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Deng YD, Zhang WH, Zuo ZH, Zhang H, Xu J, Gao JJ, Wang B, Li ZJ, Fu XY, Wang LJ, Wang Y, Tian YS, Peng RH, Yao QH. The complete degradation of 1,2-dichloroethane in Escherichia coli by metabolic engineering. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134476. [PMID: 38691996 DOI: 10.1016/j.jhazmat.2024.134476] [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: 01/24/2024] [Revised: 04/01/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
1,2-Dichloroethane (1,2-DCA), a widely utilized chemical intermediate and organic solvent in industry, frequently enters the environment due to accidental leaks and mishandling during application processes. Thus, the in-situ remediation of contaminated sites has become increasingly urgent. However, traditional remediation methods are inefficient and costly, while bioremediation presents a green, efficient, and non-secondary polluting alternative. In this study, an engineered strain capable of completely degrading 1,2-DCA was constructed. We introduced six exogenous genes of the 1,2-DCA degradation pathway into E. coli and confirmed their normal transcription and efficient expression in this engineered strain through qRT-PCR and proteomics. The degradation experiments showed that the strain completely degraded 2 mM 1,2-DCA within 12 h. Furthermore, the results of isotope tracing verified that the final degradation product, malic acid, entered the tricarboxylic acid cycle (TCA) of E. coli and was ultimately fully metabolized. Also, morphological changes in the engineered strain and control strain exposed to 1,2-DCA were observed under SEM, and the results revealed that the engineered strain is more tolerant to 1,2-DCA than the control strain. In conclusion, this study paved a new way for humanity to deal with the increasingly complex environmental challenges.
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Affiliation(s)
- Yong-Dong Deng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Wen-Hui Zhang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Zhi-Hao Zuo
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Hao Zhang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Jing Xu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Jian-Jie Gao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Bo Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Zhen-Jun Li
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Xiao-Yan Fu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Li-Juan Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Yu Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Yong-Sheng Tian
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Ri-He Peng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China.
| | - Quan-Hong Yao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, P.R. China.
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Sun S, Wang S, Yin Y, Yang Y, Wang Y, Zhang J, Wang W. Competitive mechanism of salt-tolerance/degradation-performance of organic pollutant in bacteria: Na +/H + antiporters contribute to salt-stress resistance but impact phenol degradation. WATER RESEARCH 2024; 255:121448. [PMID: 38503180 DOI: 10.1016/j.watres.2024.121448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 03/21/2024]
Abstract
Phenolic-laden wastewater is typically characterized by its high toxicity and high salinity, imposing serious limits on the application of bioremediation. Although a few halotolerant microorganisms have been reported to degrade phenol, their removal efficiency on high concentrations of phenol remains unsatisfactory. What's more, the deep interaction molecular mechanism of salt-tolerance/phenol-degradation performance has not been clearly revealed. Here, a halotolerant strain Aeribacillus pallidus W-12 employed a meta-pathway to efficiently degrade high concentration of phenol even under high salinity conditions. Investigation of salt-tolerance strategy indicated that four Na+/H+ antiporters, which are widely distributed in bacteria, synergistically endowed the strain with excellent salt adaptability. All these antiporters differentially but positively responded to salinity changes and induction of phenol, forming a synergistic transport effect on salt ions and phenol. In-depth analysis revealed a competitive relationship between salt tolerance and degradation performance, which significantly impaired the degradation efficiency at relatively high salinity. The efficient degradation performance of W-12 under different phenol concentrations and salinity conditions indicated its bioremediation potential for multiple types of phenolic wastewater. Collectively, the competitive mechanism of salt tolerance and degradation performance enlightens a new strategy of introducing or re-constructing Na+/H+ antiporters to further improve bioremediation efficiency of hypersaline organic wastewater.
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Affiliation(s)
- Shenmei Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Shuo Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Yalin Yin
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Yue Yang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Yijia Wang
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, Tianjin 300121, PR China
| | - Jingjing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.
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Wang J, Zhang L, He Y, Ji R. Biodegradation of phenolic pollutants and bioaugmentation strategies: A review of current knowledge and future perspectives. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133906. [PMID: 38430590 DOI: 10.1016/j.jhazmat.2024.133906] [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: 11/02/2023] [Revised: 01/28/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
The widespread use of phenolic compounds renders their occurrence in various environmental matrices, posing ecological risks especially the endocrine disruption effects. Biodegradation-based techniques are efficient and cost-effective in degrading phenolic pollutants with less production of secondary pollution. This review focuses on phenol, 4-nonylphenol, 4-nitrophenol, bisphenol A and tetrabromobisphenol A as the representatives, and summarizes the current knowledge and future perspectives of their biodegradation and the enhancement strategy of bioaugmentation. Biodegradation and isolation of degrading microorganisms were mainly investigated under oxic conditions, where phenolic pollutants are typically hydroxylated to 4-hydroxybenzoate or hydroquinone prior to ring opening. Bioaugmentation efficiencies of phenolic pollutants significantly vary under different application conditions (e.g., increased degradation by 10-95% in soil and sediment). To optimize degradation of phenolic pollutants in different matrices, the factors that influence biodegradation capacity of microorganisms and performance of bioaugmentation are discussed. The use of immobilization strategy, indigenous degrading bacteria, and highly competent exogenous bacteria are proposed to facilitate the bioaugmentation process. Further studies are suggested to illustrate 1) biodegradation of phenolic pollutants under anoxic conditions, 2) application of microbial consortia with synergistic effects for phenolic pollutant degradation, and 3) assessment on the uncertain ecological risks associated with bioaugmentation, resulting from changes in degradation pathway of phenolic pollutants and alterations in structure and function of indigenous microbial community.
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Affiliation(s)
- Jiacheng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lidan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yujie He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Quanzhou Institute for Environment Protection Industry, Nanjing University, Quanzhou 362000, China.
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Quanzhou Institute for Environment Protection Industry, Nanjing University, Quanzhou 362000, China
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Zhang M, Chen Q, Gong Z. Microbial remediation of petroleum-contaminated soil focused on the mechanism and microbial response: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33325-33346. [PMID: 38709405 DOI: 10.1007/s11356-024-33474-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
The environmental pollution caused by petroleum hydrocarbons has received considerable attention in recent years. Microbial remediation has emerged as the preferred method for the degradation of petroleum hydrocarbons, which is experiencing rapid development driven by advancements in molecular biology. Herein, the capacity of different microorganisms used for crude oil bioremediation was reviewed. Moreover, factors influencing the effectiveness of microbial remediation were discussed. Microbial remediation methods, such as bioaugmentation, biostimulation, and bioventilation, are summarized in this review. Aerobic and anaerobic degradation mechanisms were reviewed to elucidate the metabolic pathways involved. The impacts of petroleum hydrocarbons on microorganisms and the environment were also revealed. A brief overview of synthetic biology and a unique perspective of technique combinations were presented to provide insight into research trends. The challenges and future outlook were also presented to stimulate contemplation of the mechanisms involved and the development of innovative techniques.
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Affiliation(s)
- Mingjian Zhang
- School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China
| | - Qing Chen
- School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China
| | - Zheng Gong
- School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China.
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China.
