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Sun S, Wei R, Hu S, Yang M, Ni J. Isolation and characterization of distinctive pyrene-degrading bacteria from an uncontaminated soil. Biodegradation 2024; 35:657-670. [PMID: 38279065 DOI: 10.1007/s10532-023-10065-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: 09/14/2023] [Accepted: 12/13/2023] [Indexed: 01/28/2024]
Abstract
Considerable efforts that isolate and characterize degrading bacteria for polycyclic aromatic hydrocarbons (PAHs) have focused on contaminated environments so far. Here we isolated three distinctive pyrene (PYR)-degrading bacteria from a paddy soil that was not contaminated with PAHs. These included a novel Bacillus sp. PyB-9 and efficient degraders, Shigella sp. PyB-6 and Agromyces sp. PyB-10. All three strains could utilize naphthalene, phenanthrene, anthracene, fluoranthene and PYR as sole carbon sources, and degraded PYR in a range of temperatures (27-37 °C) and pH (5-8). Strains PyB-6 and PyB-10 almost completely degraded 50 mg L-1 PYR within 15 days, and 75.5% and 98.9% of 100 mg L-1 PYR in 27 days, respectively. The kinetics of PYR biodegradation was well represented by the Gompertz model. Ten and twelve PYR metabolites were identified in PYR degradation process by strains PyB-6 and PyB-10, respectively. Chemical analyses demonstrated that the degradation mechanisms of PYR were the same for strains PyB-6 and PyB-10 with initial dioxygenation mainly on C-4,5 positions of PYR. The degradation of 4,5-phenanthrenedicarboxylic acid was branched to 4-phenanthrenecarboxylic acid pathway and 5-hydroxy-4-phenanthrenecarboxylic acid pathway, both of which played important roles in PYR degradation by strains PyB-6 and PyB-10. To our knowledge, Shigella sp. and Agromyces sp. were found for the first time to possess the capability for PAHs degradation. These findings contributed to upgrading the bank of microbial resource and knowledge on PAH biodegradation.
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Affiliation(s)
- Shanshan Sun
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Ran Wei
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China.
| | - Siyi Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Meiyu Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Jinzhi Ni
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
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Lara‐Moreno A, Costa MC, Vargas‐Villagomez A, Carlier JD. New bacterial strains for ibuprofen biodegradation: Drug removal, transformation, and potential catabolic genes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13320. [PMID: 39187308 PMCID: PMC11347016 DOI: 10.1111/1758-2229.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 07/13/2024] [Indexed: 08/28/2024]
Abstract
Ibuprofen (IBU) is a significant contaminant frequently found in wastewater treatment plants due to its widespread use and limited removal during treatment processes. This leads to its discharge into the environment, causing considerable environmental concerns. The use of microorganisms has recently been recognized as a sustainable method for mitigating IBU contamination in wastewater. In this study, new bacteria capable of growing in a solid medium with IBU as the only carbon source and removing IBU from a liquid medium were isolated from environmental samples, including soil, marine, mine, and olive mill wastewater. Four bacterial strains, namely Klebsiella pneumoniae TIBU2.1, Klebsiella variicola LOIBU1.1, Pseudomonas aeruginosa LOIBU1.2, and Mycolicibacterium aubagnense HPB1.1, were identified through 16S rRNA gene sequencing. These strains demonstrated significant IBU removal efficiencies, ranging from 60 to 100% within 14 days, starting from an initial IBU concentration of 5 mg per litre. These bacteria have not been previously reported in the literature as IBU degraders, making this work a valuable contribution to further studies in the field of bioremediation in environments contaminated by IBU. Based on the IBU removal results, the most promising bacteria, K. pneumoniae TIBU2.1 and M. aubagnense HPB1.1, were selected for an in silico analysis to identify genes potentially involved in IBU biodegradation. Interestingly, in the tests with TIBU2.1, a peak of IBU transformation product(s) was detected by high-performance liquid chromatography, while in the tests with HPB1.1, it was not detected. The emerging peak was analysed by liquid chromatography-mass spectrometry, indicating the presence of possible conjugates between intermediates of IBU biodegradation. The proteins encoded on their whole-genome sequences were aligned with proteins involved in an IBU-degrading pathway reported in bacteria with respective catabolic genes. The analysis indicated that strain HPB1.1 possesses genes encoding proteins similar to most enzymes reported associated with the IBU metabolic pathways used as reference bacteria, while strain TIBU2.1 has genes encoding proteins similar to enzymes involved in both the upper and the lower part of that pathway. Notably, in the tests with the strain having more candidate genes encoding IBU-catabolic enzymes, no IBU transformation products were detected, while in the tests with the strain having fewer of these genes, detection occurred.
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Affiliation(s)
- Alba Lara‐Moreno
- Centre of Marine Sciences (CCMAR/CIMAR LA)University of the Algarve, Gambelas CampusFaroPortugal
- Department of Microbiology and Parasitology, Faculty of PharmacyUniversity of SevilleSevilleSpain
| | - Maria Clara Costa
- Centre of Marine Sciences (CCMAR/CIMAR LA)University of the Algarve, Gambelas CampusFaroPortugal
- Faculty of Sciences and TechnologiesUniversity of the Algarve, Gambelas CampusFaroPortugal
| | | | - Jorge Dias Carlier
- Centre of Marine Sciences (CCMAR/CIMAR LA)University of the Algarve, Gambelas CampusFaroPortugal
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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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Chen T, Fu B, Li H. Optimisation of PAHs biodegradation by Klebsiella pneumonia and Pseudomonas aeruginosa through response surface methodology. ENVIRONMENTAL TECHNOLOGY 2023:1-14. [PMID: 37970911 DOI: 10.1080/09593330.2023.2283813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/14/2023] [Indexed: 11/19/2023]
Abstract
Response Surface Methodology (RSM) with Box-Behnken Design (BBD) is used to optimise the Phenanthrene (PHE) degradation process by Klebsiella pneumoniae (K bacteria) and Pseudomonas aeruginosa (P bacteria). Wherein substrate concentration, temperature, and pH at three levels are used as independent variables, and degradation rate of PHE as dependent variables (response). The statistical analysis, via ANOVA, shows coefficient of determination R2 as 0.9848 with significant P value 0.0001 fitting in second-order quadratic regression model for PAHs removal by Klebsiella pneumonia, and R2 as 0.9847 with significant P value 0.0001 by P bacteria. According to the model analysis, temperature (P < 0.0006) is the most influential factor for PHE degradation efficiency by K bacteria, while pH (P < 0.0001) is the most influential factor for PHE degradation by P bacteria. The predicted optimum parameters for K bacteria, namely, temperature, substrate concentration, and pH are found to be 34.00℃, 50.80 mg/L, and 7.50, respectively, and those for P bacteria are 33.30℃, 52.70 mg/L, and 7.20, respectively. At these optimum conditions, the observed PHE removal rates by two bacteria are found to be 83.36% ± 2.1% and 81.23% ± 1.6% in validation experiments, respectively. Thus RSM can optimise the biodegradation conditions of both bacteria for PHE.
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Affiliation(s)
- Tao Chen
- Beijing University of Civil Engineering and Architecture, Key Laboratory of Urban Stormwater System & Water Environment Beijing, Beijing, China
| | - Bo Fu
- Beijing University of Civil Engineering and Architecture, Key Laboratory of Urban Stormwater System & Water Environment Beijing, Beijing, China
| | - Haiyan Li
- Tianjin Municipal Engineering Design and Research Institute Co. Ltd, Tianjin
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Jin J, Shi Y, Zhang B, Wan D, Zhang Q. An integrated method for studying the biodegradation of benzo[a]pyrene by Citrobacter sp. HJS-1 and interaction mechanism based on the structural model of the initial dioxygenase. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:85558-85568. [PMID: 37389752 DOI: 10.1007/s11356-023-28505-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023]
Abstract
A bacterial strain Citrobacter sp. HJS-1 was discovered from the sludge in a drainage canal of a coal mine. Firstly, its biodegradation capacity for benzo[a]pyrene (BaP) was detected under different concentrations. The results proved that the strain possessed excellent biodegradation capacity for BaP with high-efficiency degradation rates ranging from 78.9 to 86.8%. The highest degradation rate was observed in the low-concentration sample, and the high-concentration BaP had a slight influence on the biodegradation capacity due to the potential toxicity of BaP and its oxygen-containing derivatives. Meanwhile, the degradation test for the other five aromatic hydrocarbons (2- to 4-ring) proved that the strain had a comprehensive degradation potential. To clarify the biodegradation mechanism of BaP, a dioxygenase structure was constructed by homology modeling. Then, the interactions between dioxygenase and BaP were researched by molecular simulation. Combined with the identification of the vital BaP-cis-7,8-dihydrodiol intermediate and the interaction analysis, the initial oxidation mode and the binding site of BaP were revealed in the dioxygenase. Taken together, this study has offered a way to understand the biodegradation process of BaP and its interaction mechanism based on experimental and theoretical analysis.
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Affiliation(s)
- Jingnan Jin
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, No. 100 Lianhua Street, High-tech Industrial Development District, Zhengzhou, 450001, Henan, China.
| | - Yahui Shi
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, No. 100 Lianhua Street, High-tech Industrial Development District, Zhengzhou, 450001, Henan, China
| | - Baozhong Zhang
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, No. 100 Lianhua Street, High-tech Industrial Development District, Zhengzhou, 450001, Henan, China
| | - Dongjin Wan
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, No. 100 Lianhua Street, High-tech Industrial Development District, Zhengzhou, 450001, Henan, China
| | - Qingye Zhang
- College of informatics, Huazhong Agricultural University, Wuhan, 430070, China
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Panwar R, Mathur J. Microbial-assisted phytodegradation for the amelioration of pyrene-contaminated soil using Pseudomonas aeruginosa and Aspergillus oryzae with alfalfa and sunflower. 3 Biotech 2023; 13:251. [PMID: 37388857 PMCID: PMC10299988 DOI: 10.1007/s13205-023-03664-2] [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: 11/16/2022] [Accepted: 06/06/2023] [Indexed: 07/01/2023] Open
Abstract
Environmental pollution caused by polycyclic aromatic hydrocarbons (PAHs) jeopardizes nature. PAHs are the most toxic, mutagenic, and carcinogenic pollutants and their cleanup is important for the environment. In the current research, to assess and evaluate three remediation strategies for pyrene removal from the soil, a pot experiment was performed: (a) bioremediation with Pseudomonas aeruginosa and Aspergillus oryzae, (b) phytoremediation with sunflower (Helianthus annuus) and alfalfa (Medicago sativa L.) and (c) microbial-assisted phytoremediation for the treatment of pyrene (700 mg kg-1). Results depict that P. aeruginosa significantly promoted the growth and tolerance of taken plants and reduced pyrene concentration in soil. Compared with those planted in pyrene-contaminated soil without inoculation. The highest percentage of pyrene removal was observed in P. aeruginosa inoculated alfalfa (91%), alfalfa inoculated with A. oryzae (83.96%), and without inoculation (78.20%). Moreover, alfalfa planted in P. aeruginosa augmented soil had the highest dehydrogenase activity (37.83 μg TPF g-1 soil h-1), and fluorescein diacetate hydrolysis (91.67 μg fluorescein g-1 dry soil). DHA and FDA are the indicators of bioaugmentation influence on the indigenous microbial activity of contaminated soil. As a result of the findings, the rhizospheric association of plants and microbes is beneficial for pyrene removal. Therefore, P. aeruginosa-assisted phytodegradation might be a more successful remediation technique for pyrene-contaminated soil than bioremediation and phytodegradation solely.
