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Frantsuzova E, Bogun A, Kopylova O, Vetrova A, Solyanikova I, Streletskii R, Delegan Y. Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135. BIOLOGY 2024; 13:339. [PMID: 38785821 PMCID: PMC11117675 DOI: 10.3390/biology13050339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the "panIGRome" of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Olga Kopylova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Pushchino Branch of Federal State Budgetary Educational Institution of Higher Education “Russian Biotechnology University (ROSBIOTECH)”, 142290 Pushchino, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Inna Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Regional Microbiological Center, Belgorod State University, 308015 Belgorod, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
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Zavala-Meneses SG, Firrincieli A, Chalova P, Pajer P, Checcucci A, Skultety L, Cappelletti M. Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source. Microorganisms 2024; 12:753. [PMID: 38674697 PMCID: PMC11052242 DOI: 10.3390/microorganisms12040753] [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: 03/18/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 µg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.
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Affiliation(s)
- Sofía G. Zavala-Meneses
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Faculty of Science, Charles University, Vinicna 5, 12844 Prague, Czech Republic
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy or (A.F.); (M.C.)
| | - Petra Chalova
- Biomedical Research Center, Slovak Academy of Sciences, Dubravska c. 9, 845 05 Bratislava, Slovakia;
- Faculty of Pharmacy, Comenius University, Odbojarov 10, 832 32 Bratislava, Slovakia
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, U Vojenske Nemocnice 1200, 16902 Prague, Czech Republic;
| | - Alice Checcucci
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50100 Firenze, Italy;
| | - Ludovit Skultety
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Biomedical Research Center, Slovak Academy of Sciences, Dubravska c. 9, 845 05 Bratislava, Slovakia;
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy or (A.F.); (M.C.)
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Li J, Peng W, Yin X, Wang X, Liu Z, Liu Q, Deng Z, Lin S, Liang R. Identification of an efficient phenanthrene-degrading Pseudarthrobacter sp. L1SW and characterization of its metabolites and catabolic pathway. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133138. [PMID: 38086304 DOI: 10.1016/j.jhazmat.2023.133138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/25/2023] [Accepted: 11/28/2023] [Indexed: 02/08/2024]
Abstract
Phenanthrene, a typical chemical of polycyclic aromatic hydrocarbons (PAHs) pollutants, severely threatens health of wild life and human being. Microbial degradation is effective and environment-friendly for PAH removal, while the phenanthrene-degrading mechanism in Gram-positive bacteria is unclear. In this work, one Gram-positive strain of plant growth-promoting rhizobacteria (PGPR), Pseudarthrobacter sp. L1SW, was isolated and identified with high phenanthrene-degrading efficiency and great stress tolerance. It degraded 96.3% of 500 mg/L phenanthrene in 72 h and kept stable degradation performance with heavy metals (65 mg/L of Zn2+, 5.56 mg/L of Ni2+, and 5.20 mg/L of Cr3+) and surfactant (10 CMC of Tween 80). Strain L1SW degraded phenanthrene mainly through phthalic acid pathway, generating intermediate metabolites including cis-3,4-dihydrophenanthrene-3,4-diol, 1-hydroxy-2-naphthoic acid, and phthalic acid. A novel metabolite (m/z 419.0939) was successfully separated and identified as an end-product of phenanthrene, suggesting a unique metabolic pathway. With the whole genome sequence alignment and comparative genomic analysis, 19 putative genes associated with phenanthrene metabolism in strain L1SW were identified to be distributed in three gene clusters and induced by phenanthrene and its metabolites. These findings advance the phenanthrene-degrading study in Gram-positive bacteria and promote the practical use of PGPR strains in the bioremediation of PAH-contaminated environments.
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Affiliation(s)
- Junlan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xianqi Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhixiang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qinchen Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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Li B, Chen J, Huang P, Weng T, Wen Y, Yang H, Liu Y, Xia L. Induction of attenuated Nocardia seriolae and their use as live vaccine trials against fish nocardiosis. FISH & SHELLFISH IMMUNOLOGY 2022; 131:10-20. [PMID: 36162777 DOI: 10.1016/j.fsi.2022.09.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/09/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Nocardia seriolae, a Gram-positive facultative intercellular pathogen, has been identified as the causative agent of fish nocardiosis, causing substantial mortality and morbidity of a wide range of fish species. Looking into that fact, the effective vaccine against this pathogen is urgently needed to control the significant losses in aquaculture practices. In order to induct attenuated strains for developing the potential live vaccines, the mutagenic N. seriolae strain S-250 and U-20 were obtained from wild-type strain ZJ0503 through continuous passaging and ultraviolet (UV) irradiation, respectively. Additionally, the biological characteristic, virulence, stability, mediating immune response and supplying protective efficacy to hybrid snakehead of the S-250 and U-20 strains were determined in the present study. The results showed that U-20 strain displayed dramatic changes in morphological characteristic and significant decreased in the virulence to hybrid snakehead, while that of S-250 strain had no obvious different in comparison to ZJ0503 strain. When hybrid snakehead were intraperitoneally injected with ZJ0503, S-250 and U-20 strains at their respective sub-clinical dosage, the non-specific immunity parameters (serum LYZ, POD, ACP, AKP and SOD activities), specific antibody (IgM) titers production and immune-related genes (CC1, CC2, IL-1β, IL-8, TNFα, IFNγ, MHCIα, MHCIIα, CD4, CD8α, TCRα and TCRβ) expression were up-regulated, indicating that they were able to trigger humoral and cell-mediated immune responses. Furthermore, the protective efficacy in hybrid snakehead after vaccination with ZJ0503, S-250 and U-20 strains, in terms of relative percentage survival (RPS), were 28.85%, 56.89% and 89.65% respectively. Taken together, two attenuated N. seriolae strains S-250 and U-20 were obtained successfully and they could elicit strong immune response and supply protective efficacy to hybrid snakehead against N. seriolae, which suggested that these two attenuated strains were the potential candidates for live vaccine development to control fish nocardiosis in aquaculture.
