基于非培养手段的多环芳烃降解微生物解析

Abstract
Figure/Table
References (134)
Related Citation (15)

Download: PDF (524 KB) HTML (1 KB)
Export: BibTeX | EndNote (RIS)

Abstract

This review discussed the cultivation-independent approaches which have been developed to identify functional-yet-uncultivated soil microbes in situ and revealed their functions in PAHs degradation. PAHs-degrading microbes, degradation mechanisms and functional genes were summarized. The principles, characteristics and applications of cultivation-independent methods, including Fluorescence in situ hybridization (FISH), Stable-isotope probing (SIP), Metagenomics, Transcriptomics, Single-cell technology and Magnetic nanoparticle-Mediated Isolation technology (MMI) were also discussed. Examples were given on the application of these cultivation-independent approaches in identifying PAHs-degrading microbes. SIP technology is the most stable and widely used in the study of PAHs degradation mechanism. As a novel cultivation-independent approach, MMI technology provides a deep insight into exploring functional-yet-uncultivated PAHs-degrading microbes, which stands out for its ability to separate active functional microbes.

Key words： functional-yet-uncultivated microbes PAHs biodegradation soils functional microorganisms cultivation-independent approaches

Received: 09 March 2018

X53

	Service

	E-mail this article
	Add to my bookshelf
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors
	CHEN Ya-ting
	JIANG Bo
	XING Yi
	ZHANG Na-na
	LIAN Lu-ning
	LU Pei

Cite this article:

CHEN Ya-ting,JIANG Bo,XING Yi等. Identification and characterization on PAHs-degrading microorganisms via cultivation-independent approaches[J]. CHINA ENVIRONMENTAL SCIENCECE, 2018, 38(9): 3562-3575.

URL:

