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Yang L, Chen C, Xu X, Wang XT, Xing D, Ren N, Lee DJ. Genome and metabolome analysis of Bacillus sp. Hex-HIT36: A newly screened functional microorganism for the degradation of 1-hexadecene in industrial wastewater. ENVIRONMENTAL RESEARCH 2024; 260:119594. [PMID: 39002630 DOI: 10.1016/j.envres.2024.119594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/02/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
1-Hexadecene has been detected at a level of mg/L in both influent and effluent of wastewater treatment plants situated in chemical/pharmaceutical industrial parks, which poses a potential threat to the environment. However, few reports are available on aerobic metabolic pathways and microorganisms involved in 1-Hexadecene degradation. In this study, a new strain of 1-Hexadecene-degrading bacteria, Bacillus sp. Hex-HIT36 (HIT36), was isolated from the activated sludge of a wastewater treatment plants located in an industrial park. The physicochemical properties and degradation efficacy of HIT36 were investigated. HIT36 was cultured on a medium containing 1-Hexadecene as a sole carbon source; it was found to remove ∼67% of total organic carbon as confirmed by mass spectrometric analysis of intermediate metabolites. Metabolomic and genomic analysis showed that HIT36 possesses various enzymes, namely, pyruvate dehydrogenase, dihydropolyhydroxyl dehydrogenase, and 2-oxoglutarate-2-oxoiron oxidoreductase (subunit alpha), which assist in the metabolization of readily available carbon source or long chain hydrocarbons present in the growth medium/vicinity. This suggests that HIT36 has efficient long-chain alkane degradation efficacy, and understanding the alkane degradation mechanism of this strain can help in developing technologies for the degradation of long-chain alkanes present in wastewater, thereby assisting in the bioremediation of environment.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Xijun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Xue-Ting Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China.
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li, 32003, Taiwan
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2
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Muthukumar B, Duraimurugan R, Parthipan P, Rajamohan R, Rajagopal R, Narenkumar J, Rajasekar A, Malik T. Synthesis and characterization of iron oxide nanoparticles from Lawsonia inermis and its effect on the biodegradation of crude oil hydrocarbon. Sci Rep 2024; 14:11335. [PMID: 38760417 PMCID: PMC11101646 DOI: 10.1038/s41598-024-61760-6] [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: 07/24/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
Crude oil hydrocarbons are considered major environmental pollutants and pose a significant threat to the environment and humans due to having severe carcinogenic and mutagenic effects. Bioremediation is one of the practical and promising technology that can be applied to treat the hydrocarbon-polluted environment. In this present study, rhamnolipid biosurfactant (BS) produced by Pseudomonas aeruginosa PP4 and green synthesized iron nanoparticles (G-FeNPs) from Lawsonia inermis was used to evaluate the biodegradation efficiency (BE) of crude oil. The surface analysis of G-FeNPs was carried out by using FESEM and HRTEM to confirm the size and shape. Further, the average size of the G-FeNPs was observed around 10 nm by HRTEM analysis. The XRD and Raman spectra strongly confirm the presence of iron nanoparticles with their respective peaks. The BE (%) of mixed degradation system-V (PP4+BS+G-FeNPs) was obtained about 82%. FTIR spectrum confirms the presence of major functional constituents (C=O, -CH3, C-O, and OH) in the residual oil content. Overall, this study illustrates that integrated nano-based bioremediation could be an efficient approach for hydrocarbon-polluted environments. This study is the first attempt to evaluate the G-FeNPs with rhamnolipid biosurfactant on the biodegradation of crude oil.
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Affiliation(s)
- Balakrishnan Muthukumar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India
| | - Ramanathan Duraimurugan
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India
| | - Punniyakotti Parthipan
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, 603203, India
| | - Rajaram Rajamohan
- Organic Materials Synthesis Lab, School of Chemical Engineering, Yeungnam University, Gyeongsan-si, 38541, Republic of Korea.
| | - Rajakrishnan Rajagopal
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Jayaraman Narenkumar
- Department of Environmental & Water Resources Engineering, School of Civil Engineering (SCE), Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Aruliah Rajasekar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India.
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University, 378, Jimma, Ethiopia.
- Adjunct Faculty, Division of Research and Development, Lovely Professional University, Phagwara, Punjab, 144411, India.
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Mupamhadzi TL, Machona O, Chidzwondo F, Mangoyi R. Molecular Detection and Phylogenetic Analysis of the alkB Gene in Klebsiella oxytoca Strains Isolated from the Gut of Tenebrio molitor. ScientificWorldJournal 2024; 2024:3350591. [PMID: 38756480 PMCID: PMC11098606 DOI: 10.1155/2024/3350591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/17/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The challenge in polystyrene disposal has caused researchers to look for urgent innovative and ecofriendly solutions for plastic degradation. Some insects have been reported to use polystyrene as their sole carbon source, and this has been linked to the presence of microbes in their guts that aid in plastic digestion. Thus, this study focuses on the molecular detection and phylogenetic analysis of the alkane-1-monooxygenase (alkB) gene in Klebsiella oxytoca strains isolated from the gut of Tenebrio molitor. The alkB gene encodes for alkane-1-monooxygenase, an enzyme involved in the oxidation of inactivated alkanes. This gene can be used as a marker to assess bacteria's ability to biodegrade polystyrene. Three bacterial strains were isolated from the guts of T. molitor mealworms and were confirmed using polymerase chain reaction (PCR) of the 16S ribosomal RNA gene. The primers used in the amplification of the 16S ribosomal RNA region were designed using NCBI, a bioinformatics tool. To detect the presence of the alkB gene in the isolated bacterial strains, a set of primers used in the amplification of this gene was manually designed from the conserved regions of the alkB nucleotide sequences of eleven bacterial species from GenBank. TCOFFE online tool was used to align the alkB sequences of the bacteria, while Jalview and ConSurf were used to view the alignment. The amplified alkB gene was then sequenced using the Sanger sequencing technique, blasted on NCBI to look for similar sequences, and a phylogenetic tree was constructed. Based on the 16S ribosomal RNA gene sequences, the isolated bacterial strains were confirmed to be Klebsiella oxytoca NBRC 102593, Klebsiella oxytoca JCM 1665, and Klebsiella oxytoca ATCC 13182. The alkB gene sequence identical to fourteen alkB gene sequences derived from Actinobacteria whole genome was detected in Klebsiella oxytoca for the first time to the best of our knowledge. The novel nucleotide sequence was published in the NCBI database under accession number OP959069. This gene sequence was found to be for the enzyme alkane-1-monooxygenase and may be one of the enzymes responsible for polystyrene degradation by the putative Klebsiella oxytoca ATCC 13182 in T. molitor.