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Affiliation(s)
- Bei Li
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Jianlin Chen
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China.
| | - Pujiang Huang
- Shenzhen Fishery Development and Research Center, Shenzhen, Guangdong, China
| | - Tingting Weng
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yiming Wen
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Huiyuan Yang
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yansheng Liu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Liqun Xia
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong Ocean University, Zhanjiang, Guangdong, China.
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Wen L, Huang Y, Wang W, Zhang L, Xu J, Li Z, Xu P, Tang H. A novel Diaphorobacter sp. strain isolated from saponification wastewater shows highly efficient phenanthrene degradation. ENVIRONMENTAL RESEARCH 2022; 214:114047. [PMID: 35964667 DOI: 10.1016/j.envres.2022.114047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene, are a type of organic pollutants that exist widely in the environment. Of the currently known degradation methods, bioremediation is a desirable and feasible option. A novel Diaphorobacter sp. Strain MNS-0 was isolated from saponification wastewater and showed the ability to degrade phenanthrene, fluorene, acenaphthene, anthracene, benzo[a]anthracene, or chrysene using phenanthrene as the sole carbon source. Gas chromatography mass spectroscopy analysis of catabolic intermediates indicates that phenanthrene degradation occurs through the phthalic acid pathway in strain MNS-0. Genome sequencing shows that strain MNS-0 has two plasmids and one chromosome containing a presumptive phenanthrene degradation gene cluster. Strain MNS-0 was able to completely degrade 100 mg/L phenanthrene within 40 h and tolerate up to 10 g/L NaCl at pH 9.0, while maintaining phenanthrene degradation activity. We thus propose that strain MNS-0 is an effective degrader for bioremediation of PAHs pollution, even in relatively harsh alkali environments such as saponification wastewater.
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Affiliation(s)
- Lingyu Wen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, And School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yiqun Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, And School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, And School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Lige Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, And School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jijun Xu
- Befar Group Co., LTD., Binzhou, Shandong, 256619, China
| | - Zhao Li
- Befar Group Co., LTD., Binzhou, Shandong, 256619, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, And School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, And School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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Zain Ul Arifeen M, Ma Y, Wu T, Chu C, Liu X, Jiang J, Li D, Xue YR, Liu CH. Anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungi isolated from anaerobic coal-associated sediments at 2.5 km below the seafloor. CHEMOSPHERE 2022; 303:135062. [PMID: 35618067 DOI: 10.1016/j.chemosphere.2022.135062] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Fungi represent the dominant eukaryotic group in the deep biosphere and well-populated in the anaerobic coal-bearing sediments up to ∼2.5 km below seafloor (kmbsf). But whether fungi are able to degrade and utilize coal to sustain growth in the anaerobic sub-seafloor environment remains unknown. Based on biodegradation investigation, we found that fungi isolated from sub-seafloor sediments at depths of ∼1.3-∼2.5 kmbsf showed a broad range of polycyclic aromatic hydrocarbons (PAHs) anaerobic degradation rates (3-25%). Among them, the white-rot fungus Schizophyllium commune 20R-7-F01 exhibited the highest degradation, 25%, 18% and 13%, of phenanthrene (Phe), pyrene (Pyr) and benzo[a]pyrene (BaP); respectively, after 10 days of anaerobic incubation. Phe was utilized well and about 40.4% was degraded by the fungus, after 20 days of anaerobic incubation. Moreover, the ability of fungi to degrade PAHs was positively correlated with the anaerobic growth of fungi, indicating that fungi can use PAHs as a sole carbon source under anoxic conditions. In addition, fungal degradation of PAHs was found to be related to the activity of carboxylases, but little or nothing to do with the activity of lignin modifying enzymes such as laccase (Lac), manganese peroxidase (MnP) and lignin peroxidase (LiP). These results suggest that sub-seafloor fungi possess a special mechanism to degrade and utilize PAHs as a carbon and energy source under anaerobic conditions. Furthermore, fungi living in sub-seafloor sediments may not only play an important role in carbon cycle in the anaerobic environments of the deep biosphere, but also be able to persist in deep sediment below seafloor for millions of years by using PAHs or related compounds as carbon and energy source. This anaerobic biodegradation ability could make these fungi suitable candidates for bioremediation of toxic pollutants such as PAHs from anoxic environments.
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Affiliation(s)
- Muhammad Zain Ul Arifeen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yunan Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tianshang Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chen Chu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Junpeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dongxu Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ya-Rong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
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Qiu X, Wang W, Zhang L, Guo L, Xu P, Tang H. A thermophile Hydrogenibacillus sp. strain efficiently degrades environmental pollutants polycyclic aromatic hydrocarbons. Environ Microbiol 2021; 24:436-450. [PMID: 34897956 DOI: 10.1111/1462-2920.15869] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/06/2021] [Indexed: 11/27/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants threatening ecosystems and human health. Here, we isolated and characterized a new strain, Hydrogenibacillus sp. N12, which is a thermophilic PAH-degrader. Strain N12 utilizes naphthalene as a sole carbon and energy source above 60°C and co-metabolizes many other PAHs as well. The metabolites were identified in the catabolism of naphthalene by gas chromatography-mass spectrometry (GC-MS) and stable isotopic analysis. Based on the identified metabolites, we proposed two possible metabolic pathways, one via salicylic acid and the other via phthalic acid. Whole-genome sequencing reveals that strain N12 possesses a small chromosome of 2.6 Mb. Combining genetic and transcriptional information, we reveal a new gene cluster for the naphthalene degradation. The genes, designated as narAaAb that are predicted to encode the alpha and beta subunits of naphthalene dioxygenase, were subsequently subcloned into Escherichia coli and the enzyme activity was detected by whole-cell transformation. Capacity to degrade several other tricyclic-PAHs was also characterized, suggesting co-existence of other constitutively expressed enzyme systems in strain N12 in addition to the naphthalene degradation gene cluster. Our study provides insights into the potential of the thermophilic PAH-degrader in biotechnology and environmental management applications.
