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Tao W, Song Y, Singhal N, McGoverin C, Vanholsbeeck F, Swift S. A novel optical biosensor for in situ and small-scale monitoring of bacterial transport in saturated columns. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112452. [PMID: 33813297 DOI: 10.1016/j.jenvman.2021.112452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
In situ monitoring techniques can provide new insight into bacterial transport after inoculating exogenous bacteria into contaminated soils for bioremediation. A real-time and non-destructive optical sensor (the optrode) was employed to monitor in situ transport of two fluorescently labelled bacteria - Green Fluorescent Protein (Gfp)-labelled, hydrophilic Pseudomonas putida and Tomato Fluorescent Protein (td)-labelled, hydrophobic Rhodococcus erythropolis, in a saturated sand column with and without rhamnolipid surfactant. In situ measurements were made at three sampling ports in the column with the optrode in two sets of column experiments. In Experiment 1, liquid samples were extracted for ex situ analyses (plate counts and fluorescence), while in Experiment 2 no liquid samples were extracted. Extracting liquid samples for ex situ analyses in Experiment 1 disturbed in situ measurements; in situ measured bacterial concentrations were lower, or a significant lag in breakthrough occurred relative to ex situ measurements. In Experiment 2, the optrode worked well in monitoring bacterial transport, which gave consistent transport parameters at each sampling port. Moreover, the optrode enabled the impact of bacterial hydrophobicity and rhamnolipid surfactant on bacterial transport to be observed. Specifically, hydrophilic P. putida was transported faster through the column than hydrophobic R. erythropolis; we infer from this result that fewer P. putida cells adsorb to sand particles than do R. erythropolis cells. The rhamnolipid surfactant enhanced the transport of both hydrophilic and hydrophobic bacteria. These two observations are consistent with Lifshitz-van der Waals forces and acid-base interactions between bacteria and sand.
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Affiliation(s)
- Wei Tao
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, PR China; Department of Civil and Environmental Engineering, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Yantao Song
- Department of Civil and Environmental Engineering, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Naresh Singhal
- Department of Civil and Environmental Engineering, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Cushla McGoverin
- The Dodds-Walls Centre for Photonic and Quantum Technologies, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand; Department of Physics, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Frédérique Vanholsbeeck
- The Dodds-Walls Centre for Photonic and Quantum Technologies, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand; Department of Physics, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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Generation of Genetic Tools for Gauging Multiple-Gene Expression at the Single-Cell Level. Appl Environ Microbiol 2021; 87:AEM.02956-20. [PMID: 33608300 DOI: 10.1128/aem.02956-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/11/2021] [Indexed: 11/20/2022] Open
Abstract
Key microbial processes in many bacterial species are heterogeneously expressed in single cells of bacterial populations. However, the paucity of adequate molecular tools for live, real-time monitoring of multiple-gene expression at the single-cell level has limited the understanding of phenotypic heterogeneity. To investigate phenotypic heterogeneity in the ubiquitous opportunistic pathogen Pseudomonas aeruginosa, a genetic tool that allows gauging multiple-gene expression at the single-cell level has been generated. This tool, named pRGC, consists of a promoter-probe vector for transcriptional fusions that carries three reporter genes coding for the fluorescent proteins mCherry, green fluorescent protein (GFP), and cyan fluorescent protein (CFP). The pRGC vector has been characterized and validated via single-cell gene expression analysis of both constitutive and iron-regulated promoters, showing clear discrimination of the three fluorescence signals in single cells of a P. aeruginosa population without the need for image processing for spectral cross talk correction. In addition, two pRGC variants have been generated for either (i) integration of the reporter gene cassette into a single neutral site of P. aeruginosa chromosome that is suitable for long-term experiments in the absence of antibiotic selection or (ii) replication in bacterial genera other than Pseudomonas The easy-to-use genetic tools generated in this study will allow rapid and cost-effective investigation of multiple-gene expression in populations of environmental and pathogenic bacteria, hopefully advancing the understanding of microbial phenotypic heterogeneity.IMPORTANCE Within a bacterial population, single cells can differently express some genes, even though they are genetically identical and experience the same chemical and physical stimuli. This phenomenon, known as phenotypic heterogeneity, is mainly driven by gene expression noise and results in the emergence of bacterial subpopulations with distinct phenotypes. The analysis of gene expression at the single-cell level has shown that phenotypic heterogeneity is associated with key bacterial processes, including competence, sporulation, and persistence. In this study, new genetic tools have been generated that allow easy cloning of up to three promoters upstream of distinct fluorescent genes, making it possible to gauge multiple-gene expression at the single-cell level by fluorescence microscopy without the need for advanced image-processing procedures. A proof of concept has been provided by investigating iron uptake and iron storage gene expression in response to iron availability in P. aeruginosa.
