Internal arsenite bioassay calibration using multiple bioreporter cell lines

A brief note on substantial sub-daily arsenic variability in pumping drinking-water wells in New Hampshire

Large variations in redox-related water parameters, like pH and dissolved oxygen (DO), have been documented in New Hampshire (United States) drinking-water wells over the course of a few hours under pumping conditions. These findings suggest that comparable sub-daily variability in dissolved concentrations of redox-reactive and toxic arsenic (As) also may occur, representing a potentially critical public-health data gap and a fundamental challenge for long-term As-trends monitoring. To test this hypothesis, discrete groundwater As samples were collected approximately hourly during one day in May and again in August 2019 from three New Hampshire drinking-water wells (2 public-supply, 1 private) under active pumping conditions. Collected samples were assessed by laboratory analysis (total As [AsTot], As(III), As(V)) and by field analysis (AsTot) using a novel integrated biosensor system. Laboratory analysis revealed sub-daily variability (range) in AsTot concentrations equivalent to 16 % - 36 % of that observed in the antecedent 3-year bimonthly trend monitoring. Thus, the results indicated that, along with previously demonstrated seasonality effects, the timing and duration of pumping are important considerations when assessing trends in drinking-water As exposures and concomitant risks. Results also illustrated the utility of the field sensor for monitoring and management of AsTot exposures in near-real-time.

A critical review of on-site inorganic arsenic screening methods

Approximately 94 to 220 million people worldwide are at risk of drinking well water containing arsenic > 10 µg/L, the WHO guideline value. To identify non-compliant domestic wells, assess health risks and reduce exposure, accurate and rapid on-site inorganic arsenic screening methods are desirable because all domestic wells worldwide need to be tested. Here, the principles, advantages and limitations of commonly used colorimetry, electrochemistry, and biosensing methods are critically reviewed, with the performance compared with laboratory-based benchmark methods. Most commercial kits are based on the classic Gutzeit reaction. Despite being semi-quantitative, the more recent and more expensive products display improved and acceptable accuracy and shorter testing time (∼10 min). Carried out by trained professionals, electrochemical methods are also feasible for on-site analysis, although miniaturization is desirable yet challenging. Biosensing using whole bacterial cells or bio-engineered materials such as aptamers is promising, if incorporated with function specific nanomaterials and biomaterials. Since arsenic is frequently found as arsenite in reducing groundwater and subject to oxidation during sampling, transportation and storage, on-site separation and sample preservation are feasible but the specific methods should be chosen based on sample matrix and tested before use. To eliminate arsenic exposure among hundreds of millions of mostly rural residents worldwide, we call for concerted efforts in research community and regulatory authority to develop accurate, rapid, and affordable tests for on-site screening and monitoring of arsenic in drinking water. Access to affordable testing will benefit people who are socioeconomically disadvantaged.

A Novel Whole-Cell Biosensor for Bioavailable Antimonite in Water and Sediments

Antimony (Sb) is an emerging contaminant, and its on-site speciation analysis is central to the accurate evaluation of its bioavailability and toxicity. The whole-cell biosensors (WCBs) for Sb(III) are promising but challenging due to the lack of Sb(III)-specific recognition components. Here, we constructed a novel Sb(III)-specific WCB using an Sb(III) transcriptional regulator (antR) and its cognate promoter (P_ant). To prevent the promoter leakage of P_ant, an additional regulatory gene, antR, was inserted downstream of the Sb(III)-inducible promoter, improving the sensitivity of the WCB by an order of magnitude and reaching the detection limit at 0.009 μM, which is lower than the WHO drinking water standard of Sb. Moreover, the WCB with double antR showed a high specificity toward Sb(III) compared with interfering ions at 3 orders of magnitude higher concentrations. This WCB was capable of measuring Sb(III) bioavailability in natural waters and sediments on-site, and its results were not statistically different from the chemical analysis. The insights gained from this work demonstrate that the addition of regulatory genes prevents promoter leakage and improves the sensitivity of WCBs in field applications. IMPORTANCE Antimony (Sb) is a redox-sensitive pollutant ubiquitous in the environment. Sb(III) is dominant in the subsurface and is readily oxidized to less toxic Sb(V) upon exposure to air, and therefore, on-site Sb speciation analysis is essential to evaluate its bioavailability and toxicity. Dissolved Sb concentration and speciation can be determined accurately using on-site chemical sensors, but chemical sensors have difficulty determining the bioavailable Sb(III) that is taken up by the cells. Here, we constructed an Sb(III)-specific whole-cell biosensor (WCB) using double Sb(III) transcriptional regulators (antR) downstream of its cognate promoter P_ant. With an additional antR, the sensitivity of the WCB was improved by approximately 10 times, and the promoter leakage commonly found in WCBs was inhibited. Integrated with a tea-bag design, the WCB is able to measure Sb(III) bioavailability in natural water and sediments on-site. This study demonstrates the importance of inserting one more regulatory gene to improve sensitivity.

