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Abstract
Abstract
Biosensors can be excellent analytical tools for monitoring programs working to implement legislation. In this article, biosensors for environmental analysis and monitoring are extensively reviewed. Examples of biosensors for the most important families of envi-ronmental pollutants, including some commercial devices, are presented. Finally, future trends in biosensor development are discussed. In this context, bioelectronics, nanotechnology, miniaturization, and especially biotechnology seem to be growing areas that will have a marked influence on the development of new biosensing strategies in the next future.
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de las Heras A, Carreño CA, de Lorenzo V. Stable implantation of orthogonal sensor circuits in Gram-negative bacteria for environmental release. Environ Microbiol 2008; 10:3305-16. [DOI: 10.1111/j.1462-2920.2008.01722.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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53
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Borin S, Crotti E, Mapelli F, Tamagnini I, Corselli C, Daffonchio D. DNA is preserved and maintains transforming potential after contact with brines of the deep anoxic hypersaline lakes of the Eastern Mediterranean Sea. SALINE SYSTEMS 2008; 4:10. [PMID: 18681968 PMCID: PMC2531117 DOI: 10.1186/1746-1448-4-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 08/05/2008] [Indexed: 11/25/2022]
Abstract
Background Extracellular dissolved DNA has been demonstrated to be present in many terrestrial and aquatic environments, actively secreted, or released by decaying cells. Free DNA has the genetic potential to be acquired by living competent cells by horizontal gene transfer mediated by natural transformation. The aim of this work is to study the persistence of extracellular DNA and its biological transforming activity in extreme environments like the deep hypersaline anoxic lakes of the Mediterranean Sea. The brine lakes are separated from the upper seawater by a steep chemocline inhabited by stratified prokaryotic networks, where cells sinking through the depth profile encounter increasing salinity values and osmotic stress. Results Seven strains belonging to different taxonomic groups isolated from the seawater-brine interface of four hypersaline lakes were grown at medium salinity and then incubated in the brines. The osmotic stress induced the death of all the inoculated cells in variable time periods, between 2 hours and 144 days, depending on the type of brine rather than the taxonomic group of the strains, i.e. Bacillaceae or gamma-proteobacteria. The Discovery lake confirmed to be the most aggressive environment toward living cells. In all the brines and in deep seawater dissolved plasmid DNA was substantially preserved for a period of 32 days in axenic conditions. L'Atalante and Bannock brines induced a decrease of the supercoiled form up to 70 and 40% respectively; in the other brines only minor changes in plasmid conformation were observed. Plasmid DNA after incubation in the brines maintained the capacity to transform naturally competent cells of Acinetobacter baylii strain BD413. Conclusion Free dissolved DNA is likely to be released by the lysis of cells induced by osmotic stress in the deep hypersaline anoxic lakes. Naked DNA was demonstrated to be preserved and biologically active in these extreme environments, and hence could constitute a genetic reservoir of traits acquirable by horizontal gene transfer.
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Affiliation(s)
- Sara Borin
- University of Milan, Department of Food Science and Microbiology, Milan, Italy.
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54
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Bacterial Biosensors for Measuring Availability of Environmental Pollutants. SENSORS 2008; 8:4062-4080. [PMID: 27879922 PMCID: PMC3697161 DOI: 10.3390/s8074062] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/06/2008] [Accepted: 07/09/2008] [Indexed: 11/24/2022]
Abstract
Traditionally, pollution risk assessment is based on the measurement of a pollutant's total concentration in a sample. The toxicity of a given pollutant in the environment, however, is tightly linked to its bioavailability, which may differ significantly from the total amount. Physico-chemical and biological parameters strongly influence pollutant fate in terms of leaching, sequestration and biodegradation. Bacterial sensor-reporters, which consist of living micro-organisms genetically engineered to produce specific output in response to target chemicals, offer an interesting alternative to monitoring approaches. Bacterial sensor-reporters detect bioavailable and/or bioaccessible compound fractions in samples. Currently, a variety of environmental pollutants can be targeted by specific biosensor-reporters. Although most of such strains are still confined to the lab, several recent reports have demonstrated utility of bacterial sensing-reporting in the field, with method detection limits in the nanomolar range. This review illustrates the general design principles for bacterial sensor-reporters, presents an overview of the existing biosensor-reporter strains with emphasis on organic compound detection. A specific focus throughout is on the concepts of bioavailability and bioaccessibility, and how bacteria-based sensing-reporting systems can help to improve our basic understanding of the different processes at work.
