Genetically engineered microbial biosensors for in situ monitoring of environmental pollution

Cyanobacterial bioreporter of nitrate bioavailability in aquatic ecosystems

The water eutrophication, resulting from the discharge of industrial and agricultural wastewater, leads to ecological degradation. However, to date, how to assess and manage the risks of water pollution, especially nitrogen pollution, remains a particularly noteworthy issue. Nitrate, the most important nitrogen compound, has become a bottleneck restricting total nitrogen management. The development of bioreporters monitoring nitrate pollution contributes to the estimation of water quality, especially the availability of nutrients. In this study, we obtained 9 bioreporters from 40 cyanobacterial derivatives which were constructed based on different hosts, copy numbers, and sensing elements and evaluated the performance of bioreporters. The results showed that single-celled Synechocystis was more sensitive to nitrate than filamentous Anabaena, that the reporter gene luxABCDE responded faster than sfgfp in most bioreporters, and that relatively medium-copy plasmid improved the performance of sensing elements. Nine bioreporters performed well in bioavailable nitrate detection, of which AD-AS-X and AR-NI-X, activated by nitrate repletion, had the shortest response time (2 h) and the widest response range (20-800 μM), respectively. Moreover, SR-GLN-SG, activated by nitrate deficiency, exhibited the best linear response (R2 = 0.998). After parameter optimization, exponential growth phase bioreporters, culture temperature of 30 °C, sample volume of 200 μL were determined as optimal monitoring conditions. We found that common water contaminants (copper, cadmium, and phosphorus) had no impact on the performance of bioreporters, indicating the stability of bioreporters. Six out of 9 bioreporters, especially the SR-NB-X, were highly effective in detecting the bioavailable nitrate in wastewater sample. This study provides valuable references for developing more cyanobacterial bioreporters and their practical application in nitrate detection.

Advances in bacterial whole-cell biosensors for the detection of bioavailable mercury: A review

Mercury (Hg) and its organic compounds, especially monomethylmercury (MeHg), cause major damage to the ecosystem and human health. In surface water or sediments, microorganisms play a crucial role in the methylation and demethylation of Hg. Given that Hg transformation processes are intracellular reactions, accurate assessment of the bioavailability of Hg(II)/MeHg in the environment, particularly for microorganisms, is of major importance. Compared with traditional analytical methods, bacterial whole-cell biosensors (BWCBs) provide a more accurate, convenient, and cost-effective strategy to assess the environmental risks of Hg(II)/MeHg. This Review summarizes recent progress in the application of BWCBs in the detection of bioavailable Hg(II)/MeHg, providing insight on current challenges and strategies. The principle and components of BWCBs for Hg(II)/MeHg bioavailability analysis are introduced. Furthermore, the impact of water chemical factors on the bioavailability of Hg is discussed as are future perspectives of BWCBs in bioavailable Hg analysis and optimization of BWCBs.

Biological and technical challenges for implementation of yeast-based biosensors

Biosensors are low-cost and low-maintenance alternatives to conventional analytical techniques for biomedical, industrial and environmental applications. Biosensors based on whole microorganisms can be genetically engineered to attain high sensitivity and specificity for the detection of selected analytes. While bacteria-based biosensors have been extensively reported, there is a recent interest in yeast-based biosensors, combining the microbial with the eukaryotic advantages, including possession of specific receptors, stability and high robustness. Here, we describe recently reported yeast-based biosensors highlighting their biological and technical features together with their status of development, that is, laboratory or prototype. Notably, most yeast-based biosensors are still in the early developmental stage, with only a few prototypes tested for real applications. Open challenges, including systematic use of advanced molecular and biotechnological tools, bioprospecting, and implementation of yeast-based biosensors in electrochemical setup, are discussed to find possible solutions for overcoming bottlenecks and promote real-world application of yeast-based biosensors.

