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Zhao J, Wang C, Liu J, Zhang N, Zhao Y, Zhao J, Wang X, Wei W. A biocompatible surface display approach in Shewanella promotes current output efficiency. Biosens Bioelectron 2024; 259:116422. [PMID: 38797034 DOI: 10.1016/j.bios.2024.116422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/04/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
The biology-material hybrid method for chemical-electricity conversion via microbial fuel cells (MFCs) has garnered significant attention in addressing global energy and environmental challenges. However, the efficiency of these systems remains unsatisfactory due to the complex manufacturing process and limited biocompatibility. To overcome these challenges, here, we developed a simple bio-inorganic hybrid system for bioelectricity generation in Shewanella oneidensis (S. oneidensis) MR-1. A biocompatible surface display approach was designed, and silver-binding peptide AgBP2 was expressed on the cell surface. Notably, the engineered Shewanella showed a higher electrochemical sensitivity to Ag+, and a 60 % increase in power density was achieved even at a low concentration of 10 μM Ag+. Further analysis revealed significant upregulations of cell surface negative charge intensity, ATP metabolism, and reducing equivalent (NADH/NAD+) ratio in the engineered S. oneidensis-Ag nanoparticles biohybrid. This work not only provides a novel insight for electrochemical biosensors to detect metal ions, but also offers an alternative biocompatible surface display approach by combining compatible biomaterials with electricity-converting bacteria for advancements in biohybrid MFCs.
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Affiliation(s)
- Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Chen Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jingjing Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Nuo Zhang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yuqin Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China; School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; NJU Xishan Institute of Applied Biotechnology, Wuxi, 214000, China.
| | - Xiuxiu Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China; School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; NJU Xishan Institute of Applied Biotechnology, Wuxi, 214000, China.
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China; NJU Xishan Institute of Applied Biotechnology, Wuxi, 214000, China.
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2
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Mahto KU, Das S. Electroactive biofilm communities in microbial fuel cells for the synergistic treatment of wastewater and bioelectricity generation. Crit Rev Biotechnol 2024:1-20. [PMID: 39009474 DOI: 10.1080/07388551.2024.2372070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/09/2024] [Indexed: 07/17/2024]
Abstract
Increasing industrialization and urbanization have contributed to a significant rise in wastewater discharge and exerted extensive pressure on the existing natural energy resources. Microbial fuel cell (MFC) is a sustainable technology that utilizes wastewater for electricity generation. MFC comprises a bioelectrochemical system employing electroactive biofilms of several aerobic and anaerobic bacteria, such as Geobacter sulfurreducens, Shewanella oneidensis, Pseudomonas aeruginosa, and Ochrobacterum pseudiintermedium. Since the electroactive biofilms constitute a vital part of the MFC, it is crucial to understand the biofilm-mediated pollutant metabolism and electron transfer mechanisms. Engineering electroactive biofilm communities for improved biofilm formation and extracellular polymeric substances (EPS) secretion can positively impact the bioelectrochemical system and improve fuel cell performance. This review article summarizes the role of electroactive bacterial communities in MFC for wastewater treatment and bioelectricity generation. A significant focus has been laid on understanding the composition, structure, and function of electroactive biofilms in MFC. Various electron transport mechanisms, including direct electron transfer (DET), indirect electron transfer (IET), and long-distance electron transfer (LDET), have been discussed. A detailed summary of the optimization of process parameters and genetic engineering strategies for improving the performance of MFC has been provided. Lastly, the applications of MFC for wastewater treatment, bioelectricity generation, and biosensor development have been reviewed.
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Affiliation(s)
- Kumari Uma Mahto
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
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3
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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4
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Li F, Zhang J, Liu D, Yu H, Li C, Liu Q, Chen Z, Song H. Engineering extracellular polymer substrates biosynthesis and carbon felt-carbon nanotube hybrid electrode to promote biofilm electroactivity and bioelectricity production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166595. [PMID: 37659546 DOI: 10.1016/j.scitotenv.2023.166595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Organic-rich thin stillage is a significant by-product of the liquor brewing industry, and its direct release into the environment can cause severe water pollution. Microbial fuel cells (MFCs) offer the possibility for converting organic matters in thin stillage into clean electricity. However, limited biofilm formation and conductivity are crucial bottlenecks in restricting the power harvest of MFCs. Here, to efficiently harvest electricity power from thin stillage of liquor industry, we adopted a modular engineering strategy to increase biofilm formation and conductivity of Shewanella oneidensis via enhancing the component biosynthesis of extracellular polymer substrates (EPS) matrix, regulating intracellular c-di-GMP level, and constructing of artificial hybrid system. The results showed that the constructed CNTs@CF-EnBF2 hybrid system with low charge-transfer resistance enabled a maximum output power density of 576.77 mW/m2 in lactate-fed MFCs. Also, to evaluate the capability of harvesting electricity from actual wastewater, the CNTs@CF-EnBF2 system was employed to treat actual thin stillage, obtaining a maximum output power density of 495.86 mW/m2, 3.3-fold higher than the wild-type strain. Our research suggested that engineering and regulating EPS biosynthesis effectively promoted bioelectricity harvest, providing a green and sustainable treatment strategy for thin stillage.
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Affiliation(s)
- Feng Li
- Frontier Science Center for Synthetic Biology (MOE), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Junqi Zhang
- Frontier Science Center for Synthetic Biology (MOE), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (MOE), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology (MOE), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chao Li
- Frontier Science Center for Synthetic Biology (MOE), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (MOE), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zheng Chen
- Frontier Science Center for Synthetic Biology (MOE), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology (MOE), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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5
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Xie C, Gu W, Chen Z, Liang Z, Huang S, Zhang LH, Chen S. Polyamine signaling communications play a key role in regulating the pathogenicity of Dickeya fangzhongdai. Microbiol Spectr 2023; 11:e0196523. [PMID: 37874149 PMCID: PMC10715095 DOI: 10.1128/spectrum.01965-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Dickeya fangzhongdai is a newly identified plant bacterial pathogen with a wide host range. A clear understanding of the cell-to-cell communication systems that modulate the bacterial virulence is of key importance for elucidating its pathogenic mechanisms and for disease control. In this study, we present evidence that putrescine molecules from the pathogen and host plants play an essential role in regulating the bacterial virulence. The significance of this study is in (i) demonstrating that putrescine signaling system regulates D. fangzhongdai virulence mainly through modulating the bacterial motility and production of PCWD enzymes, (ii) outlining the signaling and regulatory mechanisms with which putrescine signaling system modulates the above virulence traits, and (iii) validating that D. fangzhongdai could use both arginine and ornithine pathways to synthesize putrescine signals. To our knowledge, this is the first report to show that putrescine signaling system plays a key role in modulating the pathogenicity of D. fangzhongdai.
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Affiliation(s)
- Congcong Xie
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University Integrative Microbiology Research Centre, Guangzhou, China
| | - Weihan Gu
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University Integrative Microbiology Research Centre, Guangzhou, China
| | - Zhongqiao Chen
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University Integrative Microbiology Research Centre, Guangzhou, China
| | - Zhibin Liang
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University Integrative Microbiology Research Centre, Guangzhou, China
| | - Shufen Huang
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University Integrative Microbiology Research Centre, Guangzhou, China
| | - Lian-Hui Zhang
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University Integrative Microbiology Research Centre, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaohua Chen
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University Integrative Microbiology Research Centre, Guangzhou, China
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6
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Chen S, Ding Y. A bibliography study of Shewanella oneidensis biofilm. FEMS Microbiol Ecol 2023; 99:fiad124. [PMID: 37796898 PMCID: PMC10630087 DOI: 10.1093/femsec/fiad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/28/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
This study employs a bibliography study method to evaluate 472 papers focused on Shewanella oneidensis biofilms. Biofilms, which are formed when microorganisms adhere to surfaces or interfaces, play a crucial role in various natural, engineered, and medical settings. Within biofilms, microorganisms are enclosed in extracellular polymeric substances (EPS), creating a stable working environment. This characteristic enhances the practicality of biofilm-based systems in natural bioreactors, as they are less susceptible to temperature and pH fluctuations compared to enzyme-based bioprocesses. Shewanella oneidensis, a nonpathogenic bacterium with the ability to transfer electrons, serves as an example of a species isolated from its environment that exhibits extensive biofilm applications. These applications, such as heavy metal removal, offer potential benefits for environmental engineering and human health. This paper presents a comprehensive examination and review of the biology and engineering aspects of Shewanella biofilms, providing valuable insights into their functionality.
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Affiliation(s)
- Shan Chen
- Department of Applied Social Sciences, The Hong Kong Polytechnic University, 11 Yuk Choi Rd, Hung Hom, Hong Kong, China
| | - Yuanzhao Ding
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY, United Kingdom
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7
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Armalytė J, Čepauskas A, Šakalytė G, Martinkus J, Skerniškytė J, Martens C, Sužiedėlienė E, Garcia-Pino A, Jurėnas D. A polyamine acetyltransferase regulates the motility and biofilm formation of Acinetobacter baumannii. Nat Commun 2023; 14:3531. [PMID: 37316480 DOI: 10.1038/s41467-023-39316-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 06/07/2023] [Indexed: 06/16/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen highly resistant to environmental changes and antimicrobial treatments. Regulation of cellular motility and biofilm formation is important for its virulence, although it is poorly described at the molecular level. It has been previously reported that Acinetobacter genus specifically produces a small positively charged metabolite, polyamine 1,3-diaminopropane, that has been associated with cell motility and virulence. Here we show that A. baumannii encodes novel acetyltransferase, Dpa, that acetylates 1,3-diaminopropane, directly affecting the bacterium motility. Expression of dpa increases in bacteria that form pellicle and adhere to eukaryotic cells as compared to planktonic bacterial cells, suggesting that cell motility is linked to the pool of non-modified 1,3-diaminopropane. Indeed, deletion of dpa hinders biofilm formation and increases twitching motion confirming the impact of balancing the levels of 1,3-diaminopropane on cell motility. The crystal structure of Dpa reveals topological and functional differences from other bacterial polyamine acetyltransferases, adopting a β-swapped quaternary arrangement similar to that of eukaryotic polyamine acetyltransferases with a central size exclusion channel that sieves through the cellular polyamine pool. The structure of catalytically impaired DpaY128F in complex with the reaction product shows that binding and orientation of the polyamine substrates are conserved between different polyamine-acetyltransferases.
