Microfluidic Based Whole-Cell Biosensors for Simultaneously On-Site Monitoring of Multiple Environmental Contaminants

Whole Cells of Microorganisms-A Powerful Bioanalytical Tool for Measuring Integral Parameters of Pollution: A Review

Microbial biosensors are bioanalytical devices that can measure the toxicity of pollutants or detect specific substances. This is the greatest advantage of microbial biosensors which use whole cells of microorganisms as powerful tools for measuring integral parameters of environmental pollution. This review explores the core principles of microbial biosensors including biofuel devices, emphasizing their capacity to evaluate biochemical oxygen demand (BOD), toxicity, heavy metals, surfactants, phenols, pesticides, inorganic pollutants, and microbiological contamination. However, practical challenges, such as sensitivity to environmental factors like pH, salinity, and the presence of competing substances, continue to hinder their broader application and long-term stability. The performance of these biosensors is closely tied to both technological advancement and the scientific understanding of biological systems, which influence data interpretation and device optimization. The review further examines cutting-edge developments, including the integration of electroactive biofilms with nanomaterials, molecular biology techniques, and artificial intelligence, all of which significantly enhance biosensor functionality and analytical accuracy. Commercial implementations and improvement strategies are also discussed, providing a comprehensive overview of the state-of-the-art in this field. Overall, this work consolidates recent progress and identifies both the potential and limitations of microbial biosensors, offering valuable insights into their future development for environmental monitoring.

Accelerating the Understanding of Biosensors Through the Lens of Cells: State of the Field, Emerging Directions, Advances, and Challenges

Cell-based biosensors are evolving as versatile tools for biological research, drug development, and environmental monitoring. Living cells are used to detect elements in these biosensors, which offer significant advantages over standard transducers. The purpose of this review article is to provide an in-depth overview of cell-based biosensors, emphasizing their working principles, fabrication processes, and applications. The potential of living cells to respond to particular analytes or stimuli supports the design and operation of cell-based biosensors. Real-time and label-free identification can be accomplished by combining these cells with transducers like microelectrodes or optical sensors. Genetically engineered cells or changed microenvironments can be used in cell-based biosensors to improve performance by optimizing cell types for increased dynamic range, sensitivity, and selectivity. Cell-based biosensors are developed by meticulously cultivating and immobilizing cells on transducer surfaces while retaining their vitality and performance. Cell-based biosensors have a wide range of applications, including monitoring the environment, healthcare, and pharmaceutical research. These biosensors have been used to detect diseases, toxic substances, pollutants, and therapeutic drug screening. Cell-based biosensors are cutting-edge technology that brings together the capabilities of live cells and transducers to detect analytes in a sensitive and specific manner. These biosensors illustrate the tremendous potential for upcoming uses in healthcare and monitoring environmental conditions with further developments in fabrication methods and the inclusion of artificial intelligence.

Microfluidic biosensors: revolutionizing detection in DNA analysis, cellular analysis, and pathogen detection

Microfluidic chips have emerged as versatile and powerful tools that enable the precise manipulation of fluids and bioparticles at the microscale. Their impact on detection applications is profound, offering advantages such as miniaturization, enhanced sensitivity, multiplexing capability, and integrated functions. These chips can be customized for specific techniques, such as DNA analysis, immunoassays, chemical sensing, and cell-based assays. With a wide range of types available, including Lab-on-a-Chip, droplet-based, paper-based, electrochemical, optical, and magnetic chips, they find applications in diverse fields such as medical diagnostics, DNA analysis, cell analysis, food safety testing, environmental monitoring, and industrial processes. This powerful technology replicates laboratory capabilities on miniature chip-scale devices, resulting in time and cost savings while enabling portability and field-use capability. Its impact spans genetic analysis, proteomic analysis, cell culture, biosensors, pathogen detection, and point-of-care diagnostics, playing a pivotal role in advancing chemical and biological analysis. The overall aim of this review is to provide an overview of the development of microfluidic biochips for biological detection and discuss their various applications.

Challenges and opportunities in commercializing whole-cell bioreporters in environmental application

Since the initial introduction of whole-cell bioreporters (WCBs) nearly 30 years ago, their high sensitivity, selectivity, and suitability for on-site detection have rendered them highly promising for environmental monitoring, medical diagnosis, food safety, biomanufacturing, and other fields. Especially in the environmental field, the technology provides a fast and efficient way to assess the bioavailability of pollutants in the environment. Despite these advantages, the technology has not been commercialized. This lack of commercialization is confusing, given the broad application prospects of WCBs. Over the years, numerous research papers have focused primarily on enhancing the sensitivity and selectivity of WCBs, with little attention paid to their wider commercial applications. So far, there is no a critical review has been published yet on this topic. Therefore, in this article we critically reviewed the research progress of WCBs over the past three decades, assessing the performance and limitations of current systems to understand the barriers to commercial deployment. By identifying these obstacles, this article provided researchers and industry stakeholders with deeper insights into the challenges hindering market entry and inspire further research toward overcoming these barriers, thereby facilitating the commercialization of WCBs as a promising technology for environmental monitoring.

