Optical biosensor for environmental on-line monitoring of naphthalene and salicylate bioavailability with an immobilized bioluminescent catabolic reporter bacterium

Detection of GroEL in activated sludge: a model for detection of system stress

GroEL is a ubiquitous constitutively synthesized protein that is also stress inducible. Activated sludge, which is a standard biological process used in wastewater treatment systems, is made up of a diverse microbial consortium. The synthesis of GroEL in activated sludge was significantly induced after heat (42 degrees C) shock. The increased level of GroEL expression was shown to be due to de novo protein synthesis. We have demonstrated a method which shows that stress proteins can be detected in activated sludge, and propose their use as specific indicators of system stress.

Reporter gene technology: the future looks bright

Reporter gene technology is widely used to monitor the cellular events associated with signal transduction and gene expression. Based upon the splicing of transcriptional control elements to a variety of reporter genes (with easily measurable phenotypes), it "reports" the effects of a cascade of signalling events on gene expression inside cells. The principal advantage of these assays is their high sensitivity, reliability, convenience, and adaptability to large-scale measurements. This review summarises the current status of reporter gene technology including its role in monitoring gene transfer and expression and its development as a biological screen. With the advances in this technology and in detection methods, it is likely that luciferase and green fluorescent protein will become increasingly popular for the non-invasive monitoring of gene expression in living tissues and cells. Such techniques will be important in defining the molecular events associated with gene transcription, which has implications for our understanding of the molecular basis of disease and will influence our approach to gene therapy and drug development.

Factors influencing expression of luxCDABE and nah genes in Pseudomonas putida RB1353(NAH7, pUTK9) in dynamic systems

Bioluminescent reporter organisms have been successfully exploited as analytical tools for in situ determination of bioavailable levels of contaminants in static environmental samples. Continued characterization and development of such reporter systems is needed to extend the application of these bioreporters to in situ monitoring of degradation in dynamic environmental systems. In this study, the naphthalene-degrading, lux bioreporter bacterium Pseudomonas putida RB1353 was used to evaluate the relative influences of cell growth stage, cell density, substrate concentration, oxygen tension, and background carbon substrates on both the magnitude of the light response and the rate of salicylate disappearance. The effect of these variables on the lag time required to obtain maximum luminescence and degradation was also monitored. Strong correlations were observed between the first three factors and both the magnitude and induction time of luminescence and degradation rate. The maximum luminescence response to nonspecific background carbon substrates (soil extract broth or Luria broth) was 50% lower than that generated in response to 1 mg of sodium salicylate liter(-1). Oxygen tension was evaluated over the range of 0.5 to 40 mg liter(-1), with parallel inhibition to luminescence and degradation rate (20 mg of sodium salicylate liter(-1)) observed at 1.5 mg liter(-1) and below and no effect observed above 5 mg liter(-1). Oxygen tensions from 2 to 4 mg liter(-1) influenced the magnitude of luminescence but not the salicylate degradation rate. The results suggest that factors causing parallel shifts in the magnitude of both luminescence and degradation rate were influencing regulation of the nah operon promoters. For factors that cause nonparallel shifts, other regulatory mechanisms are explored. This study demonstrates that lux reporter bacteria can be used to monitor both substrate concentration and metabolic response in dynamic systems. However, each lux reporter system and application will require characterization and calibration.

Green fluorescent protein in the design of a living biosensing system for L-arabinose

Analysis of monosaccharides is typically performed using analytical systems that involve a separation step followed by a detection step. The separation step is usually necessary because of the high degree of structural similarity between different monosaccharides. A novel sensing system for monosaccharides is described here in which living bacteria were designed to detect a model monosaccharide, L-arabinose, without the need for a separation step. In such sensing systems, analytes are detected by employing the selective recognition properties found in certain bacterial proteins. These systems are designed so that a reporter protein is expressed by the bacteria in response to the analyte. The concentration of the analyte can be related to the signal generated by the reporter protein. In the sensing system described here, the green fluorescent protein (GFP) was used as the reporter protein. L-Arabinose concentrations can be determined by monitoring the fluorescence emitted by the bacteria at 509 nm after excitation of GFP at 395 nm. The system can detect L-arabinose at concentrations as low as 5 x 10(-7) M and is selective over D-arabinose, the stereoisomer of the analyte, as well as over a variety of pentose and hexose sugars.