Use of whole-cell bioreporters to assess bioavailability of contaminants in aquatic systems

Water contamination has become increasingly a critical global environmental issue that threatens human and ecosystems’ health. Monitoring and risk assessment of toxic pollutants in water bodies is essential to identifying water pollution treatment needs. Compared with the traditional monitoring approaches, environmental biosensing via whole-cell bioreporters (WCBs) has exhibited excellent capabilities for detecting bioavailability of multiple pollutants by providing a fast, simple, versatile and economical way for environmental risk assessment. The performance of WCBs is determined by its elements of construction, such as host strain, regulatory and reporter genes, as well as experimental conditions. Previously, numerous studies have focused on the design and construction of WCB rather than improving the detection process and commercialization of this technology. For investigators working in the environmental field, WCB can be used to detect pollutants is more important than how they are constructed. This work provides a review of the development of WCBs and a brief introduction to genetic construction strategies and aims to summarize key studies on the application of WCB technology in detection of water contaminants, including organic pollutants and heavy metals. In addition, the current status of commercialization of WCBs is highlighted.

Development of Whole-Cell Biosensors for Screening of Peptidoglycan-Targeting Antibiotics in a Gram-Negative Bacterium

There is an urgent need to develop novel antibiotics since antibiotic resistance is an increasingly serious threat to global public health. Whole-cell biosensors are one of the promising strategies for new antibiotic discovery. The peptidoglycan (PG) of the bacterial cell wall is one of the most important targets for antibiotics. However, the biosensors for the detection of PG-targeting antibiotics in Gram-negative bacteria have not been developed, mainly because of the lack of the regulatory systems that sense and respond to PG stress. Recently, we identified a novel two-component signal transduction system (PghKR) that is responsible for sensing and responding to PG damage in the Gram-negative bacterium Shewanella oneidensis. Based on this system, we developed biosensors for the detection of PG-targeting antibiotics. Using ampicillin as an inducer for PG stress and the bacterial luciferase LuxCDABE as the reporter, we found that the PghKR biosensors are specific to antibiotics targeting PG synthesis, including β-lactams, vancomycin, and d-cycloserine. Deletion of genes encoding PG permease AmpG and β-lactamase BlaA improves the sensitivity of the biosensors substantially. The PghKR biosensor in the background of ΔblaA is also functional on agar plates, providing a simple method for screening bacteria that produce PG-targeting antibiotics. IMPORTANCE The growing problem of antibiotic resistance in Gram-negative bacteria urgently needs new strategies so that researchers can develop novel antibiotics. Microbial whole-cell biosensors are capable of sensing various stimuli with a quantifiable output and show tremendous potential for the discovery of novel antibiotics. As the Achilles' heel of bacteria, the synthesis of the peptidoglycan (PG) is targeted by many antibiotics. However, the regulatory systems that sense and respond to PG-targeting stress in Gram-negative bacteria are reported rarely, restricting the development of biosensors for the detection of PG-targeting antibiotics. In this study, we developed a highly sensitive and specific biosensor based on a novel two-component system in the Gram-negative bacterium Shewanella oneidensis that is responsible for the sensing and responding to PG stress. Our biosensors have great potential for discovering novel antibiotics and determining the mode of action of antibiotics.

Exploiting Catabolite Repression and Stringent Response to Control Delay and Multimodality of Bioluminescence Signal by Metal Whole-Cell Biosensors: Interplay between Metal Bioavailability and Nutritional Medium Conditions

The time-dependent response of metal-detecting whole-cell luminescent bacterial sensors is impacted by metal speciation/bioavailability in solution. The comprehensive understanding of such connections requires the consideration of the bacterial energy metabolism at stake and the effects of supplied food on cells’ capability to convert bioaccumulated metals into light. Accordingly, we investigated the time response (48 h assay) of PzntA-luxCDABE Escherichia coli Cd biosensors in media differing with respect to sources of amino acids (tryptone or Lysogeny Broth) and carbon (glucose, xylose and mixtures thereof). We show that the resulting coupling between the stringent cell response and glucose/xylose-mediated catabolite repressions lead to well-defined multimodalities and shapes of the bioluminescence signal over time. Based on a recent theory for the time–response of metal-sensing luminescent bacteria, successful theoretical reconstructions of the bioluminescence signals are reported under all Cd concentrations (0–20 nM) and nutritive conditions examined. This analysis leads to the evaluation of time-dependent cell photoactivity and qualitative information on metal speciation/bioavailability in solution. Biosensor performance and the position, shape, number, and magnitude of detected peaks are discussed in relation to the metabolic pathways operative during the successive light emission modes identified here over time. Altogether, the results clarify the contributions of metal/nutrient bio-availabilities and food quality to cell response typology.