Duckweed: a potential phytosensor for heavy metals

Globally, heavy metal (HM) contamination is one of the primary causes of environmental pollution leading to decreased quality of life for those affected. In particular, HM contamination in groundwater poses a serious risk to human health and the potential for destabilization of aquatic ecosystems. At present, strategies to remove HM contamination from wastewater are inefficient, costly, laborious, and often the removal poses as much risk to the environment as the initial contamination. Phytoremediation, plant-based removal of contaminants from soil or water, has long been viewed as an economical and sustainable solution to remove toxic metals from the environment. However, to date, phytoremediation has demonstrated limited successes despite a large volume of literature supporting its potential. A key aspect for achieving robust and meaningful phytoremediation is the selection of a plant species that is well suited to the task. For the removal of pollutants from wastewater, hydrophytes, like duckweed, exhibit significant potential due to their rapid growth on nutrient-rich water, ease of collection, and ability to survive in various ecosystems. As a model for ecotoxicity studies, duckweed is an ideal candidate, as it is easy to cultivate under controlled and even sterile conditions, and the rapid growth enables multi-generational studies. Similarly, recent advances in the genetic engineering and genome-editing of duckweed will enable the transition from fundamental ecotoxicity studies to engineered solutions for phytoremediation of HMs. This review will provide insight into the suitability of duckweeds for phytoremediation of HMs and strategies for engineering next-generation duckweed to provide real-world environmental solutions.

Highly Sensitive Whole-Cell Biosensor for Cadmium Detection Based on a Negative Feedback Circuit

Although many whole-cell biosensors (WCBs) for the detection of Cd2+ have been developed over the years, most lack sensitivity and specificity. In this paper, we developed a Cd2+ WCB with a negative feedback amplifier in P. putida KT2440. Based on the slope of the linear detection curve as a measure of sensitivity, WCB with negative feedback amplifier greatly increased the output signal of the reporter mCherry, resulting in 33% greater sensitivity than in an equivalent WCB without the negative feedback circuit. Moreover, WCB with negative feedback amplifier exhibited increased Cd2+ tolerance and a lower detection limit of 0.1 nM, a remarkable 400-fold improvement compared to the WCB without the negative feedback circuit, which is significantly below the World Health Organization standard of 27 nM (0.003 mg/L) for cadmium in drinking water. Due to the superior amplification of the output signal, WCB with negative feedback amplifier can provide a detectable signal in a much shorter time, and a fast response is highly preferable for real field applications. In addition, the WCB with negative feedback amplifier showed an unusually high specificity for Cd2+ compared to other metal ions, giving signals with other metals that were between 17.6 and 41.4 times weaker than with Cd2+. In summary, the negative feedback amplifier WCB designed in this work meets the requirements of Cd2+ detection with very high sensitivity and specificity, which also demonstrates that genetic negative feedback amplifiers are excellent tools for improving the performance of WCBs.