Isolation of carbon- and nitrogen-deprivation-induced loci of Sinorhizobium meliloti 1021 by Tn5-luxAB mutagenesis

Soil bacteria, such as Sinorhizobium meliloti, are subject to variation in environmental conditions, including carbon- and nitrogen-deprivation. The ability of bacteria to sense changes in their environment and respond accordingly is of vital importance to their survival and persistence in the soil and rhizosphere. A derivative of Tn5 which creates transcriptional fusions to the promoterless luxAB genes was used to mutagenize S. meliloti 1021 and 5000 insertion mutants were subsequently screened for gene fusions induced by selected environmental stresses. The isolation of 21 gene fusions induced by nitrogen-deprivation and 12 induced by carbon-deprivation is described. Cloning and partial DNA sequence analysis of the transposon-tagged loci revealed a variety of novel genes, as well as S. meliloti genes with significant similarity to known bacterial loci. In addition, nodule occupancy studies were carried out with selected Tn5-luxAB insertion mutants to examine the role of the tagged genes in competition.

Identification and quantification of toxic chemicals by use of Escherichia coli carrying lux genes fused to stress promoters

The luxCDABE bioluminescence genes of the Vibrio fischeri lux system have been used as a reporter system for different stress and regulatory promoters of Escherichia coli. Selected E. coli strains carrying lux genes fused to different promoters were exposed to various toxic chemicals, and the recorded luminescence was used for the characterization of the biologic signature of each compound. Analysis of these data with the aid of a proper algorithm allowed quantitative and qualitative assessment of toxic chemicals. Of the 25 tested chemicals, 23 were identified by this novel strategy in a 3-h procedure. This system can also be adapted for the identification of simple mixtures of toxic agents when the biologic signatures of the individual compounds are known. This biologic recognition strategy also provides a tool for evaluating the degree of similarity between the modes of action of different toxic agents.

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

A tod-luxCDABE fusion was constructed and introduced into the chromosome of Pseudomonas putida F1, yielding the strain TVA8. This strain was used to examine the induction of the tod operon when exposed to benzene, toluene, ethylbenzene, and xylene (BTEX) compounds and aqueous solutions of JP-4 jet fuel constituents. Since this system contained the complete lux cassette (luxCDABE), bacterial bioluminescence in response to putative chemical inducers of the tod operon was measured on-line in whole cells without added aldehyde substrate. There was an increasing response to toluene concentrations from 30 micrograms/liter to 50 mg/liter, which began to saturate at higher concentrations. The detection limit was 30 micrograms/liter. There was a significant light response to benzene, m- and p-xylenes, phenol, and water-soluble JP-4 jet fuel components, but there was no bioluminescence response upon exposure to o-xylene. The transposon insertion was stable and had no negative effect on cell growth.

The detection and characterization of genetically programmed responses to environmental stress

The rapid, accurate, and inexpensive detection of environmental contaminants (and the stress that they engender) is still a major problem worldwide. Though assays exist for monitoring these pollutants, they can often be expensive, time-consuming, and require extensive equipment and/or training in order to be effective. Research over the past decade has pointed to the measurement of enzymes encoded by genes programmed to respond to particular classes of environmental stress as a means of quantifying altered environmental health. The detection of physical and chemical contaminants can thus be performed using standard enzyme assays, by measuring the quantity of these enzymes (e.g. via immunoassays), or through the use of the technology of "gene-fusions." In this latter case, the genes encoding easily quantified enzymes are "fused" (cloned) such that their expression is under the control of genes whose expression is induced in the presence of these contaminants. In these cases, the measurement of the reporter gene's activity from the sample would signal the presence of a particular chemical and/or physical contaminant. The advantages of this system are its rapidity, ease of use, and single end-point measurement, thus allowing a "one box" (single detector) solution to measurements of environmental quality and health. Moreover, these systems can be designed for on-line monitoring and computer-aided operation for use in a wide variety of settings.