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Affiliation(s)
| | - Oleen Machona
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - Farisai Chidzwondo
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - Rumbidzai Mangoyi
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
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Meng L, Li W, Zhao L, Yan H, Zhao H. Influences of extracellular polymeric substances (EPS) recovered from waste sludge on the ability of Jiaozhou Bay to self-remediate of diesel-polluted seawater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 353:120196. [PMID: 38290259 DOI: 10.1016/j.jenvman.2024.120196] [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: 09/02/2023] [Revised: 12/10/2023] [Accepted: 01/20/2024] [Indexed: 02/01/2024]
Abstract
The introduction of EPS recovered from waste sludge may have an impact on the process of microbial remediation of oil-contaminated seawater. This study investigated the effect of EPS on the self-remediation capacity of diesel-polluted seawater in Jiaozhou Bay. Hydrocarbon attenuation and microbial activity were monitored in seawater collected from five islands after diesel and N, P addition, with and without EPS, incubated under aerobic conditions. Compared to seawater without EPS, degradation of TPH (total petroleum hydrocarbon) doubled and improved degradation of non-volatile (C16-C24) hydrocarbons to some extent in EPS-added seawater. The introduction of EPS led to changes in microbiota richness and diversity, significantly stimulating the growth of Proteobacteria and Firmicutes phyla or Bacillus and Pseudomonas genera. RT-qPCR analysis indicated EPS caused higher increases in cytochrome P450 gene copies than alkB. Prediction of alkane decay genes from 16S rRNA sequencing data revealed that EPS addition obviously promoted genes related to ethanol dehydrogenation function in the microbial community. Additionally, EPS enhanced the enzymatic activities of alkane hydroxylase, ethanol dehydrogenase, phosphatase and lipase, but increased protease and catalase inconspicuously. The above outlook that environmental sustainability of EPS from waste sludge for diesel-contaminated seawater remediation may provide new perspectives for oil spill bioremediation.
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Affiliation(s)
- Long Meng
- Department of Bioengineering, College of Chemical and Bioengineering, Shandong University of Science and Technology, 579 Qianwangang Road, Huangdao District, Qingdao, Shandong Province, 266590, PR China.
| | - Wen Li
- Biofilm Research institute, Qingdao Spring water Treatment Co. Ltd, Qingdao, 266555, PR China
| | - Lanmei Zhao
- Department of Bioengineering, College of Chemical and Bioengineering, Shandong University of Science and Technology, 579 Qianwangang Road, Huangdao District, Qingdao, Shandong Province, 266590, PR China
| | - Huaxiao Yan
- Department of Bioengineering, College of Chemical and Bioengineering, Shandong University of Science and Technology, 579 Qianwangang Road, Huangdao District, Qingdao, Shandong Province, 266590, PR China
| | - Hui Zhao
- Department of Bioengineering, College of Chemical and Bioengineering, Shandong University of Science and Technology, 579 Qianwangang Road, Huangdao District, Qingdao, Shandong Province, 266590, PR China
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5
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Hu F, Wang P, Li Y, Ling J, Ruan Y, Yu J, Zhang L. Bioremediation of environmental organic pollutants by Pseudomonas aeruginosa: Mechanisms, methods and challenges. ENVIRONMENTAL RESEARCH 2023; 239:117211. [PMID: 37778604 DOI: 10.1016/j.envres.2023.117211] [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: 07/02/2023] [Revised: 09/10/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
The development of the chemical industry has led to a boom in daily consumption and convenience, but has also led to the release of large amounts of organic pollutants, such as petroleum hydrocarbons, plastics, pesticides, and dyes. These pollutants are often recalcitrant to degradation in the environment, whereby the most problematic compounds may even lead to carcinogenesis, teratogenesis and mutagenesis in animals and humans after accumulation in the food chain. Microbial degradation of organic pollutants is efficient and environmentally friendly, which is why it is considered an ideal method. Numerous studies have shown that Pseudomonas aeruginosa is a powerful platform for the remediation of environmental pollution with organic chemicals due to its diverse metabolic networks and its ability to secrete biosurfactants to make hydrophobic substrates more bioavailable, thereby facilitating degradation. In this paper, the mechanisms and methods of the bioremediation of environmental organic pollutants (EOPs) by P. aeruginosa are reviewed. The challenges of current studies are highlighted, and new strategies for future research are prospected. Metabolic pathways and critical enzymes must be further deciphered, which is significant for the construction of a bioremediation platform based on this powerful organism.
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Affiliation(s)
- Fanghui Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, Nanjing, 210023, China
| | - Panlin Wang
- School of Bioengineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yunhan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, Nanjing, 210023, China
| | - Jiahuan Ling
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, Nanjing, 210023, China
| | - Yongqiang Ruan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, Nanjing, 210023, China
| | - Jiaojiao Yu
- School of Medical Imaging, Tianjin Medical University, Tianjin, 300203, China.
| | - Lihui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, Nanjing, 210023, China.
