Prokaryotic gene profiling assays to detect sediment toxicity: evaluating the ecotoxicological relevance of a cell-based assay

Qualitative and quantitative assessment of genotoxins usingSRRzlysis reporter under the control of a newly designed SOS responsive promoter inEscherichia coli

A new bacterial genotoxicity detection strain was constructed, in which the cell lysis gene of SRRz from a lambda phage was controlled by a new designed SOS responsive element, designated as Escherichia coli BL21/pUC-PST. The biosensor responded only after 0.5 h contact with mutagens and the changes in cell culture turbidity could be easily differentiated with the naked eyes from the control sample. This SOS/SRRz system presented a dose-dependent manner to five model DNA-damaging agents with an improved detection sensitivity. The limits of detection (LODs) were 0.026 μM for mitomycin C, 320.4 μM for azinphos-methyl, 34.4 μM for methyl methanesulfonate, 4.6 μM for dithianone and 6.0 μM for dichlofluanid, which were much lower than previously reported. By performing binary and ternary mixture experiments, the toxic equivalency concept was validated in the E. coli SOS/SRRz system by comparison with bioanalytical equivalent concentrations (BEQ) and overall toxic equivalent concentration (TEQ_mixture) using Cr(vi) as the reference compound. Pearson analysis indicated that a strong correlation existed between the TEQ_mixture and BEQ values. Thus the TEQ_mixture could be presented as the Cr(vi) equivalent concentration from its dose–effect lysis profiles for the environmental sample. The proposed genotoxicity reporter strain allows for easier qualitative characterization and quantitative interpretation of the TEQ_mixture values using Cr(vi) as the reference for environmental water samples.

A new bacterial genotoxicity detection strain was constructed, in which the cell lysis gene of SRRz from a lambda phage was controlled by a new designed SOS responsive element, designated as Escherichia coli BL21/pUC-PST.

In vitro or not in vitro: a short journey through a long history

The aim of ecotoxicology is to study toxic effects on constituents of ecosystems, with the protection goal being populations and communities rather than individual organisms. In this ecosystem perspective, the use of in vitro methodologies measuring cellular and subcellular endpoints at a first glance appears to be odd. Nevertheless, more recently in vitro approaches gained momentum in ecotoxicology. In this article, we will discuss important application domains of in vitro methods in ecotoxicology. One area is the use of in vitro assays to replace, reduce, and refine (3R) in vivo tests. Research in this field has focused mainly on the use of in vitro cytotoxicity assays with fish cells as non-animal alternative to the in vivo lethality test with fish and on in vitro biotransformation assays as part of an alternative testing strategy for bioaccumulation testing with fish. Lessons learned from this research include the importance of a critical evaluation of the sensitivity, specificity and exposure conditions of in vitro assays, as well as the availability of appropriate in vitro-in vivo extrapolation models. In addition to this classical 3R application, other application domains of in vitro assays in ecotoxicology include the screening and prioritization of chemical hazards, the categorization of chemicals according to their modes of action and the provision of mechanistic information for the pathway-based prediction of adverse outcomes. The applications discussed in this essay may highlight the potential of in vitro technologies to enhance the environmental hazard assessment of single chemicals and complex mixtures at a reduced need of animal testing.

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.

Towards improved biomonitoring tools for an intensified sustainable multi-use environment

The increasing use of our environment for multiple contrasting activities (e.g. fisheries, tourism) will have to be accompanied by improved monitoring of environmental quality, to avoid transboundary conflicts and ensure long-term sustainable intensified usage. Biomonitoring approaches are appropriate for this, since they can integrate biological effects of environmental exposure rather than measure individual compound concentrations. Recent advances in biomonitoring concepts and tools focus on single-cell assays and purified biological components that can be miniaturized and integrated in automated systems. Despite these advances, we are still very far from being able to deploy bioassays routinely in environmental monitoring, mostly because of lack of experience in interpreting responses and insufficient robustness of the biosensors for their environmental application. Further future challenges include broadening the spectrum of detectable compounds by biosensors, accelerate response times and combining sample pretreatment strategies with bioassays.

Changes in the expression of cyp35a family genes in the soil nematode Caenorhabditis elegans under controlled exposure to chlorpyrifos using passive dosing

In order to use sensitive molecular-level biomarkers for the evaluation of environmental risks, it is necessary to establish a quantitative dose-response relationship. Passive dosing is regarded as a promising new technique for maintaining a constant exposure condition of hydrophobic chemicals in the assay medium. The main goals of the present study were (1) to quantitatively compare gene expression results obtained using the passive dosing method and the conventional spiking method and (2) to investigate changes in gene expression with respect to the free concentration and exposure duration using passive dosing. Chlorpyrifos (CP), which is oxidized by the cytochrome P450 monooxygenases, was selected as a model chemical, and the expression of cytochrome P450 subfamily protein 35A gene series (cyp-35a1-5) was analyzed by quantitative real-time PCR on soil nematode Caenorhabditis elegans. Whereas the free concentration of CP rapidly decreased and the expression of cyp genes varied with the volume of exposure medium and the test duration when the spiking method was used, the free concentration in the assay medium was stable throughout the experiment when the passive dosing method was used. In addition, the level of gene expression increased with exposure time up to 8 h and with increasing CP concentration. The observed increased gene expression could be explained by increasing body residue concentration of CP with exposure time. In conclusion, quantitative dose-response relationships for gene expression biomarkers could be obtained for highly hydrophobic chemicals when the constant exposure condition is provided and the free concentration is used as the dose-metric.