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Affiliation(s)
- Xiaoyu Qiu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lige Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lihua Guo
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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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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9
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Mahto KU, Das S. Whole genome characterization and phenanthrene catabolic pathway of a biofilm forming marine bacterium Pseudomonas aeruginosa PFL-P1. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 206:111087. [PMID: 32871516 DOI: 10.1016/j.ecoenv.2020.111087] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 05/02/2023]
Abstract
Pseudomonas aeruginosa is a small rod shaped Gram-negative bacterium of Gammaproteobacteria class known for its metabolic versatility. P. aeruginosa PFL-P1 was isolated from Polycyclic Aromatic Hydrocarbons (PAHs) contaminated site of Paradip Port, Odisha Coast, India. The strain showed excellent biofilm formation and could retain its ability to form biofilm grown with different PAHs in monoculture as well as co-cultures. To explore mechanistic insights of PAHs metabolism, the whole genome of the strain was sequenced. Next generation sequencing unfolded a genome size of 6,333,060 bp encoding 5857 CDSs. Gene ontology distribution assigned to a total of 2862 genes, wherein 2235 genes were allocated to biological process, 1549 genes to cellular component and 2339 genes to molecular function. A total of 318 horizontally transferred genes were identified when the genome was compared with the reference genomes of P. aeruginosa PAO1 and P. aeruginosa DSM 50071. Further comparison of P. aeruginosa PFL-P1 genome with P. putida containing TOL plasmids revealed similarities in the meta cleavage pathway employed for degradation of aromatic compounds like xylene and toluene. Gene annotation and pathway analysis unveiled 145 genes involved in xenobiotic biodegradation and metabolism. The biofilm cultures of P. aeruginosa PFL-P1 could degrade ~74% phenanthrene within 120 h while degradation increased up to ~76% in co-culture condition. GC-MS analysis indicated presence of diverse metabolites indicating the involvement of multiple pathways for one of the PAHs (phenanthrene) degradation. The strain also possesses the genetic machinery to utilize diverse toxic aromatic compounds such as naphthalene, benzoate, aminobenzoate, fluorobenzoate, toluene, xylene, styrene, atrazine, caprolactam etc. Common catabolic gene clusters such as benABCD, xylXYZ and catAB were observed within the genome of P. aeruginosa PFL-P1 which play key roles in the degradation of various toxic aromatic compounds.
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Affiliation(s)
- Kumari Uma Mahto
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Al Farraj DA, Hadibarata T, Yuniarto A, Alkufeidy RM, Alshammari MK, Syafiuddin A. Exploring the potential of halotolerant bacteria for biodegradation of polycyclic aromatic hydrocarbon. Bioprocess Biosyst Eng 2020; 43:2305-2314. [DOI: 10.1007/s00449-020-02415-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/22/2020] [Indexed: 12/27/2022]
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Mishra A, Rathour R, Singh R, Kumari T, Thakur IS. Degradation and detoxification of phenanthrene by actinobacterium Zhihengliuella sp. ISTPL4. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:27256-27267. [PMID: 31172432 DOI: 10.1007/s11356-019-05478-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are universal environmental contaminants of great concern with regard to their potential exposure and deleterious effect on human health. The current study is the first report of phenanthrene degradation by a psychrotolerant (15 °C), halophilic (5% NaCl), and alkalophilic (pH 8) bacterial strain Zhihengliuella sp. ISTPL4, isolated from the sediment sample of the Pangong Lake, Ladakh, Jammu and Kashmir, India. Degradation studies revealed that the optimum specific growth rate was observed at 250 ppm of phenanthrene with 81% and 87% removal of phenanthrene in 72 h and 168 h, respectively. During the degradation of phenanthrene; 9,10-dihydrophenanthrene; 1-phenanthrenecarboxylic acid; and phthalic acid were detected as intermediates. Whole-genome sequencing of strain ISTPL4 has predicted phenanthrene; 9,10-monooxygense; and epoxide hydrolase B that are involved in the phenanthrene metabolism. Phenanthrene cytotoxicity was evaluated with human hepatic carcinoma cell line (HepG2) and it was observed that the cytotoxicity decreased with increased duration of bacterial incubation and maximum cell viability was observed at 168 h (89.92%). Our results suggest, Zhihengliuella sp. ISTPL4 may promise a great potential for environmental remediation applications.
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Affiliation(s)
- Arti Mishra
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rashmi Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Taruna Kumari
- Department of Statistics, University of Delhi, New Delhi, 110007, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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12
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Wang D, Lin J, Lin J, Wang W, Li S. Biodegradation of Petroleum Hydrocarbons by Bacillus subtilis BL-27, a Strain with Weak Hydrophobicity. Molecules 2019; 24:molecules24173021. [PMID: 31438460 PMCID: PMC6749392 DOI: 10.3390/molecules24173021] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 12/17/2022] Open
Abstract
The biodegradation of petroleum hydrocarbons has many potential applications and has attracted much attention recently. The hydrocarbon-degrading bacterium BL-27 was isolated from petroleum-polluted soil and was compounded with surfactants to improve biodegradation. Its 16S rDNA and rpoD gene sequences indicated that it was a strain of Bacillus subtilis. Strain BL-27 had extensive adaptability and degradability within a broad range of temperatures (25–50 °C), pH (4.0–10.0) and salinity (0–50 g/L NaCl). Under optimal conditions (45 °C, pH 7.0, 1% NaCl), the strain was able to degrade 65% of crude oil (0.3%, w/v) within 5 days using GC-MS analysis. Notably, strain BL-27 had weak cell surface hydrophobicity. The adherence rate of BL-27 to n-hexadecane was 29.6% with sucrose as carbon source and slightly increased to 33.5% with diesel oil (0.3%, w/v) as the sole carbon source, indicating that the cell surface of BL-27 is relatively hydrophilic. The strain was tolerant to SDS, Tween 80, surfactin, and rhamnolipids at a concentration of 500 mg/L. The cell surface hydrophobicity reduced more with the addition of surfactants, while the chemical dispersants, SDS (50–100 mg/L) and Tween 80 (200–500 mg/L), significantly increased the strain’s ability to biodegrade, reaching 75–80%. These results indicated that BL-27 has the potential to be used for the bioremediation of hydrocarbon pollutants and could have promising applications in the petrochemical industry.