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Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
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7
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Yu X, Zhang C, Wang H, Li Y, Kang Y, Yang K. High-Temperature Pyrolysis of N-Tetracosane Based on ReaxFF Molecular Dynamics Simulation. ACS OMEGA 2023; 8:20823-20833. [PMID: 37332798 PMCID: PMC10268645 DOI: 10.1021/acsomega.3c01525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
In order to further understand the high-temperature reaction process and pyrolysis mechanism of hydrocarbon fuels, the high-temperature pyrolysis behavior of n-tetracosane (C24H50) was investigated in this paper via the reaction force field (ReaxFF) method-based molecular dynamics approach. There are two main types of initial reaction channels for n-heptane pyrolysis, C-C and C-H bond fission. At low temperatures, there is little difference in the percentage of the two reaction channels. With the temperature increase, C-C bond fission dominates, and a small amount of n-tetracosane is decomposed by reaction with intermediates. It is found that H radicals and CH3 radicals are widely present throughout the pyrolysis process, but the amount is little at the end of the pyrolysis. In addition, the distribution of the main products H2, CH4, and C2H4, and related reactions are investigated. The pyrolysis mechanism was constructed based on the generation of major products. The activation energy of C24H50 pyrolysis is 277.19 kJ/mol, obtained by kinetic analysis in the temperature range of 2400-3600 K.
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Xiang W, Hong S, Xue Y, Ma Y. Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91. Microorganisms 2023; 11:1537. [PMID: 37375039 DOI: 10.3390/microorganisms11061537] [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: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate the functional role of alkB1 and alkB2 genes in the n-alkane degradation of strain CH91. RT-qPCR analyses revealed that the two genes were induced by n-alkanes ranging from C16 to C36 and the expression of the alkB2 gene was up-regulated much higher than that of alkB1. The knockout of the alkB1 or alkB2 gene in strain CH91 resulted in the obvious reduction of growth and degradation rates on C16-C36 n-alkanes and the alkB2 knockout mutant exhibited lower growth and degradation rate than the alkB1 knockout mutant. When gene alkB1 or alkB2 was heterologously expressed in Pseudomonas fluorescens KOB2Δ1, the two genes could restore its alkane degradation activity. These results demonstrated that both alkB1 and alkB2 genes were responsible for C16-C36 n-alkanes' degradation of strain CH91, and alkB2 plays a more important role than alkB1. The functional characteristics of the two alkB genes in the degradation of a broad range of n-alkanes make them potential gene candidates for engineering the bacteria used for bioremediation of petroleum hydrocarbon contaminations.
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Affiliation(s)
- Wei Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Hong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Das S. Cell surface hydrophobicity and petroleum hydrocarbon degradation by biofilm-forming marine bacterium Pseudomonas furukawaii PPS-19 under different physicochemical stressors. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131795. [PMID: 37301070 DOI: 10.1016/j.jhazmat.2023.131795] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/19/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
Biofilm-forming marine bacterium Pseudomonas furukawaii PPS-19 showed strong hydrophobicity under different physicochemical stressors, such as pH and salinity. Strong aggregation of P. furukawaii PPS-19 was observed at hydrophobic interfaces of n-dodecane and crude oil, while uptake of pyrene resulted in blue fluorescence of the bacterium. Changes in biofilm microcolonies were observed under different physicochemical stressors with maximum biofilm thickness of 15.15 µm and 15.77 µm at pH 7% and 1% salinity, respectively. Relative expression analysis of alkB2 gene revealed the maximum expression in n-dodecane (10.5 fold) at pH 7 (1 fold) and 1% salinity (8.3 fold). During the degradation process, a significant drop in surface tension resulted in increased emulsification activity. P. furukawaii PPS-19 showed the respective n-dodecane and pyrene degradation of 94.3% and 81.5% at pH 7% and 94.5% and 83% at 1% salinity. A significant positive correlation was obtained between cell surface hydrophobicity (CSH), biofilm formation, and PHs degradation (P < 0.05) under all the physicochemical stressors, with the highest value at pH 7% and 1% salinity. Analysis of metabolites indicated that mono-terminal oxidation and multiple pathways were followed for n-dodecane and pyrene biodegradation, respectively. Thus, P. furukawaii PPS-19 is an efficient hydrocarbonoclastic bacterium that may be exploited for large-scale oil pollution abatement.
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Affiliation(s)
- Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
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Wu HJ, Du XY, Wu WJ, Zheng J, Song JY, Xie JC. Metagenomic analysis reveals specific BTEX degrading microorganisms of a bacterial consortium. AMB Express 2023; 13:48. [PMID: 37195357 DOI: 10.1186/s13568-023-01541-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/23/2023] [Indexed: 05/18/2023] Open
Abstract
Petroleum hydrocarbon contamination is of environmental and public health concerns due to its toxic components. Bioremediation utilizes microbial organisms to metabolism and remove these contaminants. The aim of this study was to enrich a microbial community and examine its potential to degrade petroleum hydrocarbon. Through successive enrichment, we obtained a bacterial consortium using crude oil as sole carbon source. The 16 S rRNA gene analysis illustrated the structural characteristics of this community. Metagenomic analysis revealed the specific microbial organisms involved in the degradation of cyclohexane and all the six BTEX components, with a demonstration of the versatile metabolic pathways involved in these reactions. Results showed that our consortium contained the full range of CDSs that could potentially degrade cyclohexane, benzene, toluene, and (o-, m-, p-) xylene completely. Interestingly, a single taxon that possessed all the genes involved in either the activation or the central intermediates degrading pathway was not detected, except for the Novosphingobium which contained all the genes involved in the upper degradation pathway of benzene, indicating the synergistic interactions between different bacterial genera during the hydrocarbon degradation.