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Affiliation(s)
- Julija Armalytė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Albinas Čepauskas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050, Brussels, Belgium
| | - Gabija Šakalytė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Julius Martinkus
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Jūratė Skerniškytė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Chloé Martens
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Bruxelles, Belgium. Building BC, Boulevard du Triomphe, 1050, Brussels, Belgium
| | - Edita Sužiedėlienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050, Brussels, Belgium.
| | - Dukas Jurėnas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania.
- Laboratoire de Génétique et Physiologie Bactérienne, Faculté des Sciences, Université Libre de Bruxelles (ULB), 12 Rue des Profs. Jeener et Brachet, B-6041, Gosselies, Belgium.
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Zhang Y, Plymale A, Son J, Huang Q, Chen W, Yu XY. Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture. Front Chem 2023; 11:1203314. [PMID: 37304684 PMCID: PMC10248399 DOI: 10.3389/fchem.2023.1203314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.
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Affiliation(s)
- Yuchen Zhang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Andrew Plymale
- Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA, United States
| | - Jiyoung Son
- Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA, United States
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Ying Yu
- Oak Ridge National Laboratory, Materials Science and Technology Division, Oak Ridge, TN, United States
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Deciphering Molecular Factors That Affect Electron Transfer at the Cell Surface of Electroactive Bacteria: The Case of OmcA from Shewanella oneidensis MR-1. Microorganisms 2022; 11:microorganisms11010079. [PMID: 36677373 PMCID: PMC9861303 DOI: 10.3390/microorganisms11010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Multiheme cytochromes play a central role in extracellular electron transfer, a process that allows microorganisms to sustain their metabolism with external electron acceptors or donors. In Shewanella oneidensis MR-1, the decaheme cytochromes OmcA and MtrC show functional specificity for interaction with soluble and insoluble redox partners. In this work, the capacity of extracellular electron transfer by mutant variants of S. oneidensis MR-1 OmcA was investigated. The results show that amino acid mutations can affect protein stability and alter the redox properties of the protein, without affecting the ability to perform extracellular electron transfer to methyl orange dye or a poised electrode. The results also show that there is a good correlation between the reduction of the dye and the current generated at the electrode for most but not all mutants. This observation opens the door for investigations of the molecular mechanisms of interaction with different electron acceptors to tailor these surface exposed cytochromes towards specific bio-based applications.
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10
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Dynamic Changes in Biofilm Structures under Dynamic Flow Conditions. Appl Environ Microbiol 2022; 88:e0107222. [PMID: 36300948 PMCID: PMC9680615 DOI: 10.1128/aem.01072-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Detachment is an important process determining the structure and function of bacterial biofilm, which has significant implications for biogeochemical cycling of elements, biofilm application, and infection control in clinical settings. Quantifying the responses of biofilm structure to hydrodynamics is crucial for understanding biofilm detachment mechanisms in aquatic environments.
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11
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Ren H, Deng Y, Ma L, Wei Z, Ma L, Yang D, Wang B, Luo ZY. Enhanced biodegradation of oil-contaminated soil oil in shale gas exploitation by biochar immobilization. Biodegradation 2022; 33:621-639. [PMID: 36214905 DOI: 10.1007/s10532-022-09999-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
Abstract
The enhanced biodegradation of oil-contaminated soil by fixing microorganisms with corn cob biochar was investigated. It was found that the components of oil in the test soil were mainly straight-chain alkanes and branched alkanes. When using corn cob biochar as a carrier to immobilize microorganisms, the best particle size of corn cob biochar as an immobilization carrier was 0.08 mm, and the best immobilization time was 18 h. SEM analysis confirmed that the microorganisms were immobilized on the corn cob biochar. Immobilized microorganisms exhibited high biodegradability under stress to high concentrations of petroleum pollutants, heavy metals, and organic pollutants. Infrared spectroscopy analysis showed that oxygen-containing groups such as hydroxyl, carboxyl, and methoxy on the surface of biochar were involved in the complexation of heavy metals. The mechanism of immobilization promoted microbial degradation of oil contamination was explained by gas chromatography mass. First, alkanes and aromatics were adsorbed by corn cob biochar and passed to immobilized microorganisms to promote their degradation. Their bioavailability increased, especially for aromatics. Second, biochar provided a more suitable environment for microorganisms to degrade. Third, the conversion of ketones to acids was accelerated during the biodegradation of alkanes, and the biodegradation of alkanes was accelerated by immobilization. The biodegradable efficiency of oil by immobilized microorganisms in soil was 70.10% within 60 days, 28.80% higher than that of free microorganisms. The degradation of immobilized microorganisms was highly correlated with the activities of catalase, urease, and polyphenol oxidase.
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Affiliation(s)
- Hongyang Ren
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China. .,State Environmental Protection Key Laboratory of Collaborative Control and Remediation of Soil and Water Pollution, Chengdu, 610059, China. .,Oil & Gas Field Applied Chemistry Key Laboratory of Sichuan Province, Chengdu, 610500, China.
| | - Yuanpeng Deng
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China
| | - Liang Ma
- Department of Quality, Health, Safety and Environmental Protection, PetroChina Zhejiang Oilfield Company, Hangzhou, 310000, People's Republic of China
| | - Zijing Wei
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China
| | - Lingli Ma
- Ecological and Environmental Monitoring Center of Chongqing, Chongqing, 401147, China
| | - Demin Yang
- National Joint Local Engineering Research Center for Shale Gas Exploration and Development, Chongqing Institute of Geology and Mineral Resources, Chongqing, 401120, China
| | - Bing Wang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China
| | - Zheng-Yu Luo
- State Environmental Protection Key Laboratory of Collaborative Control and Remediation of Soil and Water Pollution, Chengdu, 610059, China
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Abstract
Improving the availability of representative isolates from the coral microbiome is essential for investigating symbiotic mechanisms and applying beneficial microorganisms to improve coral health. However, few studies have explored the diversity of bacteria which can be isolated from a single species. Here, we isolated a total of 395 bacterial strains affiliated with 49 families across nine classes from the coral Pocillopora damicornis. Identification results showed that most of the strains represent potential novel bacterial species or genera. We also sequenced and assembled the genomes of 118 of these isolates, and then the putative functions of these isolates were identified based on genetic signatures derived from the genomes and this information was combined with isolate-specific phenotypic data. Genomic information derived from the isolates identified putative functions including nitrification and denitrification, dimethylsulfoniopropionate transformation, and supply of fixed carbon, amino acids, and B vitamins which may support their eukaryotic partners. Furthermore, the isolates contained genes associated with chemotaxis, biofilm formation, quorum sensing, membrane transport, signal transduction, and eukaryote-like repeat-containing and cell-cell attachment proteins, all of which potentially help the bacterium establish association with the coral host. Our work expands on the existing culture collection of coral-associated bacteria and provides important information on the metabolic potential of these isolates which can be used to refine understanding of the role of bacteria in coral health and are now available to be applied to novel strategies aimed at improving coral resilience through microbiome manipulation. IMPORTANCE Microbes underpin the health of corals which are the building blocks of diverse and productive reef ecosystems. Studying the culturable fraction of coral-associated bacteria has received less attention in recent times than using culture-independent molecular methods. However, the genomic and phenotypic characterization of isolated strains allows assessment of their functional role in underpinning coral health and identification of beneficial microbes for microbiome manipulation. Here, we isolated 395 bacterial strains from tissues of Pocillopora damicornis with many representing potentially novel taxa and therefore providing a significant contribution to coral microbiology through greatly enlarging the existing cultured coral-associated bacterial bank. Through analysis of the genomes obtained in this study for the coral-associated bacteria and coral host, we elucidate putative metabolic linkages and symbiotic establishment. The results of this study will help to elucidate the role of specific isolates in coral health and provide beneficial microbes for efforts aimed at improving coral health.
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Chen Y, Niu X, Cheng M, Wang L, Sun P, Song H, Cao Y. CRISPR/dCas9-RpoD-Mediated Simultaneous Transcriptional Activation and Repression in Shewanella oneidensis MR-1. ACS Synth Biol 2022; 11:2184-2192. [PMID: 35608070 DOI: 10.1021/acssynbio.2c00149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extracellular electron transfer (EET) of electroactive microorganisms (EAMs) is the dominating factor for versatile applications of bio-electrochemical systems. Shewanella oneidensis MR-1 is one of the model EAMs for the study of EET, which is associated with a variety of cellular activities. However, due to the lack of a transcriptional activation tool, regulation of multiple genes is labor-intensive and time-consuming, which hampers the advancement of improving the EET efficiency in S. oneidensis. In this study, we developed an easily operated and multifunctional regulatory tool, that is, a simultaneous clustered regularly interspaced short palindromic repeats (CRISPR)-mediated transcriptional activation (CRISPRa) and interference (CRISPRi) system, for application in S. oneidensis. First, a large number of activators were screened, and RpoD (σ70) was determined as the optimal activator. Second, the effective activation range was identified to be 190-216 base upstream of the transcriptional start site. Third, up- and downregulation was achieved in concert by two orthogonal single guide RNAs targeting different positions. The activation of the cell division gene (minCDE) and repression of the cytotoxic gene (SO_3166) were concurrently implemented, increasing the power density by 2.5-fold and enhancing the degradation rate of azo dyes by 2.9-fold. The simultaneous CRISPRa and CRISPRi system enables simultaneous multiplex genetic regulation, offering the potential to further advance studies of the EET mechanism and application in S. oneidensis.
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Affiliation(s)
- Yaru Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xiaolong Niu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Meijie Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Luxin Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Panxing Sun
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
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Liu L, Wang W, Wu S, Gao H. Recent Advances in the Siderophore Biology of Shewanella. Front Microbiol 2022; 13:823758. [PMID: 35250939 PMCID: PMC8891985 DOI: 10.3389/fmicb.2022.823758] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the abundance of iron in nature, iron acquisition is a challenge for life in general because the element mostly exists in the extremely insoluble ferric (Fe3+) form in oxic environments. To overcome this, microbes have evolved multiple iron uptake strategies, a common one of which is through the secretion of siderophores, which are iron-chelating metabolites generated endogenously. Siderophore-mediated iron transport, a standby when default iron transport routes are abolished under iron rich conditions, is essential under iron starvation conditions. While there has been a wealth of knowledge about the molecular basis of siderophore synthesis, uptake and regulation in model bacteria, we still know surprisingly little about siderophore biology in diverse environmental microbes. Shewanella represent a group of γ-proteobacteria capable of respiring a variety of organic and inorganic substrates, including iron ores. This respiratory process relies on a large number of iron proteins, c-type cytochromes in particular. Thus, iron plays an essential and special role in physiology of Shewanella. In addition, these bacteria use a single siderophore biosynthetic system to produce an array of macrocyclic dihydroxamate siderophores, some of which show particular biological activities. In this review, we first outline current understanding of siderophore synthesis, uptake and regulation in model bacteria, and subsequently discuss the siderophore biology in Shewanella.
