微生物降解石油烃的代谢机制及研究进展

胡梦杰; 钟磊; 蔡晓鲜; 卿晋武; 孙于茹; 栗高源; 阮海华; 陈冠益

doi:10.13205/j.hjgc.202302031

微生物降解石油烃的代谢机制及研究进展

doi: 10.13205/j.hjgc.202302031

1. 天津商业大学, 天津 300134;
2. 天津大学, 天津 300072;
3. 污染场地安全修复技术国家工程实验室北京建工环境修复股份有限公司, 北京 100015

基金项目:

天津市自然科学基金项目(19JCQNJC13900)

详细信息

作者简介:
胡梦杰(1997-),女,硕士研究生,主要研究方向为石油烃污染修复。humengjie_2021@163.com

通讯作者:
阮海华(1976-),女,教授。ruanhaihua@tjcu.edu.cn

计量
- 文章访问数: 445
- HTML全文浏览量: 60
- PDF下载量: 16
- 被引次数: 0
出版历程
- 收稿日期: 2022-04-28
- 网络出版日期: 2023-05-25
- 刊出日期: 2023-02-01

METABOLIC MECHANISM OF MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS AND ITS RESEARCH PROGRESS

1. Tianjin University of Commerce, Tianjin 300314, China;
2. Tianjin University, Tianjin 300072, China;
3. National Engineering Laboratory for Site Remediation Technologies, Beijing Construction Engineering Group Environmental Remediation Co., Ltd, Beijing 100015, China

摘要

摘要: 石油烃类污染物是复杂的有机化合物,对生态环境和公众健康具有较大危害。目前微生物技术已成为修复石油烃污染环境的主要方法,微生物可利用目标污染物作为碳源,通过一系列的酶催化对其进行代谢降解。研究了微生物降解石油烃的代谢机制,可通过合理设计降解途径中关键步骤的酶,降低限制因素对石油烃微生物降解的影响,提高限速步骤的反应速度,从而提高对石油烃的降解率,以更好地应用于石油烃污染场地的修复。通过梳理总结石油烃的主要组成和结构、代谢途径、功能基因和关键酶种类,以及组学和合成生物学技术在石油烃降解代谢机制研究中的应用现状,为进一步优化提升微生物修复技术在石油烃污染领域的应用前景提供参考。
- 石油烃 /
- 微生物降解 /
- 降解机制 /
- 功能基因 /
- 酶 /
- 组学技术
Abstract: Petroleum hydrocarbon contaminants are complex organic compounds, and it would cause great risk to the ecological environment and public health. Currently, microbial technology becomes a popular remediation technology for petroleum hydrocarbon contaminations. Microorganisms use the pollutants as a carbon source and metabolize and degrade it through a series of enzymatic catalysis. For increasing the application of microbial remediation of petroleum hydrocarbon pollution, the method of rational design of enzymes at key steps can be used to increase the microbial degradation rates of petroleum hydrocarbons. This review summarizes the main components and structures of petroleum hydrocarbons, metabolic pathways, functional genes and key enzyme types, as well as the application status of omics and synthetic biology technologies in the research of petroleum hydrocarbon degradation and metabolism mechanism, providing a reference for further improving the application prospects of microbial remediation technology in the field of petroleum hydrocarbon pollution.
- petroleum hydrocarbons /
- microbial degradation /
- degradation mechanism /
- functional genes /
- enzymes /
- omics technology

HTML全文

参考文献(117)

