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Chang S, Gui Y, He X, Xue L. Transcriptome analysis of Acinetobacter calcoaceticus HX09 strain with outstanding crude-oil-degrading ability. Braz J Microbiol 2024:10.1007/s42770-024-01392-0. [PMID: 38837015 DOI: 10.1007/s42770-024-01392-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/15/2024] [Indexed: 06/06/2024] Open
Abstract
Microbial remediation plays a pivotal role in the elimination of petroleum pollutants, making it imperative to investigate the capabilities of microorganisms in degrading petroleum. The present study describes the isolation of a promising strain, Acinetobacter sp. HX09, from petroleum-contaminated water. GC-MS analysis revealed a remarkable removal efficiency for short and medium-chain alkanes, with a rate of approximately 64% after a 7-days incubation at 30 °C. Transcriptome analysis of HX09 exhibited a predominant upregulation in gene expression levels by the induce of crude oil. Notably, genes such as alkane 1-monooxygenase, dehydrogenases and fatty acid metabolic enzymes exhibited fold changes range from 3.16 to 1.3. Based on the alkB gene sequences in HX09, the Phyre2 algorithm generated a three-dimensional structure that exhibited similarity to segments of acyl coenzyme desaturases and acyl lipid desaturases. Furthermore, three biodegradation-related gene clusters were predicted in HX09 based on the reference genome sequence. These findings contribute to our understanding of the hydrocarbon-degrading mechanisms employed by Acinetobacter species and facilitate the development of effective remediation strategies for crude oil- polluted environments.
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Affiliation(s)
- Sijing Chang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China.
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China.
| | - Yanwen Gui
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
| | - Xiaoyan He
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
| | - Lingui Xue
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
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Yang H, Yu F, Qian Z, Huang T, Peng T, Hu Z. Cytochrome P450 for environmental remediation: catalytic mechanism, engineering strategies and future prospects. World J Microbiol Biotechnol 2023; 40:33. [PMID: 38057619 DOI: 10.1007/s11274-023-03823-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/29/2023] [Indexed: 12/08/2023]
Abstract
Environmental pollution is a global concern. Various organic compounds are released into the environment through wastewater, waste gas, and waste residue, ultimately accumulating in the environment and the food chain. This poses a significant threat to both human health and ecology. Currently, a growing body of research has demonstrated that microorganisms employ their Cytochrome P450 (CYP450) system for biodegradation, offering a crucial approach for eliminating these pollutants in environmental remediation. CYP450, a ubiquitous catalyst in nature, includes a vast array of family members distributed widely across various organisms, including bacteria, fungi, and mammals. These enzymes participate in the metabolism of diverse organic compounds. Furthermore, the rapid advancements in enzyme and protein engineering have led to increased utilization of engineered CYP450s in environmental remediation, enhancing their efficiency in pollutant removal. This article presents an overview of the current understanding of various members of the CYP450 superfamily involved in transforming organic pollutants and the engineering of biodegrading CYP450s. Additionally, it explores the catalytic mechanisms, current practical applications of CYP450-based systems, their potential applications, and the prospects in bioremediation.
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Affiliation(s)
- Haichen Yang
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Fei Yu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Zhihui Qian
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
- Guangdong Research Center of Offshore Environmental Pollution Control Engineering, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
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Ma J, Zhuang Y, Wang Y, Zhu N, Wang T, Xiao H, Chen J. Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:93345-93362. [PMID: 37548784 DOI: 10.1007/s11356-023-28894-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.
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Affiliation(s)
- Jinglin Ma
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Yan Zhuang
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ning Zhu
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ting Wang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Hongbin Xiao
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China.
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Qian Z, Peng T, Huang T, Hu Z. Oxidization of benzo[a]pyrene by CYP102 in a novel PAHs-degrader Pontibacillus sp. HN14 with potential application in high salinity environment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 321:115922. [PMID: 36027730 DOI: 10.1016/j.jenvman.2022.115922] [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: 04/13/2022] [Revised: 07/25/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Benzo [a]pyrene (BaP) is a type of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) with potent carcinogenicity; however, there are limited studies on its degradation mechanism. Here, a strain of Pontibacillus sp. HN14 with BaP degradation ability was isolated from mangrove sediments in Dongzhai Port, Hainan Province. Our study showed that biodegradation efficiencies reached 42.15% after Pontibacillus sp. HN14 was cultured with 20 mg L-1 BaP as the sole carbon source for 25 days and still had degradability of BaP at a 25% high salinity level. Moreover, 9,10-dihydrobenzo [a]pyrene-7(8H)-one, an intermediate metabolite, was detected during BaP degradation in the HN14 strain. Genome analysis identified a gene encoding the CYP102(HN14) enzyme. The results showed that the E. coli strain with CYP102(HN14) overexpression could transfer BaP to 9,10-dihydrobenzo [a]pyrene-7(8H)-one with a conversion rate of 43.5%, indicating that CYP102(HN14) played an essential role in BaP degradation in Pontibacillus sp. HN14. Thus, our results provide a novel BaP biodegradation molecule, which could be used in BaP bioremediation in high salinity conditions. This study is the first to show that CYP102(HN14) had the BaP oxidization ability in bacteria. CYP102(HN14) could be essential in removing PAHs in saline-alkali soil and other high salt environments through enzyme immobilization.