Modular tuning engineering and versatile applications of genetically encoded biosensors

Genetically encoded biosensors have a diverse range of detectable signals and potential applications in many fields, including metabolism control and high-throughput screening. Their ability to be used in situ with minimal interference to the bioprocess of interest could revolutionize synthetic biology and microbial cell factories. The performance and functions of these biosensors have been extensively studied and have been rapidly improved. We review here current biosensor tuning strategies and attempt to unravel how to obtain ideal biosensor functions through experimental adjustments. Strategies for expanding the biosensor input signals that increases the number of detectable compounds have also been summarized. Finally, different output signals and their practical requirements for biotechnology and biomedical applications and environmental safety concerns have been analyzed. This in-depth review of the responses and regulation mechanisms of genetically encoded biosensors will assist to improve their design and optimization in various application scenarios.

Sensitive and Specific Whole-Cell Biosensor for Arsenic Detection

Whole-cell biosensors (WCBs) have been designed to detect As(III), but most suffer from poor sensitivity and specificity. In this paper, we developed an arsenic WCB with a positive feedback amplifier in Escherichia coli DH5α. The output signal from the reporter mCherry was significantly enhanced by the positive feedback amplifier. The sensitivity of the WCB with positive feedback is about 1 order of magnitude higher than that without positive feedback when evaluated using a half-saturation As(III) concentration. The minimum detection limit for As(III) was reduced by 1 order of magnitude to 0.1 µM, lower than the World Health Organization standard for the arsenic level in drinking water, 0.01 mg/liter or 0.13 µM. Due to the amplification of the output signal, the WCB was able to give detectable signals within a shorter period, and a fast response is essential for in situ operations. Moreover, the WCB with the positive feedback amplifier showed exceptionally high specificity toward As(III) when compared with other metal ions. Collectively, the designed positive feedback amplifier WCB meets the requirements for As(III) detection with high sensitivity and specificity. This work also demonstrates the importance of genetic circuit engineering in designing WCBs, and the use of genetic positive feedback amplifiers is a good strategy to improve the performance of WCBs.IMPORTANCE Arsenic poisoning is a severe public health issue. Rapid and simple methods for the sensitive and specific monitoring of arsenic concentration in drinking water are needed. In this study, we designed an arsenic WCB with a positive feedback amplifier. It is highly sensitive and able to detect arsenic below the WHO limit level. In addition, it also significantly improves the specificity of the biosensor toward arsenic, giving a signal that is about 10 to 20 times stronger in response to As(III) than to other metals. This work not only provides simple but effective arsenic biosensors but also demonstrates the importance of genetic engineering, particularly the use of positive feedback amplifiers, in designing WCBs.

Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals

Cell-based biosensors have great potential to detect various toxic and pathogenic contaminants in aqueous environments. However, frequently they cannot meet practical requirements due to insufficient sensing performance. To address this issue, we investigated a modular, cascaded signal amplifying methodology. We first tuned intracellular sensory receptor densities to increase sensitivity, and then engineered multi-layered transcriptional amplifiers to sequentially boost output expression level. We demonstrated these strategies by engineering ultrasensitive bacterial sensors for arsenic and mercury, and improved detection limit and output up to 5,000-fold and 750-fold, respectively. Coupled by leakage regulation approaches, we developed an encapsulated microbial sensor cell array for low-cost, portable and precise field monitoring, where the analyte can be readily quantified via displaying an easy-to-interpret volume bar-like pattern. The ultrasensitive signal amplifying methodology along with the background regulation and the sensing platform will be widely applicable to many other cell-based sensors, paving the way for their real-world applications.

Miniaturized Sample Preparation and Rapid Detection of Arsenite in Contaminated Soil Using a Smartphone

Conventional methods for analyzing heavy metal contamination in soil and water generally require laboratory equipped instruments, complex procedures, skilled personnel and a significant amount of time. With the advancement in computing and multitasking performances, smartphone-based sensors potentially allow the transition of the laboratory-based analytical processes to field applicable, simple methods. In the present work, we demonstrate the novel miniaturized setup for simultaneous sample preparation and smartphone-based optical sensing of arsenic As(III) in the contaminated soil. Colorimetric detection protocol utilizing aptamers, gold nanoparticles and NaCl have been optimized and tested on the PDMS-chip to obtain the high sensitivity with the limit of detection of 0.71 ppm (in the sample) and a correlation coefficient of 0.98. The performance of the device is further demonstrated through the comparative analysis of arsenic-spiked soil samples with standard laboratory method, and a good agreement with a correlation coefficient of 0.9917 and the average difference of 0.37 ppm, are experimentally achieved. With the android application on the device to run the experiment, the whole process from sample preparation to detection is completed within 3 hours without the necessity of skilled personnel. The approximate cost of setup is estimated around 1 USD, weight 55 g. Therefore, the presented method offers the simple, rapid, portable and cost-effective means for onsite sensing of arsenic in soil. Combined with the geometric information inside the smartphones, the system will allow the monitoring of the contamination status of soils in a nation-wide manner.