[1]	CHEN M, XU P, ZENG G M, et al. Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting:applications, microbes and future research needs[J]. Biotechnology Advances, 2015, 33(6, Part 1):745-755.
[2]	WU Y, XU M, XUE J, et al. Characterization and enhanced degradation potentials of biosurfactant-producing bacteria isolated from a marine environment[J]. ACS Omega, 2019, 4(1):1645-1651.
[3]	RODRÍGUEZ-URIBE M L, PEÑA-CABRIALES J J, RIVERA-CRUZ M D C, et al. Native bacteria isolated from weathered petroleum oil-contaminated soils in Tabasco, Mexico, accelerate the degradation petroleum hydrocarbons in saline soil microcosms[J]. Environmental Technology & Innovation, 2021, 23:101781.
[4]	田春雨. 湄洲湾水体石油烃含量、分布特征及其组分研究[D]. 厦门:厦门大学, 2009.
[5]	OSSAI I C, AHMED A, HASSAN A, et al. Remediation of soil and water contaminated with petroleum hydrocarbon:a review[J]. Environmental Technology & Innovation, 2020, 17:100526.
[6]	GAUR V K, GUPTA S, PANDEY A. Evolution in mitigation approaches for petroleum oil-polluted environment:recent advances and future directions[J]. Environmental Science and Pollution Research, 2021. DOI: 10.1007/s11356-021-16047-y.
[7]	AL-HAWASH A B, DRAGH M A, LI S, et al. Principles of microbial degradation of petroleum hydrocarbons in the environment[J]. The Egyptian Journal of Aquatic Research, 2018, 44(2):71-76.
[8]	WILPISZESKI R L, AUFRECHT J A, RETTERER S T, et al. Soil aggregate microbial communities:towards understanding microbiome interactions at biologically relevant scales[J]. Applied and Environmental Microbiology, 2019, 85(14). DOI: 10.1128/AEM.00324-19.
[9]	BAI X R, NIE M Q, DIWU Z J, et al. Simultaneous biodegradation of phenolics and petroleum hydrocarbons from semi-coking wastewater:construction of bacterial consortium and their metabolic division of labor[J]. Bioresource Technology, 2022, 347:126377.
[10]	LI X, HE W, DU M, et al. Design of a microbial remediation inoculation program for petroleum hydrocarbon contaminated sites based on degradation pathways[J]. International Journal of Environmental Research and Public Health, 2021, 18(16):8794.
[11]	BAGI A, KNAPIK K, BAUSSANT T. Abundance and diversity of n-alkane and PAH-degrading bacteria and their functional genes-Potential for use in detection of marine oil pollution[J]. Science of the Total Environment, 2022, 810:152238.
[12]	HOANG S A, SARKAR B, SESHADRI B, et al. Mitigation of petroleum-hydrocarbon-contaminated hazardous soils using organic amendments:a review[J]. Journal of Hazardous Materials, 2021, 416:125702.
[13]	HEAD I M, JONES D M, RÖLING W F M. Marine microorganisms make a meal of oil[J]. Nature Reviews Microbiology, 2006, 4(3):173-182.
[14]	PÉREZ-PANTOJA D, GONZÁLEZ B, PIEPER D H. Aerobic degradation of aromatic hydrocarbons[J]. Handbook of hydrocarbon and lipid microbiology(ed Rojo F), 2019:157-200.
[15]	BOLL M. Dearomatizing Benzene Ring Reductases[J]. Microbial Physiology, 2005, 10(2/3/4):132-142.
[16]	SHARMA A, SINGH S B, SHARMA R, et al. Enhanced biodegradation of PAHs by microbial consortium with different amendment and their fate in in-situ condition[J]. Journal of environmental management, 2016, 181:728-736.
[17]	AL-HAWASH A B, AL-QURNAWI W S, ABBOOD H A, et al. Pyrene-Degrading Fungus Ceriporia lacerata RF-7 from contaminated soil in Iraq[J]. Polycyclic Aromatic Compounds, 2020(2):1-9.
[18]	MARSTON C P, PEREIRA C, FERGUSON J, et al. Effect of a complex environmental mixture from coal tar containing polycyclic aromatic hydrocarbons (PAH) on the tumor initiation, PAH-DNA binding and metabolic activation of carcinogenic PAH in mouse epidermis[J]. Carcinogenesis, 2001, 22(7):1077-1086.
