A chromosomally based tod-luxCDABE whole-cell reporter for benzene, toluene, ethybenzene, and xylene (BTEX) sensing

Construction of Whole Cell Bacterial Biosensors as an Alternative Environmental Monitoring Technology to Detect Naphthenic Acids in Oil Sands Process-Affected Water

After extraction of bitumen from oil sands deposits, the oil sand process-affected water (OSPW) is stored in tailings ponds. Naphthenic acids (NA) in tailings ponds have been identified as the primary contributor to toxicity to aquatic life. As an alternative to other analytical methods, here we identify bacterial genes induced after growth in naphthenic acids and use synthetic biology approaches to construct a panel of candidate biosensors for NA detection in water. The main promoters of interest were the atuAR promoters from a naphthenic acid degradation operon and upstream TetR regulator, the marR operon which includes a MarR regulator and downstream naphthenic acid resistance genes, and a hypothetical gene with a possible role in fatty acid biology. Promoters were printed and cloned as transcriptional lux reporter plasmids that were introduced into a tailings pond-derived Pseudomonas species. All candidate biosensor strains were tested for transcriptional responses to naphthenic acid mixtures and individual compounds. The three priority promoters respond in a dose-dependent manner to simple, acyclic, and complex NA mixtures, and each promoter has unique NA specificities. The limits of NA detection from the various NA mixtures ranged between 1.5 and 15 mg/L. The atuA and marR promoters also detected NA in small volumes of OSPW samples and were induced by extracts of the panel of OSPW samples. While biosensors have been constructed for other hydrocarbons, here we describe a biosensor approach that could be employed in environmental monitoring of naphthenic acids in oil sands mining wastewater.

Microbial whole-cell biosensors: Current applications, challenges, and future perspectives

Microbial Whole-Cell Biosensors (MWCBs) have seen rapid development with the arrival of 21st century biological and technological capabilities. They consist of microbial species which produce, or limit the production of, a reporter protein in the presence of a target analyte. The quantifiable signal from the reporter protein can be used to determine the bioavailable levels of the target analyte in a variety of sample types at a significantly lower cost than most widely used and well-established analytical instrumentation. Furthermore, the versatile and robust nature of MWCBs shows great potential for their use in otherwise unavailable settings and environments. While MWCBs have been developed for use in biomedical, environmental, and agricultural monitoring, they still face various challenges before they can transition from the laboratory into industrialized settings like their enzyme-based counterparts. In this comprehensive and critical review, we describe the underlying working principles of MWCBs, highlight developments for their use in a variety of fields, detail challenges and current efforts to address them, and discuss exciting implementations of MWCBs helping redefine what is thought to be possible with this expeditiously evolving technology.

Bacterial luciferase: Molecular mechanisms and applications

Bacterial luciferase is a flavin-dependent monooxygenase which is remarkable for its distinctive feature in transforming chemical energy to photons of visible light. The bacterial luciferase catalyzes bioluminescent reaction using reduced flavin mononucleotide, long-chain aldehyde and oxygen to yield oxidized flavin, corresponding acid, water and light at λ_max around 490nm. The enzyme comprises of two non-identical α and β subunits, where α subunit is a catalytic center and β subunit is crucially required for maintaining catalytic function of the α subunit. The crystal structure with FMN bound and mutagenesis studies have assigned a number of amino acid residues that are important in coordinating critical reactions and stabilizing intermediates to attain optimum reaction efficiency. The enzyme achieves monooxygenation by generating C4a-hydroperoxyflavin intermediate that later changes its protonation status to become C4a-peroxyflavin, which is necessary for the nucleophilic attacking with aldehyde substrate. The decomposing of C4a-peroxyhemiacetal produces excited C4a-hydroxyflavin and acid product. The chemical basis regrading bioluminophore generation in Lux reaction remains an inconclusive issue. However, current data can, at least, demonstrate the involvement of electron transfer to create radical molecules which is the key step in this mechanism. Lux is a self-sufficient bioluminescent system in which all substrates can be recycled and produced by a group of enzymes from the lux operon. This makes Lux distinctively advantageous over other luciferases for reporter enzyme application. The progression of understanding of Lux catalysis is beneficial to improve light emitting efficiency in order to expand the robustness of Lux application.

Repetitive Detection of Aromatic Hydrocarbon Contaminants with Bioluminescent Bioreporters Attached on Tapered Optical Fiber Elements

In this study, we show the repetitive detection of toluene on a tapered optical fiber element (OFE) with an attached layer of Pseudomonas putida TVA8 bioluminescent bioreporters. The bioluminescent cell layer was attached on polished quartz modified with (3-aminopropyl)triethoxysilane (APTES). The repeatability of the preparation of the optical probe and its use was demonstrated with five differently shaped OFEs. The intensity of measured bioluminescence was minimally influenced by the OFE shape, possessing transmittances between 1.41% and 5.00%. OFE probes layered with P. putida TVA8 were used to monitor liquid toluene over a two-week period. It was demonstrated that OFE probes layered with positively induced P. putida TVA8 bioreporters were reliable detectors of toluene. A toluene concentration of 26.5 mg/L was detected after <30 min after immersion of the probe in the toluene solution. Additional experiments also immobilized constitutively bioluminescent cells of E. coli 652T7, on OFEs with polyethyleneimine (PEI). These OFEs were repetitively induced with Lauria-Bertani (LB) nutrient medium. Bioluminescence appeared 15 minutes after immersion of the OFE in LB. A change in pH from 7 to 6 resulted in a decrease in bioluminescence that was not restored following additional nutrient inductions at pH 7. The E. coli 652T7 OFE probe was therefore sensitive to negative influences but could not be repetitively used.

