluorescence upon exposure to 0–40 μM toxic Hg(II) and red fluorescence upon exposure to toxic Cd(II) below 200 μM. Bioavailable Hg(II) could be quantitatively determined using double-color fluorescence within a narrow concentration range (0–5 μM). But bioavailable Cd(II) could be quantitatively measured using red fluorescence over a wide concentration range (0–200 μM). The dual-sensing biosensor was applied to detect bioavailable Hg(II) and Cd(II) simultaneously. Significant higher red fluorescence reflected the predominant pollution of Cd(II), and significant higher green fluorescence suggested the predominant pollution of Hg(II). Our findings show that the synergistic application of various sensory modules contributes to an efficient biological device that responds to concurrent heavy metal pollutants in the environment.

Potential hazards associated with the consumption of Scombridae fish: Infection and toxicity from raw material and processing

Scombridae fish (tuna, bonito, and mackerel) have significant ecological and economic values. They are very appreciated by consumers worldwide for their high-quality flesh and for their high nutritional value. However, consumption of Scombridae fish is potentially hazardous. Indeed, several cases of infections and toxicity linked to the consumption of Scombridae fish as raw, or processed food products have been reported worldwide. In this review, we presented the most common health risks associated with Scombridae fish consumption. Diseases associated with the consumption of these fish are generally infectious or toxic and are caused by biological hazards such as bacteria, viruses, parasites, or chemicals hazards that enter the body through contaminated fish (Polycyclic Aromatic Hydrocarbons, histamine) or by physical contaminants such as heavy metals. The risks of contamination exist throughout the food chain, from primary production to the preparation of products for consumption.

Effectively auto-regulated adsorption and recovery of rare earth elements via an engineered E. coli

Conventional mining processes of rare earth elements (REEs) usually produce REEs-rich industrial waterwastes, which leads to a significant waste of REEs resources and causes serious environmental pollution. Biosorption using engineered microorganisms is an attractive technology for the recovery of REEs from aqueous solution. To regulate the REEs' adsorption and recovery by sensing extraneous REEs, an engineered cascaded induction system, pmrCAB operon containing a lanthanide-binding tag (LBT) for sensing REEs, was incorporated into E. coli in conjunction with a silica-binding protein (Si-tag) and dLBT anchored onto the cell membrane. The sensing and adsorption capacities for Terbium (Tb), a typical study subject of REEs, were enhanced by screening an effective LBT and increasing the dLBT copy number. The adsorption capacity for Tb reached the highest reported value of 41.9 mgg^-1 dry cell weight (DCW). After adhering the engineered cells onto the silica column surface through overexpressed Si-tag, a high recovering efficiency (> 90%) of Tb desorption could be obtained with 3 bed volumes of citrate solution. In addition, the engineered cells also possessed fairly good adsorption capacity of other tested REEs. Our findings showed that the recovery of REEs with high efficiency, selectivity and controllability from aqueous solution can be well achieved via specifically bio-engineered strains.

Structural Identification of Metalloproteomes in Marine Diatoms, an Efficient Algae Model in Toxic Metals Bioremediation

The biosorption of pollutants using microbial organisms has received growing interest in the last decades. Diatoms, the most dominant group of phytoplankton in oceans, are (i) pollution tolerant species, (ii) excellent biological indicators of water quality, and (iii) efficient models in assimilation and detoxification of toxic metal ions. Published research articles connecting proteomics with the capacity of diatoms for toxic metal removal are very limited. In this work, we employed a structural based systematic approach to predict and analyze the metalloproteome of six species of marine diatoms: Thalassiosira pseudonana, Phaeodactylum tricornutum, Fragilariopsis cylindrus, Thalassiosira oceanica, Fistulifera solaris, and Pseudo-nitzschia multistriata. The results indicate that the metalloproteome constitutes a significant proportion (~13%) of the total diatom proteome for all species investigated, and the proteins binding non-essential metals (Cd, Hg, Pb, Cr, As, and Ba) are significantly more than those identified for essential metals (Zn, Cu, Fe, Ca, Mg, Mn, Co, and Ni). These findings are most likely related to the well-known toxic metal tolerance of diatoms. In this study, metalloproteomes that may be involved in metabolic processes and in the mechanisms of bioaccumulation and detoxification of toxic metals of diatoms after exposure to toxic metals were identified and described.

Thermoresponsive Metallo-protein-based Hybrid Hydro-gels for Reversible and Highly Selective Removal of Lead(II) from Water

It is interesting to develop biomaterials for easily removing ultra-trace toxic metal ions from the environment. Herein, we have synthesized a thermoresponsive hybrid hydrogel PNIPAM-co-PbrRP by incorporating a reconstituted lead-binding...