Design and evaluation of an incoherent feed-forward loop for an arsenic biosensor based on standard iGEM parts

The diversity and flexibility of life offers a wide variety of molecules and systems useful for biosensing. A biosensor device should be robust, specific and reliable. Inorganic arsenic is a highly toxic water contaminant with worldwide distribution that poses a threat to public health. With the goal of developing an arsenic biosensor, we designed an incoherent feed-forward loop (I-FFL) genetic circuit to correlate its output pulse with the input signal in a relatively time-independent manner. The system was conceived exclusively based on the available BioBricks in the iGEM Registry of Standard Biological Parts. The expected behavior in silico was achieved; upon arsenic addition, the system generates a short-delayed reporter protein pulse that is dose dependent to the contaminant levels. This work is an example of the power and variety of the iGEM Registry of Standard Biological Parts, which can be reused in different sophisticated system designs like I-FFLs. Besides the scientific results, one of the main impacts of this synthetic biology project is the influence it had on team’s members training and career choices which are summarized at the end of this article.

An automated microreactor for semi-continuous biosensor measurements

Living bacteria or yeast cells are frequently used as bioreporters for the detection of specific chemical analytes or conditions of sample toxicity. In particular, bacteria or yeast equipped with synthetic gene circuitry that allows the production of a reliable non-cognate signal (e.g., fluorescent protein or bioluminescence) in response to a defined target make robust and flexible analytical platforms. We report here how bacterial cells expressing a fluorescence reporter ("bactosensors"), which are mostly used for batch sample analysis, can be deployed for automated semi-continuous target analysis in a single concise biochip. Escherichia coli-based bactosensor cells were continuously grown in a 13 or 50 nanoliter-volume reactor on a two-layered polydimethylsiloxane-on-glass microfluidic chip. Physiologically active cells were directed from the nl-reactor to a dedicated sample exposure area, where they were concentrated and reacted in 40 minutes with the target chemical by localized emission of the fluorescent reporter signal. We demonstrate the functioning of the bactosensor-chip by the automated detection of 50 μgarsenite-As l(-1) in water on consecutive days and after a one-week constant operation. Best induction of the bactosensors of 6-9-fold to 50 μg l(-1) was found at an apparent dilution rate of 0.12 h(-1) in the 50 nl microreactor. The bactosensor chip principle could be widely applicable to construct automated monitoring devices for a variety of targets in different environments.

Arsenic bioavailability in soils before and after soil washing: the use of Escherichia coli whole-cell bioreporters

We investigated the quantification of bioavailable arsenic in contaminated soils and evaluation of soil-washing processes in the aspect of bioavailability using a novel bacterial bioreporter developed in present study. The whole-cell bioreporter (WCB) was genetically engineered by fusing the promoter of nik operon from Escherichia coli and green fluorescent protein as a sensing domain and reporter domain. Among eight well-known hazardous heavy metals and metalloid, this system responded specifically to arsenic, thereby inferring association of As(III) with NikR inhibits the repression. Moreover, the response was proportional to the concentration of As(III), thereby it was capable to determine the amount of bioavailable arsenic quantitatively in contaminated soils. The bioavailable portion of arsenic was 5.9 (3.46-10.96) and 0.9 (0.27-1.74) % of total from amended and site soils, respectively, suggesting the bioavailability of arsenic in soils was related to the soil properties and duration of aging. On the other hand, only 1.37 (0.21-2.97) % of total arsenic was extracted into soil solutions and 19.88 (11.86-28.27) % of arsenic in soil solution was bioavailable. This result showed that the soluble arsenic is not all bioavailable and most of bioavailable arsenic in soils is water non-extractable. In addition, the bioavailable arsenic was increased after soil-washing while total amount was decreased, thereby suggesting the soil-washing processes release arsenic associated with soil materials to be bioavailable. Therefore, it would be valuable to have a tool to assess bioavailability and the bioavailability should be taken into consideration for soil remediation plans.