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55
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Li YF, Li FY, Ho CL, Liao VHC. Construction and comparison of fluorescence and bioluminescence bacterial biosensors for the detection of bioavailable toluene and related compounds. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2008; 152:123-9. [PMID: 17583401 DOI: 10.1016/j.envpol.2007.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 04/16/2007] [Accepted: 05/03/2007] [Indexed: 05/15/2023]
Abstract
Environmental pollution with petroleum products such as benzene, toluene, ethylbenzene, and xylenes (BTEX) has garnered increasing awareness because of its serious consequences for human health and the environment. We have constructed toluene bacterial biosensors comprised of two reporter genes, gfp and luxCDABE, characterized by green fluorescence and luminescence, respectively, and compared their abilities to detect bioavailable toluene and related compounds. The bacterial luminescence biosensor allowed faster and more-sensitive detection of toluene; the fluorescence biosensor strain was much more stable and thus more applicable for long-term exposure. Both luminescence and fluorescence biosensors were field-tested to measure the relative bioavailability of BTEX in contaminated groundwater and soil samples. The estimated BTEX concentrations determined by the luminescence and fluorescence bacterial biosensors were closely comparable to each other. Our results demonstrate that both bacterial luminescence and fluorescence biosensors are useful in determining the presence and the bioavailable fractions of BTEX in the environment.
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Affiliation(s)
- Yueh-Fen Li
- Department of Bioenvironmental Systems Engineering, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan
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56
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Schottel JL, Orwin PM, Anderson CR, Flickinger MC. Spatial expression of a mercury-inducible green fluorescent protein within a nanoporous latex-based biosensor coating. J Ind Microbiol Biotechnol 2008; 35:283-90. [DOI: 10.1007/s10295-007-0288-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 11/07/2007] [Indexed: 11/30/2022]
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Busam S, McNabb M, Wackwitz A, Senevirathna W, Beggah S, van der Meer JR, Wells M, Breuer U, Harms H. Artificial Neural Network Study of Whole-Cell Bacterial Bioreporter Response Determined Using Fluorescence Flow Cytometry. Anal Chem 2007; 79:9107-14. [DOI: 10.1021/ac0713508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sirisha Busam
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Maia McNabb
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Anke Wackwitz
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Wasana Senevirathna
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Siham Beggah
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Mona Wells
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Uta Breuer
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Hauke Harms
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505, Department of Environmental Microbiology, Helmholtz Center for Environmental Research, UFZ, D-04318, Leipzig, Germany, and Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
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Andreoni V, Gianfreda L. Bioremediation and monitoring of aromatic-polluted habitats. Appl Microbiol Biotechnol 2007; 76:287-308. [PMID: 17541581 DOI: 10.1007/s00253-007-1018-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 04/25/2007] [Accepted: 04/25/2007] [Indexed: 10/23/2022]
Abstract
Bioremediation may restore contaminated soils through the broad biodegradative capabilities evolved by microorganisms towards undesirable organic compounds. Understanding bioremediation and its effectiveness is rapidly advancing, bringing available molecular approaches for examining the presence and expression of the key genes involved in microbial processes. These methods are continuously improving and require further development and validation of primer- and probe-based analyses and expansion of databases for alternative microbial markers. Phylogenetic marker approaches provide tools to determine which organisms are present or generally active in a community; functional gene markers provide only information concerning the distribution or transcript levels (deoxyribonucleic acid [DNA]- or messenger ribonucleic acid [mRNA]-based approaches) of specific gene populations across environmental gradients. Stable isotope probing methods offer great potential to identify microorganisms that metabolize and assimilate specific substrates in environmental samples, incorporating usually a rare isotope (i.e., (13)C) into their DNA and RNA. DNA and RNA in situ characterization allows the determination of the species actually involved in the processes being measured. DNA microarrays may analyze the expression of thousands of genes in a soil simultaneously. A global analysis of which genes are being expressed under various conditions in contaminated soils will reveal the metabolic status of microorganisms and indicate environmental modifications accelerating bioremediation.