Derivation of pb(II)-sensing Escherichia coli cell-based biosensors from arsenic responsive genetic systems

Heavy metal-responsive operons were used for the generation of Escherichia coli cell-based biosensors. The selectivity and specificity of the biosensors were determined based on the interaction between heavy metals and regulatory proteins; thereby, the modulating target selectivity of biosensors could be achieved by changing target sensing properties of regulatory proteins. The results of this study demonstrated that Pb(II)-sensing biosensors could be generated from an arsenic-responsive genetic system, which was originally used for arsenic-sensing biosensors. The amino acids around to As(III)-binding sites of ArsR were mutated and cysteine residues were relocated to modulate the metal selectivity. In addition, genes encoding metal ion-translocating P-type ATPases, such as copA and zntA, were deleted to enhance the specificity by increasing the intercellular levels of divalent metal ions. Based on the results, channel protein deleted E. coli cells harboring a pair of recombinant genes, engineered ArsR and arsAp::egfp, showed enhanced responses upon Pb exposure and could be used to quantify the amount of Pb(II) in artificially contaminated water and plants grown in media containing Pb(II). Although we focused on generating Pb(II)-specific biosensors in this study, the proposed strategy has a great potential for the generation of diverse heavy metal-sensing biosensors and risk assessment of heavy metals in environmental samples as well as in plants.

Rapid field testing of mercury pollution by designed fluorescent biosensor and its cells-alginate hydrogel-based paper assay

With increasing industrial activities, mercury has been largely discharged into environment and caused serious environmental problems. The growing level of mercury pollution has become a huge threat to human health due to its significant biotoxicity. Therefore, the simple and fast means for on-site monitoring discharged mercury pollution are highly necessary to protect human beings from its pernicious effects in time. Herein, a "turn off" fluorescent biosensor (mCherry L199C) for sensing Hg²⁺ was successfully designed based on direct modification of the chromophore environment of fluorescent protein mCherry. For rapid screening and characterization, the designed variant of mCherry (mCherry L199C) was directly expressed on outer-membrane of  Escherichia coli cells by cell surface display technique. The fluorescent biosensor was characterized to have favorable response to Hg²⁺ at micromole level among other metal ions and over a broad pH range. Further, the cells of the fluorescent biosensor were encapsulated in alginate hydrogel to develop the cells-alginate hydrogel-based paper. The cells-alginate hydrogel-based paper could detect mercury pollution in 5 min with simple operation process and inexpensive equipment, and it could keep fluorescence and activity stable at 4 °C for 24 hr, which would be a high-throughput screening tool in preliminarily reporting the presence of mercury pollution in natural setting.

Roles of cation efflux pump in biomineralization of cadmium into quantum dots in Escherichia coli

Cadmium (Cd) is a typical and widely present toxic heavy metals in environments. Biomineralization of Cd ions could alleviate the toxicity and produce valuable products in certain waste streams containing selenite. However, the impact of the intrinsic Cd(II) efflux system on the biotransformation process remains unrevealed. In this work, the significance of the efflux system on Cd biomineralization was evaluated by constructing engineered Escherichia coli strains, including ΔzntA with suppressed Cd(II) efflux system and pYYDT-zntA with strengthened Cd(II) efflux system. Compared to the wild type (WT), 20% more Cd ions were accumulated in ΔzntA and 17% less were observed in pYYDT-zntA in the presence of selenite as determined by inductively coupled plasma atomic emission spectrometer. Through combination with X-ray absorption fine structure analysis, it was discovered that 50% higher production of CdS_xSe_1-x quantum dots (QDs) was achieved in the ΔzntA cells than that in the WT cells. Moreover, the ΔzntA cells exhibited the same viability as the WT cells and the pYYDT-zntA cells because accumulated Cd ions were transformed into biocompatible QDs. In addition, the biosynthesized QDs had a uniform particle size (3.82 ± 0.53 nm) and a long fluorescence lifetime (45.6 ns), which could potentially be utilized for bio-imaging. These results not only elucidate the significance of Cd(II) efflux system in the biotransformation of Cd ions and selenite, but also provide a promising way to recover Cd and Se as valuable products in certain waste streams.