Microbial Acoustical Analyzer for Antibiotic Indication

In this study, a compact acoustic analyzer for express analysis of antibiotics based on a piezoelectric resonator with a lateral electric field and combined with a computer was developed. The possibility of determining chloramphenicol in aqueous solutions in the concentration range of 0.5-15 μg/mL was shown. Bacterial cells that are sensitive to this antibiotic were used as a sensory element. The change in the electrical impedance modulus of the resonator upon addition of the antibiotic to the cell suspension served as an analytical signal. The analysis time did not exceed 4 min. The correlation of the experimental results of an acoustic sensor with the results obtained using the light phase-contrast microscopy and standard microbiological analysis was established. The compact biological analyzer demonstrated stability, reproducibility, and repeatability of results.

Construction of a highly selective and sensitive carbohydrate-detecting biosensor utilizing Computational Identification of Non-disruptive Conjugation sites (CINC) for flexible and streamlined biosensor design

Fluorescently-labeled solute-binding proteins that alter their fluorescence output in response to ligand binding have been utilized as biosensors for a variety of applications. Coupling protein ligand binding to altered fluorescence output often requires trial and error-based testing of both multiple labeling positions and fluorophores to produce a functional biosensor with the desired properties. This approach is laborious and can lead to reduced ligand binding affinity or altered ligand specificity. Here we report the Computational Identification of Non-disruptive Conjugation sites (CINC) for streamlined identification of fluorophore conjugation sites. By exploiting the structural dynamics properties of proteins, CINC identifies positions where conjugation of a fluorophore results in a fluorescence change upon ligand binding without disrupting protein function. We show that a CINC-developed maltooligosaccharide (MOS)-detecting biosensor is capable of rapid (k_on = 20 μM^-1s^-1), sensitive (sub-μM K_D) and selective MOS detection. The MOS-detecting biosensor is modular with respect to the spectroscopic properties and demonstrates portability to detecting MOS released via α-amylase-catalyzed depolymerization of starch using both a stopped-flow and a microplate reader assay. Our MOS-detecting biosensor represents a first-in-class probe whose design was guided by changes in localized dynamics of individual amino acid positions, supporting expansion of the CINC pipeline as an indispensable tool for a wide range of protein engineering applications.

A novel, rapidly preparable and easily maintainable biocathode electrochemical biosensor for the continuous and stable detection of nitrite in water

Nitrite is a highly toxic and pathogenic pollutant that is widely distributed in various nitrogenous wastewaters. Therefore, there is an urgent need for fast and stable nitrite detection to avoid water pollution and protect human health. In this study, we developed a novel rapidly preparable and easily maintainable biocathode electrochemical biosensor (BEB) using nitrite-reducing bacteria as the detectors to realize continuous nitrite monitoring in wastewater. The preparation of the biocathode was shortened by the polarity inversion method to less than 6 d. The BEB could detect nitrite solution samples in the range of 0.1- 16.0 mg NO₂^--N L^-1 within 1.7 min. The BEB was also successfully used to detect nitrite in real wastewater with a relative error < 4.0% and a relative standard deviation < 5.8%. In addition, the BEB could be easily maintained by an operation mode of microbial fuel cells and stably detected nitrite for at least 150 tests. Our study provided a feasible and convenient way to develop electrochemical biosensors based on the biocathode for continuous and stable monitoring of pollutants in wastewater.

Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges

Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.

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.

Engineering and application of a biosensor with focused ligand specificity

Cell factories converting bio-based precursors to chemicals present an attractive avenue to a sustainable economy, yet screening of genetically diverse strain libraries to identify the best-performing whole-cell biocatalysts is a low-throughput endeavor. For this reason, transcriptional biosensors attract attention as they allow the screening of vast libraries when used in combination with fluorescence-activated cell sorting (FACS). However, broad ligand specificity of transcriptional regulators (TRs) often prohibits the development of such ultra-high-throughput screens. Here, we solve the structure of the TR LysG of Corynebacterium glutamicum, which detects all three basic amino acids. Based on this information, we follow a semi-rational engineering approach using a FACS-based screening/counterscreening strategy to generate an l-lysine insensitive LysG-based biosensor. This biosensor can be used to isolate l-histidine-producing strains by FACS, showing that TR engineering towards a more focused ligand spectrum can expand the scope of application of such metabolite sensors.