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Affiliation(s)
- Ritu Panwar
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan 304022 India
| | - Jyoti Mathur
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan 304022 India
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Ahmad M, Ling J, Yin J, Chen L, Yang Q, Zhou W, Zhang Y, Huang X, Khan I, Dong J. Evaluation of the Different Nutritional and Environmental Parameters on Microbial Pyrene Degradation by Mangrove Culturable Bacteria. Int J Mol Sci 2023; 24:ijms24098282. [PMID: 37175988 PMCID: PMC10179275 DOI: 10.3390/ijms24098282] [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: 03/31/2023] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Mangrove ecosystems play curial roles in providing many ecological services and alleviating global climate change. However, they are in decline globally, mainly threatened by human activities and global warming, and organic pollutants, especially PAHs, are among the crucial reasons. Microbial remediation is a cost-effective and environmentally friendly way of alleviating PAH contamination. Therefore, understanding the effects of environmental and nutritional parameters on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) is significant for the bioremediation of PAH contamination. In the present study, five bacterial strains, designated as Bp1 (Genus Rhodococcus), Sp8 (Genus Nitratireductor), Sp13 (Genus Marinobacter), Sp23 (Genus Pseudonocardia), and Sp24 (Genus Mycolicibacterium), have been isolated from mangrove sediment and their ring hydroxylating dioxygenase (RHD) genes have been successfully amplified. Afterward, their degradation abilities were comprehensively evaluated under normal cultural (monoculture and co-culture) and different nutritional (tryptone, yeast extract, peptone, glucose, sucrose, and NPK fertilizer) and environmental (cetyl trimethyl ammonium bromide (CTAB), sodium dodecyl sulfate (SDS)) parameters, as well with different co-contaminants (phenanthrene and naphthalene) and heavy metals (Cd2+, Cu2+, Fe3+, Ni2+, Mg2+, Mn2+, and Co2+). The results showed that strain Sp24 had the highest pyrene degradation rate (85%) in the monoculture experiment after being cultured for 15 days. Adding nitrogen- and carbon-rich sources, including tryptone, peptone, and yeast extract, generally endorsed pyrene degradation. In contrast, the effects of carbon sources (glucose and sucrose) on pyrene degradation were distinct for different bacterial strains. Furthermore, the addition of NPK fertilizer, SDS, Tween-80, phenanthrene, and naphthalene enhanced the bacterial abilities of pyrene removal significantly (p < 0.05). Heavy metals significantly reduced all bacterial isolates' degradation potentials (p < 0.05). The bacterial consortia containing high bio-surfactant-producing strains showed substantially higher pyrene degradation. Moreover, the consortia of three and five bacterial strains showed more degradation efficiency than those of two bacterial strains. These results provide helpful microbial resources for mangrove ecological remediation and insight into optimized culture strategies for the microbial degradation of PAHs.
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Affiliation(s)
- Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou 515041, China
| | - Jianping Yin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Luxiang Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou 515041, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Yuhang Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Xiaofang Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Imran Khan
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou 515041, China
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Yesankar PJ, Patil A, Kapley A, Qureshi A. Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons. World J Microbiol Biotechnol 2023; 39:166. [PMID: 37076735 DOI: 10.1007/s11274-023-03617-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023]
Abstract
Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.
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Affiliation(s)
- Prerna J Yesankar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - Ayurshi Patil
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - Asifa Qureshi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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9
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Goveas LC, Selvaraj R, Vinayagam R, Sajankila SP, Pugazhendhi A. Biodegradation of benzo(a)pyrene by Pseudomonas strains, isolated from petroleum refinery effluent: Degradation, inhibition kinetics and metabolic pathway. CHEMOSPHERE 2023; 321:138066. [PMID: 36781003 DOI: 10.1016/j.chemosphere.2023.138066] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/19/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Benzo(a)pyrene, a five-ring polyaromatic hydrocarbon, originating from coal tar, crude oil, tobacco, grilled foods, car exhaust etc, is highly persistent in the environment. It has been classified as a Group I carcinogen, as on its ingestion in human body, diol epoxide metabolites are generated, which bind to DNA causing mutations and eventual cancer. Among various removal methods, bioremediation is most preferred as it is a sustainable approach resulting in complete mineralization of benzo(a)pyrene. Therefore, in this study, biodegradation of benzo(a)pyrene was performed by two strains of Pseudomonas, i. e WDE11 and WD23, isolated from refinery effluent. Maximum benzo(a)pyrene tolerance was 250 mg/L and 225 mg/L against Pseudomonas sp. WD23 and Pseudomonas sp. WDE11 correspondingly. Degradation rate constants varied between 0.0468 and 0.0513/day at 50 mg/L with half-life values between 13.5 and 14.3 days as per first order kinetics, while for 100 mg/L, the respective values varied between 0.006 and 0.007 L/mg. day and 15.28-16.67 days, as per second order kinetics. The maximum specific growth rate of strains WDE11 and WD23 was 0.3512/day and 0.38/day accordingly, while concentrations over 75 mg/L had an inhibitory effect on growth. Major degradation metabolites were identified as dihydroxy-pyrene, naphthalene-1,2-dicarboxylic acid, salicylic acid, and oxalic acid, indicating benzo(a)pyrene was degraded via pyrene intermediates by salicylate pathway through catechol meta-cleavage. The substantial activity of the catechol 2,3 dioxygenase enzyme was noted during the benzo(a)pyrene metabolism by both strains with minimal catechol 1,2 dioxygenase activity. This study demonstrates the exceptional potential of indigenous Pseudomonas strains in complete metabolism of benzo(a)pyrene.
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Affiliation(s)
- Louella Concepta Goveas
- Nitte (Deemed to be University), Department of Biotechnology Engineering, NMAM Institute of Technology, Nitte - 574110, Karnataka, India.
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shyama Prasad Sajankila
- Nitte (Deemed to be University), Department of Biotechnology Engineering, NMAM Institute of Technology, Nitte - 574110, Karnataka, India
| | - Arivalagan Pugazhendhi
- School of Engineering, Lebanese American University, Byblos, Lebanon; University Centre for Research & Development, Department of Civil Engineering, Chandigarh University, Mohali, India.
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10
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Gunasekaran V, Canela N, Constantí M. Comparative Proteomic Analysis of an Ethyl Tert-Butyl Ether-Degrading Bacterial Consortium. Microorganisms 2022; 10:microorganisms10122331. [PMID: 36557584 PMCID: PMC9781318 DOI: 10.3390/microorganisms10122331] [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: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
A bacterial consortium capable of degrading ethyl tert-butyl ether (ETBE) as a sole carbon source was enriched and isolated from gasoline-contaminated water. Arthrobacter sp., Herbaspirillum sp., Pseudacidovorax sp., Pseudomonas sp., and Xanthomonas sp. were identified as the initial populations with the 16S rDNA analysis. The consortium aerobically degraded 49% of 50 mg/L of ETBE, in 6 days. The ETBE degrading efficiency of the consortium increased to 98% even with the higher concentrations of ETBE (1000 mg/L) in the subsequent subcultures, which accumulated tert-butyl alcohol (TBA). Xanthomonas sp. and Pseudomonas sp. were identified as the predominant ETBE degrading populations in the final subculture. The metaproteome of the ETBE-grown bacterial consortium was compared with the glucose-grown bacterial consortium, using 2D-DIGE. Proteins related to the ETBE metabolism, stress response, carbon metabolism and chaperones were found to be abundant in the presence of ETBE while proteins related to cell division were less abundant. The metaproteomic study revealed that the ETBE does have an effect on the metabolism of the bacterial consortium. It also enabled us to understand the responses of the complex bacterial consortium to ETBE, thus revealing interesting facts about the ETBE degrading bacterial community.
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Affiliation(s)
- Vijayalakshmi Gunasekaran
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans, 26, 43007 Tarragona, Spain
- FA Bio, Harpenden AL5 2JQ, UK
- Correspondence: (V.G.); (M.C.); Tel.: +34-977-558457 (M.C.)
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Av. Universitat 1, 43204 Reus, Spain
| | - Magda Constantí
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans, 26, 43007 Tarragona, Spain
- Correspondence: (V.G.); (M.C.); Tel.: +34-977-558457 (M.C.)
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11
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Teng T, Liang J, Zhu J, Jin P, Zhang D. Altered active pyrene degraders in biosurfactant-assisted bioaugmentation as revealed by RNA stable isotope probing. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120192. [PMID: 36126767 DOI: 10.1016/j.envpol.2022.120192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Bioaugmentation is an effective approach for removing pyrene from contaminated sites, and its performance is enhanced by a biosurfactant. To reveal the mechanisms of biosurfactant-assisted bioaugmentation, we introduced RNA stable isotope probing (RNA-SIP) in the pyrene-contaminated soils and explored the impacts of rhamnolipid on the pyrene degradation process. After 12-day degradation, residual pyrene was the lowest in the bioaugmentation treatment (7.76 ± 1.57%), followed by biosurfactant-assisted bioaugmentation (9.86 ± 2.58%) and enhanced natural attenuation (23.97 ± 1.05%). Thirteen well-known and two novel pyrene-degrading bacteria were confirmed to participate in the pyrene degradation. Pyrene degradation was accelerated in the biosurfactant-assisted bioaugmentation, manifested by the high diversity of active pyrene degraders. Our findings expand the knowledge on pyrene degrading bacteria and the mechanisms of pyrene degradation in a bioaugmentation process.
