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Huang H, Xie C, Xia Z, Sun Z, Chen Y, Gou M, Tang Y, Cui H, Wu X. Multi-omics association study of hexadecane degradation in haloarchaeal strain Halogranum rubrum RO2-11. ENVIRONMENTAL RESEARCH 2024; 252:118751. [PMID: 38522738 DOI: 10.1016/j.envres.2024.118751] [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: 12/17/2023] [Revised: 03/01/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Haloarchaea with the capacity to degrade alkanes is promising to deal with petroleum pollution in hypersaline environments. However, only a limited number of haloarchaeal species are investigated, and their pathway and mechanism for alkane degradation remain unclear. In this study, Halogranum rubrum RO2-11, a haloarchaeal strain, verified the ability to degrade kerosene and hexadecane in 184 g/L NaCl, with 53% and 52% degradation rates after 9 and 4 days, respectively. Genome sequencing and gene annotation indicated that strain RO2-11 possesses a complete potential alkane-degrading pathway, of which alkane hydroxylases may include CYP450, AlmA, and LadA. Transcriptome and metabolome analyses revealed that the upregulation of related genes in TCA cycle, lysine biosynthesis, and acetylation may help improve hexadecane degradation. Additionally, an alternative degrading pathway of hexadecane based on dual-terminal β-oxidation may occur in strain RO2-11. It is likely to be the first report of alkane degradation by the genus Halogranum, which may be helpful for applications of oil-pollution bioremediation under high-salt conditions.
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Affiliation(s)
- HeLang Huang
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China; Chengdu Surveying Geotechnical Research Institute Co. Ltd. of MCC, Chengdu, 610023, China.
| | - CaiYun Xie
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - ZiYuan Xia
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - ZhaoYong Sun
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - YaTing Chen
- Institute for Disaster Management and Reconstruction, Sichuan University, Sichuan, 610207, China.
| | - Min Gou
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - HengLin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - XiaoLei Wu
- College of Engineering, Peking University, Beijing, 100871, China.
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2
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Wang J, Zhang Y, Ding Y, Song H, Liu T, Zhang Y, Xu W, Shi Y. Comparing the indigenous microorganism system in typical petroleum-contaminated groundwater. CHEMOSPHERE 2023; 311:137173. [PMID: 36356804 DOI: 10.1016/j.chemosphere.2022.137173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 10/29/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The environmental conditions at a contaminated site will impact on the indigenous microbial communities, with implications for the removal of pollutants. An analysis of the characteristics of microbial communities in petroleum-contaminated groundwater can give insights into the relationships between microbial community and environmental factors, and provide guidance about how microbes can be used to remediate and regulate petroleum-contaminated groundwater. This study focuses on two petroleum-contaminated sites in northeast China, the physico-chemical-biological changes in petroleum-contaminated groundwater were analyzed, the response relationship between hydro-chemical indicators and microbial communities was characterized, and the bioindicator that can reflect the petroleum contamination status were established for environmental monitoring and management. The results showed that Proteobacteria was the dominant bacteria in petroleum-contaminated groundwater, with a relative abundance of 42.45%-91.19%. pH, TDS, DO, NO3-, NO2-, SO42-, NH4+, Al, and Mn have significant effects on microbial community. The effect of petroleum pollutants on microbial communities is not only related to the concentration and composition of the pollutants themselves, but also could indirectly affect microbial communities by changing the content of inorganic electron acceptor components such as iron, manganese, sulfate and nitrate in groundwater, and this indirect effect is significantly greater than the direct impact of pollutants on microbial communities. In petroleum-contaminated groundwater, the dominant genera (Polaromonas, Caulobacter) and microbial metabolic functions (methanol oxidation, methylotrophy, ureolysis, and reductive biosynthesis) of the indigenous microbial community can be used as bioindicators to indicate petroleum contamination status. The higher abundance of these bioindicators in petroleum-contaminated groundwater, the more serious petroleum pollution in groundwater.