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Affiliation(s)
- Dan Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Jiahui Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Junzhang Lin
- Oil Production Research Institute, Shengli Oil Field Ltd. Co. SinoPEC, Dongying 257000, China
| | - Weidong Wang
- Oil Production Research Institute, Shengli Oil Field Ltd. Co. SinoPEC, Dongying 257000, China
| | - Shuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China.
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Bourguignon N, Irazusta V, Isaac P, Estévez C, Maizel D, Ferrero MA. Identification of proteins induced by polycyclic aromatic hydrocarbon and proposal of the phenanthrene catabolic pathway in Amycolatopsis tucumanensis DSM 45259. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 175:19-28. [PMID: 30878660 DOI: 10.1016/j.ecoenv.2019.02.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
In the present study the polycyclic aromatic hydrocarbon removal and metabolic adaptation of Amycolatopsis tucumanensis DSM 45259 were investigated. Analysis of one-dimensional gel electrophoresis of crude cell extracts revealed differential synthesis of proteins which were identified by MALDI-TOF. To elucidate the phenanthrene metabolic pathway in A. tucumanensis DSM45259, two-dimensional electrophoresis and detection of phenanthrene degradation intermediates by GS-MS were performed. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in the metabolism of aromatic compounds, oxidative stress response, energy production and protein synthesis. The obtained results allowed us to clarify the phenanthrene catabolic pathway, by confirming the roles of several proteins involved in the degradation process and comprehensive adaptation. This may clear the way for more efficient engineering of bacteria in the direction of more effective bioremediation applications.
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Affiliation(s)
- Natalia Bourguignon
- Universidad Tecnológica Nacional (UTN), Facultad Regional de Haédo, París 532, 1706 Haedo, Buenos Aires, Argentina.
| | - Verónica Irazusta
- Instituto de Investigaciones para la Industria Química (INIQUI), CONICET-UNSa, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina
| | - Paula Isaac
- Centro de Investigaciones y Transferencia de Villa María (CIT Villa María), CONICET-Instituto de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa María, Córdoba, Argentina
| | - Cristina Estévez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Tucumán, Argentina
| | - Daniela Maizel
- Instituto de Astronomía y Física del Espacio, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Buenos Aires, Intendente Güiraldes 2160, C1428EGA CABA, Argentina
| | - Marcela A Ferrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Tucumán, Argentina
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Kosek K, Kozioł K, Luczkiewicz A, Jankowska K, Chmiel S, Polkowska Ż. Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1585-1596. [PMID: 30446169 DOI: 10.1016/j.scitotenv.2018.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L-1 (R12) and 3901 ng L-1 (R13) in June, and 2179 ng L-1 (R12) and 1349 ng L-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L-1 in June and 0.35 mg L-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.
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Affiliation(s)
- Klaudia Kosek
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Krystyna Kozioł
- Institute of Geography, Faculty of Geography and Biology, Pedagogical University in Cracow, Podchorążych 2, Cracow 30-084, Poland; Institute of Geophysics, Polish Academy of Sciences, 64 Księcia Janusza St., Warsaw 01-452, Poland
| | - Aneta Luczkiewicz
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Katarzyna Jankowska
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Stanisław Chmiel
- Faculty of Earth Sciences and Spatial Management, Maria Curie-Skłodowska University, 2 C-D Kraśnicka Ave., Lublin 20-718, Poland
| | - Żaneta Polkowska
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Current Status of the Degradation of Aliphatic and Aromatic Petroleum Hydrocarbons by Thermophilic Microbes and Future Perspectives. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15122782. [PMID: 30544637 PMCID: PMC6313336 DOI: 10.3390/ijerph15122782] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 01/10/2023]
Abstract
Contamination of the environment by petroleum products is a growing concern worldwide, and strategies to remove these contaminants have been evaluated. One of these strategies is biodegradation, which consists of the use of microorganisms. Biodegradation is significantly improved by increasing the temperature of the medium, thus, the use of thermophiles, microbes that thrive in high-temperature environments, will render this process more efficient. For instance, various thermophilic enzymes have been used in industrial biotechnology because of their unique catalytic properties. Biodegradation has been extensively studied in the context of mesophilic microbes, and the mechanisms of biodegradation of aliphatic and aromatic petroleum hydrocarbons have been elucidated. However, in comparison, little work has been carried out on the biodegradation of petroleum hydrocarbons by thermophiles. In this paper, a detailed review of the degradation of petroleum hydrocarbons (both aliphatic and aromatic) by thermophiles was carried out. This work has identified the characteristics of thermophiles, and unraveled specific catabolic pathways of petroleum products that are only found with thermophiles. Gaps that limit our understanding of the activity of these microbes have also been highlighted, and, finally, different strategies that can be used to improve the efficiency of degradation of petroleum hydrocarbons by thermophiles were proposed.
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Wang W, Wang L, Shao Z. Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1. Appl Environ Microbiol 2018; 84:AEM.01261-18. [PMID: 30171002 PMCID: PMC6193391 DOI: 10.1128/aem.01261-18 10.1016/j.biotechadv.2015.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/19/2018] [Indexed: 06/12/2023] Open
Abstract
Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by CycloclasticusCycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in CycloclasticusIMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lin Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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17
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Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1. Appl Environ Microbiol 2018; 84:AEM.01261-18. [PMID: 30171002 DOI: 10.1128/aem.01261-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by Cycloclasticus Cycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in Cycloclasticus IMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.