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Affiliation(s)
- Tingting Teng
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China; College of New Energy and Environment, Jilin University, Changchun, 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, PR China
| | - Jidong Liang
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China.
| | - Jinwei Zhu
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China; Shaanxi Electrical Equipment Institute, Xi'an, 710025, PR China
| | - Pengkang Jin
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, PR China
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12
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Xu P, Chen X, Li K, Meng R, Pu Y. Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12039. [PMID: 36231339 PMCID: PMC9565075 DOI: 10.3390/ijerph191912039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Polycyclic aromatic hydrocarbons are a widespread organic pollutant worldwide. In this study, a highly efficient phenanthrene (PHE)-degrading microbial community was enriched from oil extraction soil, which could degrade 500 mg/L PHE within 4 days. Using 16S rRNA sequencing, the dominant bacteria in this community at the phylum level were found to be Proteobacteria, Actinobacteria, and Firmicutes. Metagenomic annotation of genes revealed the metabolic pathways and the contribution of different bacteria to the degradation process. Pseudomonadaceae contributed multiple functional genes in the degradation process. This study revealed the functional genes, metabolic pathways, and microbial interactions of the microbial community, which are expected to provide guidance for practical management.
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Affiliation(s)
- Pan Xu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xiaoxiao Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Kai Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Rong Meng
- The Husbandry Technology Promotion Center of Inner Mongolia, Hohhot 010051, China
| | - Yuewu Pu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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13
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Biodegradation of high molecular weight hydrocarbons under saline condition by halotolerant Bacillus subtilis and its mixed cultures with Pseudomonas species. Sci Rep 2022; 12:13227. [PMID: 35918482 PMCID: PMC9345985 DOI: 10.1038/s41598-022-17001-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/19/2022] [Indexed: 11/08/2022] Open
Abstract
Biodegradation of high-molecular-weight petroleum hydrocarbons in saline conditions appears to be complicated and requires further investigation. This study used heavy crude oil to enrich petroleum-degrading bacteria from oil-contaminated saline soils. Strain HG 01, with 100% sequence similarity to Bacillus subtilis, grew at a wide range of salinities and degraded 55.5 and 77.2% of 500 mg/l pyrene and 500 mg/l tetracosane, respectively, at 5% w/v NaCl. Additionally, a mixed-culture of HG 01 with Pseudomonas putida and Pseudomonas aeruginosa, named TMC, increased the yield of pyrene, and tetracosane degradation by about 20%. Replacing minimal medium with treated seawater (C/N/P adjusted to 100/10/1) enabled TMC to degrade more than 99% of pyrene and tetracosane, but TMC had lesser degradation in untreated seawater than in minimal medium. Also, the degradation kinetics of pyrene and tetracosane were fitted to a first-order model. Compared to B. subtilis, TMC increased pyrene and tetracosane's removal rate constant (K1) from 0.063 and 0.110 per day to 0.123 and 0.246 per day. TMC also increased the maximum specific growth rate of B. subtilis, P. putida, and P. aeruginosa, respectively, 45% higher in pyrene, 24.5% in tetracosane, and 123.4% and 95.4% higher in pyrene and tetracosane.
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14
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Gabriele I, Race M, Papirio S, Papetti P, Esposito G. Phytoremediation of a pyrene-contaminated soil by Cannabis sativa L. at different initial pyrene concentrations. CHEMOSPHERE 2022; 300:134578. [PMID: 35417760 DOI: 10.1016/j.chemosphere.2022.134578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/24/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
This study proposes the phytoremediation of a pyrene (PYR)-contaminated soil by Cannabis sativa L. The experimental campaign was conducted along a 60 days period using three different initial PYR concentrations (i.e., 50, 100 and 150 mg kg TS-1 of soil) in 300 mL volume pots under greenhouse conditions (18-25 °C and 45-55% humidity). After 60 days of hemp growth and flourishing, the highest PYR removal reached approximately 95% in planted soil, 35% higher than in the unplanted control. PYR accumulation was observed in both roots and aerial parts of the plant, with a higher PYR uptake at increasing initial PYR concentrations in soil. The initial PYR concentration affected the growth and, thus, the phytoremediation potential of C. sativa L., which was the result of different removal mechanisms. Overall, the lowest initial PYR concentration was the one that resulted in the highest PYR removal. The interaction between the plant roots and microorganisms in rhizosphere was likely associated with PYR removal in this study. The highest DHO activity of 66.26 μg INTF g-1 TS-1 was observed in the soil spiked with 50 mg PYR·kg TS-1.
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Affiliation(s)
- Ilaria Gabriele
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy.
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy
| | - Stefano Papirio
- Department of Civil, Architectural and Environmental Engineering, University of Napoli Federico II, Via Claudio 21, 80125, Napoli, Italy
| | - Patrizia Papetti
- Department of Economics and Law, Territorial and Products Analysis Laboratory, University of Cassino and Southern Lazio, Via S. Angelo, Folcara, 03043, Cassino, Italy
| | - Giovanni Esposito
- Department of Civil, Architectural and Environmental Engineering, University of Napoli Federico II, Via Claudio 21, 80125, Napoli, Italy
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15
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Medić AB, Karadžić IM. Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation. World J Microbiol Biotechnol 2022; 38:165. [PMID: 35861883 DOI: 10.1007/s11274-022-03349-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/26/2022] [Indexed: 10/17/2022]
Abstract
Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.
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Affiliation(s)
- Ana B Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
| | - Ivanka M Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
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16
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A Review of Pyrene Bioremediation Using Mycobacterium Strains in a Different Matrix. FERMENTATION 2022. [DOI: 10.3390/fermentation8060260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Polycyclic aromatic hydrocarbons are compounds with 2 or more benzene rings, and 16 of them have been classified as priority pollutants. Among them, pyrene has been found in higher concentrations than recommended, posing a threat to the ecosystem. Many bacterial strains have been identified as pyrene degraders. Most of them belong to Gram-positive strains such as Mycobacterium sp. and Rhodococcus sp. These strains were enriched and isolated from several sites contaminated with petroleum products, such as fuel stations. The bioremediation of pyrene via Mycobacterium strains is the main objective of this review. The scattered data on the degradation efficiency, formation of pyrene metabolites, bio-toxicity of pyrene and its metabolites, and proposed degradation pathways were collected in this work. The study revealed that most of the Mycobacterium strains were capable of degrading pyrene efficiently. The main metabolites of pyrene were 4,5-dihydroxy pyrene, phenanthrene-4,5-dicarboxylate, phthalic acid, and pyrene-4,5-dihydrodiol. Some metabolites showed positive results for the Ames mutagenicity prediction test, such as 1,2-phenanthrenedicarboxylic acid, 1-hydroxypyrene, 4,5-dihydropyrene, 4-phenanthrene-carboxylic acid, 3,4-dihydroxyphenanthrene, monohydroxy pyrene, and 9,10-phenanthrenequinone. However, 4-phenanthrol showed positive results for experimental and prediction tests. This study may contribute to enhancing the bioremediation of pyrene in a different matrix.
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17
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Alfaify AM, Mir MA, Alrumman SA. Klebsiella oxytoca: an efficient pyrene-degrading bacterial strain isolated from petroleum-contaminated soil. Arch Microbiol 2022; 204:248. [PMID: 35397012 DOI: 10.1007/s00203-022-02850-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are the hazardous xenobiotic agents of oil production. One of the methods to eliminate hazardous compounds is bioremediation, which is the most efficient and cost-effective method to eliminate the harmful byproducts of crude petroleum processing. In this study, five pure bacterial isolates were isolated from petroleum-contaminated soil, four of which showed a robust growth on the PAH pyrene, as a sole carbon source. Various methods viz mass spectroscopy, biochemical assays, and 16S RNA sequencing employed to identify the isolates ascertained the consistent identification of Klebsiella oxytoca by all three methods. Scanning electron microscopy and Gram staining further demonstrated the characterization of the K. oxytoca. High-performance liquid chromatography of the culture supernatant of K. oxytoca grown in pyrene containing media showed that the cells started utilizing pyrene from the 6th day onwards and by the 12th day of growth, 70% of the pyrene was completely degraded. A genome search for the genes predicted to be involved in pyrene degradation using Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their presence in the genome of K. oxytoca. These results suggest that K. oxytoca would be a suitable candidate for removing soil aromatic hydrocarbons.
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Affiliation(s)
- Abdulkhaleg M Alfaify
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Mushtaq Ahmad Mir
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P. O. Box 3665, Abha, 61421, Saudi Arabia.
| | - Sulaiman A Alrumman
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
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18
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Wang H, Chen P, Zhang S, Jiang J, Hua T, Li F. Degradation of pyrene using single-chamber air-cathode microbial fuel cells: Electrochemical parameters and bacterial community changes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150153. [PMID: 34509835 DOI: 10.1016/j.scitotenv.2021.150153] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Pyrene, a typical four-ring polycyclic aromatic hydrocarbon, is abundantly present in the environment and is potentially harmful to the human body. In this study, single-chamber air-cathode microbial fuel cells (MFCs) were used to treat pyrene, and the ensuing degradation, electrical parameters, and microbial changes were analyzed. The results showed that MFCs could degrade pyrene, and the maximum degradation rate for 30 mg/L reached 88.1 ± 5.4%. The addition of pyrene reduced the electrical performance of the MFCs and suppressed the power output. Analysis of the anodic microbial community showed that the proportion of Alcaligenes and Stenotrophomonas increased with an increase in pyrene concentration, which may explain the high degradation rate of pyrene.
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Affiliation(s)
- Haonan Wang
- Key Laboratory of Pollution Processes and Environmental Criteria at (Ministry of Education), Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Peng Chen
- Key Laboratory of Pollution Processes and Environmental Criteria at (Ministry of Education), Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Shixuan Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria at (Ministry of Education), Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Jiwei Jiang
- Key Laboratory of Pollution Processes and Environmental Criteria at (Ministry of Education), Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Tao Hua
- Key Laboratory of Pollution Processes and Environmental Criteria at (Ministry of Education), Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Fengxiang Li
- Key Laboratory of Pollution Processes and Environmental Criteria at (Ministry of Education), Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China.