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5
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Wang L, Deng Y, Gao J, Wang B, Han H, Li Z, Zhang W, Wang Y, Fu X, Peng R, Yao Q, Tian Y, Xu J. Biosynthesis of melatonin from L-tryptophan by an engineered microbial cell factory. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:27. [PMID: 38369525 PMCID: PMC10874579 DOI: 10.1186/s13068-024-02476-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/10/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND The demand for melatonin is increasing due to its health-promoting bioactivities such as antioxidant and sleep benefits. Although melatonin is present in various organisms, its low content and high extraction cost make it unsustainable. Biosynthesis is a promising alternative method for melatonin production. However, the ectopic production of melatonin in microorganisms is very difficult due to the low or insoluble expression of melatonin synthesis genes. Hence, we aim to explore the biosynthesis of melatonin using Escherichia coli as a cell factory and ways to simultaneously coordinated express genes from different melatonin synthesis pathways. RESULTS In this study, the mXcP4H gene from Xanthomonas campestris, as well as the HsAADC, HsAANAT and HIOMT genes from human melatonin synthesis pathway were optimized and introduced into E. coli via a multi-monocistronic vector. The obtained strain BL7992 successfully synthesized 1.13 mg/L melatonin by utilizing L-tryptophan (L-Trp) as a substrate in a shake flask. It was determined that the rate-limiting enzyme for melatonin synthesis is the arylalkylamine N-acetyltransferase, which is encoded by the HsAANAT gene. Targeted metabolomics analysis of L-Trp revealed that the majority of L-Trp flowed to the indole pathway in BL7992, and knockout of the tnaA gene may be beneficial for increasing melatonin production. CONCLUSIONS A metabolic engineering approach was adopted and melatonin was successfully synthesized from low-cost L-Trp in E. coli. This study provides a rapid and economical strategy for the synthesis of melatonin.
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Affiliation(s)
- Lijuan Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms Ministry of Agriculture and Rural Affairs, 2901 Beidi Road, Shanghai, China
| | - Yongdong Deng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms Ministry of Agriculture and Rural Affairs, 2901 Beidi Road, Shanghai, China
| | - Jianjie Gao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Hongjuan Han
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Zhenjun Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Wenhui Zhang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Yu Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Xiaoyan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms Ministry of Agriculture and Rural Affairs, 2901 Beidi Road, Shanghai, China
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms Ministry of Agriculture and Rural Affairs, 2901 Beidi Road, Shanghai, China
| | - Yongsheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China.
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms Ministry of Agriculture and Rural Affairs, 2901 Beidi Road, Shanghai, China.
| | - Jing Xu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China.
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms Ministry of Agriculture and Rural Affairs, 2901 Beidi Road, Shanghai, China.
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Sui X, Wang J, Zhao Z, Liu B, Liu M, Liu M, Shi C, Feng X, Fu Y, Shi D, Li S, Qi Q, Xian M, Zhao G. Phenolic compounds induce ferroptosis-like death by promoting hydroxyl radical generation in the Fenton reaction. Commun Biol 2024; 7:199. [PMID: 38368473 PMCID: PMC10874397 DOI: 10.1038/s42003-024-05903-5] [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: 11/05/2023] [Accepted: 02/08/2024] [Indexed: 02/19/2024] Open
Abstract
Phenolic compounds are industrially versatile chemicals, also the most ubiquitous pollutants. Recently, biosynthesis and biodegradation of phenols has attracted increasing attention, while phenols' toxicity is a major issue. Here, we evolved phloroglucinol-tolerant Escherichia coli strains via adaptive evolution, and three mutations (ΔsodB, ΔclpX and fetAB overexpression) prove of great assistance in the tolerance improvement. We discover that phloroglucinol complexes with iron and promotes the generation of hydroxyl radicals in Fenton reaction, which leads to reducing power depletion, lipid peroxidation, and ferroptosis-like cell death of E. coli. Besides phloroglucinol, various phenols can trigger ferroptosis-like death in diverse organisms, from bacteria to mammalian cells. Furthermore, repressing this ferroptosis-like death improves phloroglucinol production and phenol degradation by corresponding strains respectively, showing great application potential in microbial degradation or production of desired phenolic compounds, and phloroglucinol-induced ferroptosis suppresses tumor growth in mice, indicating phloroglucinol as a promising drug for cancer treatment.
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Affiliation(s)
- Xinyue Sui
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jichao Wang
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zhiqiang Zhao
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Miaomiao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Min Liu
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Cong Shi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xinjun Feng
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yingxin Fu
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Dayong Shi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China.
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
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Zhao ZM, Liu ZH, Zhang T, Meng R, Gong Z, Li Y, Hu J, Ragauskas AJ, Li BZ, Yuan YJ. Unleashing the capacity of Rhodococcus for converting lignin into lipids. Biotechnol Adv 2024; 70:108274. [PMID: 37913947 DOI: 10.1016/j.biotechadv.2023.108274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/11/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
Bioconversion of bioresources/wastes (e.g., lignin, chemical pulping byproducts) represents a promising approach for developing a bioeconomy to help address growing energy and materials demands. Rhodococcus, a promising microbial strain, utilizes numerous carbon sources to produce lipids, which are precursors for synthesizing biodiesel and aviation fuels. However, compared to chemical conversion, bioconversion involves living cells, which is a more complex system that needs further understanding and upgrading. Various wastes amenable to bioconversion are reviewed herein to highlight the potential of Rhodococci for producing lipid-derived bioproducts. In light of the abundant availability of these substrates, Rhodococcus' metabolic pathways converting them to lipids are analyzed from a "beginning-to-end" view. Based on an in-depth understanding of microbial metabolic routes, genetic modifications of Rhodococcus by employing emerging tools (e.g., multiplex genome editing, biosensors, and genome-scale metabolic models) are presented for promoting the bioconversion. Co-solvent enhanced lignocellulose fractionation (CELF) strategy facilitates the generation of a lignin-derived aromatic stream suitable for the Rhodococcus' utilization. Novel alkali sterilization (AS) and elimination of thermal sterilization (ETS) approaches can significantly enhance the bioaccessibility of lignin and its derived aromatics in aqueous fermentation media, which promotes lipid titer significantly. In order to achieve value-added utilization of lignin, biodiesel and aviation fuel synthesis from lignin and lipids are further discussed. The possible directions for unleashing the capacity of Rhodococcus through synergistically modifying microbial strains, substrates, and fermentation processes are proposed toward a sustainable biological lignin valorization.
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Affiliation(s)
- Zhi-Min Zhao
- Frontiers 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; Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States; Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Zhi-Hua Liu
- Frontiers 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
| | - Tongtong Zhang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Rongqian Meng
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Zhiqun Gong
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yibing Li
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Jing Hu
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Arthur J Ragauskas
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States; Joint Institute of Biological Science, Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, United States; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996, United States.
| | - Bing-Zhi Li
- Frontiers 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.
| | - Ying-Jin Yuan
- Frontiers 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
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8
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Aminian-Dehkordi J, Rahimi S, Golzar-Ahmadi M, Singh A, Lopez J, Ledesma-Amaro R, Mijakovic I. Synthetic biology tools for environmental protection. Biotechnol Adv 2023; 68:108239. [PMID: 37619824 DOI: 10.1016/j.biotechadv.2023.108239] [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: 04/15/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.
