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Li Y, Liu Y, Guo D, Dong H. Differential degradation of petroleum hydrocarbons by Shewanella putrefaciens under aerobic and anaerobic conditions. Front Microbiol 2024; 15:1389954. [PMID: 38659987 PMCID: PMC11040095 DOI: 10.3389/fmicb.2024.1389954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
The complexity of crude oil composition, combined with the fluctuating oxygen level in contaminated environments, poses challenges for the bioremediation of oil pollutants, because of compound-specific microbial degradation of petroleum hydrocarbons under certain conditions. As a result, facultative bacteria capable of breaking down petroleum hydrocarbons under both aerobic and anaerobic conditions are presumably effective, however, this hypothesis has not been directly tested. In the current investigation, Shewanella putrefaciens CN32, a facultative anaerobic bacterium, was used to degrade petroleum hydrocarbons aerobically (using O2 as an electron acceptor) and anaerobically (using Fe(III) as an electron acceptor). Under aerobic conditions, CN32 degraded more saturates (65.65 ± 0.01%) than aromatics (43.86 ± 0.03%), with the following order of degradation: dibenzofurans > n-alkanes > biphenyls > fluorenes > naphthalenes > alkylcyclohexanes > dibenzothiophenes > phenanthrenes. In contrast, under anaerobic conditions, CN32 exhibited a higher degradation of aromatics (53.94 ± 0.02%) than saturates (23.36 ± 0.01%), with the following order of degradation: dibenzofurans > fluorenes > biphenyls > naphthalenes > dibenzothiophenes > phenanthrenes > n-alkanes > alkylcyclohexanes. The upregulation of 4-hydroxy-3-polyprenylbenzoate decarboxylase (ubiD), which plays a crucial role in breaking down resistant aromatic compounds, was correlated with the anaerobic degradation of aromatics. At the molecular level, CN32 exhibited a higher efficiency in degrading n-alkanes with low and high carbon numbers relative to those with medium carbon chain lengths. In addition, the degradation of polycyclic aromatic hydrocarbons (PAHs) under both aerobic and anaerobic conditions became increasingly difficult with increased numbers of benzene rings and methyl groups. This study offers a potential solution for the development of targeted remediation of pollutants under oscillating redox conditions.
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Affiliation(s)
- Yang Li
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing, China
| | - Yuan Liu
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing, China
| | - Dongyi Guo
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing, China
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2
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Liu Y, Zhao N, Dai S, He R, Zhang Y. Metagenomic insights into phenanthrene biodegradation in electrical field-governed biofilms for groundwater bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133477. [PMID: 38218033 DOI: 10.1016/j.jhazmat.2024.133477] [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: 10/23/2023] [Revised: 12/21/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024]
Abstract
Electrical fields (EFs)-assisted in-situ bioremediation of petroleum-contaminated groundwater, such as polycyclic aromatic hydrocarbons, has drawn increasing attention. However, the long-term stability, the EFs influence, and metabolic pathways are still poorly understood, hindering the further development of robust technology design. Herein, a series of EFs was applied to the phenanthrene-contaminated groundwater, and the corresponding system performance was investigated. The highest removal capacity of phenanthrene (phe) (7.63 g/(m3·d)) was achieved with EF_0.8 V biofilm at a hydrolytic retention time of 0.5 d. All the biofilms with four EFs exhibited a high removal efficiency of phe over 80% during a 100-d continuous-flow operation. Intermediates analysis revealed the main pathways of phe degradation: phthalate and salicylate via hydroxylation, methylation, carboxylation, and ring cleavage steps. Synergistic effects between phe-degraders (Dechloromonas), fermentative bacteria (Delftia), and electroactive microorganisms (Geobacter) were the main contributors to the complete phe mineralization. Genes encoding various proteins of methyl-accepting (mcp), response regulator (cheABDRY), and type IV pilus (pilABCMQV) were dominant, revealing the importance of cell motility and extracellular electron transfer. Metagenomics analysis unveiled phe-degrading genes, including ring reduction enzymes (bamBCDE), carboxylase of aromatics (ubiD), and methyltransferase protein (ubiE, pcm). These findings offered a molecular understanding of refractory organics' decompositions in EFs-governed biotechnology.
