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Zhou J, Lin WH, Yu YL, Dong CD, Zhang H, Hu Z, Kao CM. Transitioning weathered oil fields towards new energy: A review on utilizing hydrogenotrophic methanogens for petroleum hydrocarbons remediation. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135279. [PMID: 39047569 DOI: 10.1016/j.jhazmat.2024.135279] [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: 05/26/2024] [Revised: 07/06/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
The weathering process can cause the volatilization of light components in crude oil, leading to the accumulation of total petroleum hydrocarbons (TPH) in weathered oil field soils. These TPH compounds are relatively resistant to biodegradation, posing a significant environmental hazard by contributing to soil degradation. TPH represents a complex mixture of petroleum-based hydrocarbons classified as persistent organic pollutants in soil and groundwater. The release of TPH pollutants into the environment poses serious threats to ecosystems and human health. Currently, various methods are available for TPH-contaminated soil remediation, with bioremediation technology recognized as an environmentally friendly and cost-effective approach. While converting TPH to CO2 is a common remediation method, the complex structures and diverse types of petroleum hydrocarbons (PHs) involved can result in excessive CO2 generation, potentially exacerbating the greenhouse effect. Alternatively, transforming TPH into energy forms like methane through bioremediation, followed by collection and reuse, can reduce greenhouse gas emissions and energy consumption. This process relies on the synergistic interaction between Methanogens archaea and syntrophic bacteria, forming a consortium known as the oil-degrading bacterial consortium. Methanogens produce methane through anaerobic digestion (AD), with hydrogenotrophic methanogens (HTMs) utilizing H2 as an electron donor, playing a crucial role in biomethane production. Candidatus Methanoliparia (Ca. Methanoliparia) was found in the petroleum archaeal community of weathered Oil field in northeast China. Ca. Methanoliparia has demonstrated its independent ability to decompose and produce new energy (biomethane) without symbiosis, contribute to transitioning weathered oil fields towards new energy. Therefore, this review focuses on the principles, mechanisms, and developmental pathways of HTMs during new energy production in the degradation of PHs. It also discusses strategies to enhance TPH degradation and recovery methods.
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Affiliation(s)
- Jiaping Zhou
- China University of Petroleum-Beijing at Karamay, Karamay, PR China
| | - Wei-Han Lin
- China University of Petroleum-Beijing at Karamay, Karamay, PR China
| | - Ying-Liang Yu
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
| | - Cheng-Di Dong
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Haibing Zhang
- China University of Petroleum-Beijing at Karamay, Karamay, PR China
| | - Zhongtao Hu
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, Australia
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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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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3
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Dornelles HS, Sabatini CA, Adorno MAT, Silva EL, Lee PH, Varesche MBA. Microbial synergies drive simultaneous biodegradation of ethoxy and alkyl chains of Nonylphenol Ethoxylate in fluidized bed reactors. CHEMOSPHERE 2024; 358:142084. [PMID: 38642772 DOI: 10.1016/j.chemosphere.2024.142084] [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: 02/17/2024] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 04/22/2024]
Abstract
The widely-used surfactant Nonylphenol Ethoxylate (NPEO) produces endocrine-disrupting compounds during biodegradation, with these byproducts being more harmful than untreated NPEO. This study investigates the effectiveness of a Fluidized Bed Reactor (FBR) in reducing the production of 4-Nonylphenol (4-NP) during the biodegradation of NPEO. Two identical FBR filled with sand were used to assess the NPEO degradation and to enhance the microbial consortia capable of breaking down the complex byproducts, ethanol and fumarate were introduced as co-substrates. Our findings demonstrate the significant potential of the FBR, especially when coupled with fumarate, for enhancing the surfactant degradation. It outperforms the efficiency achieved with ethanol as the primary electron donor, albeit with a higher rate of byproduct production. Microbial community taxonomy and metabolic prediction revealed the high abundance of Geobacter (1.51-31.71%) and Methanobacterium (1.08-13.81%) in non-conductive sand. This may hint a new metabolic interaction and expand our understanding of Direct Interspecies Electron Transfer (DIET) in bioreactors applied to micropollutants degradation. Such an intricate relationship between facultative and anaerobes working together to simultaneously biodegrade the ethoxy and alkyl chains presents a new perspective on NPEO degradation and can potentially be extended to other micropollutants.