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Affiliation(s)
| | - Shadi Rahimi
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Mehdi Golzar-Ahmadi
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada
| | - Amritpal Singh
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | - Javiera Lopez
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | | | - Ivan Mijakovic
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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9
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Zhang C, Li S, Sun Z, Geng Y, Zhang Y, Shi T, Hua R, Fang L. Dual metabolic pathways co-determine the efficient aerobic biodegradation of phenol in Cupriavidus nantongensis X1. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132424. [PMID: 37651933 DOI: 10.1016/j.jhazmat.2023.132424] [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: 06/11/2023] [Revised: 08/23/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
Phenol, as an important chemical raw material, often exists in wastewater from chemical plants and pollutes soil and groundwater. Aerobic biodegradation is a promising method for remediation of phenolic wastewater. In this study, degradation characteristics and mechanisms of phenol in Cupriavidus nantongensis X1 were explored. Strain X1 could completely degrade 1.5 mM phenol within 32 h and use it as the sole carbon source for growth. The optimal degradation temperature and pH for phenol by strain X1 were 30 °C and 7.0. The detection of 3-oxoadipate and 4-hydroxy-2-oxopentanoate indicated that dual metabolic pathways coexist in strain X1 for phenol degradation, ortho- and meta-pathway. Genome and transcriptome sequencing revealed the whole gene clusters for phenol biomineralization, in which C12O and C23O were key enzymes in two metabolic pathways. The ribosome proteins were also involved in the regulation of phenol degradation. Meanwhile, the degradation activities of enzyme C23O was 188-fold higher than that of C12O in vitro, which indicated that the meta-pathway was more efficient than ortho-pathway for catechol degradation in strain X1. This study provides an efficient strain resource for phenol degradation, and the discovery of dual metabolic pathways provides new insight into the aerobic biological metabolism and bioremediation of phenol.
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Affiliation(s)
- Chuansong Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Shengyang Li
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zhanxiang Sun
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yuehan Geng
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yanwei Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Taozhong Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Rimao Hua
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Liancheng Fang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China.
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10
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Bai B, Zhang L, Dong H, Huang Y. Coupled Fe(III) reduction and phenanthrene degradation by marine-derived Kocuria oceani FXJ8.057 under aerobic condition. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132237. [PMID: 37595472 DOI: 10.1016/j.jhazmat.2023.132237] [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: 03/02/2023] [Revised: 06/29/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
Diverse aerobic actinobacteria possess the capacity to degrade polycyclic aromatic hydrocarbons (PAHs) and have recently been shown to reduce Fe(III). However, the coupling of the two processes under oxic conditions remains unclear. Here, the co-metabolism of phenanthrene (PHE) and Fe(III) by marine-derived Kocuria oceani FXJ8.057 was realized under aerobic condition. In the presence of both PHE and Fe(III), the rates of PHE degradation (83.91 %) and Fe(III) reduction (50.00 %) were synchronously enhanced, compared to those with PHE (67.34 %) or Fe(III) (38.00 %) alone. Transcriptome analysis detected upregulation of PHE biodegradation and riboflavin biosynthesis in the strain cultured with both PHE and Fe(III) compared to that with PHE alone. Metabolite analysis indicated that, with the addition of Fe(III), the strain could efficiently degrade PHE via three pathways. Moreover, the strain secreted riboflavin, which acted as a shuttle to promote electron transfer from PHE to Fe(III). It also secreted organic acids that could delay Fe(II) reoxidation. Finally, H2O2 secreted by the strain caused extracellular Fenton reaction to generate •OH, which also played a minor role in the PHE degradation. These findings provide the first example of an aerobic bacterium that couples PAH degradation to Fe(III) reduction and extend our understanding of Fe(III)-reducing microorganisms.
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Affiliation(s)
- Bingbing Bai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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Wang Y, Tian YS, Gao JJ, Xu J, Li ZJ, Fu XY, Han HJ, Wang LJ, Zhang WH, Deng YD, Qian C, Zuo ZH, Wang B, Peng RH, Yao QH. Complete biodegradation of the oldest organic herbicide 2,4-Dichlorophenoxyacetic acid by engineering Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131099. [PMID: 36868133 DOI: 10.1016/j.jhazmat.2023.131099] [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: 11/12/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
After nearly 80 years of extensive application, the oldest organic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has caused many problems of environmental pollution and ecological deterioration. Bioremediation is an ideal method for pollutant treatment. However, difficult screening and preparation of efficient degradation bacteria have largely hindered its application in 2,4-D remediation. We have created a novel engineering Escherichia coli with a reconstructed complete degradation pathway of 2,4-D to solve the problem of screening highly efficient degradation bacteria in this study. The results of fluorescence quantitative PCR demonstrated that all nine genes in the degradation pathway were successfully expressed in the engineered strain. The engineered strains can quickly and completely degrade 0.5 mM 2, 4-D within 6 h. Inspiring, the engineered strains grew with 2,4-D as the sole carbon source. By using the isotope tracing method, the metabolites of 2,4-D were found incorporated into the tricarboxylic acid cycle in the engineering strain. Scanning electron microscopy showed that 2,4-D had less damage on the engineered bacteria than the wild-type strain. Engineered strain can also rapidly and completely remedy 2,4-D pollution in natural water and soil. Assembling the metabolic pathways of pollutants through synthetic biology was an effective method to create pollutant-degrading bacteria for bioremediation.
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Affiliation(s)
- Yu Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yong-Sheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jian-Jie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhen-Jun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiao-Yan Fu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hong-Juan Han
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Li-Juan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wen-Hui Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yong-Dong Deng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Cen Qian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhi-Hao Zuo
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
| | - Ri-He Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
| | - Quan-Hong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
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Anand U, Dey S, Bontempi E, Ducoli S, Vethaak AD, Dey A, Federici S. Biotechnological methods to remove microplastics: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2023; 21:1787-1810. [PMID: 36785620 PMCID: PMC9907217 DOI: 10.1007/s10311-022-01552-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/25/2022] [Indexed: 05/14/2023]
Abstract
Microplastics pollution is major threat to ecosystems and is impacting abiotic and biotic components. Microplastics are diverse and highly complex contaminants that transport other contaminants and microbes. Current methods to remove microplastics include biodegradation, incineration, landfilling, and recycling. Here we review microplastics with focus on sources, toxicity, and biodegradation. We discuss the role of algae, fungi, bacteria in the biodegradation, and we present biotechnological methods to enhance degradation, e.g., gene editing tools and bioinformatics.