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Affiliation(s)
- Lulu Liu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
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Kumar A, Ng DHP, Bairoliya S, Cao B. The Dark Side of Microbial Processes: Accumulation of Nitrate During Storage of Surface Water in the Dark and the Underlying Mechanism. Microbiol Spectr 2022; 10:e0223221. [PMID: 34985332 PMCID: PMC8729765 DOI: 10.1128/spectrum.02232-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/03/2021] [Indexed: 11/20/2022] Open
Abstract
In densely populated cities with limited land, storage of surface water in underground spaces is a potential solution to meet the rising demand of clean water. In addition, due to the imperative need of renewable solar energy and limited land resources, the deployment of floating solar photovoltaic (PV) systems over water has risen exponentially. In both scenarios, microbial communities in the water do not have access to sunlight. How the absence of sunlight influences microbial community function and the water quality is largely unknown. The objective of this study was to reveal microbial processes in surface water stored in the dark and water quality dynamics. Water from a freshwater reservoir was stored in the dark or light (control) for 6 months. Water quality was monitored at regular intervals. RNA sequencing was performed on the Illumina MiSeq platform and qPCR was used to substantiate the findings arising from the sequencing data. Our results showed that storage of surface water in the dark resulted in the accumulation of nitrate in the water. Storage in the dark promoted the decay of algal cells, increasing the amount of free nitrogen in the water. Most of the free nitrogen was eventually transformed into nitrate through microbial processes. RNA sequencing-based microbial community analyses and pure culture experiments using nitrifying bacteria Nitrosomonas europaea and Nitrobacter sp. revealed that the accumulation of nitrate in the dark was likely due to an increase in nitrification rate and a decrease in the assimilation rate of nitrate back into the biomass. IMPORTANCE Microbial communities play an essential role in maintaining a healthy aquatic ecosystem. For example, in surface water reservoirs, microorganisms produce oxygen, break down toxic contaminants and remove excess nitrogen. In densely populated cities with limited land, storing surface water in underground spaces and deploying floating solar photovoltaic (PV) systems over water are potential solutions to address water and energy sustainability challenges. In both scenarios, surface water is kept in the dark. In this work, we revealed how the absence of sunlight influences microbial community function and water quality. We showed that storage of surface water in the dark affected bacterial activities responsible for nitrogen transformation, resulting in the accumulation of nitrate in the water. Our findings highlight the importance of monitoring nitrate closely if raw surface water is to be stored in the dark and the potential need of downstream treatment to remove nitrate.
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Affiliation(s)
- Amit Kumar
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Daphne H. P. Ng
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Sakcham Bairoliya
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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16
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Wang YX, Hou N, Liu XL, Mu Y. Advances in interfacial engineering for enhanced microbial extracellular electron transfer. BIORESOURCE TECHNOLOGY 2022; 345:126562. [PMID: 34910968 DOI: 10.1016/j.biortech.2021.126562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The extracellular electron transfer (EET) efficiency between electroactive microbes (EAMs) and electrode is a key factor determining the development of microbial electrochemical technology (MET). Currently, the low EET efficiency of EAMs limits the application of MET in the fields of organic matter degradation, electric energy production, seawater desalination, bioremediation and biosensing. Enhancement of the interaction between EAMs and electrode by interfacial engineering methods brings bright prospects for the improvement of the EET efficiency of EAMs. In view of the research in recent years, this mini-review systematically summarizes various interfacial engineering strategies ranging from electrode surface modification to hybrid biofilm formation, then to single cell interfacial engineering and intracellular reformation for promoting the electron transfer between EAMs and electrode, focusing on the applicability and limitations of these methodologies. Finally, the possible key directions, challenges and opportunities for future interfacial engineering to strengthen the microbial EET are proposed in this mini-review.
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Affiliation(s)
- Yi-Xuan Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Nannan Hou
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Xiao-Li Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Yang Mu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
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Beneficial biofilms: A mini-review of strategies to enhance biofilm formation for biotechnological applications. Appl Environ Microbiol 2021; 88:e0199421. [PMID: 34851721 DOI: 10.1128/aem.01994-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The capacity of bacteria to form biofilms is an important trait for their survival and persistence. Biofilms occur naturally in soil and aquatic environments, are associated with animals ranging from insects to humans and are also found in built environments. They are typically encountered as a challenge in healthcare, food industry, and water supply ecosystems. In contrast, they are known to play a key role in the industrial production of commercially valuable products, environmental remediation processes, and in microbe-catalysed electrochemical systems for energy and resource recovery from wastewater. While there are many recent articles on biofilm control and removal, review articles on promoting biofilm growth for biotechnological applications are unavailable. Biofilm formation is a tightly regulated response to perturbations in the external environment. The multi-stage process, mediated by an assortment of proteins and signaling systems, involves the attachment of bacterial cells to a surface followed by their aggregation in a matrix of extracellular polymeric substances. Biofilms can be promoted by altering the external environment in a controlled manner, supplying molecules that trigger the aggregation of cells and engineering genes associated with biofilm development. This mini-review synthesizes findings from studies that have described such strategies and highlights areas needing research attention.
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Edel M, Sturm G, Sturm-Richter K, Wagner M, Ducassou JN, Couté Y, Horn H, Gescher J. Extracellular riboflavin induces anaerobic biofilm formation in Shewanella oneidensis. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:130. [PMID: 34082787 PMCID: PMC8176591 DOI: 10.1186/s13068-021-01981-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Some microorganisms can respire with extracellular electron acceptors using an extended electron transport chain to the cell surface. This process can be applied in bioelectrochemical systems in which the organisms produce an electrical current by respiring with an anode as electron acceptor. These organisms apply flavin molecules as cofactors to facilitate one-electron transfer catalyzed by the terminal reductases and in some cases as endogenous electron shuttles. RESULTS In the model organism Shewanella oneidensis, riboflavin production and excretion trigger a specific biofilm formation response that is initiated at a specific threshold concentration, similar to canonical quorum-sensing molecules. Riboflavin-mediated messaging is based on the overexpression of the gene encoding the putrescine decarboxylase speC which leads to posttranscriptional overproduction of proteins involved in biofilm formation. Using a model of growth-dependent riboflavin production under batch and biofilm growth conditions, the number of cells necessary to produce the threshold concentration per time was deduced. Furthermore, our results indicate that specific retention of riboflavin in the biofilm matrix leads to localized concentrations, which by far exceed the necessary threshold value. CONCLUSION This study describes a new quorum-sensing mechanism in S. oneidensis. Biofilm formation of S. oneidensis is induced by low concentrations of riboflavin resulting in an upregulation of the ornithine-decarboxylase speC. The results can be applied for the development of strains catalyzing increased current densities in bioelectrochemical systems.
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Affiliation(s)
- Miriam Edel
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Gunnar Sturm
- Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Katrin Sturm-Richter
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Michael Wagner
- Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | | | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, Grenoble, France
| | - Harald Horn
- Engler-Bunte-Institute, Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Karlsruhe, Germany
- DVGW Research Laboratories for Water Chemistry and Water Technology, Karlsruhe, Germany
| | - Johannes Gescher
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany.
- Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
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Sivakumar K, Lehmann R, Rachmadi AT, Augsburger N, Zaouri N, Tegner J, Hong PY. Elucidating the Role of Virulence Traits in the Survival of Pathogenic E. coli PI-7 Following Disinfection. Front Bioeng Biotechnol 2021; 8:614186. [PMID: 33415102 PMCID: PMC7783314 DOI: 10.3389/fbioe.2020.614186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
Reuse and discharge of treated wastewater can result in dissemination of microorganisms into the environment. Deployment of disinfection strategies is typically proposed as a last stage remediation effort to further inactivate viable microorganisms. In this study, we hypothesize that virulence traits, including biofilm formation, motility, siderophore, and curli production along with the capability to internalize into mammalian cells play a role in survival against disinfectants. Pathogenic E. coli PI-7 strain was used as a model bacterium that was exposed to diverse disinfection strategies such as chlorination, UV and solar irradiation. To this end, we used a random transposon mutagenesis library screening approach to generate 14 mutants that exhibited varying levels of virulence traits. In these 14 isolated mutants, we observed that an increase in virulence traits such as biofilm formation, motility, curli production, and internalization capability, increased the inactivation half-lives of mutants compared to wild-type E. coli PI-7. In addition, oxidative stress response and EPS production contributed to lengthening the lag phase duration (defined as the time required for exposure to disinfectant prior to decay). However, traits related to siderophore production did not help with survival against the tested disinfection strategies. Taken together, the findings suggested that selected virulence traits facilitate survival of pathogenic E. coli PI-7, which in turn could account for the selective enrichment of pathogens over the non-pathogenic ones after wastewater treatment. Further, the study also reflected on the effectiveness of UV as a more viable disinfection strategy for inactivation of pathogens.