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Affiliation(s)
- Jili Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yuling Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China.
| | - Yang Ding
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Hewei Song
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Ting Liu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yi Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Weiqing Xu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yujia Shi
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun, 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
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3
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Cao Z, Yan W, Ding M, Yuan Y. Construction of microbial consortia for microbial degradation of complex compounds. Front Bioeng Biotechnol 2022; 10:1051233. [PMID: 36561050 PMCID: PMC9763274 DOI: 10.3389/fbioe.2022.1051233] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Increasingly complex synthetic environmental pollutants are prompting further research into bioremediation, which is one of the most economical and safest means of environmental restoration. From the current research, using microbial consortia to degrade complex compounds is more advantageous compared to using isolated bacteria, as the former is more adaptable and stable within the growth environment and can provide a suitable catalytic environment for each enzyme required by the biodegradation pathway. With the development of synthetic biology and gene-editing tools, artificial microbial consortia systems can be designed to be more efficient, stable, and robust, and they can be used to produce high-value-added products with their strong degradation ability. Furthermore, microbial consortia systems are shown to be promising in the degradation of complex compounds. In this review, the strategies for constructing stable and robust microbial consortia are discussed. The current advances in the degradation of complex compounds by microbial consortia are also classified and detailed, including plastics, petroleum, antibiotics, azo dyes, and some pollutants present in sewage. Thus, this paper aims to support some helps to those who focus on the degradation of complex compounds by microbial consortia.
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Affiliation(s)
- Zhibei Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Wenlong Yan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Mingzhu Ding
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China,*Correspondence: Mingzhu Ding,
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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4
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Sah D, Rai JPN, Ghosh A, Chakraborty M. A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils. 3 Biotech 2022; 12:218. [PMID: 35965658 PMCID: PMC9365905 DOI: 10.1007/s13205-022-03277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/21/2022] [Indexed: 11/01/2022] Open
Abstract
The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.
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Affiliation(s)
- Diksha Sah
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - J. P. N. Rai
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Ankita Ghosh
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Moumita Chakraborty
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
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5
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Kalia A, Sharma S, Semor N, Babele PK, Sagar S, Bhatia RK, Walia A. Recent advancements in hydrocarbon bioremediation and future challenges: a review. 3 Biotech 2022; 12:135. [PMID: 35620568 PMCID: PMC9127022 DOI: 10.1007/s13205-022-03199-y] [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] [Received: 02/19/2022] [Accepted: 05/04/2022] [Indexed: 11/01/2022] Open
Abstract
Petrochemicals are important hydrocarbons, which are one of the major concerns when accidently escaped into the environment. On one hand, these cause soil and fresh water pollution on land due to their seepage and leakage from automobile and petrochemical industries. On the other hand, oil spills occur during the transport of crude oil or refined petroleum products in the oceans around the world. These hydrocarbon and petrochemical spills have not only posed a hazard to the environment and marine life, but also linked to numerous ailments like cancers and neural disorders. Therefore, it is very important to remove or degrade these pollutants before their hazardous effects deteriorate the environment. There are varieties of mechanical and chemical methods for removing hydrocarbons from polluted areas, but they are all ineffective and expensive. Bioremediation techniques provide an economical and eco-friendly mechanism for removing petrochemical and hydrocarbon residues from the affected sites. Bioremediation refers to the complete mineralization or transformation of complex organic pollutants into the simplest compounds by biological agents such as bacteria, fungi, etc. Many indigenous microbes present in nature are capable of detoxification of various hydrocarbons and their contaminants. This review presents an updated overview of recent advancements in various technologies used in the degradation and bioremediation of petroleum hydrocarbons, providing useful insights to manage such problems in an eco-friendly manner.
