Biotechnology Bulletin ›› 2017, Vol. 33 ›› Issue (10): 46-51.doi: 10.13560/j.cnki.biotech.bull.1985.2017-0368
• Review • Previous Articles Next Articles
KONG De-kang, WANG Hong-qi, XU Jie, LIU Zi-li, WU Xiao-xiong
Received:
2017-05-08
Online:
2017-10-29
Published:
2017-10-29
Contact:
王红旗,男,博士,研究方向:地下水污染治理,环境科学;E-mail:whongqi@126.com
KONG De-kang, WANG Hong-qi, XU Jie, LIU Zi-li, WU Xiao-xiong. Applications of Genomics,Proteomics and Metabolomics in Microbial Degradation of PAHs[J]. Biotechnology Bulletin, 2017, 33(10): 46-51.
[1]Dubrovskaya E, Pozdnyakova N, Golubev S, et al. Peroxidases from root exudates of Medicago sativa and Sorghum bicolor:Catalytic properties and involvement in PAH degradation[J]. Chemosphere, 2017, 169:224-232. [2]Liu SH, Zeng GM, Niu QY, et al. Bioremediation mechanisms of combined pollution of PAHs and heavy metals by bacteria and fungi:A mini review[J]. Bioresour Technol, 2017, 224:25-33. [3]Tian W, Zhao J, Zhou Y, et al. Effects of root exudates on gel-beads/reeds combination remediation of high molecular weight polycyclic aromatic hydrocarbons[J]. Ecotoxicol Environ Saf, 2017, 135:158-164. [4]Zhao OY, Zhang XN, Feng SD, et al. Starch-enhanced degradation of HMW PAHs by Fusarium sp. in an aged polluted soil from a coal mining area[J]. Chemosphere, 2017, 174:774-780. [5]Jiang J, Liu H, Li Q, et al. Combined remediation of Cd-phenanthrene co-contaminated soil by Pleurotus cornucopiae and Bacillus thuringiensis FQ1 and the antioxidant responses in Pleurotus cornucopiae[J]. Ecotoxicol Environ Saf, 2015, 120:386-393. [6]Lee H, Jang Y, Lee YM, et al. Enhanced removal of PAHs by Peniophora incarnata and ascertainment of its novel ligninolytic enzyme genes[J]. J Environ Manage, 2015, 164:10-18. [7]方翔, 曾伟伟, 王庆, 等. 基因组学、转录组学、蛋白质组学和结构生物学在水产科学中的应用[J]. 动物医学进展, 2015, 36(7):108-112. [8]Marin AJ. Sequecing your genome:What does it mean?[J]. Methodist Debakey Cardiovasc J, 2014, 10(1):3-6. [9]Barbosa EG, Aburjaile FF, Ramos RT, et al. Value of a newly sequenced bacterial genome[J]. World J Biol Chem, 2014, 5(2):161-168. [10]刘娟, 高彦征. 第六届全国环境化学大会暨环境科学仪器与分析仪器展览会摘要集[C]. 上海:土壤化学, 2011. [11]Song M, Jiang L, Zhang D, et al. Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil[J]. J Hazard Mater, 2016, 308:50, 57. [12]Jones MD, Crandell DW, Singleton DR, et al. Stable-isotope probing of the polycyclic aromatic hydrocarbon-degrading bacterial guild in a contaminated soil[J]. Environ Microbiol, 2011, 13(10):2623-2632. [13]Gutierrez T, Biddle JF, Teske A, et al. Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments[J]. Front Microbiol, 2015, 6:695. [14]Pathak A, Chauhan A, Blom J, et al. Comparative genomics and metabolic analysis reveals peculiar characteristics of Rhodococcus opacus strain M213 particularly for naphthalene degradation[J]. PLoS One, 2016, 11(8):e0161032. [15]Li J, Luo C, Song M, et al. Biodegradation of phenanthrene in polycyclic aromatic hydrocarbon-contaminated wastewater revealed by coupling cultivation-dependent and -independent approaches[J]. Environ Sci Technol, 2017, 51(6):3391-3401. [16]Zafra G, Taylor TD, Absalon AE, et al. Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium[J]. J Hazard Mater, 2016, 318:702-710. [17]Fang T, Pan R, Jiang J, et al. Effect of salinity on community structure and naphthalene dioxygenase gene diversity of a halophilic bacterial consortium[J]. Frontiers of Environmental Science & Engineering, 2016, 10(6):16. [18]Zhao H, Zhang Y, Xiao X, et al. Different phenanthrene-degrading bacteria cultured by in situ soil substrate membrane system and traditional cultivation[J]. International Biodeterioration & Biodegradation, 2017, 117:269-277. [19]Tyers M, Mann M. From genomics to proteomics[J]. Nature, 2003, 422(6928):193-197. [20]Vandera E, Samiotaki M, Parapouli M, et al. Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose[J]. J Proteomics, 2015, 113:73-89. [21]Kim SJ, Kweon O, Cerniglia CE. Proteomic applications to elucidate bacterial aromatic hydrocarbon metabolic pathways[J]. Curr Opin Microbiol, 2009, 12(3):301-309. [22]Jain A, Singh A, Singh S, et al. Comparative proteomic analysis in pea treated with microbial consortia of beneficial microbes reveals changes in the protein network to enhance resistance against Sclerotinia sclerotiorum[J]. J Plant Physiol, 2015, 182:79-94. [23]Lee SY, Sekhon SS, Ban YH, et al. Proteomic analysis of polycyclic aromatic hydrocarbons(PAHs)degradation and detoxification in Sphingobium chungbukense DJ77[J]. J Microbiol Biotechnol, 2016, 26(11):1943-1950. [24]Wei K, Yin H, Peng H, et al. Characteristics and proteomic analysis of pyrene degradation by Brevibacillus brevis in liquid medium[J]. Chemosphere, 2017, 178:80-87. [25]Lee SE, Seo JS, Keum YS, et al. Fluoranthene metabolism and associated proteins in Mycobacterium sp. JS14[J]. Proteomics, 2007, 7(12):2059-2069. [26]Liu S, Guo C, Dang Z, et al. Comparative proteomics reveal the mechanism of Tween80 enhanced phenanthrene biodegradation by Sphingomonas sp. GY2B[J]. Ecotoxicol Environ Saf, 2017, 137:256-264. [27]Yun SH, Park GW, Kim JY, et al. Proteomic characterization of the Pseudomonas putida KT2440 global response to a monocyclic aromatic compound by iTRAQ analysis and 1DE-MudPIT[J]. J Proteomics, 2011, 74(5):620-628. [28]Liu H, Sun WB, Liang RB, et al. iTRAQ-based quantitative proteomic analysis of Pseudomonas aeruginosa SJTD-1:A global response to n-octadecane induced stress[J]. J Proteomics, 2015, 123:14-28. [29]Carvalho RN, Lettieri T. Proteomic analysis of the marine diatom Thalassiosira pseudonana upon exposure to benzo(a)pyrene[J]. BMC Genomics, 2011, 12:159. [30]Herbst FA, Taubert M, Jehmlich N, et al. Sulfur-34S stable isotope labeling of amino acids for quantification(SULAQ34)of proteomic changes in Pseudomonas fluorescens during naphthalene degradation[J]. Molecular & Cellular Proteomics, 2013, 12(10):2060-2069. [31]Léonie MR, Bas T, David B, et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations[J]. Nature Biotechnology, 2001, 19(1):45-50. [32]Palsson B. Metabolic systems biology[J]. FEBS Lett, 2009, 583(24):3900-3904. [33]席晓敏, 张和平. 微生物代谢组学研究及应用进展[J]. 食品科学, 2016, 37(11)::283-289. [34]Bean HD, Dimandja JM, Hill JE. Bacterial volatile discovery using solid phase microextraction and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry[J]. J Chromatogr B Analyt Technol Biomed Life Sci, 2012, 901:41-46. [35]Samelis J, Bleicher A, Delbès-Paus C, et al. FTIR-based polyphasic identification of lactic acid bacteria isolated from traditional Greek Graviera cheese[J]. Food Microbiology, 2011, 28(1):76-83. [36]Ghosal D, Dutta A, Chakraborty J, et al. Characterization of the metabolic pathway involved in assimilation of acenaphthene in Acinetobacter sp. strain AGAT-W[J]. Res Microbiol, 2013, 164(2):155-163. [37] Zhong J, Luo L, Chen B, et al. Degradation pathways of 1-methylph-enanthrene in bacterial Sphingobium sp. MP9-4 isolated from petroleum-contaminated soil[J]. Mar Pollut Bull, 2017, 114(2):926-933. [38]Zhao JK, Li XM, Ai GM, et al. Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil[J]. J Hazard Mater, 2016, 318:90-98. [39]Xu J, Zhang L, Hou J, et al. iTRAQ-based quantitative proteomic analysis of the global response to 17β-estradiol in estrogen-degradation strain Pseudomonas putida SJTE-1[J]. Scientific Reports, 2017, 7:41682. [40]Han X, Hu H, Shi X, et al. Effects of different agricultural wastes on the dissipation of PAHs and the PAH-degrading genes in a PAH-contaminated soil[J]. Chemosphere, 2017, 172:286-293. [41]Khara P, Roy M, Chakraborty J, et al. Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB[J]. FEBS Open Bio, 2014, 4:290-300. |
[1] | ZHANG Kun, YAN Chang, TIAN Xin-peng. Research Progress in Microbial Single Cell Separation Methods [J]. Biotechnology Bulletin, 2023, 39(9): 1-11. |
[2] | ZHOU Lu-qi, CUI Ting-ru, HAO Nan, ZHAO Yu-wei, ZHAO Bin, LIU Ying-chao. Application of Chemical Proteomics in Identifying the Molecular Targets of Natural Products [J]. Biotechnology Bulletin, 2023, 39(9): 12-26. |
[3] | ZHOU Ai-ting, PENG Rui-qi, WANG Fang, WU Jian-rong, MA Huan-cheng. Analysis of Metabolic Differences of Biocontrol Strain DZY6715 at Different Growth Stages [J]. Biotechnology Bulletin, 2023, 39(9): 225-235. |
[4] | JIANG Run-hai, JIANG Ran-ran, ZHU Cheng-qiang, HOU Xiu-li. Research Progress in Mechanisms of Microbial-enhanced Phytoremediation for Lead-contaminated Soil [J]. Biotechnology Bulletin, 2023, 39(8): 114-125. |
[5] | ZHAO Lin-yan, XU Wu-mei, WANG Hao-ji, WANG Kun-yan, WEI Fu-gang, YANG Shao-zhou, GUAN Hui-lin. Effects of Applying Biochar on the Rhizosphere Fungal Community and Survival Rate of Panax notoginseng Under Continuous Cropping [J]. Biotechnology Bulletin, 2023, 39(7): 219-227. |
[6] | HAN Hua-rui, YANG Yu-lu, MEN Yi-han, HAN Shang-ling, HAN Yuan-huai, HUO Yi-qiong, HOU Si-yu. SiYABBYs Involved in Rhamnoside Biosynthesis During the Flower Development of Setaria italica, Based on Metabolomics [J]. Biotechnology Bulletin, 2023, 39(6): 189-198. |
[7] | ZHANG Jing, ZHANG Hao-rui, CAO Yun, HUANG Hong-ying, QU Ping, ZHANG Zhi-ping. Research Progress in Thermophilic Microorganisms for Cellulose Degradation [J]. Biotechnology Bulletin, 2023, 39(6): 73-87. |
[8] | YU Yang, LIU Tian-hai, LIU Li-xu, TANG Jie, PENG Wei-hong, CHEN Yang, TAN Hao. Study on Aerosol Microbial Community in the Production Workshop of Morel Spawn [J]. Biotechnology Bulletin, 2023, 39(5): 267-275. |
[9] | SANG Tian, WANG Peng-cheng. Research Progress in Plant SUMOylation [J]. Biotechnology Bulletin, 2023, 39(3): 1-12. |
[10] | ZHANG Hua-xiang, XU Xiao-ting, ZHENG Yun-ting, XIAO Chun-qiao. Roles of Phosphate-solubilizing Microorganisms in the Passivation and Phytoremediation of Heavy Metal Contaminated Soil [J]. Biotechnology Bulletin, 2023, 39(3): 52-58. |
[11] | LI Xin-yue, ZHOU Ming-hai, FAN Ya-chao, LIAO Sha, ZHANG Feng-li, LIU Chen-guang, SUN Yue, ZHANG Lin, ZHAO Xin-qing. Research Progress in the Improvement of Microbial Strain Tolerance and Efficiency of Biological Manufacturing Based on Transporter Engineering [J]. Biotechnology Bulletin, 2023, 39(11): 123-136. |
[12] | HU Jin-chao, SHEN Wen-qi, XU Chao-ye, FAN Ya-qi, LU Hao-yu, JIANG Wen-jie, LI Shi-long, JIN Hong-chen, LUO Jian-mei, WANG Min. Research Advances in the Enhancement of Microbial Tolerance to Acid Stress [J]. Biotechnology Bulletin, 2023, 39(11): 137-149. |
[13] | WANG Chen-yu, ZHOU Chu-yuan, HE Di, FAN Zi-hao, WANG Meng-meng, YANG Liu-yan. Role and Mechanism of Polyphosphate in the Microbial Response to Environmental Stresses [J]. Biotechnology Bulletin, 2023, 39(11): 168-181. |
[14] | WAN Qi-wu, BAO Xu-dong, DING Ke, MOU Hua-ming, LUO Yang. Research Progress in Microfluidic Technology in the Detection of Pathogenic Microorganisms [J]. Biotechnology Bulletin, 2023, 39(10): 107-114. |
[15] | XU Yang, DING Hong, ZHANG Guan-chu, GUO Qing, ZHANG Zhi-meng, DAI Liang-xiang. Metabolomics Analysis of Germinating Peanut Seed Under Salt Stress [J]. Biotechnology Bulletin, 2023, 39(1): 199-213. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||