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Affiliation(s)
- Henrique S Dornelles
- Department of Hydraulics and Sanitation, School of Engineering, University of São Paulo, Av. João Dagnone - 1100, 13563-120, São Carlos, São Paulo, Brazil; Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, Imperial College Road, SW7 2BU, London, England, United Kingdom
| | - Carolina A Sabatini
- Department of Hydraulics and Sanitation, School of Engineering, University of São Paulo, Av. João Dagnone - 1100, 13563-120, São Carlos, São Paulo, Brazil
| | - Maria A T Adorno
- Department of Hydraulics and Sanitation, School of Engineering, University of São Paulo, Av. João Dagnone - 1100, 13563-120, São Carlos, São Paulo, Brazil
| | - Edson L Silva
- Department of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luiz, Km 235, SP 310, 13565-905, São Carlos, São Paulo, Brazil
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, Imperial College Road, SW7 2BU, London, England, United Kingdom
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation, School of Engineering, University of São Paulo, Av. João Dagnone - 1100, 13563-120, São Carlos, São Paulo, Brazil.
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Mohamad Shahimin MF, Siddique T. Uncovering Anaerobic Hydrocarbon Biodegradation Pathways in Oil Sands Tailings from Two Different Tailings Ponds via Metabolite and Functional Gene Analyses. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04855-0. [PMID: 38376742 DOI: 10.1007/s12010-024-04855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2024] [Indexed: 02/21/2024]
Abstract
Oil sands tailings, a slurry of alkaline water, silt, clay, unrecovered bitumen, and residual hydrocarbons generated during bitumen extraction, are contained in ponds. Indigenous microbes metabolize hydrocarbons and emit greenhouse gases from the tailings. Metabolism of hydrocarbons in tailings ponds of two operators, namely, Canadian Natural Upgrading Limited (CNUL) and Canadian Natural Resources Limited (CNRL), has not been comprehensively investigated. Previous reports have revealed sequential and preferential hydrocarbon degradation of alkanes in primary cultures established from CNUL and CNRL tailings amended separately with mixtures of hydrocarbons (n-alkanes, iso-alkanes, paraffinic solvent, or naphtha). In this study, activation pathway of hydrocarbon biodegradation in these primary cultures was investigated. The functional gene analysis revealed that fumarate addition was potentially the primary activation pathway of alkanes in all cultures. However, the metabolite analysis only detected transient succinylated 2-methylpentane and 2-methylbutane metabolites during initial methanogenic biodegradation of iso-alkanes and paraffinic solvent in all CNUL and CNRL cultures amended with iso-alkanes and paraffinic solvent. Under sulfidogenic conditions (prepared only with CNUL tailings amended with iso-alkanes), succinylated 2-methylpentane persisted throughout incubation period of ~ 1100 days, implying dead-end nature of the metabolite. Though no metabolite was detected in n-alkanes- and naphtha-amended cultures during incubation, assA/masD genes related to Peptococcaceae were amplified in all CNUL and CNRL primary cultures. The findings of this present study suggest that microbial communities in different tailings ponds can biodegrade hydrocarbons through fumarate addition as activation pathway under methanogenic and sulfidogenic conditions.
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Affiliation(s)
- Mohd Faidz Mohamad Shahimin
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2G7, Canada.
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis, Aras 2, Blok S2, UniCITI Alam Campus, 02100, Padang Besar, Perlis, Malaysia.
| | - Tariq Siddique
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2G7, Canada
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Yamini V, Rajeswari VD. Metabolic capacity to alter polycyclic aromatic hydrocarbons and its microbe-mediated remediation. CHEMOSPHERE 2023; 329:138707. [PMID: 37068614 DOI: 10.1016/j.chemosphere.2023.138707] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 05/03/2023]
Abstract
The elimination of contaminants caused by anthropogenic activities and rapid industrialization can be accomplished using the widely used technology of bioremediation. Recent years have seen significant advancement in our understanding of the bioremediation of coupled polycyclic aromatic hydrocarbon contamination caused by microbial communities including bacteria, algae, fungi, yeast, etc. One of the newest techniques is microbial-based bioremediation because of its greater productivity, high efficiency, and non-toxic approach. Microbes are appealing candidates for bioremediation because they have amazing metabolic capacity to alter most types of organic material and can endure harsh environmental conditions. Microbes have been characterized as extremophiles that can survive in a variety of environmental circumstances, making them the treasure troves for environmental cleanup and the recovery of contaminated soil. In this study, the mechanisms underlying the bioremediation process as well as the current situation of microbial bioremediation of polycyclic aromatic hydrocarbon are briefly described.