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Affiliation(s)
- Hui-Jun Wu
- State Key Laboratory of Petroleum Pollution Control, National Petroleum Corporation Research Institute of Safety and Environmental Technology, 102206, Beijing, China.
| | - Xian-Yuan Du
- State Key Laboratory of Petroleum Pollution Control, National Petroleum Corporation Research Institute of Safety and Environmental Technology, 102206, Beijing, China
| | - Wen-Jing Wu
- State Key Laboratory of Petroleum Pollution Control, National Petroleum Corporation Research Institute of Safety and Environmental Technology, 102206, Beijing, China
- College of Life Science, Northwest University, 710000, Xian, China
| | - Jin Zheng
- State Key Laboratory of Petroleum Pollution Control, National Petroleum Corporation Research Institute of Safety and Environmental Technology, 102206, Beijing, China
| | - Jia-Yu Song
- State Key Laboratory of Petroleum Pollution Control, National Petroleum Corporation Research Institute of Safety and Environmental Technology, 102206, Beijing, China
| | - Jia-Cai Xie
- State Key Laboratory of Petroleum Pollution Control, National Petroleum Corporation Research Institute of Safety and Environmental Technology, 102206, Beijing, China
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Wei F, Xu R, Rao Q, Zhang S, Ma Z, Ma Y. Biodegradation of asphaltenes by an indigenous bioemulsifier-producing Pseudomonas stutzeri YWX-1 from shale oil in the Ordos Basin: Biochemical characterization and complete genome analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 251:114551. [PMID: 36669280 DOI: 10.1016/j.ecoenv.2023.114551] [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: 11/07/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Crude oil pollution is environmentally ubiquitous and has become a global public concern about its impact on human health. Asphaltenes are the key components of heavy crude oil (HCO) that are underutilized due to their high viscosity and density, and yet, the associated information about biodegradation is extremely limited in the literature. In the present study, an indigenous bacterium with effective asphaltene-degrading activity was isolated from oil shale and identified as Pseudomonas stutzeri by a polyphasic taxonomic approach, named YWX-1. Supplemented with 75 g L-1 heavy crude oil as the sole carbon source for growth in basic mineral salts liquid medium (MSM), strain YWX-1 was able to remove 49% of asphaletene fractions within 14 days, when it was cultivated with an initial inoculation size of 1%. During the degradation process, the bioemulsifier produced by strain YWX-1 could emulsify HCO obviously into particles, as well as it had the ability to solubilize asphaletenes. The bioemulsifier was identified to be a mixture of polysaccharide and protein through Fourier transform infrared spectroscopy (FT-IR). The genome of strain YWX-1 contains one circular chromosome of 4488441 bp with 63.98% GC content and 4145 protein coding genes without any plasmid. Further genome annotation indicated that strain YWX-1 possesses a serial of genes involved in bio-emulsification and asphaltenes biodegradation. This work suggested that P. stutzeri YWX-1 could be a promising species for bioremediation of HCO and its genome analysis provided insight into the molecular basis of asphaltene biodegradation and bioemulsifier production.
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Affiliation(s)
- Fengdan Wei
- College of Life Science, Northwest University, Xi´an, China
| | - Rui Xu
- College of Life Science, Northwest University, Xi´an, China
| | - Qingyan Rao
- College of Life Science, Northwest University, Xi´an, China
| | - Shuqi Zhang
- College of Life Science, Northwest University, Xi´an, China
| | - Zhiwei Ma
- College of Life Science, Northwest University, Xi´an, China
| | - Yanling Ma
- Shaanxi 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, Shaanxi 710069, China; College of Life Science, Northwest University, 229 Tai bai North Rd, Xi´an, Shaanxi 710069, China.
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12
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Duque E, Udaondo Z, Molina L, de la Torre J, Godoy P, Ramos JL. Providing octane degradation capability to Pseudomonas putida KT2440 through the horizontal acquisition of oct genes located on an integrative and conjugative element. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:934-946. [PMID: 35651318 PMCID: PMC9795978 DOI: 10.1111/1758-2229.13097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 05/17/2023]
Abstract
The extensive use of petrochemicals has produced serious environmental pollution problems; fortunately, bioremediation is considered an efficient way to fight against pollution. In line with Synthetic Biology is that robust microbial chassis with an expanded ability to remove environmental pollutants are desirable. Pseudomonas putida KT2440 is a robust lab microbe that has preserved the ability to survive in the environment and is the natural host for the self-transmissible TOL plasmid, which allows metabolism of toluene and xylenes to central metabolism. We show that the P. putida KT2440 (pWW0) acquired the ability to use octane as the sole C-source after acquisition of an almost 62-kb ICE from a microbial community that harbours an incomplete set of octane metabolism genes. The ICE bears genes for an alkane monooxygenase, a PQQ-dependent alcohol dehydrogenase and aldehyde dehydrogenase but lacks the electron donor enzymes required for the monooxygenase to operate. Host rubredoxin and rubredoxin reductase allow metabolism of octane to octanol. Proteomic assays and mutants unable to grow on octane or octanoic acid revealed that metabolism of octane is mediated by redundant host and ICE enzymes. Octane is oxidized to octanol, octanal and octanoic acid, the latter is subsequently acylated and oxidized to yield acetyl-CoA that is assimilated via the glyoxylate shunt; in fact, a knockout mutant in the aceA gene, encoding isocitrate lyase was unable to grow on octane or octanoic acid.
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Affiliation(s)
- Estrella Duque
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
| | - Zulema Udaondo
- Department of Biomedical InformaticsUniversity of Arkansas for Medical ScienceLittle RockArkansasUSA
| | - Lázaro Molina
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
| | - Jesús de la Torre
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
| | - Patricia Godoy
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
| | - Juan L. Ramos
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
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13
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Yao C, Xia W, Dou M, Du Y, Wu J. Oxidative degradation of UV-irradiated polyethylene by laccase-mediator system. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129709. [PMID: 35939906 DOI: 10.1016/j.jhazmat.2022.129709] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Polyethylene (PE) is one of the most widely used plastics. However, the chemical inertness, inefficient recycling, and random landfilling of PE waste have caused serious pollution to the natural environment. In this study, a series of laccase-mediator systems (LMS) were constructed by combination of two laccases from Botrytis aclada (BaLac) and Bacillus subtilis (BsLac) with three synthetic mediators (ABTS, HBT, and TEMPO) to oxidize LDPE films (UVPE) pretreated with high-temperature UV irradiation. Scanning electron microscopy showed aging phenomena such as etching, fragmentation, and cracking on the surface of the UVPE films after LMS incubation. The FTIR results showed that LMS-UVPE added new oxygen-containing functional groups such as -OH, -CO, and CC. High-temperature gel chromatography confirmed that the average reduction in weight-average molecular weight (Mw) was approximately 40% for the BaLac experimental group. GC-MS analysis showed the presence of oxygen-containing products, such as aldehydes, ketones, and alcohols, in the reaction mixture. To verify the oxidation process UVPE degradation by LMS, we inferred three possible pathways by combined analysis of the oxidation products of LMS on UVPE and model substrates oleic acid and squalene.