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Affiliation(s)
- Yue Liu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Nannan Zhao
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; International Science and Technology Cooperation Platform for Low-carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, China.
| | - Shuo Dai
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; International Science and Technology Cooperation Platform for Low-carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yifeng Zhang
- Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
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Zhou N, Guo H, Zhang Z, Wang H. The discrepant metabolic pathways of PAHs by facultative anaerobic bacteria under aerobic and nitrate-reducing conditions. CHEMOSPHERE 2024; 351:141230. [PMID: 38237784 DOI: 10.1016/j.chemosphere.2024.141230] [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: 08/30/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Studies regarding the facultative anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) were still in the initial stage. In this study, a facultative anaerobe which was identified as Bacillus Firmus and named as PheN7 was firstly isolated from the mixed petroleum-polluted soil samples using phenanthrene and nitrate as the solo carbon resource and electron acceptor under anaerobic condition. The degradation rates of PheN7 towards phenanthrene were detected as 33.17 μM/d, 13.81 μM/d and 7.11 μM/d at the initial phenanthrene concentration of 250.17 μM with oxygen, nitrate and sulfate as the electron acceptor, respectively. The metabolic pathways toward phenanthrene by PheN7 were deduced combining the metagenome analysis of PheN7 and intermediate metabolites of phenanthrene under aerobic and nitrate-reducing conditions. Dioxygenation and carboxylation were inferred as the initial activation reactions of phenanthrene degradation in these two pathways. This study highlighted the significance of facultative anaerobic bacteria in natural PAHs biodegradation, revealing the discrepant metabolic fates of PAHs by one solo bacteria under aerobic and anaerobic environments.
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Affiliation(s)
- Nan Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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4
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Yao Y, Wei Y, Li J, Han R, Jing C, Liu R, Niu Q. Microbial electron flow promotes naphthalene degradation in anaerobic digestion in the presence of nitrate electron acceptor: Focus on electron flow regulation and microbial interaction succession. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132293. [PMID: 37597391 DOI: 10.1016/j.jhazmat.2023.132293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
Microbial electron flow (MEF) is produced from microbial degradation of organic compounds. Regulating MEF to promote organic pollutants biodegradation such as naphthalene (Nap) is a potential way but remains a lack of theoretical basis. Here, we regulated MEF by adding electron acceptor NO3- to achieve 2.6 times increase of Nap biodegradation with cyclodextrin as co-metabolism carbon source. With the NO3- addition, the genes inhibited by Nap of electron generation significantly up-regulated. Especially, key genes ubiD and nahD for anaerobic Nap degradation significantly up-regulated respectively 3.7 times and 6.7 times. Moreover, the ability of electron transfer in MEF was also improved consistent with 7.2 times increase of electron transfer system (ETS) activity. Furthermore, total 60 metagenome-assembled genomes (MAGs) were reconstructed through the metagenomic sequencing data with assembly and binning strategies. Interestingly, it was also first found that the Klebsiella MAG. SDU (Shandong University) 14 had the ability of simultaneous Nap biodegradation and denitrification. Our results firstly offered an effective method of regulating MEF to promote polycyclic aromatic hydrocarbons (PAHs) degradation and simultaneous methanogenesis.
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Affiliation(s)
- Yilin Yao
- China-America CRC for Environment & Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Yanhao Wei
- China-America CRC for Environment & Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Jingyi Li
- China-America CRC for Environment & Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Ruotong Han
- China-America CRC for Environment & Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Chuanyong Jing
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Rutao Liu
- China-America CRC for Environment & Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China; Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China; Qingdao Key Laboratory of Marine Pollutant Prevention, Shandong University, Qingdao, Shandong 266237, China.
| | - Qigui Niu
- China-America CRC for Environment & Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China; Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China; Qingdao Key Laboratory of Marine Pollutant Prevention, Shandong University, Qingdao, Shandong 266237, China.