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Wang S, Payne GF, Bentley WE. Quorum Sensing Communication: Molecularly Connecting Cells, Their Neighbors, and Even Devices. Annu Rev Chem Biomol Eng 2020; 11:447-468. [DOI: 10.1146/annurev-chembioeng-101519-124728] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quorum sensing (QS) is a molecular signaling modality that mediates molecular-based cell–cell communication. Prevalent in nature, QS networks provide bacteria with a method to gather information from the environment and make decisions based on the intel. With its ability to autonomously facilitate both inter- and intraspecies gene regulation, this process can be rewired to enable autonomously actuated, but molecularly programmed, genetic control. On the one hand, novel QS-based genetic circuits endow cells with smart functions that can be used in many fields of engineering, and on the other, repurposed QS circuitry promotes communication and aids in the development of synthetic microbial consortia. Furthermore, engineered QS systems can probe and intervene in interkingdom signaling between bacteria and their hosts. Lastly, QS is demonstrated to establish conversation with abiotic materials, especially by taking advantage of biological and even electronically induced assembly processes; such QS-incorporated biohybrid devices offer innovative ways to program cell behavior and biological function.
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Affiliation(s)
- Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
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Han J, Xia A, Huang Y, Ni L, Chen W, Jin Z, Yang S, Jin F. Simultaneous Visualization of Multiple Gene Expression in Single Cells Using an Engineered Multicolor Reporter Toolbox and Approach of Spectral Crosstalk Correction. ACS Synth Biol 2019; 8:2536-2546. [PMID: 31596563 DOI: 10.1021/acssynbio.9b00223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Synthetic biology aims to make biology easier to engineer and focuses on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria, and the assembly of these smaller parts and devices into larger integrated systems to solve specific problems. Here, we designed and engineered a multicolor fluorescent reporter toolbox to simultaneously monitor the activities of multiple genes in single cells. The toolbox contained standardized and well-characterized genetic building blocks for the convenient and reproducible assembly of multiple promoter-reporter fusions (ranging from 1 to 4) into a single plasmid. Given the common problem of spectral crosstalk among multiple fluorescent proteins, we deciphered multiple spectral signatures within cells through a deduced linear unmixing algorithm. Our approach enabled the quantification of gene expression with direct FP concentrations, instead of mix-contributed fluorescence intensities, thus enabling true signal separation with high confidence. This approach performed well in the imaging of mixing cells with single FP labels. Additionally, combining with the multicolor toolbox, we succeeded in simultaneously monitoring the genetic dynamics of four selected quorum-sensing genes in response to the induction of two exogenously added autoinducers and were able to examine gene regulatory connections within the QS signaling network in Pseudomonas aeruginosa. Overall, this synthetic framework (i.e., the genetic toolbox and the well-evaluated approach of spectral correction) will be useful for applied synthetic biology projects, multicolor imaging, and analyzing interactions of multiple genes of natural genetic networks or assembling synthetic ones.
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Affiliation(s)
- Jundong Han
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering , University of Science and Technology of China , No. 96, JinZhai Road Baohe District , Hefei , Anhui 230026 , PR China
| | - Aiguo Xia
- Institute of Synthetic Biology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , PR China
| | - Yajia Huang
- Institute of Synthetic Biology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , PR China
| | - Lei Ni
- Institute of Synthetic Biology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , PR China
| | - Wenhui Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering , University of Science and Technology of China , No. 96, JinZhai Road Baohe District , Hefei , Anhui 230026 , PR China
| | - Zhenyu Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering , University of Science and Technology of China , No. 96, JinZhai Road Baohe District , Hefei , Anhui 230026 , PR China
| | - Shuai Yang
- Institute of Synthetic Biology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , PR China
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering , University of Science and Technology of China , No. 96, JinZhai Road Baohe District , Hefei , Anhui 230026 , PR China
- Institute of Synthetic Biology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , PR China
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