Transcriptional biosensors represent powerful tools for the screening of vast strain libraries, but the broad ligand specificity of some transcriptional regulators (TRs) can prohibit such applications. Here authors present the engineering of a LysG-based biosensor with a focused ligand specificity to isolate L-histidine-producing strains.

Ion Selective Amperometric Biosensors for Environmental Analysis of Nitrate, Nitrite and Sulfate

Inorganic ions that can be redox-transformed by living cells can be sensed by biosensors, where the redox transformation gives rise to a current in a measuring circuit. Such biosensors may be based on enzymes, or they may be based on application of whole cells. In this review focus will be on biosensors for the environmentally important ions NO₃⁻, NO₂⁻, and SO₄²⁻, and for comparison alternative sensor-based detection will also be mentioned. The developed biosensors are generally characterized by a high degree of specificity, but unfortunately also by relatively short lifetimes. There are several investigations where biosensor measurement of NO₃⁻ and NO₂⁻ have given new insight into the functioning of nitrogen transformations in man-made and natural environments such as sediments and biofilms, but the biosensors have not become routine tools. Future modifications resulting in better long-term stability may enable such general use.

Portable, Disposable, Paper-Based Microbial Fuel Cell Sensor Utilizing Freeze-Dried Bacteria for In Situ Water Quality Monitoring

Water quality monitoring is becoming an essential part of our lives as increasing human activities continue to spill unknown and unexpected contaminants into our water systems. To ensure the provision of safe and clean water to the public and the ecosystem, the development of rapid and sensitive in situ early warning systems for water toxicity monitoring is crucial. In this work, an entirely paper-based microbial fuel cell sensor utilizing freeze-dried bacteria is demonstrated as a portable and disposable water toxicity sensor. The bacterial cells were preinoculated on the anode reservoir of the device, and they were freeze-dried, making their on-site and on-demand applications possible. Upon rehydration of the bacteria with the water samples, current readings were obtained, and inhibition ratios (IRs) were calculated for different concentrations of formaldehyde as a model toxin. For 0.001, 0.01, and 0.02% of formaldehyde, IRs of 7.88, 16.08, and 23.14% were obtained, respectively. These IRs showed a very good linearity with the formaldehyde concentrations at R ² = 0.995. Additionally, the shelf life of the freeze-dried microbial fuel cell sensor was investigated. Even after 14 days of storage in the desiccator, at 4, and at -20 °C, the performance outputs compared to the new device were all at 96%.

Novel surface plasmon resonance biosensor that uses full-length Det7 phage tail protein for rapid and selective detection of Salmonella enterica serovar Typhimurium

We report a novel surface plasmon resonance (SPR) biosensor that uses the full-length Det7 phage tail protein (Det7T) to rapidly and selectively detect Salmonella enterica serovar Typhimurium (S. Typhimurium). Det7T, which was obtained using recombinant protein expression and purification in Escherichia coli, demonstrated a size of ∼75 kDa upon SDS-PAGE and was homotrimeric in its native structure. Microagglutination and transmission electron microscopy (TEM) data revealed that the protein specifically bound to the host, S. Typhimurium, but not to nonhost E. coli K-12 cells. The observed protein agglutination occurred over a concentration range of 0.8-24.6 µg/mL. The Det7T proteins were immobilized on gold-coated surfaces using amine-coupling to generate a novel Det7T-functionalized SPR biosensor, wherein the specific binding of these proteins with bacteria was detected by SPR. We observed rapid detection of (∼20 Min) and typical binding kinetics with S. Typhimurium in the range of 5 × 10⁴ -5 × 10⁷  CFU/mL, but not with E. coli at any tested concentration, indicating that the sensor exhibited recognition specificity. Similar binding was observed with 10% apple juice spiked with S. Typhimurium, suggesting that this strategy provides promise for the rapid, real-time, and selective monitoring of target microorganisms in the environment, and thus has great potential for supporting health by enabling early disease prevention.