Bacterial bioreporter detection of arsenic associated with iron oxides

Bacterial bioreporters are engineered microorganisms that have found recent application as a low-cost method of detecting arsenic (As) in environmental systems. However, no assessment exists of bioreporter detection of particle-bound As. We applied an Escherichia coli-based bioreporter to assess the bioavailability of As(v) adsorbed by goethite (α-FeOOH), 2-line ferrihydrite and As(v) co-precipitated with Fe(iii). We found that As(v) bound to the surface of crystalline goethite was not detected by the bioreporters, which contrasted sharply the 50% detection of As(v) adsorbed by ferrihydrite. In addition, the presence of Ca2+ caused a systematic decrease in the bioreporter-detected As(v) fraction in the ferrihydrite samples. For co-precipitated As(v)-Fe(iii) samples, we found a similar bioreporter-detected As(v) fraction (<0.2) regardless of crystallite size (0.7-2.5 nm) or As Fe-1 surface loading (10-60 mol%). Our results reveal that the bioreporter response depends largely on aggregated particle size, which is expected to physically isolate As(v) from bioreporters by encapsulating surface-bound As(v) in coagulated flocs. Our results show that while bioreporters do not perform optimally in water that contains Fe particles, this method could be developed for sludge testing and for monitoring As levels in the product water of decentralized Fe-based As treatment systems.

The emerging use of bioluminescence in medical research

Bioluminescence is the light produced by a living organism and is commonly emitted by sea life with Ca²⁺-regulated photoproteins being the most responsible for bioluminescence emission. Marine coelenterates provide important functions involved in essential purposes such as defense, feeding, and breeding. In this review, the main characteristics of marine photoproteins including aequorin, clytin, obelin, berovin, pholasin and symplectin from different marine organisms will be discussed. We will focused on the recent use of recombinant photoproteins in different biomedical research fields including the measurement of Ca²⁺ in different intracellular compartments of animal cells, as labels in the design and development of binding assays. This review will also outline how bioluminescent photoproteins have been used in a plethora of analytical methods including ultra-sensitive assays and in vivo imaging of cellular processes. Due to their unique properties including elective intracellular distribution, wide dynamic range, high signal-to-noise ratio and low Ca²⁺-buffering effect, recombinant photoproteins represent a promising future analytical tool in several in vitro and in vivo experiments.

Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants

In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a biphenyl-degrading bacterium, is reported and analyzed in relation to its extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes. The genome harbors a bph gene cluster, permitting degradation of biphenyl and many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling benzoate and its derivatives to be degraded, and phe gene cluster, which permits phenol degradation. In addition, P. alcaliphila JAB1 is capable of cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol. The strain carries both catechol and protocatechuate branches of the β-ketoadipate pathway, which is used to funnel the pollutants to the central metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with closest phylogenetic relatives should be used when taxonomically classifying the isolated bacterium; this, together with 16S rRNA gene sequence and chemotaxonomic data analyses, enables more precise identification of the culture at the species level.

Reporter Gene Assays in Ecotoxicology

The need for simple and rapid means for evaluating the potential toxic effects of environmental samples has prompted the development of reporter gene assays, based on tester cells (bioreporters) genetically engineered to report on sample toxicity by producing a readily quantifiable signal. Bacteria are especially suitable to serve as bioreporters owing to their fast responses, low cost, convenient preservation, ease of handling, and amenability to genetic manipulations. Various bacterial bioreporters have been introduced for general toxicity and genotoxicity assessment, and the monitoring of endocrine disrupting and dioxin-like compounds has been mostly covered by similarly engineered eukaryotic cells. Some reporter gene assays have been validated, standardized, and accredited, and many others are under constant development. Efforts are aimed at broadening detection spectra, lowering detection thresholds, and combining toxicity identification capabilities with characterization of the toxic effects. Taking advantage of bacterial robustness, attempts are also being made to incorporate bacterial bioreporters into field instrumentation for online continuous monitoring or on-site spot checks. However, key hurdles concerning test validation, cell preservation, and regulatory issues related to the use of genetically modified organisms still remain to be overcome.

Smartphone-based low light detection for bioluminescence application

We report a smartphone-based device and associated imaging-processing algorithm to maximize the sensitivity of standard smartphone cameras, that can detect the presence of single-digit pW of radiant flux intensity. The proposed hardware and software, called bioluminescent-based analyte quantitation by smartphone (BAQS), provides an opportunity for onsite analysis and quantitation of luminescent signals from biological and non-biological sensing elements which emit photons in response to an analyte. A simple cradle that houses the smartphone, sample tube, and collection lens supports the measuring platform, while noise reduction by ensemble averaging simultaneously lowers the background and enhances the signal from emitted photons. Five different types of smartphones, both Android and iOS devices, were tested, and the top two candidates were used to evaluate luminescence from the bioluminescent reporter Pseudomonas fluorescens M3A. The best results were achieved by OnePlus One (android), which was able to detect luminescence from ~10⁶ CFU/mL of the bio-reporter, which corresponds to ~10⁷ photons/s with 180 seconds of integration time.