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Affiliation(s)
- Vincenza Andreoni
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
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59
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Wells M, Gösch M, Rigler R, Harms H, Lasser T, van der Meer JR. Ultrasensitive reporter protein detection in genetically engineered bacteria. Anal Chem 2007; 77:2683-9. [PMID: 15859581 DOI: 10.1021/ac048127k] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the use of laser-induced fluorescence confocal spectroscopy to measure analyte-stimulated enhanced green fluorescent protein (egfp) synthesis by genetically modified Escherichia coli bioreporter cells. Induction is measured in cell lysates and, since the spectroscopic focal volume is approximately the size of one bioreporter cell, also in individual live bacteria. This is, to our knowledge, the first ever proof-of-concept work utilizing instrumentation with single-molecule detection capability to monitor bioreporter response. Although we use arsenic inducible bioreporters here, the method is extensible to gfp/egfp bioreporters that are responsive to other substances.
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Affiliation(s)
- Mona Wells
- Laboratory of Soil Science, Swiss Federal Institute of Technology (EPFL), CH-1015, Lausanne, Switzerland.
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60
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Abstract
Despite the vast surface area of terrestrial plant leaves and the large microbial communities they support, little is known of the ability of leaf-associated microorganisms to access and degrade airborne pollutants. Here, we examined bacterial acquisition and degradation of phenol on leaves by an introduced phenol degrader and by natural phyllosphere communities. Whole-cell gfp-based Pseudomonas fluorescens bioreporter cells detected phenol on leaves that had previously been transiently exposed to gaseous phenol, indicating that leaves accumulated phenol; moreover, they accumulated it in sites that were accessible to epiphytic bacteria and to concentrations that were at least 10-fold higher than those in the air. After inoculated leaves were exposed to gaseous 14C-phenol, leaves harbouring the phenol-degrading Pseudomonas sp. strain CF600 released eight times more 14CO2 than did leaves harbouring a non-degrading mutant, demonstrating that CF600 actively mineralized phenol on leaves. We evaluated phenol degradation by natural microbial communities on green ash leaves that were collected from a field site rich in airborne organic pollutants. We found that significantly more phenol was mineralized by these leaves when the communities were present than by these leaves following surface sterilization. Thus, phenol-degrading organisms were present in these natural communities and were metabolically capable of phenol degradation. Collectively, these results provide the first direct evidence that bacteria on leaves can degrade an organic pollutant from the air, and indicate that bacteria on leaves could potentially contribute to the natural attenuation of organic air pollutants.
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Affiliation(s)
- Amarjyoti Sandhu
- Department of Plant Pathology and Interdepartmental Microbiology Program, Iowa State University, Ames, IA 50011-3211, USA
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61
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Yagi K. Applications of whole-cell bacterial sensors in biotechnology and environmental science. Appl Microbiol Biotechnol 2007; 73:1251-8. [PMID: 17111136 DOI: 10.1007/s00253-006-0718-6] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Revised: 09/30/2006] [Accepted: 10/12/2006] [Indexed: 11/26/2022]
Abstract
Biosensors have major advantages over chemical or physical analyses with regard to specificity, sensitivity, and portability. Recently, many types of whole-cell bacterial biosensors have been developed using recombinant DNA technology. The bacteria are genetically engineered to respond to the presence of chemicals or physiological stresses by synthesizing a reporter protein, such as luciferase, beta-galactosidase, or green fluorescent protein. In addition to an overview of conventional biosensors, this minireview discusses a novel type of biosensor using a photosynthetic bacterium as the sensor strain and the crtA gene, which is responsible for carotenoid synthesis, as the reporter. Since bacteria possess a wide variety of stress-response mechanisms, including antioxidation, heat-shock responses, nutrient-starvation, and membrane-damage responses, DNA response elements for several stress-response proteins can be fused with various reporter genes to construct a versatile set of bacterial biosensors for a variety of analytes. Portable biosensors for on-site monitoring have been developed using a freeze-dried biosensing strain, and cell array biosensors have been designed for high-throughput analysis. Moreover, in the future, the use of single-cell biosensors will permit detailed analyses of samples. Signals from such sensors could be detected with digital imaging, epifluorescence microscopy, and/or flow cytometry.
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Affiliation(s)
- Kiyohito Yagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka, 565-0871, Japan.
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62
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Rodriguez-Mozaz S, Lopez de Alda MJ, Barceló D. Biosensors as useful tools for environmental analysis and monitoring. Anal Bioanal Chem 2006; 386:1025-41. [PMID: 16807703 DOI: 10.1007/s00216-006-0574-3] [Citation(s) in RCA: 195] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 04/23/2006] [Accepted: 05/22/2006] [Indexed: 10/24/2022]
Abstract
Recent advances in the development and application of biosensors for environmental analysis and monitoring are reviewed in this article. Several examples of biosensors developed for relevant environmental pollutants and parameters are briefly overviewed. Special attention is paid to the application of biosensors to real environmental samples, taking into consideration aspects such as sample pretreatment, matrix effects and validation of biosensor measurements. Current trends in biosensor development are also considered and commented on in this work. In this context, nanotechnology, miniaturisation, multi-sensor array development and, especially, biotechnology arise as fast-growing areas that will have a marked influence on the development of new biosensing strategies in the near future.