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Affiliation(s)
- V Yamini
- Department of Biomedical Sciences, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - V Devi Rajeswari
- Department of Biomedical Sciences, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India.
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Ventura J, Camargo FP, Sakamoto IK, Silva EL, Varesche MBA. Potential methanogenic and degradation of nonylphenol ethoxylate from domestic sewage: unravelling the essential roles of nutritional conditions and microbial community. ENVIRONMENTAL TECHNOLOGY 2023; 44:1996-2010. [PMID: 34907848 DOI: 10.1080/09593330.2021.2018504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/07/2021] [Indexed: 05/25/2023]
Abstract
Nonylphenol ethoxylathe (NPEO) is a non-ionic surfactant of increasing concern, used in the formulation of laundry detergents and is frequently found in aquatic environments. The purpose of this study was to evaluate the effects of yeast extract (YE) and sodium fumarate (SF) in NPEO removal from domestic sewage under anaerobic conditions via central composite rotatable design (CCRD) and response surface methodology (RSM). Experiments were designed by varying concentrations of NPEO (1.6-5.8 mg L-1), YE (131.8-468.2 mg L-1) and SF (97.7-602.3 mg L-1) in batch reactors. SF and YE addition significantly influenced NPEO removal and CH4 production. Optimal values of YE (400 mg L-1) and SF (200 mg L-1) result in removal efficiency of 97% for 5 mg L-1 of NPEO, being mostly removed by biodegradation (86%). Meanwhile COD removal was 95% and methane yield was 134 ± 4 NmLCH4 g-¹CODremoved. The most abundant Bacteria genus identified were Macellibacteroides, Longilinea, Petrimonas and Proteiniphilum, while for Archaea, Methanosaeta and Methanoregula were the genera identified in higher relative abundances in optimized conditions.
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Affiliation(s)
- Jeny Ventura
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone 1100, Jardim Santa Angelina, São Carlos 13563120, Brazil
| | - Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone 1100, Jardim Santa Angelina, São Carlos 13563120, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone 1100, Jardim Santa Angelina, São Carlos 13563120, Brazil
| | - Edson Luiz Silva
- Federal University of São Carlos, Chemical Engineering, São Carlos, Brazil
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone 1100, Jardim Santa Angelina, São Carlos 13563120, Brazil
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7
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Abstract
Petroleum is the most common global fossil fuel. It is a complex multi-component system mainly composed of various hydrocarbons such as alkanes, cycloalkanes, mono-, bi- and polyaromatic compounds, resins and asphaltenes. In spite of humanity’s need for petroleum, it negatively affects the environment due to its toxicity. The ecological problem is especially serious at petroleum mining sites or during petroleum transportation. Since it is not possible to replace petroleum with less toxic fuel, ways to reduce the toxic impact of petroleum hydrocarbons on the environment need to be developed. This review addresses bioremediation, a biological approach to petroleum degradation, which is mainly performed by microbes. The pathways of degradation of alkanes, alkenes and aromatic hydrocarbons are presented in detail. The effects of temperature, aeration and the presence of biogenic elements on microbial degradation of petroleum are discussed. Plant–microbe interactions involved with the bioremediation of petroleum-polluted soils are specifically addressed. The data presented in this review point to the great potential of bioremediation practices for cleaning soils of petroleum.
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8
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Pavlova ON, Izosimova ON, Chernitsyna SM, Ivanov VG, Pogodaeva TV, Khabuev AV, Gorshkov AG, Zemskaya TI. Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions. MICROBIAL ECOLOGY 2022; 83:899-915. [PMID: 34255112 DOI: 10.1007/s00248-021-01802-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.
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Affiliation(s)
- O N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia.
| | - O N Izosimova
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - S M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - V G Ivanov
- Laboratory of Hydrology and Hydrophysics, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A V Khabuev
- Laboratory of Lake Baikal Geology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A G Gorshkov
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
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Cabral L, Giovanella P, Pellizzer EP, Teramoto EH, Kiang CH, Sette LD. Microbial communities in petroleum-contaminated sites: Structure and metabolisms. CHEMOSPHERE 2022; 286:131752. [PMID: 34426136 DOI: 10.1016/j.chemosphere.2021.131752] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.
