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Zhao L, Sun P, Gao J, Li Y, Pu Q, Lyu C, Zhao W. Improved microbial-plant soil bioremediation of PAHs and heavy metal through in silico methods. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135524. [PMID: 39181001 DOI: 10.1016/j.jhazmat.2024.135524] [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: 03/16/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024]
Abstract
The combined pollution of polycyclic aromatic hydrocarbons (PAHs) and organic cadmium (Cd) in farmland soils, and the field controlling strategy need to be studied urgently. In this study, 5 PAHs, 5 Cd and 11 soil conditioners were selected to explore the co-exposure risk and remediation efficiency. Firstly, a significant combination Fl-alkylalkoxy cadmium was obtained using forward and reverse methods coupling variation coefficient methods (the combined pollution value was 0.173). Secondly, the interaction energy of microbial degradation / plant absorption of Fl under Cd stress, and microbial mineralization / plant absorption of alkylalkoxy cadmium under PAHs stress were characterized using factorial experimental design, molecular docking and molecular dynamics simulation. The combined pollution of alkylalkoxy cadmium and dialkyl cadmium, phenanthrene and Benzo [a] pyrene was significant (synergistic contribution rates were 17.58 % and 19.22 %, respectively). In addition, 6 soil conditioners with significant efficiency were selected to design Taguchi orthogonal experimental schemes, indicating the microbial degradation / mineralization and plant absorption were significantly effective (the maximum increase of remediation efficiency was 93.81 %) under the combinations (i.e., trratone, coumarol, fulvamic acid, potassium fertilizer and others, etc.). Finally, it was found that the soil conditioners affected the hydrophobic groups and forces, and the efficiency was proportional to the highest peak value and minimum distance in the RDF curve. This study identifies the risk characteristics of co-exposure of PAHs and Cd and screens effective soil conditioners, providing theoretical guidance for risk controlling.
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Affiliation(s)
- Lei Zhao
- College of New Energy and Environment, Jilin University, Changchun 130012, China.
| | - Peixuan Sun
- College of New Energy and Environment, Jilin University, Changchun 130012, China.
| | - Jiaxuan Gao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
| | - Yunxiang Li
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
| | - Qikun Pu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
| | - Cong Lyu
- College of New Energy and Environment, Jilin University, Changchun 130012, China.
| | - Wenjin Zhao
- College of New Energy and Environment, Jilin University, Changchun 130012, China.
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2
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Davletgildeeva AT, Kuznetsov NA. Bioremediation of Polycyclic Aromatic Hydrocarbons by Means of Bacteria and Bacterial Enzymes. Microorganisms 2024; 12:1814. [PMID: 39338488 PMCID: PMC11434427 DOI: 10.3390/microorganisms12091814] [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: 08/12/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread, persistent, and toxic environmental pollutants. Many anthropogenic and some natural factors contribute to the spread and accumulation of PAHs in aquatic and soil systems. The effective and environmentally friendly remediation of these chemical compounds is an important and challenging problem that has kept scientists busy over the last few decades. This review briefly summarizes data on the main sources of PAHs, their toxicity to living organisms, and physical and chemical approaches to the remediation of PAHs. The basic idea behind existing approaches to the bioremediation of PAHs is outlined with an emphasis on a detailed description of the use of bacterial strains as individual isolates, consortia, or cell-free enzymatic agents.
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Affiliation(s)
- Anastasiia T. Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia;
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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3
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Xu Q, Ali S, Afzal M, Nizami AS, Han S, Dar MA, Zhu D. Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172967. [PMID: 38705297 DOI: 10.1016/j.scitotenv.2024.172967] [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: 02/15/2024] [Revised: 04/06/2024] [Accepted: 05/01/2024] [Indexed: 05/07/2024]
Abstract
The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.
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Affiliation(s)
- Qi Xu
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Shehbaz Ali
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Muhammad Afzal
- Soil & Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Abdul-Sattar Nizami
- Sustainable Development Study Centre, Government College University, Lahore 54000, Pakistan
| | - Song Han
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Mudasir A Dar
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Daochen Zhu
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China.
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4
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Naloka K, Kuntaveesuk A, Muangchinda C, Chavanich S, Viyakarn V, Chen B, Pinyakong O. Pseudomonas and Pseudarthrobacter are the key players in synergistic phenanthrene biodegradation at low temperatures. Sci Rep 2024; 14:11976. [PMID: 38796616 PMCID: PMC11127967 DOI: 10.1038/s41598-024-62829-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
Hydrocarbon contamination, including contamination with polycyclic aromatic hydrocarbons (PAHs), is a major concern in Antarctica due to the toxicity, recalcitrance and persistence of these compounds. Under the Antarctic Treaty, nonindigenous species are not permitted for use in bioremediation at polluted sites in the Antarctic region. In this study, three bacterial consortia (C13, C15, and C23) were isolated from Antarctic soils for phenanthrene degradation. All isolated bacterial consortia demonstrated phenanthrene degradation percentages ranging from 45 to 85% for 50 mg/L phenanthrene at 15 ℃ within 5 days. Furthermore, consortium C13 exhibited efficient phenanthrene degradation potential across a wide range of environmental conditions, including different temperature (4-30 ℃) and water availability (without polyethylene glycol (PEG) 6000 or 30% PEG 6000 (w/v)) conditions. Sequencing analysis of 16S rRNA genes revealed that Pseudomonas and Pseudarthrobacter were the dominant genera in the phenanthrene-degrading consortia. Moreover, six cultivable strains were isolated from these consortia, comprising four strains of Pseudomonas, one strain of Pseudarthrobacter, and one strain of Paeniglutamicibacter. These isolated strains exhibited the ability to degrade 50 mg/L phenanthrene, with degradation percentages ranging from 4 to 22% at 15 ℃ within 15 days. Additionally, the constructed consortia containing Pseudomonas spp. and Pseudarthrobacter sp. exhibited more effective phenanthrene degradation (43-52%) than did the individual strains. These results provide evidence that Pseudomonas and Pseudarthrobacter can be potential candidates for synergistic phenanthrene degradation at low temperatures. Overall, our study offers valuable information for the bioremediation of PAH contamination in Antarctic environments.
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Affiliation(s)
- Kallayanee Naloka
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Bangkok, 10330, Thailand
| | - Aunchisa Kuntaveesuk
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chanokporn Muangchinda
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
- International Postgraduate Programs in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suchana Chavanich
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Voranop Viyakarn
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Bo Chen
- Polar Biological Science Division, Polar Research Institute of China, Shanghai, China
| | - Onruthai Pinyakong
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Bangkok, 10330, Thailand.
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de Melo Carlos L, Camacho KF, Duarte AW, de Oliveira VM, Boroski M, Rosa LH, Vieira R, Neto AA, Ottoni JR, Passarini MRZ. Bioprospecting the potential of the microbial community associated to Antarctic marine sediments for hydrocarbon bioremediation. Braz J Microbiol 2024; 55:471-485. [PMID: 38052770 PMCID: PMC10920520 DOI: 10.1007/s42770-023-01199-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/27/2023] [Indexed: 12/07/2023] Open
Abstract
Microorganisms that inhabit the cold Antarctic environment can produce ligninolytic enzymes potentially useful in bioremediation. Our study focused on characterizing Antarctic bacteria and fungi from marine sediment samples of King George and Deception Islands, maritime Antarctica, potentially affected by hydrocarbon influence, able to produce enzymes for use in bioremediation processes in environments impacted with petroleum derivatives. A total of 168 microorganism isolates were obtained: 56 from sediments of King George Island and 112 from Deception Island. Among them, five bacterial isolates were tolerant to cell growth in the presence of diesel oil and gasoline and seven fungal were able to discolor RBBR dye. In addition, 16 isolates (15 bacterial and one fungal) displayed enzymatic emulsifying activities. Two isolates were characterized taxonomically by showing better biotechnological results. Psychrobacter sp. BAD17 and Cladosporium sp. FAR18 showed pyrene tolerance (cell growth of 0.03 g mL-1 and 0.2 g mL-1) and laccase enzymatic activity (0.006 UL-1 and 0.10 UL-1), respectively. Our results indicate that bacteria and fungi living in sediments under potential effect of hydrocarbon pollution may represent a promising alternative to bioremediate cold environments contaminated with polluting compounds derived from petroleum such as polycyclic aromatic hydrocarbons and dyes.