An integrated overview of bacterial carboxylesterase: Structure, function and biocatalytic applications

Carboxylesterases (CEs) are members of prominent esterase, and as their name imply, they catalyze the cleavage of ester linkages. By far, a considerable number of novel CEs have been identified to investigate their exquisite physiological and biochemical properties. They are abundant enzymes in nature, widely distributed in relatively broad temperature range and in various sources; both macroorganisms and microorganisms. Given the importance of these enzymes in broad industries, interest in the study of their mechanisms and structural-based engineering are greatly increasing. This review presents the current state of knowledge and understanding about the structure and functions of this ester-metabolizing enzyme, primarily from bacterial sources. In addition, the potential biotechnological applications of bacterial CEs are also encompassed. This review will be useful in understanding the molecular basis and structural protein of bacterial CEs that are significant for the advancement of enzymology field in industries.

Versatile artificial mer operons in Escherichia coli towards whole cell biosensing and adsorption of mercury

Mercury exists naturally and mainly as a man-made pollutant in the environment, where it exerts adverse effects on local ecosystems and living organisms. It is important to develop an appropriate synthetic biological device that recognizes, detects and removes the bioavailable fraction of environmental mercury. Both single-signal and double-signal output mercury biosensors were assembled using a natural mer operon as a template. Selectivity and sensitivity of whole-cell biosensors based on artificial mer operons were determined. Three whole-cell biosensors were highly stable at very high concentrations of mercuric chloride, and could detect bioavailable Hg(II) in the concentration range of 6.25-200 μM HgCl2. A novel Hg(II) bioadsorption coupled with biosensing artificial mer operon was assembled. This would allow Hg(II)-induced Hg(II) binding protein cell surface display and green fluorescence emission to be achieved simultaneously while retaining the linear relationship between fluorescent signal and Hg(II) exposure concentration. The present study provides an innovative way to simultaneously detect, quantify, and remove bioavailable heavy metal ions using an artificially reconstructed heavy metal resistance operon.

A simplified protein purification method through nickel cleavage of the recombinant protein from the Escherichia coli cell surface

To simplify the protein purification process, we developed a novel one-step purification method in which the recombinant protein can be cleaved directly from the Escherichia coli cell surface. This method involves fusion of the target protein to the C-terminus of a LOS tag comprising a surface anchor protein (Lpp-OmpA) and a sequence-specific nickel-assisted cleavage (SNAC)-tag. The LOS tag facilitates the anchoring of the target protein to the outer membrane of E. coli cells and its separation from the cell membrane through Ni2+ cleavage. Intact, biologically active protein with a purity of 95% and a yield of approximately 100 mg per liter of culture can be readily obtained through Ni2+ cleavage in resuspension solution followed by centrifugation. In this study, a practical and promising protein purification method has been established with minimal labor and cost, as no cell disruption and chromatographic separation are required downstream.

Gut Escherichia coli expressing Pb2+-adsorption protein reduces lead accumulation in grass carp, Ctenopharyngodon idellus

Lead (Pb²⁺) is easy to accumulate in fish which become a major source of Pb²⁺ exposure to humans. In this study, a recombinant Escherichia coli strain expressing Pb²⁺-specific surface-binding protein anchored by the ice nucleation protein was introduced into grass carp (Ctenopharyngodon idellus) gut to investigate its protective effect against dietary Pb²⁺ exposure. Pb²⁺ mostly precipitated on the surface of the engineered strain through Pb²⁺-specific surface-binding protein, with a maximum adsorption efficiency of 73% and an adsorption capacity of 163 μmol/g dry cells. The Pb²⁺ concentration in engineered bacteria-fed grass carp was reduced significantly, and the residual level of Pb²⁺ in feces was increased by 76%, compared with the control group. Meantime, the engineered bacteria were able to mitigate the oxidative stress and histological alterations of intestines and dysbiosis of gut microbiota induced by Pb²⁺exposure. Thus, the engineered bacterium that can effectively reduce Pb²⁺ residue in grass carp might be a useful tool for decontamintion of lead in aquatic organisms.

Deciphering and engineering photosynthetic cyanobacteria for heavy metal bioremediation

Environmental pollution caused by heavy metals has received worldwide attentions due to their ubiquity, poor degradability and easy bioaccumulation in host cells. As one potential solution, photosynthetic cyanobacteria have been considered as promising remediation chassis and widely applied in various bioremediation processes of heavy-metals. Meanwhile, deciphering resistant mechanisms and constructing tolerant chassis towards heavy metals could greatly contribute to the successful application of the cyanobacteria-based bioremediation in the future. In this review, first we summarized recent application of cyanobacteria in heavy metals bioremediation using either live or dead cells. Second, resistant mechanisms and strategies for enhancing cyanobacterial bioremediation of heavy metals were discussed. Finally, potential challenges and perspectives for improving bioremediation of heavy metals by cyanobacteria were presented.