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Affiliation(s)
- Krishnakumar Sivakumar
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Robert Lehmann
- Living Systems Laboratory, Environmental Epigenetic Program, Biological and Environmental Science and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Andri Taruna Rachmadi
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nicolas Augsburger
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Noor Zaouri
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jesper Tegner
- Living Systems Laboratory, Environmental Epigenetic Program, Biological and Environmental Science and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Liu W, Chen Y, Zhou X, Liu J, Zhu J, Wang S, Liu C, Sun D. The Cyclic AMP Receptor Protein, Crp, Is Required for the Decolorization of Acid Yellow 36 in Shewanella putrefaciens CN32. Front Microbiol 2020; 11:596372. [PMID: 33362744 PMCID: PMC7755654 DOI: 10.3389/fmicb.2020.596372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/15/2020] [Indexed: 01/20/2023] Open
Abstract
Shewanella shows good application potentials in the decolorization and detoxification of azo dye wastewater. However, the molecular mechanism of decolorization is still lacking. In this study, it was found that Shewanella putrefaciens CN32 exhibited good decolorization ability to various azo dyes, and a global regulatory protein cAMP receptor protein (Crp) was identified to be required for the decolorization of acid yellow 36 (AY) by constructing a transposon mutant library. Then, the molecular mechanism of AY decolorization regulated by Crp was further investigated. RT-qPCR and electrophoretic mobility shift assay (EMSA) results showed that Crp was able to directly bind to the promoter region of the cymA gene and promote its expression. Riboflavin acting as an electron shuttle could accelerate the AY decolorization efficiency of S. putrefaciens CN32 wild-type (WT) but did not show a promoting effect to Δcrp mutant and ΔcymA mutant, further confirming that Crp promotes the decolorization through regulating electron transport chains. Moreover, the mutant with cymA overexpression could slightly enhance the AY decolorization efficiency compared with the WT strain. In addition, it was found that MtrA, MtrB, and MtrC partially contribute to the electron transfer from CymA to dye molecules, and other main electron transport chains need to be identified in future experiments. This study revealed the molecular mechanism of a global regulator Crp regulating the decolorization of azo dye, which is helpful in understanding the relationship between the decolorization and other metabolic processes in S. putrefaciens CN32.
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Affiliation(s)
- Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ying Chen
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xuge Zhou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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Engineering S. oneidensis for Performance Improvement of Microbial Fuel Cell-a Mini Review. Appl Biochem Biotechnol 2020; 193:1170-1186. [PMID: 33200267 DOI: 10.1007/s12010-020-03469-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/09/2020] [Indexed: 02/02/2023]
Abstract
Microbial fuel cell (MFC) is a promising technology that utilizes exoelectrogens cultivated in the form of biofilm to generate power from various types of sources supplied. A metal-reducing pathway is utilized by these organisms to transfer electrons obtained from the metabolism of substrate from anaerobic respiration extracellularly. A widely established model organism that is capable of extracellular electron transfer (EET) is Shewanella oneidensis. This review highlights the strategies used in the transformation of S. oneidensis and the recent development of MFC in terms of intervention through genetic modifications. S. oneidensis was genetically engineered for several aims including the study on the underlying mechanisms of EET, and the enhancement of power generation and wastewater treating potential when used in an MFC. Through engineering S. oneidensis, genes responsible for EET are identified and strategies on enhancing the EET efficiency are studied. Overexpressing genes related to EET to enhance biofilm formation, mediator biosynthesis, and respiration appears as one of the common approaches.
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Chen H, Simoska O, Lim K, Grattieri M, Yuan M, Dong F, Lee YS, Beaver K, Weliwatte S, Gaffney EM, Minteer SD. Fundamentals, Applications, and Future Directions of Bioelectrocatalysis. Chem Rev 2020; 120:12903-12993. [DOI: 10.1021/acs.chemrev.0c00472] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hui Chen
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Olja Simoska
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Koun Lim
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Matteo Grattieri
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Mengwei Yuan
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Fangyuan Dong
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Yoo Seok Lee
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Kevin Beaver
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Samali Weliwatte
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Erin M. Gaffney
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
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Mukherjee M, Zaiden N, Teng A, Hu Y, Cao B. Shewanella biofilm development and engineering for environmental and bioenergy applications. Curr Opin Chem Biol 2020; 59:84-92. [PMID: 32750675 DOI: 10.1016/j.cbpa.2020.05.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 12/31/2022]
Abstract
The genus Shewanella comprises about 70 species of Gram-negative, facultative anaerobic bacteria inhabiting various environments, which have shown great potential in various biotechnological applications ranging from environmental bioremediation, metal(loid) recovery and material synthesis to bioenergy generation. Most environmental and energy applications of Shewanella involve the biofilm mode of growth on surfaces of solid minerals or electrodes. In this article, we first provide an overview of Shewanella biofilm biology with the focus on biofilm dynamics, biofilm matrix, and key signalling systems involved in Shewanella biofilm development. Then we review strategies recently exploited to engineer Shewanella biofilms to improve biofilm-mediated bioprocesses.
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Affiliation(s)
- Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore
| | - Norazean Zaiden
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, 637335, Singapore
| | - Aloysius Teng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, 637335, Singapore
| | - Yidan Hu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, 637335, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore.
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Wu Y, Zaiden N, Liu X, Mukherjee M, Cao B. Responses of Exogenous Bacteria to Soluble Extracellular Polymeric Substances in Wastewater: A Mechanistic Study and Implications on Bioaugmentation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:6919-6928. [PMID: 32348125 DOI: 10.1021/acs.est.0c00015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Compared with the chemically defined synthetic wastewater (SynWW), real wastewater has been reported to exhibit distinct effects on microbial community development. Whether and how soluble microbial products in real wastewater contribute to different effects of synthetic and real wastewater on the fate of exogenous bacteria remains elusive. In this study, using a model wastewater bacterium Comamonas testosteroni, we first examined the influences of microfiltration filter-sterilized real wastewater (MF-WW) and SynWW on the retention of C. testosteroni in established wastewater flocs during bioaugmentation. In bioreactors fed with MF-WW, augmentation of C. testosteroni to wastewater flocs resulted in a substantially higher abundance of the augmented bacterial cells than those fed with SynWW. To identify the soluble microbial products in MF-WW contributing to the observed differences between bioaugmentation reactors fed with MF-WW and SynWW, we examined the effect of MF-WW and SynWW on the growth, floc formation, and biofilm development of C. testosteroni. When C. testosteroni grew in MF-WW, visible flocs formed within 2 h, which is in contrast to cell growth in SynWW where floc formation was not observed. We further demonstrated that the observed differences were mainly attributed to the high molecular weight fraction of the soluble extracellular polymeric substances (EPS) in MF-WW, in particular, proteins and extracellular DNA. The DLVO analysis suggested that, in the presence of soluble EPS, the bacterial cell surface exhibits an increased hydrophobicity and a diminished energy barrier, leading to irreversible attachment of planktonic cells and floc formation. The RNA-seq based transcriptional analysis revealed that, in the presence of soluble EPS, genes involved in nonessential metabolisms were downregulated while genes coding for Cco (cbb3-type) and Cox (aa3-type) oxidases with different oxygen affinities were upregulated, facilitating bacterial survival in flocs. Taken together, this study reveals the mechanisms underlying the contribution of soluble EPS in real wastewater to the recruitment of exogenous bacteria by microbial aggregates and provides implications to bioaugmentation.
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Affiliation(s)
- Yichao Wu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Norazean Zaiden
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Xin Liu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
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25
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Promiscuous Enzymes Cause Biosynthesis of Diverse Siderophores in Shewanella oneidensis. Appl Environ Microbiol 2020; 86:AEM.00030-20. [PMID: 32005730 DOI: 10.1128/aem.00030-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/23/2020] [Indexed: 02/05/2023] Open
Abstract
The siderophore synthetic system in Shewanella species is able to synthesize dozens of macrocyclic siderophores in vitro with synthetic precursors. In vivo, however, although three siderophores are produced naturally in Shewanella algae B516, which carries a lysine decarboxylase (AvbA) specific for siderophore synthesis, only one siderophore can be detected from many other Shewanella species. In this study, we examined a siderophore-overproducing mutant of Shewanella oneidensis which lacks an AvbA counterpart, and we found that it can also produce these three siderophores. We identified both SpeC and SpeF as promiscuous decarboxylases for both lysine and ornithine to synthesize the siderophore precursors cadaverine and putrescine, respectively. Intriguingly, putrescine is mainly synthesized from arginine through an arginine decarboxylation pathway in a constitutive manner, not liable to the concentrations of iron and siderophores. Our results provide further evidence that the substrate availability plays a determining role in siderophore production. Furthermore, we provide evidence to suggest that under iron starvation conditions, cells allocate more putrescine for siderophore biosynthesis by downregulating the expression of the enzyme that transforms putrescine into spermidine. Overall, this study provides another example of the great flexibility of bacterial metabolism that is honed by evolution to better fit living environments of these bacteria.IMPORTANCE The simultaneous production of multiple siderophores is considered a general strategy for microorganisms to rapidly adapt to their ever-changing environments. In this study, we show that some Shewanella spp. may downscale their capability for siderophore synthesis to facilitate adaptation. Although S. oneidensis lacks an enzyme specifically synthesizing cadaverine, it can produce it by using promiscuous ornithine decarboxylases. Despite this ability, this bacterium predominately produces the primary siderophore while restraining the production of secondary siderophores by regulating substrate availability. In addition to using the arginine decarboxylase (ADC) pathway for putrescine synthesis, cells optimize the putrescine pool for siderophore production. Our work provides an insight into the coordinated synthesis of multiple siderophores by harnessing promiscuous enzymes in bacteria and underscores the importance of substrate pools for the biosynthesis of natural products.
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26
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Cheng L, Min D, Liu DF, Zhu TT, Wang KL, Yu HQ. Deteriorated biofilm-forming capacity and electroactivity of Shewanella oneidnsis MR-1 induced by insertion sequence (IS) elements. Biosens Bioelectron 2020; 156:112136. [PMID: 32174561 DOI: 10.1016/j.bios.2020.112136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/17/2022]
Abstract
Shewanella oneidensis MR-1, a model species of exoelectrogenic bacteria (EEB), has been widely applied in bioelectrochemical systems. Biofilms of EEB grown on electrodes are essential in governing the current output and power density of bioelectrochemical systems. The MR-1 genome is exceptionally dynamic due to the existence of a large number of insertion sequence (IS) elements. However, to date, the impacts of IS elements on the biofilm-forming capacity of EEB and performance of bioelectrochemical systems remain unrevealed. Herein, we isolated a non-motile mutant (NMM) with biofilm-deficient phenotype from MR-1. We found that the insertion of an ISSod2 element into the flrA (encoding the master regulator for flagella synthesis and assembly) of MR-1 resulted in the non-motile and biofilm-deficient phenotypes in NMM cells. Notably, such a variant was readily confused with the wild-type strain because there were no obvious differences in growth rates and colonial morphologies between the two strains. However, the reduced biofilm formation on the electrodes and the deteriorated performances of bioelectrochemical systems and Cr(VI) immobilization for the strain NMM were observed. Given the wide distribution of IS elements in EEB, appropriate cultivation and preservation conditions should be adopted to reduce the likelihood that IS elements-mediated mutation occurs in EEB. These findings reveal the negative impacts of IS elements on the biofilm-forming capacity of EEB and performance of bioelectrochemical systems and suggest that great attention should be given to the actual physiological states of EEB before their applications.