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Affiliation(s)
- Arun Kalia
- Center for Environmental Science and Technology, Central University of Punjab, Bhatinda, 151001 India
| | - Samriti Sharma
- Department of Biotechnology, Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, India
| | - Nisha Semor
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005 India
| | - Piyoosh Kumar Babele
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, 284003 Uttar Pradesh India
| | - Shweta Sagar
- Department of Microbiology, College of Basic Sciences, CSKHPKV, Palampur, 176062 Himachal Pradesh India
| | - Ravi Kant Bhatia
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005 India
| | - Abhishek Walia
- Department of Microbiology, College of Basic Sciences, CSKHPKV, Palampur, 176062 Himachal Pradesh India
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Guo Y, Wen Z, Zhang C, Jakada H. Contamination characteristics of chlorinated hydrocarbons in a fractured karst aquifer using TMVOC and hydro-chemical techniques. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 794:148717. [PMID: 34323754 DOI: 10.1016/j.scitotenv.2021.148717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
In this study, we investigated a fractured karst aquifer polluted by chlorinated hydrocarbons to determine the contamination characteristics of the main hydrocarbon components. The natural attenuation processes of representative components were simulated and forecasted using TMVOC and hydro-chemical components (NO3-, SO42-, HCO3- Cl- and δ13CDIC). The impact of hydrocarbon compounds on the hydro-chemical ions were estimated, and their historical contamination characteristics were also reconstructed. Results showed that the dynamic characteristics of Trichloromethane and 1,1,2-Trichlorethane can indicate those of chlorinated hydrocarbons, where the rate of natural attenuation was observed to decrease with decreasing concentrations of hydrocarbon compounds. Additionally, the long-term variation characteristics in groundwater levels showed that the relatively stable hydrodynamic field conditions enabled the simulation of the natural attenuation processes of chlorinated hydrocarbons. The simulation which also considered the biodegradation processes showed that the use of TMVOC and hydro-chemical parameters may better describe natural attenuation processes. Over 3 years (from 2017 to 2019), the average percentage of biodegradation in the total natural attenuation was estimated to be 88.35%. Similarly, Trichloromethane and 1,1,2-Trichlorethane are forecasted to have no health hazards in 10 and 15 years, respectively. The contribution rates of biodegradation to HCO3- and Cl- in the fractured karst aquifer varied with the concentrations of chlorinated hydrocarbons. Overall, the findings and methods in this work have significant contributions for advancing remediation developments of petroleum hydrocarbons, especially in karst environments that are highly susceptible to contamination.
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Affiliation(s)
- Yongli Guo
- Institute of Karst Geology, Chinese Academy of Geological Sciences, Key Laboratory of Karst Dynamics, MNR and GZAR, Guilin 541004, People's Republic of China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, People's Republic of China
| | - Zhang Wen
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430074, People's Republic of China.
| | - Cheng Zhang
- Institute of Karst Geology, Chinese Academy of Geological Sciences, Key Laboratory of Karst Dynamics, MNR and GZAR, Guilin 541004, People's Republic of China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, People's Republic of China
| | - Hamza Jakada
- Department of Civil Engineering, Baze University, Abuja, Nigeria
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7
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Zhang J, Gao H, Xue Q. Potential applications of microbial enhanced oil recovery to heavy oil. Crit Rev Biotechnol 2020; 40:459-474. [PMID: 32166983 DOI: 10.1080/07388551.2020.1739618] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Heavy oil accounts for around one-third of total global oil and gas resources. The progressive depletion of conventional energy reserves has led to an increased emphasis on the efficient exploitation of heavy oil and bitumen reserves in order to meet energy demand. Therefore, it is imperative to develop new technologies for heavy oil upgrading and recovery. Biologically-based technology that involves using microorganisms or their metabolites to mobilize heavy oil trapped in reservoir rocks can make a significant contribution to the recovery of heavy oils. Here, the results of laboratory experiments and field trials applying microbial enhanced oil recovery (MEOR) technologies are summarized. This review provides an overview of the basic concepts, mechanisms, advantages, problems, and trends in MEOR, and demonstrates the credibility of MEOR methods for applications in enhanced heavy oil recovery and the petroleum refining processes. This technology is cost-effective and environmentally-friendly. The feasibility of MEOR technologies for heavier oil has not yet been fully realized due to the perceived process complexity and a lack of sufficient laboratory research and field test data. However, novel developments such as enzyme-enhanced oil recovery continues to improve MEOR methods.HighlightsHeavy oil represents the largest known potentially-recoverable petroleum energy resource.Novel biotechnological processes are needed to recover or upgrade heavy oil.Microbial technologies have great potential for heavy oil recovery.Microorganisms can produce metabolic byproducts to mobilize oil trapped in reservoirs.More technological research is needed to develop microbial enhanced oil recovery.