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Affiliation(s)
- Congyu Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Wei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Mingde Dou
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Yanyi Du
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
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14
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A Novel FadL Homolog, AltL, Mediates Transport of Long-Chain Alkanes and Fatty Acids in Acinetobacter venetianus RAG-1. Appl Environ Microbiol 2022; 88:e0129422. [PMID: 36169310 PMCID: PMC9599521 DOI: 10.1128/aem.01294-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Due to the barrier effect of lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria, transporters are required for hydrophobic alkane uptake. However, there are few reports on long-chain alkane transporters. In this study, a potential long-chain alkane transporter (AltL) was screened in Acinetobacter venetianus RAG-1 by comparative transcriptome analysis. Growth and degradation experiments showed that altL deletion led to the loss of n-octacosane utilization capacity of RAG-1. To identify the function of AltL, we measured the existence and accumulation of alkanes in cells through the constructed alkane detection system and isotope transport experiment, which proved its long-chain alkane transport function. Growth experiments using different chain-length n-alkanes and fatty acids as substrates showed that AltL was responsible for the transport of (very) long-chain n-alkanes (C20 to C38) and fatty acids (C18A to C28A) and was also involved in the uptake of medium-chain n-alkanes (C16 to C18). Subsequently, we analyzed the distribution of AltL in bacteria, and found that AltL homologs are widespread in Gamma-, Beta-, and Deltaproteobacteria. An AltL homolog in Pseudomonas aeruginosa was also identified to participate in long-chain alkane transport by a gene deletion and growth assay. We also found that overexpression of altL in Pseudomonas aeruginosa enhanced the degradation of C16 to C32 n-alkanes. In addition, structure analysis showed that AltL has longer extracellular loops than other FadL family members, which may be involved in the binding of alkanes. These results showed that AltL is a novel transporter and that it is mainly responsible for the transport of long-chain n-alkanes and (very) long-chain fatty acids and has broad application potential. IMPORTANCE Petroleum pollution has caused great harm to the natural environment, and alkanes are the main components of petroleum. Many Gram-negative bacteria can use alkanes as carbon and energy sources, which is an important strategy for oil pollution remediation. Alkane uptake is the first step for its utilization. Hence, the characterization of transport proteins is of great significance for the recovery of oil pollution and other potential applications in industrial engineering bacteria. At present, some short- and medium-chain alkane transporters have been identified, but stronger hydrophobic long-chain alkane transporters have received little attention. In this study, the broad-spectrum transporter AltL, identified in RAG-1, makes up for the lack of research on the transport of long-chain alkanes and (very) long-chain fatty acids. Meanwhile, the structural features of longer extracellular loops might be related to its unique transport function on more hydrophobic and larger substrates, indicating it is a novel type alkane transporter.
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15
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Perera M, Wijesundera S, Wijayarathna CD, Seneviratne G, Jayasena S. Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis. Front Microbiol 2022; 13:898456. [PMID: 36110294 PMCID: PMC9468676 DOI: 10.3389/fmicb.2022.898456] [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: 03/17/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Efficient degradation of alkanes in crude oil by the isolated Aspergillus flavus MM1 alluded to the presence of highly active alkane-degrading enzymes in this fungus. A long-chain alkane-degrading, LadA-like enzyme family in A. flavus was identified, and possible substrate-binding modes were analyzed using a computational approach. By analyzing publicly available protein databases, we identified six uncharacterized proteins in A. flavus NRRL 3357, of which five were identified as class LadAα and one as class LadAβ, which are eukaryotic homologs of bacterial long-chain alkane monooxygenase (LadA). Computational models of A. flavus LadAα homologs (Af1-Af5) showed overall structural similarity to the bacterial LadA and the unique sequence and structural elements that bind the cofactor Flavin mononucleotide (FMN). A receptor-cofactor-substrate docking protocol was established and validated to demonstrate the substrate binding in the A. flavus LadAα homologs. The modeled Af1, Af3, Af4, and Af5 captured long-chain n-alkanes inside the active pocket, above the bound FMN. Isoalloxazine ring of reduced FMN formed a π–alkyl interaction with the terminal carbon atom of captured alkanes, C16–C30, in Af3–Af5 and C16–C24 in Af1. Our results confirmed the ability of identified A. flavus LadAα monooxygenases to bind long-chain alkanes inside the active pocket. Hence A. flavus LadAα monooxygenases potentially initiate the degradation of long-chain alkanes by oxidizing bound long-chain alkanes into their corresponding alcohol.