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Affiliation(s)
- Sara Rodriguez-Mozaz
- Department of Environmental Chemistry, IIQAB-CSIC, C/ Jordi Girona 18-26, 08034, Barcelona, Spain.
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63
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Galvão TC, de Lorenzo V. Transcriptional regulators à la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol 2006; 17:34-42. [PMID: 16359854 DOI: 10.1016/j.copbio.2005.12.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 11/15/2005] [Accepted: 12/05/2005] [Indexed: 11/27/2022]
Abstract
For many regulators of bacterial biodegradation pathways, small molecule/effector binding is the signal for triggering transcriptional activation. Thus, regulation results from a cross-talk between chemicals sensed by transcriptional factors and operon expression status. These features can be utilised in the construction of biosensors for a wide range of target compounds as, in principle, any regulatory protein whose activity is modulated by binding to a small molecule can have its effector/inducer profile artificially altered. The cognate specificities of a number of regulatory proteins have been modified as an astute approach to developing, among others, bacterial biosensors for environmentally relevant compounds.
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Affiliation(s)
- Teca Calcagno Galvão
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología-CSIC, Madrid 28049, Spain.
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64
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Tecon R, van der Meer JR. Information from single-cell bacterial biosensors: what is it good for? Curr Opin Biotechnol 2006; 17:4-10. [PMID: 16326092 DOI: 10.1016/j.copbio.2005.11.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 11/10/2005] [Accepted: 11/23/2005] [Indexed: 11/26/2022]
Abstract
Bacterial reporter cells (i.e. strains engineered to produce easily measurable signals in response to one or more chemical targets) can principally be used to quantify chemical signals and analytes, physicochemical conditions and gradients on a microscale (i.e. micrometer to submillimeter distances), when the reporter signal is determined in individual cells. This makes sense, as bacterial life essentially thrives in microheterogenic environments and single-cell reporter information can help us to understand the microphysiology of bacterial cells and its importance for macroscale processes like pollutant biodegradation, beneficial bacteria-eukaryote interactions, and infection. Recent findings, however, showed that clonal bacterial populations are essentially always physiologically, phenotypically and genotypically heterogeneous, thus emphasizing the need for sound statistical approaches for the interpretation of reporter response in individual bacterial cells. Serious attempts have been made to measure and interpret single-cell reporter gene expression and to understand variability in reporter expression among individuals in a population.
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Affiliation(s)
- Robin Tecon
- Department of Fundamental Microbiology, Bâtiment Biophore, Quartier UNIL-Sorge, University of Lausanne, CH 1015 Lausanne, Switzerland
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65
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Larrainzar E, O'Gara F, Morrissey JP. Applications of autofluorescent proteins for in situ studies in microbial ecology. Annu Rev Microbiol 2006; 59:257-77. [PMID: 16153170 DOI: 10.1146/annurev.micro.59.030804.121350] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
When autofluorescent proteins (AFPs), such as green fluorescent protein (GFP) and Discosoma striata red fluorescent protein (DsRed), are excited with light of a specific wavelength, they emit light of a longer wavelength, without the further addition of substrates. A range of AFPs have been identified and cloned from marine organisms, and mutagenesis techniques have been employed to develop improved variant AFPs for applications in biological research. In recent years, AFP technology has become an important tool for microbiologists and microbial ecologists studying processes such as microbe-plant interactions, biosensors, biofilm formation, and horizontal gene transfer. The ability to use AFPs with differing fluorescent spectra within a single cell has allowed simultaneous monitoring of several aspects of microbial physiology and gene expression in situ in real time. This provides a tremendous insight into microbial function and behavior in natural environments. Furthermore, the integration of AFP reporters with other markers and technologies is facilitating a systems approach to research in microbial ecology.