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Affiliation(s)
- Uttpal Anand
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000 Midreshet Ben Gurion, Israel
| | - Satarupa Dey
- Department of Botany, Shyampur Siddheswari Mahavidyalaya, University of Calcutta, Ajodhya, Shyampur, Howrah, 711312 India
| | - Elza Bontempi
- Department of Mechanical and Industrial Engineering, INSTM Unit of Brescia, University of Brescia, Via Branze 38, 25123 Brescia, Italy
| | - Serena Ducoli
- Department of Mechanical and Industrial Engineering, INSTM Unit of Brescia, University of Brescia, Via Branze 38, 25123 Brescia, Italy
| | - A. Dick Vethaak
- Department of Environment and Health, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Institute for Risk Assessment Sciences, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
| | - Stefania Federici
- Department of Mechanical and Industrial Engineering, INSTM Unit of Brescia, University of Brescia, Via Branze 38, 25123 Brescia, Italy
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13
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Yaashikaa PR, Devi MK, Kumar PS. Engineering microbes for enhancing the degradation of environmental pollutants: A detailed review on synthetic biology. ENVIRONMENTAL RESEARCH 2022; 214:113868. [PMID: 35835162 DOI: 10.1016/j.envres.2022.113868] [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: 02/23/2022] [Revised: 05/28/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Anthropogenic activities resulted in the deposition of huge quantities of contaminants such as heavy metals, dyes, hydrocarbons, etc into an ecosystem. The serious ill effects caused by these pollutants to all living organisms forced in advancement of technology for degrading or removing these pollutants. This degrading activity is mostly depending on microorganisms owing to their ability to survive in harsh adverse conditions. Though native strains possess the capability to degrade these pollutants the development of genetic engineering and molecular biology resulted in engineering approaches that enhanced the efficiency of microbes in degrading pollutants at faster rate. Many bioinformatics tools have been developed for altering/modifying genetic content in microbes to increase their degrading potency. This review provides a detailed note on engineered microbes - their significant importance in degrading environmental contaminants and the approaches utilized for modifying microbes. The genes responsible for degrading the pollutants have been identified and modified fir increasing the potential for quick degradation. The methods for increasing the tolerance in engineered microbes have also been discussed. Thus engineered microbes prove to be effective alternate compared to native strains for degrading pollutants.
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Affiliation(s)
- P R Yaashikaa
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - M Keerthana Devi
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India.
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Sharma P, Bano A, Singh SP, Sharma S, Xia C, Nadda AK, Lam SS, Tong YW. Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals. CHEMOSPHERE 2022; 306:135538. [PMID: 35792210 DOI: 10.1016/j.chemosphere.2022.135538] [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: 03/22/2022] [Revised: 06/04/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.
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Affiliation(s)
- Pooja Sharma
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore
| | - Ambreen Bano
- IIRC-3, Plant-Microbe Interaction and Molecular Immunology Laboratory, Department of Biosciences, Faculty of Sciences, Integral University, Lucknow, UP, India
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208001, India
| | - Swati Sharma
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Changlei Xia
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, China; Dehua Tubao New Decoration Material Co., Ltd., Huzhou, Zhejiang 313200, China
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173 234, India.
| | - Su Shiung Lam
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India.
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, 117585, Singapore.
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Deng YD, Wang LJ, Zhang WH, Xu J, Gao JJ, Wang B, Fu XY, Han HJ, Li ZJ, Wang Y, Tian YS, Peng RH, Yao QH. Construction of complete degradation pathway for nitrobenzene in Escherichia coli. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 243:114016. [PMID: 36027713 DOI: 10.1016/j.ecoenv.2022.114016] [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: 03/20/2022] [Revised: 07/31/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Nitrobenzene is widely present in industrial wastewater and soil. Biodegradation has become an ideal method to remediate organic pollutants due to its low cost, high efficiency, and absence of secondary pollution. In the present study, 10 exogenous genes that can completely degrade nitrobenzene were introduced into Escherichia coli, and their successful expression in the strain was verified by fluorescence quantitative polymerase chain reaction and proteomic analysis. The results of the degradation experiment showed that the engineered strain could completely degrade 4 mM nitrobenzene within 8 h. The formation of intermediate metabolites was detected, and the final metabolites entered the E. coli tricarboxylic acid cycle smoothly. This process was discovered by isotope tracing method. Results indicated the integrality of the degradation pathway and the complete degradation of nitrobenzene. Finally, further experiments were conducted in soil to verify its degradation ability and showed that the engineered strain could also degrade 1 mM nitrobenzene within 10 h. In this study, engineered bacteria that can completely degrade nitrobenzene have been constructed successfully. The construction of remediation-engineered bacteria by synthetic biology laid the foundation for the industrial application of biological degradation of organic pollutants.
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Affiliation(s)
- Yong-Dong Deng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Li-Juan Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Wen-Hui Zhang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Jing Xu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Jian-Jie Gao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Bo Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xiao-Yan Fu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Hong-Juan Han
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Zhen-Jun Li
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yu Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yong-Sheng Tian
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China.
| | - Ri-He Peng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China.
| | - Quan-Hong Yao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, 2901, Beidi Road, Shanghai, China; Key Laboratory for Safety Assessment (Enviornment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China.
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Tian YS, Deng YD, Zhang WH, Yu-Wang, Xu J, Gao JJ, Bo-Wang, Fu XY, Han HJ, Li ZJ, Wang LJ, Peng RH, Yao QH. Metabolic engineering of Escherichia coli for direct production of vitamin C from D-glucose. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:86. [PMID: 35996146 PMCID: PMC9396866 DOI: 10.1186/s13068-022-02184-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022]
Abstract
Background Production of vitamin C has been traditionally based on the Reichstein process and the two-step process. However, the two processes share a common disadvantage: vitamin C cannot be directly synthesized from D-glucose. Therefore, significant effort has been made to develop a one-step vitamin C fermentation process. While, 2-KLG, not vitamin C, is synthesized from nearly all current one-step fermentation processes. Vitamin C is naturally synthesized from glucose in Arabidopsis thaliana via a ten-step reaction pathway that is encoded by ten genes. The main objective of this study was to directly produce vitamin C from D-glucose in Escherichia coli by expression of the genes from the A. thaliana vitamin C biosynthetic pathway. Results Therefore, the ten genes of whole vitamin C synthesis pathway of A. thaliana were chemically synthesized, and an engineered strain harboring these genes was constructed in this study. The direct production of vitamin C from D-glucose based on one-step fermentation was achieved using this engineered strain and at least 1.53 mg/L vitamin C was produced in shaking flasks. Conclusions The study demonstrates the feasibility of one-step fermentation for the production of vitamin C from D-glucose. Importantly, the one-step process has significant advantages compared with the currently used fermentation process: it can save multiple physical and chemical steps needed to convert D-glucose to D-sorbitol; it also does not involve the associated down-streaming steps required to convert 2-KLG into vitamin C. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02184-0.