http://www.zghjkx.com.cn/EN/ OR http://www.zghjkx.com.cn/EN/Y2018/V38/I9/3562

[1]	Tarafdar A, Sinha A. Public health risk assessment with bioaccessibility considerations for soil PAHs at oil refinery vicinity areas in India[J]. The Science of the Total Environment, 2017,616-617:1477-1484.
[2]	Yin W, Hou J, Xu T, et al. Obesity mediated the association of exposure to polycyclic aromatic hydrocarbon with risk of cardiovascular events[J]. The Science of the Total Environment, 2018,616-617:841-854.
[3]	Tavera B I, Tames F, Silva J A, et al. Biomonitoring levels and trends of PAHs and synthetic musks associated with land use in urban environments[J]. The Science of the Total Environment, 2017,618:93-100.
[4]	Tu Y T, Ou J H, Tsang D C W, et al. Source identification and ecological impact evaluation of PAHs in urban river sediments:A case study in Taiwan[J]. Chemosphere, 2018,194:666-674.
[5]	Yadav I C, Devi N L, Li J, et al. Polycyclic aromatic hydrocarbons in house dust and surface soil in major urban regions of Nepal:Implication on source apportionment and toxicological effect[J]. The Science of the Total Environment, 2017,616-617:223-235.
[6]	康杰,胡健,朱兆洲,等.太湖及周边河流表层沉积物中PAHs的分布、来源与风险评价[J]. 中国环境科学, 2017,37(3):1162-1170.
[7]	Wang C L, Zou X Q, Zhao Y F, et al. Distribution pattern and mass budget of sedimentary polycyclic aromatic hydrocarbons in shelf areas of the Eastern China Marginal Seas[J]. Journal of Geophysical Research-Oceans, 2017,122(6):4990-5004.
[8]	Xiao Y H, Tong F C, Kuang Y W, et al. Distribution and Source Apportionment of Polycyclic Aromatic Hydrocarbons (PAHs) in Forest Soils from Urban to Rural Areas in the Pearl River Delta of Southern China[J]. International Journal of Environmental Research and Public Health, 2014,11(3):2642-2656.
[9]	Wang Y, Zhang S, Cui W, et al. Polycyclic aromatic hydrocarbons and organochlorine pesticides in surface water from the Yongding River basin, China:Seasonal distribution, source apportionment, and potential risk assessment[J]. The Science of the Total Environment, 2018,618:419-429.
[10]	Tong R P, Yang X Y, Su H R, et al. Levels, sources and probabilistic health risks of polycyclic aromatic hydrocarbons in the agricultural soils from sites neighboring suburban industries in Shanghai[J]. The Science of the Total Environment, 2018,616-617:1365-1373.
[11]	Kuppusamy S, Thavamani P, Venkateswarlu K, et al. Remediation approaches for polycyclic aromatic hydrocarbons (PAHs) contaminated soils:Technological constraints, emerging trends and future directions[J]. Chemosphere, 2017,168:944-968.
[12]	Peris P M, Gómez J C, Herbert J H, et al. Ecological restoration of a former gravel pit contaminated by a massive petroleum sulfonate spill. A case study:Arganda del Rey. Madrid (Spain)[J]. Ecological Engineering, 2017,100:73-88.
[13]	Lin W, Guo C, Zhang H, et al. Electrokinetic-Enhanced Remediation of Phenanthrene-Contaminated Soil Combined with Sphingomonas sp GY2B and Biosurfactant[J]. Applied Biochemistry and Biotechnology, 2016,178(7):1325-1338.
[14]	Srivastava V J, Hudson J M, Cassidy D P. In situ solidification and in situ chemical oxidation combined in a single application to reduce contaminant mass and leachability in soil[J]. Journal of Environmental Chemical Engineering, 2016,4(3):2857-2864.
[15]	Cheng M, Zeng G, Huang D, et al. Hydroxyl radicals based advanced oxidation processes (AOPs) for remediation of soils contaminated with organic compounds:A review[J]. Chemical Engineering Journal, 2016, 284:582-598.
[16]	Chen M, Xu P, Zeng G, 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):745-755.
[17]	Liu S H, Zeng G M, Niu Q Y, et al. Bioremediation mechanisms of combined pollution of PAHs and heavy metals by bacteria and fungi:A mini review[J]. Bioresource Technology, 2017,224:25-33.
[18]	Lin M, Hu X, Chen W, et al. Biodegradation of phenanthrene by Pseudomonas sp. BZ-3, isolated from crude oil contaminated soil[J]. International Biodeterioration and Biodegradation, 2014,94:176-181.
[19]	Song X, Xu Y, Li G, et al. Isolation, characterization of Rhodococcus sp. P14capable of degrading high-molecular-weight polycyclic aromatic hydrocarbons and aliphatic hydrocarbons[J]. Marine Pollution Bulletin, 2011,62(10):2122-2128.
[20]	Nie M, Nie H, Cao W, et al. Phenanthrene Metabolites from a New Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Aeromonas salmonicida subsp. Achromogenes Strain NY4[J]. Polycyclic Aromatic Compounds, 2016,36(2):132-151.