Toxicity ranking and toxic mode of action evaluation of commonly used agricultural adjuvants on the basis of bacterial gene expression profiles

The omnipresent group of pesticide adjuvants are often referred to as “inert” ingredients, a rather misleading term since consumers associate this term with “safe”. The upcoming new EU regulation concerning the introduction of plant protection products on the market (EC1107/2009) includes for the first time the demand for information on the possible negative effects of not only the active ingredients but also the used adjuvants. This new regulation requires basic toxicological information that allows decisions on the use/ban or preference of use of available adjuvants. In this study we obtained toxicological relevant information through a multiple endpoint reporter assay for a broad selection of commonly used adjuvants including several solvents (e.g. isophorone) and non-ionic surfactants (e.g. ethoxylated alcohols). The used assay allows the toxicity screening in a mechanistic way, with direct measurement of specific toxicological responses (e.g. oxidative stress, DNA damage, membrane damage and general cell lesions). The results show that the selected solvents are less toxic than the surfactants, suggesting that solvents may have a preference of use, but further research on more compounds is needed to confirm this observation. The gene expression profiles of the selected surfactants reveal that a phenol (ethoxylated tristyrylphenol) and an organosilicone surfactant (ethoxylated trisiloxane) show little or no inductions at EC₂₀ concentrations, making them preferred surfactants for use in different applications. The organosilicone surfactant shows little or no toxicity and good adjuvant properties. However, this study also illustrates possible genotoxicity (induction of the bacterial SOS response) for several surfactants (POEA, AE, tri-EO, EO FA and EO NP) and one solvent (gamma-butyrolactone). Although the number of compounds that were evaluated is rather limited (13), the results show that the used reporter assay is a promising tool to rank commonly used agricultural adjuvants based on toxicity and toxic mode of action data.

Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting

Mutants were produced in the A-domain of HbpR, a protein belonging to the XylR family of σ(54)-dependent transcription activators, with the purpose of changing its effector recognition specificity from 2-hydroxybiphenyl (2-HBP, the cognate effector) to 2-chlorobiphenyl (2-CBP). Mutations were introduced in the hbpR gene part for the A-domain via error-prone polymerase chain reaction, and assembled on a gene circuitry plasmid in Escherichia coli, permitting HbpR-dependent induction of the enhanced green fluorescent protein (egfp). Cells with mutant HbpR proteins responsive to 2-CBP were enriched and separated in a flow cytometry-assisted cell-sorting procedure. Some 70 mutants were isolated and the A-domain mutations mapped. One of these had acquired true 2-CBP recognition but reacted hypersensitively to 2-HBP (20-fold more than the wild type), whereas others had reduced sensitivity to 2-HBP but a gain of 2-CBP recognition. Sequencing showed that most mutants carried double or triple mutations in the A-domain gene part, and were not located in previously recognized conserved residues within the XylR family members. Further selection from a new mutant pool prepared of the hypersensitive mutant did not result in increased 2-CBP or reduced 2-HBP recognition. Our data thus demonstrate that a one-step in vitro 'evolutionary' adaptation of the HbpR protein can result in both enhancement and reduction of the native effector recognition.

Selection of scFv phages specific for chloramphenicol acetyl transferase (CAT), as alternatives for antibodies in CAT detection assays

Reporter gene assays are commonly used in applied toxicology to measure the transcription of genes involved in toxic responses. In these reporter gene assays, transgenic cells are used, which contain a promoter-operator region of a gene of interest fused to a reporter gene. The transcription of the gene of interest can be measured by the detection of the reporter protein. Chloramphenicol acetyl transferase (CAT) is frequently used as a reporter protein in mammalian reporter gene assays. Although CAT can be measured by different detection systems, like enzymatic and immune assays, most of these tests are expensive, time-consuming and labor-intensive. The excellent characteristics of phages, like their high affinity and specificity, their fast, cheap and animal-friendly manufacturing process with low batch-to-batch variations and their stability, make them appropriate as alternatives for antibodies in detection assays. Therefore, in this study single-chain variable fragment (scFv) phages were selected with affinity for CAT. Several scFv phages were selected that showed affinity towards CAT in a screening ELISA. Surface plasmon resonance analyses showed that the tested scFv phages have an affinity for CAT with a dissociation constant (K(d)) around 1 µM. The selected scFv phages in this study could be used as capture elements in a highly sensitive sandwich ELISA to detect CAT concentration as low as 0.1 ng ml⁻¹ or 4 pM. This low detection limit demonstrates the potential of the scFv phages as an alternative for capturing antibodies in a highly sensitive detection test to measure CAT concentrations in reporter gene assays.