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The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons. Microbiol Res 2022; 262:127087. [DOI: 10.1016/j.micres.2022.127087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022]
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Wang L, Peng R, Tian Y, Xu J, Wang B, Han H, Fu X, Gao J, Yao Q. Metabolic engineering of Escherichia coli for efficient degradation of 4-fluorophenol. AMB Express 2022; 12:55. [PMID: 35567640 PMCID: PMC9107566 DOI: 10.1186/s13568-022-01396-9] [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: 12/21/2021] [Accepted: 05/04/2022] [Indexed: 11/10/2022] Open
Abstract
As a kind of refractory organic pollutant, 4-fluorophenol (4-FP) can be degraded by only a few microorganisms with low efficiency because of the great electron-withdrawing ability of fluorine atoms. So it is necessary to artificially construct engineered strain to improve the degradation efficiency and meet the requirements of pollutant degradation. In this study, four genes (fpdA2, fpdB, fpdC, and fpdD) for 4-FP degradation from Arthrobacter sp. strain IF1 were optimized and synthesized and then reconstructed into Escherichia coli by a multi-monocistronic vector to obtain recombinant BL-fpd that could degrade 4-FP efficiently. Under optimized induction conditions (inducing the strain by 2 g/L L-arabinose and 1 mM IPTG at 37 ℃), BL-fpd could completely degrade 2 mM 4-FP, 4-chlorophenol, 4-bromophenol, and 4-nitrophenol into β-ketoadipate, which could be further metabolized by the bacteria. FpdA2 showed the highest activity towards 4-bromophenol. The strain could completely degrade 1 mM 4-FP in industrial wastewater within 3 h. This study provided a promising strain for the degradation of 4-FP and some other 4-substituted phenols. The construction technologies of multi-monocistronic expression vector may also be used to construct other organic pollutants degrading bacteria.
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Abstract
Crude oil is a viscous dark liquid resource composed by a mix of hydrocarbons which, after refining, is used for the elaboration of distinct products. A major concern is that many petroleum components are highly toxic due to their teratogenic, hemotoxic, and carcinogenic effects, becoming an environmental concern on a global scale, which must be solved through innovative, efficient, and sustainable techniques. One of the most widely used procedures to totally degrade contaminants are biological methods such as bioremediation. Synthetic biology is a scientific field based on biology and engineering principles, with the purpose of redesigning and restructuring microorganisms to optimize or create new biological systems with enhanced features. The use of this discipline offers improvement of bioremediation processes. This article will review some of the techniques that use synthetic biology as a platform to be used in the area of hydrocarbon bioremediation.
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Xu J, Wang B, Wang MQ, Gao JJ, Li ZJ, Tian YS, Peng RH, Yao QH. Metabolic Engineering of Escherichia coli for Methyl Parathion Degradation. Front Microbiol 2022; 13:679126. [PMID: 35222319 PMCID: PMC8874220 DOI: 10.3389/fmicb.2022.679126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
Organophosphate compounds are widely used in pesticides to control weeds, crop diseases, and insect pests. Unfortunately, these synthetic compounds are hazardous and toxic to all types of living organisms. In the present work, Escherichia coli was bioengineered to achieve methyl parathion (MP) degradation via the introduction of six synthetic genes, namely, opdS, pnpAS, pnpBS, pnpCS, pnpDS, and pnpES, to obtain a new transformant, BL-MP. MP and its subsequent decomposition intermediates were completely degraded by this transformant to enter the metabolites of multiple anabolic pathways. The MP-degraded strain created in this study may be a promising candidate for the bioremediation of MP and potential toxic intermediates.
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Zhang G, Yang X, Zhao Z, Xu T, Jia X. Artificial Consortium of Three E. coli BL21 Strains with Synergistic Functional Modules for Complete Phenanthrene Degradation. ACS Synth Biol 2022; 11:162-175. [PMID: 34914358 DOI: 10.1021/acssynbio.1c00349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly toxic and persistent organic pollutions that can accumulate in the environment. In this study, an aromatic ring cleavage module, a salicylic acid synthesis module, and a catechol metabolism module were respectively constructed in three Escherichia coli BL21 strains. Subsequently, the engineered strains were cocultured as an artificial consortium for the biodegradation of phenanthrene, a typical PHA. Single factor experiments and response surface methodology were used to identify the optimal degradation conditions, including an inoculation interval of 6 h, inoculation ratio of 1:1:1, and IPTG concentration of 2 mM. Under these conditions, the 7-day degradation ratio of 100 mg/L phenanthrene reached 72.67%. Moreover, the engineered Escherichia coli BL21 strains showed good phenanthrene degradation ability at substrate concentrations 10 mg/L up to 500 mg/L. Enzyme activity assays combined with gas chromatography-mass spectrometry measurements confirmed that the three engineered strains behaved as a synergistic consortium in the phenanthrene degradation process. Based on the analysis of the key metabolites, the engineered bacteria were supplemented at 7-day intervals in batches so that each engineered strain maintained its optimal degradation ability. The 21-day degradation ratio finally reached 90.66%, which was much higher than what was observed with simultaneous inoculation. These findings suggest that the three engineered strains with separate modules constructed in this study offer an attractive solution for removing PAHs from the environment.
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Affiliation(s)
- Guangbao Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaohui Yang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhenhua Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Tao Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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Ji R, Jie X, Zhou Y, Wang Y, Li B, Liu X, Zhao J. Light-assisted Ullmann coupling of phenols and aryl halides: The synergetic effect between plasmonic copper nanoparticles and carbon nanotubes from various sources. Chemistry 2021; 28:e202103703. [PMID: 34919296 DOI: 10.1002/chem.202103703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Indexed: 11/11/2022]
Abstract
Utilizing light and plastic wastes as resources to turn the wasted phenols and hazardous aryl halides into value added chemicals seems to be an attractive idea for alleviating the energy crisis and environmental problems. In this work, we loaded plasmonic copper nanoparticles (Cu NPs) onto carbon nanotubes (CNTs) from various sources including commercial CNTs and those derived from plastic wastes. Under visible-light irradiation, the catalyst could efficiently convert phenols and aryl halides to diaryl ethers. Similar with commercial CNTs, excellent activity is also achieved when utilizing CNTs derived from different kinds of plastic wastes as support for the system. Further investigation shows that the visible-light irradiation and light-excited plasmonic Cu NPs are necessary to inhibit the phenol degradation on CNTs and in turn promote the cross-coupling of phenol and aryl halides. Compared with metal oxides and other carbon materials, the excellent capability of CNTs to absorb light, to convert light to heat, and to adsorb both two reactants simultaneously are critical to enhance the activity of Cu NPs, achieving the high yield of diaryl ethers. We believe that this study could provide a novel strategy for catalyst design and generate a more economically-sustainable process.