New family of biosensors for monitoring BTX in aquatic and edaphic environments

Benzene, toluene, ethylbenzene and xylenes (BTEX) contamination is a serious threat to public health and the environment, and therefore, there is an urgent need to detect its presence in nature. The use of whole-cell reporters is an efficient, easy-to-use and low-cost approach to detect and follow contaminants outside specialized laboratories; this is especially important in oil spills that are frequent in marine environments. The aim of this study is the construction of a bioreporter system and its comparison and validation for the specific detection of monocyclic aromatic hydrocarbons in different host bacteria and environmental samples. Our bioreporter system is based on the two component regulatory system TodS-TodT of P. putida DOT-T1E, and the PtodX promoter fused to the GFP protein as the reporter protein. For the construction of different biosensors, this bioreporter was transferred into three different bacterial strains isolated from three different environments, and their performance was measured. Validation of the biosensors on water samples spiked with petrol, diesel and crude oil on contaminated waters from oil spills and on contaminated soils demonstrated that they can be used in mapping and monitoring some BTEX compounds (specifically benzene, toluene and two xylene isomers). Validation of biosensors is an important issue for the integration of these devices into pollution-control programmes.

The Repetitive Detection of Toluene with Bioluminescence Bioreporter Pseudomonas putida TVA8 Encapsulated in Silica Hydrogel on an Optical Fiber

Living cells of the lux-based bioluminescent bioreporter Pseudomonas putida TVA8 were encapsulated in a silica hydrogel attached to the distal wider end of a tapered quartz fiber. Bioluminescence of immobilized cells was induced with toluene at high (26.5 mg/L) and low (5.3 mg/L) concentrations. Initial bioluminescence maxima were achieved after >12 h. One week after immobilization, a biofilm-like layer of cells had formed on the surface of the silica gel. This resulted in shorter response times and more intensive bioluminescence maxima that appeared as rapidly as 2 h after toluene induction. Considerable second bioluminescence maxima were observed after inductions with 26.5 mg toluene/L. The second and third week after immobilization the biosensor repetitively and semiquantitatively detected toluene in buffered medium. Due to silica gel dissolution and biofilm detachment, the bioluminescent signal was decreasing 20-32 days after immobilization and completely extinguished after 32 days. The reproducible formation of a surface cell layer on the wider end of the tapered optical fiber can be translated to various whole cell bioluminescent biosensor devices and may serve as a platform for in-situ sensors.

Construction of a bioreporter by heterogeneously expressing a Vibrio natriegens recA::luxCDABE fusion in Escherichia coli, and genotoxicity assessments of petrochemical-contaminated groundwater in northern China

Here, we constructed an Escherichia coli recA::luxCDABE bioreporter for genotoxicity assessments. The recA promoter was cloned from the marine bacterium Vibrio natriegens. This bioreporter showed a dose-response relationship following induction by mitomycin C, and other pollutants or environmental samples could be calculated as mitomycin C equivalents, which provided a way to quantitatively compare the genotoxicities of different environmental samples. This bioreporter was used to evaluate the genotoxicity under a wide range of external environmental conditions, like temperatures ranging from 15 °C to 42 °C, pH between 4.0 and 9.0, and salinity ranging from 0% to 3%. This successfully extended its application from the laboratory to the field, and allowed the bioreporter to assess the genotoxicity and bioavailability of genotoxins in various environmental media, including surface water, groundwater, seawater, and soil matrix. Expression of V. natriegens recA in E. coli indicated a LexA-like regulator in V. natriegens, and the putative SOS box of V. natriegens recA was similar to that of E. coli. The genotoxicities of groundwater samples from a petrochemical-contaminated site in northern China were evaluated by this bioreporter assay, and the genotoxic levels were in accordance with contamination levels obtained by chemical analyses.

Hydrothermal synthesis and enhanced xylene-sensing properties of pompon-like Cr-doped Co3O4hierarchical nanostructures

Unique pompon-like Cr-doped Co₃O₄hierarchical nanostructures were preparedviaa hydrothermal method, showing extraordinary sensing properties towards xylene.

Application of genetically engineered microbial whole-cell biosensors for combined chemosensing

The progress of genetically engineered microbial whole-cell biosensors for chemosensing and monitoring has been developed in the last 20 years. Those biosensors respond to target chemicals and produce output signals, which offer a simple and alternative way of assessment approaches. As actual pollution caused by human activities usually contains a combination of different chemical substances, how to employ those biosensors to accurately detect real contaminant samples and evaluate biological effects of the combined chemicals has become a realistic object of environmental researches. In this review, we outlined different types of the recent method of genetically engineered microbial whole-cell biosensors for combined chemical evaluation, epitomized their detection performance, threshold, specificity, and application progress that have been achieved up to now. We also discussed the applicability and limitations of this biosensor technology and analyzed the optimum conditions for their environmental assessment in a combined way.