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Degradation of petroleum hydrocarbons and treatment of refinery wastewater under saline condition by a halophilic bacterial consortium enriched from marine environment (Red Sea), Jeddah, Saudi Arabia. 3 Biotech 2018; 8:276. [PMID: 29872607 DOI: 10.1007/s13205-018-1296-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/20/2018] [Indexed: 01/05/2023] Open
Abstract
A halophilic bacterial consortium was enriched from Red Sea saline water and sediment samples collected from Abhor, Jeddah, Saudi Arabia. The consortium potentially degraded different low (above 90% for phenanthrene and fluorene) and high (69 ± 1.4 and 56 ± 1.8% at 50 and 100 mg/L of pyrene) molecular weight polycyclic aromatic hydrocarbons (PAHs) at different concentrations under saline condition (40 g/L NaCl concentration). The cell hydrophobicity (91° ± 1°) and biosurfactant production (30 mN/m) confirmed potential bacterial cell interaction with PAHs to facilitate biodegradation process. Co-metabolic study with phenanthrene as co-substrate during pyrene degradation recorded 90% degradation in 12 days. The consortium in continuous stirred tank reactor with petroleum refinery wastewater showed complete and 90% degradation of low and high molecular weight PAHs, respectively. The reactor study also revealed 94 ± 1.8% chemical oxygen demand removal by the halophilic consortium under saline condition (40 g/L NaCl concentration). The halophilic bacterial strains present in the consortium were identified as Ochrobactrum halosaudis strain CEES1 (KX377976), Stenotrophomonas maltophilia strain CEES2 (KX377977), Achromobacter xylosoxidans strain CEES3 (KX377978) and Mesorhizobium halosaudis strain CEES4 (KX377979). Thus, the promising halophilic consortium was highly recommended to be employed in petroleum saline wastewater treatment process.
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Jiang Y, Qi H, Zhang XM. Co-biodegradation of anthracene and naphthalene by the bacterium Acinetobacter johnsonii. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2018; 53:448-456. [PMID: 29300682 DOI: 10.1080/10934529.2017.1409579] [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] [Indexed: 06/07/2023]
Abstract
NAP (Naphthalene) and ANT (anthracene) usually co-exist in environment and possessed interactional effects on their biodegradation in environment. Presently, a strain of Acinetobacter johnsonii was employed to degrade NAP and ANT in single- and dual-substrate systems. NAP was utilized as prefer substrate by cells to accelerate ANT biodegradation. As much as 200 mg L-1 ANT could be entirely degraded with 1,500 mg L-1 NAP, which was beyond bacterial potential in single substrate system. Especially, the shortest biodegradation period (103 h) for ANT was observed with the presence of 50 mg L-1 NAP. By contrast, ANT showed strong inhibition on NAP degradation, while the peak biodegradation of 1,950 mg L-1 NAP with 50 mg L-1 ANT could still proceed. By introducing an inhibition constant parameter to fit the inhibition on cells, modeling indicated the substrate inhibition for NAP and ANT over the concentrations of 174 and 49 mg L-1, respectively. Furthermore, enzyme assay revealed the pathway of meta fission in NAP biodegradation due to the appearance of catechol 2,3-dioxygenase activity, and low-level lipase excretion was also found in both NAP and ANT biodegradation, but hardly affect NAP and ANT biodegradation in the present study. To research the interplay of NAP and ANT is conducive to targeted decontamination.
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Affiliation(s)
- Yan Jiang
- a Engineering Research Centre for Waste Oil Recovery Technology and Equipment , Ministry Education, Chongqing Technology and Business University , Chongqing , P R China
| | - Hui Qi
- b College of Foreign Languages , Chongqing Technology and Business University , Chongqing , P R China
| | - Xian M Zhang
- a Engineering Research Centre for Waste Oil Recovery Technology and Equipment , Ministry Education, Chongqing Technology and Business University , Chongqing , P R China
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Pugazhendi A, Abbad Wazin H, Qari H, Basahi JMAB, Godon JJ, Dhavamani J. Biodegradation of low and high molecular weight hydrocarbons in petroleum refinery wastewater by a thermophilic bacterial consortium. ENVIRONMENTAL TECHNOLOGY 2017; 38:2381-2391. [PMID: 27852158 DOI: 10.1080/09593330.2016.1262460] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
Clean-up of contaminated wastewater remains to be a major challenge in petroleum refinery. Here, we describe the capacity of a bacterial consortium enriched from crude oil drilling site in Al-Khobar, Saudi Arabia, to utilize polycyclic aromatic hydrocarbons (PAHs) as sole carbon source at 60°C. The consortium reduced low molecular weight (LMW; naphthalene, phenanthrene, fluorene and anthracene) and high molecular weight (HMW; pyrene, benzo(e)pyrene and benzo(k)fluoranthene) PAH loads of up to 1.5 g/L with removal efficiencies of 90% and 80% within 10 days. PAH biodegradation was verified by the presence of PAH metabolites and evolution of carbon dioxide (90 ± 3%). Biodegradation led to a reduction of the surface tension to 34 ± 1 mN/m thus suggesting biosurfactant production by the consortium. Phylogenetic analysis of the consortium revealed the presence of the thermophilic PAH degrader Pseudomonas aeruginosa strain CEES1 (KU664514) and Bacillus thermosaudia (KU664515) strain CEES2. The consortium was further found to treat petroleum wastewater in continuous stirred tank reactor with 96 ± 2% chemical oxygen demand removal and complete PAH degradation in 24 days.
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Affiliation(s)
- Arulazhagan Pugazhendi
- a Center of Excellence in Environmental Studies , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Hadeel Abbad Wazin
- a Center of Excellence in Environmental Studies , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Huda Qari
- a Center of Excellence in Environmental Studies , King Abdulaziz University , Jeddah , Saudi Arabia
| | | | - Jean Jacques Godon
- b Laboratorie de Biotechnologie de l'Environnement , Institut National de la Recherche Agronomique , Narbonne , France
| | - Jeyakumar Dhavamani
- a Center of Excellence in Environmental Studies , King Abdulaziz University , Jeddah , Saudi Arabia
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21
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Biodegradation of polycyclic aromatic hydrocarbons by an acidophilic Stenotrophomonas maltophilia strain AJH1 isolated from a mineral mining site in Saudi Arabia. Extremophiles 2016; 21:163-174. [DOI: 10.1007/s00792-016-0892-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
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Jin J, Yao J, Zhang Q. Biodegradation of Phenanthrene by Pseudomonas sp. JPN2 and Structure-Based Degrading Mechanism Study. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2016; 97:689-694. [PMID: 27631505 DOI: 10.1007/s00128-016-1917-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
The strain Pseudomonas sp. JPN2 had a high potential to degrade phenanthrene degrading 98.52 % of the initial amount of 100 mg L-1 after 10 days incubation. The analysis of metabolites demonstrated that the cleavage of phenanthrene started at the C9 and C10 positions on the aromatic ring by the dioxygenation reaction, and then further degraded via a phthalate pathway. To understand the interaction between phenanthrene and the amino acid residues in the active site of the target enzyme, a molecular docking simulation was performed. The results showed that the distances of C9-O1 and C10-O2 atoms were 3.47 and 3.67 Å, respectively. The C9 and C10 positions of the phenanthrene ring are much closer to the dioxygen molecule in the active site relative to the other atoms. Therefore, the C9 and C10 positions are vulnerable to attack in the initial oxygenation process.