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Affiliation(s)
- Rongrong Ji
- Tianjin University of Technology, School of Chemistry and Chemical Engineering, CHINA
| | - Xiangyu Jie
- Oxford University: University of Oxford, Department of Chemistry, UNITED KINGDOM
| | - Yiwei Zhou
- Tianjin University of Technology, School of Chemistry and Chemical Engineering, CHINA
| | - Yuanhui Wang
- Tianjin University of Technology, School of Chemistry and Chemical Engineering, CHINA
| | - Bing Li
- Tianjin University of Technology, School of Chemistry and Chemical Engineering, CHINA
| | - Xuguang Liu
- Tianjin University of Technology, School of Chemistry and Chemical Engineering, CHINA
| | - Jian Zhao
- Tianjin University of Technology, School of Chemistry and Chemical Engineering, Xiqing District, Tianjin, 300384, Tianjin, CHINA
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Chang D, Islam ZU, Zheng J, Zhao J, Cui X, Yu Z. Inhibitor tolerance and bioethanol fermentability of levoglucosan-utilizing Escherichia coli were enhanced by overexpression of stress-responsive gene ycfR: The proteomics-guided metabolic engineering. Synth Syst Biotechnol 2021; 6:384-395. [PMID: 34853817 PMCID: PMC8605246 DOI: 10.1016/j.synbio.2021.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/28/2021] [Accepted: 11/08/2021] [Indexed: 01/06/2023] Open
Abstract
Pretreatment of lignocellulosic biomass is crucial for the release of biofermentable sugars for biofuels production, which could greatly alleviate the burgeoning environment and energy crisis caused by the massive usage of traditional fossil fuels. Pyrolysis is a cost-saving pretreatment process that can readily decompose biomass into levoglucosan, a promising anhydrosugar; however, many undesired toxic compounds inhibitory to downstream microbial fermentation are also generated during the pyrolysis, immensely impeding the bioconversion of levoglucosan-containing pyrolysate. Here, we took the first insight into the proteomic responses of a levoglucosan-utilizing and ethanol-producing Escherichia coli to three representative biomass-derived inhibitors, identifying large amounts of differentially expressed proteins (DEPs) that could guide the downstream metabolic engineering for the development of inhibitor-resistant strains. Fifteen up- and eight down-regulated DEPs were further identified as the biomarker stress-responsive proteins candidate for cellular tolerance to multiple inhibitors. Among these biomarker proteins, YcfR exhibiting the highest expression fold-change level was chosen as the target of overexpression to validate proteomics results and develop robust strains with enhanced inhibitor tolerance and fermentation performance. Finally, based on four plasmid-borne genes encoding the levoglucosan kinase, pyruvate decarboxylase, alcohol dehydrogenase, and protein YcfR, a new recombinant strain E. coli LGE-ycfR was successfully created, showing much higher acetic acid-, furfural-, and phenol-tolerance levels compared to the control without overexpression of ycfR. The specific growth rate, final cell density, ethanol concentration, ethanol productivity, and levoglucosan consumption rate of the recombinant were also remarkably improved. From the proteomics-guided metabolic engineering and phenotypic observations, we for the first time corroborated that YcfR is a stress-induced protein responsive to multiple biomass-derived inhibitors, and also developed an inhibitors-resistant strain that could produce bioethanol from levoglucosan in the presence of inhibitors of relatively high concentration. The newly developed E. coli LGE-ycfR strain that could eliminate the commonly-used costly detoxicification processes, is of great potential for the in situ cost-effective bioethanol production from the biomass-derived pyrolytic substrates.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zia Ul Islam
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Junfang Zheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, PR China
| | - Jie Zhao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiaoyong Cui
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, No. 380 Huaibei Town, Huairou District, Beijing, 101408, PR China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, 100085, PR China
- Corresponding author. College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China.
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Chang D, Wang C, Ndayisenga F, Yu Z. Mutations in adaptively evolved Escherichia coli LGE2 facilitated the cost-effective upgrading of undetoxified bio-oil to bioethanol fuel. BIORESOUR BIOPROCESS 2021; 8:105. [PMID: 38650237 PMCID: PMC10991953 DOI: 10.1186/s40643-021-00459-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Levoglucosan is a promising sugar present in the lignocellulose pyrolysis bio-oil, which is a renewable and environment-friendly source for various value-added productions. Although many microbial catalysts have been engineered to produce biofuels and chemicals from levoglucosan, the demerits that these biocatalysts can only utilize pure levoglucosan while inhibited by the inhibitors co-existing with levoglucosan in the bio-oil have greatly limited the industrial-scale application of these biocatalysts in lignocellulose biorefinery. In this study, the previously engineered Escherichia coli LGE2 was evolved for enhanced inhibitor tolerance using long-term adaptive evolution under the stress of multiple inhibitors and finally, a stable mutant E. coli-H was obtained after ~ 374 generations' evolution. In the bio-oil media with an extremely acidic pH of 3.1, E. coli-H with high inhibitor tolerance exhibited remarkable levoglucosan consumption and ethanol production abilities comparable to the control, while the growth of the non-evolved strain was completely blocked even when the pH was adjusted to 7.0. Finally, 8.4 g/L ethanol was achieved by E. coli-H in the undetoxified bio-oil media with ~ 2.0% (w/v) levoglucosan, reaching 82% of the theoretical yield. Whole-genome re-sequencing to monitor the acquisition of mutations identified 4 new mutations within the globally regulatory genes rssB, yqhA, and basR, and the - 10 box of the putative promoter of yqhD-dgkA operon. Especially, yqhA was the first time to be revealed as a gene responsible for inhibitor tolerance. The mutations were all responsible for improved fitness, while basR mutation greatly contributed to the fitness improvement of E. coli-H. This study, for the first time, generated an inhibitor-tolerant levoglucosan-utilizing strain that could produce cost-effective bioethanol from the toxic bio-oil without detoxification process, and provided important experimental evidence and valuable genetic/proteinic information for the development of other robust microbial platforms involved in lignocellulose biorefining processes.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Cong Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, 100085, People's Republic of China.
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25
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Wang B, Gao J, Xu J, Fu X, Han H, Li Z, Wang L, Zhang F, Tian Y, Peng R, Yao Q. Optimization and reconstruction of two new complete degradation pathways for 3-chlorocatechol and 4-chlorocatechol in Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126428. [PMID: 34171665 DOI: 10.1016/j.jhazmat.2021.126428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/11/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Chlorinated aromatic compounds are a serious environmental concern because of their widespread occurrence throughout the environment. Although several microorganisms have evolved to gain the ability to degrade chlorinated aromatic compounds and use them as carbon sources, they still cannot meet the diverse needs of pollution remediation. In this study, the degradation pathways for 3-chlorocatechol (3CC) and 4-chlorocatechol (4CC) were successfully reconstructed by the optimization, synthesis, and assembly of functional genes from different strains. The addition of a 13C-labeled substrate and functional analysis of different metabolic modules confirmed that the genetically engineered strains can metabolize chlorocatechol similar to naturally degrading strains. The strain containing either of these artificial pathways can degrade catechol, 3CC, and 4CC completely, although differences in the degradation efficiency may be noted. Proteomic analysis and scanning electron microscopy observation showed that 3CC and 4CC have toxic effects on Escherichia coli, but the engineered bacteria can significantly eliminate these inhibitory effects. As core metabolic pathways for the degradation of chloroaromatics, the two chlorocatechol degradation pathways constructed in this study can be used to construct pollution remediation-engineered bacteria, and the related technologies may be applied to construct complete degradation pathways for complex organic hazardous materials.
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Affiliation(s)
- Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jianjie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Xiaoyan Fu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Hongjuan Han
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Zhenjun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Fujian Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Rihe Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Quanhong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
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Tran KM, Lee HM, Thai TD, Shen J, Eyun SI, Na D. Synthetically engineered microbial scavengers for enhanced bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126516. [PMID: 34218189 DOI: 10.1016/j.jhazmat.2021.126516] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.
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Affiliation(s)
- Kha Mong Tran
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Thi Duc Thai
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea.