Implementation of Combinatorial Genetic and Microenvironmental Engineering to Microbial-Based Field-Deployable Microbead Biosensors for Highly Sensitive and Remote Chemical Detection

Bioreporters, microbial species genetically engineered to provide measurable signals in response to specific chemicals, have been widely investigated as sensors for biomedical and environmental monitoring. More specifically, the bioreporter encapsulated within a biocompatible material, such as a hydrogel that can provide a suitable microenvironment for its prolonged activity as well as efficient scalable production, has been viewed as a more broadly applicable mode of biosensors. In this study, alginate-based microbeads encapsulated with the bacterial bioreporter capable of expressing green fluorescence protein in response to nitro compounds (e.g., trinitrotoluene and dinitrotoluene) are developed as biosensors. To significantly enhance the sensitivity of the microbial-based microbead biosensors, "multifaceted" modification strategies are simultaneously employed: (1) multiple genetic modifications of the bioreporter, (2) tuning the physicomechanical properties of the encapsulating microbeads, (3) controlling the initial cell density within the microbeads, and (4) enrichment of nitro compounds inside microbeads via functional nanomaterials. These microbial and microenvironmental engineering approaches combine to significantly enhance the sensing capability, even allowing highly sensitive remote detection under a low-vapor phase. Thus, the strategy developed herein is expected to contribute to various cell-based biosensors.

Strategies of Immobilizing Cells in Whole-cell Microbial Biosensor Devices Targeted for Analytical Field Applications

This review summarizes the development of whole-cell biosensors with a special focus on device development and cell immobilization. Integration of biosensor functions in a device will pave the way for field applications in remote areas and resource-limited settings. Firstly, an introduction to the field of whole-cell biosensors is provided, followed by examples of genetic engineering of cells in order to fulfill sensor functions. A framework of requirements to enable future field applications of biosensors is elaborated. A special focus is on different cell immobilization techniques ranging from polymers, to microfluidic devices, immobilization on paper and combinations of these methods. Looking at globally successfully implemented point of care devices such as a home pregnancy test or a blood glucose meter, we conclude the review with thoughts on long-term stability, portability, ease of use and user safety design guidelines for whole-cell biosensor devices.

Engineering the effector specificity of regulatory proteins for the in vitro detection of biomarkers and pesticide residues

Transcriptional regulatory proteins (TRPs)-based whole-cell biosensors are promising owing to their specificity and sensitivity, but their applications are currently limited. Herein, TRPs were adapted for the extracellular detection of a disease biomarker, uric acid, and a typical pesticide residue, carbaryl. A mutant regulatory protein that specifically recognizes carbaryl as its non-natural effector and activates transcription upon carbaryl binding was developed by engineering the regulatory protein TtgR from Pseudomonas putida. The TtgR mutant responsive to carbaryl and a regulatory protein responsive to uric acid were used for in vitro detection, based on their allosteric binding of operator DNA and inducer molecules. Based on the quantitative polymerase chain reactions (qPCRs) output, the minimum detectable concentration was between 1 nM-1 μM and 1-10 nM for uric acid and carbaryl, respectively. Our results demonstrated that engineering the effector specificity of regulatory proteins is a potential technique for generating molecular recognition elements for not only in vivo but also in vitro applications.

Vibrio fischeri bioluminescence inhibition assay for ecotoxicity assessment: A review

Vibrio fischeri bioluminescence inhibition bioassay (VFBIA) has been widely applied for the monitoring of toxicity on account of multiple advantages encompassing shorter test duration, sensitive, cost-effective and ease of operation. Moreover, this bioassay found to be equally applicable to all types of matrices (organic & inorganic compounds, metals, wastewater, river water, sewage sludge, landfill leachate, herbicides, treated wastewater etc.) for toxicity monitoring. This review highlights the apparent significance of Vibrio fischeri bioluminescence inhibition assay for ecotoxicological screening and evaluation of diverse chemical substances toxicity profile. The biochemical and genetic basis of the bioluminescence assay and its regulatory mechanism have been concisely discussed. The basic test protocol with ongoing improvements, widespread applications, typical advantages and probable limitations of the assay have been overviewed. The sensitivity of VFBIA and toxicity bioassays has also been compared.

