Towards the development of a new generation of whole-cell bioreporters to sense iron bioavailability in oceanic systems—learning from the case of Synechococcus sp. PCC7002 iron bioreporter

Whole-cell bioreporters are genetically modified micro-organisms designed to sense bioavailable forms of nutrients or toxic compounds in aquatic systems. As they represent the most promising cost-efficient tools available for such purpose, engineering and use of bioreporters is rapidly growing in association with wide applicability. Bioreporters are urgently needed to determine phytoplankton iron (Fe) limitation, which has been reported in up to 30% of the ocean, with consequences affecting Earth's global carbon cycle and climate. This study presents a critical evaluation and optimization of the only Cyanobacteria bioreporter available to sense Fe limitation in marine systems (Synechococcus sp. PCC7002). The nonmonotonic biphasic dose–response curve between the bioreporters’ signal and Fe bioavailability impairs an appropriate data interpretation, highlighting the need for new carefully designed bioreporters. Here, limitations under low Fe concentrations were related to cellular energy stress, nonlinear expression of the targeted promoter and siderophore expression. Furthermore, we provide critical standard criteria for the development of new Fe bioreporters. Finally, based on gene expression data under a range of marine Fe concentrations, we propose novel sensor genes for the development of new Cyanobacteria Fe bioreporters for distinct marine regions.     

Advances in optical detection strategies for reporter signal measurements

Many recent advances in bioreporter technology focus on challenges related to bioengineering, yet in many applications implementation of optical signal measurement is equally susceptible to improvement. For bioluminescent bioreporters, one area of effort lies in the development of semiconductor chip-based detector modules; this holds great promise for ultra-compact and field-deployable instrumentation, but has not yet had a palpable impact on improved detection limits. Regarding lower detection limits, single-molecule detection techniques have seen their first application to bioreporters, and preliminary results serve as an indication of future promise. Another technique applicable to fluorescent bioreporters is fluorescence flow cytometry, which is rapid, suitable for high-throughput screening, and lends itself to increased analytical specificity through simple algorithmic approaches to data treatment.     

Improving the sensitivity of bacterial bioreporters for heavy metals

Whole-cell bacterial bioreporters represent a convenient testing method for quantifying the bioavailability of contaminants in environmental samples. Despite the fact that several bioreporters have been constructed for measuring heavy metals, their application to environmental samples has remained minimal. The major drawbacks of the available bioreporters include a lack of sensitivity and specificity. Here, we report an improvement in the limit of detection of bacterial bioreporters by interfering with the natural metal homeostasis system of the host bacterium. The limit of detection of a Pseudomonas putida KT2440-based Zn/Cd/Pb-biosensor was improved by a factor of up to 45 by disrupting four main efflux transporters for Zn/Cd/Pb and thereby causing the metals to accumulate in the cell. The specificity of the bioreporter could be modified by changing the sensor element. A Zn-specific bioreporter was achieved by using the promoter of the cadA1 gene from P. putida as a sensor element. The constructed transporter-deficient P. putida reporter strain detected Zn(2+) concentrations about 50 times lower than that possible with other available Zn-bioreporters. The achieved detection limits were significantly below the permitted limit values for Zn and Pb in water and in soil, allowing for reliable detection of heavy metals in the environment.     

Development of Bioluminescent Bioreporters for In Vitro and In Vivo Tracking of Yersinia pestis

Yersinia pestis causes an acute infection known as the plague. Conventional techniques to enumerate Y. pestis can be labor intensive and do not lend themselves to high throughput assays. In contrast, bioluminescent bioreporters produce light that can be detected using plate readers or optical imaging platforms to monitor bacterial populations as a function of luminescence. Here, we describe the development of two Y. pestis chromosomal-based luxCDABE bioreporters, Lux_PtolC and Lux_PcysZK. These bioreporters use constitutive promoters to drive expression of luxCDABE that allow for sensitive detection of bacteria via bioluminescence in vitro. Importantly, both bioreporters demonstrate a direct correlation between bacterial numbers and bioluminescence, which allows for bioluminescence to be used to compare bacterial numbers. We demonstrate the use of these bioreporters to test antimicrobial inhibitors (Lux_PtolC) and monitor intracellular survival (Lux_PtolC and Lux_PcysZK) in vitro. Furthermore, we show that Y. pestis infection of the mouse model can be monitored using whole animal optical imaging in real time. Using optical imaging, we observed Y. pestis dissemination and differentiated between virulence phenotypes in live animals via bioluminescence. Finally, we demonstrate that whole animal optical imaging can identify unexpected colonization patterns in mutant-infected animals.     