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Nandy S, Arora U, Tarar P, Viggor S, Jõesaar M, Kivisaar M, Kapley A. Monitoring the growth, survival and phenol utilization of the fluorescent-tagged Pseudomonas oleovorans immobilized and free cells. BIORESOURCE TECHNOLOGY 2021; 338:125568. [PMID: 34274579 DOI: 10.1016/j.biortech.2021.125568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Bioaugmentation in wastewater treatment plants (WWTPs) is challenging due to low survival and persistence of applied microbes. This study aimed to track the capacity and survival of fluorescent-tagged Pseudomonas oleovoransICTN13 as a model organism applicable in bioaugmentation of phenol-containing wastewater. The isolate was immobilized in alginate biopolymer, and enhanced efficacy and survival for biodegradation of phenol against free cells were studied. Encapsulated cells resulted in enhanced phenol removal efficiency (~94%) compared to free cells (~72%). Encapsulation of cells facilitated an extended storage time of 30 days. Remarkably, phenol and COD removal efficacy of encapsulated cells was sustained up to ~ 92-93% in a reactor after 45 days, while free cells could produce ~ 80-84% removal efficiency. Fluorescence microscopy showed high survival of the encapsulated cells, whereas gradual deterioration of free cells was observed. Thus, the findings highlight the importance of bio augmented strain in WWTPs where encapsulation is a crucial factor.
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Affiliation(s)
- Sampurna Nandy
- Director's Research Cell, CSIR-National Environmental Engineering Research Institute, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Upasana Arora
- Director's Research Cell, CSIR-National Environmental Engineering Research Institute, Nagpur 440020, India
| | - Pranay Tarar
- Director's Research Cell, CSIR-National Environmental Engineering Research Institute, Nagpur 440020, India
| | - Signe Viggor
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Merike Jõesaar
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Atya Kapley
- Director's Research Cell, CSIR-National Environmental Engineering Research Institute, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Xu J, Wang B, Zhang WH, Zhang FJ, Deng YD, Wang Y, Gao JJ, Tian YS, Peng RH, Yao QH. Biodegradation of p-nitrophenol by engineered strain. AMB Express 2021; 11:124. [PMID: 34463855 PMCID: PMC8408293 DOI: 10.1186/s13568-021-01284-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/19/2021] [Indexed: 01/30/2023] Open
Abstract
p-Nitrophenol (PNP) is an important environmental pollutant and can causes significant environmental and health risks. Compared with the traditional methods, biodegradation is a useful one to completely remove the harmful pollutants from the environment. Here, an engineered strain was first constructed by introducing PNP biodegradation pathway via the hydroquinone (HQ) pathway into Escherichia coli. In the engineered strain BL-PNP, PNP was completely degraded to β-ketoadipate and subsequently enter the metabolites of multiple anabolic pathways. The high tolerance and rapid degradation ability to PNP enable the engineered strain to have the potential to degrade toxic substances. The engineered strain created in this study can be used as a functional strain for bioremediation of PNP and potential toxic intermediates, and the method of assembling aromatic hydrocarbons metabolic pathway can be used to eradicate nitroaromatic pollutants in the environment.
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Differential Effects of Homologous Transcriptional Regulators NicR2A, NicR2B1, and NicR2B2 and Endogenous Ectopic Strong Promoters on Nicotine Metabolism in Pseudomonas sp. Strain JY-Q. Appl Environ Microbiol 2021; 87:AEM.02457-20. [PMID: 33187996 DOI: 10.1128/aem.02457-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 01/27/2023] Open
Abstract
Nicotine is a toxic environmental pollutant that widely exists in tobacco wastes. As a natural nicotine-degrading strain, Pseudomonas sp. strain JY-Q still has difficulties degrading high concentrations of nicotine. In this study, we investigated the effect of two homologous transcriptional regulators and endogenous ectopic strong promoters on the efficiency of nicotine degradation. Comparative genomics analysis showed that two homologous transcriptional regulators, namely, NicR2A and NicR2Bs (NicR2B1 plus NicR2B2), can repress nicotine degradation gene expression. When both nicR2A and nicR2Bs were deleted, the resulting mutant JY-Q ΔnicR2A ΔnicR2B1 ΔnicR2B2 (QΔABs) exhibits a 17% higher nicotine degradation efficiency than wild-type JY-Q. Transcriptome sequencing (RNA-seq) analysis showed that the transcription levels (fragments per kilobase per million [FPKM] value) of six genes were higher than those of the other genes in JY-Q. Based on the genetic organization of these genes, three putative promoters, PRS28250 , PRS09985 , and PRS24685 , were identified. Their promoter activities were evaluated by comparing their expression levels using reverse transcriptase quantitative PCR (RT-qPCR). We found that the transcription levels of RS28250, RS09985, and RS24685 were respectively 16.8, 2.6, and 1.6 times higher than that of hspB2, encoding 6-hydroxy-3-succinylpyridine hydroxylase, which is involved in nicotine degradation. Thus, two strong endogenous promoters, namely, PRS28250 and PRS09985 , were selected to replace the original promoters of nic2 gene clusters. The effect of the endogenous ectopic promoter was also related to the position of target gene clusters. When the promoter PRS28250 replaced the promoter of hspB2, the resultant mutant QΔABs-ΔPhspB2 ::PRS28250 exhibited nicotine-degrading efficiency 69% higher than that of JY-Q. This research suggests a feasible strategy to enhance strains' capacity for nicotine degradation by removal of repressing regulatory proteins and replacing the target promoter with strong endogenous ectopic promoters.IMPORTANCE This study evaluated the differential effects of homologous NicR2A and NicR2Bs and endogenous ectopic strong promoters on nicotine metabolism in Pseudomonas sp. strain JY-Q. Based on our differential analysis, a feasible strategy is presented to modify wild-type (WT) strain JY-Q by removing repressing regulatory proteins NicR2A and NicR2Bs and replacing the target promoter with strong endogenous ectopic promoters. The resulting mutants exhibited high tolerance and degradation of nicotine. These findings should be beneficial for improving the pollutant-degrading capacity of natural strains through genomic modification.
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30
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Jaiswal S, Kumar Gupta G, Panchal K, Mandeep, Shukla P. Synthetic Organic Compounds From Paper Industry Wastes: Integrated Biotechnological Interventions. Front Bioeng Biotechnol 2021; 8:592939. [PMID: 33490048 PMCID: PMC7820897 DOI: 10.3389/fbioe.2020.592939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Synthetic organic compounds (SOCs) are reported as xenobiotics compounds contaminating the environment from various sources including waste from the pulp and paper industries: Since the demand and production of paper is growing increasingly, the release of paper and pulp industrial waste consisting of SOCs is also increasing the SOCs' pollution in natural reservoirs to create environmental pollution. In pulp and paper industries, the SOCs viz. phenol compounds, furans, dioxins, benzene compounds etc. are produced during bleaching phase of pulp treatment and they are principal components of industrial discharge. This review gives an overview of various biotechnological interventions for paper mill waste effluent management and elimination strategies. Further, the review also gives the insight overview of various ways to restrict SOCs release in natural reservoirs, its limitations and integrated approaches for SOCs bioremediation using engineered microbial approaches. Furthermore, it gives a brief overview of the sustainable remediation of SOCs via genetically modified biological agents, including bioengineering system innovation at industry level before waste discharge.