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Affiliation(s)
- Layssa de Melo Carlos
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000 - Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Karine Fernandes Camacho
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000 - Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | | | | | - Marcela Boroski
- Programa de Pós-Graduação Em Energia & Sustentabilidade, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, Brazil
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rosemary Vieira
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Arthur A Neto
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Júlia Ronzella Ottoni
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000 - Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Michel R Z Passarini
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000 - Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
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6
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Li J, Hong M, Tang R, Cui T, Yang Y, Lv J, Liu N, Lei Y. Isolation of Diaphorobacter sp. LW2 capable of degrading Phenanthrene and its migration mediated by Pythium ultimum. ENVIRONMENTAL TECHNOLOGY 2024; 45:1497-1507. [PMID: 36384417 DOI: 10.1080/09593330.2022.2145914] [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: 07/03/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Phenanthrene, one of the polycyclic aromatic hydrocarbons, is stubborn and persistent and exists widely in petroleum-contaminated soil. Filamentous fungi are good assistants to bacterial transport, by hyphae passing through soil pores and reaching further positions. An isolated bacterial strain, from the contaminated soil of the coking plant, was identified as Diaphorobacter and named LW2, which could use phenanthrene as the only carbon source and energy for its growth. LW2 could degrade phenanthrene in a wide range of pH, temperature and initial concentration. When pH was 6 and 10, the removal rate of phenanthrene was 38.59% and 76.44%, respectively, and the removal rate of phenanthrene was 68.25% at 15 ℃. And LW2 could degrade 86.64% phenanthrene when the initial concentration was 100 mg L-1. The detection of DI-N-octyl phthalate, phthalic acid and p-hydroxybenzoic acid revealed that the strain LW2 metabolised phenanthrene through the phthalic acid pathway. Meanwhile, swimming and swarming test results suggested that LW2 was motile. The auxiliary effect of Pythium ultimum on LW2 migration was assessed. In the presence of Pythium ultimum, LW2 could migrate within the range of centimters by its mycelium, which was also observed by fluorescence microscopy. Meanwhile, the degradation ability of LW2 after the migration was also explored. The results proved that the migration process had no significant effect on its degradation ability, and LW2 still showed good phenanthrene metabolism ability. This study provides more possibilities for the bioremediation of phenanthrene-contaminated soil by screening the degradation bacteria and testing the effect of fungi on its migration.
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Affiliation(s)
- Jialu Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Mei Hong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Rui Tang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Tingchen Cui
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Yadong Yang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Jing Lv
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Na Liu
- Institute of Groundwater and Earth Science, Jinan University, Guangzhou City, People's Republic of China
| | - Yutao Lei
- South China Institute of Environmental Sciences, MEP, Guangzhou, People's Republic of China
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7
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Chen R, Zhao Z, Xu T, Jia X. Microbial Consortium HJ-SH with Very High Degradation Efficiency of Phenanthrene. Microorganisms 2023; 11:2383. [PMID: 37894041 PMCID: PMC10609217 DOI: 10.3390/microorganisms11102383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/04/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH, with very high degradation efficiency was isolated from soil exposed to long-term PHE contamination. The results of GC analysis showed that the consortium HJ-SH degraded 98% of 100 mg/L PHE in 3 days and 93% of 1000 mg/L PHE in 5 days, an efficiency higher than that of any other natural consortia, and even most of the engineered strains and consortia reported so far. Seven dominating strains were isolated from the microbial consortium HJ-SH, named SH-1 to SH-7, which were identified according to morphological observation and 16S rDNA sequencing as Pseudomonas sp., Stenotrophomonas sp., Delftia sp., Pseudomonas sp., Brevundimonas sp., Curtobacterium sp., and Microbacterium sp., respectively. Among all the seven single strains, SH-4 showed the strongest PHE degradation ability, and had the biggest degradation contribution. However, it is very interesting that the microbial consortium can hold its high degradation ability only with the co-existence of all these seven single strains. Moreover, HJ-SH exhibited a very high tolerance for PHE, up to 4.5 g/L, and it can degrade some other typical organic pollutants such as biphenyl, anthracene, and n-hexadecane with the degradation ratios of 93%, 92% and 70%, respectively, under 100 mg/L initial concentration in 5 days. Then, we constructed an artificial consortium HJ-7 consisting of the seven single strains, SH-1 to SH-7. After comparing the degradation ratios, cell growth, and relative degradation rates, it was concluded that the artificial consortium HJ-7 with easier reproducibility, better application stability, and larger room for modification can largely replace the natural consortium HJ-SH. In conclusion, this research provided novel tools and new insights for the bioremediation of PHE and other typical organic pollutants using microbial consortia.
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Affiliation(s)
- Rui Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (R.C.); (Z.Z.); (T.X.)
| | - Zhenhua Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (R.C.); (Z.Z.); (T.X.)
| | - Tao Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (R.C.); (Z.Z.); (T.X.)
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (R.C.); (Z.Z.); (T.X.)
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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8
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Dietz-Vargas C, Valenzuela-Ibaceta F, Carrasco V, Pérez-Donoso JM. Solid medium for the direct isolation of bacterial colonies growing with polycyclic aromatic hydrocarbons or 2,4,6-trinitrotoluene (TNT). Arch Microbiol 2023; 205:271. [PMID: 37358740 DOI: 10.1007/s00203-023-03610-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Isolation of hydrocarbon-degrading bacteria is a key step for the study of microbiological diversity, metabolic pathways, and bioremediation. However current strategies lack simplicity and versatility. We developed an easy method for the screening and isolation of bacterial colonies capable of degrading hydrocarbons, such as diesel or polycyclic aromatic hydrocarbons (PAHs), as well as the pollutant explosive, 2,4,6-trinitrotoluene (TNT). The method uses a two-layer solid medium, with a layer of M9 medium, and a second layer containing the carbon source deposited through the evaporation of ethanol. Using this medium we grew hydrocarbon-degrading strains, as well as TNT-degrading isolates. We were able to isolate PAHs-degrading bacterial colonies directly from diesel-polluted soils. As a proof of concept, we used this method to isolate a phenanthrene-degrading bacteria, identified as Acinetobacter sp. and determined its ability to biodegrade this hydrocarbon.
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Affiliation(s)
- Claudio Dietz-Vargas
- Bionanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República #330, Santiago, Chile
| | - Felipe Valenzuela-Ibaceta
- Bionanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República #330, Santiago, Chile
| | - Valentina Carrasco
- Bionanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República #330, Santiago, Chile
| | - José M Pérez-Donoso
- Bionanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República #330, Santiago, Chile.
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Egas C, Galbán-Malagón C, Castro-Nallar E, Molina-Montenegro MA. Role of Microbes in the degradation of organic semivolatile compounds in polar ecosystems: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163046. [PMID: 36965736 DOI: 10.1016/j.scitotenv.2023.163046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
The Arctic and the Antarctic Continent correspond to two eco-regions with extreme climatic conditions. These regions are exposed to the presence of contaminants resulting from human activity (local and global), which, in turn, represent a challenge for life forms in these environments. Anthropogenic pollution by semi-volatile organic compounds (SVOCs) in polar ecosystems has been documented since the 1960s. Currently, various studies have shown the presence of SVOCs and their bioaccumulation and biomagnification in the polar regions with negative effects on biodiversity and the ecosystem. Although the production and use of these compounds has been regulated, their persistence continues to threaten biodiversity and the ecosystem. Here, we summarize the current literature regarding microbes and SVOCs in polar regions and pose that bioremediation by native microorganisms is a feasible strategy to mitigate the presence of SVOCs. Our systematic review revealed that microbial communities in polar environments represent a wide reservoir of biodiversity adapted to extreme conditions, found both in terrestrial and aquatic environments, freely or in association with vegetation. Microorganisms adapted to these environments have the potential for biodegradation of SVOCs through a variety of genes encoding enzymes with the capacity to metabolize SVOCs. We suggest that a comprehensive approach at the molecular and ecological level is required to mitigate SVOCs presence in these regions. This is especially patent when considering that SVOCs degrade at slow rates and possess the ability to accumulate in polar ecosystems. The implications of SVOC degradation are relevant for the preservation of polar ecosystems with consequences at a global level.
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Affiliation(s)
- Claudia Egas
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Instituto de Ciencias Biológicas (ICB), Universidad de Talca, Campus Lircay, Talca, Chile
| | - Cristóbal Galbán-Malagón
- Centro de Genómica, Ecología y Medio Ambiente (GEMA), Universidad Mayor, Campus Huechuraba, Santiago, Chile; Institute of Environment, Florida International University, University Park, Miami, FL 33199, USA
| | - Eduardo Castro-Nallar
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Lircay, Talca, Chile
| | - Marco A Molina-Montenegro
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Instituto de Ciencias Biológicas (ICB), Universidad de Talca, Campus Lircay, Talca, Chile; Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile.