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Affiliation(s)
- Zhihui Qian
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, PR China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, PR China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, PR China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, Guangdong, PR China.
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Huang Y, Wang B, Yang Y, Yang S, Dong M, Xu M. Microbial carriers promote and guide pyrene migration in sediments. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127188. [PMID: 34597936 DOI: 10.1016/j.jhazmat.2021.127188] [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: 06/22/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Microbial carriers may co-transport polycyclic aromatic hydrocarbons (PAHs), but lack substantial experimental evidence. Cable bacteria use gliding or twitching motility to access sulfide; hence, they could be important microbial carriers in co-transporting PAHs from the sediment-water interface into suboxic zones. In this study, the effect of cable bacteria on pyrene migration was investigated by connecting or blocking the paths of cable bacteria to the suboxic zones. The results showed that downward migration of pyrene in the connecting groups were significantly higher (17.3-49.2%, p < 0.01) than those in the control groups. Meanwhile, significant downward migration of microbial communities in the connecting groups were also observed, including abundant filamentous-motile microorganisms, especially cable bacteria. The adsorption of surrounding particles by cable bacteria were morphologically evidenced. The biomechanical model based on the Peclet number indicated that filamentous-motile microorganisms demonstrated stronger adsorption ability for pyrene than other microorganisms. Supposedly, the downward migration of microbial communities, especially cable bacteria, significantly enhanced pyrene migration, thus influencing the distribution and ecological risk of pyrene in sediments. This study provides new insights into the important roles of motile microorganisms in the migration of PAHs in sediments, shedding lights on guidance for ecological risk assessment of PAHs.
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Affiliation(s)
- Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Meijun Dong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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Hwangbo M, Gill JJ, Young R, Chu KH. Dual-function oleaginous biocatalysts for non-sterile cultivation and solvent-free biolipid bioextraction to reduce biolipid-based biofuel production costs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143969. [PMID: 33333303 PMCID: PMC8061307 DOI: 10.1016/j.scitotenv.2020.143969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/31/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
Triacylglycerols (TAGs) are starting materials for the production of biolipid-based fuels such as biodiesel and biojet fuel. While various microorganisms can produce TAGs from renewable resources, the cultivation of TAG-producing microorganisms under sterilization conditions to avoid microbial contamination and application of solvent to extract TAGs from the TAG-filled microorganisms are costly. To overcome these challenges, this study reports the feasibility of a non-sterile cultivation of an oleaginous bacterium Rhodococcus opacus PD631SpAHB under saline conditions, followed by the use of a solvent-free, phage-lysis-protein-based bioextraction approach for TAGs release. The engineered strain PD631SpAHB was developed by introducing a recombinant plasmid carrying a phage lytic gene cassette (pAHB) into Rhodococcus opacus PD631 via transformation, followed by adaptive evolution under saline conditions. This newly developed strain is a salt-tolerant strain with the inducible plasmid pAHB to enable TAGs release into the supernatant upon induction. Cell lysis of PD631SpAHB was confirmed by the decrease of the optical density of cell suspension, by the loss of cell membrane integrity, and by the detection of TAGs in the culture medium. Up to 38% of the total TAGs accumulated in PD631SpAHB was released into supernatant after the expression of the lytic genes. PD631SpAHB strain is a promising candidate to produce TAGs from non-sterile growth medium and release of its TAGs without solvent extraction - a new approach to reduce the overall cost of biolipid-based biofuel production.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Jason J Gill
- Department of Animal Science, Texas A&M University, College Station, TX 77843, United States; Center for Phage Technology, Texas A&M University, College Station, TX 77843, United States
| | - Ry Young
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, United States; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, United States.