Functionalization of whole‐cell bacterial reporters with magnetic nanoparticles

We developed a biocompatible and highly efficient approach for functionalization of bacterial cell wall with magnetic nanoparticles (MNPs). Three Acinetobacter baylyi ADP1 chromosomally based bioreporters, which were genetically engineered to express bioluminescence in response to salicylate, toluene/xylene and alkanes, were functionalized with 18 ± 3 nm iron oxide MNPs to acquire magnetic function. The efficiency of MNPs functionalization of Acinetobacter bioreporters was 99.96 ± 0.01%. The MNPs‐functionalized bioreporters (MFBs) can be remotely controlled and collected by an external magnetic field. The MFBs were all viable and functional as good as the native cells in terms of sensitivity, specificity and quantitative response. More importantly, we demonstrated that salicylate sensing MFBs can be applied to sediments and garden soils, and semi‐quantitatively detect salicylate in those samples by discriminably recovering MFBs with a permanent magnet. The magnetically functionalized cells are especially useful to complex environments in which the indigenous cells, particles and impurities may interfere with direct measurement of bioreporter cells and conventional filtration is not applicable to distinguish and harvest bioreporters. The approach described here provides a powerful tool to remotely control and selectively manipulate MNPs‐functionalized cells in water and soils. It would have a potential in the application of environmental microbiology, such as bioremediation enhancement and environment monitoring and assessment.     

Highly Sensitive,Highly Specific Whole-Cell Bioreporters for the Detection of Chromate in Environmental Samples

Microbial bioreporters offer excellent potentialities for the detection of the bioavailable portion of pollutants in contaminated environments, which currently cannot be easily measured. This paper describes the construction and evaluation of two microbial bioreporters designed to detect the bioavailable chromate in contaminated water samples. The developed bioreporters are based on the expression of gfp under the control of the chr promoter and the chrB regulator gene of TnOtChr determinant from Ochrobactrum tritici 5bvl1. pCHRGFP1 Escherichia coli reporter proved to be specific and sensitive, with minimum detectable concentration of 100 nM chromate and did not react with other heavy metals or chemical compounds analysed. In order to have a bioreporter able to be used under different environmental toxics, O. tritici type strain was also engineered to fluoresce in the presence of micromolar levels of chromate and showed to be as specific as the first reporter. Their applicability on environmental samples (spiked Portuguese river water) was also demonstrated using either freshly grown or cryo-preserved cells, a treatment which constitutes an operational advantage. These reporter strains can provide on-demand usability in the field and in a near future may become a powerful tool in identification of chromate-contaminated sites.     

Field‐compatible protocol for detecting tetracyclines with bioluminescent bioreporters without pipetting steps

Whole‐cell bioreporters are living organisms and thus using them for detecting environmental contaminants would reflect biological effects of these pollutants. However, bioreporters are not widely used in field studies. Many of the bioreporter field protocols are suitable for liquid samples or include pipetting steps, which is a demanding task outside the laboratory. We present a bioreporter protocol without pipetting or sample type requirements. The protocol utilizes polyester swabs, commonly used in cleanroom technology. As an example contaminant, we used tetracycline and generated test samples with known concentrations up to the maximum tetracycline residue limit of milk set by the European Union (EU) regulation. The matrices of the test samples were Milli‐Q water, milk and soil. The swabs were first dipped in the bioreporter cell cultures and then to test samples and luminescence was measured after incubation. The standard deviation of measurements from ten replicate swabs was in the same range as commonly in pipetting protocols (4–19%). The test samples with lowest tetracycline concentration (5 ng mL^?1) were distinguished from the control samples (0 ng mL^?1 tetracycline). Our results show that swabs can be used together with luminescent whole cell bioreporters, making it possible to conduct the measurements in field conditions.     

Bioreporters: gfp versus lux revisited and single-cell response

Genetically engineered organisms expressing spectroscopically active reporter molecules in response to chemical effectors display great potential as living transducers in sensing applications. Green fluorescent protein (gfp gene) bioreporters have distinct advantages over luminescent couterparts (lux gene), including applicability at the single-cell level, but are typically less sensitive. Here we describe a gfp-bearing bioreporter that is sensitive to naphthalene (a poorly water soluble pollutant behaving like a large class of hydrophobic compounds), is suitable for use in chemical assays and bioavailability studies, and has detection limits comparable to lux-bearing bioreporters for higher efficiency detection strategies. Simultaneously, we find that the exploitation of population response data from single-cell analysis is not an algorithmic conduit to enhanced signal detection and hence lower effector detection limits, as normally assumed. The assay reported functions to equal effect with or without biocide.     