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66
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Marqués S, Aranda-Olmedo I, Ramos JL. Controlling bacterial physiology for optimal expression of gene reporter constructs. Curr Opin Biotechnol 2005; 17:50-6. [PMID: 16359853 DOI: 10.1016/j.copbio.2005.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Revised: 11/15/2005] [Accepted: 12/05/2005] [Indexed: 10/25/2022]
Abstract
Bacterial biosensors for the detection of pollutants are based on the regulatory elements that control the corresponding degradation pathways. An increasing number of catabolic pathways under the control of specific regulators are now known to be influenced by the presence of alternative carbon sources, which to different extents repress expression of the pathway despite the presence of the inducer. The molecular basis underlying the control of each catabolic pathway is different, although all sense a high energy state of the cell resulting from the presence of more favourable carbon sources. Biosensor tests mimicking field conditions point to global regulation being relevant for biosensor performance; thus, this global regulation must be taken into account when designing whole-cell biosensors.
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Affiliation(s)
- Silvia Marqués
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Apartado de Correos 419, E-18008, Granada, Spain.
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Huang WE, Wang H, Zheng H, Huang L, Singer AC, Thompson I, Whiteley AS. Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate. Environ Microbiol 2005; 7:1339-48. [PMID: 16104857 DOI: 10.1111/j.1462-5822.2005.00821.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acinetobacter sp. ADP1 is a common soil-associated bacterium with high natural competency, allowing it to efficiently integrate foreign DNA fragments into its chromosome. This property was exploited to engineer salicylate-inducible luxCDABE and green fluorescent protein (GFP) variants of Acinetobacter sp. ADP1. Specifically, Acinetobacter sp. ADPWH_lux displayed the higher sensitivity when comparing the two variants (minimum detection c. 0.5-1 microM salicylate) and a faster turnover of the lux marker gene, making it suitable for whole-cell luminescence assays of salicylate concentration. In contrast, the longer maturation and turnover times of the GFP protein make the Acinetobacter sp. ADPWH_gfp variant more suited to applications involving whole-cell imaging of the presence of salicylate. The sensitivity of the luxCDABE variant was demonstrated by assaying salicylate production in naphthalene-degrading cultures. Assays using ADPWH_lux specifically mapped the kinetics of salicylate production from naphthalene and were similar to that observed by high-performance liquid chromatography (HPLC) data. However, ADPWH_lux exhibited the higher sensitivity, when compared with HPLC, for detecting salicylate production during the first 24 h of naphthalene metabolism. These data demonstrate that the engineered Acinetobacter variants have significant potential for salicylate detection strategies in laboratory and field studies, especially in scenarios where genetic stability of the construct is required for in situ monitoring.
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Affiliation(s)
- Wei E Huang
- Molecular Microbial Ecology, CEH-Oxford, Mansfield Road, Oxford OX1 3SR, UK
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68
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Paitan Y, Biran I, Shechter N, Biran D, Rishpon J, Ron EZ. Monitoring aromatic hydrocarbons by whole cell electrochemical biosensors. Anal Biochem 2005; 335:175-83. [PMID: 15556555 DOI: 10.1016/j.ab.2004.08.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Indexed: 10/26/2022]
Abstract
In this article, we describe a bacterial whole cell electrochemical biosensors system that can be used for monitoring aromatic hydrocarbons. These bacterial biosensors are based on fusions of a promoter that is sensitive to aromatic compounds (the promoter region of the xylS gene and the xylR gene coding for the transcriptional regulator of the xyl operon) to reporter genes that can be monitored electrochemically at real-time and on-line. The xylS promoter was fused upstream of two promoterless genes coding the lacZ gene and phoA. These constructs reacted specifically to aromatic compounds but not to nonaromatic compounds, and we could detect, within minutes, micromolar concentrations of different aromatic hydrocarbons such as xylene and toluene. The use of two different reporter genes allows the future construction of a multianalyte detection system for simultaneous monitoring of several pollutants. These whole cell biosensors are potentially useful for on-line and in situ detection of aromatic compounds and as early warning systems of environmental hazards.
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Affiliation(s)
- Yossi Paitan
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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69
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Response Characteristics of Arsenic-Sensitive Bioreporters Expressing the gfp Reporter Gene. Mikrochim Acta 2005. [DOI: 10.1007/s00604-005-0401-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Chapter 10 Non-affinity sensing technology: the exploitation of biocatalytic events for environmental analysis. BIOSENSORS AND MODERN BIOSPECIFIC ANALYTICAL TECHNIQUES 2005. [DOI: 10.1016/s0166-526x(05)44010-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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71
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Abstract
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.
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Affiliation(s)
- Jan Roelof van der Meer
- Department of Fundamental Microbiology, Bâtiment de Biologie, University of Lausanne, 1015 Lausanne, Switzerland.