Genetically engineered microorganisms for the detection of explosives' residues

The manufacture and use of explosives throughout the past century has resulted in the extensive pollution of soils and groundwater, and the widespread interment of landmines imposes a major humanitarian risk and prevents civil development of large areas. As most current landmine detection technologies require actual presence at the surveyed areas, thus posing a significant risk to personnel, diverse research efforts are aimed at the development of remote detection solutions. One possible means proposed to fulfill this objective is the use of microbial bioreporters: genetically engineered microorganisms “tailored” to generate an optical signal in the presence of explosives’ vapors. The use of such sensor bacteria will allow to pinpoint the locations of explosive devices in a minefield. While no study has yet resulted in a commercially operational system, significant progress has been made in the design and construction of explosives-sensing bacterial strains. In this article we review the attempts to construct microbial bioreporters for the detection of explosives, and analyze the steps that need to be undertaken for this strategy to be applicable for landmine detection.

Programmable living material containing reporter micro-organisms permits quantitative detection of oligosaccharides

The increasing molecular understanding of many diseases today permits the development of new diagnostic methods. However, few easy-to-handle and inexpensive tools exist for common diseases such as food disorders. Here we present a living material based analytical sensor (LiMBAS) containing genetically modified bacteria (Escherichia coli) immobilized and protected in a thin layer between a nanoporous and support polymer membrane for a facile quantification of disease-relevant oligosaccharides. The bacteria were engineered to fluoresce in response to the analyte to reveal its diffusion behavior when using a blue-light source and optical filter. We demonstrated that the diffusion zone diameter was related semi-logarithmically to the analyte concentration. LiMBAS could accurately quantify lactose or galactose in undiluted food samples and was able to measure food intolerance relevant concentrations in the range of 1-1000 mM requiring a sample volume of 1-10 μL. LiMBAS was storable for at least seven days without losing functionality at 4 °C. A wide range of genetic tools for E. coli are readily available thus allowing the reprogramming of the material to serve as biosensor for other molecules. In combination with smartphones, an automated diagnostic analysis becomes feasible which would also allow untrained people to use LiMBAS.

Toxicity bioassays for water from black-odor rivers in Wenzhou, China

Following urbanization, a large number of urban rivers were contaminated and turned to black-odor rivers. The traditional approach for detecting water quality is based on chemical or physical analysis. However, biological toxicity of black-odor water has been less addressed. As two typical black-odor rivers, Jiushanwai River (JS) and Shanxia River (SX) are tributaries of Wen-Rui Tang River in Wenzhou (south of China). The eco-safety of the urban rivers was evaluated by bioassay for water toxicity in this study. Ten and 5 sampling sites were respectively set along JS and SX. Water samples were collected monthly from October 2010 to October 2011. The general physical and chemical parameters of river water were monitored. In order to investigate the ecotoxicological effects of black-odor water, the following bioassays were used: (1) Fish acute toxicity test (Danio rerio, comprehensive toxicity), (2) luminescent bacteria bioassay (Qinghaiensis vibrio, toxicity to bacteria), and (3) tropical claw embryo assay (Xenopus tropicalis, embryo toxicity). Biotoxicity of black-odor rivers water was demonstrated by D. rerio, Q. vibrio, and X. tropicalis embryos. Toxicological effects of black-odor water were respectively shown by mortality of zebrafish, and by the relative inhibitory light rate of luminescent bacteria. However, luminescent bacteria were more sensitive to inspect biotoxicity than zebrafish. In X. tropicalis embryos test, toxicological effects of black-odor water were mostly shown by embryos' survival rate and teratogenic rate. Bioassay results showed that toxicity of SX water was higher than that of JS water, especially in summer. Statistical analysis of luminescent bacteria toxicity test showed that biotoxicity of SX and JS was high in summer, but low in winter and spring. The seasonal changes of water toxicity of the black-odor river were positively correlative with changes of water temperature (p < 0.05), and related to pH and ammonium nitrogen of water. Typical black-odor river water displays different degrees of biotoxicity to D. rerio, luminescent bacteria, and X. tropicalis embryos. The ecotoxicological risk of black-odor rivers was demonstrated in urban area, which suggests bioassay is necessary for evaluation of water quality. In the present study, spatial and seasonal bioassay for toxicity of JS and SX provides a complete example for evaluation of urban rivers.

Detection of organic compounds with whole-cell bioluminescent bioassays

Natural and manmade organic chemicals are widely deposited across a diverse range of ecosystems including air, surface water, groundwater, wastewater, soil, sediment, and marine environments. Some organic compounds, despite their industrial values, are toxic to living organisms and pose significant health risks to humans and wildlife. Detection and monitoring of these organic pollutants in environmental matrices therefore is of great interest and need for remediation and health risk assessment. Although these detections have traditionally been performed using analytical chemical approaches that offer highly sensitive and specific identification of target compounds, these methods require specialized equipment and trained operators, and fail to describe potential bioavailable effects on living organisms. Alternatively, the integration of bioluminescent systems into whole-cell bioreporters presents a new capacity for organic compound detection. These bioreporters are constructed by incorporating reporter genes into catabolic or signaling pathways that are present within living cells and emit a bioluminescent signal that can be detected upon exposure to target chemicals. Although relatively less specific compared to analytical methods, bioluminescent bioassays are more cost-effective, more rapid, can be scaled to higher throughput, and can be designed to report not only the presence but also the bioavailability of target substances. This chapter reviews available bacterial and eukaryotic whole-cell bioreporters for sensing organic pollutants and their applications in a variety of sample matrices.