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Affiliation(s)
- Jingnan Jin
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Jun Yao
- School of Civil 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
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Genomic Changes Associated with the Loss of Nocardia brasiliensis Virulence in Mice after 200 In Vitro Passages. Infect Immun 2016; 84:2595-606. [PMID: 27354446 DOI: 10.1128/iai.00329-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/18/2016] [Indexed: 11/20/2022] Open
Abstract
Nocardia species, particularly Nocardia brasiliensis, are etiologic agents of mycetoma, a chronic subcutaneous infection. Until now, little has been known about the pathogenic mechanisms involved in nocardial infection. Traditionally, subculture in rich media has been a simple way to induce attenuation. In this work, we report the changes in virulence toward mice and in genomic constitution of N. brasiliensis produced after 200 continuous subcultures in brain heart infusion (BHI) medium (P-200 strain). The ability of the N. brasiliensis P-200 strain to produce experimental infection was tested using BALB/c mice. P-200 was also used to immunize mice to determine whether it could induce resistance against a challenge with a nonsubcultured isolate (P-0). Comparative proteomic analysis between N. brasiliensis P-0 and P-200 was performed by two-dimensional (2-D) electrophoresis, and the genome sequence was obtained through Roche 454 sequence analysis. Virulence in BALB/c mice was completely lost, and BALB/c mice immunized with P-200 bacterial cells were resistant to mycetoma production by the nonsubcultured strain. Whole-genome sequence analysis revealed that P-200 lost a total of 262,913 bp distributed in 19 deleted regions, involving a total of 213 open reading frames (ORFs). The deleted genes included those encoding bacterial virulence factors, e.g., catalase, nitrate reductase enzymes, and a group of mammalian cell entry (MCE) family proteins, which may explain the loss of virulence of the isolate. Thus, completely attenuated N. brasiliensis was obtained after 200 passages in BHI medium, and putative Nocardia virulence genes were identified for the first time.
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Sakulthaew C, Comfort S, Chokejaroenrat C, Harris C, Li X. A combined chemical and biological approach to transforming and mineralizing PAHs in runoff water. CHEMOSPHERE 2014; 117:1-9. [PMID: 25433987 DOI: 10.1016/j.chemosphere.2014.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 06/04/2023]
Abstract
The water quality of lakes, rivers and streams associated with metropolitan areas is declining from increased inputs of urban runoff that contain polycyclic aromatic hydrocarbons (PAHs). Our objective was to transform and mineralize PAHs in runoff using a combined chemical and biological approach. Using (14)C-labeled phenanthrene, (14)C-benzo(a)pyrene and a mixture of 16 PAHs, we found that ozone transformed all PAHs in a H2O matrix within minutes but complete mineralization to CO2 took several weeks. When urban runoff water (7.6 mg CL(-1)) replaced H2O as the background matrix, some delays in degradation rates were observed but transforming a mixture of PAHs was still complete within 10 min. Comparing the biodegradability of the ozonated products to the parent structures in unsaturated soil microcosms showed that the 3-ring phenanthrene was more biodegradable (as evidence by (14)CO2 released) than its ozonated products but for the 5-ring benzo(a)pyrene, the products produced by ozone were much more biodegradable (22% vs. 3% mineralized). For phenanthrene, we identified diphenaldehyde as the initial degradation product produced from ozonation. By continuing to pump the ozonated products ((14)C-labeled diphenaldehyde or ozone-treated benzo(a)pyrene) onto glass beads coated with microorganisms, we verified that biological mineralization could be achieved in a flow-through system and mineralization rates improved with acclimation of the microbial population (i.e., time and exposure to the substrate). These results support a combined ozone and biological approach to treating PAHs in urban runoff water.
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Affiliation(s)
- Chainarong Sakulthaew
- School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0915, USA; Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand.
| | - Steve Comfort
- School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0915, USA.
| | - Chanat Chokejaroenrat
- Department of Civil Engineering, University of Nebraska, Lincoln, NE 68588-6105, USA; School of Environmental Engineering, Institute of Engineering, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
| | - Clifford Harris
- Department of Chemistry, Albion College, Albion, MI 49224, USA.
| | - Xu Li
- Department of Civil Engineering, University of Nebraska, Lincoln, NE 68588-6105, USA.
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Zhang J, Zhang X, Liu J, Li R, Shen B. Isolation of a thermophilic bacterium, Geobacillus sp. SH-1, capable of degrading aliphatic hydrocarbons and naphthalene simultaneously, and identification of its naphthalene degrading pathway. BIORESOURCE TECHNOLOGY 2012; 124:83-89. [PMID: 22985850 DOI: 10.1016/j.biortech.2012.08.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/06/2012] [Accepted: 08/10/2012] [Indexed: 06/01/2023]
Abstract
A thermophilic naphthalene- and aliphatic hydrocarbon-degrading bacterium SH-1 was isolated from a deep oil well and identified as Geobacillus sp. n-alkanes from C12 to C33 in crude oil and naphthalene were effectively degraded by strain SH-1, and this strain could readily utilize these compounds as its sole carbon and energy resources. During the degradation of naphthalene, strain SH-1 initiated its attack on naphthalene by a monooxygenation at its C-1 to give 1-naphthol and further monooxygenation at C-2 to produce 1,2-dihydroxynaphthalene. The ring of 1,2-dihydroxynaphthalene was cleaved to form trans-o-hydroxybenzylidenepyruvate. Subsequently, trans-o-hydroxybenzylidenepyruvate was transformed to (2E)-3-(2-hydroxyphenyl)prop-2-enal by losing a carboxyl group. Additionally, benzoic acid was identified as an intermediate in the naphthalene degradation pathway of this Geobacillus strain. This study highlights an important potential use of the thermophilic degradative strain SH-1 in the cleanup of environmental contamination by naphthalene and crude oil and presents a mechanism for naphthalene metabolism.