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10
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Wang Y, Tian X, Song T, Jiang Z, Zhang G, He C, Li P. Linking DOM characteristics to microbial community: The potential role of DOM mineralization for arsenic release in shallow groundwater. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131566. [PMID: 37148792 DOI: 10.1016/j.jhazmat.2023.131566] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/23/2023] [Accepted: 05/02/2023] [Indexed: 05/08/2023]
Abstract
Dissolved organic matter (DOM) play critical roles in arsenic (As) biotransformation in groundwater, but its compositional characteristics and interactions with indigenous microbial communities remain unclear. In this study, DOM signatures coupled with taxonomy and functions of microbial community were characterized in As-enriched groundwater by excitation-emission matrix, Fourier transform ion cyclotron resonance mass spectrometry and metagenomic sequencing. Results showed that As concentrations were significantly positively correlated with DOM humification (r = 0.707, p < 0.01) and the most dominant humic acid-like DOM components (r = 0.789, p < 0.01). Molecular characterization further demonstrated high DOM oxidation degree, with the prevalence of unsaturated oxygen-low aromatics, nitrogen (N1/N2)-containing compounds and unique CHO molecules in high As groundwater. These DOM properties were consistent with microbial composition and functional potentials. Both taxonomy and binning analyses demonstrated the dominance of Pseudomonas stutzeri, Microbacterium and Sphingobium xenophagum in As-enriched groundwater which possessed abundant As-reducing gene, with organic carbon degrading genes capable of labile to recalcitrant compounds degradation and high potentials of organic nitrogen mineralization to generate ammonium. Besides, most assembled bins in high As groundwater presented strong fermentation potentials which could facilitate carbon utilization by heterotrophic microbes. This study provides better insight into the potential role of DOM mineralization for As release in groundwater system.
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Affiliation(s)
- Yanhong Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, PR China
| | - Xuege Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China
| | - Tenglong Song
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Zhou Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Guanglong Zhang
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, PR China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, PR China.
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11
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Xin Q, Saborimanesh N, Greer CW, Farooqi H, Dettman HD. The effect of temperature on hydrocarbon profiles and the microbial community composition in North Saskatchewan River water during mesoscale tank tests of diluted bitumen spills. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160161. [PMID: 36379338 DOI: 10.1016/j.scitotenv.2022.160161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/21/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Despite many studies of diluted bitumen (DB) behavior during spills in saltwater, limited information is available on DB behavior in fresh water. This study examined the collective weathering processes on changes of fresh DB spilled in the North Saskatchewan River water and sediment mixture in a mesoscale spill tank under average air/water temperatures of 14 °C/15 °C and 6 °C/2 °C. Temporal changes of the hydrocarbon and microbial community compositions in the water column were assessed during the two 35-day tests under intermittent wave action. The contents of total organic carbon (TOC), benzene/toluene/ethylbenzene/xylenes (BTEX) and polycyclic aromatic hydrocarbons (PAHs) in water decreased with time during both tests. The final contents remained at higher values in warm water (15 °C) than in cold water (2 °C) after the collective weathering processes. A quick response of the main phyla, Proteobacteria and Actinobacteria, was observed, where the members of Proteobacteria enriched during both DB spills. In contrast, the members of Actinobacteria reduced with time. The microbial shifts coincided with the changes of PAHs in the waters at both temperatures. A comparison of the physical properties and chemical compositions of fresh and weathered DBs at both temperatures showed that the oil had undergone weathering that increased oil density and viscosity due to losing the light oil fraction with boiling points < 204 °C and emulsifying with water. This corresponded to losses of 19.0 wt% and 17.2 wt% of the fresh DB at 15 °C and 2 °C tests, respectively. For organic compounds in the DB with boiling points > 204 °C, there were small losses of saturates and 2- & 3-ring PAH aromatics (more during the 15 °C test than the 2 °C test), and negligible losses in the subfractions of resins and asphaltenes by the ends of the tests. <1.0 wt% of the DB was recovered from the bottom sediment, regardless of the temperature.
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Affiliation(s)
- Qin Xin
- Natural Resources Canada (NRCan), CanmetENERGY, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada.
| | - Nayereh Saborimanesh
- Natural Resources Canada (NRCan), CanmetENERGY, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2, Canada; McGill University, Natural Resource Sciences, 21111 Lakeshore, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
| | - Hena Farooqi
- Natural Resources Canada (NRCan), CanmetENERGY, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
| | - Heather D Dettman
- Natural Resources Canada (NRCan), CanmetENERGY, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
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12
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Cappello S, Corsi I, Patania S, Bergami E, Azzaro M, Mancuso M, Genovese M, Lunetta A, Caruso G. Characterization of Five Psychrotolerant Alcanivorax spp. Strains Isolated from Antarctica. Microorganisms 2022; 11:microorganisms11010058. [PMID: 36677350 PMCID: PMC9861381 DOI: 10.3390/microorganisms11010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Five psychrotolerant Alcanivorax spp. strains were isolated from Antarctic coastal waters. Strains were screened for molecular and physiological properties and analyzed regarding their growth capacity. Partial 16S rDNA, alk-B1, and P450 gene sequencing was performed. Biolog EcoPlates and the API 20E test were used to evaluate metabolic and biochemical profiles. Bacterial growth in sodium acetate was determined at 4, 15, 20, and 25 °C to evaluate the optimal temperature. Furthermore, the ability of each strain to grow in a hydrocarbon mixture at 4 and 25 °C was assayed. Biosurfactant production tests (drop-collapse and oil spreading) and emulsification activity tests (E24) were also performed. Concerning results of partial gene sequencing (16S rDNA, alk-B1, and P450), a high similarity of the isolates with the same genes isolated from other Alcanivorax spp. strains was observed. The metabolic profiles obtained by Biolog assays showed no significant differences in the isolates compared to the Alcanivorax borkumensis wild type. The results of biodegradative tests showed their capability to grow at different temperatures. All strains showed biosurfactant production and emulsification activity. Our findings underline the importance to proceed in the isolation and characterization of Antarctic hydrocarbon-degrading bacterial strains since their biotechnological and environmental applications could be useful even for pollution remediation in polar areas.
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Affiliation(s)
- Simone Cappello
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (CNR-IRBIM), 98122 Messina, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, 53100 Siena, Italy
| | - Sabrina Patania
- PhD School in “Applied Biology and Experimental Medicine”, University of Messina, 98166 Messina, Italy
| | - Elisa Bergami
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council (CNR-ISP), 98122 Messina, Italy
| | - Monique Mancuso
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (CNR-IRBIM), 98122 Messina, Italy
| | - Maria Genovese
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (CNR-IRBIM), 98122 Messina, Italy
| | - Alessia Lunetta
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (CNR-IRBIM), 98122 Messina, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences, National Research Council (CNR-ISP), 98122 Messina, Italy
- Correspondence: ; Tel.: +39-090-6015423
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13
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Silva JB, Centurion VB, Duarte AWF, Galazzi RM, Arruda MAZ, Sartoratto A, Rosa LH, Oliveira VM. Unravelling the genetic potential for hydrocarbon degradation in the sediment microbiome of Antarctic islands. FEMS Microbiol Ecol 2022; 99:6847214. [PMID: 36427064 DOI: 10.1093/femsec/fiac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/08/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022] Open
Abstract
Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.