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19
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Xue SW, Tian YX, Pan JC, Liu YN, Ma YL. Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1. Sci Rep 2021; 11:21317. [PMID: 34716364 PMCID: PMC8556375 DOI: 10.1038/s41598-021-00783-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/18/2021] [Indexed: 11/11/2022] Open
Abstract
Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His217-His222-Asp372 for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C7-C8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C7-O and C8-O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.
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Affiliation(s)
- Shu-Wen Xue
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Yue-Xin Tian
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Jin-Cheng Pan
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Ya-Ni Liu
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Yan-Ling Ma
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
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20
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Li L, Zhang X, Zhu P, Yong X, Wang Y, An W, Jia H, Zhou J. Enhancing biomethane production and pyrene biodegradation by addition of bio-nano FeS or magnetic carbon during sludge anaerobic digestion. ENVIRONMENTAL TECHNOLOGY 2021; 42:3496-3507. [PMID: 32085684 DOI: 10.1080/09593330.2020.1733674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/14/2020] [Indexed: 05/22/2023]
Abstract
Pyrene exerts toxic effects on methanogens during anaerobic digestion of sludge, thus affecting the efficiency of sludge treatment. This study evaluated the facilitated direct interspecific electron transfer (DIET) between bacteria and methanogens when bio-nano FeS or magnetic carbon is added into anaerobic reactors. Results showed that adding 200 mg/L bio-nano FeS or magnetic carbon clearly reduced the accumulation of short-chain fatty acids and avoided acidification during 25 days of anaerobic digestion. The methane productions were 98.38 L/kg total solid (TS) and 73.69 L/kg TS in the bio-nano FeS and magnetic carbon systems, respectively, which accelerated methane production by 58.1% and 33.4%, respectively, compared with the control system (40.26 L/kg TS). The pyrene removal rates reached 77.5% and 72.1% in the bio-nano FeS and magnetic carbon systems, whereas it was only 40.8% in the control system. Analysis of microbial community structure revealed that methanogens (e.g. Methanosarcina and Methanosaeta) and extracellular electron-transfer bacteria (e.g. Pseudomonas, Cloastridia, and Synergistetes) were enriched in the reactors added with bio-nano FeS or magnetic carbon. This result indicates that the addition of bio-nano FeS or magnetic carbon may promote the activity and growth of microorganisms to improve the efficiency of methane production and pyrene degradation by enhancing DIET.
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Affiliation(s)
- Lian Li
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing, People's Republic of China
- College of Environment, Nanjing TECH University, Nanjing, People's Republic of China
| | - Xueying Zhang
- College of Environment, Nanjing TECH University, Nanjing, People's Republic of China
| | - Peiru Zhu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing, People's Republic of China
- College of Environment, Nanjing TECH University, Nanjing, People's Republic of China
| | - Xiaoyu Yong
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing, People's Republic of China
| | - Yajun Wang
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, People's Republic of China
| | - Wei An
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, People's Republic of China
| | - Honghua Jia
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing, People's Republic of China
| | - Jun Zhou
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing, People's Republic of China
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21
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Ferraro A, Massini G, Miritana VM, Panico A, Pontoni L, Race M, Rosa S, Signorini A, Fabbricino M, Pirozzi F. Bioaugmentation strategy to enhance polycyclic aromatic hydrocarbons anaerobic biodegradation in contaminated soils. CHEMOSPHERE 2021; 275:130091. [PMID: 33984916 DOI: 10.1016/j.chemosphere.2021.130091] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
This paper proposes an innovative bioaugmentation approach for the remediation of polycyclic aromatic hydrocarbon (PAH) contaminated soils, based on a novel habitat-based strategy. This approach was tested using two inocula (i-24 and i-96) previously enriched through an anaerobic digestion process on wheat straw. It relies on the application of allochthonous microorganisms characterized by specific functional roles obtained by mimicking a natural hydrolytic environment such as the rumen. The inocula efficiency was tested in presence of naphthalene alone, benzo[a]pyrene alone, and a mix of both of them. In single-contamination tests, i-24 inoculum showed the highest biodegradation rates (84.7% for naphthalene and 51.7% for benzo[a]pyrene). These values were almost 1.2 times higher than those obtained for both contaminants with i-96 inoculum and in the control test in presence of naphthalene alone, while they were 3 times higher compared to the control test in presence of benzo[a]pyrene alone. In mixed-contamination tests, i-96 inoculum showed final biodegradation efficiencies for naphthalene and benzo[a]pyrene between 1.1 and 1.5 higher than i-24 inoculum or autochthonous biomass. Total microbial abundances increased in the bioaugmented tests in line with the PAH degradation. The microbial community structure showed the highest diversity at the end of the experiment in almost all cases. Values of the Firmicutes active fraction up to 7 times lower were observed in the i-24 bioaugmented tests compared to i-96 and control tests. This study highlights a successful bioaugmentation strategy with biological components that can be reused in multiple processes supporting an integrated and environmentally sustainable bioremediation system.
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Affiliation(s)
- Alberto Ferraro
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125, Naples, Italy; Department of Civil, Environmental, Land, Building Engineering and Chemistry, Polytechnic University of Bari, Via E. Orabona 4, 70125, Bari, Italy
| | - Giulia Massini
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Valentina Mazzurco Miritana
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Antonio Panico
- Department of Engineering, University of Campania "L. Vanvitelli", Via Roma, 29, 81031, Aversa, Italy; Telematic University Pegaso, Piazza Trieste e Trento 48, Naples, Italy.
| | - Ludovico Pontoni
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125, Naples, Italy
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via di Biasio 43, 03043, Cassino, Italy
| | - Silvia Rosa
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Antonella Signorini
- Department of Energy Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Massimiliano Fabbricino
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125, Naples, Italy
| | - Francesco Pirozzi
- Department of Civil, Architectural and Environmental Engineering, University of Naples "Federico II", Via Claudio 21, 80125, Naples, Italy
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Cecchi G, Cutroneo L, Di Piazza S, Besio G, Capello M, Zotti M. Port Sediments: Problem or Resource? A Review Concerning the Treatment and Decontamination of Port Sediments by Fungi and Bacteria. Microorganisms 2021; 9:microorganisms9061279. [PMID: 34208305 PMCID: PMC8231108 DOI: 10.3390/microorganisms9061279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
Contamination of marine sediments by organic and/or inorganic compounds represents one of the most critical problems in marine environments. This issue affects not only biodiversity but also ecosystems, with negative impacts on sea water quality. The scientific community and the European Commission have recently discussed marine environment and ecosystem protection and restoration by sustainable green technologies among the main objectives of their scientific programmes. One of the primary goals of sustainable restoration and remediation of contaminated marine sediments is research regarding new biotechnologies employable in the decontamination of marine sediments, to consider sediments as a resource in many fields such as industry. In this context, microorganisms—in particular, fungi and bacteria—play a central and crucial role as the best tools of sustainable and green remediation processes. This review, carried out in the framework of the Interreg IT-FR Maritime GEREMIA Project, collects and shows the bioremediation and mycoremediation studies carried out on marine sediments contaminated with ecotoxic metals and organic pollutants. This work evidences the potentialities and limiting factors of these biotechnologies and outlines the possible future scenarios of the bioremediation of marine sediments, and also highlights the opportunities of an integrated approach that involves fungi and bacteria together.
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Affiliation(s)
- Grazia Cecchi
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
| | - Laura Cutroneo
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
| | - Simone Di Piazza
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
| | - Giovanni Besio
- DICCA, University of Genoa, 1 Via Montallegro, I-16145 Genoa, Italy;
| | - Marco Capello
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
- Correspondence:
| | - Mirca Zotti
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
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Effect of pyrene and phenanthrene in shaping bacterial communities in seagrass meadows sediments. Arch Microbiol 2021; 203:4259-4272. [PMID: 34100100 DOI: 10.1007/s00203-021-02410-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), originating from anthropogenic and natural sources, are highly concerned environmental pollutants. This study investigated the impact of two model PAHs (pyrene and phenanthrene) on bacterial community succession in the seagrass meadows sediment in a lab-scale microcosm. Halophila ovalis sediment slurry microcosms were established, one group was placed as a control, and the other two were treated with pyrene and phenanthrene. Bacterial community succession in response to respective PAHs was investigated by 16S rRNA amplicon sequencing. The results demonstrated that bacterial diversity decrease in each microcosm during the incubation process; however, the composition of bacterial communities in each microcosm was significantly different. Proteobacteria (37-89%), Firmicutes (9-41%), and Bacteroides (7-21%) were the predominant group at the phylum levels. Their abundance varies during the incubation process. Several previously reported hydrocarbon-degrading genera, such as Pseudomonas, Spinghobium, Sphingobacterium, Mycobacterium, Pseudoxanthomonas, Idiomarina, Stenotrophomonas, were detected in higher abundance in pyrene- and phenanthrene-treated microcosms. However, these genera were distinctly distributed in the pyrene and phenanthrene treatments, suggesting that certain bacterial groups favorably degrade different PAHs. Statistical analyses, such as ANOSIM and PERMANOVA, also revealed that significant differences existed among the treatments' bacterial consortia (P < 0.05). This work showed that polycyclic aromatic hydrocarbon significantly affects bacterial community succession, and different PAHs might influence the bacterial community succession differently.
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Pandya DK, Kumar MA. Chemo-metric engineering designs for deciphering the biodegradation of polycyclic aromatic hydrocarbons. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125154. [PMID: 33858107 DOI: 10.1016/j.jhazmat.2021.125154] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are non-polar organic compounds that are omnipresent in the environment and released due to anthropogenic activities through emissions and discharges. PAHs, being xenobiotic and exerts health impacts, thus they attract serious concern by the environmentalists. The stringent regulations and the need of sustainable development urges the hunt for a technically feasible and cost-effective wastewater treatment. Although the conventional physico-chemical treatment are widely preferred, they cause secondary pollution problems and demand subsequent treatment options. This comprehensive review intends to address the (a) different PAHs and their associated toxicity, (b) the remedial strategies, particularly biodegradation. The biological wastewater treatment techniques that involve microbial systems are highly influenced by the different physio-chemical and environmental parameters. Therefore, suitable optimization techniques are prerequisite for effective functioning of the biological treatment that sustains judiciously and interpreted in a lesser time. Here we have aimed to discuss (a) different chemo-metric tools involved in the design of experiments (DoE), (b) design equations and models, (c) tools for evaluating the model's adequacy and (d) plots for graphically interpreting the chemo-metric designs. However, to best of our knowledge, this is a first review to discuss the PAHs biodegradation that are tailored by chemo-metric designs. The associated challenges, available opportunities and techno-economic aspects of PAHs degradation using chemo-metric engineering designs are explained. Additionally, the review highlights how well these DoE tools can be suited for the sustainable socio-industrial sectors. Concomitantly, the futuristic scope and prospects to undertake new areas of research exploration were emphasized to unravel the least explored chemo-metric designs.