Feed-additive of bioengineering strain with surface-displayed laccase degrades sulfadiazine in broiler manure and maintains intestinal flora structure

Sulfonamide antibiotics (SAs) are excreted into the ecosystem unchanged through feces and urine because of their low adsorption and degradation in the guts of humans and animals. In this study, a novel whole-cell biocatalyst with fungal laccase on the cell surface of Escherichia coli Nissle 1917 was developed to degrade sulfadiazine (SDZ). Engineered strain EcN-IL showed laccase enzyme activity of 2 ± 1 U/mg dry weight of cell and degraded 37 ± 1% of SDZ at temperature 40 °C and pH 5 within 3 h in vitro. Strain EcN-IL with 500 mg/kg of SDZ was employed as a food supplement to feed chicken broilers, which can reduce the residue of SDZ in broiler manure by 58 ± 2% and also reduced dysbiosis of the gut microbiota due to overuse of antibiotics. The genetically engineered EcN-IL has laid a foundation for degrading SDZ in broilers and their manure.

Whole-Cell Microbial Bioreporter for Soil Contaminants Detection

Anthropogenic activities have released various contaminants into soil that pose a serious threat to the ecosystem and human well-being. Compared to conventional analytical methodologies, microbial cell-based bioreporters are offering a flexible, rapid, and cost-effective strategy to assess the environmental risks. This review aims to summarize the recent progress in the application of bioreporters in soil contamination detection and provide insight into the challenges and current strategies. The biosensing principles and genetic circuit engineering are introduced. Developments of bioreporters to detect and quantify heavy metal and organic contaminants in soil are reviewed. Moreover, future opportunities of whole-cell bioreporters for soil contamination monitoring are discussed.

Bacterial tolerance strategies against lead toxicity and their relevance in bioremediation application

Among heavy metals, lead (Pb) is a non-essential metal having a higher toxicity and without any crucial known biological functions. Being widespread, non-biodegradable and persistent in every sphere of soil, air and water, Pb is responsible for severe health and environmental issues, which need appropriate remediation measures. However, microbes inhabiting Pb-contaminated area are found to have evolved distinctive mechanisms to successfully thrive in the Pb-contaminated environment without exhibiting any negative effects on their growth and metabolism. The defensive strategies used by bacteria to ameliorate the toxic effects of lead comprise biosorption, efflux, production of metal chelators like siderophores and metallothioneins and synthesis of exopolysaccharides, extracellular sequestration and intracellular bioaccumulation. Lead remediation technologies by employing microbes may appear as potential advantageous alternatives to the conventional physical and chemical means due to specificity, suitability for applying in situ condition and feasibility to upgrade by genetic engineering. Developing strategies by designing transgenic bacterial strain having specific metal binding properties and metal chelating proteins or higher metal adsorption ability and using bacterial activity such as incorporating plant growth-promoting rhizobacteria for improved Pb resistance, exopolysaccharide and siderophores and metallothionein-mediated immobilization may prove highly effective for formulating bioremediation vis-a-vis phytoremediation strategies.

Using a Riboswitch Sensor to Detect Co2+/Ni2+ Transport in E. coli

Intracellular concentrations of essential mental ions must be tightly maintained to avoid metal deprivation and toxicity. However, their levels in cells are still difficult to monitor. In this report, the combination of a Co2+Ni2+-specific riboswitch and an engineered downstream mCherry fluorescent protein allowed a highly sensitive and selective whole-cell Co2+/Ni2+ detection process. The sensors were applied to examine the resistance system of Co2+/Ni2+ in E. coli, and the sensors were able to monitor the effects of genetic deletions. These results indicate that riboswitch-based sensors can be employed in the study of related cellular processes.

Development of Cadmium Multiple-Signal Biosensing and Bioadsorption Systems Based on Artificial Cad Operons

The development of genetic engineering, especially synthetic biology, greatly contributes to the development of novel metal biosensors. The cad operon encoding cadmium resistance was previously characterized from Pseudomonas putida. In this study, single-, dual-, and triple-signal output Cd(II) biosensors were successfully developed using artificial translationally coupled cad operons. Sensitivity, selectivity, and response toward Cd(II) and Hg(II), of three biosensors were all determined. Reporter signals of three biosensors all increased within the range 0.1-3.125 μM Cd(II). Three biosensors responded strongly to Cd(II), and weakly to Hg(II). However, the detection ranges of Cd(II) and Hg(II) do not overlap in all three biosensors. Next, novel Cd(II) biosensing coupled with bioadsorptive artificial cad operons were assembled for the first time. Cd(II)-induced fluorescence emission, enzymatic indication, and Cd(II) binding protein surface display can be achieved simultaneously. This study provides an example of one way to realize multiple signal outputs and bioadsorption based on the redesigned heavy metal resistance operons, which may be a potential strategy for biodetection and removal of toxic metal in the environment, facilitating the study of the mechanism and dynamics of bioremediation.

Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models

The coordination of Pb(II) in aqueous solutions containing thiols is a pivotal topic to the understanding of the pollutant potential of this cation. Based on its hard/soft borderline nature, Pb(II) forms stable hydrated ions as well as stable complexes with the thiol groups of proteins. In this paper, the modeling of Pb(II) coordination via classical molecular dynamics simulations was investigated to assess the possible use of non-bonded potentials for the description of the metal–ligand interaction. In particular, this study aimed at testing the capability of cationic dummy atom schemes—in which part of the mass and charge of the Pb(II) is fractioned in three or four sites anchored to the metal center—in reproducing the correct coordination geometry and, also, in describing the hard/soft borderline character of this cation. Preliminary DFT calculations were used to design two topological schemes, PB3 and PB4, that were subsequently implemented in the Amber force field and employed in molecular dynamics simulation of either pure water or thiol/thiolate-containing aqueous solutions. The PB3 scheme was then tested to model the binding of Pb(II) to the lead-sensing protein pbrR. The potential use of CDA topological schemes in the modeling of Pb(II) coordination was here critically discussed.

Display of lead-binding proteins on Escherichia coli surface for lead bioremediation

Cell surface display of heavy metal-binding proteins has been used to enhance the adsorption capacity of heavy metals and the engineered microbial cells can be potentially used for the bioremediation of heavy metals. In this study, the proteins PbrR, PbrR691, and PbrD from the Cupriavidus metallidurans strain CH34 were displayed on the extracellular membrane of Escherichia coli BL21 cells, with the N-domain of ice-nucleation protein as the anchor protein to achieve specific adsorption of lead ions (Pb²⁺ ) and bioremediation of lead in the soil. The localization of fusion proteins was confirmed by western blot analysis. We investigated the effects of fusion pattern, expression level, heavy metal concentration, and the presence of other heavy metal ions on the adsorption of Pb²⁺ by these engineered bacteria, and the optimal linker peptide (flexible linker) and inducer concentration (0.5 mM) were obtained. The engineered bacteria showed specific selectivity and strong adsorption capacity for Pb²⁺ . The maximum Pb²⁺ adsorption capacity of strains displaying the three proteins (PbrR, PbrR691, and PbrD) were 942.1-, 754.3-, and 864.8-μmol/g cell dry weight, respectively, which was the highest reported to date. The engineered E. coli bacteria were also applied to Pb²⁺ -contaminated soil and the detoxification effects were observed via the seed germination test and the growth of Nicotiana benthamiana in comparison with the control BL21, which provides the proof-of-concept for in situ remediations of Pb²⁺ -contaminated water or soil.

Screening strains for microbial biosorption technology of cadmium

Heavy metals contaminate the environment and provide a threat to public health through drinking water and food chain. Microbial biosorption technology provides a more economical and competitive solution for bioremediation of toxicants such as heavy metals, and microbial genetic modification may modify microbes towards optimal sorption. It is very important to screen suitable strains for this purpose. In this study, three different types of microorganisms Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae were isolated and identified, from uncontaminated soils, and compared their sorption differences with respect to cadmium (Cd²⁺). We evaluated the effects of contact time and initial concentration on Cd²⁺ uptake, and found pseudo-second-order kinetic models were more suitable to describe biosorption processes. Adsorption isotherms were used to reflect their biosorption capacity. The maximum biosorption capacities of three strains calculated by the Langmuir model were 37.764, 56.497, and 22.437 mg Cd/g biomass, respectively. In bacteria, Cd²⁺ biosorption mainly occurred on cell wall, while the difference in biosorption between yeast inside and outside the cell was not significant. We found that due to the structural differences, the removal rate of E. coli surface decreased at a high concentration, while S. cerevisiae still had a lower biosorption capacity. FTIR spectroscopy reflected the difference in functional groups involved in biosorption by three strains. SEM-EDS analysis showed the binding of Cd²⁺ to microorganisms mainly relied on ion exchange mechanism. Based on the above results, we suggested that B. subtilis is more suitable to get genetically modified for heavy metal biosorption.