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5
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Bai B, Zhang L, Dong H, Huang Y. Coupled Fe(III) reduction and phenanthrene degradation by marine-derived Kocuria oceani FXJ8.057 under aerobic condition. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132237. [PMID: 37595472 DOI: 10.1016/j.jhazmat.2023.132237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/29/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
Diverse aerobic actinobacteria possess the capacity to degrade polycyclic aromatic hydrocarbons (PAHs) and have recently been shown to reduce Fe(III). However, the coupling of the two processes under oxic conditions remains unclear. Here, the co-metabolism of phenanthrene (PHE) and Fe(III) by marine-derived Kocuria oceani FXJ8.057 was realized under aerobic condition. In the presence of both PHE and Fe(III), the rates of PHE degradation (83.91 %) and Fe(III) reduction (50.00 %) were synchronously enhanced, compared to those with PHE (67.34 %) or Fe(III) (38.00 %) alone. Transcriptome analysis detected upregulation of PHE biodegradation and riboflavin biosynthesis in the strain cultured with both PHE and Fe(III) compared to that with PHE alone. Metabolite analysis indicated that, with the addition of Fe(III), the strain could efficiently degrade PHE via three pathways. Moreover, the strain secreted riboflavin, which acted as a shuttle to promote electron transfer from PHE to Fe(III). It also secreted organic acids that could delay Fe(II) reoxidation. Finally, H2O2 secreted by the strain caused extracellular Fenton reaction to generate •OH, which also played a minor role in the PHE degradation. These findings provide the first example of an aerobic bacterium that couples PAH degradation to Fe(III) reduction and extend our understanding of Fe(III)-reducing microorganisms.
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Affiliation(s)
- Bingbing Bai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Chen C, Zhang Z, Xu P, Hu H, Tang H. Anaerobic biodegradation of polycyclic aromatic hydrocarbons. ENVIRONMENTAL RESEARCH 2023; 223:115472. [PMID: 36773640 DOI: 10.1016/j.envres.2023.115472] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Although many anaerobic microorganisms that can degrade PAHs have been harnessed, there is still a large gap between laboratory achievements and practical applications. Here, we review the recent advances in the biodegradation of PAHs under anoxic conditions and highlight the mechanistic insights into the metabolic pathways and functional genes. Achievements of practical application and enhancing strategies of anaerobic PAHs bioremediation in soil were summarized. Based on the concerned issues during research, perspectives of further development were proposed including time-consuming enrichment, byproducts with unknown toxicity, and activity inhibition with low temperatures. In addition, meta-omics, synthetic biology and engineering microbiome of developing microbial inoculum for anaerobic bioremediation applications are discussed. We anticipate that integrating the theoretical research on PAHs anaerobic biodegradation and its successful application will advance the development of anaerobic bioremediation.
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Affiliation(s)
- Chao Chen
- College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhan Zhang
- China Tobacco Henan Industrial Co. Ltd., Zhengzhou, 450000, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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7
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Bonatti E, Dos Santos A, Birolli WG, Rodrigues-Filho E. Endophytic, extremophilic and entomophilic fungi strains biodegrade anthracene showing potential for bioremediation. World J Microbiol Biotechnol 2023; 39:152. [PMID: 37029326 DOI: 10.1007/s11274-023-03590-8] [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: 09/29/2022] [Accepted: 03/21/2023] [Indexed: 04/09/2023]
Abstract
Anthropogenic activities have been increasing Polycyclic Aromatic Hydrocarbons (PAHs) release, promoting an urgent need for decontamination methods. Therefore, anthracene biodegradation by endophytic, extremophilic, and entomophilic fungi was studied. Moreover, a salting-out extraction methodology with the renewable solvent ethanol and the innocuous salt K2HPO4 was employed. Nine of the ten employed strains biodegraded anthracene in liquid medium (19-56% biodegradation) after 14 days at 30 °C, 130 rpm, and 100 mg L-1. The most efficient strain Didymellaceae sp. LaBioMMi 155, an entomophilic strain, was employed for optimized biodegradation, aiming at a better understanding of how factors like pollutant initial concentration, pH, and temperature affected this process. Biodegradation reached 90 ± 11% at 22 °C, pH 9.0, and 50 mg L-1. Futhermore, 8 different PAHs were biodegraded and metabolites were identified. Then, experiments with anthracene in soil ex situ were performed and bioaugmentation with Didymellaceae sp. LaBioMMi 155 presented better results than natural attenuation by the native microbiome and biostimulation by the addition of liquid nutrient medium into soil. Therefore, an expanded knowledge about PAHs biodegradation processes was achieved with emphasis to the action of Didymellaceae sp. LaBioMMi 155, which can be further employed for in situ biodegradation (after strain security test), or for enzyme identification and isolation aiming at oxygenases with optimal activity under alkaline conditions.