Bioluminescent bioreporter for assessment of arsenic contamination in water samples of India

In the present study the most efficient R-factor controlling the ars operon was selected after screening of 39 Escherichia coli isolates by minimum inhibitory concentration test (MIC) studies from water samples of different geographical locations of India. Among all, strain isolated from Hooghly River (West Bengal) was found to have maximum tolerance towards arsenic and was further used for the development of bioreporter bacteria. Cloning of the ars regulatory element along with operator-promotor and luxCDABE from Photobacteria into expression vector has been accomplished by following recombinant DNA protocols. The bioreporter sensor system developed in this study can measure the estimated range of 0.74-60 mu g of As/L and is both specific and selective for sensing bioavailable As. The constructed bacterial biosensor was further used for the determination of arsenic ion concentration in different environmental samples of India.

Genetically modified whole-cell bioreporters for environmental assessment

Living whole-cell bioreporters serve as environmental biosentinels that survey their ecosystems for harmful pollutants and chemical toxicants, and in the process act as human and other higher animal proxies to pre-alert for unfavorable, damaging, or toxic conditions. Endowed with bioluminescent, fluorescent, or colorimetric signaling elements, bioreporters can provide a fast, easily measured link to chemical contaminant presence, bioavailability, and toxicity relative to a living system. Though well tested in the confines of the laboratory, real-world applications of bioreporters are limited. In this review, we will consider bioreporter technologies that have evolved from the laboratory towards true environmental applications, and discuss their merits as well as crucial advancements that still require adoption for more widespread utilization. Although the vast majority of environmental monitoring strategies rely upon bioreporters constructed from bacteria, we will also examine environmental biosensing through the use of less conventional eukaryotic-based bioreporters, whose chemical signaling capacity facilitates a more human-relevant link to toxicity and health-related consequences.

Joint action and lethal levels of toluene, ethylbenzene, and xylene on midge (Chironomus plumosus) larvae

Aquatic ecosystems are vulnerable to the exposure with petrochemicals such as toluene, ethylbenzene, and xylene (o-, m-, and p-xylene) (TEX) and their adverse effects. Considering the widespread use, occurrence, and high toxicity of TEX, the aim of this work was to investigate the differential toxicity of TEX against midge (Chironomus plumosus) larvae and reveal the joint action of binary and ternary mixtures of TEX using the predictive concentration addition model. More importantly, this research can afford the basic toxicity data and scientific reference for the establishment of water quality criteria or benchmark, water pollution control, and aquatic risk assessment. Single and joint toxic effects of TEX on C. plumosus larvae were investigated using a semi-static bioassay, and the type of joint effects of TEX was ascertained. In the single toxicant experiments, the toxicity of the three pollutants could be sequenced as ethylbenzene > xylene > toluene. Specifically, LC(50s) of T, E, and X after a 48-h exposure were 64.9, 37.8, and 42.0 mg/L, respectively. In the binary mixture experiments, the interaction between toluene and ethylbenzene, ethylbenzene and xylene, and toluene and xylene was largely in conformity with partial additive or additive effect as determined by isobologram representation and toxic unit models. In the ternary mixture experiments, the interaction was basically dependent on the use of additive index and mixture toxicity index methods. However, the antagonistic and synergistic actions were not significant. Thus, the tertiary mixture interaction could be regarded as additive action. The concentration addition model could successfully predict the joint action of TEX mixtures on C. plumosus larvae. Particularly, the additive action of TEX on C. plumosus larvae can be further recommended to evaluate water quality criteria of TEX.

Tactic responses to pollutants and their potential to increase biodegradation efficiency

A significant number of bacterial strains are able to use toxic aromatic hydrocarbons as carbon and energy sources. In a number of cases, the evolution of the corresponding degradation pathway was accompanied by the evolution of tactic behaviours either towards or away from these toxic carbon sources. Reports are reviewed which show that a chemoattraction to heterogeneously distributed aromatic pollutants increases the bioavailability of these compounds and their biodegradation efficiency. An extreme form of chemoattraction towards aromatic pollutants, termed 'hyperchemotaxis', was described for Pseudomonas putida DOT-T1E, which is based on the action of the plasmid-encoded McpT chemoreceptor. Cells with this phenotype were found of being able to approach and of establishing contact with undiluted crude oil samples. Although close McpT homologues are found on other degradation plasmids, the sequence of their ligand-binding domains does not share significant similarity with that of NahY, the other characterized chemoreceptor for aromatic hydrocarbons. This may suggest the existence of at least two families of chemoreceptors for aromatic pollutants. The use of receptor chimers comprising the ligand-binding region of McpT for biosensing purposes is discussed.

Construction and application of an Escherichia coli bioreporter for aniline and chloroaniline detection

Aniline and chlorinated anilines (CAs) are classified as priority pollutants; therefore, an effective method for detection and monitoring is required. In this study, a green-fluorescence protein-based bioreporter for the detection of aniline and CAs was constructed in Escherichia coli DH5α, characterized and tested with soil and wastewater. The sensing capability relied on the regulatory control between a two-component regulatory protein, TodS/TodT, and the P( todX ) promoter of Pseudomonas putida T-57 (PpT57), since the gene expression of todS, todT, and todC2 are positively induced with 4-chloroaniline. The bioreporter system (DH5α/pPXGFP-pTODST) is markedly unique with the two co-existing plasmids. The inducibility of the fluorescence response was culture-medium- and time-dependent. Cells grown in M9G medium exhibited a low background fluorescence level and were readily induced by 4CA after 3-h exposure, reaching the maximum induction level at 9 h. When tested with benzene, toluene, ethyl-benzene and xylene, aniline and CAs, the response data were best fit by a sigmoidal dose-response relationship, from which the K(½) value was determined for the positive effectors. 3CA and 4CA were relatively powerful inducers, while some poly-chlorinated anilines could also induce green fluorescence protein expression. The results indicated a broader recognition range of PpT57'sTodST than previously reported for P. putida. The test results with environmental samples were reliable, indicating the potential application of this bioreporter in the ecotoxicology assessment and bioremediation of areas contaminated with aniline- and/or CAs.