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Affiliation(s)
- Jéssica B Silva
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil.,Institute of Biology, UNICAMP, Zip code 13083-862, Campinas, São Paulo, Brazil
| | - Victor B Centurion
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil.,Institute of Biology, UNICAMP, Zip code 13083-862, Campinas, São Paulo, Brazil
| | - Alysson W F Duarte
- Federal University of Alagoas, Campus Arapiraca (UFAL), Zip code 57309-005, Araparica, Alagoas, Brazil
| | - Rodrigo M Galazzi
- Spectrometry, Sample Preparation and Mechanization Group (GEPAM), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas São Paulo, Brazil.,National Institute of Science and Technology for Bioanalytics (INCTBio), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas, São Paulo, Brazil
| | - Marco A Z Arruda
- Spectrometry, Sample Preparation and Mechanization Group (GEPAM), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas São Paulo, Brazil.,National Institute of Science and Technology for Bioanalytics (INCTBio), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas, São Paulo, Brazil
| | - Adilson Sartoratto
- Organic Chemistry and Pharmaceutical Division, Pluridisciplinary Research Center for Chemistry, Biology, and Agriculture (CPQBA), UNICAMP, Zip code 13081-970, Paulínia, São Paulo, Brazil
| | - Luiz H Rosa
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Zip code 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Valéria M Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil
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14
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Fathiah Mohamed Zuki, Pourzolfaghar H, Edyvean RGJ, Hernandez JE. Interpretation of Initial Adhesion of Pseudomonas putida on Hematite and Quartz Using Surface Thermodynamics, DLVO, and XDLVO Theories. SURFACE ENGINEERING AND APPLIED ELECTROCHEMISTRY 2022. [DOI: 10.3103/s1068375522050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Abbasi M, Kafilzadeh F, Sabokbar A, Haddadi A. Biodegradation of Phenanthrene Polluted Soil through Native Strains in the Darkhouvin Oil Field. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2097272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Maryam Abbasi
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Farshid Kafilzadeh
- Department of Biology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Azar Sabokbar
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Azam Haddadi
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
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16
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Boss BL, Wanees AE, Zaslow SJ, Normile TG, Izquierdo JA. Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata. BMC Genomics 2022; 23:508. [PMID: 35831788 PMCID: PMC9281055 DOI: 10.1186/s12864-022-08738-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Background The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biodegradation and bioremediation in sediments and sandy soils. A Sphingobium sp. isolate was obtained from the rhizosphere of the beachgrass Ammophila breviligulata with a variety of plant growth-promoting properties and designated as Sphingobium sp. strain AEW4. Results Analysis of the 16S rRNA gene as well as full genome nucleotide and amino acid identities revealed that this isolate is most similar to Sphingobium xenophagum and Sphingobium hydrophobicum. Comparative genomics analyses indicate that the genome of strain AEW4 contains unique features that explain its relationship with a plant host as a PGPR, including pathways involved in monosaccharide utilization, fermentation pathways, iron sequestration, and resistance to osmotic stress. Many of these unique features are not broadly distributed across the genus. In addition, pathways involved in the metabolism of salicylate and catechol, phenyl acetate degradation, and DNA repair were also identified in this organism but not in most closely related organisms. Conclusion The genome of Sphingobium sp. strain AEW4 contains a number of distinctive features that are crucial to explain its role as a plant-growth promoting rhizobacterium, and comparative genomics analyses support its classification as a relevant Sphingobium strain involved in plant growth promotion of beachgrass and other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08738-8.
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Affiliation(s)
- Brianna L Boss
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Abanoub E Wanees
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Shari J Zaslow
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Tyler G Normile
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
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17
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The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel. NPJ Biofilms Microbiomes 2022; 8:32. [PMID: 35484166 PMCID: PMC9050737 DOI: 10.1038/s41522-022-00299-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 04/04/2022] [Indexed: 11/08/2022] Open
Abstract
Bioprospecting of microorganisms suitable for bioremediation of fuel or oil spills is often carried out in contaminated environments such as gas stations or polluted coastal areas. Using next-generation sequencing (NGS) we analyzed the microbiota thriving below the lids of the fuel deposits of diesel and gasoline cars. The microbiome colonizing the tank lids differed from the diversity found in other hydrocarbon-polluted environments, with Proteobacteria being the dominant phylum and without clear differences between gasoline or diesel-fueled vehicles. We observed differential growth when samples were inoculated in cultures with gasoline or diesel as the main carbon source, as well as an increase in the relative abundance of the genus Pseudomonas in diesel. A collection of culturable strains was established, mostly Pseudomonas, Stenotrophomonas, Staphylococcus, and Bacillus genera. Strains belonging to Bacillus, Pseudomonas, Achromobacter, and Isoptericola genera showed a clear diesel degradation pattern when analyzed by GC-MS, suggesting their potential use for bioremediation and a possible new species of Isoptericola was further characterized as hydrocarbon degrader.
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18
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Mezzasoma A, Coleine C, Sannino C, Selbmann L. Endolithic Bacterial Diversity in Lichen-Dominated Communities Is Shaped by Sun Exposure in McMurdo Dry Valleys, Antarctica. MICROBIAL ECOLOGY 2022; 83:328-339. [PMID: 34081148 PMCID: PMC8891110 DOI: 10.1007/s00248-021-01769-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.
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Affiliation(s)
- Ambra Mezzasoma
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
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19
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Behera BK, Dehury B, Rout AK, Patra B, Mantri N, Chakraborty HJ, Sarkar DJ, Kaushik NK, Bansal V, Singh I, Das BK, Rao AR, Rai A. Metagenomics study in aquatic resource management: Recent trends, applied methodologies and future needs. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Ausuri J, Vitale GA, Coppola D, Palma Esposito F, Buonocore C, de Pascale D. Assessment of the Degradation Potential and Genomic Insights towards Phenanthrene by Dietzia psychralcaliphila JI1D. Microorganisms 2021; 9:microorganisms9061327. [PMID: 34205451 PMCID: PMC8235520 DOI: 10.3390/microorganisms9061327] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Extreme marine environments are potential sources of novel microbial isolations with dynamic metabolic activity. Dietzia psychralcaliphila J1ID was isolated from sediments originated from Deception Island, Antarctica, grown over phenanthrene. This strain was also assessed for its emulsifying activity. In liquid media, Dietzia psychralcaliphila J1ID showed 84.66% degradation of phenanthrene examined with HPLC-PDA. The identification of metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 4,216,480 bp with 3961 annotated genes. The presence of a wide range of monooxygenase and dioxygenase, as well as dehydrogenase catabolic genes provided the genomic basis for the biodegradation. The strain possesses the genetic compartments for a wide range of toxic aromatic compounds, which includes the benABCD and catABC clusters. COG2146, COG4638, and COG0654 through COG analysis confirmed the genes involved in the oxygenation reaction of the hydrocarbons by the strain. Insights into assessing the depletion of phenanthrene throughout the incubation process and the genetic components involved were obtained. This study indicates the degradation potential of the strain, which can also be further expanded to other model polyaromatic hydrocarbons.
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Affiliation(s)
- Janardhan Ausuri
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy; (J.A.); (C.B.)
| | - Giovanni Andrea Vitale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
| | - Daniela Coppola
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
| | - Fortunato Palma Esposito
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
| | - Carmine Buonocore
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy; (J.A.); (C.B.)
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
| | - Donatella de Pascale
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy; (J.A.); (C.B.)
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
- Correspondence: ; Tel.: +39-081-5833-319
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21
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Yap HS, Zakaria NN, Zulkharnain A, Sabri S, Gomez-Fuentes C, Ahmad SA. Bibliometric Analysis of Hydrocarbon Bioremediation in Cold Regions and a Review on Enhanced Soil Bioremediation. BIOLOGY 2021; 10:biology10050354. [PMID: 33922046 PMCID: PMC8143585 DOI: 10.3390/biology10050354] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Anthropogenic activities in cold regions require petroleum oils to support various purposes. With the increased demand of petroleum, accidental oil spills are generated during transportation or refuelling processes. Soil is one of the major victims in petroleum pollution, hence studies have been devoted to find solutions to remove these petroleum hydrocarbons. However, the remote and low-temperature conditions in cold regions hindered the implementation of physical and chemical removal treatments. On the other hand, biological treatments in general have been proposed as an innovative approach to attenuate these hydrocarbon pollutants in soils. To understand the relevancy of biological treatments for cold regions specifically, bibliometric analysis has been applied to systematically analyse studies focused on hydrocarbon removal treatment in a biological way. To expedite the understanding of this analysis, we have summarised these biological treatments and suggested other biological applications in the context of cold conditions. Abstract The increased usage of petroleum oils in cold regions has led to widespread oil pollutants in soils. The harsh environmental conditions in cold environments allow the persistence of these oil pollutants in soils for more than 20 years, raising adverse threats to the ecosystem. Microbial bioremediation was proposed and employed as a cost-effective tool to remediate petroleum hydrocarbons present in soils without significantly posing harmful side effects. However, the conventional hydrocarbon bioremediation requires a longer time to achieve the clean-up standard due to various environmental factors in cold regions. Recent biotechnological improvements using biostimulation and/or bioaugmentation strategies are reported and implemented to enhance the hydrocarbon removal efficiency under cold conditions. Thus, this review focuses on the enhanced bioremediation for hydrocarbon-polluted soils in cold regions, highlighting in situ and ex situ approaches and few potential enhancements via the exploitation of molecular and microbial technology in response to the cold condition. The bibliometric analysis of the hydrocarbon bioremediation research in cold regions is also presented.