[21]	Moody J D, Freeman J P, Doerge D R, et al. Degradation of phenanthrene and anthracene by cell suspensions of Mycobacterium sp. strain PYR-1[J]. Applied and Environmental Microbiology, 2001, 67(4):1476-1483.
[22]	Chikere C B, Chikere B O, Okpokwasili G C. Bioreactor-based bioremediation of hydrocarbon-polluted Niger Delta marine sediment, Nigeria[J]. Biotech., 2012,2(1):53-66.
[23]	Ni N, Song Y, Shi R, et al. Biochar reduces the bioaccumulation of PAHs from soil to carrot (Daucus carota L.) in the rhizosphere:A mechanism study[J]. The Science of the Total Environment, 2017,601:1015-1023.
[24]	Song M, Luo C, Jiang L, et al. Identification of Benzo a pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing[J]. Applied and Environmental Microbiology, 2015,81(21):7368-7376.
[25]	Hesham A E, Mawad A M M., Mostafa Y M, et al. Biodegradation Ability and Catabolic Genes of Petroleum-Degrading Sphingomonas koreensis Strain ASU-06Isolated from Egyptian Oily Soil[J]. Biomed Research International, 2014,2014(1):127674.
[26]	Seo J S, Keum Y S, Hu Y, et al. Phenanthrene degradation in Arthrobacter sp P1-1:Initial 1,2-, 3,4-and 9,10-dioxygenation, and meta-and ortho-cleavages of naphthalene-1,2-diol after its formation from naphthalene-1,2-dicarboxylic acid and hydroxyl naphthoic acids[J]. Chemosphere, 2006,65(11):2388-2394.
[27]	Saito A, Iwabuchi T, Harayama S. Characterization of genes for enzymes involved in the phenanthrene degradation in Nocardioides sp. KP7[J]. Chemosphere, 1999,38(6):1331-1337.
[28]	Yen K M, Gunsalus I C. Regulation of naphthalene catabolic genes of plasmid NAH7[J]. Journal of Bacteriology, 1985,162(3):1008-1013.
[29]	Chebbi A, Hentati D, Zaghden H, et al. Polycyclic aromatic hydrocarbon degradation and biosurfactant production by a newly isolated Pseudomonas sp. strain from used motor oil-contaminated soil[J]. International Biodeterioration and Biodegradation, 2017,122:128-140.
[30]	Xu H S. Survival and viability of nonculturableEscherichia coli andVibrio cholerae in the estuarine and marine environment[J]. Microbial Ecology, 1982,8(4):313-323.
[31]	Tarafdar A, Sinha A, Masto R E. Biodegradation of anthracene by a newly isolated bacterial strain, Bacillus thuringiensis AT.ISM.1, isolated from a fly ash deposition site[J]. Letters in Applied Microbiology, 2017,65(4):327-334.
[32]	Meena S S, Sharma R S, Gupta P, et al. Isolation and identification of Bacillus megaterium YB3 from an effluent contaminated site efficiently degrades pyrene[J]. Journal of Basic Microbiol., 2016, 56(4):369-378.
[33]	Cao J, Lai Q, Yuan J, et al. Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73(T)[J]. Scientific Reports, 2015,5:7741.
[34]	Schuler L, Jouanneau Y, Chadhain S M N, et al. Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp. strain LH128able to oxidize benz a anthracene[J]. Applied Microbiology and Biotechnology, 2009,83(3):465-475.
[35]	Nojiri H, Nam J W, Kosaka M, et al. Diverse oxygenations catalyzed by carbazole 1,9a-dioxygenase from Pseudomonas sp. Strain CA10[J]. Journal of Bacteriology, 1999,181(10):3105-3113.
[36]	Schuler L, Chadhain S M N, Jouanneau Y, et al. Characterization of a novel angular dioxygenase from fluorene-degrading Spingomonas sp. strain LB126[J]. Applied and Environmental Microbiology, 2008, 74(4):1050-1057.
[37]	Pinyakong O, Habe H, Yoshida T, et al. Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2[J]. Biochemical and Biophysical Research Communications, 2003,301(2):350-357.
[38]	Bosch R, Garcíavaldés E, Moore E R. Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10[J]. Gene, 2000,245(1):65-74.
[39]	Park H H, Lim W K, Shin H J. In vitro binding of purified NahR regulatory protein with promoter Psal [J]. Biochimica Et Biophysica Acta-General Subjects, 2005,1725(2):247-255.
[40]	Izmalkova T Y, Sazonova O I, Kosheleva I A, et al. Phylogenetic Analysis of the Genes for Naphthalene and Phenanthrene Degradation in Burkholderia sp. Strains[J]. Russian Journal of Genetics., 2013, 49(6):609-616.
[41]	Segura A, Hernándezsánchez V, Marqués S, et al. Insights in the regulation of the degradation of PAHs in Novosphingobium sp. HR1a and utilization of this regulatory system as a tool for the detection of PAHs[J]. The Science of the Total Environment., 2017,590:381-393.
[42]	Liu T T, Xu Y, Liu H, et al. Functional characterization of a gene cluster involved in gentisate catabolism in Rhodococcus sp. strain NCIMB 12038[J]. Applied Microbiology and Biotechnology, 2011,90(2):671-678.