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Affiliation(s)
- Lei Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China.
| | - Ting-Ting Zhu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Kai-Li Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China.
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27
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Herrero Del Valle A, Seip B, Cervera-Marzal I, Sacheau G, Seefeldt AC, Innis CA. Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. Nat Microbiol 2020; 5:554-561. [PMID: 32094585 PMCID: PMC7250644 DOI: 10.1038/s41564-020-0669-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Polyamines are essential metabolites that play an important role in cell growth, stress adaptation, and microbial virulence1–3. In order to survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues2. Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF4, via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryo-EM structure of an Escherichia coli (E. coli) ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor RF1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens.
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Affiliation(s)
- Alba Herrero Del Valle
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France
| | - Britta Seip
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Evotec International GmbH, Göttingen, Germany
| | - Iñaki Cervera-Marzal
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Aix Marseille Université, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Guénaël Sacheau
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Sopra Steria, Saint-Herblain, France
| | - A Carolin Seefeldt
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France. .,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France. .,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.
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28
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Hu Y, Liu X, Ren ATM, Gu JD, Cao B. Optogenetic Modulation of a Catalytic Biofilm for the Biotransformation of Indole into Tryptophan. CHEMSUSCHEM 2019; 12:5142-5148. [PMID: 31621183 DOI: 10.1002/cssc.201902413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/15/2019] [Indexed: 06/10/2023]
Abstract
In green chemical synthesis, biofilms as biocatalysts have shown great promise. Efficient biofilm-mediated biocatalysis requires the modulation of biofilm formation. Optogenetic tools are ideal to control biofilms because light is noninvasive, easily controllable, and cost-efficient. In this study, a gene circuit responsive to near-infrared (NIR) light was used to modulate the cellular level of bis-(3'-5') cyclic dimeric guanosine monophosphate (c-di-GMP), a central regulator of the prokaryote biofilm lifestyle, which allowed the regulation of biofilm formation by using NIR light. The engineered biofilm was applied to catalyze the biotransformation of indole into tryptophan in submerged biofilm reactors and NIR-light-enhanced biofilm formation resulted in an approximately 30 % increase in tryptophan yield, which demonstrates the feasibility of the application of light to modulate the formation and performance of catalytic biofilms for chemical production. The c-di-GMP-targeted optogenetic approach to modulate catalytic biofilms showcases applications for biofilm-mediated biocatalysis.
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Affiliation(s)
- Yidan Hu
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Xiaobo Liu
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Dr, Singapore, 637551, Singapore
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, P.R. China
| | - Aloysius Teng Min Ren
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, P.R. China
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, 60 Nanyang Dr, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore, 639798, Singapore
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29
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Zhang Z, Weng Y, Ding Y, Qian S. Use of Genetically Modified Bacteria to Repair Cracks in Concrete. MATERIALS 2019; 12:ma12233912. [PMID: 31779264 PMCID: PMC6926745 DOI: 10.3390/ma12233912] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/13/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022]
Abstract
In this paper, we studied the crack-repair by spraying bacteria-based liquid around the cracks in concrete. To enhance the repair efficiency and speed up the repair process, the transposon mutagenesis method was employed to modify the genes of Bacillus halodurans and create a mutant bacterial strain with higher efficiency of calcium carbonate productivity by catalyzing the combination of carbonate and calcium ion. The efficiency of crack-repairing in concrete by spraying two kinds of bacterial liquid was evaluated via image analysis, X-ray computed tomography (X-CT) scanning technology and the sorptivity test. The results show that the crack-repair efficiency was enhanced very evidently by spraying genetically modified bacterial-liquid as no microbiologically induced calcite precipitation (MICP) was found within the cracks for concrete samples sprayed using wild type bacterial-liquid. In addition, the crack-repair process was also shortened significantly in the case of genetically modified bacteria.
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Affiliation(s)
- Zhigang Zhang
- Key Laboratory of New Technology for Construction of Cities in Mountain Area, Chongqing University, Ministry of Education, Chongqing 400045, China;
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 637551, Singapore; (Y.W.); (Y.D.)
| | - Yiwei Weng
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 637551, Singapore; (Y.W.); (Y.D.)
- Singapore Centre for 3D Printing, School of Mechanical and Aerospace Engineering, Singapore 639798, Singapore
| | - Yuanzhao Ding
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 637551, Singapore; (Y.W.); (Y.D.)
| | - Shunzhi Qian
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 637551, Singapore; (Y.W.); (Y.D.)
- Correspondence:
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30
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Geng N, Wu Y, Zhang M, Tsang DCW, Rinklebe J, Xia Y, Lu D, Zhu L, Palansooriya KN, Kim KH, Ok YS. Bioaccumulation of potentially toxic elements by submerged plants and biofilms: A critical review. ENVIRONMENT INTERNATIONAL 2019; 131:105015. [PMID: 31369978 DOI: 10.1016/j.envint.2019.105015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 05/28/2023]
Abstract
The accumulation of potentially toxic elements (PTEs) in aquatic ecosystems has become a global concern, as PTEs may exert a wide range of toxicological impacts on aquatic organisms. Submerged plants and the microorganisms attached to their surfaces, however, have displayed great potential as a means of coping with such pollution. Therefore, it is crucial to understand the transport pathways of PTEs across sediment and organisms as well as their accumulation mechanisms in the presence of submerged plants and their biofilms. The majority of previous studies have demonstrated that submerged plants and their biofilms are indicators of PTE pollution in the aquatic environment, yet relatively little is known about PTE accumulation in epiphytic biofilms. In this review, we describe the transport pathways of PTEs in the aquatic environment in order to offer remarkable insights into bioaccumulation mechanisms in submerged plants and their biofilms. Based on the literature cited in this review, the roles of epiphytic biofilms in bioaccumulation and as an indicator of ecosystem health are discussed.
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Affiliation(s)
- Nan Geng
- College of Water Conservancy and Environment Engineering, Zhejiang University of Water Resources and Electric Power, Hangzhou, China; Korea Biochar Research Center, O-Jeong Eco-Resilience Institute (OJERI) & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Yichao Wu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Ming Zhang
- Department of Environmental Engineering, China Jiliang University, Hangzhou, China
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Jörg Rinklebe
- School of Architecture and Civil Engineering, Institute of Soil Engineering, Waste- and Water Science, Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; Department of Environment, Energy and Geoinformatics, Sejong University, Seoul, Republic of Korea
| | - Yinfeng Xia
- College of Water Conservancy and Environment Engineering, Zhejiang University of Water Resources and Electric Power, Hangzhou, China; Korea Biochar Research Center, O-Jeong Eco-Resilience Institute (OJERI) & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Debao Lu
- College of Water Conservancy and Environment Engineering, Zhejiang University of Water Resources and Electric Power, Hangzhou, China; Korea Biochar Research Center, O-Jeong Eco-Resilience Institute (OJERI) & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Lifang Zhu
- College of Water Conservancy and Environment Engineering, Zhejiang University of Water Resources and Electric Power, Hangzhou, China
| | - Kumuduni Niroshika Palansooriya
- Korea Biochar Research Center, O-Jeong Eco-Resilience Institute (OJERI) & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seoul, Republic of Korea.
| | - Yong Sik Ok
- Korea Biochar Research Center, O-Jeong Eco-Resilience Institute (OJERI) & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
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31
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A polyamine-independent role for S-adenosylmethionine decarboxylase. Biochem J 2019; 476:2579-2594. [DOI: 10.1042/bcj20190561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 11/17/2022]
Abstract
AbstractThe only known function of S-adenosylmethionine decarboxylase (AdoMetDC) is to supply, with its partner aminopropyltransferase enzymes such as spermidine synthase (SpdSyn), the aminopropyl donor for polyamine biosynthesis. Polyamine spermidine is probably essential for the growth of all eukaryotes, most archaea and many bacteria. Two classes of AdoMetDC exist, the prokaryotic class 1a and 1b forms, and the eukaryotic class 2 enzyme, which is derived from an ancient fusion of two prokaryotic class 1b genes. Herein, we show that ‘eukaryotic' class 2 AdoMetDCs are found in bacteria and are enzymatically functional. However, the bacterial AdoMetDC class 2 genes are phylogenetically limited and were likely acquired from a eukaryotic source via transdomain horizontal gene transfer, consistent with the class 2 form of AdoMetDC being a eukaryotic invention. We found that some class 2 and thousands of class 1b AdoMetDC homologues are present in bacterial genomes that also encode a gene fusion of an N-terminal membrane protein of the Major Facilitator Superfamily (MFS) class of transporters and a C-terminal SpdSyn-like domain. Although these AdoMetDCs are enzymatically functional, spermidine is absent, and an entire fusion protein or its SpdSyn-like domain only, does not biochemically complement a SpdSyn deletion strain of E. coli. This suggests that the fusion protein aminopropylates a substrate other than putrescine, and has a role outside of polyamine biosynthesis. Another integral membrane protein found clustered with these genes is DUF350, which is also found in other gene clusters containing a homologue of the glutathionylspermidine synthetase family and occasionally other polyamine biosynthetic enzymes.
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32
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Shi Z, Wang Q, Li Y, Liang Z, Xu L, Zhou J, Cui Z, Zhang LH. Putrescine Is an Intraspecies and Interkingdom Cell-Cell Communication Signal Modulating the Virulence of Dickeya zeae. Front Microbiol 2019; 10:1950. [PMID: 31497009 PMCID: PMC6712546 DOI: 10.3389/fmicb.2019.01950] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/08/2019] [Indexed: 11/13/2022] Open
Abstract
The infections caused by Dickeya zeae become a severe problem in recent years, but the regulatory mechanisms that govern the bacterial virulence remain to be fragmental. Here we report the investigation of potential involvement of polyamines in regulation of D. zeae virulence. We showed that null mutation of speA encoding arginine decarboxylase dramatically decreased the bacterial swimming motility, swarming motility and biofilm formation, and exogenous addition of putrescine effectively rescues the defective phenotypes of D. zeae. HPLC and mass spectrometry analysis validated that speA was essential for production of putrescine in D. zeae. In addition, we demonstrated that D. zeae EC1 could detect and response to putrescine molecules produced by itself or from host plant through specific transporters. Among the two transporters identified, the one represented by PotF played a dominated role over the other represented by PlaP in modulation of putrescine-dependent biological functions. Furthermore, we provided evidence that putrescine signal is critical for D. zeae EC1 bacterial invasion and virulence against rice seeds. Our data depict a novel function of putrescine signal in pathogen-host communication and in modulation of the virulence of an important plant bacterial pathogen.