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Affiliation(s)
- How Swen Yap
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
| | - Nur Nadhirah Zakaria
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence:
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22
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Sineli PE, Herrera HM, Aparicio JD, Guerrero DS, Polti MA, Dávila Costa JS. Genomic analysis and proteomic response of the chromium-resistant and phenanthrene-degrading strain Streptomyces sp. MC1. J Appl Microbiol 2021; 131:719-727. [PMID: 33434397 DOI: 10.1111/jam.15002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/26/2020] [Accepted: 01/08/2021] [Indexed: 11/28/2022]
Abstract
AIM Chemically disparate toxic organic and/or inorganic molecules produced by anthropogenic activities often hinder the bioremediation process. This research was conducted to understand the capacity of Streptomyces sp. MC1 to remove chemically disparate toxics such as Cr(VI) or phenanthrene. METHODS AND RESULTS Genomic, metabolic modeling and proteomic approaches were used in this study. Our results demonstrated that Streptomyces sp. MC1 has the genetic determinants to remove Cr(VI) or degrade phenanthrene. Proteomics showed that these genetic determinants were expressed. Metabolic versatility of the strain was confirmed by two metabolic models in complex and minimal media. Interestingly, our results also suggested a connection between the degradation of phenanthrene and synthesis of specialized metabolites. CONCLUSIONS Streptomyces sp. MC1 has the genetic and physiological potential to remove Cr(VI) or degrade phenanthrene SIGNIFICANCE AND IMPACT OF STUDY: The probability of a microorganism to survive in the presence of different contaminants depends on its genetic potential and the ability to express it. The genetic and proteomic profiles obtained for Streptomyces sp. MC1 can be recommended as model and predict if other Streptomyces strains can be used in bioremediation processes. Our work also hypothesized that intermediates of the phenanthrene degradation serve as precursors for the specialized metabolism.
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Affiliation(s)
- P E Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| | - H M Herrera
- Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - J D Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina.,Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - D S Guerrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| | - M A Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina.,Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - J S Dávila Costa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
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Verasoundarapandian G, Wong CY, Shaharuddin NA, Gomez-Fuentes C, Zulkharnain A, Ahmad SA. A Review and Bibliometric Analysis on Applications of Microbial Degradation of Hydrocarbon Contaminants in Arctic Marine Environment at Metagenomic and Enzymatic Levels. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:1671. [PMID: 33572432 PMCID: PMC7916232 DOI: 10.3390/ijerph18041671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/20/2022]
Abstract
The globe is presently reliant on natural resources, fossil fuels, and crude oil to support the world's energy requirements. Human exploration for oil resources is always associated with irreversible effects. Primary sources of hydrocarbon pollution are instigated through oil exploration, extraction, and transportation in the Arctic region. To address the state of pollution, it is necessary to understand the mechanisms and processes of the bioremediation of hydrocarbons. The application of various microbial communities originated from the Arctic can provide a better interpretation on the mechanisms of specific microbes in the biodegradation process. The composition of oil and consequences of hydrocarbon pollutants to the various marine environments are also discussed in this paper. An overview of emerging trends on literature or research publications published in the last decade was compiled via bibliometric analysis in relation to the topic of interest, which is the microbial community present in the Arctic and Antarctic marine environments. This review also presents the hydrocarbon-degrading microbial community present in the Arctic, biodegradation metabolic pathways (enzymatic level), and capacity of microbial degradation from the perspective of metagenomics. The limitations are stated and recommendations are proposed for future research prospects on biodegradation of oil contaminants by microbial community at the low temperature regions of the Arctic.
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Affiliation(s)
| | - Chiew-Yen Wong
- School of Health Sciences, International Medical University, Kuala Lumpur 57000, Malaysia;
- National Antarctic Research Center, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (G.V.); (N.A.S.)
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama-shi 337-8570, Saitama, Japan;
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (G.V.); (N.A.S.)
- National Antarctic Research Center, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile
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24
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Sakdapetsiri C, Kuntaveesuk A, Ngaemthao W, Suriyachadkun C, Muangchinda C, Chavanich S, Viyakarn V, Chen B, Pinyakong O. Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33555249 DOI: 10.1099/ijsem.0.004689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated strain ANT13_2T, was isolated from a phenanthrene-degrading consortium enriched from a soil sample collected near the Great Wall Station located in the southwestern area of King George Island, Antarctica. Following a polyphasic taxonomic study, a novel species belonging to the genus Paeniglutamicibacter was described. The strain was a Gram-stain-positive bacterium that exhibited a rod-coccus growth cycle. Strain ANT13_2T grew aerobically at an optimum temperature of 20-25 °C and at pH 7.0-8.0. Ribose, arabinose and glucose were detected as whole-cell sugars. The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C15 : 0 (67.7 %) and anteiso-C17 : 0 (11.2 %). The DNA G+C content of the genomic DNA was 60.6 mol%. Based on 16S rRNA gene sequence analysis, strain ANT13_2T showed the highest similarities to Paeniglutamicibacter antarcticus SPC26T (98.9 %) followed by Paeniglutamicibacter gangotriensis Lz1yT (98.4 %), Paeniglutamicibacter sulfureus DSM 20167T (98.3%) and Paeniglutamicibacter kerguelensis KGN15T (97.9 %). The average nucleotide identity values between strain ANT13_2T and the type strains of P. antarcticus SPC26T and P. gangotriensis Lz1yT were 73.8 and 77.5 %, respectively, which are well below the 95-96 % species circumscription threshold. On the basis of this polyphasic taxonomic study, strain ANT13_2T is proposed to represent a novel species to be named Paeniglutamicibacter terrestris sp. nov. The type strain is ANT13_2T (=TBRC 11756T=NBRC 114615T).
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Affiliation(s)
- Chatsuda Sakdapetsiri
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aunchisa Kuntaveesuk
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wipaporn Ngaemthao
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chanwit Suriyachadkun
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chanokporn Muangchinda
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suchana Chavanich
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Voranop Viyakarn
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Bo Chen
- Key Laboratory of Polar Science, MNR, Polar Research Institute of China, Shanghai, 200136, PR China
| | - Onruthai Pinyakong
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok 10330, Thailand
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25
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Wong RR, Lim ZS, Shaharuddin NA, Zulkharnain A, Gomez-Fuentes C, Ahmad SA. Diesel in Antarctica and a Bibliometric Study on Its Indigenous Microorganisms as Remediation Agent. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041512. [PMID: 33562609 PMCID: PMC7915771 DOI: 10.3390/ijerph18041512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/03/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Diesel acts as a main energy source to complement human activities in Antarctica. However, the increased expedition in Antarctica has threatened the environment as well as its living organisms. While more efforts on the use of renewable energy are being done, most activities in Antarctica still depend heavily on the use of diesel. Diesel contaminants in their natural state are known to be persistent, complex and toxic. The low temperature in Antarctica worsens these issues, making pollutants more significantly toxic to their environment and indigenous organisms. A bibliometric analysis had demonstrated a gradual increase in the number of studies on the microbial hydrocarbon remediation in Antarctica over the year. It was also found that these studies were dominated by those that used bacteria as remediating agents, whereas very little focus was given on fungi and microalgae. This review presents a summary of the collective and past understanding to the current findings of Antarctic microbial enzymatic degradation of hydrocarbons as well as its genotypic adaptation to the extreme low temperature.
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Affiliation(s)
- Rasidnie Razin Wong
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Zheng Syuen Lim
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, Shibaura Institute of Technology, College of Systems Engineering and Science, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile
- National Antarctic Research Centre, Universiti Malaya B303 Level 3, Block B, IPS Building, Kuala Lumpur 50603, Malaysia
- Correspondence:
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26
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Bioremediation of Diesel Contaminated Marine Water by Bacteria: A Review and Bibliometric Analysis. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9020155] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oil pollution can cause tremendous harm and risk to the water ecosystem and organisms due to the relatively recalcitrant hydrocarbon compounds. The current chemical method used to treat the ecosystem polluted with diesel is incompetent and expensive for a large-scale treatment. Thus, bioremediation technique seems urgent and requires more attention to solve the existing environmental problems. Biological agents, including microorganisms, carry out the biodegradation process where organic pollutants are mineralized into water, carbon dioxide, and less toxic compounds. Hydrocarbon-degrading bacteria are ubiquitous in the nature and often exploited for their specialty to bioremediate the oil-polluted area. The capability of these bacteria to utilize hydrocarbon compounds as a carbon source is the main reason behind their species exploitation. Recently, microbial remediation by halophilic bacteria has received many positive feedbacks as an efficient pollutant degrader. These halophilic bacteria are also considered as suitable candidates for bioremediation in hypersaline environments. However, only a few microbial species have been isolated with limited available information on the biodegradation of organic pollutants by halophilic bacteria. The fundamental aspect for successful bioremediation includes selecting appropriate microbes with a high capability of pollutant degradation. Therefore, high salinity bacteria are remarkable microbes for diesel degradation. This paper provides an updated overview of diesel hydrocarbon degradation, the effects of oil spills on the environment and living organisms, and the potential role of high salinity bacteria to decontaminate the organic pollutants in the water environment.