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Affiliation(s)
- Madushika Perera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Sulochana Wijesundera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | | | | | - Sharmila Jayasena
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
- *Correspondence: Sharmila Jayasena,
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16
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Muthukumar B, Al Salhi MS, Narenkumar J, Devanesan S, Kim W, Rajasekar A. Characterization of two novel strains of Pseudomonas aeruginosa on biodegradation of crude oil and its enzyme activities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119223. [PMID: 35351596 DOI: 10.1016/j.envpol.2022.119223] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/03/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Crude oil contaminant is one of the major problem to environment and its removal process considered as most challenging tool currently across the world. In this degradation study, crude oil hydrocarbons are degraded on various pH optimization conditions (pH 2, 4,6,7,8 and 10) by using two biosurfactant producing bacterial strains Pseudomonas aeruginosa PP3 and Pseudomonas aeruginosa PP4. During crude oil biodegradation, degradative enzymes alkane hydroxylase and alcohol dehydrogenase were examined and found to be higher in PP4 than PP3. Biodegradation efficiency (BE) of crude oil by both PP3 and PP4 were analysed by gas chromatography mass spectroscopy (GCMS). Based on strain PP3, the highest BE was observed in pH 2 and pH 4 were found to be 62% and 69% than pH 6, 7, 8 and 10 (47%, 47%, 49% and 45%). It reveals that PP3 was survived effectively in acidic condition and utilized the crude oil hydrocarbons. In contrast, the highest BE of PP4 was observed in pH 7 (78%) than pH4 (68%) and pH's 2, 6, 8 and 10 (52%, 52%, 43% and 53%) respectively. FTIR spectra results revealed that the presence of different functional group of hydrocarbons (OH, -CH3, CO, C-H) in crude oil. GCMS results confirmed that both strains PP3 and PP4 were survived in acidic condition and utilized the crude oil hydrocarbons as sole carbon sources. This is the first observation on biodegradation of crude oil by the novel strains of Pseudomonas aeruginosa in acidic condition with higher BE. Overall, the extracellular enzymes and surface active compounds (biosurfactant) produced by bacterial strains were played a key role in crude oil biodegradation process.
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Affiliation(s)
- Balakrishnan Muthukumar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India
| | - Mohamad S Al Salhi
- Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box-2455, Riyadh, 11451, Saudi Arabia
| | - Jayaraman Narenkumar
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Selaiyur, Chennai, Tamil Nadu 600073. India
| | - Sandhanasamy Devanesan
- Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box-2455, Riyadh, 11451, Saudi Arabia
| | - Woong Kim
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, South Korea
| | - Aruliah Rajasekar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India.
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17
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Li Y, Wang J, Wang F, Wang L, Wang L, Xu Z, Yuan H, Yang X, Li P, Su J, Wang R. Production of 10-Hydroxy-2-decenoic Acid from Decanoic Acid via Whole-Cell Catalysis in Engineered Escherichia coli. CHEMSUSCHEM 2022; 15:e202102152. [PMID: 34796684 DOI: 10.1002/cssc.202102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Indexed: 06/13/2023]
Abstract
10-Hydroxy-2-decenoic acid (10-HDA) is a terminal hydroxylated medium-chain α,β-unsaturated carboxylic acid that performs various unique physiological activities and has a wide market value. Therefore, development of an environmentally friendly, safe, and high-efficiency route to synthesize 10-HDA is required. Here, the β-oxidation pathway of Escherichia coli was modified and a P450 terminal hydroxylase (CYP153A33-CPRBM3 ) was rationally designed to synthesize 10-HDA using decanoic acid as a substrate via two-step whole-cell catalysis. Different homologues of FadDs, FadEs, and YdiIs were analyzed in the first step of the conversion of decanoic acid to trans- -2- decenoic acid. In the second step, CYP153A33 (M228L)-CPRBM3 efficiently catalyzed the conversion of trans- -2- decenoic acid to 10-HDA. Finally, 217 mg L-1 10-HDA was obtained with 500 mg L-1 decanoic acid. This study provides a strategy for biosynthesis of 10-HDA and other α, β-unsaturated carboxylic acid derivatives from specific fatty acids.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Fen Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Li Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Leilei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Ziqi Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Xiaohui Yang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
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18
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Tooker BC, Kandel SE, Work HM, Lampe JN. Pseudomonas aeruginosa cytochrome P450 CYP168A1 is a fatty acid hydroxylase that metabolizes arachidonic acid to the vasodilator 19-HETE. J Biol Chem 2022; 298:101629. [PMID: 35085556 PMCID: PMC8913318 DOI: 10.1016/j.jbc.2022.101629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 01/08/2023] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen that is highly prevalent in individuals with cystic fibrosis (CF). A major problem in treating CF patients infected with P. aeruginosa is the development of antibiotic resistance. Therefore, the identification of novel P. aeruginosa antibiotic drug targets is of the utmost urgency. The genome of P. aeruginosa contains four putative cytochrome P450 enzymes (CYPs) of unknown function that have never before been characterized. Analogous to some of the CYPs from Mycobacterium tuberculosis, these P. aeruginosa CYPs may be important for growth and colonization of CF patients’ lungs. In this study, we cloned, expressed, and characterized CYP168A1 from P. aeruginosa and identified it as a subterminal fatty acid hydroxylase. Spectral binding data and computational modeling of substrates and inhibitors suggest that CYP168A1 has a large, expansive active site and preferentially binds long chain fatty acids and large hydrophobic inhibitors. Furthermore, metabolic experiments confirm that the enzyme is capable of hydroxylating arachidonic acid, an important inflammatory signaling molecule present in abundance in the CF lung, to 19-hydroxyeicosatetraenoic acid (19-HETE; Km = 41 μM, Vmax = 220 pmol/min/nmol P450), a potent vasodilator, which may play a role in the pathogen’s ability to colonize the lung. Additionally, we found that the in vitro metabolism of arachidonic acid is subject to substrate inhibition and is also inhibited by the presence of the antifungal agent ketoconazole. This study identifies a new metabolic pathway in this important human pathogen that may be of utility in treating P. aeruginosa infections.
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Affiliation(s)
- Brian C Tooker
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, Colorado, USA
| | - Sylvie E Kandel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, Colorado, USA
| | - Hannah M Work
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, Colorado, USA
| | - Jed N Lampe
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, Colorado, USA.