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Affiliation(s)
- Darshita Ketan Pandya
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India
| | - Madhava Anil Kumar
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India.
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25
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Effects of Different Continuous Cropping Years on Bacterial Community and Diversity of Cucumber Rhizosphere Soil in Solar-Greenhouse. Curr Microbiol 2021; 78:2380-2390. [PMID: 33871692 DOI: 10.1007/s00284-021-02485-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
The rhizosphere soils from 1, 3, 5, and 7 years of cucumber continuous cropping in solar-greenhouse were used as the research objects. The region of bacterial 16S rRNA was analyzed by Illumina MiSeq high-throughput sequencing technology. The effect of continuous cropping years on the microbial community structure and diversity in cucumber soil in the greenhouse was investigated. The physical and chemical properties of soil and the activities of urease and catalase were determined. The results showed that cucumber crop succession for different years affected the community composition of the bacteria at the phylum level, and the abundance of Proteobacteria, Chloroflexi, Gemmatimonadetes, Patescibacteria and Firmicutes gradually increased, while Actinobacteria in the soil significantly decreased. Among the top 15 significantly different genera, with the extension of successive years, the relative abundance of most genera in bacteria decreased after a small increase in year 3. The diversity results indicated that soil samples from continuous cropping for 7 years had the lowest community diversity. PICRUSt analysis showed a decreasing trend in soil bacterial function as the cucumber crop succession age increased. In environmental factor clustering analysis, the soil bacterial community was significantly correlated with pH, available nitrogen (AN), soil urease (SUR) and available phosphorus (AP), and the effect on the bacterial community was expressed as SUR > AP > AN > pH.
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26
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Wang P, Gao J, Zhao Y, Zhang M, Zhou S. Biodegradability of di-(2-ethylhexyl) phthalate by a newly isolated bacterium Achromobacter sp. RX. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142476. [PMID: 33035973 DOI: 10.1016/j.scitotenv.2020.142476] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 05/12/2023]
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is a chemical plasticizer that has been commonly used in the manufacture of polyvinyl chloride. DEHP is one of the environmental pollution sources. In this study, a gram-negative strain RX bacterium utilizing DEHP as sole carbon source was isolated from activated sludge through screening test. This strain RX was identified as Achromobacter sp. RX based on its morphology, physiological properties and 16S rRNA gene sequence analysis. The results showed that the optimal conditions for the DEHP degradation were 30.0 °C and pH 7.0. The DEHP degradation induced by strain RX demonstrated nitrogen source dependent, while followed a decreasing degradation rate under the source of: NO3- > NH4+ > NO2-. The biodegradability of Achromobacter sp. RX was enhanced with Masson pine seed powder as a co-metabolic substrate and Tween-80 as a solubilizing agent. Meanwhile, the degrading kinetics analysis was performed in the condition of DEHP as sole carbon source. The DEHP degradation curves fitted well with the first-order kinetic model at 50-300 mg/L of DEHP, with the half-life ranging from 13.0 to 16.4 h. During the biodegradation of DEHP, mono-(2-ehtylhexyl) phthalate (MEHP) was firstly generated through de-esterification, followed by the formation of phthalic acid and benzoic acid after further de-esterification of MEHP. Benzoic acid was finally mineralized to CO2 and H2O. The decontamination of DEHP-contaminated soil by Achromobacter sp. RX was investigated using a rotating-drum bioreactor. Evolution of total organic carbon from the contaminated soil showed that 86.4%-91.7% of DEHP was mineralized at pH 7.0 and 30.0 °C within 96 h. Reusability of Achromobacter sp. RX and its lifetime were observed over six consecutive cycles. Thus, Achromobacter sp. RX possessed high DEHP biodegradability, which provided a good potential in dealing with DEHP-contaminated soil.
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Affiliation(s)
- Ping Wang
- School of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
| | - Jingjing Gao
- School of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Zhao
- School of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- School of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Sijie Zhou
- School of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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Wang P, Zhang Y, Jin J, Wang T, Wang J, Jiang B. A high-efficiency phenanthrene-degrading Diaphorobacter sp. isolated from PAH-contaminated river sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:140455. [PMID: 32758981 DOI: 10.1016/j.scitotenv.2020.140455] [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: 03/09/2020] [Revised: 06/18/2020] [Accepted: 06/21/2020] [Indexed: 05/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are typical persistent organic pollutants that accumulate in the environment, mainly from anthropogenic activities. Microbial degradation is the main pathway of PAHs degradation in the natural environment. Therefore, the widen of the available bank of microbial resources and exploration of the molecular degradation mechanisms of PAHs are crucial to the proper management of PAHs-polluted sites. In this work, a bacterial strain, YM-6, which has a high ability to utilize phenanthrene (PHE) as its sole source of carbon and energy, was isolated from sediment contaminated with PAHs. The strain YM-6 was found to degrade 96.3% of 100 mg/L of PHE in liquid cultures within 52 h. The strain was identified as Diaphorobacter sp. by 16S rDNA sequencing. The optimum growth conditions of the YM-6 strain were studied, and the results indicated that the optimum growth temperature of the strain was 30 °C, and the optimum growth pH was 7. The stain is well-suited for high-temperature stress (40 °C), and it could withstand 400 mg/L of PHE. The strain's PHE metabolism was assayed using GC-MS analyses. The results revealed that the YM-6 strain metabolized PHE via the phthalic acid pathway because the intermediates, such as phthalic acid, diethyl ester and phthalaldehydic acid, methyl ester, were detected. The use of this strain may be an attractive alternative for the bioremediation of polycyclic aromatic hydrocarbons in an aquatic environment.
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Affiliation(s)
- Ping Wang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China; Engineering Research Center of Biomembrane Water Purification and Utilization Technology, Ministry of Education, Maanshan 243002, China.
| | - Yongmin Zhang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China
| | - Jie Jin
- Appraisal Center for Environment & Engineering, Ministry of Ecology and Environment,Beijing 100012,China
| | - Tianhui Wang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China
| | - Jie Wang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China
| | - Bingyu Jiang
- College of Energy and Environment, Anhui University of Technology, Maanshan 243002, China
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Li X, Zhang X, Li L, Lin C, Dong W, Shen W, Yong X, Jia H, Wu X, Zhou J. Anaerobic biodegradation of pyrene by Klebsiella sp. LZ6 and its proposed metabolic pathway. ENVIRONMENTAL TECHNOLOGY 2020; 41:2130-2139. [PMID: 30522413 DOI: 10.1080/09593330.2018.1556348] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Pyrene is one of the polycyclic aromatic hydrocarbons, which are a potential threat to ecosystems due to their mutagenicity, carcinogenicity, and teratogenicity. In this study, several bacteria were isolated from oil contaminated sludge and their capacity to biodegrade pyrene was investigated. Of these bacteria, the monoculture strain LZ6 showed the highest pyrene anaerobic biodegradation rate of 33% after 30 days when the initial concentration was 50 mg/L, and was identified as Klebsiella sp. LZ6 by morphological observation, the GENIII technology of Biolog, and 16S rDNA gene sequence analysis. The influence of various culture parameters on the biodegradation of pyrene were evaluated, and Klebsiella sp. LZ6 all showed the high degradation rate at an inoculum of 10-20% (v/v), pH 6.0-8.4, temperature 30-38°C, and initial pyrene concentration of 50-150 mg/L. The intermediate metabolites of the anaerobic biodegradation were analyzed by GC-MS. Several metabolites were identified, such as pyrene, 4,5-dihydro-, phenanthrene, dibenzo-p-dioxin, and 4-hydroxycinnamate acid. The anaerobic metabolic pathway for the degradation of pyrene was inferred by the products. It seems that pyrene was first reduced to pyrene,4,5-dihydro- by the adding of two hydrogen atoms, and then the carbon-carbon bond cleavage at saturated carbon atoms generated phenanthrene.
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Affiliation(s)
- Xiang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- College of Environment, Nanjing Tech University, Nanjing, People's Republic of China
| | - Xueying Zhang
- College of Environment, Nanjing Tech University, Nanjing, People's Republic of China
| | - Lian Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- College of Environment, Nanjing Tech University, Nanjing, People's Republic of China
| | - Chaoba Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Weiran Shen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- College of Environment, Nanjing Tech University, Nanjing, People's Republic of China
| | - Xiaoyu Yong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Honghua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Xiayuan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Jun Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- Bioenergy Research Institute, Nanjing Tech University, Nanjing, People's Republic of China
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Gupta B, Puri S, Thakur IS, Kaur J. Comparative evaluation of growth kinetics for pyrene degradation by Acinetobacter pittii NFL and Enterobacter cloacae BT in the presence of biosurfactant. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2019.100369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Sangkharak K, Choonut A, Rakkan T, Prasertsan P. The Degradation of Phenanthrene, Pyrene, and Fluoranthene and Its Conversion into Medium-Chain-Length Polyhydroxyalkanoate by Novel Polycyclic Aromatic Hydrocarbon-Degrading Bacteria. Curr Microbiol 2020; 77:897-909. [PMID: 31960091 DOI: 10.1007/s00284-020-01883-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/10/2020] [Indexed: 11/25/2022]
Abstract
Screening of high-efficient polycyclic aromatic hydrocarbon (PAH)-degrading bacteria is important due to environmental contamination by PAHs. In this study, sediment contaminated with phenanthrene (Phe), pyrene (Pyr), and fluoranthene (Fluo) was used as a source of bacteria. The ability of these isolated bacteria to convert PAHs into valuable products was determined. Based on a primary screening, 20 bacterial isolates were obtained; however, only three strains showed a good PAH-degrading ability, and were identified as Pseudomonas aeruginosa, Pseudomonas sp., and Ralstonia sp. PAH-degrading genes were detected in all isolates. Notably, all selected strains could degrade PAHs using the ortho or meta cleavage pathways due to the presence of catechol dioxygenase genes. The ability of isolated strains to convert PAHs into polyhydroxyalkanoate (PHA) was also evaluated in both single and mixed cultures. Single cultures of P. aeruginosa PAH-P02 showed 100% degradation of PAHs, with the highest biomass (1.27 ± 0.02 g l-1) and PHA content (38.20 ± 1.92% dry cell weight). However, degradative ability and PHA production were decreased when mixtures of PAHs were used. This study showed that P. aeruginosa, Pseudomonas sp., and Ralstonia sp. were able to degrade PAHs and convert them into medium-chain-length (mcl)-PHA. A high content of 3-hydroxydecanoate (3HD, C10) was observed in this study. The formation of mcl-PHA with high 3HD content from Pyr and Fluo, and the assessment of mixed cultures converting PAHs to mcl-PHA, were novel contributions.