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Affiliation(s)
- Lucélia Cabral
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Patricia Giovanella
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elisa Pais Pellizzer
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elias Hideo Teramoto
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Chang Hung Kiang
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Lara Durães Sette
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
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10
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Pal S, Dutta A, Sarkar J, Roy A, Sar P, Kazy SK. Exploring the diversity and hydrocarbon bioremediation potential of microbial community in the waste sludge of Duliajan oil field, Assam, India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:50074-50093. [PMID: 33945094 DOI: 10.1007/s11356-021-13744-6] [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: 07/05/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min-1 mg-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.
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Affiliation(s)
- Siddhartha Pal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
- School of Bio Science, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India.
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11
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Yang Y, Zhang ZW, Liu RX, Ju HY, Bian XK, Zhang WZ, Zhang CB, Yang T, Guo B, Xiao CL, Bai H, Lu WY. Research progress in bioremediation of petroleum pollution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:46877-46893. [PMID: 34254241 DOI: 10.1007/s11356-021-15310-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
With the enhancement of environmental protection awareness, research on the bioremediation of petroleum hydrocarbon environmental pollution has intensified. Bioremediation has received more attention due to its high efficiency, environmentally friendly by-products, and low cost compared with the commonly used physical and chemical restoration methods. In recent years, bacterium engineered by systems biology strategies have achieved biodegrading of many types of petroleum pollutants. Those successful cases show that systems biology has great potential in strengthening petroleum pollutant degradation bacterium and accelerating bioremediation. Systems biology represented by metabolic engineering, enzyme engineering, omics technology, etc., developed rapidly in the twentieth century. Optimizing the metabolic network of petroleum hydrocarbon degrading bacterium could achieve more concise and precise bioremediation by metabolic engineering strategies; biocatalysts with more stable and excellent catalytic activity could accelerate the process of biodegradation by enzyme engineering; omics technology not only could provide more optional components for constructions of engineered bacterium, but also could obtain the structure and composition of the microbial community in polluted environments. Comprehensive microbial community information lays a certain theoretical foundation for the construction of artificial mixed microbial communities for bioremediation of petroleum pollution. This article reviews the application of systems biology in the enforce of petroleum hydrocarbon degradation bacteria and the construction of a hybrid-microbial degradation system. Then the challenges encountered in the process and the application prospects of bioremediation are discussed. Finally, we provide certain guidance for the bioremediation of petroleum hydrocarbon-polluted environment.
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Affiliation(s)
- Yong Yang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Zhan-Wei Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Rui-Xia Liu
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Hai-Yan Ju
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Xue-Ke Bian
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Wan-Ze Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Chuan-Bo Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Ting Yang
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Bing Guo
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Chen-Lei Xiao
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - He Bai
- China Offshore Environmental Service Ltd., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China.
- Tianjin Huakan Environmental Protection Technology Co. Ltd., No. 67 Guangrui West Rd, Hedong District, Tianjin, 300170, China.
| | - Wen-Yu Lu
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China.
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12
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Sengupta K, Pal S. A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40288-40307. [PMID: 33844144 DOI: 10.1007/s11356-021-13666-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Microbial activities within oil reservoirs have adversely impacted the world's majority of oil by lowering its quality, thereby increasing its recovery and refining cost. Moreover, conventional method of extraction leaves behind nearly two-thirds of the fossil fuels in the oil fields. This huge potential can be extracted if engineered methanogenic consortium is adapted to convert the hydrocarbons into natural gas. This process involves conversion of crude oil hydrocarbons into methanogenic substrates by syntrophic and fermentative bacteria, which are subsequently utilized by methanogens to produce methane. Microbial diversity of such environments supports the viability of this process. This review illuminates the potentials of abundant microbial groups such as Syntrophaceae, Anaerolineaceae, Clostridiales and Euryarchaeota in petroleum hydrocarbon-related environment, their genetic markers, biochemical process and omics-based bioengineering methods involved in methane generation. Increase in the copy numbers of catabolic genes during methanogenesis highlights the prospect of developing engineered biofuel recovery technology. Several lab-based methanogenic consortia from depleted petroleum reservoirs and microcosm studies so far would not be enough for field application without the advent of multi-omics-based technologies to trawl out the bottleneck parameters of the enhanced fuel recovery process. The adaptability of efficient consortium of versatile hydrocarbonoclastic and methanogenic microorganisms under environmental stress conditions is further needed to be investigated. The improved process might hold the potential of methane extraction from petroleum waste like oil tank and refinery sludge, oil field deposits, etc. What sounds as biodegradation could be a beginning of converting waste into wealth by recovery of stranded energy assets.