A whole-cell bioreporter assay for quantitative genotoxicity evaluation of environmental samples

Whole-cell bioreporters have emerged as promising tools for genotoxicity evaluation, due to their rapidity, cost-effectiveness, sensitivity and selectivity. In this study, a method for detecting genotoxicity in environmental samples was developed using the bioluminescent whole-cell bioreporter Escherichia coli recA::luxCDABE. To further test its performance in a real world scenario, the E. coli bioreporter was applied in two cases: i) soil samples collected from chromium(VI) contaminated sites; ii) crude oil contaminated seawater collected after the Jiaozhou Bay oil spill which occurred in 2013. The chromium(VI) contaminated soils were pretreated by water extraction, and directly exposed to the bioreporter in two phases: aqueous soil extraction (water phase) and soil supernatant (solid phase). The results indicated that both extractable and soil particle fixed chromium(VI) were bioavailable to the bioreporter, and the solid-phase contact bioreporter assay provided a more precise evaluation of soil genotoxicity. For crude oil contaminated seawater, the response of the bioreporter clearly illustrated the spatial and time change in genotoxicity surrounding the spill site, suggesting that the crude oil degradation process decreased the genotoxic risk to ecosystem. In addition, the performance of the bioreporter was simulated by a modified cross-regulation gene expression model, which quantitatively described the DNA damage response of the E. coli bioreporter. Accordingly, the bioluminescent response of the bioreporter was calculated as the mitomycin C equivalent, enabling quantitative comparison of genotoxicities between different environmental samples. This bioreporter assay provides a rapid and sensitive screening tool for direct genotoxicity assessment of environmental samples.

A portable bioelectronic sensing system (BESSY) for environmental deployment incorporating differential microbial sensing in miniaturized reactors

Current technologies are lacking in the area of deployable, in situ monitoring of complex chemicals in environmental applications. Microorganisms metabolize various chemical compounds and can be engineered to be analyte-specific making them naturally suited for robust chemical sensing. However, current electrochemical microbial biosensors use large and expensive electrochemistry equipment not suitable for on-site, real-time environmental analysis. Here we demonstrate a miniaturized, autonomous bioelectronic sensing system (BESSY) suitable for deployment for instantaneous and continuous sensing applications. We developed a 2x2 cm footprint, low power, two-channel, three-electrode electrochemical potentiostat which wirelessly transmits data for on-site microbial sensing. Furthermore, we designed a new way of fabricating self-contained, submersible, miniaturized reactors (m-reactors) to encapsulate the bacteria, working, and counter electrodes. We have validated the BESSY’s ability to specifically detect a chemical amongst environmental perturbations using differential current measurements. This work paves the way for in situ microbial sensing outside of a controlled laboratory environment.

Development of Colorimetric-Based Whole-Cell Biosensor for Organophosphorus Compounds by Engineering Transcription Regulator DmpR

It is useful for whole-cell biosensors to be based on colorimetric detection because the output signal can be easily visualized. However, colorimetric-based whole-cell biosensors suffer higher detection limits as compared to bioluminescence- or fluorescence-based biosensors. In this work, we attempt to reduce the detection limit for a colorimetric-based whole-cell biosensor by applying directed evolution techniques on a transcription regulator, DmpR, to alter the expression level of its cognate promoter, which was fused to mRFP1 to output red coloration in the presence of organophosphate pesticides containing a phenolic group. We selected the two best-performing mutants, DM01 and DM12, which were able to develop red coloration in the presence of parathion as low as 10 μM after just 6 h of induction at 30 °C. This suggests that engineering of the transcription regulator in the sensing domain is useful for improving various properties of whole-cell biosensors, such as reducing the detection limit for simple colorimetric detection of organophosphate pesticides.

Detection of Metal and Organometallic Compounds with Bioluminescent Bacterial Bioassays

Chemical detection of metal and organometallic compounds is very specific and sensitive, but these techniques are time consuming and expensive. Although these techniques provide information about the concentrations of compounds, they fail to inform us about the toxicity of a sample. Because the toxic effects of metals and organometallic compounds are influenced by a multitude of environmental factors, such as pH, the presence of chelating agents, speciation, and organic matter, bioassays have been developed for ecotoxicological studies. Among these bioassays, recombinant luminescent bacteria have been developed over the past 20 years, and many of them are specific for the detection of metals and metalloids. These bioassays are simple to use, are inexpensive, and provide information on the bioavailable fraction of metals and organometals. Thus, they are an essential complementary tool for providing information beyond chemical analysis. In this chapter, we propose to investigate the detection of metals and organometallic compounds with bioluminescent bacterial bioassays and the applications of these bioassays to environmental samples. Graphical Abstract.