Development and testing of a bacterial biosensor for toluene-based environmental contaminants

A bacterial biosensor for benzene, toluene, and similar compounds has been constructed, characterized, and field tested on contaminated water and soil. The biosensor is based on a plasmid incorporating the transcriptional activator xylR from the TOL plasmid of Pseudomonas putida mt-2. The XylR protein binds a subset of toluene-like compounds and activates transcription at its promoter, Pu. A reporter plasmid was constructed by placing the luc gene for firefly luciferase under the control of XylR and Pu. When Escherichia coli cells were transformed with this plasmid vector, luminescence from the cells was induced in the presence of benzene, toluene, xylenes, and similar molecules. Accurate concentration dependencies of luminescence were obtained and exhibited K1/2 values ranging from 39.0 +/- 3.8 microM for 3-xylene to 2,690 +/- 160 microM for 3-methylbenzylalcohol (means +/- standard deviations). The luminescence response was specific for only toluene-like molecules that bind to and activate XylR. The biosensor cells were field tested on deep aquifer water, for which contaminant levels were known, and were able to accurately detect toluene derivative contamination in this water. The biosensor cells were also shown to detect BETX (benzene, toluene, and xylene) contamination in soil samples. These results demonstrate the capability of such a bacterial biosensor to accurately measure environmental contaminants and suggest a potential for its inexpensive application in field-ready assays.

Bioremediation: towards a credible technology

Bioremediation is the technological process whereby biological systems are harnessed to effect the clean-up of environmental pollutants. Currently, microbial systems are most widely employed in bioremediation programmes, generally in the treatment of soils and waters contaminated with organic pollutants. Micro-organisms have a huge metabolic repertoire that enables them to degrade a panoply of organic pollutants and in many cases the complex biochemistry and molecular biology of the catabolic pathways involved have been unravelled (e.g. Gibson, 1984; Frantz et al., 1987; Evans & Fuchs, 1988; Burlage et al., 1989; Abramowicz, 1990; Assinder & Williams, 1990; Chaudhry & Chapalamadugu, 1991; Cerniglia, 1992; Knackmuss, 1996). Despite valuable basic knowledge on the mechanisms of pollutant bio-degradation, bioremediation has yet to be accepted as a routine treatment technology and the environmental industry is wary of applying bioremediation for the treatment of contaminated sites.

Bioluminescence-based assays for detection and characterization of bacteria and chemicals in clinical laboratories

OBJECTIVES

To survey recent advances in the application of bioluminescence to public health problems. The usefulness of bacterial (lux) and eucaryotic (luc) luciferase genes is presented, along with several examples that demonstrate their value as "reporters" of many endpoints of clinical concern.

CONCLUSIONS

The development of new technologies for monitoring biological and chemical contaminants is in continuous progress. Recent excitement in this area has come from the use of genes encoding enzymes for bioluminescence as reporter systems. Applications of the recombinant luciferase reporter phage concept now provide a sensitive approach for bacterial detection, their viability, and sensitivity to antimicrobial agents. Moreover, a number of fusions of the lux and luc genes to stress inducible genes in different bacteria can allow a real-time measurement of gene expression and determination of cellular viability, and also constitute a new tool to detect toxic chemicals and their bioavailability.

Development and characterization of a whole-cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples

A microbial whole-cell biosensor was developed, and its potential to measure water-dissolved concentrations of middle-chain-length alkanes and some related compounds by bioluminescence was characterized. The biosensor strain Escherichia coli DH5 alpha(pGEc74, pJAMA7) carried the regulatory gene alkS from Pseudomonas oleovorans and a transcriptional fusion of PalkB from the same strain with the promoterless luciferase luxAB genes from Vibrio harveyi on two separately introduced plasmids. In standardized assays, the biosensor cells were readily inducible with octane, a typical inducer of the alk system. Light emission after induction periods of more than 15 min correlated well with octane concentration. In well-defined aqueous samples, there was a linear relationship between light output and octane concentrations between 24 and 100 nM. The biosensor responded to middle-chain-length alkanes but not to alicyclic or aromatic compounds. In order to test its applicability for analyzing environmentally relevant samples, the biosensor was used to detect the bioavailable concentration of alkanes in heating oil-contaminated groundwater samples. By the extrapolation of calibrated light output data to low octane concentrations with a hyperbolic function, a total inducer concentration of about 3 nM in octane equivalents was estimated. The whole-cell biosensor tended to underestimate the alkane concentration in the groundwater samples by about 25%, possibly because of the presence of unknown inhibitors. This was corrected for by spiking the samples with a known amount of an octane standard. Biosensor measurements of alkane concentrations were further verified by comparing them with the results of chemical analyses.