Whole-cell biochips for online water monitoring

Chip-integrated luminescent recombinant reporter bacteria were combined with fluidics and light detection systems to form a real-time water biomonitor. The biomonitor was exposed to a continuous water flow for up to ten days, in the course of which it was challenged with spikes of both model toxic compounds and toxic environmental samples. All simulated contamination events were reported within 0.5-2.5 h. Furthermore, the response pattern of the reporter bacteria was indicative of the nature of the contaminating chemicals. Efforts were aimed at improving signal quality and at the development of an alarm management software. Following further research, a device of the proposed design could be implemented in monitoring networks as an early warning system against water pollution by toxic chemicals.

The evolution of the bacterial luciferase gene cassette (lux) as a real-time bioreporter

The bacterial luciferase gene cassette (lux) is unique among bioluminescent bioreporter systems due to its ability to synthesize and/or scavenge all of the substrate compounds required for its production of light. As a result, the lux system has the unique ability to autonomously produce a luminescent signal, either continuously or in response to the presence of a specific trigger, across a wide array of organismal hosts. While originally employed extensively as a bacterial bioreporter system for the detection of specific chemical signals in environmental samples, the use of lux as a bioreporter technology has continuously expanded over the last 30 years to include expression in eukaryotic cells such as Saccharomyces cerevisiae and even human cell lines as well. Under these conditions, the lux system has been developed for use as a biomedical detection tool for toxicity screening and visualization of tumors in small animal models. As the technologies for lux signal detection continue to improve, it is poised to become one of the first fully implantable detection systems for intra-organismal optical detection through direct marriage to an implantable photon-detecting digital chip. This review presents the basic biochemical background that allows the lux system to continuously autobioluminesce and highlights the important milestones in the use of lux-based bioreporters as they have evolved from chemical detection platforms in prokaryotic bacteria to rodent-based tumorigenesis study targets. In addition, the future of lux imaging using integrated circuit microluminometry to image directly within a living host in real-time will be introduced and its role in the development of dose/response therapeutic systems will be highlighted.

Online monitoring of water toxicity by use of bioluminescent reporter bacterial biochips

We describe a flow-through biosensor for online continuous water toxicity monitoring. At the heart of the device are disposable modular biochips incorporating agar-immobilized bioluminescent recombinant reporter bacteria, the responses of which are probed by single-photon avalanche diode detectors. To demonstrate the biosensor capabilities, we equipped it with biochips harboring both inducible and constitutive reporter strains and exposed it to a continuous water flow for up to 10 days. During these periods we challenged the biosensor with 2-h pulses of water spiked with model compounds representing different classes of potential water pollutants, as well as with a sample of industrial wastewater. The biosensor reporter panel detected all simulated contamination events within 0.5-2.5 h, and its response was indicative of the nature of the contaminating chemicals. We believe that a biosensor of the proposed design can be integrated into future water safety and security networks, as part of an early warning system against accidental or intentional water pollution by toxic chemicals.

Are luminescent bacteria suitable for online detection and monitoring of toxic compounds in drinking water and its sources?

Biosensors based on luminescent bacteria may be valuable tools to monitor the chemical quality and safety of surface and drinking water. In this review, an overview is presented of the recombinant strains available that harbour the bacterial luciferase genes luxCDABE, and which may be used in an online biosensor for water quality monitoring. Many bacterial strains have been described for the detection of a broad range of toxicity parameters, including DNA damage, protein damage, membrane damage, oxidative stress, organic pollutants, and heavy metals. Most lux strains have sensitivities with detection limits ranging from milligrams per litre to micrograms per litre, usually with higher sensitivities in compound-specific strains. Although the sensitivity of lux strains can be enhanced by various molecular manipulations, most reported detection thresholds are still too high to detect levels of individual contaminants as they occur nowadays in European drinking waters. However, lux strains sensing specific toxic effects have the advantage of being able to respond to mixtures of contaminants inducing the same effect, and thus could be used as a sensor for the sum effect, including the effect of compounds that are as yet not identified by chemical analysis. An evaluation of the suitability of lux strains for monitoring surface and drinking water is therefore provided.