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Affiliation(s)
- Zurong Shi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agricluture and Engineering, Guangzhou, China
| | - Qingwei Wang
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yasheng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zhibing Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Linghui Xu
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zining Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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33
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Ng CK, Karahan HE, Loo SCJ, Chen Y, Cao B. Biofilm-Templated Heteroatom-Doped Carbon-Palladium Nanocomposite Catalyst for Hexavalent Chromium Reduction. ACS APPLIED MATERIALS & INTERFACES 2019; 11:24018-24026. [PMID: 31251015 DOI: 10.1021/acsami.9b04095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, we report an interdisciplinary and novel strategy toward biofilm engineering for the development of a biofilm-templated heteroatom-doped catalytic system through bioreduction and biofilm matrix-facilitated immobilization of the in situ-formed catalytic nanoparticles followed by controlled pyrolysis. We showed that (i) even under room temperature and bulk aerobic conditions, Shewanella oneidensis MR-1 biofilms reduced Pd(II) to form Pd(0) nanocrystals (∼10 to 20 nm) that were immobilized in the biofilm matrix and in cellular membranes, (ii) the MR-1 biofilms with the immobilized Pd(0) nanocrystals exhibited nanocatalytic activity, (iii) exposure to Pd(II) greatly increased the rate of cell detachment from the biofilm and posed a risk of biofilm dispersal, (iv) controlled pyrolysis (carbonization) of the biofilm led to the formation of a stable heteroatom-doped carbon-palladium (C-Pd) nanocomposite catalyst, and (v) the biofilm-templated C-Pd nanocomposite catalyst exhibited a high Cr(VI) reduction activity and maintained a high reduction rate over multiple catalytic cycles. Considering that bacteria are capable of synthesizing a wide range of metal and metalloid nanoparticles, the biofilm-templated approach for the fabrication of the catalytic C-Pd nanocomposite we have demonstrated here should prove to be widely applicable for the production of different nanocomposites that are of importance to various environmental applications.
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Affiliation(s)
- Chun Kiat Ng
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School , Nanyang Technological University , 637551 Singapore
- Department of Engineering Science , University of Oxford , Oxford OX1 3PJ , United Kingdom
| | - H Enis Karahan
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 637459 Singapore
| | - Say Chye Joachim Loo
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School , Nanyang Technological University , 637551 Singapore
| | - Yuan Chen
- The University of Sydney, School of Chemical and Biomolecular Engineering , Sydney , New South Wales 2006 , Australia
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School , Nanyang Technological University , 637551 Singapore
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34
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Ding Y, Zhou Y, Yao J, Xiong Y, Zhu Z, Yu XY. Molecular evidence of a toxic effect on a biofilm and its matrix. Analyst 2019; 144:2498-2503. [DOI: 10.1039/c8an02512f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Shewanella oneidensisMR-1 wild-type and a hyper-adhesive mutant CP2-1-S1 model organisms and Cr(vi) are used to study biofilm and toxic chemical interactions.
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Affiliation(s)
- Yuanzhao Ding
- Earth and Biological Sciences Directorate
- Pacific Northwest National Laboratory
- Richland
- USA
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE)
| | - Yufan Zhou
- Environmental and Molecular Science Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Juan Yao
- Earth and Biological Sciences Directorate
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Yijia Xiong
- College of Osteopathic Medicine of the Pacific-Northwest
- Western University of Health Sciences
- Oregon 97355
- USA
| | - Zihua Zhu
- Environmental and Molecular Science Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Xiao-Ying Yu
- Earth and Biological Sciences Directorate
- Pacific Northwest National Laboratory
- Richland
- USA
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Mukherjee M, Hu Y, Tan CH, Rice SA, Cao B. Engineering a light-responsive, quorum quenching biofilm to mitigate biofouling on water purification membranes. SCIENCE ADVANCES 2018; 4:eaau1459. [PMID: 30539145 PMCID: PMC6286168 DOI: 10.1126/sciadv.aau1459] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 11/07/2018] [Indexed: 05/05/2023]
Abstract
Quorum quenching (QQ) has been reported to be a promising approach for membrane biofouling control. Entrapment of QQ bacteria in porous matrices is required to retain them in continuously operated membrane processes and to prevent uncontrollable biofilm formation by the QQ bacteria on membrane surfaces. It would be more desirable if the formation and dispersal of biofilms by QQ bacteria could be controlled so that the QQ bacterial cells are self-immobilized, but the QQ biofilm itself still does not compromise membrane performance. In this study, we engineered a QQ bacterial biofilm whose growth and dispersal can be modulated by light through a dichromatic, optogenetic c-di-GMP gene circuit in which the bacterial cells sense near-infrared (NIR) light and blue light to adjust its biofilm formation by regulating the c-di-GMP level. We also demonstrated the potential application of the engineered light-responsive QQ biofilm in mitigating biofouling of water purification forward osmosis membranes. The c-di-GMP-targeted optogenetic approach for controllable biofilm development we have demonstrated here should prove widely applicable for designing other controllable biofilm-enabled applications such as biofilm-based biocatalysis.
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Affiliation(s)
- Manisha Mukherjee
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yidan Hu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Chuan Hao Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- iThree Institute, University of Technology Sydney, New South Wales, Sydney, Australia
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Corresponding author.
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Wan N, Wang H, Ng CK, Mukherjee M, Ren D, Cao B, Tang YJ. Bacterial Metabolism During Biofilm Growth Investigated by 13C Tracing. Front Microbiol 2018; 9:2657. [PMID: 30515135 PMCID: PMC6255981 DOI: 10.3389/fmicb.2018.02657] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/17/2018] [Indexed: 01/27/2023] Open
Abstract
This study investigated the metabolism of Pseudomonas aeruginosa PAO1 during its biofilm development via microscopy imaging, gene expression analysis, and 13C-labeling. First, dynamic labeling was employed to investigate glucose utilization rate in fresh biofilms (thickness 40∼60 micrometer). The labeling turnover time of glucose-6-P indicated biofilm metabolism was substantially slower than planktonic cells. Second, PAO1 was cultured in continuous tubular biofilm reactors or shake flasks. Then 13C-metabolic flux analysis of PAO1 was performed based on the isotopomer patterns of proteinogenic amino acids. The results showed that PAO1 biofilm cells during growth conserved the flux features as their planktonic mode. (1) Glucose could be degraded by two cyclic routes (the TCA cycle and the Entner-Doudoroff-Embden-Meyerhof-Parnas loop) that facilitated NAD(P)H supplies. (2) Anaplerotic pathways (including pyruvate shunt) increased flux plasticity. (3) Biofilm growth phenotype did not require significant intracellular flux rewiring (variations between biofilm and planktonic flux network, normalized by glucose uptake rate as 100%, were less than 20%). (4) Transcription analysis indicated that key catabolic genes in fresh biofilm cells had expression levels comparable to planktonic cells. Finally, PAO1, Shewanella oneidensis (as the comparing group), and their c-di-GMP transconjugants (with different biofilm formation capabilities) were 13C-labeled under biofilm reactors or planktonic conditions. Analysis of amino acid labeling variances from different cultures indicated Shewanella flux network was more flexibly changed than PAO1 during its biofilm formation.
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Affiliation(s)
- Ni Wan
- Mechanical Engineering and Materials Science, Washington University, St. Louis, MO, United States
| | - Hao Wang
- Department of Biomedical and Chemical Engineering, Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY, United States
| | - Chun Kiat Ng
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Manisha Mukherjee
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY, United States.,Department of Civil and Environmental Engineering, and Biology, Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY, United States
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yinjie J Tang
- Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, United States
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Zhang Y, Li C, Wu Y, Zhang Y, Zhou Z, Cao B. A microfluidic gradient mixer-flow chamber as a new tool to study biofilm development under defined solute gradients. Biotechnol Bioeng 2018; 116:54-64. [DOI: 10.1002/bit.26852] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/17/2018] [Accepted: 10/12/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yingdan Zhang
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Cheng Li
- School of Mechanical and Aerospace Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Yichao Wu
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Yilei Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University; Singapore
| | - Zhi Zhou
- Division of Environmental and Ecological Engineering and School of Civil Engineering, Purdue University; Indiana USA
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
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38
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Li B, Maezato Y, Kim SH, Kurihara S, Liang J, Michael AJ. Polyamine-independent growth and biofilm formation, and functional spermidine/spermine N-acetyltransferases in Staphylococcus aureus and Enterococcus faecalis. Mol Microbiol 2018; 111:159-175. [PMID: 30281855 DOI: 10.1111/mmi.14145] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2018] [Indexed: 01/07/2023]
Abstract
Polyamines such as spermidine and spermine are primordial polycations that are ubiquitously present in the three domains of life. We have found that Gram-positive bacteria Staphylococcus aureus and Enterococcus faecalis have lost either all or most polyamine biosynthetic genes, respectively, and are devoid of any polyamine when grown in polyamine-free media. In contrast to bacteria such as Pseudomonas aeruginosa, Campylobacter jejuni and Agrobacterium tumefaciens, which absolutely require polyamines for growth, S. aureus and E. faecalis grow normally over multiple subcultures in the absence of polyamines. Furthermore, S. aureus and E. faecalis form biofilms normally without polyamines, and exogenous polyamines do not stimulate growth or biofilm formation. High levels of external polyamines, including norspermidine, eventually inhibit biofilm formation through inhibition of planktonic growth. We show that spermidine/spermine N-acetyltransferase (SSAT) homologues encoded by S. aureus USA300 and E. faecalis acetylate spermidine, spermine and norspermidine, that spermine is the more preferred substrate, and that E. faecalis SSAT is almost as efficient as human SSAT with spermine as substrate. The polyamine auxotrophy, polyamine-independent growth and biofilm formation, and presence of functional polyamine N-acetyltransferases in S. aureus and E. faecalis represent a new paradigm for bacterial polyamine biology.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yukari Maezato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sok Ho Kim
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shin Kurihara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jue Liang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anthony J Michael
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Zou L, Qiao Y, Li CM. Boosting Microbial Electrocatalytic Kinetics for High Power Density: Insights into Synthetic Biology and Advanced Nanoscience. ELECTROCHEM ENERGY R 2018. [DOI: 10.1007/s41918-018-0020-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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40
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Abstract
Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products, such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species, ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A and the agmatine modification of tRNAIle As with bacterial hyperthermophiles, archaeal thermophiles require long-chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research.