[19]	AGULLó L, CÁMARA B, MARTÍNEZ P, et al. Response to (chloro)biphenyls of the polychlorobiphenyl-degrader Burkholderia xenovorans LB400 involves stress proteins also induced by heat shock and oxidative stress[J]. FEMS Microbiology Letters, 2007, 267(2):167-175.
[20]	VARJANI S J, GNANSOUNOU E. Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs[J]. Bioresource Technology, 2017, 245:1258-1265.
[21]	ABBASIAN F, LOCKINGTON R, MALLAVARAPU M, et al. A comprehensive review of aliphatic hydrocarbon biodegradation by bacteria[J]. Applied Biochemistry and Biotechnology, 2015, 176(3):670-699.
[22]	CHAN S I, CHEN K H C, YU S S F, et al. Toward delineating the structure and function of the particulate methane monooxygenase from methanotrophic bacteria[J]. Biochemistry, 2004, 43(15):4421-4430.
[23]	MCDONALD I R, MIGUEZ C B, ROGGE G, et al. Diversity of soluble methane monooxygenase-containing methanotrophs isolated from polluted environments[J]. FEMS Microbiology Letters, 2006, 255(2):225-232.
[24]	YONG N, FANG H, LI Y, et al. The genome of the moderate halophile amycolicicoccus subflavus DQS3-9A1T reveals four alkane hydroxylation systems and provides some clues on the genetic basis for its adaptation to a petroleum environment[J]. PLos One, 2013, 8:e70986.
[25]	ROJO F. Degradation of alkanes by bacteria[J]. Environ Microbiol, 2009, 11(10):2477-2490.
[26]	RATAJCZAK A, GEISSDÖRFER W, HILLEN W. Alkane hydroxylase from Acinetobacter sp. strain ADP1 is encoded by alkM and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases[J]. Applied and Environmental Microbiology, 1998, 64(4):1175-1179.
[27]	van BEILEN J B, FUNHOFF E G, van LOON A, et al. Cytochrome P450 alkane hydroxylases of the CYP153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases[J]. Appl Environ Microbiol, 2006, 72(1):59-65.
[28]	WANG X B, CHI C Q, NIE Y, et al. Degradation of petroleum hydrocarbons (C6~C40) and crude oil by a novel Dietzia strain[J]. Bioresource Technology, 2011, 102(17):7755-7761.
[29]	LI L, LIU X Q, YANG W, et al. Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN:unveiling the long-chain alkane hydroxylase[J]. J Mol Biol, 2008, 376(2):453-465.
[30]	THRONE-HOLST M, WENTZEL A, ELLINGSEN TROND E, et al. Identification of novel genes involved in long-chain n-Alkane degradation by Acinetobacter sp. strain DSM 17874[J]. Applied and Environmental Microbiology, 2007, 73(10):3327-3332.
[31]	WILKES H, BUCKEL W, GOLDING B T, et al. Metabolism of hydrocarbons in n-alkane-utilizing anaerobic bacteria[J]. Microbial Physiology, 2016, 26(1/2/3):138-151.
[32]	JIANG Y, YANG X, LIU B, et al. Catechol 2, 3-dioxygenase from Pseudomonas sp. strain ND6:gene sequence and enzyme characterization[J]. Bioscience, Biotechnology, and Biochemistry, 2004, 68(8):1798-1800.
[33]	VON NETZER F, KUNTZE K, VOGT C, et al. Functional gene markers for fumarate-adding and dearomatizing key enzymes in anaerobic aromatic hydrocarbon degradation in terrestrial environments[J]. Microbial Physiology, 2016, 26(1/2/3):180-194.
[34]	HEIDER J. Adding handles to unhandy substrates:anaerobic hydrocarbon activation mechanisms[J]. Curr Opin Chem Biol, 2007, 11(2):188-194.
[35]	SEO J, KANG S I, RYU J Y, et al. Location of flavone B-ring controls regioselectivity and stereoselectivity of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4[J]. Applied Microbiology and Biotechnology, 2010, 86(5):1451-1462.
[36]	AGBAJI J E, NWAICHI E O, ABU G O. Attenuation of petroleum hydrocarbon fractions using rhizobacterial isolates possessing alkB, C23O, and nahR genes for degradation of n-alkane and aromatics[J]. Journal of Environmental Science and Health, Part A, 2021, 56(6):635-645.