[43]	Krivobok S, Kuony S, Meyer C, et al. Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1:Evidence for two ring-hydroxylating dioxygenases[J]. Journal of Bacteriology, 2003, 185(13):3828-3841.
[44]	Takizawa N, Iida T, Sawada T, et al. Nucleotide sequences and characterization of genes encoding naphthalene upper pathway of pseudomonas aeruginosa PaK1 and Pseudomonas putida OUS82[J]. Journal of Bioscience and Bioengineering, 1999,87(6):721-731.
[45]	Denome S A, Stanley D C, Olson E S, et al. Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains:complete DNA sequence of an upper naphthalene catabolic pathway[J]. Journal of Bacteriology, 1993,175(21):6890-6901.
[46]	Stingley R L, Khan A A, Cerniglia C E. Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1[J]. Biochemical and Biophysical Research Communications, 2004,322(1):133-146.
[47]	Hickey W J, Chen S, Zhao J. The phn island:a new genomic island encoding catabolism of polynuclear aromatic hydrocarbons[J]. Frontiers in Microbiology, 2012:3(125):1-12.
[48]	张作艳,原野,丁立建,等.未培养微生物原位培养技术研究进展[J]. 天然产物研究与开发, 2018,38(5):907-913.
[49]	Pulschen A A, Bendia A G, Fricker A D, et al. Isolation of Uncultured Bacteria from Antarctica Using Long Incubation Periods and Low Nutritional Media[J]. Frontiers in Microbiology, 2017,8(12):1346.
[50]	崔晓龙,徐丽华,文孟良,等.未培养微生物资源[J]. 微生物学通报, 2005,(3):144-146.
[51]	Kim M, Yu Z. Quantitative comparisons of select cultured and uncultured microbial populations in the rumen of cattle fed different diets[J]. Journal of Animal Science and Biotechnology, 2012,3(4):193-198.
[52]	Ouyang E, Liu Y, Ouyang J, et al. Effects of different wastewater characteristics and treatment techniques on the bacterial community structure in three pharmaceutical wastewater treatment systems[J]. Environmental Technology, 2017,(11):1-13.
[53]	Konstantinidis K T, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy[J]. ISME Journal, 2017, 11(11):2399-2406.
[54]	Neufeld J D, Wagner M, Murrell J C. Who eats what, where and when? Isotope-labelling experiments are coming of age[J]. Isme Journal, 2007,1(2):103.
[55]	Sanches S, Martins M, Silva A F, et al. Bioremoval of priority polycyclic aromatic hydrocarbons by a microbial community with high sorption ability[J]. Environmental Science and Pollution Research International, 2017,24(4):3550-3561.
[56]	Hesham E L, Khan S, Yu T, et al. Biodegradation of high molecular weight PAHs using isolated yeast mixtures:application of meta-genomic methods for community structure analyses[J]. Environmental Science and Pollution Research International., 2012,19(8):3568-3578.
[57]	Johnsen A R, Winding A, Karlson U, et al. Linking of microorganisms to phenanthrene metabolism in soil by analysis of C-13-labeled cell lipids[J]. Applied and Environmental Microbiology, 2002,68(12):6106-6113.
[58]	Coyotzi S, Pratscher J, Murrell J C, et al. Targeted metagenomics of active microbial populations with stable-isotope probing[J]. Current Opinion in Biotechnology, 2016,41:1-8.
[59]	Gkarmiri K, Mahmood S, Ekblad A, et al. Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape[J]. Applied and Environmental Microbiology, 2017,83(22):AME.01938-17.
[60]	Jehmlich N, Vogt C, Lünsmann V, et al. Protein-SIP in environmental studies[J]. Current Opinion in Biotechnology, 2016,41:26-33.
[61]	Boschker H T S, Nold S C, Wellsbury P, et al. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers[J]. Nature, 1998,392(6678):801-805.
[62]	Radajewski S, Ineson P, Parekh N R, et al. Stable-isotope probing as a tool in microbial ecology[J]. Nature, 2000,403(6770):646-649.
[63]	Lueders T, Dumont M G, Bradford L, et al. RNA-stable isotope probing:from carbon flow within key microbiota to targeted transcriptomes[J]. Current Opinion in Biotechnology, 2016,41:83-89.
[64]	Youngblut N D, Buckley D H. Intra-genomic variation in G plus C content and its implications for DNA stable isotope probing[J]. Environmental Microbiology Reports, 2014,6(6):767-775.
[65]	Gao J, Pan K, Li H, et al. Application of GelGreen (TM) in Cesium Chloride Density Gradients for DNA -Stable Isotope Probing Experiments[J]. PLos One, 2017,12(1):1-13.
[66]	Martinezcruz K, Leewis M C, Herriott I C, et al. Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments[J]. The Science of the Total Environment, 2017,607-608:23-31.
[67]	Srithep P, Pornkulwat P, Limpiyakorn T. Contribution of ammonia-oxidizing archaea and ammonia-oxidizing bacteria to ammonia oxidation in two nitrifying reactors[J]. Environmental Science and Pollution Research International, 2018,25(3):1-12.