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27
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Ahmad F, Zhu D, Sun J. Bacterial chemotaxis: a way forward to aromatic compounds biodegradation. ENVIRONMENTAL SCIENCES EUROPE 2020; 32:52. [DOI: 10.1186/s12302-020-00329-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/23/2020] [Indexed: 07/23/2024]
Abstract
AbstractWorldwide industrial development has released hazardous polycyclic aromatic compounds into the environment. These pollutants need to be removed to improve the quality of the environment. Chemotaxis mechanism has increased the bioavailability of these hydrophobic compounds to microorganisms. The mechanism, however, is poorly understood at the ligand and chemoreceptor interface. Literature is unable to furnish a compiled review of already published data on up-to-date research on molecular aspects of chemotaxis mechanism, ligand and receptor-binding mechanism, and downstream signaling machinery. Moreover, chemotaxis-linked biodegradation of aromatic compounds is required to understand the chemotaxis role in biodegradation better. To fill this knowledge gap, the current review is an attempt to cover PAHs occurrence, chemical composition, and potential posed risks to humankind. The review will cover the aspects of microbial signaling mechanism, the structural diversity of methyl-accepting chemotaxis proteins at the molecular level, discuss chemotaxis mechanism role in biodegradation of aromatic compounds in model bacterial genera, and finally conclude with the potential of bacterial chemotaxis for aromatics biodegradation.
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Gran-Scheuch A, Ramos-Zuñiga J, Fuentes E, Bravo D, Pérez-Donoso JM. Effect of Co-contamination by PAHs and Heavy Metals on Bacterial Communities of Diesel Contaminated Soils of South Shetland Islands, Antarctica. Microorganisms 2020; 8:microorganisms8111749. [PMID: 33171767 PMCID: PMC7695015 DOI: 10.3390/microorganisms8111749] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 01/04/2023] Open
Abstract
Diesel oil is the main source of energy used in Antarctica. Since diesel is composed of toxic compounds such as polycyclic aromatic hydrocarbons (PAHs) and heavy metals, it represents a constant threat to the organisms inhabiting this continent. In the present study, we characterized the chemical and biological parameters of diesel-exposed soils obtained from King George Island in Antarctica. Contaminated soils present PAH concentrations 1000 times higher than non-exposed soils. Some contaminated soil samples also exhibited high concentrations of cadmium and lead. A 16S metagenome analysis revealed the effect of co-contamination on bacterial communities. An increase in the relative abundance of bacteria known as PAH degraders or metal resistant was determined in co-contaminated soils. Accordingly, the soil containing higher amounts of PAHs exhibited increased dehydrogenase activity than control soils, suggesting that the microorganisms present can metabolize diesel. The inhibitory effect on soil metabolism produced by cadmium was lower in diesel-contaminated soils. Moreover, diesel-contaminated soils contain higher amounts of cultivable heterotrophic, cadmium-tolerant, and PAH-degrading bacteria than control soils. Obtained results indicate that diesel contamination at King George island has affected microbial communities, favoring the presence of microorganisms capable of utilizing PAHs as a carbon source, even in the presence of heavy metals.
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Affiliation(s)
- Alejandro Gran-Scheuch
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica # 330, Santiago 8370146, Chile; (A.G.-S.); (J.R.-Z.)
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone Pohlhammer # 1007, Santiago 8380000, Chile;
| | - Javiera Ramos-Zuñiga
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica # 330, Santiago 8370146, Chile; (A.G.-S.); (J.R.-Z.)
| | - Edwar Fuentes
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone Pohlhammer # 1007, Santiago 8380000, Chile;
| | - Denisse Bravo
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Sergio Livingstone Pohlhammer # 943, Santiago 8380453, Chile;
| | - José M. Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica # 330, Santiago 8370146, Chile; (A.G.-S.); (J.R.-Z.)
- Correspondence:
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29
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Mishra A, Rathour R, Singh R, Kumari T, Thakur IS. Degradation and detoxification of phenanthrene by actinobacterium Zhihengliuella sp. ISTPL4. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:27256-27267. [PMID: 31172432 DOI: 10.1007/s11356-019-05478-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are universal environmental contaminants of great concern with regard to their potential exposure and deleterious effect on human health. The current study is the first report of phenanthrene degradation by a psychrotolerant (15 °C), halophilic (5% NaCl), and alkalophilic (pH 8) bacterial strain Zhihengliuella sp. ISTPL4, isolated from the sediment sample of the Pangong Lake, Ladakh, Jammu and Kashmir, India. Degradation studies revealed that the optimum specific growth rate was observed at 250 ppm of phenanthrene with 81% and 87% removal of phenanthrene in 72 h and 168 h, respectively. During the degradation of phenanthrene; 9,10-dihydrophenanthrene; 1-phenanthrenecarboxylic acid; and phthalic acid were detected as intermediates. Whole-genome sequencing of strain ISTPL4 has predicted phenanthrene; 9,10-monooxygense; and epoxide hydrolase B that are involved in the phenanthrene metabolism. Phenanthrene cytotoxicity was evaluated with human hepatic carcinoma cell line (HepG2) and it was observed that the cytotoxicity decreased with increased duration of bacterial incubation and maximum cell viability was observed at 168 h (89.92%). Our results suggest, Zhihengliuella sp. ISTPL4 may promise a great potential for environmental remediation applications.
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Affiliation(s)
- Arti Mishra
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rashmi Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Taruna Kumari
- Department of Statistics, University of Delhi, New Delhi, 110007, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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30
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Cabrera MÁ, Márquez SL, Quezada CP, Osorio MI, Castro-Nallar E, González-Nilo FD, Pérez-Donoso JM. Biotransformation of 2,4,6-Trinitrotoluene by Pseudomonas sp. TNT3 isolated from Deception Island, Antarctica. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:113922. [PMID: 32443190 DOI: 10.1016/j.envpol.2020.113922] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 12/11/2019] [Accepted: 01/05/2020] [Indexed: 06/11/2023]
Abstract
2,4,6-Trinitrotoluene (TNT) is a nitroaromatic explosive, highly toxic and mutagenic for organisms. In this study, we report for the first time the screening and isolation of TNT-degrading bacteria from Antarctic environmental samples with potential use as bioremediation agents. Ten TNT-degrading bacterial strains were isolated from Deception Island. Among them, Pseudomonas sp. TNT3 was selected as the best candidate since it showed the highest tolerance, growth, and TNT biotransformation capabilities. Our results showed that TNT biotransformation involves the reduction of the nitro groups. Additionally, Pseudomonas sp. TNT3 was capable of transforming 100 mg/L TNT within 48 h at 28 °C, showing higher biotransformation capability than Pseudomonas putida KT2440, a known TNT-degrading bacterium. Functional annotation of Pseudomonas sp. TNT3 genome revealed a versatile set of molecular functions involved in xenobiotic degradation pathways. Two putative xenobiotic reductases (XenA_TNT3 and XenB_TNT3) were identified by means of homology searches and phylogenetic relationships. These enzymes were also characterized at molecular level using homology modelling and molecular dynamics simulations. Both enzymes share different levels of sequence similarity with other previously described TNT-degrading enzymes and with their closest potential homologues in databases.
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Affiliation(s)
- Ma Ángeles Cabrera
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Sebastián L Márquez
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Carolina P Quezada
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Manuel I Osorio
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Fernando D González-Nilo
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - José M Pérez-Donoso
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile.
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31
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Yin C, Xiong W, Qiu H, Peng W, Deng Z, Lin S, Liang R. Characterization of the Phenanthrene-Degrading Sphingobium yanoikuyae SJTF8 in Heavy Metal Co-Existing Liquid Medium and Analysis of Its Metabolic Pathway. Microorganisms 2020; 8:E946. [PMID: 32586023 PMCID: PMC7355620 DOI: 10.3390/microorganisms8060946] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 01/27/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are common organic pollutants with great carcinogenic threaten, and metal/PAH-contaminated environments represent one of the most difficult remedial challenges. In this work, Sphingobium yanoikuyae SJTF8 was isolated and identified with great and stable PAH-degrading efficiency even under stress conditions. It could utilize typical PAHs (naphthalene, phenanthrene, and anthracene) and heterocyclic and halogenated aromatic compounds (dibenzothiophene and 9-bromophenanthrene) as the sole carbon source. It could degrade over 98% of 500 mg/L phenanthrene in 4 days, and the cis-3,4-dihydrophenanthrene-3,4-diol was the first-step intermediate. Notably, strain SJTF8 showed great tolerance to heavy metals and acidic pH. Supplements of 0.30 mM of Cu2+, 1.15 mM of Zn2+, and 0.01 mM of Cd2+ had little effect on its cell growth and phenanthrene degradation; phenanthrene of 250 mg/L could still be degraded completely in 48 h. Further, the whole genome sequence of S. yanoikuyae SJTF8 was obtained, and three plasmids were found. The potential genes participating in stress-tolerance and PAH-degradation were annotated and were found mostly distributed in plasmids 1 and 2. Elimination of plasmid 2 resulted in the loss of the PAH-degradation ability. On the basis of genome mining results, the possible degrading pathway and the metabolites of S. yanoikuyae SJTF8 to phenanthrene were predicted.