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Affiliation(s)
- Kanokphorn Sangkharak
- Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung, 93210, Thailand.
| | - Aophat Choonut
- Ph.D. Program in Biotechnology, Department of Biology, Faculty of Science, Thaksin University, Phatthalung, 93210, Thailand
| | - Thanaphorn Rakkan
- Ph.D. Program in Biotechnology, Department of Biology, Faculty of Science, Thaksin University, Phatthalung, 93210, Thailand
| | - Poonsuk Prasertsan
- Research and Development Office, Prince of Songkla University, Songkhla, 90112, Thailand
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Zango ZU, Jumbri K, Sambudi NS, Hanif Abu Bakar NH, Fathihah Abdullah NA, Basheer C, Saad B. Removal of anthracene in water by MIL-88(Fe), NH 2-MIL-88(Fe), and mixed-MIL-88(Fe) metal-organic frameworks. RSC Adv 2019; 9:41490-41501. [PMID: 35541585 PMCID: PMC9076480 DOI: 10.1039/c9ra08660a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
Three adsorbents based on the metal-organic frameworks (MOFs), viz.; MIL-88(Fe), NH2-MIL-88(Fe), and mixed-MIL-88(Fe) were synthesized using a microwave-assisted solvothermal technique. The as-synthesized MOFs were characterized by X-ray diffraction (XRD), Brunauer-Emmett-Teller (BET), field emission scanning microscopy (FESEM), X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), and Fourier transform infrared spectroscopy (FTIR). The MOFs were shown to possess highly crystalline and porous structures with specific surface areas of 1240, 941, and 1025 m2 g-1 and pore volumes of 0.7, 0.6 and 0.6 m3 g-1 for MIL-88(Fe), NH2-MIL-88(Fe) and mixed-MIL-88(Fe), respectively. Faster removal of a model polycyclic aromatic hydrocarbon, anthracene (ANT) within 25 minutes, was achieved when these MOFs were used as adsorbents in water. The removal efficiency was 98.3, 92.4 and 95.8% for MIL-88(Fe), NH2-MIL-88(Fe) and mixed-MIL-88(Fe), respectively. The kinetics and isotherms of the process were best statistically described by pseudo-second-order and Langmuir models, respectively, while the thermodynamic studies revealed the exothermic and spontaneous nature of the process. Docking simulations were found to be consistent with the experimental results with MIL-88(Fe) showing the best binding capacity with the ANT molecule.
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Affiliation(s)
- Zakariyya Uba Zango
- Fundamental and Applied Sciences Department, Universiti Teknologi PETRONAS Seri Iskandar Perak Malaysia
| | - Khairulazhar Jumbri
- Fundamental and Applied Sciences Department, Universiti Teknologi PETRONAS Seri Iskandar Perak Malaysia
| | - Nonni Soraya Sambudi
- Chemical Engineering Department, Universiti Teknologi PETRONAS Seri Iskandar Perak Malaysia
| | | | - Nor Ain Fathihah Abdullah
- Fundamental and Applied Sciences Department, Universiti Teknologi PETRONAS Seri Iskandar Perak Malaysia
| | - Chanbasha Basheer
- Department of Chemistry, King Fahd University of Petroleum and Minerals Dhahran Saudi Arabia
| | - Bahruddin Saad
- Fundamental and Applied Sciences Department, Universiti Teknologi PETRONAS Seri Iskandar Perak Malaysia
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Patel AB, Singh S, Patel A, Jain K, Amin S, Madamwar D. Synergistic biodegradation of phenanthrene and fluoranthene by mixed bacterial cultures. BIORESOURCE TECHNOLOGY 2019; 284:115-120. [PMID: 30927648 DOI: 10.1016/j.biortech.2019.03.097] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 05/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly recalcitrant compounds and difficult to degrade. Therefore in this work, using a bioremediation approach, mixed bacterial cultures (ASPF) was developed and enriched from polluted marine sediments capable of degrading 400 mg/L of phenanthrene and fluoranthene in Bushnell Hass medium. ASPF consists of 22 bacterial genera dominated by Azoarcus and Chelativorans. The biostimulation effect of three water soluble fertilizers (NPK, urea, and ammonium sulfate) showed that NPK and ammonium sulfate have enhanced the degradation, whereas urea has decreased their degradation. ASPF was also able to degrade phenanthrene and fluoranthene in the presence of petroleum hydrocarbons. But degradation was found to decrease in the presence of pathway intermediates (phthalic acid and catechol) due to enzymatic feedback inhibition. Optimum degradation of both PAHs was observed under room temperature, suggesting the practical applicability of ASPF.
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Affiliation(s)
- Avani Bharatkumar Patel
- Department of Biosciences, UGC Center of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol 388 315, Anand, Gujarat, India
| | - Shilpi Singh
- Department of Biosciences, UGC Center of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol 388 315, Anand, Gujarat, India
| | - Aaishwarya Patel
- P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, Charusat Campus, Changa 388 421, Anand, Gujarat, India
| | - Kunal Jain
- Department of Biosciences, UGC Center of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol 388 315, Anand, Gujarat, India
| | - Seema Amin
- P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, Charusat Campus, Changa 388 421, Anand, Gujarat, India
| | - Datta Madamwar
- Department of Biosciences, UGC Center of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol 388 315, Anand, Gujarat, India.
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Zhou Y, Gao X. Characterization of Biofilm Formed by Phenanthrene-Degrading Bacteria on Rice Root Surfaces for Reduction of PAH Contamination in Rice. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E2002. [PMID: 31195653 PMCID: PMC6603869 DOI: 10.3390/ijerph16112002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 01/13/2023]
Abstract
One effective method in to reduce the uptake of organic contaminants by plants is the development of a root barrier. In this study, the characterization of biofilm structure and function by phenanthrene-degrading Pseudomonas sp. JM2-gfp on rice root surfaces were carried out. Our results showed that root surfaces from three rice species, namely Liaojing401, Koshihikari, and Zhenzhuhong all present hydrophobicity and a high initial adhesion of strain JM2-gfp. Matured robust biofilm formation occurred at 48 h on the root surfaces. The biofilm exhibited cell dense aggregates and biomass embedded in the extracellular polymeric substance (EPS) matrix. EPS composition results showed that the proteins, carbohydrates, lipids and nucleic acids are produced in the biofilm, while the content varied with rice species. Under the initial concentration of phenanthrene 50 mg·L-1, the residual phenanthrene in plant roots from 'Zhengzhuhong', 'Koshihikari' and 'Liaojing401' with biofilm mediated were significantly decreased by 71.9%, 69.3% and 58.7%, respectively, compared to those without biofilm groups after 10 days of exposure. Thus, the biofilm colonized on roots plays an important role of degradation in order to reduce the level of phenanthrene uptake of plants. Thereby, the present work provides significant new insights into lowering the environmental risks of polycyclic aromatic hydrocarbons (PAHs) in crop products from contaminated agriculture soils.
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Affiliation(s)
- Yuman Zhou
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, China.
| | - Xiaorong Gao
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, China.
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Luo J, Wu L, Chen Y, Feng L, Cao J. Integrated approach to enhance the anaerobic biodegradation of benz[α]anthracene: A high-molecule-weight polycyclic aromatic hydrocarbon in sludge by simultaneously improving the bioavailability and microbial activity. JOURNAL OF HAZARDOUS MATERIALS 2019; 365:322-330. [PMID: 30447640 DOI: 10.1016/j.jhazmat.2018.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 10/20/2018] [Accepted: 11/04/2018] [Indexed: 06/09/2023]
Abstract
The biodegradation of benz[α]anthracene (BaA), which was a high-molecule-weight PAH, was enhanced via a combination of alkaline and alkyl polyglucosides (APG) treatment during waste activated sludge (WAS) anaerobic fermentation. The biodegradation efficiency of BaA was increased from 14.1% in the control to 30.2 and 47.8% in pH 10 and pH 10 & APG reactors, respectively. Mechanism investigations found that the alkaline and APG treatments stimulated the processes of BaA desorption from sludge and transfer/entry into microorganisms, and ultimately improved the BaA bioavailability. Meanwhile, the huge released substrates from WAS not only served as carbon sources but also involved in the electron transfer among microorganisms which contributed to the BaA biodegradation process. Moreover, the microbial activities involved in BaA biodegradation, including the abundances of functional bacteria, activities of enzymes and quantities of genes, were also incremented due to the alkaline and APG treatments. Overall, the simultaneous improvement of BaA bioavailability and microbial activities enhanced its biodegradation efficiency.