[68]	Ziels R M, Sousa D Z, Stensel H D, et al. DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies[J]. ISME Journal, 2018,12(1):112-123.
[69]	Cunliffe M, Hollingsworth A, Bain C, et al. Algal polysaccharide utilisation by saprotrophic planktonic marine fungi[J]. Fungal Ecology, 2017,30:135-138.
[70]	Bryson S, Zhou L, Chavez F, et al. Phylogenetically conserved resource partitioning in the coastal microbial loop[J]. ISME Journal, 2017,11(12):2781-2792.
[71]	Orsi W D, Wilken S, Campo J D, et al. Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing[J]. Environmental Microbiology, 2018,20(2):815-827.
[72]	Costa D P D, Dias A C F, Cotta S R, et al. Changes of bacterial communities in the rhizosphere of sugarcane under elevated concentration of atmospheric CO2[J]. Global Change Biology Bioenergy, 2018,10(2):137-145.
[73]	Dai S, Liu Q, Zhao J, et al. Ecological niche differentiation of ammonia-oxidising archaea and bacteria in acidic soils due to land use change[J]. Soil Research, 2018,56(1):71-79.
[74]	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]. Journal of Hazardous Materials, 2016,308:50-57.
[75]	Rochman F F, Sheremet A, Tamas I, et al. Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond[J]. Front Microbiol., 2017,8(12):1845.
[76]	Jeon C O, Park W, Padmanabhan P, et al. Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment[J]. Proceedings of the National Academy of Sciences of the United States of America, 2003,100(23):13591-13596.
[77]	Singleton D R, Powell S N, Sangaiah R, et al. Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a Bioreactor treating contaminated soil[J]. Applied and Environmental Microbiology, 2005,71(3):1202-1209.
[78]	Jones M D, Crandell D W, Singleton D R, et al. Stable-isotope probing of the polycyclic aromatic hydrocarbon-degrading bacterial guild in a contaminated soil[J]. Environmental Microbiology, 2011, 13(10):2623-2632.
[79]	Jones M D, Singleton D R, Sun W, et al. Multiple DNA Extractions Coupled with Stable-Isotope Probing of Anthracene-Degrading Bacteria in Contaminated Soil[J]. Applied and Environmental Microbiology, 2011,77(9):2984-2991.
[80]	Jiang L, Song M, Luo C, et al. Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing[J]. Plos One, 2015,10(6):1-14.
[81]	Corteselli E M, Aitken M D, Singleton D R. Rugosibacter aromaticivorans gen. nov., sp nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds[J]. International Journal of Systematic and Evolutionary Microbiology, 2017,67(2):311-318.
[82]	Song M, Luo C, Jiang L, et al. Identification of Benzo a pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing[J]. Applied and Environmental Microbiology, 2015, 81(21):7368-7376.
[83]	Handelsman J, Rondon M R, Brady S F, et al. Molecular biological access to the chemistry of unknown soil microbes:a new frontier for natural products[J]. Chemistry and Biology, 1998,5(10):245-249.
[84]	Montella S, Amore A, Faraco V. Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development[J]. Critical Reviews in Biotechnology, 2016,36(6):998-1009.
[85]	Kim M, Lee K H, Yoon S W, et al. Analytical tools and databases for metagenomics in the next-generation sequencing era[J]. Genomics and Informatics, 2013,11(3):102-113.
[86]	Neelakanta G, Sultana H. The use of metagenomic approaches to analyze changes in microbial communities[J]. Microbiology Insights, 2013,6:37-48.
[87]	Zhou J, He Z, Yang Y, et al. High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis:Open and Closed Formats[J]. Microbiology, 2015,6(1):1-17.
[88]	Lindgreen S, Adair K L, Gardner P P. An evaluation of the accuracy and speed of metagenome analysis tools[J]. Scientific Reports, 2016,6:1-14.
[89]	Klemetsen T, Raknes I A, Fu J, et al. The MAR databases:development and implementation of databases specific for marine metagenomics[J]. Nucleic Acids Research, 2018,46(D1):D692-D699.
[90]	Smith T E, Pond C D, Pierce E, et al. Accessing chemical diversity from the uncultivated symbionts of small marine animals[J]. Nature Chemical Biology, 2018,14(2):179-185.
[91]	Mendes L W, Tsai S M. Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil[J]. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2018, 111(1):101-114.
[92]	Becraft E D, Dodsworth J A, Murugapiran S K, et al. Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1Archaeal Lineage from Chemically and Geographically Disparate Hot Springs[J]. Frontiers in Microbiology, 2017,8(10):1-10.