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Affiliation(s)
- Erika Bonatti
- Laboratory of Micromolecular Biochemistry of Microorganisms (LaBioMMi), Center for Exact Sciences and Technology, Federal University of São Carlos, Via Washington Luiz, Km 235, P.O. Box 676, São Carlos, SP, 13.565-905, Brazil
| | - Alef Dos Santos
- Laboratory of Micromolecular Biochemistry of Microorganisms (LaBioMMi), Center for Exact Sciences and Technology, Federal University of São Carlos, Via Washington Luiz, Km 235, P.O. Box 676, São Carlos, SP, 13.565-905, Brazil
| | - Willian Garcia Birolli
- Laboratory of Micromolecular Biochemistry of Microorganisms (LaBioMMi), Center for Exact Sciences and Technology, Federal University of São Carlos, Via Washington Luiz, Km 235, P.O. Box 676, São Carlos, SP, 13.565-905, Brazil.
| | - Edson Rodrigues-Filho
- Laboratory of Micromolecular Biochemistry of Microorganisms (LaBioMMi), Center for Exact Sciences and Technology, Federal University of São Carlos, Via Washington Luiz, Km 235, P.O. Box 676, São Carlos, SP, 13.565-905, Brazil.
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Zhang J, Hai Y, Shi M, Bing W, Bao N, Liang J. Selective assembly of microbe on patterned porous interfaces as potential membrane reactors for enhanced biodegradation of phenol. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Castro AR, Martins G, Salvador AF, Cavaleiro AJ. Iron Compounds in Anaerobic Degradation of Petroleum Hydrocarbons: A Review. Microorganisms 2022; 10:2142. [PMID: 36363734 PMCID: PMC9695802 DOI: 10.3390/microorganisms10112142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 09/22/2023] Open
Abstract
Waste and wastewater containing hydrocarbons are produced worldwide by various oil-based industries, whose activities also contribute to the occurrence of oil spills throughout the globe, causing severe environmental contamination. Anaerobic microorganisms with the ability to biodegrade petroleum hydrocarbons are important in the treatment of contaminated matrices, both in situ in deep subsurfaces, or ex situ in bioreactors. In the latter, part of the energetic value of these compounds can be recovered in the form of biogas. Anaerobic degradation of petroleum hydrocarbons can be improved by various iron compounds, but different iron species exert distinct effects. For example, Fe(III) can be used as an electron acceptor in microbial hydrocarbon degradation, zero-valent iron can donate electrons for enhanced methanogenesis, and conductive iron oxides may facilitate electron transfers in methanogenic processes. Iron compounds can also act as hydrocarbon adsorbents, or be involved in secondary abiotic reactions, overall promoting hydrocarbon biodegradation. These multiple roles of iron are comprehensively reviewed in this paper and linked to key functional microorganisms involved in these processes, to the underlying mechanisms, and to the main influential factors. Recent research progress, future perspectives, and remaining challenges on the application of iron-assisted anaerobic hydrocarbon degradation are highlighted.