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Affiliation(s)
- Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Lijuan Wu
- Jiangsu Provincial Academy of Environmental Science, Nanjing, China
| | - Yinguang Chen
- State key laboratory of pollution control and Resources reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Leiyu Feng
- State key laboratory of pollution control and Resources reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
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Li X, Chu Z, Du X, Qiu Y, Li Y. Combined molecular docking, homology modelling and density functional theory studies to modify dioxygenase to efficiently degrade aromatic hydrocarbons. RSC Adv 2019; 9:11465-11475. [PMID: 35520246 PMCID: PMC9063381 DOI: 10.1039/c8ra10663k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/06/2019] [Indexed: 01/16/2023] Open
Abstract
To promote the biodegradation of aromatic hydrocarbons in petroleum-contaminated soils, naphthalene dioxygenase (NDO), which is the key metabolic enzyme that degrades aromatic hydrocarbons, was modified using molecular docking and homology modelling. The novel NDO enzymes screened can efficiently degrade the target aromatic hydrocarbons naphthalene, anthracene, pyrene and benzo[a]pyrene. The docking showed that the key amino acid residues at the binding site of the NDO enzyme include both hydrophilic residues (Asn201, Asp205, His208, His213, His295 and Asn297) and hydrophobic residues (Phe202, Ala206, Val209, Leu307, Phe352 and Trp358), and the hydrophilic residues were replaced by hydrophobic residues to design 54 kinds of NDO enzyme modification schemes. A total of 14 kinds of novel NDO enzymes designed were found to simultaneously increase the binding affinity to the target aromatic hydrocarbons. The energy barrier and rate constant of the degradation reaction for the NDO enzyme modification were calculated using Gaussian09 software and the KiSThelP program. The novel NDO-7 enzyme exhibited decreases in the energy barrier of 76.28, 26.35, 4.39 and 1.88 kcal mol−1 and increases in the rate constant of 54, 18, 12 and 5 orders of magnitude in the degradation reactions with naphthalene, anthracene, pyrene and benzo[a]pyrene, respectively. These results provide a theoretical basis for the efficient degradation of aromatic hydrocarbons and the modification of their key metabolic enzymes. To promote the biodegradation of aromatic hydrocarbons in petroleum-contaminated soils, naphthalene dioxygenase (NDO), which is the key metabolic enzyme that degrades aromatic hydrocarbons, was modified using molecular docking and homology modelling.![]()
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Affiliation(s)
- Xingchun Li
- State Key Laboratory of Petroleum Pollution Control
- Beijing 102206
- China
| | - Zhenhua Chu
- College of Environmental Science and Engineering
- North China Electric Power University
- Beijing 102206
- China
| | - Xianyuan Du
- State Key Laboratory of Petroleum Pollution Control
- Beijing 102206
- China
| | - Youli Qiu
- College of Environmental Science and Engineering
- North China Electric Power University
- Beijing 102206
- China
| | - Yu Li
- College of Environmental Science and Engineering
- North China Electric Power University
- Beijing 102206
- China
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Rathour R, Gupta J, Tyagi B, Kumari T, Thakur IS. Biodegradation of pyrene in soil microcosm by Shewanella sp. ISTPL2, a psychrophilic, alkalophilic and halophilic bacterium. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.biteb.2018.10.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Jiang Y, Zhang Z, Zhang X. Co-biodegradation of pyrene and other PAHs by the bacterium Acinetobacter johnsonii. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 163:465-470. [PMID: 30075449 DOI: 10.1016/j.ecoenv.2018.07.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/15/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) usually co-exist in environment with interactional effects. Currently, Acinetobacter johnsonii was employed to degrade 400 mg L-1 of pyrene (PYR) and kinetic modeling indicated substrate inhibition over 76 mg L-1 by introducing an inhibition constant parameter. In PAHs co-biodegradation, naphthalene (NAP) dominated biodegradation processes through the preferential utilization as growth substrate. The peak biodegradation of PYR increased to 415 mg L-1 with 65 mg L-1 of NAP. Furthermore, phenanthrene (PHE), PYR and anthracene (ANT) were degraded in turn and ended in reverse order. When the concentrations reached their respective limiting concentration of 22%, ANT could not be degraded and PHE and PYR biodegradations also respectively terminated at 66 and 45 h later with a removal rate of 40% and 26% due to very low specific activities of salicylate hydroxylase and catechol 2,3-dioxygenase. However, by introducing 125-133 mg L-1 of NAP, the bacterial potential was effectively enhanced to 29% after cell underwent a re-stimulation stage with the exhaustion of NAP. NAP prominently contributed to cell growth to stimulate secretion of key enzymes, but the advantage would gradually get lost with the decline of its titer. To research the interplay of PAHs is conducive to targeted decontamination.
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Affiliation(s)
- Yan Jiang
- Engineering Research Centre for Waste Oil Recovery Technology and Equipment, Ministry Education, Chongqing Technology and Business University, Chongqing, PR China.
| | - Zhe Zhang
- Engineering Research Centre for Waste Oil Recovery Technology and Equipment, Ministry Education, Chongqing Technology and Business University, Chongqing, PR China
| | - Xianming Zhang
- Engineering Research Centre for Waste Oil Recovery Technology and Equipment, Ministry Education, Chongqing Technology and Business University, Chongqing, PR China
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Kamyabi A, Nouri H, Moghimi H. Characterization of pyrene degradation and metabolite identification by Basidioascus persicus and mineralization enhancement with bacterial-yeast co-culture. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 163:471-477. [PMID: 30075450 DOI: 10.1016/j.ecoenv.2018.07.098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
In this paper, we introduce pyrene degrader halotolerant yeast, Basidioascus persicus EBL-C16 and characterize its growth in different salt concentrations. Investigation of the removal of different concentrations of pyrene showed that B. persicus EBL-C16 was able to eliminate 50-90% of pyrene in the presence of 2.5% salt and also mineralize phenanthrene and anthracene. Growth and depletion kinetics of 500 mg L-1 of pyrene removal revealed 79% degradation and the growth rate reached 1.4 g L-1 of dry weight, decomposition constant rate was obtained as 0.074 day-1 and the half-life was 9.33 days. When minimal medium was replaced with Persian Gulf water, 48% increase in pyrene removal was detected by yeast strain. The mass spectrometry of the treated samples specified the phthalic acid pathway as the metabolic pathway of pyrene degradation by B. persicus. Study of the synergistic effect of using rhamnolipid and co-culture of yeast with Pseudomonas putida ATCC 12633 revealed that the combination of both of them with B. persicus increased 21% pyrene elimination. The findings of this study can be used to comprehend the mechanisms of oil hydrocarbon degradation by yeasts. Furthermore, the results demonstrated the promising potential of yeast-bacteria co-culture for cleaning of oil spills in marine and saline soil contaminated areas.
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Affiliation(s)
- A Kamyabi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - H Nouri
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - H Moghimi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
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Carlos C, Fan H, Currie CR. Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers. Front Microbiol 2018; 9:364. [PMID: 29545786 PMCID: PMC5839234 DOI: 10.3389/fmicb.2018.00364] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/15/2018] [Indexed: 01/05/2023] Open
Abstract
Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.
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Affiliation(s)
- Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,U.S. Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Huan Fan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,U.S. Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
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40
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Sommaggio LRD, Mazzeo DEC, Sant' Anna DDAES, Levy CE, Marin-Morales MA. Ecotoxicological and microbiological assessment of sewage sludge associated with sugarcane bagasse. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:550-557. [PMID: 28918337 DOI: 10.1016/j.ecoenv.2017.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
Sewage sludge (SS) obtained after sewage treatment process may contain several toxic substances. Bioremediation can decrease the toxicity of the sludge, mainly when it is associated with stimulant agents, such as sugarcane bagasse (B). Samples of pure SS (SSP); SS+B; SS+Soil; and SS+B+Soil were bioremediated for 1, 3, and 6 months (T1, T2, and T3, respectively). After each period, the cytotoxic, genotoxic, and mutagenic potentials of the solid samples and their respective aqueous extracts (aqueous eluate and percolate water) were evaluated by the Allium cepa test. A microbiological analysis of the samples was also performed after each period tested. All solid samples of SS+B (in T1, T2, and T3) and the solid sample of SSP (treatment T3) showed a significant decrease of cell division (cytotoxic effects). The aqueous eluate extracts of SS+B (T1 and T3) and SSP (T2 and T3) induced cytotoxic effect. The solid sample of SS+B (T2 and T3) and aqueous extracts of SSP (T1) were genotoxic, indicating a harmful effect of SS on A. cepa, even after 6 months of bioremediation. There was an alternation in the microbial community both in diversity and in abundance, with the predominance of nonfermenting gram-negative bacilli. The tested bioremediation periods were not sufficient for the complete detoxification of SS, and the use of B did not seem to contribute to the degradation of the pollutants to inert compounds. These data emphasize that a specific relationship should exist between the sludge characteristic and the biostimulating agent used to promote a more efficient bioremediation. These results suggest the necessity to study longer periods of biodegradation and the use of other decomposing agents for greater safety and sustainability for the agricultural use of this residue.
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Affiliation(s)
- Lais Roberta Deroldo Sommaggio
- Department of Biology, Institute of Biosciences, São Paulo State University (Unesp), Av. 24-A, 1515, 13506-900 Rio Claro, SP, Brazil.
| | - Dânia Elisa Christofoletti Mazzeo
- Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University (Unesp), Rua Professor Francisco Degni, 55, 14800-060, Araraquara, SP, Brazil.
| | - Débora de Andrade E Silva Sant' Anna
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Rua Alexander Fleming, 105, 13081-970 Campinas, SP, Brazil.
| | - Carlos Emílio Levy
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Rua Alexander Fleming, 105, 13081-970 Campinas, SP, Brazil.
| | - Maria Aparecida Marin-Morales
- Department of Biology, Institute of Biosciences, São Paulo State University (Unesp), Av. 24-A, 1515, 13506-900 Rio Claro, SP, Brazil.
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Biodegradation of fluoranthene by Paenibacillus sp. strain PRNK-6: a pathway for complete mineralization. Arch Microbiol 2017; 200:171-182. [DOI: 10.1007/s00203-017-1431-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/04/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
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42
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Fang Y, Zhang LS, Wang J, Zhou Y, Ye BC. Identification of the di-n-butyl phthalate-biodegrading strains and the biodegradation pathway in strain LMB-1. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s000368381703005x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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Zhang H, Li M, Li J, Wang G, Liu Y. Purification and properties of a novel quizalofop-p-ethyl-hydrolyzing esterase involved in quizalofop-p-ethyl degradation by Pseudomonas sp. J-2. Microb Cell Fact 2017; 16:80. [PMID: 28490371 PMCID: PMC5424357 DOI: 10.1186/s12934-017-0695-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/04/2017] [Indexed: 11/22/2022] Open
Abstract
Quizalofop-p-ethyl (QPE) is a post-emergence herbicide that effectively controls grass weeds and is often detected in the environment. However, the biochemical and molecular mechanisms of QPE degradation in the environment remains unclear. In this study, a highly effective QPE-degrading bacterial strain J-2 was isolated from acclimated activated sludge and identified as a Pseudomonas sp., containing the QPE breakdown metabolite quizalofop acid (QA) identified by Liquid Chromatography-Ion Trap-Mass Spectrometry (LC-IT-MSn) analysis. A novel QPE hydrolase esterase-encoding gene qpeH was cloned from strain J-2 and functionally expressed in Escherichia coli BL21 (DE3). The specific activity of recombinant QpeH was 198.9 ± 2.7 U mg−1 for QPE with Km and Kcat values of 41.3 ± 3.6 μM and 127.3 ± 4.5 s−1. The optimal pH and temperature for the recombinant QpeH were 8.0 and 30 °C, respectively and the enzyme was activated by Ca2+, Cd2+, Li+, Fe3+ and Co2+ and inhibited by Ni2+, Fe2+, Ag+, DEPC, SDS, Tween 80, Triton X, β-mercaptoethanol, PMSF, and pCMB. In addition, the catalytic efficiency of QpeH toward different AOPP herbicides in descending order was as follows: fenoxaprop-P-ethyl > quizalofop-P-tefuryl > QPE > haloxyfop-P-methyl > cyhalofopbutyl > clodinafop-propargyl. On the basis of the phylogenetic analysis and multiple sequence alignment, the identified enzyme QpeH, was clustered with esterase family V, suggesting a new member of this family because of its low similarity of amino acid sequence with esterases reported previously.