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73
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Smirnova IA, Dian C, Leonard GA, McSweeney S, Birse D, Brzezinski P. Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR. J Mol Biol 2004; 340:405-18. [PMID: 15210343 DOI: 10.1016/j.jmb.2004.04.071] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2003] [Revised: 04/19/2004] [Accepted: 04/19/2004] [Indexed: 11/22/2022]
Abstract
The transcriptional regulator DntR, a member of the LysR family, is a central element in a prototype bacterial cell-based biosensor for the detection of hazardous contamination of soil and groundwater by dinitrotoluenes. To optimise the sensitivity of the biosensor for such compounds we have chosen a rational design of the inducer-binding cavity based on knowledge of the three-dimensional structure of DntR. We report two crystal structures of DntR with acetate (resolution 2.6 angstroms) and thiocyanate (resolution 2.3 angstroms), respectively, occupying the inducer-binding cavity. These structures allow for the construction of models of DntR in complex with salicylate (Kd approximately or = 4 microM) and 2,4-dinitrotoluene that provide a basis for the design of mutant DntR with enhanced specificity for dinitrotoluenes. In both crystal structures DntR crystallises as a homodimer with a "head-to-tail" arrangement of monomers in the asymmetric unit. Analysis of the crystal structure has allowed the building of a full-length model of DntR in its biologically active homotetrameric form consisting of two "head-to-head" dimers. The implications of this model for the mechanism of transcription regulation by LysR proteins are discussed.
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Affiliation(s)
- Irina A Smirnova
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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74
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Abstract
A biosensor composed of a high-density living bacterial cell array was fabricated by inserting bacteria into a microwell array formed on one end of an imaging fiber bundle. The size of each microwell allows only one cell to occupy each well. In this biosensor, E. coli cells carrying a recA::gfp fusion were used as sensing components for genotoxin detection. Each fiber in the array has its own light pathway, enabling thousands of individual cell responses to be monitored simultaneously with both spatial and temporal resolution. The biosensor was capable of performing cell-based functional sensing of a genotoxin with high sensitivity and short incubation times (1 ng/mL mitomycin C after 90 min). Dose-response curves for several genotoxins were obtained. The biosensors demonstrated an active sensing lifetime of more than 6 h and a shelf lifetime of two weeks.
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Affiliation(s)
- Yina Kuang
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, USA
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75
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Saini R, Halverson LJ, Lorimor JC. Rainfall timing and frequency influence on leaching of Escherichia coli RS2G through soil following manure application. JOURNAL OF ENVIRONMENTAL QUALITY 2003; 32:1865-1872. [PMID: 14535331 DOI: 10.2134/jeq2003.1865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The time between swine (Sus scrofa) manure application to soil as a crop fertilizer, the first rainfall event, and the frequency of rainfall events should influence leaching potential of fecal pathogens. Soil microcosms were inoculated in the lab with a swine manure isolate of Escherichia coli, strain RS2G, expressing green fluorescent protein, to examine how timing and frequency of rainfall events influences RS2G leaching and survival in soil. Liquid swine manure inoculated with RS2G was applied to intact soil cores (20 cm in diameter x 30 cm long) 4, 8, or 16 d before the first rainfall event (50.8 mm over a 4-h period), and each core received one to three rainfall events. Manure application methods (no-till surface-broadcast, broadcast and incorporated, and tilled before broadcast) had no affect on leaching, although there was greater survival in soils when the manure had been incorporated. Most of the RS2G in the leachate appeared following the first rainfall event and RS2G leaching decreased with increasing time between manure application and the first rainfall, although leachates contained as much as 3.4 to 4.5 log colony forming units (CFU) 100 mL(-1) of RS2G when the first rainfall occurred 16 d after manure application. With increasing frequency of rainfalls there was a decrease in subsequent concentrations of RS2G in the leachate. There was no correlation between leachate RS2G and total coliforms or fecal streptococci concentrations. Soil RS2G numbers were 1 to 10% of the inoculum regardless of the length of time between manure application and the first rainfall. RS2G leaching was mostly influenced by the time between manure application and first rainfall event, and significant leaching and survival in soil was possible even if the first rain occurred 16 d after manure application.