[37]	PARK J W, CROWLEY D E. Dynamic changes in nahAc gene copy numbers during degradation of naphthalene in PAH-contaminated soils[J]. Applied microbiology and biotechnology, 2006, 72(6):1322-1329.
[38]	SOWANI H, KULKARNI M, ZINJARDE S. Uptake and detoxification of diesel oil by a tropical soil Actinomycete Gordonia amicalis HS-11:cellular responses and degradation perspectives[J]. Environmental Pollution, 2020, 263:114538.
[39]	DAS N, CHANDRAN P. Microbial degradation of petroleum hydrocarbon contaminants:an overview[J]. Biotechnol Res Int 2011, 2011:941810.
[40]	JI Y R, MAO G W, WANG Y Y, et al. Structural insights into diversity and n-alkane biodegradation mechanisms of alkane hydroxylases[J]. Frontiers in Microbiology, 2013, 4. DOI: 10.3389/fmicb.2013.00058.
[41]	CABRAL L, GIOVANELLA P, PELLIZZER E P, et al. Microbial communities in petroleum-contaminated sites:structure and metabolisms[J]. Chemosphere, 2022, 286:131752.
[42]	张腾飞, 黄玉杰, 王磊磊, 等. 正十二烷降解菌株的筛选及降解特性研究[J]. 环境科学与技术, 2021, 44(增刊2):238-244.
[43]	SINGH J S, SENEVIRATNE G. Agro-environmental sustainability[M]. Springer, 2017.
[44]	SLUIS M K, SAYAVEDRA-SOTO L A, ARP D J. Molecular analysis of the soluble butane monooxygenase from 'Pseudomonas butanovora'[J]. Microbiology (Reading), 2002, 148(Pt 11):3617-3629.
[45]	FUNHOFF ENRICO G, BAUER U, GARCÍA-RUBIO I, et al. CYP153A6, a Soluble P450 oxygenase catalyzing terminal-alkane hydroxylation[J]. Journal of Bacteriology, 2006, 188(14):5220-5227.
[46]	SAZYKIN I, MAKARENKO M, KHMELEVTSOVA L, et al. Cyclohexane, naphthalene, and diesel fuel increase oxidative stress, CYP153, sodA, and recA gene expression in Rhodococcus erythropolis[J]. Microbiologyopen, 2019, 8(9):e00855.
[47]	RATAJCZAK A, GEISSDÖRFER W, HILLEN W. Alkane hydroxylase from Acinetobacter sp. strain ADP1 is encoded by alkM and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases[J]. Appl Environ Microbiol, 1998, 64(4):1175-1179.
[48]	LIU C, WANG W, WU Y, et al. Multiple alkane hydroxylase systems in a marine alkane degrader, Alcanivorax dieselolei B-5[J]. Environ Microbiol, 2011, 13(5):1168-1178.
[49]	MINERDI D, SADEGHI S J, DI NARDO G, et al. CYP116B5:a new class Ⅶ catalytically self-sufficient cytochrome P450 from Acinetobacter radioresistens that enables growth on alkanes[J]. Mol Microbiol, 2015, 95(3):539-554.
[50]	WATKINSON R J, MORGAN P. Physiology of aliphatic hydrocarbon-degrading microorganisms[J]. Physiology of biodegradative microorganisms, 1991,1(2):79-92.
[51]	LIN H, LIU J Y, WANG H B, et al. Biocatalysis as an alternative for the production of chiral epoxides:a comparative review[J]. Journal of Molecular Catalysis B:Enzymatic, 2011, 72(3):77-89.
[52]	WANG S, WANG D, YU Z C, et al. Advances in research on petroleum biodegradability in soil[J]. Environ Sci Process Impacts, 2021, 23(1):9-27.
[53]	SALAMANCA D, KARANDE R, SCHMID A, et al. Novel cyclohexane monooxygenase from Acidovorax sp. CHX100[J]. Appl Microbiol Biotechnol, 2015, 99(16):6889-6897.
[54]	KAWAKAMI N, SHOJI O, WATANABE Y. Use of perfluorocarboxylic acids to trick cytochrome P450BM3 into initiating the hydroxylation of gaseous alkanes[J]. Angewandte Chemie, 2011, 123(23):5427-5430.
[55]	GHOSAL D, GHOSH S, DUTTA T K, et al. Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs):a review[J]. Frontiers in Microbiology, 2016, 7:1369.
[56]	PHALE P S, SHAH B A, MALHOTRA H. Variability in assembly of degradation operons for naphthalene and its derivative, carbaryl, suggests mobilization through horizontal gene transfer[J]. Genes, 2019, 10(8):569.
[57]	JOUANNEAU Y, MEYER C. Purification and Characterization of an arene cis-dihydrodiol dehydrogenase endowed with broad substrate specificity toward polycyclic aromatic hydrocarbon dihydrodiols[J]. Applied and Environmental Microbiology, 2006, 72(7):4726-4734.