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Affiliation(s)
| | | | | | | | | | | | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (C.Y.); (W.X.); (H.Q.); (W.P.); (Z.D.); (S.L.)
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32
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Sharma M, Nandy A, Taylor N, Venkatesan SV, Ozhukil Kollath V, Karan K, Thangadurai V, Tsesmetzis N, Gieg LM. Bioelectrochemical remediation of phenanthrene in a microbial fuel cell using an anaerobic consortium enriched from a hydrocarbon-contaminated site. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:121845. [PMID: 31862354 DOI: 10.1016/j.jhazmat.2019.121845] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/15/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAH) are organic pollutants that require remediation due to their detrimental impact on human and environmental health. In this study, we used a novel approach of sequestering a model PAH, phenanthrene, onto a solid carbon matrix bioanode in a microbial fuel cell (MFC) to assess its biodegradation coupled with power generation. Here, the bioanode serves as a site for enrichment of electroactive and hydrocarbon-degrading microorganisms, which can simultaneously act to biodegrade a pollutant and generate power. Carbon cloth electrodes loaded with two rates of phenanthrene (2 and 20 mg cm-2) were compared using dual chamber MFCs that were operated for 50 days. The lower loading rate of 2 mg cm-2 was most efficient in the degradation of phenanthrene and had higher power production capacities (37 mW m-2) as compared to the higher loading rate of 20 mg cm-2 (power production of 19.2 mW m-2). FTIR (Fourier-Transform Infrared Spectroscopy) analyses showed a depletion in absorbance peak signals associated with phenanthrene. Microbes known to have electroactive properties or phenanthrene biodegradation abilities like Pseudomonas, Rhodococcus, Thauera and Ralstonia were enriched over time in the MFCs, substantiating the electrochemical and FTIR analyses. The MFC approach taken here thus offers great promise towards PAH bioelectroremediation.
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Affiliation(s)
- Mohita Sharma
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Arpita Nandy
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Nicole Taylor
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Senthil Velan Venkatesan
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Vinayaraj Ozhukil Kollath
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Kunal Karan
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Venkataraman Thangadurai
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., 3333 Highway 6 South, Houston, Texas, 77251-7171, USA
| | - Lisa M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
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Ji D, Mao Z, He J, Peng S, Wen H. Characterization and genomic function analysis of phenanthrene-degrading bacterium Pseudomonas sp. Lphe-2. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 55:549-562. [PMID: 31913782 DOI: 10.1080/10934529.2019.1711352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 12/24/2019] [Accepted: 12/28/2019] [Indexed: 06/10/2023]
Abstract
A stain of Pseudomonas sp. Lphe-2, which could degrade phenanthrene as the main carbon and energy source, was isolated from the aerobic sludge of a coking plant. Then its biodegradation characteristics, whole genome sequence and biodegradation pathway were examined. The Lphe-2 strain exhibited broad-spectrum degradation activities for various polycyclic aromatic hydrocarbons (PAHs), including naphthalene (NAP), phenanthrene (PHE), and pyrene (PYR). Under the optimal conditions, the degradation efficiency of phenanthrene (100 mg/L) is 92.76% on the 7th day, and 2-carboxybenzaldehyde and 1-hydroxy-2-naphthoic acid are the major metabolites found in phenanthrene metabolism. Genomic analysis of Pseudomonas sp. Lphe-2 showed that a total of 3879 genes from the Lphe-2 strain were annotated based on the COG classification, and the genomic information was annotated to 185 metabolic pathways. Based on the intermediate metabolites detected by Gas Chromatography-Mass Spectrometer (GC-MS) and all potential phenanthrene-degrading genes identified by BLAST search, a phenanthrene biodegradation pathway of Lphe-2 strain was proposed. These results suggested that Lphe-2 strain has a good prospect in the bioremediation of PAHs pollution.
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Affiliation(s)
- Dan Ji
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, Jiangsu, China
| | - Zhen Mao
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, Jiangsu, China
| | - Jian He
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, Jiangsu, China
| | - Sihan Peng
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, Jiangsu, China
| | - Hongyu Wen
- School of life Sciences, Jiangsu Normal University, Xuzhou, China
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Sharma Ghimire P, Tripathee L, Zhang Q, Guo J, Ram K, Huang J, Sharma CM, Kang S. Microbial mercury methylation in the cryosphere: Progress and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134150. [PMID: 32380618 DOI: 10.1016/j.scitotenv.2019.134150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 06/11/2023]
Abstract
Mercury (Hg) is one of the most toxic heavy metals, and its cycle is mainly controlled by oxidation-reduction reactions carried out by photochemical or microbial process under suitable conditions. The deposition and accumulation of methylmercury (MeHg) in various ecosystems, including the cryospheric components such as snow, meltwater, glaciers, and ice sheet, and subsequently in the food chain pose serious health concerns for living beings. Unlike the abundance of knowledge about the processes of MeHg production over land and oceans, little is known about the sources and production/degradation rate of MeHg in cryosphere systems. In addition, processes controlling the concentration of Hg and MeHg in the cryosphere remains poorly understood, and filling this scientific gap has been challenging. Therefore, it is essential to study and review the deposition and accumulation by biological, physical, and chemical mechanisms involved in Hg methylation in the cryosphere. This review attempts to address knowledge gaps in understanding processes, especially biotic and abiotic, applicable for Hg methylation in the cryosphere. First, we focus on the variability in Hg concentration and mechanisms of Hg methylation, including physical, chemical, microbial, and biological processes, and transportation in the cryosphere. Then, we elaborate on the mechanism of redox reactions and biotic and abiotic factors controlling Hg methylation and biogeochemistry of Hg in the cryosphere. We also present possible mechanisms of Hg methylation with an emphasis on microbial transformation and molecular function to understand variability in Hg concentration in the cryosphere. Recent advancements in the genetic and physicochemical mechanisms of Hg methylation are also presented. Finally, we summarize and propose a method to study the unsolved issues of Hg methylation in the cryosphere.
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Affiliation(s)
- Prakriti Sharma Ghimire
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; Himalayan Environment Research Institute (HERI), Kathmandu, Nepal
| | - Lekhendra Tripathee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; Himalayan Environment Research Institute (HERI), Kathmandu, Nepal.
| | - Qianggong Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China
| | - Junming Guo
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Kirpa Ram
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Jie Huang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China; Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Chhatra Mani Sharma
- Himalayan Environment Research Institute (HERI), Kathmandu, Nepal; Central Department of Environmental Science, Tribhuvan University, Kathmandu, Nepal
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China.
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35
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Farber R, Rosenberg A, Rozenfeld S, Banet G, Cahan R. Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste. Microorganisms 2019; 7:E497. [PMID: 31661854 PMCID: PMC6921085 DOI: 10.3390/microorganisms7110497] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/19/2019] [Accepted: 10/26/2019] [Indexed: 11/16/2022] Open
Abstract
Bioaugmentation is a bioremediation option based on increasing the natural in-situ microbial population that possesses the ability to degrade the contaminating pollutant. In this study, a diesel-degrading consortium was obtained from an oil-contaminated soil. The diesel-degrading consortium was grown on wood waste that was plasma-pretreated. This plasma treatment led to an increase of bacterial attachment and diesel degradation rates. On the 7th day the biofilm viability on the plasma-treated wood waste reached 0.53 ± 0.02 OD 540 nm, compared to the non-treated wood waste which was only 0.34 ± 0.02. Biofilm attached to plasma-treated and untreated wood waste which was inoculated into artificially diesel-contaminated soil (0.15% g/g) achieved a degradation rate of 9.3 mg day-1 and 7.8 mg day-1, respectively. While, in the soil that was inoculated with planktonic bacteria, degradation was only 5.7 mg day-1. Exposing the soil sample to high temperature (50 °C) or to different soil acidity did not influence the degradation rate of the biofilm attached to the plasma-treated wood waste. The two most abundant bacterial distributions at the family level were Xanthomonadaceae and Sphingomonadaceae. To our knowledge, this is the first study that showed the advantages of biofilm attached to plasma-pretreated wood waste for diesel biodegradation in soil.