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agricultural, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, Jiangsu Province, PR China
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26
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Seo JS, Keum YS, Li QX. Mycobacterium aromativorans JS19b1(T) Degrades Phenanthrene through C-1,2, C-3,4 and C-9,10 Dioxygenation Pathways. INTERNATIONAL BIODETERIORATION & BIODEGRADATION 2012; 70:96-103. [PMID: 22485067 PMCID: PMC3319295 DOI: 10.1016/j.ibiod.2012.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Mycobacterium aromativorans strain JS19b1(T) can utilize phenanthrene as a sole source of carbon and energy. Strain JS19b1(T) degrades phenanthrene through highly branched metabolic pathways, including dioxygenation on C-1,2, C-3,4 and C-9,10 positions and ring opening by both ortho- and meta-cleavage. The presence of novel metabolic pathways was confirmed by replacement cultivation using synthetic metabolite standards. The metabolites were isolated and identified by gas chromatography-mass spectrometry. Both ortho and meta-cleavage products of 1,2- and 3,4-dihydroxyphenanthrene were detected. Two ortho-cleavage products, 1-[(E)-2-carboxyvinyl]-2-naphthoic acid and 2-[(E)-2-carboxyvinyl]-1-napthoic acid were further metabolized to naphthalene-1,2-dicarboxylic acid and then to 1,2-dihydroxynaphthalene, which can also be produced from the meta-cleavage products hydroxynaphthoic acids. These results suggest that part of the branched pathways is merged into 1,2-dihydroxynaphthalene. The concentrations of the products from C-9,10 dioxygenation were higher than those from other pathways. C-9,10 dioxygenation of phenanthrene produced phthalic acid through decarboxylation and mono-/di-oxygenation. The diverse phenanthrene metabolic pathways in JS19b1(T) give a new insight of the bacterial degradation of polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Jong-Su Seo
- Environmental Toxicology Research Center, Korea Institute of Toxicology, 100 Jangdong, Yuseonggu, Daejeon 305-343, Korea
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Young-Soo Keum
- Department of Molecular Biotechnology, KonKuk University, Seoul 143-701, Korea
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA
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Ghosal D, Chakraborty J, Khara P, Dutta TK. Degradation of phenanthrene via meta-cleavage of 2-hydroxy-1-naphthoic acid by Ochrobactrum sp. strain PWTJD. FEMS Microbiol Lett 2010; 313:103-10. [DOI: 10.1111/j.1574-6968.2010.02129.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Mallick S, Chakraborty J, Dutta TK. Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular-weight polycyclic aromatic hydrocarbons: a review. Crit Rev Microbiol 2010; 37:64-90. [PMID: 20846026 DOI: 10.3109/1040841x.2010.512268] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Widespread environmental pollution by polycyclic aromatic hydrocarbons (PAHs) poses an immense risk to the environment. Bacteria-mediated attenuation has a great potential for the restoration of PAH-contaminated environment in an ecologically accepted manner. Bacterial degradation of PAHs has been extensively studied and mining of biodiversity is ever expanding the biodegradative potentials with intelligent manipulation of catabolic genes and adaptive evolution to generate multiple catabolic pathways. The present review of bacterial degradation of low-molecular-weight (LMW) PAHs describes the current knowledge about the diverse metabolic pathways depicting novel metabolites, enzyme-substrate/metabolite relationships, the role of oxygenases and their distribution in phylogenetically diverse bacterial species.
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Affiliation(s)
- Somnath Mallick
- Department of Chemistry, Saldiha College, Bankura, West Bengal, India
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Bandowe BAM, Wilcke W. Analysis of polycyclic aromatic hydrocarbons and their oxygen-containing derivatives and metabolites in soils. JOURNAL OF ENVIRONMENTAL QUALITY 2010; 39:1349-58. [PMID: 20830923 DOI: 10.2134/jeq2009.0298] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Although polycyclic aromatic hydrocarbons (PAHs) have been extensively studied, the knowledge of their oxygen-containing derivatives and metabolites (OPAHs) in soils is limited. We modified and tested an existing analytical protocol involving pressurized liquid extraction of soil followed by fractionation of target compounds into PAHs and OPAHs on a silica gel column and gas chromatography/ mass spectrometry-based separation and quantification. Polycyclic aromatic hydrocarbons and carbonyl-OPAHs were quantified directly after separation on silica gel columns, and hydroxyl/carboxyl-OPAHs were quantified after silylation with N,O-bis(trimethylsilyl)trifluoroacetamide. Recoveries between 78 and 97% (relative standard deviation [RSD], 5-12%) were obtained for six carbonyl-OPAHs, whereas 1,2-acenaphthenequinone and 1,4-naphthoquinone showed lower recoveries of 34 and 44% (RSD, 19 and 28%, respectively). Five hydroxyl/carboxyl-OPAHs had recoveries between 36 and 70% (RSD, 13-46%), six others had between 2 and 7% (RSD, 8-25%), and nine were lost in sample preparation. Limits of detection ranged from 0.1 to 1.6 ng g(-1) for OPAHs and from 0.01 to 0.56 ng g(-1) for PAHs. The protocol was applied to soils from a former gasworks site, Berlin, an urban soil from Mainz, both in Germany, and a forest soil from near Manaus, Brazil. The sums of 34 PAH concentrations were 107,000, 3505, and 21 ng g(-1); those of seven carbonyl-OPAHs were 15,690, 170, and 7 ng g(-1); and those of 11 hydroxyl/carboxyl-OPAHs 518, 36, and 16 ng g(-1) for Berlin, Mainz, and Manaus soils, respectively. Several OPAHs were present at concentrations higher than or equal to their parent PAHs, demonstrating the importance of OPAH measurement for the assessment of PAH-related environmental risks.