Design and characterization of an aequorin-based bacterial biosensor for detection of toluene and related compounds

An aequorin-based Escherichia coli strain JM109 biosensor was constructed and characterized for its potential to detect toluene and related compounds in aqueous solutions. The biosensor was constructed based on a PGL2 plasmid carrying the lower pathway promoter (Pu) of the xyl operon of Pseudomonas putida mt-2, which was incorporated with transcriptional activator xylR and fused to aequorin cDNA named pGL2-aequorin. Binding of xylR protein to a subset of toluene-like compounds activates transcription at the Pu promoter, thus expression of aequorin is controlled by xylR and Pu. In this work we have compared the effect of Shine-Dalgarno (SD) and T2 rrnβ terminator sequence in the expression of aequorin. According to the sensitivity of aequorin and increase in the signal-to-noise ratio, this reporter enzyme has reasonable sensitivity compared with other reporter systems. The results indicate higher expression of aequorin in the presence of SD and T2 rrnβ. The activity of aequorin in recombinant whole-cell biosensor was linear from 1 to 500 μm of toluene. The bioluminescence response was specific for toluene-like molecules, so this biosensor cells would be able to detect toluene derivative contamination in environmental samples, accurately.

Use of reporter-gene based bacteria to quantify phenanthrene biodegradation and toxicity in soil

A phenanthrene-degrading bacterium, Sphingomonas paucimobilis EPA505 was used to construct two fluorescence-based reporter strains. Strain D harboring gfp gene was constructed to generate green fluorescence when the strain started to biodegrade phenanthrene. Strain S possessing gef gene was designed to die once phenanthrene biodegradation was initiated and thus to lose green fluorescence when visualized by a live/dead cell staining. Confocal laser scanning microscopic observation followed by image analysis demonstrates that the fluorescence intensity generated by strain D increased and the intensity by strain S decreased linearly at the phenanthrene concentration of up to 200 mg/L. Such quantitative increase and decrease of fluorescence intensity in strain D (i.e., from 1 to 11.90 ± 0.72) and strain S (from 1 to 0.40 ± 0.07) were also evident in the presence of Ottawa sand spiked with the phenanthrene up to 1000 mg/kg. The potential use of the reporter strains in quantitatively determining biodegradable or toxic phenanthrene was discussed.

Microbial degradation of petroleum hydrocarbon contaminants: an overview

One of the major environmental problems today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. Accidental releases of petroleum products are of particular concern in the environment. Hydrocarbon components have been known to belong to the family of carcinogens and neurotoxic organic pollutants. Currently accepted disposal methods of incineration or burial insecure landfills can become prohibitively expensive when amounts of contaminants are large. Mechanical and chemical methods generally used to remove hydrocarbons from contaminated sites have limited effectiveness and can be expensive. Bioremediation is the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization. Bioremediation functions basically on biodegradation, which may refer to complete mineralization of organic contaminants into carbon dioxide, water, inorganic compounds, and cell protein or transformation of complex organic contaminants to other simpler organic compounds by biological agents like microorganisms. Many indigenous microorganisms in water and soil are capable of degrading hydrocarbon contaminants. This paper presents an updated overview of petroleum hydrocarbon degradation by microorganisms under different ecosystems.

Whole-cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls

Whole-cell microbial biosensors are one of the newest molecular tools used in environmental monitoring. Such biosensors are constructed through fusing a reporter gene such as lux, gfp or lacZ, to a responsive promoter. There have been many reports of the applications of biosensors, particularly their use in assaying pollutant toxicity and bioavailability. This paper reviews the basic concepts behind the construction of whole-cell microbial biosensors for pollutant monitoring, and describes the applications of two such biosensors for detecting the bioavailability and biodegradation of Polychlorinated Biphenyls (PCBs).

Immobilization of bioluminescent Escherichia coli cells using natural and artificial fibers treated with polyethyleneimine

Biosensors based on whole-cell bioluminescence have the potential to become a cost-effective alternative to conventional detection methods upon validation of target selectivity and sensitivity. However, quantitative analysis of bioluminescence is greatly hindered due to lack of control over the total number of cells in a suspending culture. In this study, the effect of surface properties of genetically engineered luminous E. coli cells and fibrous matrices on the immobilization capacity and effectiveness under various environmental conditions were characterized. Four different fibers, including cotton, polyester, viscose rayon, and silk, were investigated. Although cell adhesion was observed on untreated viscose and cotton fibers, viscose fiber pretreated with 0.667% polyethyleneimine (PEI) was found capable of immobilizing the most viable E. coli DPD2234 cells, followed by viscose treated with 0.33% and 1% PEI. The cells immobilized on PEI-treated viscose remained viable and yielded 20% or more bioluminescence signals immediately upon contact with the inducer up to 72 h without feeding nutrients to the cells, suggesting that viscose treated with 0.667% PEI could provide a stable immobilization mechanism for bioluminescent E. coli cells with long sensing period, quick response time, and good signal reproducibility.

Predicting bioremediation of hydrocarbons: laboratory to field scale

There are strong drivers to increasingly adopt bioremediation as an effective technique for risk reduction of hydrocarbon impacted soils. Researchers often rely solely on chemical data to assess bioremediation efficiently, without making use of the numerous biological techniques for assessing microbial performance. Where used, laboratory experiments must be effectively extrapolated to the field scale. The aim of this research was to test laboratory derived data and move to the field scale. In this research, the remediation of over thirty hydrocarbon sites was studied in the laboratory using a range of analytical techniques. At elevated concentrations, the rate of degradation was best described by respiration and the total hydrocarbon concentration in soil. The number of bacterial degraders and heterotrophs as well as quantification of the bioavailable fraction allowed an estimation of how bioremediation would progress. The response of microbial biosensors proved a useful predictor of bioremediation in the absence of other microbial data. Field-scale trials on average took three times as long to reach the same endpoint as the laboratory trial. It is essential that practitioners justify the nature and frequency of sampling when managing remediation projects and estimations can be made using laboratory derived data. The value of bioremediation will be realised when those that practice the technology can offer transparent lines of evidence to explain their decisions.