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19
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Crude Oil Degradation by a Novel Strain Pseudomonas aeruginosa AQNU-1 Isolated from an Oil-Contaminated Lake Wetland. Processes (Basel) 2022. [DOI: 10.3390/pr10020307] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In this study, a novel crude oil degrading bacterium was isolated from an oil-contaminated freshwater lake using crude oil as the sole carbon source. The strain was named Pseudomonas aeruginosa AQNU-1 based on the analyses of its morphological characteristics and 16S rRNA gene sequencing. Gas chromatography-mass spectrometry (GC-MS) was carried out to investigate the degradation of crude oil fractions under dynamic (37 °C, 180 r/min) and static (37 °C, 0 r/min) cultivation over three months of continuous enrichment in the laboratory. It was found that strain AQNU-1 exhibited stronger biodegradation efficiency for n-alkanes of C13–C35 under dynamic cultivation with degradation ratios of 87–100% compared to ratios of 74–100% under static cultivation. Furthermore, this strain could fully utilize alkylcyclohexane (M/Z 82), alkylbenzene (M/Z 92) and alkyltoluene (M/Z 106) in crude oil under both conditions. It also had better biodegradability of partial aromatic compounds in the crude oil, showing differences within compound families of aromatic hydrocarbons. Further, the potential degradation ability of this isolated strain decreased with increasing molecular weight, with the dynamic condition performing better in general. These results suggest that the isolated strain has great potential to assimilate indigestible crude-oil contaminants under different hydrological conditions, providing a valuable microbiological resource for in situ remediation of natural wetlands.
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20
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Khot V, Zorz J, Gittins DA, Chakraborty A, Bell E, Bautista MA, Paquette AJ, Hawley AK, Novotnik B, Hubert CRJ, Strous M, Bhatnagar S. CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. Front Microbiol 2022; 12:764058. [PMID: 35069469 PMCID: PMC8767102 DOI: 10.3389/fmicb.2021.764058] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 02/04/2023] Open
Abstract
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.
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Affiliation(s)
- Varada Khot
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jackie Zorz
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Daniel A Gittins
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Anirban Chakraborty
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Emma Bell
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - María A Bautista
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Alexandre J Paquette
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K Hawley
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Breda Novotnik
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Casey R J Hubert
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Srijak Bhatnagar
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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21
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Pan J, Wei F, Liu Y, Xu Y, Ma Y. Unraveling the role of GntR on the regulation of alkane hydroxylase AlkB
2
in
Pseudomonas aeruginosa
DN1 based on transcriptome analysis. J Appl Microbiol 2022; 132:2812-2822. [DOI: 10.1111/jam.15453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Jincheng Pan
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University 229 Taibai North Rd Xi’an Shaanxi 710069 China
| | - Fengdan Wei
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University 229 Taibai North Rd Xi’an Shaanxi 710069 China
| | - Yani Liu
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University 229 Taibai North Rd Xi’an Shaanxi 710069 China
| | - Yuanyuan Xu
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University 229 Taibai North Rd Xi’an Shaanxi 710069 China
| | - Yanling Ma
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University 229 Taibai North Rd Xi’an Shaanxi 710069 China
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22
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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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Kim NK, Lee SH, Yoon H, Jeong G, Jung YJ, Hur M, Lee BH, Park HD. Microbiome degrading linear alkylbenzene sulfonate in activated sludge. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126365. [PMID: 34329019 DOI: 10.1016/j.jhazmat.2021.126365] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/20/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
As the most widely used anionic surfactant, linear alkylbenzene sulfonate (LAS) requires biological alkane degradation when it is treated using an activated sludge (AS) process in a wastewater treatment plant because of its structural carboxylic unavailability. As consumption of LAS is gradually increasing, LAS loading into the WWTP is accordingly increasing. However, fewer studies have examined the involvement of the AS microbial community in the LAS degradation. In this study, metagenomic approaches were used to define microbiomes involved in LAS degradation in AS, with a particular focus on ω-hydroxylation. The abundance and diversity of alkane-degrading genes were investigated, and these genes were integrated with reconstructed metagenome-assembled genomes (MAGs). Additionally, the association of functional genes and MAGs with respect to LAS degradation was investigated. The results showed that alkB and cytochrome P450 genes were only shared within specific MAGs. Unique sets of genes with diverse abundances were detected in each sample. The MAGs with the alkB and cytochrome P450 genes were strongly associated with the other MAGs and involved in positive commensal interactions. The findings provided significant insights into how the AS microbiomes, which have continuously treated anionic surfactants for decades, potentially metabolize LAS and interact with commensal bacteria.
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Affiliation(s)
- Na-Kyung Kim
- Research Institute of Engineering and Technology, Korea University, Seoul, South Korea
| | - Sang-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Hyeokjun Yoon
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Garam Jeong
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - You-Jung Jung
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Moonsuk Hur
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Byoung-Hee Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea.
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Yeom SJ, Le TK, Yun CH. P450-driven plastic-degrading synthetic bacteria. Trends Biotechnol 2021; 40:166-179. [PMID: 34243985 DOI: 10.1016/j.tibtech.2021.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/27/2022]
Abstract
Plastic contamination currently threatens a wide variety of ecosystems and presents damaging repercussions and negative consequences for many wildlife species. Sustainable plastic waste management is an important approach to environmental protection and a necessity in the current life cycle of plastics in nature. Plastic biodegradation by microorganisms is a notable possible solution. This opinion article includes a proposal to use hypothetical P450 enzymes with an engineered active site as potent trigger biocatalysts to biodegrade polyethylene (PE) via in-chain hydroxylation into smaller products of linear aliphatic alcohols and alkanoic acids based on cascade enzymatic reactions. Furthermore, we propose the adoption of P450 into plastic-eating synthetic bacteria for PE biodegradation. This strategy can be applicable to other dense plastics, such as polypropylene (PP) and polystyrene (PS).
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Affiliation(s)
- Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.
| | - Thien-Kim Le
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.
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25
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Kong W, Zhao C, Gao X, Wang L, Tian Q, Liu Y, Xue S, Han Z, Chen F, Wang S. Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18126365. [PMID: 34208299 PMCID: PMC8296198 DOI: 10.3390/ijerph18126365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022]
Abstract
Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain n-alkanes (C8–C16). The degradation rate of C20 was 91.25%, followed by C18, C22, C24, C32, and C36 with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C20 or CH3COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C20 compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C20, C24, and C32, and almA induction extent by C24 and C32 was higher than that with C20. Furthermore, ladA2 expression was only induced by C32, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.