Integrated phytobial remediation for sustainable management of arsenic in soil and water

Arsenic (As), cited as the most hazardous substance by the U.S. Agency for Toxic Substance and Disease Registry (ATSDR, 2005), is an ubiquitous metalloid which when ingested for prolonged periods cause extensive health effects leading to ultimate untimely death. Plants and microbes can help mitigate soil and groundwater As problem since they have evolved elaborate detoxification machineries against this toxic metalloid as a result of their coexistence with this since the origin of life on earth. Utilization of the phytoremediation and bioremediation potential of the plants and microbes, respectively, is now regarded as two innovative tools that encompass biology, geology, biotechnology and allied sciences with cutting edge applications for sustainable mitigation of As epidemic. Discovery of As hyperaccumulating plants that uptake and concentrate large amounts of this toxic metalloid in their shoots or roots offered new hope to As phytoremediation, solar power based nature's own green remediation. This review focuses on how phytoremediation and bioremediation can be merged together to form an integrated phytobial remediation which could synergistically achieve the goal of large scale removal of As from soil, sediment and groundwater and overcome the drawbacks of the either processes alone. The review also points to the feasibility of the introduction of transgenic plants and microbes that bring new hope for more efficient treatment of As. The review identifies one critical research gap on the importance of remediation of As contaminated groundwater not only for drinking purpose but also for irrigation purpose and stresses that more research should be conducted on the use of constructed wetland, one of the most suitable areas of application of phytobial remediation. Finally the review has narrowed down on different phytoinvestigation and phytodisposal methods, which constitute the most essential and the most difficult part of pilot scale and field scale applications of phytoremediation programs.

Nickel nanoparticle-doped paper as a bioactive scaffold for targeted and robust immobilization of functional proteins

Cellulose-based materials are widely used in analytical chemistry as platforms for chromatographic and immunodiagnostic techniques. Due to its countless advantages (e.g., mechanical properties, three-dimensional structure, large surface to volume area, biocompatibility and biodegradability, and high industrial availability), paper has been rediscovered as a valuable substrate for sensors. Polymeric materials such as cellulosic paper present high protein capture ability, resulting in a large increase of detection signal and improved assay sensitivity. However, cellulose is a rather nonreactive material for direct chemical coupling. Aiming at developing an efficient method for controlled conjugation of cellulose-based materials with proteins, we devised and fabricated a hybrid scaffold based on the adsorption and in situ self-assembly of surface-oxidized Ni nanoparticles on filter paper, which serve as "docking sites" for the selective immobilization of proteins containing polyhistidine tags (His-tag). We demonstrate that the interaction between the nickel substrate and the His-tagged protein G is remarkably resilient toward chemicals at concentrations that quickly disrupt standard Ni-NTA and Ni-IDA complexes, so that this system can be used for applications in which a robust attachment is desired. The bioconjugation with His-tagged protein G allowed the binding of anti-Salmonella antibodies that mediated the immuno-capture of live and motile Salmonella bacteria. The versatility and biocompatibility of the nickel substrate were further demonstrated by enzymatic reactions.

Functional characterization of a StyS sensor kinase reveals distinct domains associated with intracellular and extracellular sensing of styrene in P. putida CA-3

Bacterial two-component systems (TCSs) are of vital importance in the translation of rapidly changing environmental conditions into appropriate cellular regulatory responses enabling adaptation, growth, and survival. The diverse range of environmental signals that TCSs can process, coupled with discrete modular domains within TCS proteins, offers considerable potential for the rational design of bio-sensor and/or bio-reporter strains. In this study we functionally characterize the multi-domain StyS sensor kinase associated with sensing of the aromatic pollutant styrene by Pseudomonas putida CA-3. Deletion analysis of discrete domains was performed and the ability of the truncated StyS sensor proteins to activate a cognate reporter system in an E. coli host assessed. The essential histidine kinase and PAS input domains were identified for StyS dependent activation of the reporter system. However, co-expression of an ABC-transporter protein StyE, previously linked to styrene transport in P. putida CA-3, enabled activation of the reporter system with a StyS construct containing a non-essential PAS input domain, suggesting a novel role for intracellular detection and/or activation. Site directed mutagenesis and amino acid deletions were employed to further characterize the PAS sensing domains of both input regions. The potential implications of these findings in the use of multi-domain sensor kinases in rational design strategies and the potential link between transport and intracellular sensing are discussed.