Construction of recombinant Nitrosomonas europaea expressing green fluorescent protein in response to co-oxidation of chloroform

Transcriptional fusions with gfp driven by the promoter region of mbla (NE2571) in pPRO/mbla4 and clpB (NE2402) in pPRO/clpb7 were used to transform the ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718). The two genes were chosen because their transcript levels were found at much higher levels in N. europaea in response to oxidation of chloroform and chloromethane. In N. europaea transformed with pPRO/mbla4, green fluorescent protein (GFP)-dependent fluorescence increased from 3- to 18-fold above control levels in response to increasing chloroform concentrations (7 to 28 microM), and from 8- to 10-fold in response to increasing hydrogen peroxide concentrations (2.5-7.5 mM). The GFP-dependent fluorescence of N. europaea transformed with pPRO/clpb7 also showed an increase of 6- to 10-fold in response to chloroform (28-100 microM) but did not respond to H(2)O(2). Our data provide proof of concept that biosensors can be fabricated in ammonia-oxidizing bacteria using "sentinel" genes that up-regulate in response to stress caused either by co-oxidation of chlorinated solvents or by the presence of H(2)O(2). The fabricated biosensors had a consistent concentration-dependent response to chloroform; however, these did not respond to other chlorinated compounds that cause similar cellular stress.

Toxicant identification by a luminescent bacterial bioreporter panel: application of pattern classification algorithms

Genetically engineered microorganisms, tailored to respond by a dose-dependent signal to the presence of toxic chemicals, are a potentially useful tool for environmental monitoring. One manifestation of this approach is based on a panel of luminescent bacterial bioreporters, harboring fusions of the luxCDABE operon to various stress-responsive gene promoters. Such sensors can report by a dose-dependent luminescent signal on the stress sensed by the cells and thus on the presence of toxic compound(s), but they lack the ability to identify the chemicals involved. Here, we demonstrate how the use of a panel of such sensors might offer a solution to this drawback. Five selected Escherichia coli reporter strains harboring fusions of selected gene promoters (grpE, nhoA, oraA, lacZ, and mipA) to luxCDABE were exposed to five model toxicants and to a toxicant-free control in a 40-repetition format. Each of the six treatments activated different promoters to different extents, producing its own unique fingerprint. Two machine learning schemes were challenged with the obtained data set: Bayesian decision theory and the nonparametric nearest-neighbor technique. The Bayesian classifiers performed better and were able to identify the sample's contents within 30 min with an error rate estimate that did not exceed 3% at a 95% confidence level and with zero false negatives. Performance in tap water and wastewater samples was similar. Given the coming of age of whole-cell sensing devices, pattern classification algorithms such as the ones described here offer a step toward the incorporation of reporter cells into future biosensor formats, including whole-cell arrays.

Bacterial Biosensors for Measuring Availability of Environmental Pollutants

Traditionally, pollution risk assessment is based on the measurement of a pollutant's total concentration in a sample. The toxicity of a given pollutant in the environment, however, is tightly linked to its bioavailability, which may differ significantly from the total amount. Physico-chemical and biological parameters strongly influence pollutant fate in terms of leaching, sequestration and biodegradation. Bacterial sensor-reporters, which consist of living micro-organisms genetically engineered to produce specific output in response to target chemicals, offer an interesting alternative to monitoring approaches. Bacterial sensor-reporters detect bioavailable and/or bioaccessible compound fractions in samples. Currently, a variety of environmental pollutants can be targeted by specific biosensor-reporters. Although most of such strains are still confined to the lab, several recent reports have demonstrated utility of bacterial sensing-reporting in the field, with method detection limits in the nanomolar range. This review illustrates the general design principles for bacterial sensor-reporters, presents an overview of the existing biosensor-reporter strains with emphasis on organic compound detection. A specific focus throughout is on the concepts of bioavailability and bioaccessibility, and how bacteria-based sensing-reporting systems can help to improve our basic understanding of the different processes at work.

Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodoccocus sp. strain TFB

Rhodococcus sp. strain TFB is a versatile gram-positive bacterium able to grow on a wide variety of aromatic compounds as carbon and energy sources. Since the strain is refractory to genetic analysis, a proteomic approach was used to study the metabolic pathways involved in the catabolism of such compounds by analyzing differentially induced proteins. The most marked difference was observed when the proteome profiles of phthalate-grown cells were compared with those cultured in the presence of tetralin- or naphthalene, suggesting that different metabolic pathways are involved in the degradation of mono- and polyaromatic compounds. Comparison with the proteome of glucose-grown cells indicated that each pathway was specifically induced by the corresponding aromatic compound. A combination of proteomics and molecular biology led to the identification of 14 proteins (65-80% identical to known Pht proteins) that describe a complete pathway for the catabolism of phthalate to central metabolites via intradiol cleavage of protochatechuic acid. Chaperonins were also induced in phthalate-grown cells, indicating that growth on this compound induces a stress response. Absence of catabolite repression by glucose was observed by both transcriptional and proteome analysis, suggesting that Rhodococcus sp. strain TFB may have advantages over other tightly regulated strains in bioremediation.