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Affiliation(s)
- Ana R. Castro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Gilberto Martins
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Andreia F. Salvador
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Ana J. Cavaleiro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
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Zhou N, Guo H, Liu Q, Zhang Z, Sun J, Wang H. Bioaugmentation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil with the nitrate-reducing bacterium PheN7 under anaerobic condition. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129643. [PMID: 35908400 DOI: 10.1016/j.jhazmat.2022.129643] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/10/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
The remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil under anaerobic condition is still a huge challenge. In this study, an anaerobic Bacillus firmus strain named PheN7 was firstly isolated from mixture of contaminated soil and sludge samples with phenanthrene as the sole carbon resource under nitrate reducing environment. The anaerobic strain was then inoculated combining with nitrate into the phenanthrene-spiked PAH-contaminated soil to investigate the remediation efficiency by anaerobic bioaugmentation (BA). Results showed that the synergy between PheN7 and indigenous degrading bacteria promoted the remediation efficiency of soil. The average removal efficiencies of phenanthrene in 56 days were 1.73 mg/kg soil·d in BA group, much higher than biostimulation group (sole nitrate addition) and natural degradation which achieved 1.48 mg/kg soil·d and 1.24 mg/kg soil·d of degradation rate, respectively. The outstanding adaptability of PheN7 made it become the dominant species in soil in the terminal period, but the invasion of PheN7 also resulted in the decline of diversity of the indigenous microbial community. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt 2) results showed that a series of functional genes encoding anaerobic phenanthrene degradation and nitrate reductase enzymes in soil were remarkably strengthened with the addition of PheN7. This study confirmed the contribution of PheN7 as the anaerobic inoculum in PAH-contaminated soil remediation, further evaluating the practical applicability of anaerobic bioaugmentation technology in on-site remediation of real PAH-contaminated sites.
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Affiliation(s)
- Nan Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Qingxin Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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11
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Sun J, Zhang Z, Wang H, Rogers MJ, Guo H, He J. Exploration of the biotransformation of phenanthrene degradation coupled with methanogensis by metabolites and enzyme analyses. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 293:118491. [PMID: 34780757 DOI: 10.1016/j.envpol.2021.118491] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/21/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
The ubiquitous environmental contaminants, polycyclic aromatic hydrocarbons (PAHs), can be aerobically biodegraded. Strategies for biodegradation of PAHs are needed for the persisted character of it in anoxic environments. In current study, we obtained a highly enriched anaerobic, PAHs-degrading co-culture DYM1, from petroleum-polluted soil. DYM1 significantly degrades a range of PAHs in 4 days without supplementary terminal electron acceptors. Co-culture DYM1 is consists of two microorganisms (a degrading bacterium Paracoccus sp. strain PheM1 and an aceticlastic methanogen Methanosaeta concilii.) that utilize different carbon sources in a syntrophic metabolic process of phenanthrene. About 93% of phenanthrene (104.5 μM) has been removed under methanogenic conditions after incubation with co-culture DYM1 for 4 d, and produced 33.68 μmol CH4. Carboxylation, which is catalyzed by UbiD-like carboxylase, was proposed as the initial steps of methanogenic phenanthrene-degrading pathway based upon the detection of 2-phenanthroic acid and 4-phenanthrene acid. Reduction and hydration of the benzene rings were followed by the initial reaction. Hydrated phenanthroic acid metabolites were newly detected and characterized under anaerobic conditions. Anaerobic degradation of phenanthrene without terminal electron acceptor addition not only sheds light on a poorly understood and environmentally relevant biological process, but also supply a novel approach to recover the energy of toxic pollutant in forms of methane.
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Affiliation(s)
- Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China.
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive, 3117576, Singapore
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive, 3117576, Singapore
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12
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Yi M, Zhang L, Qin C, Lu P, Bai H, Han X, Yuan S. Temporal changes of microbial community structure and nitrogen cycling processes during the aerobic degradation of phenanthrene. CHEMOSPHERE 2022; 286:131709. [PMID: 34340117 DOI: 10.1016/j.chemosphere.2021.131709] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g-1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%-194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.