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Affiliation(s)
- Weina Kong
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Cheng Zhao
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Xingwang Gao
- Hulangmao Oil Production Area in No.3 Oil Production Plant of Changqing Oilfield Company, Yan’an 717500, China;
| | - Liping Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Qianqian Tian
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Yu Liu
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Shuwen Xue
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Zhuang Han
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China;
| | - Fulin Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
- Correspondence: (F.C.); (S.W.)
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
- Correspondence: (F.C.); (S.W.)
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Liu J, Zhao B, Lan Y, Ma T. Enhanced degradation of different crude oils by defined engineered consortia of Acinetobacter venetianus RAG-1 mutants based on their alkane metabolism. BIORESOURCE TECHNOLOGY 2021; 327:124787. [PMID: 33556770 DOI: 10.1016/j.biortech.2021.124787] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial consortia offer an attractive biodegradation strategy for removing hydrocarbons from oil-contaminated sites. In this study, we explored the degradation properties of Acinetobacter venetianus strain RAG-1 (RAG-1). RAG-1 effectively degrades three crude oils with excellent emulsification activity and cell surface hydrophobicity, while exhibiting broad environmental tolerance. RAG-1 accepts a range of alkane substrates (C10-C38) using three alkane hydroxylases (AlkMa, AlkMb, and AlmA). Bacterial mutant with alkMa or alkMb deletion enhanced degradation of C10-C20 or C22-C32 n-alkanes, respectively. Based on the substrate metabolism of the mutants, adjustable and targeted consortia consisting of ΔalkMa/almA and ΔalkMb were constructed, achieving enhanced degradation (10 days) of light crude oil (73.42% to 88.65%), viscous crude oil (68.40% to 90.05%), and high waxy crude oil (47.46% to 60.52%) compared with the single wild-type strain. The degradation properties of RAG-1 and the engineered consortia strategy may have potential use in microbial biodegradation applications.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Bo Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yazheng Lan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
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27
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Furlan JPR, Lopes R, Stehling EG. Whole-genome sequence-based analysis of the Paenibacillus aquistagni strain DK1, a polyethylene-degrading bacterium isolated from landfill. World J Microbiol Biotechnol 2021; 37:80. [PMID: 33839943 DOI: 10.1007/s11274-021-03045-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/29/2021] [Indexed: 11/25/2022]
Abstract
Polyethylene-degrading bacteria have been emerging as a rational and safe alternative in bioremediation strategies. In this context, some Paenibacillus species produce enzymes involved in the biodegradation of pollutants. Among the enzymes involved in the biodegradation of polyethylene, the alkane hydroxylases, encoded by alkB homologous genes, play a key role in this process. Therefore, this study aimed to identify and perform a genomic investigation of the first polyethylene-degrading Paenibacillus sp. strain, named DK1. The whole-genome sequence-based analysis revealed that the DK1 strain belonged to the species Paenibacillus aquistagni and shared a total of 4327 CDSs with P. aquistagni strain 11. On the other hand, a comparison of the gene clusters showed that DK1 strain harbored a genetic context surrounding the alkB-like gene similar to that found in Pseudomonas sp. strains. The percentage of similarity ranged from 47.88 to 99.76% among all complete amino acid sequences of AlkB-like proteins analyzed. Nevertheless, the predicted amino acid sequences of AlkB-like contained typical structural motifs of alkane hydroxylases, such as His boxes and the HYG motif. These findings associated with the previously reported phenotypic results highlighted the potential of P. aquistagni strain DK1 to biodegrade polyethylene. Therefore, further studies focusing on the biochemical and structural properties of the AlkB-like protein from Paenibacillus may also contribute to the development of sustainable bioremediation strategies.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Ralf Lopes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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28
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Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation. Microorganisms 2020; 9:microorganisms9010003. [PMID: 33374976 PMCID: PMC7822026 DOI: 10.3390/microorganisms9010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/19/2020] [Accepted: 12/19/2020] [Indexed: 12/12/2022] Open
Abstract
The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. n-hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.
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Sangkharak K, Paichid N, Yunu T, Prasertsan P. Enhancing the degradation of mixed polycyclic aromatic hydrocarbon and medium-chain-length polyhydroxyalkanoate production by mixed bacterial cultures using modified repeated batch fermentation. J Appl Microbiol 2020; 129:554-564. [PMID: 32162457 DOI: 10.1111/jam.14638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
AIMS To increase the biodegradation of phenanthrene (PHE), pyrene (PYR) and fluoranthene (FLU) through mixed cultures of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria, using modified repeated batch fermentation. METHODS AND RESULTS Novel bacterial strains of Pseudomonas putida, Pseudomonas sp. and Ralstonia eutropha were cultivated and the biodegradation and conversion of mixed PAH to medium-chain-length polyhydroxyalkanoates (MCL-PHA) was determined. The highest degradation of PAH (100%) and PHA production (50·0%) was obtained in medium containing 30 mmol l-1 of mixed PAH after three cycles of repeated batch fermentation. The concentration of PAH in the reactor was increased from 30 to 90 mmol l-1 with repeated additions of PAH, and bacteria were able to produce PHA at 40% of cell dry mass. The MCL-PHA were identified by gas chromatography/mass spectroscopy, with the 3-hydroxydecanoate (3-HD) monomer higher than 75 mol.%. CONCLUSIONS This study demonstrated that the biodegradation of PHE, PYR and FLU was enhanced by modified repeated batch fermentation using a mixed culture of bacteria. In addition, this fermentation strategy also increased the production of PHA, with an increase in monomer composition. SIGNIFICANCE AND IMPACT OF THE STUDY This was the first study to describe the enhancement of the degradation of mixed solutions of PHE, PYR and FLU, and PHA production, using novel mixed bacterial cultures and modified repeated batch fermentation. The MCL-PHA formed had uniquely high 3-HD content.
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Affiliation(s)
- K Sangkharak
- Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung, Thailand
| | - N Paichid
- Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung, Thailand
| | - T Yunu
- Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung, Thailand
| | - P Prasertsan
- Research and Development Office, Prince of Songkla University, Songkhla, Thailand
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