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Affiliation(s)
- Junhui Zhang
- College of Resource and Environment Sciences, Xinjiang University, Urumqi, China.,Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi, China
| | - Hui Gao
- College of Natural Resources and Environment, Northwest A & F University, Yangling, China
| | - Quanhong Xue
- College of Natural Resources and Environment, Northwest A & F University, Yangling, China
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8
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Bio-Methanol Production Using Treated Domestic Wastewater with Mixed Methanotroph Species and Anaerobic Digester Biogas. WATER 2018. [DOI: 10.3390/w10101414] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The development of cost-effective methods, which generate minimal chemical wastewater, for methanol production is an important research goal. In this study, treated wastewater (TWW) was utilized as a culture solution for methanol production by mixed methanotroph species as an alternative to media prepared from commercial or chemical agents, e.g., nitrate mineral salts medium. Furthermore, a realistic alternative for producing methanol in wastewater treatment plants using biogas from anaerobic digestion was proposed. By culturing mixed methanotroph species with nitrate and phosphate-supplemented TWW in municipal wastewater treatment plants, this study demonstrates, for the first time, the application of biogas generated from the sludge digester of municipal wastewater treatment plants. NaCl alone inhibited methanol dehydrogenase and the addition of 40 mM formate as an electron donor increased methanol production to 6.35 mM. These results confirmed that this practical energy production method could enable cost-effective methanol production. As such, methanol produced in wastewater treatment plants can be used as an eco-friendly energy and carbon source for biological denitrification, which can be an alternative to reducing the expenses required for the waste water treatment process.
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9
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Varjani SJ. Microbial degradation of petroleum hydrocarbons. BIORESOURCE TECHNOLOGY 2017; 223:277-286. [PMID: 27789112 DOI: 10.1016/j.biortech.2016.10.037] [Citation(s) in RCA: 482] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 05/14/2023]
Abstract
Petroleum hydrocarbon pollutants are recalcitrant compounds and are classified as priority pollutants. Cleaning up of these pollutants from environment is a real world problem. Bioremediation has become a major method employed in restoration of petroleum hydrocarbon polluted environments that makes use of natural microbial biodegradation activity. Petroleum hydrocarbons utilizing microorganisms are ubiquitously distributed in environment. They naturally biodegrade pollutants and thereby remove them from the environment. Removal of petroleum hydrocarbon pollutants from environment by applying oleophilic microorganisms (individual isolate/consortium of microorganisms) is ecofriendly and economic. Microbial biodegradation of petroleum hydrocarbon pollutants employs the enzyme catalytic activities of microorganisms to enhance the rate of pollutants degradation. This article provides an overview about bioremediation for petroleum hydrocarbon pollutants. It also includes explanation about hydrocarbon metabolism in microorganisms with a special focus on new insights obtained during past couple of years.
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Affiliation(s)
- Sunita J Varjani
- School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar 382007, Gujarat, India.
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10
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Regulation of the Alkane Hydroxylase CYP153 Gene in a Gram-Positive Alkane-Degrading Bacterium, Dietzia sp. Strain DQ12-45-1b. Appl Environ Microbiol 2015; 82:608-19. [PMID: 26567302 DOI: 10.1128/aem.02811-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/31/2015] [Indexed: 01/07/2023] Open
Abstract
CYP153, one of the most common medium-chain n-alkane hydroxylases belonging to the cytochrome P450 superfamily, is widely expressed in n-alkane-degrading bacteria. CYP153 is also thought to cooperate with AlkB in degrading various n-alkanes. However, the mechanisms regulating the expression of the protein remain largely unknown. In this paper, we studied CYP153 gene transcription regulation by the potential AraC family regulator (CypR) located upstream of the CYP153 gene cluster in a broad-spectrum n-alkane-degrading Gram-positive bacterium, Dietzia sp. strain DQ12-45-1b. We first identified the transcriptional start site and the promoter of the CYP153 gene cluster. Sequence alignment of upstream regions of CYP153 gene clusters revealed high conservation in the -10 and -35 regions in Actinobacteria. Further analysis of the β-galactosidase activity in the CYP153 gene promoter-lacZ fusion cell indicated that the CYP153 gene promoter was induced by n-alkanes comprised of 8 to 14 carbon atoms, but not by derived decanol and decanic acid. Moreover, we constructed a cypR mutant strain and found that the CYP153 gene promoter activities and CYP153 gene transcriptional levels in the mutant strain were depressed compared with those in the wild-type strain in the presence of n-alkanes, suggesting that CypR served as an activator for the CYP153 gene promoter. By comparing CYP153 gene arrangements in Actinobacteria and Proteobacteria, we found that the AraC family regulator is ubiquitously located upstream of the CYP153 gene, suggesting its universal regulatory role in CYP153 gene transcription. We further hypothesize that the observed mode of CYP153 gene regulation is shared by many Actinobacteria.