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Affiliation(s)
- Meiling Yi
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Lilan Zhang
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Cunli Qin
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Peili Lu
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Hongcheng Bai
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Xinkuan Han
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shupei Yuan
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
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Liu J, Zhang AN, Liu YJ, Liu Z, Liu Y, Wu XJ. Analysis of the mechanism for enhanced pyrene biodegradation based on the interactions between iron-ions and Rhodococcus ruber strain L9. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112789. [PMID: 34560613 DOI: 10.1016/j.ecoenv.2021.112789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
A slow degradation rate and low transformation efficiency are the main problems in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). This study selected pyrene as the target PAH to investigate the effect of ferrous ion and ferric ion on pyrene degradation. The driving effect and mechanism, including the interaction between pyrene and iron ions and the bacterial physiological response during the biodegradation process by Rhodococcus ruber strain L9, were investigated. The results showed that iron ions did not enhance bacterial growth but improved bacteria's pyrene removal capacity, contributing to the total efficiency of pyrene biodegradation. The process started with an initial formation of "cation-π" between Fe (III) and pyrene, which subsequently drove the pyrene removal process and accelerated the bacterial metabolic process. Moreover, a significant increase in the protein concentration, catechol dioxygenase (C12O and C23O) activities, and intracellular protein regulation in crude enzyme solution indicate a positive response of the bacteria during the iron ion-enhanced pyrene degradation process.
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Affiliation(s)
- Jing Liu
- School of Civil Engineering, Yulin University, Yulin 719000, China; Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Ai-Ning Zhang
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Yong-Jun Liu
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China.
| | - Zhe Liu
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Yu Liu
- School of Petroleum and Environment Engineering, Yanan University, Yanan 716000, China
| | - Xi-Jun Wu
- School of Civil Engineering, Yulin University, Yulin 719000, China
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14
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Shen X, Dong W, Wan Y, Feng K, Liu Y, Wei Y. Influencing mechanisms of siderite and magnetite, on naphthalene biodegradation: Insights from degradability and mineral surface structure. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113648. [PMID: 34479148 DOI: 10.1016/j.jenvman.2021.113648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/18/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Biodegradation is the most economical and efficient process for remediating polycyclic aromatic hydrocarbons (PAHs) such as naphthalene (Nap). Soil composition is pivotal in controlling PAH migration and transformation. Iron minerals such as siderite and magnetite are the primary components of soil and sediment and play key roles in organic pollutant biodegradation. However, it is unclear whether siderite and magnetite promote or inhibit Nap biodegradation. The effects of siderite and magnetite on Nap biodegradation were investigated through batch experiments in this study. The results indicated that siderite increased Nap biodegradation efficiency by 7.87%, whereas magnetite inhibited Nap biodegradation efficiency by 3.54%. In the presence of siderite, Nap-degrading bacteria with acid-producing effects promoted siderite dissolution via metabolic activity, resulting in an increased Fe (II) concentration in solution which accelerated the iron reduction process and promoted Nap biodegradation. In addition, the presence of iron minerals altered the genus-level community structure. Anaerobic sulfate-reducing bacteria such as Desulfosporosinus occurred in the presence of siderite, indicating that sulfate reduction occurred in advance under the influence of siderite. In the presence of magnetite, Fe (III) in iron minerals were converted to Fe (II), and under the mediation of microorganisms, Fe (II) combined with carbonate to form secondary minerals (e.g., siderite). Secondary minerals were attached to the surface of magnetite, which inhibited magnetite dissolution and reduced the efficiency of Fe (III) utilization by microorganisms. Furthermore, as the reaction proceeds, acid-producing microorganisms promoted magnetite further dissolution, resulting in a longer duration of the Fe (III) reduction process. Bacteria utilizing sulfuric acid as the terminal electron acceptor consumed organic matter more rapidly than those using iron as the terminal electron acceptor. Therefore, magnetite inhibited Nap degradation. These observations enhance our understanding of the interaction mechanisms of iron minerals, organic pollutants, and degrading bacteria during the biodegradation process.
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Affiliation(s)
- Xiaofang Shen
- College of Construction Engineering, Jilin University, Changchun, Jilin, 130021, China; Key Laboratory of Groundwater Resources and Environments, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China
| | - Weihong Dong
- Key Laboratory of Groundwater Resources and Environments, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China
| | - Yuyu Wan
- Key Laboratory of Groundwater Resources and Environments, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China.
| | - Kaijie Feng
- Hubei Coal Geological Exploration Institute, Wuhan, Hubei, 430070, China
| | - Yu Liu
- Key Laboratory of Groundwater Resources and Environments, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China
| | - Yujie Wei
- College of Construction Engineering, Jilin University, Changchun, Jilin, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China
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