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Affiliation(s)
- Kriti Sengupta
- Bioenergy Group, Agharkar Research Institute, Pune, 411004, India
| | - Siddhartha Pal
- National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.
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13
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Liu JF, Lu YW, Zhou L, Li W, Hou ZW, Yang SZ, Wu XL, Gu JD, Mu BZ. Simultaneous detection of transcribed functional assA gene and the corresponding metabolites of linear alkanes (C 4, C 5, and C 7) in production water of a low-temperature oil reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141290. [PMID: 32745846 DOI: 10.1016/j.scitotenv.2020.141290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/25/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
Methanogenic hydrocarbon degradation is an important biogeochemical process in oil reservoirs; however, genomic DNA-based analysis of microorganisms and metabolite detection are not conclusive for identification of the ongoing nature of this bioprocess. In this study, a suite of analyses, involving the study of microbial community and selective gene quantification of both genomic DNA and RNA together with signature metabolites, were performed to comprehensively advance the understanding of the methanogenic biodegradation of hydrocarbons in a low-temperature oilfield. The fumarate addition products for alkanes-C4, C5, and C7-alkylsuccinates-and transcribed assA and mcrA genes were simultaneously detected in the production water sample, providing robust and convincing evidence for both the initial activation of n-alkanes and methane metabolism in this oilfield. The clone library of assA gene transcripts showed that Smithella was active and most likely responsible for the addition of fumarate to n-alkanes, whereas Methanoculleus and Methanothrix were the dominant and active methane-producers via CO2 reduction and acetoclastic pathways, respectively. Additionally, qPCR results of assA and mcrA genes and their transcribed gene copy numbers revealed a roughly similar transcriptional activity in both n-alkanes-degraders and methane producers, implying that they were the major participants in the methanogenic degradation of n-alkanes in this oilfield. To the best of our knowledge, this is the first report presenting sufficient speculation, through detection of signature intermediates, corresponding gene quantification at transcriptional levels, and microbial community analysis, of methanogenic degradation of n-alkanes in production water of an oil reservoir.
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Affiliation(s)
- Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China; Engineering Research Center of Microbial Enhanced Oil Recovery, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Yu-Wei Lu
- State Key Laboratory of Bioreactor Engineering, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China; Engineering Research Center of Microbial Enhanced Oil Recovery, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China; Engineering Research Center of Microbial Enhanced Oil Recovery, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Wei Li
- Exploration and Development Research Institute of Daqing Oilfield Company Limited, PetroChina, Daqing, Heilongjiang 163712, PR China
| | - Zhao-Wei Hou
- Exploration and Development Research Institute of Daqing Oilfield Company Limited, PetroChina, Daqing, Heilongjiang 163712, PR China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China; Engineering Research Center of Microbial Enhanced Oil Recovery, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Xiao-Lin Wu
- Exploration and Development Research Institute of Daqing Oilfield Company Limited, PetroChina, Daqing, Heilongjiang 163712, PR China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, PR China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China; Engineering Research Center of Microbial Enhanced Oil Recovery, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China.