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Affiliation(s)
- Anthony J Michael
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Kera K, Nagayama T, Nanatani K, Saeki-Yamoto C, Tominaga A, Souma S, Miura N, Takeda K, Kayamori S, Ando E, Higashi K, Igarashi K, Uozumi N. Reduction of Spermidine Content Resulting from Inactivation of Two Arginine Decarboxylases Increases Biofilm Formation in Synechocystis sp. Strain PCC 6803. J Bacteriol 2018; 200:e00664-17. [PMID: 29440257 PMCID: PMC5892111 DOI: 10.1128/jb.00664-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/09/2018] [Indexed: 12/14/2022] Open
Abstract
The phototropic bacterium Synechocystis sp. strain PCC 6803 is able to adapt its morphology in order to survive in a wide range of harsh environments. Under conditions of high salinity, planktonic cells formed cell aggregates in culture. Further observations using crystal violet staining, confocal laser scanning microscopy, and field emission-scanning electron microscopy confirmed that these aggregates were Synechocystis biofilms. Polyamines have been implicated in playing a role in biofilm formation, and during salt stress the content of spermidine, the major polyamine in Synechocystis, was reduced. Two putative arginine decarboxylases, Adc1 and Adc2, in Synechocystis were heterologously expressed in Escherichia coli and purified. Adc2 had high arginine decarboxylase activity, whereas Adc1 was much less active. Disruption of the adc genes in Synechocystis resulted in decreased spermidine content and formation of biofilms even under nonstress conditions. Based on the characterization of the adc mutants, Adc2 was the major arginine decarboxylase whose activity led to inhibition of biofilm formation, and Adc1 contributed only minimally to the process of polyamine synthesis. Taken together, in Synechocystis the shift from planktonic lifestyle to biofilm formation was correlated with a decrease in intracellular polyamine content, which is the inverse relationship of what was previously reported in heterotroph bacteria.IMPORTANCE There are many reports concerning biofilm formation in heterotrophic bacteria. In contrast, studies on biofilm formation in cyanobacteria are scarce. Here, we report on the induction of biofilm formation by salt stress in the model phototrophic bacterium Synechocystis sp. strain PCC 6803. Two arginine decarboxylases (Adc1 and Adc2) possess function in the polyamine synthesis pathway. Inactivation of the adc1 and adc2 genes leads to biofilm formation even in the absence of salt. The shift from planktonic culture to biofilm formation is regulated by a decrease in spermidine content in Synechocystis This negative correlation between biofilm formation and polyamine content, which is the opposite of the relationship reported in other bacteria, is important not only in autotrophic but also in heterotrophic bacteria.
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Affiliation(s)
- Kota Kera
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Tatsuya Nagayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Kei Nanatani
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Chika Saeki-Yamoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Akira Tominaga
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Satoshi Souma
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Nozomi Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Kota Takeda
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Syunsuke Kayamori
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Eiji Ando
- Clinical and Biotechnology B.U., Shimadzu Corporation, Kyoto, Japan
| | - Kyohei Higashi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kazuei Igarashi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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42
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Zhao X, He X, Xi B, Gao R, Tan W, Zhang H, Huang C, Li D, Li M. Response of humic-reducing microorganisms to the redox properties of humic substance during composting. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 70:37-44. [PMID: 28927850 DOI: 10.1016/j.wasman.2017.09.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 09/11/2017] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
Humic substance (HS) could be utilized by humus-reducing microorganisms (HRMs) as the terminal acceptors. Meanwhile, the reduction of HS can support the microbial growth. This process would greatly affect the redox conversion of inorganic and organic pollutants. However, whether the redox properties of HS lined with HRMs community during composting still remain unclear. This study aimed to assess the relationships between the redox capability of HS [i.e. humic acids (HA) and fulvic acids (FA)] and HRMs during composting. The results showed that the changing patterns of electron accepting capacity and electron donating capacity of HS were diverse during seven composting. Electron transfer capacities (ETC) of HA was significantly correlated with the functional groups (i.e. alkyl C, O-alkyl C, aryl C, carboxylic C, aromatic C), aromaticity and molecular weight of HA. Aromatic C, phenols, aryl C, carboxylic C, aromaticity and molecular weight of HS were the main structuralfeatures associated with the ETC of FA. Ten key genera of HRMs were found significantly determine these redox-active functional groups of HS during composting, thus influencing the ETC of HS in composts. In addition, a regulating method was suggested to enhance the ETC of HS during composting based on the relationships between the key HRMs and redox-active functional groups as well as environmental variables.
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Affiliation(s)
- Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China
| | - Xiaosong He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China.
| | - Rutai Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China
| | - Hui Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China
| | - Caihong Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China
| | - Dan Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China
| | - Meng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Innovation Base of Groundwater & Environmental System Engineering, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Beijing 100012, China
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Ornithine Decarboxylase-Mediated Production of Putrescine Influences Ganoderic Acid Biosynthesis by Regulating Reactive Oxygen Species in Ganoderma lucidum. Appl Environ Microbiol 2017; 83:AEM.01289-17. [PMID: 28802268 DOI: 10.1128/aem.01289-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/07/2017] [Indexed: 12/23/2022] Open
Abstract
Putrescine is an important polyamine that participates in a variety of stress responses. Ornithine decarboxylase (ODC) is a key enzyme that catalyzes the biosynthesis of putrescine. A homolog of the gene encoding ODC was cloned from Ganoderma lucidum In the ODC-silenced strains, the transcript levels of the ODC gene and the putrescine content were significantly decreased. The ODC-silenced strains were more sensitive to oxidative stress. The content of ganoderic acid was increased by approximately 43 to 46% in the ODC-silenced strains. The content of ganoderic acid could be recovered after the addition of exogenous putrescine. Additionally, the content of reactive oxygen species (ROS) was significantly increased by approximately 1.3-fold in the ODC-silenced strains. The ROS content was significantly reduced after the addition of exogenous putrescine. The gene transcript levels and the activities of four major antioxidant enzymes were measured to further explore the effect of putrescine on the intracellular ROS levels. Further studies showed that the effect of the ODC-mediated production of putrescine on ROS might be a factor influencing the biosynthesis of ganoderic acid. Our study reports the role of putrescine in large basidiomycetes, providing a basis for future studies of the physiological functions of putrescine in microbes.IMPORTANCE It is well known that ODC and the ODC-mediated production of putrescine play an important role in resisting various environmental stresses, but there are few reports regarding the mechanisms underlying the effect of putrescine on secondary metabolism in microorganisms, particularly in fungi. G. lucidum is gradually becoming a model organism for studying environmental regulation and metabolism. In this study, a homolog of the gene encoding ODC was cloned in Ganoderma lucidum We found that the transcript level of the ODC gene and the content of putrescine were significantly decreased in the ODC-silenced strains. The content of ganoderic acid was significantly increased in the ODC-silenced strains. Further studies showed that the effect of the ODC-mediated production of putrescine on ROS might be a factor influencing the biosynthesis of ganoderic acid. Our study reports the role of putrescine in large basidiomycetes, providing a basis for future studies of the physiological functions of putrescine in microbes.
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Cao Y, Li X, Li F, Song H. CRISPRi-sRNA: Transcriptional-Translational Regulation of Extracellular Electron Transfer in Shewanella oneidensis. ACS Synth Biol 2017; 6:1679-1690. [PMID: 28616968 DOI: 10.1021/acssynbio.6b00374] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Extracellular electron transfer (EET) in Shewanella oneidensis MR-1, which is one of the most well-studied exoelectrogens, underlies many microbial electrocatalysis processes, including microbial fuel cells, microbial electrolysis cells, and microbial electrosynthesis. However, regulating the efficiency of EET remains challenging due to the lack of efficient genome regulation tools that regulate gene expression levels in S. oneidensis. Here, we systematically established a transcriptional regulation technology, i.e., clustered regularly interspaced short palindromic repeats interference (CRISPRi), in S. oneidensis MR-1 using green fluorescent protein (GFP) as a reporter. We used this CRISPRi technology to repress the expression levels of target genes, individually and in combination, in the EET pathways (e.g., the MtrCAB pathway and genes affecting the formation of electroactive biofilms in S. oneidensis), which in turn enabled the efficient regulation of EET efficiency. We then established a translational regulation technology, i.e., Hfq-dependent small regulatory RNA (sRNA), in S. oneidensis by repressing the GFP reporter and mtrA, which is a critical gene in the EET pathways in S. oneidensis. To achieve coordinated transcriptional and translational regulation at the genomic level, the CRISPRi and Hfq-dependent sRNA systems were incorporated into a single plasmid harbored in a recombinant S. oneidensis strain, which enabled an even higher efficiency of mtrA gene repression in the EET pathways than that achieved by the CRISPRi and Hfq-dependent sRNA system alone, as exhibited by the reduced electricity output. Overall, we developed a combined CRISPRi-sRNA method that enabled the synergistic transcriptional and translational regulation of target genes in S. oneidensis. This technology involving CRISPRi-sRNA transcriptional-translational regulation of gene expression at the genomic level could be applied to other microorganisms.