Sensing antimonite and arsenite at the subattomole level with genetically engineered bioluminescent bacteria

A highly sensitive and selective optical sensing system for antimonite has been developed using genetically engineered bacteria. The basis of this system is the ability of certain bacteria to survive in environments that are contaminated with antimonite, arsenite, and arsenate. The survival is conferred to the bacteria by the ars operon, which consists of five genes that code for three structural proteins, ArsA, ArsB, and ArsC, and two regulatory proteins, ArsD and ArsR. ArsA, ArsB, and ArsC form a protein pump system that extrudes antimonite, arsenite, and arsenate once these anions reach the cytoplasm of the bacterium. A method was developed for monitoring antimonite and arsenite by using a single plasmid that incorporates the regulatory gene of the extrusion system, arsR, and the genes of bacterial luciferase, luxA and luxB. In the designed plasmid, ArsR regulates the expression of bacterial luciferase in a manner that is dependent on the concentration of antimonite and arsenite in the sample. Thus, the bioluminescence emitted by luciferase can be related to the concentration of antimonite and arsenite in the sample. Concentrations for antimonite and arsenite in the order of 10(-5) M, which corresponds to subattomole levels, can be detected. This bacterial-based sensing system is highly selective for antimonite and arsenite.

Effector specificity mutants of the transcriptional activator NahR of naphthalene degrading Pseudomonas define protein sites involved in binding of aromatic inducers

This work reports a genetic analysis of the interactions between NahR, the LysR-type regulator of the NAH operons for biodegradation of naphthalene in Pseudomonas, and its aromatic effectors. Six mutants encoding NahR variants responsive to salicylate analogs such as benzoate, which is not an inducer for the wild type regulator, were isolated with a polymerase chain reaction-based saturation mutagenesis protocol. Most mutants displaying a specific change of effector profile bore single amino acid substitutions within a short protein segment of 60 residues located at the central portion of the NahR sequence. Some of the protein variants exhibited an increased affinity for salicylate and also for otherwise suboptimal effectors, with apparent Ks' values 5-100-fold lower than those of the wild type NahR protein. In addition, all mutants were activated by inducers bearing novel substituents at positions 1 or 2 of the aromatic ring and displayed also an enhanced tolerance to changes at positions 3 and 4. Correlation between mutations in NahR and the structures of the new effectors suggested that protein sites Met116, Arg132, Asn169, and Arg248 are involved in effector recognition and binding during the earlier steps of the process leading to transcriptional activation of cognate NAH promoters.

Survival of lux-marked bacteria introduced into soil and the rhizosphere of bean (Phaseolus vulgaris L.)

The survival of lux-marked recombinants of Escherichia coli and Bacillus subtilis was studied in the rhizosphere of bean (Phaseolus vulgaris L.) and in bulk soil. The number of E. coli (pSB343) containing a complete lux operon did not differ significantly according to whether they were introduced into soil separately or together with a non-luminescent mutant Pseudomonas fluorescens R2fN. When genetically altered strains of E. coli and B. subtilis bearing a complete or an incomplete lux-reporter system were introduced into soil, the numbers of surviving cells were the same both in the rhizosphere and bulk soil. The insertion of lux genes into bacterial strains therefore does not affect their competitiveness and survival in the rhizosphere and bulk soil.