[58]	HADDOCK J. Aerobic degradation of aromatic hydrocarbons:enzyme structures and catalytic mechanisms[M]. Handbook of Hydrocarbon and Lipid Microbiology, 2010.
[59]	GIBSON D, KOCH J, KALLIO R. Oxidative degradation of aromatic hydrocarbons by microorganisms. Ⅰ. Enzymic formation of catechol from benzene[J]. Biochemistry, 1968, 7(7):2653-2662.
[60]	LIANG C Y, HUANG Y, WANG H. pahE, a functional marker gene for polycyclic aromatic hydrocarbon-degrading bacteria[J]. Applied and environmental microbiology, 2019, 85(3). DOI: 10.1128/AEM.02399-18.
[61]	GOLUBEV S N, MURATOVA A Y, PANCHENKO L V, et al. Mycolicibacterium sp. strain PAM1, an alfalfa rhizosphere dweller, catabolizes PAHs and promotes partner-plant growth[J]. Microbiological Research, 2021, 253:126885.
[62]	LOZADA M, RIVA MERCADAL J P, GUERRERO L D, et al. Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia[J]. BMC Microbiology, 2008, 8(1):50.
[63]	VAILLANCOURT F H, BOLIN J T, ELTIS L D. The ins and outs of ring-cleaving dioxygenases[J]. Crit Rev Biochem Mol Biol, 2006, 41(4):241-267.
[64]	KOVALEVA E G, NEIBERGALL M B, CHAKRABARTY S, et al. Finding intermediates in the O₂ activation pathways of non-heme iron oxygenases[J]. Accounts of Chemical Research, 2007, 40(7):475-483.
[65]	吴慧君, 宋权威, 郑瑾, 等. 微生物降解石油烃的功能基因研究进展[J]. 微生物学通报, 2020, 47(10):3355-3368.
[66]	MECKENSTOCK R U, BOLL M, MOUTTAKI H, et al. Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons[J]. Microbial Physiology, 2016, 26(1/2/3):92-118.
[67]	WILKES H, KüHNER S, BOLM C, et al. Formation of n-alkane-and cycloalkane-derived organic acids during anaerobic growth of a denitrifying bacterium with crude oil[J]. Organic Geochemistry, 2003, 34(9):1313-1323.
[68]	CHANDRA S, SHARMA R, SINGH K, et al. Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon[J]. Annals of microbiology, 2013, 63(2):417-431.
[69]	KNIEMEYER O, MUSAT F, SIEVERT S M, et al. Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria[J]. Nature, 2007, 449(7164):898-901.
[70]	JI J H, ZHOU L, MBADINGA S M, et al. Methanogenic biodegradation of C9 to C12n-alkanes initiated by Smithella via fumarate addition mechanism[J]. AMB Express, 2020, 10(1):23.
[71]	WAWRIK B, MENDIVELSO M, PARISI V A, et al. Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin[J]. FEMS Microbiology Ecology, 2012, 81(1):26-42.
[72]	SO CHI M, PHELPS CRAIG D, YOUNG L Y. Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium, strain Hxd3[J]. Applied and Environmental Microbiology, 2003, 69(7):3892-3900.
[73]	SO C M, YOUNG L. Isolation and characterization of a sulfate-reducing bacterium that anaerobically degrades alkanes[J]. Applied and Environmental Microbiology, 1999, 65(7):2969-2976.
[74]	BOLL M, ESTELMANN S, HEIDER J. Anaerobic degradation of hydrocarbons:mechanisms of hydrocarbon activation in the absence of oxygen[J]. 2020:3-29.
[75]	ZEDELIUS J, RABUS R, GRUNDMANN O, et al. Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation[J]. Environ Microbiol Rep, 2011, 3(1):125-135.
[76]	WILKES H, BUCKEL W, GOLDING B T, et al. Metabolism of hydrocarbons in n-alkane-utilizing anaerobic bacteria[J]. J Mol Microbiol Biotechnol, 2016, 26(1/2/3):138-151.
[77]	MECKENSTOCK R U, BOLL M, MOUTTAKI H, et al. Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons[J]. Microbial Physiology, 2016, 26(1/2/3):92-118.
[78]	VON NETZER F, PILLONI G, KLEINDIENST S, et al. Enhanced gene detection assays for fumarate-adding enzymes allow uncovering of anaerobic hydrocarbon degraders in terrestrial and marine systems[J]. Applied and Environmental Microbiology, 2013, 79(2):543-552.
[79]	BOLL M, ESTELMANN S, HEIDER J. Catabolic pathways and enzymes involved in the anaerobic degradation of monocyclic aromatic compounds[J]. Anaerobic Utilization of Hydrocarbons, Oils, and Lipids, 2020:85-133.
[80]	TIERNEY M, YOUNG L Y. Anaerobic degradation of aromatic hydrocarbons[M]. Handbook of Hydrocarbon and Lipid Microbiology, 2010:925-934.
[81]	KNIEMEYER O, HEIDER J. (S)-1-phenylethanol dehydrogenase of Azoarcus sp. strain EbN1, an enzyme of anaerobic ethylbenzene catabolism[J]. Arch Microbiol, 2001, 176(1/2):129-135.
[82]	ZHANG X, YOUNG L Y. Carboxylation as an initial reaction in the anaerobic metabolism of naphthalene and phenanthrene by sulfidogenic consortia[J]. Applied and Environmental Microbiology, 1997, 63(12):4759-4764.
[83]	MECKENSTOCK R U, BOLL M, MOUTTAKI H, et al. Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons[J]. J Mol Microbiol Biotechnol, 2016, 26(1/2/3):92-118.
[84]	ABU LABAN N, SELESI D, RATTEI T, et al. Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture[J]. Environmental Microbiology, 2010, 12(10):2783-2796.
[85]	LUO F, GITIAFROZ R, DEVINE C E, et al. Metatranscriptome of an anaerobic benzene-degrading, nitrate-reducing enrichment culture reveals involvement of carboxylation in benzene ring activation[J]. Applied and Environmental Microbiology, 2014, 80(14):4095-4107.
[86]	DHAR K, SUBASHCHANDRABOSE S R, VENKATESWARLU K, et al. Anaerobic microbial degradation of polycyclic aromatic hydrocarbons:a comprehensive review[J]. Reviews of Environmental Contamination and Toxicology Volume 251, 2019:25-108.
[87]	RABUS R, WILKES H. Functional genomics of sulfate-reducing bacteria degrading hydrocarbons[J]. Anaerobic Utilization of Hydrocarbons, Oils, and Lipids, 2020:225-232.
[88]	WARTELL B, BOUFADEL M, RODRIGUEZ-FREIRE L. An effort to understand and improve the anaerobic biodegradation of petroleum hydrocarbons:a literature review[J]. International Biodeterioration & Biodegradation, 2021, 157:105156.
[89]	GIEG L M, TOTH C R. Signature metabolite analysis to determine in situ anaerobic hydrocarbon biodegradation[J]. Anaerobic Utilization of Hydrocarbons, Oils, and Lipids, 2020:361-390.
[90]	FOGHT J. Anaerobic Biodegradation of Aromatic Hydrocarbons:Pathways and Prospects[J]. Microbial Physiology, 2008, 15(2/3):93-120.
[91]	GAO H, WU M L, LIU H, et al. Effect of petroleum hydrocarbon pollution levels on the soil microecosystem and ecological function[J]. Environmental Pollution, 2022, 293:118511.
[92]	LACZI K, ERDEINÉ KIS Á, SZILÁGYI Á, et al. New frontiers of anaerobic hydrocarbon biodegradation in the multi-omics era[J]. Frontiers in Microbiology, 2020, 11. DOI: 10.3389/fmicb.2020.590049.
[93]	李伟, 印莉萍. 基因组学相关概念及其研究进展[J]. 生物学通报, 2000,35(11):1-3.
[94]	JAISWAL S, SINGH D K, SHUKLA P. Gene editing and systems biology tools for pesticide bioremediation:a review[J]. Frontiers in Microbiology, 2019, 10.DOI: 10.3389/fmicb.2019.00087.
[95]	CHEN H P, ZHU S H, CASABON I, et al. Genomic and transcriptomic studies of an RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)-degrading actinobacterium[J]. Applied and Environmental Microbiology, 2012, 78(21):7798-7800.
[96]	HE C, LI Y, HUANG C, et al. Genome sequence and metabolic analysis of a fluoranthene-degrading strain Pseudomonas aeruginosa DN1[J]. Frontiers in Microbiology, 2018,9:2595.
[97]	NELSON K, WEINEL C, PAULSEN I, et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440[J]. Environmental Microbiology, 2002, 4(12):799-808.
[98]	FILONOV A, DELEGAN Y, PUNTUS I, et al. Complete genome sequence of Pseudomonas putida BS3701, a promising Polycyclic Aromatic Hydrocarbon-Degrading strain for bioremediation technologies[J]. Microbiology Resource Announcements, 2020, 9(40). DOI: 10.1128/MRA.00892-20.
[99]	CHANDRAN H, MUKESH M, SHARMA K. Microbial biodiversity and bioremediation assessment through omics approaches[J]. Frontiers in Environmental Chemistry,2020. DOI: 10.3389/fenvc.2020.570326.
[100]	ZHANG X, LIANG C, SONG J, et al. Transcriptome analyses suggest a molecular mechanism for the SIPC response of Amphibalanus amphitrite[J]. Biochemical and Biophysical Research Communications, 2020, 525(4):823-829.
[101]	DAS D, MAWLONG G T, SARKI Y N, et al. Transcriptome analysis of crude oil degrading Pseudomonas aeruginosa strains for identification of potential genes involved in crude oil degradation[J]. Gene, 2020, 755:144909.
[102]	LIU S, GUO C, LIN W, et al. Comparative transcriptomic evidence for Tween80-enhanced biodegradation of phenanthrene by Sphingomonas sp. GY2B[J]. Science of the Total Environment, 2017, 609:1161-1171.
[103]	PEIDRO-GUZMÁN H, PÉREZ-LLANO Y, GONZÁLEZ-ABRADELO D, et al. Transcriptomic analysis of polyaromatic hydrocarbon degradation by the halophilic fungus Aspergillus sydowii at hypersaline conditions[J]. Environmental Microbiology, 2021, 23(7):3435-3459.
[104]	NESVIZHSKII A I. Proteogenomics:concepts, applications and computational strategies[J]. Nature methods, 2014, 11(11):1114-1125.
[105]	KIM S J, KWEON O, SUTHERLAND J B, et al. Dynamic response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon crude oil[J]. Applied and Environmental Microbiology, 2015, 81(13):4263-4276.
[106]	KUREEL M K, GEED S R, RAI B N, et al. Novel investigation of the performance of continuous packed bed bioreactor (CPBBR) by isolated Bacillus sp. M4 and proteomic study[J]. Bioresource Technology, 2018, 266:335-342.
[107]	BHAGANNA P, BIELECKA A, MOLINARI G, et al. Protective role of glycerol against benzene stress:insights from the Pseudomonas putida proteome[J]. Current Genetics, 2016, 62(2):419-429.
[108]	KURA B. Deepwater horizon oil spill of 2010 in the Gulf of Mexico[J]. The Magazine for Environmental Managers, 2011(7):6-7.
[109]	PARK H, MIN B, JANG Y, et al. Comprehensive genomic and transcriptomic analysis of polycyclic aromatic hydrocarbon degradation by a mycoremediation fungus, Dentipellis sp. KUC8613[J]. Applied Microbiology and Biotechnology, 2019, 103(19):8145-8155.
[110]	MALIK G, ARORA R, CHATURVEDI R, et al. Implementation of genetic engineering and novel omics approaches to enhance bioremediation:a focused review[J]. Bulletin of Environmental Contamination and Toxicology, 2022, 108(3):443-450.
[111]	PARK H, CHOI I-G. Genomic and transcriptomic perspectives on mycoremediation of polycyclic aromatic hydrocarbons[J]. Applied Microbiology and Biotechnology, 2020, 104(16):6919-6928.
[112]	BHATTACHARJEE G, GOHIL N, SINGH V. Synthetic biology approaches for bioremediation[M]. Bioremediation of Pollutants. Elsevier, 2020:303-312.
[113]	JIMÉNEZ-DÍAZ V, PEDROZA-RODRÍGUEZ A M, RAMOS-MONROY O, et al. Synthetic biology:a new era in hydrocarbon bioremediation[J]. Processes, 2022, 10(4):712.
[114]	WANG B, XU J, GAO J, et al. Construction of an Escherichia coli strain to degrade phenol completely with two modified metabolic modules[J]. Journal of Hazardous Materials, 2019, 373:29-38.
[115]	JAIN C K, GUPTA M, PRASAD Y, et al. Homology modeling and protein engineering of alkane monooxygenase in Burkholderia thailandensis MSMB121:in silico insights[J]. J Mol Model, 2014, 20(7):2340.
[116]	PATEL R, ZAVERI P, MUKHERJEE A, et al. Development of fluorescent protein-based biosensing strains:a new tool for the detection of aromatic hydrocarbon pollutants in the environment[J]. Ecotoxicology and Environmental Safety, 2019, 182:109450.
[117]	MCCARTY N S, LEDESMA-AMARO R. Synthetic biology tools to engineer microbial communities for biotechnology[J]. Trends Biotechnol, 2019, 37(2):181-197.