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Affiliation(s)
- R Saini
- Department of Agronomy, 2537 Agronomy Hall, Iowa State University, Ames, IA 50011-1010, USA
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76
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Park J, Malinverni J, Adriaens P, Kukor JJ. Quantitative structure-activity relationship (QSAR) analysis of aromatic effector specificity in NtrC-like transcriptional activators from aromatic oxidizing bacteria. FEMS Microbiol Lett 2003; 224:45-52. [PMID: 12855166 DOI: 10.1016/s0378-1097(03)00400-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A quantitative structure-activity relationship (QSAR) approach was taken to provide mechanistic insights into the interaction between the chemical structure of inducing compounds and the transcriptional activation of aromatic monooxygenase operons among the XylR/DmpR subclass of bacterial NtrC-like transcriptional regulators. Compared to XylR and DmpR, a broader spectrum of effector compounds was observed for the TbuT system from Ralstonia pickettii PKO1. The results of QSAR analysis for TbuT suggested that a steric effect, rather than hydrophobic or electronic effects, may be the predominant factor in determining aromatic effector specificity, and the active site of the regulator may positively interact not only with the methyl moiety but also with the most electron-rich aryl side of an aromatic effector.
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Affiliation(s)
- Joonhong Park
- Center for Microbial Ecology, Michigan State University, A528 PSS Building, East Lansing, MI 48824, USA
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77
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Watanabe K, Hamamura N. Molecular and physiological approaches to understanding the ecology of pollutant degradation. Curr Opin Biotechnol 2003; 14:289-95. [PMID: 12849782 DOI: 10.1016/s0958-1669(03)00059-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pollutant biodegradation in the environment occurs in the context of various interactions among microorganisms. To understand this ecological process, identification of functionally important populations is considered to be the primary step, which can be followed by isolation and laboratory pure-culture studies of the important organisms. Laboratory studies can then proceed to the analysis of in situ activity and interactions with other organisms. Such studies will shape a deeper understanding of the ecology of pollutant degradation and facilitate the development of new bioremediation strategies.
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Affiliation(s)
- Kazuya Watanabe
- Laboratory of Applied Microbiology, Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan.
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78
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Abstract
Fluorescent and luminescent marker and reporter genes provide easily detectable phenotypes to microbial cells and are therefore valuable tools for the study of microorganisms in the environment. Although these tools are becoming widely adopted, there are still issues that remain to be solved, such as the dependence of the reporter output on the physiological status of the cell. Eventually it might be the use of marker and reporter genes themselves that will contribute towards better understanding of the physiological status of specific microbial populations in nature.
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Affiliation(s)
- Janet K Jansson
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025 SE-750 07, Uppsala, Sweden.
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79
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Abstract
The past decade has witnessed the development of a novel class of tools for environmental monitoring: genetically engineered microorganisms 'tailored' to respond in a dose-dependent manner to changes in environmental conditions. Recent advances in the field include the expansion of available reporter functions with multicolored fluorescent proteins, a broadening of the detected chemical effects such as the availability of nutrients and enhancement of the spectrum of reporter microorganisms to include cyanobacteria, yeast and fungi. Most importantly, the stage has been set for the incorporation of such cells into various whole-cell array formats on silicon chips, optic fibres and other configurations. The future of such multiplex detection and analysis systems seems bright.
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Affiliation(s)
- Shimshon Belkin
- Division of Environmental Sciences, The Fredy and Nadin Herrmann Graduate School of Applied Science, Hebrew University, Jerusalem 91904, Israel.
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80
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Casavant NC, Thompson D, Beattie GA, Phillips GJ, Halverson LJ. Use of a site-specific recombination-based biosensor for detecting bioavailable toluene and related compounds on roots. Environ Microbiol 2003; 5:238-49. [PMID: 12662171 DOI: 10.1046/j.1462-2920.2003.00420.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We constructed and characterized a plasmid-based genetic system that reports the expression of a toluene-responsive promoter (PtbuA1) by effecting an irreversible, heritable change in the biosensor cell. Expression of the reporter gene gfp is strongly repressed in the absence of expression from the PtbuA1 promoter, and high level gfp expression in the original cell and its progeny is mediated by the site-specific recombination machinery of bacteriophage P22 to initiate removal of a repressor cassette. The reporter plasmid pTolLHB was functional in two soil saprophytes, Pseudomonas fluorescens A506 and Enterobacter cloacae JL1157, with the efficiency and sensitivity to low toluene concentrations being optimal in P. fluorescens A506. In culture, 80-100% of the A506 (pTolLHB) population expressed gfp following exposure to 0.2 micro m toluene for one to three hours. Compared to the response of A506 containing a plasmid-borne PtbuA1-gfp fusion, the recombination-based biosensor was more sensitive at detecting low toluene and trichloroethylene concentrations. An A506 (pTolLHB) inoculum, which had a background of 2.5% of the cells expressing gfp, was introduced onto barley roots in soil microcosms. If toluene was introduced into the microcosms, after 24 h, 72% of the A506 (pTolLHB) cells recovered from roots expressed gfp, indicating bioavailable toluene to rhizosphere bacteria. When toluene was not introduced, 16.5% of the A506 (pTolLHB) cells recovered from the roots expressed gfp, indicating that natural inducers of the PtbuA1 promoter were present in the barley rhizosphere. When introduced into rhizotrons containing barley plants and toluene vapours, the biosensor allowed localization of the availability of toluene along the seminal roots. In rhizotrons that were not exposed to toluene vapours, the biosensor exhibited high PtbuA1-promoter activity in distinct regions along the seminal roots, indicating spatial heterogeneity plant- or rhizosphere microbial community-derived inducers of the PtbuA1 promoter. This recombination-based toluene biosensor thus was useful in identifying bacterial exposure to transient or low levels of toluene, or related compounds, directly in the environment.