A low cost color-based bacterial biosensor for measuring arsenic in groundwater

Using arsenic (As) contaminated groundwater for drinking or irrigation has caused major health problems for humans around the world, raising a need to monitor As level efficiently and economically. This study developed a color-based bacterial biosensor which is easy-to-use and inexpensive for measuring As and could be complementary to current As detecting techniques. The arsR-lacZ recombinant gene cassette in nonpathogenic strain Escherichia coli DH5α was used in the color-based biosensor which could be observed by eyes or measured by spectrometer. The developed bacterial biosensor demonstrates a quantitative range from 10 to 500μgL(-1) of As in 3-h reaction time. Furthermore, the biosensor was able to successfully detect and estimate As concentration in groundwater sample by measuring optical density at 595nm (OD595). Among different storage methods used in this study, biosensor in liquid at 4°C showed the longest shelf life about 9d, and liquid storage at RT and cell pellet could also be stored for about 3-5d. In conclusion, this study showed that the As biosensor with reliable color signal and economical preservation methods is useful for rapid screening of As pollutant, providing the potential for large scale screening and better management strategies for environmental quality control.

Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors

The engineering of microbial strains for the production of small molecules of biotechnological interest is a time-consuming, laborious and expensive process. This can be mostly attributed to the fact that good producers cannot be readily obtained by high-throughput screening approaches since increased product formation usually does not confer a clear phenotype to producing strain variants. Recently, advances were made in the design and construction of genetically encoded RNA aptamer-based or transcription factor-based biosensors for detecting small molecules at the single-cell level. The first promising examples for the application of these molecular biosensors in combination with fluorescent-activated cell sorting as a high-throughput screening device demonstrated the value and potential of these new tools for microbial strain development.

Strategies for enhancing bioluminescent bacterial sensor performance by promoter region manipulation

Genetically engineered microbial reporter strains are based upon the fusion of an inducible sensing element upstream of a reporting element, so that the construct emits a dose-dependent signal when exposed to the inducing compound(s) or stress factor(s). In this communication we described several general approaches undertaken in order to enhance the sensing performance of such promoter::reporter fusions. Significant improvements in detection sensitivity, response kinetics and signal intensity were achieved by modification of the length of the promoter-containing DNA fragment, by random or site-directed mutagenesis and by promoter duplication. The general nature of these genetics manipulations makes them applicable to other types of promoter::reporter fusions.

Strategies for enhancing bioluminescent bacterial sensor performance by promoter region manipulation

Bioluminescent bacterial sensors are based upon the fusion of bacterial bioluminescence (lux) genes, acting as a reporter element, to selected bacterial stress‐response gene promoters. Depending upon the nature of the promoter, the resulting constructs react to diverse types of environmental stress, including the presence of toxic chemicals, by dose‐dependant light emission. Two bacterial sensors, harbouring sulA::luxCDABE and grpE::luxCDABE fusions, activated by the model chemicals nalidixic acid (NA) and ethanol, respectively, were subjected to molecular manipulations of the promoter region, in order to enhance the intensity and speed of their response and lower their detection thresholds. By manipulating the length of the promoter‐containing segment (both promoters), by introducing random or specific mutations in the promoter sequence or by duplicating the promoter sequence (sulA only), major improvements in sensor performance were obtained. Improvements included significantly enhanced sensitivity, earlier response times and an increase in signal intensity. The general approaches described herein may be of general applicability for optimizing bacterial sensor performance, regardless of the sensing or reporting elements employed.

Development of bacteria-based bioassays for arsenic detection in natural waters

Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor-reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor-reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams.