title: Characterization of the transcriptome of Achromobacter sp. HZ01 with the outstanding hydrocarbon-degrading ability.
abstract: Microbial remediation has become one of the most important strategies for eliminating petroleum pollutants. Revealing the transcript maps of microorganisms with the hydrocarbon-degrading ability contributes to enhance the degradation of hydrocarbons and further improve the effectiveness of bioremediation. In this study, we characterized the transcriptome of hydrocarbon-degrading Achromobacter sp. HZ01 after petroleum treatment for 16h. A total of 38,706,280 and 38,954,413 clean reads were obtained by RNA-seq for the petroleum-treated group and control, respectively. By an effective de novo assembly, 3597 unigenes were obtained, including 3485 annotated transcripts. Petroleum treatment had significantly influenced the transcriptional profile of strain HZ01, involving 742 differentially expressed genes. A part of genes were activated to exert specific physiological functions, whereas more genes were down-regulated including specific genes related to cell motility, genes associated with glycometabolism, and genes coding for ribosomal proteins. Identification of genes related to petroleum degradation revealed that the fatty acid metabolic pathway and a part of monooxygenases and dehydrogenases were activated, whereas the TCA cycle was inactive. Additionally, terminal oxidation might be a major aerobic pathway for the degradation of n-alkanes in strain HZ01. The newly obtained data contribute to better understand the gene expression profiles of hydrocarbon-degrading microorganisms after petroleum treatment, to further investigate the genetic characteristics of strain HZ01 and other related species and to develop cost-effective and eco-friendly strategies for remediation of crude oil-polluted environments.
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
authors.forename: Yue-Hui
authors.initials: YH
authors.lastname: Hong
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; Department of Food and Bioengineering, Guangdong Industry Technical College, Guangzhou 510300, PR China.
authors.forename: Mao-Cheng
authors.initials: MC
authors.lastname: Deng
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
authors.forename: Xiao-Ming
authors.initials: XM
authors.lastname: Xu
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
authors.forename: Chou-Fei
authors.initials: CF
authors.lastname: Wu
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
authors.forename: Xi
authors.initials: X
authors.lastname: Xiao
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
authors.forename: Xian-Xian
authors.initials: XX
authors.lastname: Sun
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
authors.forename: Qian-Zhi
authors.initials: QZ
authors.lastname: Zhou
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
authors.forename: Juan
authors.initials: J
authors.lastname: Peng
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China. Electronic address: yuanjp@mail.sysu.edu.cn.
authors.forename: Jian-Ping
authors.initials: JP
authors.lastname: Yuan
authors.affiliation: Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; South China Sea Bioresource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China. Electronic address: wangjhai@mail.sysu.edu.cn.
authors.forename: Jiang-Hai
authors.initials: JH
authors.lastname: Wang
mesh_terms: D042402:Achromobacter / Q000235:genetics* / Q000378:metabolism; D015536:Down-Regulation; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D006838:Hydrocarbons / Q000378:metabolism*; D014158:Transcription, Genetic; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D006838:Hydrocarbons
keywords: Achromobacter; Bioremediation; Hydrocarbon; Petroleum; RNA-seq; Transcriptome