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Affiliation(s)
- N Carol Casavant
- Department of Agronomy, and Department of Microbiology, Iowa State University, Ames, IA 50011-1010, USA
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81
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Goh YY, Ho B, Ding JL. A novel fluorescent protein-based biosensor for gram-negative bacteria. Appl Environ Microbiol 2002; 68:6343-52. [PMID: 12450859 PMCID: PMC134398 DOI: 10.1128/aem.68.12.6343-6352.2002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Site-directed mutagenesis of enhanced green fluorescent protein (EGFP) based on rational computational design was performed to create a fluorescence-based biosensor for endotoxin and gram-negative bacteria. EGFP mutants (EGFP(i)) bearing one (G10) or two (G12) strands of endotoxin binding motifs were constructed and expressed in an Escherichia coli host. The EGFP(i) proteins were purified and tested for their efficacy as a novel fluorescent biosensor. After efficient removal of lipopolysaccharide from the E. coli lysates, the binding affinities of the EGFP(i) G10 and G12 to lipid A were established. The K(D) values of 7.16 x 10(-7) M for G10 and 8.15 x 10(-8) M for G12 were achieved. With high affinity being maintained over a wide range of pH and ionic strength, the binding of lipid A/lipopolysaccharide to the EGFP(i) biosensors could be measured as a concentration-dependent fluorescence quenching of the EGFP mutants. The EGFP(i) specifically tagged gram-negative bacteria like E. coli and Pseudomonas aeruginosa, as well as other gram-negative bacteria in contaminated water sampled from the environment. This dual function of the EGFP(i) in detecting both free endotoxin and live gram-negative bacteria forms the basis of the development of a novel fluorescent biosensor.
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Affiliation(s)
- Yan Y Goh
- Department of Biological Sciences, National University of Singapore, Singapore 117543
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82
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Axtell CA, Beattie GA. Construction and characterization of a proU-gfp transcriptional fusion that measures water availability in a microbial habitat. Appl Environ Microbiol 2002; 68:4604-12. [PMID: 12200319 PMCID: PMC124082 DOI: 10.1128/aem.68.9.4604-4612.2002] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We constructed and characterized a transcriptional fusion that measures the availability of water to a bacterial cell. This fusion between the proU promoter from Escherichia coli and the reporter gene gfp was introduced into strains of E. coli, Pantoea agglomerans, and Pseudomonas syringae. The proU-gfp fusion in these bacterial biosensor strains responded in a quantitative manner to water deprivation caused by the presence of NaCl, Na(2)SO(4), KCl, or polyethylene glycol (molecular weight, 8000). The fusion was induced to a detectable level by NaCl concentrations of as low as 10 mM in all three bacterial species. Water deprivation induced proU-gfp expression in both planktonic and surface-associated cells; however, it induced a higher level of expression in the surface-associated cells. Following the introduction of P. agglomerans biosensor cells onto bean leaves, the cells detected a significant decrease in water availability within only 5 min. After 30 min, the populations were exposed, on average, to a water potential equivalent to that imposed by approximately 55 mM NaCl. These results demonstrate the effectiveness of a proU-gfp-based biosensor for evaluating water availability on leaves. Furthermore, the inducibility of proU-gfp in multiple bacterial species illustrates the potential for tailoring proU-gfp-based biosensors to specific habitats.
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Affiliation(s)
- Catherine A Axtell
- Department of Microbiology, Iowa State University, Ames, Iowa 50011, USA
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