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Affiliation(s)
- Yingxiu Cao
- Key Laboratory of Systems
Bioengineering (Ministry of Education), SynBio Research Platform,
Collaborative Innovation Center of Chemical Science and Engineering
(Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Xiaofei Li
- Key Laboratory of Systems
Bioengineering (Ministry of Education), SynBio Research Platform,
Collaborative Innovation Center of Chemical Science and Engineering
(Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Feng Li
- Key Laboratory of Systems
Bioengineering (Ministry of Education), SynBio Research Platform,
Collaborative Innovation Center of Chemical Science and Engineering
(Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Hao Song
- Key Laboratory of Systems
Bioengineering (Ministry of Education), SynBio Research Platform,
Collaborative Innovation Center of Chemical Science and Engineering
(Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
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Sodium Lactate Negatively Regulates Shewanella putrefaciens CN32 Biofilm Formation via a Three-Component Regulatory System (LrbS-LrbA-LrbR). Appl Environ Microbiol 2017; 83:AEM.00712-17. [PMID: 28500045 DOI: 10.1128/aem.00712-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/09/2017] [Indexed: 11/20/2022] Open
Abstract
The capability of biofilm formation has a major impact on the industrial and biotechnological applications of Shewanella putrefaciens CN32. However, the detailed regulatory mechanisms underlying biofilm formation in this strain remain largely unknown. In the present report, we describe a three-component regulatory system which negatively regulates the biofilm formation of S. putrefaciens CN32. This system consists of a histidine kinase LrbS (Sputcn32_0303) and two cognate response regulators, including a transcription factor, LrbA (Sputcn32_0304), and a phosphodiesterase, LrbR (Sputcn32_0305). LrbS responds to the signal of the carbon source sodium lactate and subsequently activates LrbA. The activated LrbA then promotes the expression of lrbR, the gene for the other response regulator. The bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) phosphodiesterase LrbR, containing an EAL domain, decreases the concentration of intracellular c-di-GMP, thereby negatively regulating biofilm formation. In summary, the carbon source sodium lactate acts as a signal molecule that regulates biofilm formation via a three-component regulatory system (LrbS-LrbA-LrbR) in S. putrefaciens CN32.IMPORTANCE Biofilm formation is a significant capability used by some bacteria to survive in adverse environments. Numerous environmental factors can affect biofilm formation through different signal transduction pathways. Carbon sources are critical nutrients for bacterial growth, and their concentrations and types significantly influence the biomass and structure of biofilms. However, knowledge about the underlying mechanism of biofilm formation regulation by carbon source is still limited. This work elucidates a modulation pattern of biofilm formation negatively regulated by sodium lactate as a carbon source via a three-component regulatory system in S. putrefaciens CN32, which may serve as a good example for studying how the carbon sources impact biofilm development in other bacteria.
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46
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Hobley L, Li B, Wood JL, Kim SH, Naidoo J, Ferreira AS, Khomutov M, Khomutov A, Stanley-Wall NR, Michael AJ. Spermidine promotes Bacillus subtilis biofilm formation by activating expression of the matrix regulator slrR. J Biol Chem 2017; 292:12041-12053. [PMID: 28546427 PMCID: PMC5519356 DOI: 10.1074/jbc.m117.789644] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/23/2017] [Indexed: 11/16/2022] Open
Abstract
Ubiquitous polyamine spermidine is not required for normal planktonic growth of Bacillus subtilis but is essential for robust biofilm formation. However, the structural features of spermidine required for B. subtilis biofilm formation are unknown and so are the molecular mechanisms of spermidine-stimulated biofilm development. We report here that in a spermidine-deficient B. subtilis mutant, the structural analogue norspermidine, but not homospermidine, restored biofilm formation. Intracellular biosynthesis of another spermidine analogue, aminopropylcadaverine, from exogenously supplied homoagmatine also restored biofilm formation. The differential ability of C-methylated spermidine analogues to functionally replace spermidine in biofilm formation indicated that the aminopropyl moiety of spermidine is more sensitive to C-methylation, which it is essential for biofilm formation, but that the length and symmetry of the molecule is not critical. Transcriptomic analysis of a spermidine-depleted B. subtilis speD mutant uncovered a nitrogen-, methionine-, and S-adenosylmethionine-sufficiency response, resulting in repression of gene expression related to purine catabolism, methionine and S-adenosylmethionine biosynthesis and methionine salvage, and signs of altered membrane status. Consistent with the spermidine requirement in biofilm formation, single-cell analysis of this mutant indicated reduced expression of the operons for production of the exopolysaccharide and TasA protein biofilm matrix components and SinR antagonist slrR. Deletion of sinR or ectopic expression of slrR in the spermidine-deficient ΔspeD background restored biofilm formation, indicating that spermidine is required for expression of the biofilm regulator slrR. Our results indicate that spermidine functions in biofilm development by activating transcription of the biofilm matrix exopolysaccharide and TasA operons through the regulator slrR.
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Affiliation(s)
- Laura Hobley
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390; Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD15EH, Scotland, United Kingdom
| | - Bin Li
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390; Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Jennifer L Wood
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD15EH, Scotland, United Kingdom
| | - Sok Ho Kim
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Jacinth Naidoo
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Ana Sofia Ferreira
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD15EH, Scotland, United Kingdom
| | - Maxim Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, Russia
| | - Alexey Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, Russia
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD15EH, Scotland, United Kingdom.
| | - Anthony J Michael
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390; Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390.
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47
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Li F, Li Y, Sun L, Li X, Yin C, An X, Chen X, Tian Y, Song H. Engineering Shewanella oneidensis enables xylose-fed microbial fuel cell. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:196. [PMID: 28804512 PMCID: PMC5549365 DOI: 10.1186/s13068-017-0881-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/01/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND The microbial fuel cell (MFC) is a green and sustainable technology for electricity energy harvest from biomass, in which exoelectrogens use metabolism and extracellular electron transfer pathways for the conversion of chemical energy into electricity. However, Shewanella oneidensis MR-1, one of the most well-known exoelectrogens, could not use xylose (a key pentose derived from hydrolysis of lignocellulosic biomass) for cell growth and power generation, which limited greatly its practical applications. RESULTS Herein, to enable S. oneidensis to directly utilize xylose as the sole carbon source for bioelectricity production in MFCs, we used synthetic biology strategies to successfully construct four genetically engineered S. oneidensis (namely XE, GE, XS, and GS) by assembling one of the xylose transporters (from Candida intermedia and Clostridium acetobutylicum) with one of intracellular xylose metabolic pathways (the isomerase pathway from Escherichia coli and the oxidoreductase pathway from Scheffersomyces stipites), respectively. We found that among these engineered S. oneidensis strains, the strain GS (i.e. harbouring Gxf1 gene encoding the xylose facilitator from C. intermedi, and XYL1, XYL2, and XKS1 genes encoding the xylose oxidoreductase pathway from S. stipites) was able to generate the highest power density, enabling a maximum electricity power density of 2.1 ± 0.1 mW/m2. CONCLUSION To the best of our knowledge, this was the first report on the rationally designed Shewanella that could use xylose as the sole carbon source and electron donor to produce electricity. The synthetic biology strategies developed in this study could be further extended to rationally engineer other exoelectrogens for lignocellulosic biomass utilization to generate electricity power.
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Affiliation(s)
- Feng Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Yuanxiu Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Liming Sun
- Petrochemical Research Institute, PetroChina Company Limited, Beijing, 102206 People’s Republic of China
| | - Xiaofei Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Changji Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Xingjuan An
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Xiaoli Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Yao Tian
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Hao Song
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
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48
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Lin T, Bai X, Hu Y, Li B, Yuan Y, Song H, Yang Y, Wang J. Synthetic
Saccharomyces cerevisiae
‐
Shewanella oneidensis
consortium enables glucose‐fed high‐performance microbial fuel cell. AIChE J 2016. [DOI: 10.1002/aic.15611] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tong Lin
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Xue Bai
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Yidan Hu
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Bingzhi Li
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Ying‐Jin Yuan
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Hao Song
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Yun Yang
- School of Chemistry and EnvironmentBeihang UniversityBeijing100191 China
| | - Jingyu Wang
- Dept. of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis MN55455
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49
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Greener J, Parvinzadeh Gashti M, Eslami A, Zarabadi MP, Taghavi SM. A microfluidic method and custom model for continuous, non-intrusive biofilm viscosity measurements under different nutrient conditions. BIOMICROFLUIDICS 2016; 10:064107. [PMID: 27965730 PMCID: PMC5116028 DOI: 10.1063/1.4968522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/09/2016] [Indexed: 05/24/2023]
Abstract
Straight, low-aspect ratio micro flow cells are used to support biofilm attachment and preferential accumulation at the short side-wall, which progressively reduces the effective channel width. The biofilm shifts downstream at measurable velocities under the imposed force from the constant laminar co-flowing nutrient stream. The dynamic behaviour of the biofilm viscosity is modeled semi-analytically, based on experimental measurements of biofilm dimensions and velocity as inputs. The technique advances the study of biofilm mechanical properties by strongly limiting biases related to non-Newtonian biofilm properties (e.g., shear dependent viscosity) with excellent time resolution. To demonstrate the proof of principle, young Pseudomonas sp. biofilms were analyzed under different nutrient concentrations and constant micro-flow conditions. The striking results show that large initial differences in biofilm viscosities grown under different nutrient concentrations become nearly identical in less than one day, followed by a continuous thickening process. The technique verifies that in 50 h from inoculation to early maturation stages, biofilm viscosity could grow by over 2 orders of magnitude. The approach opens the way for detailed studies of mechanical properties under a wide variety of physiochemical conditions, such as ionic strength, temperature, and shear stress.
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Affiliation(s)
- J Greener
- Department of Chemistry, Université Laval , 1045 Ave. de la Médecine, Québec, Québec G1V 0A6, Canada
| | - M Parvinzadeh Gashti
- Department of Chemistry, Université Laval , 1045 Ave. de la Médecine, Québec, Québec G1V 0A6, Canada
| | - A Eslami
- Department of Chemical Engineering, Université Laval , Québec, Québec G1V 0A6, Canada
| | - M P Zarabadi
- Department of Chemistry, Université Laval , 1045 Ave. de la Médecine, Québec, Québec G1V 0A6, Canada
| | - S M Taghavi
- Department of Chemical Engineering, Université Laval , Québec, Québec G1V 0A6, Canada
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50
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Ding Y, Zhou Y, Yao J, Szymanski C, Fredrickson J, Shi L, Cao B, Zhu Z, Yu XY. In Situ Molecular Imaging of the Biofilm and Its Matrix. Anal Chem 2016; 88:11244-11252. [DOI: 10.1021/acs.analchem.6b03909] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yuanzhao Ding
- Singapore
Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
- Interdisciplinary
Graduate School (IGS), Nanyang Technological University (NTU), 639798, Singapore
- Earth
and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yufan Zhou
- Environmental
and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Juan Yao
- Earth
and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Craig Szymanski
- Environmental
and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - James Fredrickson
- Earth
and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Liang Shi
- Earth
and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Bin Cao
- Singapore
Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
- School
of Civil and Environmental Engineering, Nanyang Technological University (NTU), 639798, Singapore
| | - Zihua Zhu
- Environmental
and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xiao-Ying Yu
- Earth
and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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