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Abstract
Emerging pollutants in nature are linked to various acute and chronic detriments in biotic components and subsequently deteriorate the ecosystem with serious hazards. Conventional methods for removing pollutants are not efficient; instead, they end up with the formation of secondary pollutants. Significant destructive impacts of pollutants are perinatal disorders, mortality, respiratory disorders, allergy, cancer, cardiovascular and mental disorders, and other harmful effects. The pollutant substrate can recognize different microbial enzymes at optimum conditions (temperature/pH/contact time/concentration) to efficiently transform them into other rather unharmful products. The most representative enzymes involved in bioremediation include cytochrome P450s, laccases, hydrolases, dehalogenases, dehydrogenases, proteases, and lipases, which have shown promising potential degradation of polymers, aromatic hydrocarbons, halogenated compounds, dyes, detergents, agrochemical compounds, etc. Such bioremediation is favored by various mechanisms such as oxidation, reduction, elimination, and ring-opening. The significant degradation of pollutants can be upgraded utilizing genetically engineered microorganisms that produce many recombinant enzymes through eco-friendly new technology. So far, few microbial enzymes have been exploited, and vast microbial diversity is still unexplored. This review would also be useful for further research to enhance the efficiency of degradation of xenobiotic pollutants, including agrochemical, microplastic, polyhalogenated compounds, and other hydrocarbons.
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Patel AB, Shaikh S, Jain KR, Desai C, Madamwar D. Polycyclic Aromatic Hydrocarbons: Sources, Toxicity, and Remediation Approaches. Front Microbiol 2020; 11:562813. [PMID: 33224110 PMCID: PMC7674206 DOI: 10.3389/fmicb.2020.562813] [Citation(s) in RCA: 341] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread across the globe mainly due to long-term anthropogenic sources of pollution. The inherent properties of PAHs such as heterocyclic aromatic ring structures, hydrophobicity, and thermostability have made them recalcitrant and highly persistent in the environment. PAH pollutants have been determined to be highly toxic, mutagenic, carcinogenic, teratogenic, and immunotoxicogenic to various life forms. Therefore, this review discusses the primary sources of PAH emissions, exposure routes, and toxic effects on humans, in particular. This review briefly summarizes the physical and chemical PAH remediation approaches such as membrane filtration, soil washing, adsorption, electrokinetic, thermal, oxidation, and photocatalytic treatments. This review provides a detailed systematic compilation of the eco-friendly biological treatment solutions for remediation of PAHs such as microbial remediation approaches using bacteria, archaea, fungi, algae, and co-cultures. In situ and ex situ biological treatments such as land farming, biostimulation, bioaugmentation, phytoremediation, bioreactor, and vermiremediation approaches are discussed in detail, and a summary of the factors affecting and limiting PAH bioremediation is also discussed. An overview of emerging technologies employing multi-process combinatorial treatment approaches is given, and newer concepts on generation of value-added by-products during PAH remediation are highlighted in this review.
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Affiliation(s)
- Avani Bharatkumar Patel
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Sardar Patel University, Anand, India
| | - Shabnam Shaikh
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Anand, India
| | - Kunal R. Jain
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Sardar Patel University, Anand, India
| | - Chirayu Desai
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Anand, India
| | - Datta Madamwar
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Sardar Patel University, Anand, India
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Anand, India
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Peng T, Kan J, Hu J, Hu Z. Genes and novel sRNAs involved in PAHs degradation in marine bacteria Rhodococcus sp. P14 revealed by the genome and transcriptome analysis. 3 Biotech 2020; 10:140. [PMID: 32206489 DOI: 10.1007/s13205-020-2133-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/11/2020] [Indexed: 01/12/2023] Open
Abstract
Rhodococcus sp. P14 is able to degrade various polycyclic aromatic hydrocarbons (PAHs). In this study, 6 ring-hydroxylating dioxygenases and 24 monooxygenases genes related to PAHs degradation were identified in its genome. Moreover, various genes, like serine hydrolase, hydratase, alcohol dehydrogenase, protocatechuate 3,4-dioxygenase, β-ketoadipate CoA transferase and β-Ketoadipyl CoA thiolase, which were supposed to be involved in PAHs degradation were also identified. Based on the genome analysis, the proposed PAHs degradation pathway was constructed in P14 strain, which showed that PAHs was degraded into the acetyl CoA and succinyl CoA, then mineralized to CO2 via the TCA cycle. Furthermore, several genes, including cytochrome P450 (RS16725; RS16695; RS12220), catalase (RS15825), dehydrogenase (RS15755; RS18420) and hydrolase (RS16460; RS24665), showed increased expression level during PAHs degradation according to the transcriptome data. In addition, 12 novel sRNAs which were supposed to have the regulation function in PAHs degradation were identified. This study gives us the outlook of PAHs degradation pathway in Rhodococcus sp. P14. Moreover, it first demonstrates that sRNAs may harbor the regulation function in PAHs degradation.
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Affiliation(s)
- Tao Peng
- 1Department of Biology, Shantou University, Shantou, 515063 Guangdong China
| | - Jie Kan
- 1Department of Biology, Shantou University, Shantou, 515063 Guangdong China
| | - Jing Hu
- 2Affiliated Hospital 1, College of Medical, Shantou University, Guangdong, 515063 China
| | - Zhong Hu
- 1Department of Biology, Shantou University, Shantou, 515063 Guangdong China
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