New quaternary ammonium camphor derivatives and their antiviral activity, genotoxic effects and cytotoxicity

The synthesis and biological evaluation of a novel series of dimeric camphor derivatives are described. The resulting compounds were studied for their antiviral activity, cyto- and genotoxicity. Compounds 3a and 3d in which the quaternary nitrogen atoms are separated by the C5H10 and С9H18 aliphatic chain, exhibited the highest efficiency as an agent inhibiting the reproduction of the influenza virus A(H1N1)pdm09. The cytotoxicity data of compounds 3 and 4 revealed their moderate activity against malignant cell lines; compound 3f had the highest activity for the CEM-13 cells. These results show close agreement with the data of independent studies on toxicity of these compounds, in particular that the toxicity of compounds strongly depends on spacer length.

Continuous, real-time bioimaging of chemical bioavailability and toxicology using autonomously bioluminescent human cell lines

Bioluminescent imaging is an emerging biomedical surveillance strategy that uses external cameras to detect in vivo light generated in small animal models of human physiology or in vitro light generated in tissue culture or tissue scaffold mimics of human anatomy. The most widely utilized of reporters is the firefly luciferase (luc) gene; however, it generates light only upon addition of a chemical substrate, thus only generating intermittent single time point data snapshots. To overcome this disadvantage, we have demonstrated substrate-independent bioluminescent imaging using an optimized bacterial bioluminescence (lux) system. The lux reporter produces bioluminescence autonomously using components found naturally within the cell, thereby allowing imaging to occur continuously and in real-time over the lifetime of the host. We have validated this technology in human cells with demonstrated chemical toxicological profiling against exotoxin exposures at signal strengths comparable to existing luc systems (~1.33 × 10⁷ photons/second). As a proof-in-principle demonstration, we have engineered breast carcinoma cells to express bioluminescence for real-time screening of endocrine disrupting chemicals and validated detection of 17β-estradiol (EC₅₀ = ~ 10 pM). These and other applications of this new reporter technology will be discussed as potential new pathways towards improved models of target chemical bioavailability, toxicology, efficacy, and human safety.

Genetic Programming as a tool for identification of analyte-specificity from complex response patterns using a non-specific whole-cell biosensor

Whole-cell biosensors are mostly non-specific with respect to their detection capabilities for toxicants, and therefore offering an interesting perspective in environmental monitoring. However, to fully employ this feature, a robust classification method needs to be implemented into these sensor systems to allow further identification of detected substances. Substance-specific information can be extracted from signals derived from biosensors harbouring one or multiple biological components. Here, a major task is the identification of substance-specific information among considerable amounts of biosensor data. For this purpose, several approaches make use of statistical methods or machine learning algorithms. Genetic Programming (GP), a heuristic machine learning technique offers several advantages compared to other machine learning approaches and consequently may be a promising tool for biosensor data classification. In the present study, we have evaluated the use of GP for the classification of herbicides and herbicide classes (chemical classes) by analysis of substance-specific patterns derived from a whole-cell multi-species biosensor. We re-analysed data from a previously described array-based biosensor system employing diverse microalgae (Podola and Melkonian, 2005), aiming on the identification of five individual herbicides as well as two herbicide classes. GP analyses were performed using the commercially available GP software 'Discipulus', resulting in classifiers (computer programs) for the binary classification of each individual herbicide or herbicide class. GP-generated classifiers both for individual herbicides and herbicide classes were able to perform a statistically significant identification of herbicides or herbicide classes, respectively. The majority of classifiers were able to perform correct classifications (sensitivity) of about 80-95% of test data sets, whereas the false positive rate (specificity) was lower than 20% for most classifiers. Results suggest that a higher number of data sets may lead to a better classification performance. In the present paper, GP-based classification was combined with a biosensor for the first time. Our results demonstrate GP was able to identify substance-specific information within complex biosensor response patterns and furthermore use this information for successful toxicant classification in unknown samples. This suggests further research to assess perspectives and limitations of this approach in the field of biosensors.