Recent advances in portable devices for environmental monitoring applications

Environmental pollution remains a major societal problem, leading to serious impacts on living organisms including humans. Human activities such as civilization, urbanization, and industrialization are major causes of pollution. Imposing stricter rules helps control environmental pollutant levels, creating a need for reliable pollutant monitoring in air, water, and soil. The application of traditional analytical techniques is limited in low-resource areas because they are sophisticated, expensive, and bulky. With the development of biosensors and microfluidics technology, environmental monitoring has significantly improved the analysis time, low cost, portability, and ease of use. This review discusses the fundamentals of portable devices, including microfluidics and biosensors, for environmental control. Recently, publications reviewing microfluidics and biosensor device applications have increased more than tenfold, showing the potential of emerging novel approaches for environmental monitoring. Strategies for enzyme-, immunoassay-, and molecular-based analyte sensing are discussed based on their mechanisms and applications. Microfluidic and biosensor platforms for detecting major pollutants, including metal ions, pathogens, pesticides, and antibiotic residues, are reviewed based on their working principles, advantages, and disadvantages. Challenges and future trends for the device design and fabrication process to improve performance are discussed. Miniaturization, low cost, selectivity, sensitivity, high automation, and savings in samples and reagents make the devices ideal alternatives for in-field detection, especially in low-resource areas. However, their operation with complicated environmental samples requires further research to improve the specificity and sensitivity. Although there is a wide range of devices available for environmental applications, their implementation in real-world situations is limited. This study provides insights into existing issues that can be used as references and a comparative analysis for future studies and applications.

Principles and challenges of whole cell microbial biosensors in the food industry

Whole cell microbial biosensors (WCMB) are mostly genetically modified microorganisms used to detect target molecules as indicators of biological and chemical contaminants as well as in the identification of compounds of interest in the food industry. The specificity and sensitivity of these biosensors are achieved through the design of genetic circuits that make use of genetic sequences such as promoters, terminators, genes encoding regulatory proteins or reporter proteins, among others. Despite the advances of WCMBs for their application, significant challenges are faced, such as cell stability, regulatory restrictions, and the need to optimize response times so that they can be a competitive detection tool in the market. This review explores the technological progress, potential and limitations of WCMBs in the food industry, starting by reviewing the operating principles of biosensors. The importance of selecting appropriate chassis cells and the integration of recognition elements and transducers to maximize their effectiveness in the detection of contaminants and compounds of interest in the food industry is highlighted.

Taguchi method: artificial neural network approach for the optimization of high-efficiency microfluidic biosensor for COVID-19

COVID-19 is a pandemic disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus is mainly spread by droplets, respiratory secretions, and direct contact. Caused by the huge spread of the COVID-19 epidemic, research is focused on the study of biosensors as it presents a rapid solution for reducing incidents and fatality rates. In this paper, a microchip flow confinement method for the rapid transport of small sample volumes to sensor surfaces is optimized in terms of the confinement coefficient β, the position of the confinement flow X, and its inclination α relative to the main channel. A numerical simulation based on two-dimensional Navier-Stokes equations has been used. Taguchi's L9(33) orthogonal array was adopted to design the numerical assays taking into account the confining flow parameters (α, β, and X) on the response time of microfluidic biosensors. Analyzing the signal-to-noise ratio allowed us to determine the most effective combinations of control parameters for reducing the response time. The contribution of the control factors to the detection time was determined via analysis of variance (ANOVA). Numerical predictive models using multiple linear regression (MLR) and an artificial neural network (ANN) were developed to accurately predict microfluidic biosensor response time. This study concludes that the best combination of control factors isα 3 β 3 X 2 that corresponds to α = 90 ∘ , β = 25 and X = 40 µm. Analysis of variance (ANOVA) shows that the position of the confinement channel (62% contribution) is the factor most responsible for the reduction in response time. Based on the correlation coefficient (R 2), and value adjustment factor (VAF), the ANN model performed better than the MLR model in terms of prediction accuracy.

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Programmable Synthesis of Biobased Materials Using Cell-Free Systems

Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.

Comparative Analysis of Cell Metabolic Activity Sensing by Escherichia coli rrnB P1-lux and Cd Responsive-Lux Biosensors: Time-Resolved Experiments and Mechanistic Modelling

Whole-cell bacterial sensors are used in medical/environmental applications to detect chemicals, and to assess medium toxicity or stress. Non-specific constitutive biosensors generally serve the latter purpose, whereas chemical detection is performed with biosensors involving a specific chemical-inducible promoter. Herein, we show that functioning principles of specific and non-specific whole-cell biosensors are not exclusive as both can probe modulations of cell metabolic activity under stressing conditions. The demonstration is based on (i) time-resolved measurements of bioluminescence produced by constitutive rrnB P1-luxCDABE Escherichia coli biosensor in media differing with respect to carbon source, (ii) theoretical reconstruction of the measured signals using a here-reported theory for bioluminescence generated by constitutive cells, (iii) comparison between time-dependent cell photoactivity (reflecting metabolic activity) retrieved by theory with that we reported recently for cadmium-inducible PzntA-luxCDABE E. coli in media of similar compositions. Whereas signals of constitutive and non-constitutive biosensors differ in terms of shape, amplitude and peak number depending on nutritional medium conditions, analysis highlights the features shared by their respective cell photoactivity patterns mediated by the interplay between stringent response and catabolite repressions. The work advocates for the benefits of a theoretical interpretation for the time-dependent response of biosensors to unravel metabolic and physicochemical contributions to the bioluminescence signal.

Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants

Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg²⁺, Zn²⁺, Pb²⁺, Au³⁺, Cd²⁺, As³⁺, Ni²⁺, Cu²⁺, and UO₂²⁺) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.

Application of Microfluidics in Detection of Circulating Tumor Cells

Tumor metastasis is one of the main causes of cancer incidence and death worldwide. In the process of tumor metastasis, the isolation and analysis of circulating tumor cells (CTCs) plays a crucial role in the early diagnosis and prognosis of cancer patients. Due to the rarity and inherent heterogeneity of CTCs, there is an urgent need for reliable CTCs separation and detection methods in order to obtain valuable information on tumor metastasis and progression from CTCs. Microfluidic technology is increasingly used in various studies of CTCs separation, identification and characterization because of its unique advantages, such as low cost, simple operation, less reagent consumption, miniaturization of the system, rapid detection and accurate control. This paper reviews the research progress of microfluidic technology in CTCs separation and detection in recent years, as well as the potential clinical application of CTCs, looks forward to the application prospect of microfluidic technology in the treatment of tumor metastasis, and briefly discusses the development prospect of microfluidic biosensor.

Harnessing the Potential of Biological Recognition Elements for Water Pollution Monitoring

Environmental monitoring of pollutants is an imperative first step to remove the genotoxic, embryotoxic, and carcinogenic toxins. Various biological sensing elements such as proteins, aptamers, whole cells, etc., have been used to track down major pollutants, including heavy metals, aromatic pollutants, pathogenic microorganisms, and pesticides in both environmental samples and drinking water, demonstrating their potential in a true sense. The intermixed use of nanomaterials, electronics, and microfluidic systems has further improved the design and enabled robust on-site detection with enhanced sensitivity. Through this perspective, we shed light on the advances in the field and entail recent efforts to optimize these systems for real-time, online sensing and on-site field monitoring.

Advanced oxidation processes in microreactors for water and wastewater treatment: Development, challenges, and opportunities

The miniaturization of reaction processes by microreactors offers many significant advantages over the use of larger, conventional reactors. Microreactors' interior structures exhibit comparatively higher surface area-to-volume ratios, which reduce reactant diffusion distances, enable faster and more efficient heat and mass transfer, and better control over process conditions. These advantages can be exploited to significantly enhance the performance of advanced oxidation processes (AOPs) commonly used for the removal of water pollutants. This comprehensive review of the rapidly emerging area of environmental microfluidics describes recent advances in the development and application of microreactors to AOPs for water and wastewater treatment. Consideration is given to the hydrodynamic properties, construction materials, fabrication techniques, designs, process features, and upscaling of microreactors used for AOPs. The use of microreactors for various AOP types, including photocatalytic, electrochemical, Fenton, ozonation, and plasma-phase processes, showcases how microfluidic technology enhances mass transfer, improves treatment efficiency, and decreases the consumption of energy and chemicals. Despite significant advancements of microreactor technology, organic pollutant degradation mechanisms that operate during microscale AOPs remain poorly understood. Moreover, limited throughput capacity of microreactor systems significantly restrains their industrial-scale applicability. Since large microreactor-inspired AOP systems are needed to meet the high-throughput requirements of the water treatment sector, scale-up strategies and recommendations are suggested as priority research opportunities. While microstructured reactor technology remains in an early stage of development, this work offers valuable insight for future research and development of AOPs in microreactors for environmental purposes.

Recent innovations in cost-effective polymer and paper hybrid microfluidic devices

Hybrid microfluidic systems that are composed of multiple different types of substrates have been recognized as a versatile and superior platform, which can draw benefits from different substrates while avoiding their limitations. This review article introduces the recent innovations of different types of low-cost hybrid microfluidic devices, particularly focusing on cost-effective polymer- and paper-based hybrid microfluidic devices. In this article, the fabrication of these hybrid microfluidic devices is briefly described and summarized. We then highlight various hybrid microfluidic systems, including polydimethylsiloxane (PDMS)-based, thermoplastic-based, paper/polymer hybrid systems, as well as other emerging hybrid systems (such as thread-based). The special benefits of using these hybrid systems have been summarized accordingly. A broad range of biological and biomedical applications using these hybrid microfluidic devices are discussed in detail, including nucleic acid analysis, protein analysis, cellular analysis, 3D cell culture, organ-on-a-chip, and tissue engineering. The perspective trends of hybrid microfluidic systems involving the improvement of fabrication techniques and broader applications are also discussed at the end of the review.