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Affiliation(s)
- Shweta Jaiswal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Guddu Kumar Gupta
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Kusum Panchal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Mandeep
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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31
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Wang B, Gao F, Xu J, Gao J, Li Z, Wang L, Zhang F, Wang Y, Tian Y, Peng R, Yao Q. Optimization, reconstruction and heterologous expression of the gene cluster encoding toluene/ o-xylene monooxygenase from Pseudomonas stutzeri in Escherichia coli and its successive hydroxylation of toluene and benzene. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1996267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, PR China
| | - Feng Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jianjie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Zhenjun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Fujian Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yu Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Rihe Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Quanhong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
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Liu H, Luo J, Shukla P. Effluents detoxification from pulp and paper industry using microbial engineering and advanced oxidation techniques. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122998. [PMID: 32502804 DOI: 10.1016/j.jhazmat.2020.122998] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Due to the high demand of paper and related items, pulp and paper industry is flourishing day by day. With increased production, come the hazards associated with the toxic elements present in the effluents. Various microorganisms are currently employed in the remediation of these toxic effluents. In addition, various techniques like ozonation, electrocoagulation, UV treatment, Fenton's reagent, and photo-Fenton based techniques are used in advanced oxidation processes to reduce these toxins from effluents. This review highlights various above mentioned advanced techniques and innovative processes along with the biological remediation of these toxic effluents with the help of some potential microbial consortia or their combinatory effects. Moreover, the present review will also disclose the ideas on utilizing the tools of metabolic engineering, systems biology, and artificial intelligence towards microbial engineering for relatively better bioremediation processes. In the future, these techniques might be helpful in increasing the capability of microbial consortia towards detoxification of effluents to make them environmentally safe. Finally, this review gives well-synchronized approaches to get more insights into these innovative methodologies and techniques and their use for various industrial applications.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, PR China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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Yu YH, Su JF, Shih Y, Wang J, Wang PY, Huang CP. Hazardous wastes treatment technologies. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2020; 92:1833-1860. [PMID: 32866315 DOI: 10.1002/wer.1447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
A review of the literature published in 2019 on topics related to hazardous waste management in water, soils, sediments, and air. The review covered treatment technologies applying physical, chemical, and biological principles for the remediation of contaminated water, soils, sediments, and air. PRACTICAL POINTS: This report provides a review of technologies for the management of waters, wastewaters, air, sediments, and soils contaminated by various hazardous chemicals including inorganic (e.g., oxyanions, salts, and heavy metals), organic (e.g., halogenated, pharmaceuticals and personal care products, pesticides, and persistent organic chemicals) in three scientific areas of physical, chemical, and biological methods. Physical methods for the management of hazardous wastes including general adsorption, sand filtration, coagulation/flocculation, electrodialysis, electrokinetics, electro-sorption ( capacitive deionization, CDI), membrane (RO, NF, MF), photocatalysis, photoelectrochemical oxidation, sonochemical, non-thermal plasma, supercritical fluid, electrochemical oxidation, and electrochemical reduction processes were reviewed. Chemical methods including ozone-based, hydrogen peroxide-based, potassium permanganate processes, and Fenton and Fenton-like process were reviewed. Biological methods such as aerobic, anoxic, anaerobic, bioreactors, constructed wetlands, soil bioremediation and biofilter processes for the management of hazardous wastes, in mode of consortium and pure culture were reviewed. Case histories were reviewed in four areas including contaminated sediments, contaminated soils, mixed industrial solid wastes and radioactive wastes.
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Affiliation(s)
- Yu Han Yu
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Jenn Fang Su
- Department of Chemical and Materials Engineering, Tamkang University, New Taipei City, Taiwan
| | - Yujen Shih
- Graduate Institute of Environmental Essngineering, National Sun yat-sen University, Kaohsiung, Taiwan
| | - Jianmin Wang
- Department of Civil Architectural and Environmental Engineering, Missouri University of Science & Technology, Rolla, Missouri
| | - Po Yen Wang
- Department of Civil Engineering, Widener University, Chester, Pennsylvania, USA
| | - Chin Pao Huang
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
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Yuan K, Li S, Zhong F. Characterization of a newly isolated strain Comamonas sp. ZF-3 involved in typical organics degradation in coking wastewater. BIORESOURCE TECHNOLOGY 2020; 304:123035. [PMID: 32111454 DOI: 10.1016/j.biortech.2020.123035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
The aim of this study was to investigate the characteristic of a newly isolated strain Comamonas sp. ZF-3 involved in typical organics degradation in coking wastewater (CWW). The results showed that the isolated strain had efficient biodegradability of phenolic compounds and heterocyclic compounds in CWW, meanwhile, phenol and indole could be respectively used as sole carbon source for its growth, which demonstrated the bioaugmentation potential of the isolated strain in CWW treatment. During phenol and indole degradation processes, part of metabolites (e.g., 2,3-hexanedione, 2-ethyl-1-hexanol, nonanal, 2-propyl-1-heptanol, butanoic acid, butyl ester and butanoic acid, anhydride) remained in effluents, with NH4+-N concentration having no obvious reduction, which implied the biological treatment of CWW should be accomplished by complex microbial communities in many steps.
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Affiliation(s)
- Ke Yuan
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Suqin Li
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Fa Zhong
- School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, Beijing 100083, China
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Pimviriyakul P, Wongnate T, Tinikul R, Chaiyen P. Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions. Microb Biotechnol 2020; 13:67-86. [PMID: 31565852 PMCID: PMC6922536 DOI: 10.1111/1751-7915.13488] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.
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Affiliation(s)
- Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn UniversityNakhon Pathom73000Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme TechnologyFaculty of ScienceMahidol UniversityBangkok10400Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
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Jia X, Zhang S, Li J, Xia J, Yao R, Zhao X, Wu B, Bai F, Xiao Y. Engineered bacterial biofloc formation enhancing phenol removal and cell tolerance. Appl Microbiol Biotechnol 2019; 104:1187-1199. [PMID: 31834438 DOI: 10.1007/s00253-019-10289-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/18/2019] [Accepted: 11/28/2019] [Indexed: 12/17/2022]
Abstract
A microbial floc consisting of a community of microbes embedded in extracellular polymeric substances matrix can provide microbial resistances to toxic chemicals and harsh environments. Phenol is a toxic environmental pollutant and a typical lignin-derived phenolic inhibitor. In this study, we genetically engineered Escherichia coli cells by expressions of diguanylate cyclases (DGCs) to promote proteinaceous and aliphatic biofloc formation. Compared with the planktonic E. coli cells, the biofloc-forming cells improved phenol removal rate by up to 2.2-folds, due to their substantially improved tolerance (up to 149%) to phenol and slightly enhanced cellular activity (20%) of phenol hydroxylase (PheH). The engineered bioflocs also improved E. coli tolerance to other toxic compounds such as furfural, 5-hydroxymethylfurfural, and guaiacol. Additionally, the strategy of the engineered biofloc formation was applicable to Pseudomonas putida and enhanced its tolerance to phenol. This study highlights a strategy to form engineered bioflocs for improved cell tolerance and removal of toxic compounds, enabling their universality of use in bioproduction and bioremediation.
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Affiliation(s)
- Xiao Jia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shun Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Juan Xia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bing Wu
- Faculty of Civil and Environmental Engineering, University of Iceland, Hjardarhagi 2-6, IS-107, Reykjavik, Iceland
| | - Fengwu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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