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Affiliation(s)
- Hui Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Mengya Li
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Jie Li
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Guangli Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
| | - Yuan Liu
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
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Singh P, Tiwary BN. Optimization of conditions for polycyclic aromatic hydrocarbons (PAHs) degradation by Pseudomonas stutzeri P2 isolated from Chirimiri coal mines. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.02.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Zhu X, Wang W, Crowley DE, Sun K, Hao S, Waigi MG, Gao Y. The endophytic bacterium Serratia sp. PW7 degrades pyrene in wheat. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:6648-6656. [PMID: 28083742 DOI: 10.1007/s11356-016-8345-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/28/2016] [Indexed: 06/06/2023]
Abstract
This research was conducted to isolate polycyclic aromatic hydrocarbon-degrading (PAH-degrading) endophytic bacteria and investigate their potential in protecting plants against PAH contamination. Pyrene-degrading endophytic bacteria were isolated from plants grown in PAH-contaminated soil. Among these endophytic bacteria, strain PW7 (Serratia sp.) isolated from Plantago asiatica was selected to investigate the suppression of pyrene accumulation in Triticum aestivum L. In the in vitro tests, strain PW7 degraded 51.2% of the pyrene in the media within 14 days. The optimal biodegradation conditions were pH 7.0, 30 °C, and MS medium supplemented with additional glucose, maltose, sucrose, and peptones. In the in vivo tests, strain PW7 successfully colonized the roots and shoots of inoculated (E+) wheat plants, and its colonization decreased pyrene accumulation and pyrene transportation from roots to shoots. Remarkably, the concentration of pyrene in shoots decreased much more than that in roots, suggesting that strain PW7 has the potential for protecting wheat against pyrene contamination and mitigating the threat of pyrene to human health via food consumption.
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Affiliation(s)
- Xuezhu Zhu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Wanqing Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - David E Crowley
- The Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Kai Sun
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Shupeng Hao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, People's Republic of China.
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Bezza FA, Chirwa EMN. Pyrene biodegradation enhancement potential of lipopeptide biosurfactant produced by Paenibacillus dendritiformis CN5 strain. JOURNAL OF HAZARDOUS MATERIALS 2017; 321:218-227. [PMID: 27627697 DOI: 10.1016/j.jhazmat.2016.08.035] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/26/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Effect of biosurfactant on biodegradation of pyrene was studied using a microbial consortium predominantly composed of Pseudomonas viridiflava (49.5%) and Pseudomonas nitroreducens (32.5%) in a batch experiment containing lipopeptidic biosurfactant, produced by Paenibacillus dendritiformis CN5 strain, and mineral salt medium. The results showed that the lipopeptide at 600 and 300mgL-1 enhanced pyrene degradation to 83.5% and 67% respectively in 24days compared to 16% degradation in its absence. However degradation of pyrene was reduced to 57% as the lipopeptide supplementation was raised to 900mgL-1. This demonstrates that the biodegradation of pyrene was found to increase with an increase in the lipopeptide concentration up to a threshold level. The experimental data were fitted to the logistic kinetic model which provided best fit with a coefficient of determination (R2) values≥0.97. Maximum specific growth rate, μmax of 0.97 and 0.69d-1 were achieved in the 600 and 300mgL-1 lipopeptide amendments in comparison to 0.54d-1 in the unamended one. The carrying capacity, Xmax increased 4.4-fold in 600mgL-1 lipopeptide supplemented samples in comparison to its absence. Generally the lipopeptide showed potential application in improving bioremediation of polycyclic aromatic hydrocarbons contaminated environmental media.
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Affiliation(s)
- Fisseha Andualem Bezza
- Water Utilisation and Environmental Engineering Division, Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa
| | - Evans M Nkhalambayausi Chirwa
- Water Utilisation and Environmental Engineering Division, Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa.
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47
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Jin J, Yao J, Liu W, Zhang Q, Liu J. Fluoranthene degradation and binding mechanism study based on the active-site structure of ring-hydroxylating dioxygenase in Microbacterium paraoxydans JPM1. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:363-371. [PMID: 27722881 DOI: 10.1007/s11356-016-7809-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
In this study, a gram-positive fluoranthene-degrading bacterial strain was isolated from crude oil in Dagang Oilfield and identified as Microbacterium paraoxydans JPM1 by the analysis of 16S rDNA sequence. After 25 days of incubation, the strain JPM1 could degrade 91.78 % of the initial amount of fluoranthene. Moreover, four metabolites 9-fluorenone-1-carboxylic acid, 9-fluorenone, phthalic acid, and benzoic acid were detected in the culture solution. The gene sequence encoding the aromatic-ring-hydroxylating dioxygenase was amplified in the strain JPM1 by PCR. Based on the translated protein sequence, a homology modeling method was applied to build the crystal structure of dioxygenase. Subsequently, the interaction mechanism between fluoranthene and the active site of dioxygenase was simulated and analyzed by molecular docking. Consequently, a feasible degrading pathway of fluoranthene in the strain JPM1 was proposed based on the metabolites and the interaction analyses. Additionally, the thermodynamic analysis showed that the strain JPM1 had high tolerance for fluoranthene, and the influence of fluoranthene for the bacterial growth activity was negligible under 100 to 400 mg L-1 concentrations. Taken together, this study indicates that the strain JPM1 has high potential for further study in bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sites.
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Affiliation(s)
- Jingnan Jin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Jun Yao
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Wenjuan Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Qingye Zhang
- College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianli Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China
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48
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Deka H, Lahkar J. Biodegradation of Benzo(a)anthracene Employing Paenibacillus sp. HD1PAH: A Novel Strain Isolated from Crude Oil Contaminated Soil. Polycycl Aromat Compd 2016. [DOI: 10.1080/10406638.2016.1253593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Hemen Deka
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - Jiumoni Lahkar
- Biological Sciences and Technology Division, CSIR- North East Institute of Science and Technology, Jorhat, Assam, India
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49
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Jin J, Yao J, Zhang Q, Liu J. Biodegradation of pyrene by pseudomonas sp. JPN2 and its initial degrading mechanism study by combining the catabolic nahAc gene and structure-based analyses. CHEMOSPHERE 2016; 164:379-386. [PMID: 27596825 DOI: 10.1016/j.chemosphere.2016.08.113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 05/02/2023]
Abstract
In this study, a pyrene-degrading bacterial strain Pseudomonas sp. JPN2 was isolated from crude oil in Dagang Oilfield, China. The degrading percent of the strain JPN2 to pyrene was increased with the extension of culture time and achieved a maximum of 82.88% after 25 d culture. Meanwhile, four metabolites 4,5-dihydroxy-4,5-dihydropyrene, 4-phenanthrol, 1-hydroxy-2-naphthoic acid and phthalate were detected in the culture solution by GC-MS analysis. In addition, DNA fragments of nahAc gene, encoding α subunit of naphthalene dioxygenase, were amplified by PCR program and sequenced. As a result, it was presumed that the initial cleavage of the aromatic rings on pyrene was occurred at C4 and C5 positions and formed the intermediate 4,5-dihydroxy-4,5-dihydropyrene. This issue had been verified by the interaction analysis between pyrene and the active site of naphthalene dioxygenase in the strain JPN2 by molecular docking. Meanwhile, the differences of the amino acid residues in the active sites of template and target enzymes may be a factor leading to the different biological activity between the strain JPN2 and the other bacteria from the genus Pseudomonas. Additionally, the microcalorimetry analysis displayed that the strain JPN2 had high tolerance for pyrene, and the effect could be negligible under the experimental concentration (100 mg L-1). Consequently, the strain JPN2 was considered as an excellent candidate for the further bioremediation study of pyrene and the other aromatic contaminants.
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Affiliation(s)
- Jingnan Jin
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jun Yao
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; State Key Laboratory of Biogeology and Environmental Geology of Chinese Ministry of Education, and Sino-Hungarian Joint Laboratory of Environmental Science and Health, China University of Geoscience, Wuhan 430074, China.
| | - Qingye Zhang
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianli Liu
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
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50
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Zhao JK, Li XM, Ai GM, Deng Y, Liu SJ, Jiang CY. Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil. JOURNAL OF HAZARDOUS MATERIALS 2016; 318:90-98. [PMID: 27415596 DOI: 10.1016/j.jhazmat.2016.06.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/26/2016] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Microbial degradation of polycyclic aromatic hydrocarbons (PAHs) is the primary process of removing PAHs from environments. The metabolic pathway of PAHs in pure cultures has been intensively studied, but cooperative metabolisms at community-level remained to be explored. In this study, we determined the dynamic composition of a microbial community and its metabolic intermediates during fluoranthene degradation using high-throughput metagenomics and gas chromatography-mass spectrometry (GC-MS), respectively. Subsequently, a cooperative metabolic network for fluoranthene degradation was constructed. The network shows that Mycobacterium contributed the majority of ring-hydroxylating and -cleavage dioxygenases, while Diaphorobacter contributed most of the dehydrogenases. Hyphomicrobium, Agrobacterium, and Sphingopyxis contributed to genes encoding enzymes involved in downstream reactions of fluoranthene degradation. The contributions of various microbial groups were calculated with the PICRUSt program. The contributions of Hyphomicrobium to alcohol dehydrogenases were 62.4% in stage 1 (i.e., when fluoranthene was rapidly removed) and 76.8% in stage 3 (i.e., when fluoranthene was not detectable), respectively; the contribution of Pseudomonas were 6.6% in stage 1 and decreased to 1.2% in subsequent stages. To the best of the author's knowledge, this report describes the first cooperative metabolic network to predict the contributions of various microbial groups during PAH-degradation at community-level.
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Affiliation(s)
- Jian-Kang Zhao
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ming Li
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China
| | - Ye Deng
- Research Center of Ecological and Environmental Science, CAS, Beijing, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China.
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