Development of bioreporter assays for the detection of bioavailability of long-chain alkanes based on the marine bacterium Alcanivorax borkumensis strain SK2

Long-chain alkanes are a major component of crude oil and therefore potentially good indicators of hydrocarbon spills. Here we present a set of new bacterial bioreporters and assays that allow to detect long-chain alkanes. These reporters are based on the regulatory protein AlkS and the alkB1 promoter from Alcanivorax borkumensis SK2, a widespread alkane degrader in marine habitats. Escherichia coli cells with the reporter construct reacted strongly to octane in short-term (6 h) aqueous suspension assays but very slightly only to tetradecane, in line with what is expected from its low water solubility. In contrast, long-term assays (up to 5 days) with A. borkumensis bioreporters showed strong induction with tetradecane and crude oil. Gel-immobilized A. borkumensis reporter cells were used to demonstrate tetradecane and crude oil bioavailability at a distance from a source. Alcanivorax borkumensis bioreporters induced fivefold more rapid and more strongly when allowed physical contact with the oil phase in standing flask assays, suggesting a major contribution of adhered cells to the overall reporter signal. Using the flask assays we further demonstrated the effect of oleophilic nutrients and biosurfactants on oil availability and degradation by A. borkumensis. The fluorescence signal from flask assays could easily be captured with a normal digital camera, making such tests feasible to be carried out on, e.g. marine oil responder vessels in case of oil accidents.     

Whole-cell living biosensors—are they ready for environmental application?

Since the development of the first whole-cell living biosensor or bioreporter about 15 years ago, construction and testing of new genetically modified microorganisms for environmental sensing and reporting has proceeded at an ever increasing rate. One and a half decades appear as a reasonable time span for a new technology to reach the maturity needed for application and commercial success. It seems, however, that the research into cellular biosensors is still mostly in a proof-of-principle or demonstration phase and not close to extensive or commercial use outside of academia. In this review, we consider the motivations for bioreporter developments and discuss the suitability of extant bioreporters for the proposed applications to stimulate complementary research and to help researchers to develop realistic objectives. This includes the identification of some popular misconceptions about the qualities and shortcomings of bioreporters.     

Illuminating the detection chain of bacterial bioreporters

Engineering bacteria for measuring chemicals of environmental or toxicological concern (bioreporter bacteria) has grown slowly into a mature research area. Despite many potential advantages, current bioreporters do not perform well enough to comply with environmental detection standards. Basically, the reasons for this are the lack of engineering principles in the detection chain in the bioreporters. Here, we dissect critical steps in the detection chain and illustrate how bioreporter design could be improved by mutagenizing specificity and selectivity of the sensing and regulatory proteins, by newer expression strategies and application of different signalling networks. Furthermore, we describe how redesigning bioreporter assays with respect to pollutant transport into the cells and application of other detection devices can decrease detection limits and increase the speed of detection.     

Calibration and deployment of custom-designed bioreporters for protecting biological remediation consortia from toxic shock

We have previously described the development of a panel of site-specific lux-based bioreporters from an industrial wastewater treatment system remediating coking effluents. The Pseudomonad strains carry a stable chromosomal copy of the luxCDABE operon from Photorhabdus luminescens and display proportional responses in bioluminescence decay with increasing phenol concentration up to 800 mg l-1. In this work we describe their deployment to provide a strategic sensing network for protecting bacterial communities involved in the biological breakdown of coking effluents. This evaluation demonstrated the utility of strategic placement of reporters around heavy industry treatment systems and the reliability of the reporter strains under normal operational conditions. Mono-phenol or total phenolic variation within the treatment system accounted for>65-80% of the luminescence response. The reporters exhibited stable luminescence output during normal operations with maximum standard deviations of luminescence over time of c. 5-15% depending on the treatment compartment. Furthermore, deployment of the bioreporters over a 5-month period allowed the determination of an operational range (OR) for each reporter for effluent samples from each compartment. The OR allowed a convenient measure of toxicity effects between treatment compartments and accurately reflected a specific pollution event occurring within compartments of the treatment system. This work demonstrates the utility of genetic modification to provide ecologically relevant bioreporters, extends the sensing capabilities currently obtained through marine derived biosensors and significantly enhances the potential for in situ deployment of reporting agents.     