Escherichia coli as a bioreporter in ecotoxicology

Ecotoxicological assessment relies to a large extent on the information gathered with surrogate species and the extrapolation of test results across species and different levels of biological organisation. Bacteria have long been used as a bioreporter for genotoxic testing and general toxicity. Today, it is clear that bacteria have the potential for screening of other toxicological endpoints. Escherichia coli has been studied for years; in-depth knowledge of its biochemistry and genetics makes it the most proficient prokaryote for the development of new toxicological assays. Several assays have been designed with E. coli as a bioreporter, and the recent trend to develop novel, better advanced reporters makes bioreporter development one of the most dynamic in ecotoxicology. Based on in-depth knowledge of E. coli, new assays are being developed or existing ones redesigned, thanks to the availability of new reporter genes and new or improved substrates. The technological evolution towards easier and more sensitive detection of different gene products is another important aspect. Often, this requires the redesign of the bacterium to make it compatible with the novel measuring tests. Recent advances in surface chemistry and nanoelectronics open the perspective for advanced reporter based on novel measuring platforms and with an online potential. In this article, we will discuss the use of E. coli-based bioreporters in ecotoxicological applications as well as some innovative sensors awaited for the future.

Application of a luminescence-based biosensor for assessing naphthalene biodegradation in soils from a manufactured gas plant

Despite numerous reviews suggesting that microbial biosensors could be used in many environmental applications, in reality they have failed to be used for which they were designed. In part this is because most of these sensors perform in an aqueous phase and a buffered medium, which is in contrast to the nature of genuine environmental systems. In this study, a range of non-exhaustive extraction techniques (NEETs) were assessed for (i) compatibility with a naphthalene responsive biosensor and (ii) correlation with naphthalene biodegradation. The NEETs removed a portion of the total soil naphthalene in the order of methanol > HPCD > betaCD > water. To place the biosensor performance to NEETs in context, a biodegradation experiment was carried out using historically contaminated soils. By coupling the HPCD extraction with the biosensor, it was possible to assess the fraction of the naphthalene capable of undergoing microbial degradation in soil.

A Determination of Metallothionein in Larvae of Freshwater Midges (Chironomus riparius) Using Brdicka Reaction

Among wide spectrum of biomolecules induced by various stress factors low molecular mass protein called metallothionein (MT) is suitable for assessment of the heavy metal environmental pollution. The aim of this work was to determine the metallothionein and total thiols content in larvae of freshwater midges (Chironomus riparius) sampled from laboratory exposure to cadmium(II) ions and from field studies using differential pulse voltammetry Brdicka reaction. Unique electrochemical instrument, stationary electrochemical analyser Autolab coupled with autosampler, was utilized for the analysis of the samples. The detection limit for MT was evaluated as 5 nM. The larvae exposed to two doses (50 ng/g or 50 μg/g) of cadmium(II) ions for fifteen days under laboratory controlled conditions were at the end of the exposure killed, homogenized and analysed. MT content in control samples was 1.2 μM, in larvae exposed to 50 ng Cd/g it was 2.0 μM and in larvae exposed to 50 μg Cd/g 2.9 μM. Moreover at field study chironomid larvae as well as sediment samples have been collected from eight field sites with different levels of pollution by heavy. The metals content (chromium, nickel, copper, zinc, arsenic, molybdenum, cadmium, tin and lead) in the sediment and or MT content in the chironomid larvae were determined by inductively coupled plasma mass spectrometry or Brdicka reaction, respectively.

Mode of action clustering of chemicals and environmental samples on the bases of bacterial stress gene inductions

Over the years, environment and the human population have seen an increasing exposure to both existing and newly developed chemicals. It is generally accepted that at least some of those are toxic, albeit as pure compound or in combination with others. In response to a growing public awareness and scientific data, the new European chemicals legislation (Registration, Evaluation and Authorization of Chemicals) is under implementation at the moment. As a consequence, during the coming years about 30,000 chemicals have to be assessed on their potential hazard for man and biota. Part of this assessment will be done using existing and new in vitro tests offering insight into the toxicity of chemicals and into their toxicological mode of action. This study presents data on a battery of 14 bacterial reporter gene assay allowing mode of action determination and statistical grouping of chemicals based on their induction profile. Gene induction results are used to group reference chemicals in a statistical cascade employing hierarchical tree and k-means clustering for initial grouping. Both complementary, yet mathematically different, algorithms are consequently confirmed by principal component analysis (PCA). The gene induction profiles of an environmental extract with documented in vivo effects and a chemical with limited toxicological are data available and projected in the PCA vector space. The projection allows correct mode of action grouping and indicates that effect predictions based on the known toxicological effects of the reference compounds can be made.