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Affiliation(s)
- Ravit Farber
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Alona Rosenberg
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Shmuel Rozenfeld
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Gabi Banet
- Dead Sea-Arava Science Center, Arava 86910, Israel.
| | - Rivka Cahan
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
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Park H, Min B, Jang Y, Kim J, Lipzen A, Sharma A, Andreopoulos B, Johnson J, Riley R, Spatafora JW, Henrissat B, Kim KH, Grigoriev IV, Kim JJ, Choi IG. Comprehensive genomic and transcriptomic analysis of polycyclic aromatic hydrocarbon degradation by a mycoremediation fungus, Dentipellis sp. KUC8613. Appl Microbiol Biotechnol 2019; 103:8145-8155. [DOI: 10.1007/s00253-019-10089-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/06/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022]
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Rego A, Raio F, Martins TP, Ribeiro H, Sousa AGG, Séneca J, Baptista MS, Lee CK, Cary SC, Ramos V, Carvalho MF, Leão PN, Magalhães C. Actinobacteria and Cyanobacteria Diversity in Terrestrial Antarctic Microenvironments Evaluated by Culture-Dependent and Independent Methods. Front Microbiol 2019; 10:1018. [PMID: 31214128 PMCID: PMC6555387 DOI: 10.3389/fmicb.2019.01018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with the development of High Throughput Sequencing (HTS) techniques. However, some of the diversity remains inaccessible by the power of sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria and cyanobacteria diversity along different soil and endolithic micro-environments of Victoria Valley in McMurdo Dry Valleys. Our results demonstrate that the Dry Valleys actinobacteria and cyanobacteria distribution is driven by environmental forces, in particular the effect of water availability and endolithic environments clearly conditioned the distribution of those communities. Data derived from HTS show that the percentage of cyanobacteria decreases from about 20% in the sample closest to the water source to negligible values on the last three samples of the transect with less water availability. Inversely, actinobacteria relative abundance increases from about 20% in wet soils to over 50% in the driest samples. Over 30% of the total HTS data set was composed of actinobacterial strains, mainly distributed by 5 families: Sporichthyaceae, Euzebyaceae, Patulibacteraceae, Nocardioidaceae, and Rubrobacteraceae. However, the 11 actinobacterial strains isolated in this study, belonged to Micrococcaceae and Dermacoccaceae families that were underrepresented in the HTS data set. A total of 10 cyanobacterial strains from the order Synechococcales were also isolated, distributed by 4 different genera (Nodosilinea, Leptolyngbya, Pectolyngbya, and Acaryochloris-like). In agreement with the cultivation results, Leptolyngbya was identified as dominant genus in the HTS data set. Acaryochloris-like cyanobacteria were found exclusively in the endolithic sample and represented 44% of the total 16S rRNA sequences, although despite our efforts we were not able to properly isolate any strain from this Acaryochloris-related group. The importance of combining cultivation and sequencing techniques is highlighted, as we have shown that culture-dependent methods employed in this study were able to retrieve actinobacteria and cyanobacteria taxa that were not detected in HTS data set, suggesting that the combination of both strategies can be usefull to recover both abundant and rare members of the communities.
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Affiliation(s)
- Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Francisco Raio
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Teresa P Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Hugo Ribeiro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - António G G Sousa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Joana Séneca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Mafalda S Baptista
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand.,School of Science, University of Waikato, Hamilton, New Zealand
| | - S Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand.,School of Science, University of Waikato, Hamilton, New Zealand
| | - Vitor Ramos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Maria F Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Pedro N Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal
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Liu XX, Hu X, Cao Y, Pang WJ, Huang JY, Guo P, Huang L. Biodegradation of Phenanthrene and Heavy Metal Removal by Acid-Tolerant Burkholderia fungorum FM-2. Front Microbiol 2019; 10:408. [PMID: 30930861 PMCID: PMC6427951 DOI: 10.3389/fmicb.2019.00408] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/18/2019] [Indexed: 11/13/2022] Open
Abstract
Phenanthrene (PHE) is a common pollutant of acidic and non-acidic environments that is recalcitrant to biodegradation. Herein, Burkholderia fungorum FM-2 (GenBank accession no. KM263605) was isolated from oil-contaminated soil in Xinjiang and characterized morphologically, physiologically, and phylogenetically. Environmental parameters including PHE concentration, pH, temperature, and salinity were optimized, and heavy metal tolerance was investigated. The MIC of strain FM-2 tolerant to Pb(II) and Cd(II) was 50 and 400 mg L−1, respectively, while the MIC of Zn(II) was >1,200 mg L−1. Atypically for a B. fungorum strain, FM-2 utilized PHE (300 mg L−1) as a sole carbon source over a wide pH range (between pH 3 and 9). PHE and heavy metal metabolism were assessed using gas chromatography (GC), inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Fourier-transform infrared (FTIR) spectroscopy and ultraviolet (UV) absorption spectrometry. The effects of heavy metals on the bioremediation of PHE in soil were investigated, and the findings suggest that FM-2 has potential for combined bioremediation of soils co-contaminated with PHE and heavy metals.
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Affiliation(s)
- Xin-Xin Liu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Xin Hu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Yue Cao
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Wen-Jing Pang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Jin-Yu Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Peng Guo
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Lei Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
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Lambrechts S, Willems A, Tahon G. Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach. Front Microbiol 2019; 10:242. [PMID: 30828325 PMCID: PMC6385771 DOI: 10.3389/fmicb.2019.00242] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.
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Affiliation(s)
- Sam Lambrechts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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40
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Antarctic Soil Microbial Communities in a Changing Environment: Their Contributions to the Sustainability of Antarctic Ecosystems and the Bioremediation of Anthropogenic Pollution. SPRINGER POLAR SCIENCES 2019. [DOI: 10.1007/978-3-030-02786-5_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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Mucilaginibacter xinganensis sp. nov., a phenanthrene-degrading bacterium isolated from wetland soil. Antonie van Leeuwenhoek 2018; 112:641-649. [DOI: 10.1007/s10482-018-1194-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
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42
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Orellana R, Macaya C, Bravo G, Dorochesi F, Cumsille A, Valencia R, Rojas C, Seeger M. Living at the Frontiers of Life: Extremophiles in Chile and Their Potential for Bioremediation. Front Microbiol 2018; 9:2309. [PMID: 30425685 PMCID: PMC6218600 DOI: 10.3389/fmicb.2018.02309] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022] Open
Abstract
Extremophiles are organisms capable of adjust, survive or thrive in hostile habitats that were previously thought to be adverse or lethal for life. Chile gathers a wide range of extreme environments: salars, geothermal springs, and geysers located at Altiplano and Atacama Desert, salars and cold mountains in Central Chile, and ice fields, cold lakes and fjords, and geothermal sites in Patagonia and Antarctica. The aims of this review are to describe extremophiles that inhabit main extreme biotopes in Chile, and their molecular and physiological capabilities that may be advantageous for bioremediation processes. After briefly describing the main ecological niches of extremophiles along Chilean territory, this review is focused on the microbial diversity and composition of these biotopes microbiomes. Extremophiles have been isolated in diverse zones in Chile that possess extreme conditions such as Altiplano, Atacama Desert, Central Chile, Patagonia, and Antarctica. Interesting extremophiles from Chile with potential biotechnological applications include thermophiles (e.g., Methanofollis tationis from Tatio Geyser), acidophiles (e.g., Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum from Atacama Desert and Central Chile copper ores), halophiles (e.g., Shewanella sp. Asc-3 from Altiplano, Streptomyces sp. HKF-8 from Patagonia), alkaliphiles (Exiguobacterium sp. SH31 from Altiplano), xerotolerant bacteria (S. atacamensis from Atacama Desert), UV- and Gamma-resistant bacteria (Deinococcus peraridilitoris from Atacama Desert) and psychrophiles (e.g., Pseudomonas putida ATH-43 from Antarctica). The molecular and physiological properties of diverse extremophiles from Chile and their application in bioremediation or waste treatments are further discussed. Interestingly, the remarkable adaptative capabilities of extremophiles convert them into an attractive source of catalysts for bioremediation and industrial processes.
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Affiliation(s)
- Roberto Orellana
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
| | - Constanza Macaya
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Guillermo Bravo
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Flavia Dorochesi
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Andrés Cumsille
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Ricardo Valencia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Claudia Rojas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
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Ren L, Jia Y, Zhang R, Lin Z, Zhen Z, Hu H, Yan Y. Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1. Front Microbiol 2018; 9:2438. [PMID: 30364317 PMCID: PMC6193132 DOI: 10.3389/fmicb.2018.02438] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/24/2018] [Indexed: 01/11/2023] Open
Abstract
The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.
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Affiliation(s)
- Lei Ren
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Jia
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China
| | - Zhong Lin
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, China
| | - Zhen Zhen
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - Hanqiao Hu
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - Yanchun Yan
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
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