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Affiliation(s)
- Benjamin A Musa Bandowe
- Earth System Science Research Center, Geographic Institute, Professorship of Soil Geography/Soil Science, Johannes Gutenberg Univ. Mainz, Johann-Joachim-Becher-Weg 21, 55128 Mainz, Germany
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Tapilatu YH, Grossi V, Acquaviva M, Militon C, Bertrand JC, Cuny P. Isolation of hydrocarbon-degrading extremely halophilic archaea from an uncontaminated hypersaline pond (Camargue, France). Extremophiles 2010; 14:225-31. [PMID: 20157750 DOI: 10.1007/s00792-010-0301-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 01/20/2010] [Indexed: 11/29/2022]
Abstract
Little information exists about the ability of halophilic archaea present in hypersaline environments to degrade hydrocarbons. In order to identify the potential actors of hydrocarbon degradation in these environments, enrichment cultures were prepared using samples collected from a shallow crystallizer pond with no known contamination history in Camargue, France, with n-alkanes provided as source of carbon and energy. Five alkane-degrading halophilic archaeal strains were isolated: one (strain MSNC 2) was closely related to Haloarcula and three (strains MSNC 4, MSNC 14, and MSNC 16) to Haloferax. Biodegradation assays showed that depending on the strain, 32 to 95% (0.5 g/l) of heptadecane was degraded after 30 days of incubation at 40 degrees C in 225 g/l NaCl artificial medium. One of the strains (MSNC 14) was also able to degrade phenanthrene. This work clearly shows for the first time the potential role of halophilic archaea belonging to the genera Haloarcula and Haloferax in the degradation of hydrocarbons in both pristine and hydrocarbon-contaminated hypersaline environments.
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Affiliation(s)
- Yosmina H Tapilatu
- Laboratoire de Microbiologie Géochimie et Ecologie Marines, CNRS/INSU, UMR 6117, Centre d'Océanologie de Marseille, Université de la Méditerranée, Campus de Luminy, Case 901, 13288, Marseille Cedex 9, France
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Chang YT, Thirumavalavan M, Lee JF. Effects of PAH biodegradation in the presence of non-ionic surfactants on a bacterial community and its exoenzymatic activity. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2010; 45:421-431. [PMID: 20390887 DOI: 10.1080/10934520903540141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The influence of two non-ionic surfactants (TX-100 and Brij 35) on a bacterial community and its exoenzymatic activity during polycyclic aromatic hydrocarbon (naphthalene, phenanthrene and pyrene) biodegradation was evaluated in this study. The result indicated the addition of the non-ionic surfactants altered the profiles of the microbial populations and produced exoenzymes. Fluorescence in situ hybridization found that, as PAH biodegradation progressed in the presence of non-ionic surfactant, the proportion of Bacteria presents increased significantly from the range 54.79%-57.00% to 64.17%-73.4% and there was parallel decrease in Archaea. The trends in five phyla/subclass of Bacteria, namely alpha -, beta -, or gamma -Proteobacteria, HGC bacteria and LGC bacteria, were influenced significantly by the addition of Brij 35 as either monomers or micelles. A change was ascribed to different cohesive energy density (CED) value between the PAH and surfactant. The percentage of genera Pseudomonas 4.76%-12.67%, which included two signals, namely most true Pseudomonas spp. and Pseudomonas aeruginosa, were dominant during biodegradation. For exoenzymaztic activities, trends were identified by principle component analysis of the API ZYM enzymatic activity dataset. The additions of non-ionic surfactant were identified strong activities of three esterase (esterase, esterase lipase and lipase), alpha -glucosidase, beta -glucosidase, leucine arylamidase and acid phosphatase during PAH biodegradation. These enzymes are selected as possible organic pollutant indicators when the in situ bioremediation was monitored in the presence of non-ionic surfactant additives.
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Affiliation(s)
- Yi-Tang Chang
- Department of Microbiology, Soochow University, Shih-Lin, Taipei, Taiwan
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Di Nardo G, Roggero C, Campolongo S, Valetti F, Trotta F, Gilardi G. Catalytic properties of catechol 1,2-dioxygenase from Acinetobacter radioresistens S13 immobilized on nanosponges. Dalton Trans 2009:6507-12. [PMID: 19672496 DOI: 10.1039/b903105g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catechol 1,2-dioxygenases are iron containing enzymes able to convert catechol into cis,cis-muconate, a precursor of the industrially important compound adipic acid. Catechol 1,2-dioxygenase from Acinetobacter radioresistens S13 was immobilized on beta-cyclodextrins cross-linked with carbonate groups (nanosponges) with a yield of 29 mg of enzyme per gram of support. This support was chosen for its low cost and its ability to offer different types of interactions with the enzyme. The activity profiles at different pH and temperatures showed a shift of the optimal pH from 8.5, for the free protein, to 9.5, for the immobilized protein and, similarly, a shift in optimal temperature from 30 degrees C to 50 degrees C. The Michaelis-Menten constant, KM, increased from 2.0 +/- 0.3 microM, for the free form, to 16.6 +/- 4.8 microM for the immobilized enzyme, whereas the rate constant, k(cat), values were found to be 32 +/- 2 s(-1) and 27 +/- 3 s(-1) for the free and immobilized forms respectively. The immobilization process also increased the thermostability of the enzyme with 60% residual activity after 90 min at 40 degrees C for the immobilized protein versus 20% for the free enzyme. A residual activity of 75% was found after 15 min at 60 degrees C for the immobilized enzyme while the free form showed a total loss of activity under the same conditions. The activity toward other substrates, such as 3- and 4-methylcatechol and 4-chlorocatechol, was retained by the immobilized enzyme. A small scale bioreactor was constructed and was able to convert catechol into cis,cis-muconic acid with high efficiency for 70 days.
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Affiliation(s)
- Giovanna Di Nardo
- Department of Human and Animal Biology, University of Torino, via Accademia Albertina 12, 10123, Torino, Italy
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