Biofilm ecology: On-line methods bring new insights into mic and microbial biofouling

Microbial biofilms were formed on coupons with defined coatings in once-through laminar flow fields of controlled bulk-phase composition and shear. Dilute media were utilized to select for biofilm growth. The formation, succession, and stability of the biofilms were monitored with non-destructive on-line methods (fluorescence, bioluminescence, attenuated total reflectance Fourier transform infrared spectrometry [ATR-FTIR] and electrochemical impedance spectroscopy) and by high resolution destructive analysts (viable and direct counts and phospholipid fatty acid signature methods) at the termination of the experiments. Biofilms of reproducible composition can be formed and the order of inoculation of multi-component biofilms affects their composition at harvest. The corrosion rates of mild steel depended on the biofilm composition but not the attached biomass. Examination of biofilms with the scanning vibrating electrode in a microscope field showed effects of heterogeneity in biofilm structure which promoted localized anodic activity. Pseudomonas stains were engineered to contain the lux gene cassette as a "reporter"; and the formation of the exopolymer alginate was shown not to promote attachment of the strain or secondary colonization by Vibrio. Examination of mutants forming different alginate structures showed differential attachment and biofilm structure. Studies of mutants of lipopolysaccharide structure showed differential attachment to substrata. Specific antifouling and fouling-release coatings showed a wide range of attachment and release properties as well as sublethal toxicity.

Luminescence-based systems for detection of bacteria in the environment

The development of techniques for detection and tracking of microorganisms in natural environments has been accelerated by the requirement for assessment of the risks associated with environmental release of genetically engineered microbial inocula. Molecular marker systems are particularly appropriate for such studies and luminescence-based markers have the broadest range of applications, involving the introduction of prokaryotic (lux) or eukaryotic (luc) genes for the enzyme luciferase. Lux or luc genes can be detected on the basis of unique DNA sequences by gene probing and PCR amplification, but the major advantage of luminescence-based systems is the ability to detect light emitted by marked organisms or by luciferase activity in cell-free extracts. Luminescent colonies can be detected by eye, providing distinction from colonies of indigenous organisms, and the sensitivity of plate counting can be increased greatly by CCD imaging. Single cells or microcolonies of luminescent organisms can also be detected in environmental samples by CCD image-enhanced microscopy, facilitating study of their spatial distribution. The metabolic activity of luminescence-marked populations can be quantified by luminometry and does not require extraction of cells or laboratory growth. Metabolic activity, and potential activity, of marked organisms therefore can be measured during colonization of soil particles and plant material in real time without disturbing the colonization process. In comparison with traditional activity techniques, luminometry provides significant increases in sensitivity, accuracy, and, most importantly, selectivity, as activity can be measured in the presence of indigenous microbial communities. The sensitivity, speed, and convenience of luminescence measurements make this a powerful technique that is being applied to the study of an increasingly wide range of ecological problems. These include microbial survival and recovery, microbial predation, plant pathogenicity, phylloplane and rhizosphere colonization and reporting of gene expression in environmental samples.

Susceptibility of suspended and surface-attached Salmonella enteritidis to biocides and elevated temperatures

The differential resistance of substratum-attached, detached, and planktonic cells of Salmonella enteritidis phage type 4 was studied by using several inimical processes and in vivo bioluminescence as a nondestructive, real-time reporter of metabolic activity. Bioluminescence in this strain was mediated by a construction containing the entire lux operon from Photorhabdus luminescens. An excellent correlation between bioluminescence and classical plate count data was obtained when we compared attachment profiles, biocide concentration exponents, and thermal inactivation D values (D value was the time required for a 10-fold reduction in the number of survivors). Biocide challenge of surface-adherent S. enteritidis resulted in concentration exponents that were experimentally indistinguishable from those obtained with Luria-Bertani broth-grown planktonic cells. It appears that cleansing regimes developed by using planktonic cell data are effective against surface-attached cells of this bacterium. Both attached and detached cells exhibited an approximately twofold increase in D values at 52 degrees C compared with values calculated for planktonic cells, strongly indicating that the detached cells exhibited an attached phenotype during the heating process. A model of a physiological adaptive response induced in attached cells and also reflected in detached cells is presented.

Marker proteins for gene expression

Reporter genes are widely used as a rapid and convenient means of measuring molecular genetic events. Their role in experimental strategies has expanded from analysis of the DNA sequences mediating RNA transcription to the broader ensemble of molecular events that define phenotype expression. The several genetic reporters available today impart a range of performance criteria to choose from, including assay convenience and reliability, sensitivity, linearity, simplicity and dynamics.