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11
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Fuentes S, Méndez V, Aguila P, Seeger M. Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications. Appl Microbiol Biotechnol 2014; 98:4781-94. [PMID: 24691868 DOI: 10.1007/s00253-014-5684-9] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 01/22/2023]
Abstract
Bioremediation is an environmental sustainable and cost-effective technology for the cleanup of hydrocarbon-polluted soils and coasts. In spite of that longer times are usually required compared with physicochemical strategies, complete degradation of the pollutant can be achieved, and no further confinement of polluted matrix is needed. Microbial aerobic degradation is achieved by the incorporation of molecular oxygen into the inert hydrocarbon molecule and funneling intermediates into central catabolic pathways. Several families of alkane monooxygenases and ring hydroxylating dioxygenases are distributed mainly among Proteobacteria, Actinobacteria, Firmicutes and Fungi strains. Catabolic routes, regulatory networks, and tolerance/resistance mechanisms have been characterized in model hydrocarbon-degrading bacteria to understand and optimize their metabolic capabilities, providing the basis to enhance microbial fitness in order to improve hydrocarbon removal. However, microbial communities taken as a whole play a key role in hydrocarbon pollution events. Microbial community dynamics during biodegradation is crucial for understanding how they respond and adapt to pollution and remediation. Several strategies have been applied worldwide for the recovery of sites contaminated with persistent organic pollutants, such as polycyclic aromatic hydrocarbons and petroleum derivatives. Common strategies include controlling environmental variables (e.g., oxygen availability, hydrocarbon solubility, nutrient balance) and managing hydrocarbon-degrading microorganisms, in order to overcome the rate-limiting factors that slow down hydrocarbon biodegradation.
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Affiliation(s)
- Sebastián Fuentes
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología & Center of Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
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12
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Ji Y, Mao G, Wang Y, Bartlam M. Structural insights into diversity and n-alkane biodegradation mechanisms of alkane hydroxylases. Front Microbiol 2013; 4:58. [PMID: 23519435 PMCID: PMC3604635 DOI: 10.3389/fmicb.2013.00058] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/28/2013] [Indexed: 11/13/2022] Open
Abstract
Environmental microbes utilize four degradation pathways for the oxidation of n-alkanes. Although the enzymes degrading n-alkanes in different microbes may vary, enzymes functioning in the first step in the aerobic degradation of alkanes all belong to the alkane hydroxylases. Alkane hydroxylases are a class of enzymes that insert oxygen atoms derived from molecular oxygen into different sites of the alkane terminus (or termini) depending on the type of enzymes. In this review, we summarize the different types of alkane hydroxylases, their degrading steps, and compare typical enzymes from various classes with regard to their three-dimensional structures, in order to provide insights into how the enzymes mediate their different roles in the degradation of n-alkanes and what determines their different substrate ranges. Through the above analyzes, the degrading mechanisms of enzymes can be elucidated and molecular biological methods can be utilized to expand their catalytic roles in the petrochemical industry or in bioremediation of oil-contaminated environments.
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Affiliation(s)
- Yurui Ji
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
| | - Guannan Mao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
- College of Life Sciences, Nankai UniversityTianjin, China
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13
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Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0543-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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14
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Engineering of LadA for enhanced hexadecane oxidation using random- and site-directed mutagenesis. Appl Microbiol Biotechnol 2012; 94:1019-29. [DOI: 10.1007/s00253-012-4035-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/14/2012] [Accepted: 03/15/2012] [Indexed: 10/28/2022]
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15
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Negi S, Kumar S. Evaluation of Techniques Used for Parameters Estimation: an Application to Bioremediation of Grease Waste. Appl Biochem Biotechnol 2012; 167:1613-21. [DOI: 10.1007/s12010-012-9562-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 01/16/2012] [Indexed: 10/14/2022]
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16
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Das N, Chandran P. Microbial degradation of petroleum hydrocarbon contaminants: an overview. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2010; 2011:941810. [PMID: 21350672 PMCID: PMC3042690 DOI: 10.4061/2011/941810] [Citation(s) in RCA: 449] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 06/28/2010] [Accepted: 07/07/2010] [Indexed: 11/20/2022]
Abstract
One of the major environmental problems today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. Accidental releases of petroleum products are of particular concern in the environment. Hydrocarbon components have been known to belong to the family of carcinogens and neurotoxic organic pollutants. Currently accepted disposal methods of incineration or burial insecure landfills can become prohibitively expensive when amounts of contaminants are large. Mechanical and chemical methods generally used to remove hydrocarbons from contaminated sites have limited effectiveness and can be expensive. Bioremediation is the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization. Bioremediation functions basically on biodegradation, which may refer to complete mineralization of organic contaminants into carbon dioxide, water, inorganic compounds, and cell protein or transformation of complex organic contaminants to other simpler organic compounds by biological agents like microorganisms. Many indigenous microorganisms in water and soil are capable of degrading hydrocarbon contaminants. This paper presents an updated overview of petroleum hydrocarbon degradation by microorganisms under different ecosystems.