A simple solid phase assay for the detection of 2,4-D in soil

Contaminated soils are usually characterized using chemical analyses. However, these do not assess the bioavailability of pollutants, a factor which may be important in estimating the risks associated with contamination. Thus there is a need to support chemical analyses with information on biological effects to determine the potential risks a pollutant may pose in the soil. Although bacterial bioreporters have been used to detect the presence of contaminants in soils, in general these studies have been carried out in slurries or soil extracts rather than soil itself. The following study presents the development of a simple solid-phase bioassay for the direct detection of the herbicide 2,4-dichlorophenoxy acetic acid (2,4-D) in soil using Ralstonia eutropha JMP 134-32, a luxCDABE-based 2,4-D whole cell bioreporter. The bioreporter was spotted onto glass microfibre filter discs that allowed its retrieval and analysis after exposure to 2,4-D amended soils. These disc-fixed cells responded in a concentration dependent manner to 2,4-D in solution (0-25 mg/L) and in spiked soil (0-50 mg/kg). The influence of environmental factors on bioavailability was demonstrated in soil with a low moisture content which prevented 2,4-D-induced bioluminescence but which did not affect bioluminescence from already induced cells. This rapid and low cost bioassay provides a proof of concept demonstrating that retrievable disk-fixed cells can be induced in soil, thus providing a measure of solid-phase bioavailability. This method overcomes some of the limitations associated with the inoculation and monitoring of bioreporters directly in soil. Additionally, this simple system should be amenable to use with other bioreporters.     

OPTIMIZATION OF IRON‐DEPENDENT CYANOBACTERIAL (SYNECHOCOCCUS,CYANOPHYCEAE) BIOREPORTERS TO MEASURE IRON BIOAVAILABILITY1

Complex chemistry and biological uptake pathways render iron bioavailability particularly difficult to assess in natural waters. Bioreporters are genetically modified organisms that are useful tools to directly sense the bioavailable fractions of solutes. In this study, three cyanobacterial bioreporters derived from Synechococcus PCC 7942 were examined for the purpose of optimizing the response to bioavailable Fe. Each bioreporter uses a Fe‐regulated promoter (isiAB, irpA and mapA), modulated by distinct mechanisms under Fe deficiency, fused to a bacterial luciferase (luxAB). In order to provide a better understanding of the way natural conditions may affect the ability of the bioreporter to sense iron bioavailability, the effect of relevant environmental parameters on the response to iron was assessed. Optimal conditions (and limits of applicability) for the use of these bioreporters on the field were determined to be: a 12 h (12–24 h) exposure time, temperature of 15°C (15°C–22°C), photon flux density of 100 μmol photons·m^?2·s^?1 (37–200 lmol photons·m^?2·s^?1), initial biomass of 0.6–0.8 lg chlorophyll a (chl a)·L^?1 (0.3–1.5 lg chl a·L^?1) or approximately 10⁵ bioreporter cells·mL^?1, high phosphate (10 lM), and low micronutrients (absent). The measured luminescence was optimal with an exogenous addition of 60 lM aqueous decanal substrate allowing a 5 min reaction time in the dark before analysis. This study provides important considerations relating to the optimization in the use of bioreporters under field conditions that can be used for method development of other algal and cyanobacterial bioreporters in aquatic systems.     

Transforming cyanobacteria into bioreporters of biological relevance

Microbial bioreporters play an important role in environmental monitoring and ecotoxicology. Microorganisms that are genetically modified with reporter genes can be used in various formats to determine the bioavailability of chemicals and their effect on living organisms. Cyanobacteria are abundant in the photosynthetic biosphere and have considerable potential with regards to broadening bioreporter applications. Two recent studies described novel cyanobacterial reporters for the detection of environmental toxicants and iron availability.     

Luciferase and fluorescent protein as dual reporters analyzing the effect of <Emphasis Type="Italic">n</Emphasis>-dodecyltrimethylammonium bromide on the physiology of <Emphasis Type="Italic">Pseudomonas putida</Emphasis>

With the growing interest in using surfactants to improve microbial cell performance for whole-cell biocatalysis and bioremediation, understanding the interactions between surfactants and bacteria is of great importance. By using cyanine fluorescent protein (CFP) and bacterial luciferase (LUX) as dual bioreporters, the effects of n-dodecyltrimethylammonium bromide (DTAB) on the whole cells and intracellular proteins in Pseudomonas putida cultures were quantitatively and systematically studied. The dual reporter system was shown to be a useful indicator to assess the effect of DTAB treatment on whole-cell metabolic activity, membrane permeability, and cellular enzyme activity. CFP was useful to assess the leakage of intracellular enzymes and the lysis of cells and was able to reflect the activities of most cellular enzymes, while LUX reflected the permeability of cell membranes and cellular metabolic activity. The validity of CFP–LUX dual bioreporters was further confirmed by detecting changes in extracellular proteins, membrane potential, oxygen consumption rate (OUR), and intracellular catechol 2,3-dioxygenase (C23O) activity with the addition of DTAB. The dual LUX–CFP bioreporter is a useful tool for analyzing the surfactant–bacterium interactions for biotechnological applications.