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14
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Liu YF, Chen J, Liu ZL, Shou LB, Lin DD, Zhou L, Yang SZ, Liu JF, Li W, Gu JD, Mu BZ. Anaerobic Degradation of Paraffins by Thermophilic Actinobacteria under Methanogenic Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10610-10620. [PMID: 32786606 DOI: 10.1021/acs.est.0c02071] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial anaerobic alkane degradation is a key process in subsurface oil reservoirs and anoxic environments contaminated with petroleum, with a major impact on global carbon cycling. However, the thermophiles capable of water-insoluble paraffins (>C17) degradation under methanogenic conditions has remained understudied. Here, we established thermophilic (55 °C) n-paraffins-degrading (C21-C30) cultures from an oil reservoir. After over 900 days of incubation, the even-numbered n-paraffins were biodegraded to methane. The bacterial communities are dominated by a novel class-level lineage of actinobacteria, 'Candidatus Syntraliphaticia'. These 'Ca. Syntraliphaticia'-like metagenome-assembled genomes (MAGs) encode a complete alkylsuccinate synthases (ASS) gene operon, as well as hydrogenases and formate dehydrogenase, and several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. Metatranscriptomic analysis suggests that n-paraffins are activated via fumarate addition reaction, and oxidized into carbon dioxide, hydrogen/formate and acetate by 'Ca. Syntraliphaticia', that could be further converted to methane by the abundant hydrogenotrophic and acetoclastic methanogens. We also found a divergent methyl-CoM reductase-like complex (MCR) and a canonical MCR in two MAGs representing 'Ca. Methanosuratus' (within candidate phylum Verstraetearchaeota), indicating the capability of methane and short-chain alkane metabolism in the oil reservoir. Ultimately, this result offers new insights into the degradability and the mechanisms of n-paraffins under methanogenic conditions at high temperatures.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, P.R. China
| | - Jing Chen
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Zhong-Lin Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Li-Bin Shou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Dan-Dan Lin
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Wei Li
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, P.R. China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, P.R. China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
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15
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Chen J, Liu YF, Zhou L, Irfan M, Hou ZW, Li W, Mbadinga SM, Liu JF, Yang SZ, Wu XL, Gu JD, Mu BZ. Long-chain n-alkane biodegradation coupling to methane production in an enriched culture from production water of a high-temperature oil reservoir. AMB Express 2020; 10:63. [PMID: 32266503 PMCID: PMC7138878 DOI: 10.1186/s13568-020-00998-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 03/21/2020] [Indexed: 11/18/2022] Open
Abstract
Paraffinic n-alkanes (C22–C30), crucial portions of residual oil, are generally considered to be difficult to be biodegraded owing to their general solidity at ambient temperatures and low water solubility, rendering relatively little known about metabolic processes in different methanogenic hydrocarbon-contaminated environments. Here, we established a methanogenic C22–C30 n-alkane-degrading enrichment culture derived from a high-temperature oil reservoir production water. During two-year incubation (736 days), unexpectedly significant methane production was observed. The measured maximum methane yield rate (164.40 μmol L−1 d−1) occurred during the incubation period from day 351 to 513. The nearly complete consumption (> 97%) of paraffinic n-alkanes and the detection of dicarboxylic acids in n-alkane-amended cultures indicated the biotransformation of paraffin to methane under anoxic condition. 16S rRNA gene analysis suggested that the dominant methanogen in n-alkane-degrading cultures shifted from Methanothermobacter on day 322 to Thermoplasmatales on day 736. Bacterial community analysis based on high-throughput sequencing revealed that members of Proteobacteria and Firmicutes exhibiting predominant in control cultures, while microorganisms affiliated with Actinobacteria turned into the most dominant phylum in n-alkane-dependent cultures. Additionally, the relative abundance of mcrA gene based on genomic DNA significantly increased over the incubation time, suggesting an important role of methanogens in these consortia. This work extends our understanding of methanogenic paraffinic n-alkanes conversion and has biotechnological implications for microbial enhanced recovery of residual hydrocarbons and effective bioremediation of hydrocarbon-containing biospheres.
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Ji JH, Zhou L, Mbadinga SM, Irfan M, Liu YF, Pan P, Qi ZZ, Chen J, Liu JF, Yang SZ, Gu JD, Mu BZ. Methanogenic biodegradation of C 9 to C 12n-alkanes initiated by Smithella via fumarate addition mechanism. AMB Express 2020; 10:23. [PMID: 32008120 PMCID: PMC6995468 DOI: 10.1186/s13568-020-0956-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/16/2020] [Indexed: 11/15/2022] Open
Abstract
In the present study, a methanogenic alkane-degrading (a mixture of C9 to C12n-alkanes) culture enriched from production water of a low-temperature oil reservoir was established and assessed. Significant methane production was detected in the alkane-amended enrichment cultures compared with alkane-free controls over an incubation period of 1 year. At the end of the incubation, fumarate addition metabolites (C9 to C12 alkylsuccinates) and assA genes (encoding the alpha subunit of alkylsuccinate synthase) were detected only in the alkane-amended enrichment cultures. Microbial community analysis showed that putative syntrophic n-alkane degraders (Smithella) capable of initiating n-alkanes by fumarate addition mechanism were enriched in the alkane-amended enrichment cultures. In addition, both hydrogenotrophic (Methanocalculus) and acetoclastic (Methanothrix) methanogens were also observed. Our results provide further evidence that alkanes can be activated by addition to fumarate under methanogenic conditions.
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