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Affiliation(s)
- Nilanjana Das
- Environmental Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
| | - Preethy Chandran
- Environmental Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
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17
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Kang YS, Park W. Protection against diesel oil toxicity by sodium chloride-induced exopolysaccharides in Acinetobacter sp. strain DR1. J Biosci Bioeng 2009; 109:118-23. [PMID: 20129094 DOI: 10.1016/j.jbiosc.2009.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 07/21/2009] [Accepted: 08/02/2009] [Indexed: 11/16/2022]
Abstract
Acinetobacter sp. strain DR1 is capable of growth on diesel oil. Interestingly, the degradation of diesel oil by the strain DR1 is enhanced in the presence of sodium chloride (NaCl). However, the growth rate of strain DR1 is not affected by the presence of NaCl. Northern blot analysis has also demonstrated that the effect of NaCl on the degradation of diesel oil is not attributable to increased levels of alkane hydroxylase (AlkM-type) gene expression. Rather, we have noted an increase in the exopolysaccharide (EPS) yields of strain DR1 under high NaCl conditions (9-fold). The lag-time of diesel oil biodegradation was significantly shorter in the strain DR1 with exogenous EPS than in the controls, although EPS alone does not support the growth of strain DR1. The recovery of strain DR1 when exposed to diesel oil was accelerated when exogenous EPS was added to the medium. The overproduction of EPS was also noted in the presence of diesel oil and n-hexadecane. The data indicated that EPS overproduction might play a protective role against diesel oil toxicity. Along with the results of the soil microcosm tests, the data presented herein demonstrated that NaCl-induced EPS is associated with a reduction in diesel oil toxicity, and thus increases diesel oil biodegradation in Acinetobacter sp. strain DR1.
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Affiliation(s)
- Yoon-Suk Kang
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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18
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Trotsenko YA, Murrell JC. Metabolic aspects of aerobic obligate methanotrophy. ADVANCES IN APPLIED MICROBIOLOGY 2008; 63:183-229. [PMID: 18395128 DOI: 10.1016/s0065-2164(07)00005-6] [Citation(s) in RCA: 248] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yuri A Trotsenko
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow 142290, Russia
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19
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Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 2007; 74:1305-15. [PMID: 18165358 DOI: 10.1128/aem.02233-07] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Schäfer F, Breuer U, Benndorf D, von Bergen M, Harms H, Müller R. Growth ofAquincola tertiaricarbonis L108 ontert-Butyl Alcohol Leads to the Induction of a Phthalate Dioxygenase-related Protein and its Associated Oxidoreductase Subunit. Eng Life Sci 2007. [DOI: 10.1002/elsc.200700011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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van Beilen JB, Funhoff EG. Alkane hydroxylases involved in microbial alkane degradation. Appl Microbiol Biotechnol 2007; 74:13-21. [PMID: 17216462 DOI: 10.1007/s00253-006-0748-0] [Citation(s) in RCA: 306] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 11/03/2006] [Accepted: 11/05/2006] [Indexed: 11/30/2022]
Abstract
This review focuses on the role and distribution in the environment of alkane hydroxylases and their (potential) applications in bioremediation and biocatalysis. Alkane hydroxylases play an important role in the microbial degradation of oil, chlorinated hydrocarbons, fuel additives, and many other compounds. Environmental studies demonstrate the abundance of alkane degraders and have lead to the identification of many new species, including some that are (near)-obligate alkanotrophs. The availability of a growing collection of alkane hydroxylase gene sequences now allows estimations of the relative abundance of the different enzyme systems and the distribution of the host organisms.
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Affiliation(s)
- Jan B van Beilen
- Département de Biologie Moléculaire Végétale, Le Biophore, Quartier Sorge, Université de Lausanne, 1015, Lausanne, Switzerland.
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