[93]	Ms. Sylwia Zielińska, Dr. Dorota Kidawa, Prof. Lech Stempniewicz, et al. Environmental DNA as a valuable and unique source of information about ecological networks in Arctic terrestrial ecosystems[J]. Environmental Reviews, 2017,25(3):282-291.
[94]	Sarkar S F, Poon J S, Lepage E, et al. Enabling a sustainable and prosperous future through science and innovation in the bioeconomy at Agriculture and Agri-Food Canada[J]. New Biotechnology, 2018,40:70-75.
[95]	Douglas G M, Hansen R, Cma J, et al. Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn's disease[J]. Microbiome, 2018,6(13):1-12.
[96]	Sahu N, Deori M, Ghosh I. Metagenomics Study of Contaminated Sediments from the Yamuna River at Kalindi Kunj, Delhi, India[J]. Genome Announcements, 2018,6(1):1-7.
[97]	Mason O U, Scott N M, Gonzalez A, et al. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill[J]. Isme Journal Multidisciplinary Journal of Microbial Ecology, 2014,8(7):1464-1475.
[98]	Zafra G, Taylor T D, Absalón A E, et al. Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium[J]. Journal of Hazardous Materials, 2016,318:702-710.
[99]	Zhao J K, Li X M, Ai G M, et al. Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil[J]. Journal of Hazardous Materials, 2016,318:90-98.
[100]	Hangauer M J, Vaughn I W, Mcmanus M T. Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs[J]. Plos Genetics, 2013,9(6):e1003569.
[101]	Todd E V, Black M A, Gemmell N J. The power and promise of RNA-seq in ecology and evolution[J]. Molecular Ecology, 2016, 25(6):1224-1241.
[102]	Conesa A, Madrigal P, Tarazona S, et al. A survey of best practices for RNA-seq data analysis[J]. Genome Biology, 2016,17(1):13.
[103]	Haile S, Corbett R D, Macleod T, et al. Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing[J]. BMC Genomics, 2017,18(1):515.
[104]	Kaluzna M, Kuras A, Mikicinski A, et al. Evaluation of different RNA extraction methods for high-quality total RNA and mRNA from Erwinia amylovora in planta [J]. European Journal of Plant Pathology, 2016,146(4):893-899.
[105]	Molyneaux P L, Willisowen S A G, Cox M J, et al. Host-Microbial Interactions in Idiopathic Pulmonary Fibrosis[J]. American Journal of Respiratory and Critical Care Medicine, 2017,195(12):1640-1650.
[106]	Gruzieva O, Xu C J, Breton C V, et al. Epigenome-Wide Meta-Analysis of Methylation in Children Related to Prenatal NO2Air Pollution Exposure[J]. Environmental Health Perspectives, 2017, 125(1):104-110.
[107]	Singh S, Parihar P, Singh R, et al. Heavy Metal Tolerance in Plants:Role of Transcriptomics, Proteomics, Metabolomics, and lonomics[J]. Frontiers in Plant Science, 2016,6(1143):1-36.
[108]	Evans T G, Padillagamiño J L, Kelly M W, et al. Ocean acidification research in the ‘ost-genomic’ era:Roadmaps from the purple sea urchin Strongylocentrotus purpuratus [J]. Comparative Biochemistry and Physiology a-Molecular and Integrative Physiology, 2015,185:33-42.
[109]	Goltsman D S A, Comolli L R, Thomas B C, et al. Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities[J]. The ISME journal, 2015,9(4):1014-1023.
[110]	Imadi S R, Kazi A G, Ahanger M A, et al. Plant transcriptomics and responses to environmental stress:an overview[J]. Journal of Genetics, 2015,94(3):525-537.
[111]	Brinkmann M, Koglin S, Eisner B, et al. Characterisation of transcriptional responses to dioxins and dioxin-like contaminants in roach (Rutilus rutilus) using whole transcriptome analysis[J]. The Science of the Total Environment, 2016,541:412-423.
[112]	Curtis L R, Bravo C F, Bayne C J, et al. Transcriptional changes in innate immunity genes in head kidneys from Aeromonas salmonicida-challenged rainbow trout fed a mixture of polycyclic aromatic hydrocarbons[J]. Ecotoxicology and Environmental Safety, 2017,142:157-163.
[113]	Labib S, Williams A, Kuo B, et al. A framework for the use of single-chemical transcriptomics data in predicting the hazards associated with complex mixtures of polycyclic aromatic hydrocarbons[J]. Archives of Toxicology, 2017,91(7):2599-2616.
[114]	De Menezes Alexandre, Clipson N, Doyle E. Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil[J]. Environmental Microbiology, 2012,14(9):2577-2588.
[115]	Meckenstock R U, Boll M, Mouttaki H, et al. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons[J]. J. Journal of Molecular Microbiology and Biotechnology, 2016,26(1-3):92-118.
[116]	Stepanauskas R. Single cell genomics:an individual look at microbes[J]. Current Opinion in Microbiology, 2012,15(5):613-620.
[117]	Tanay A, Regev A. Scaling single-cell genomics from phenomenology to mechanism[J]. Nature, 2017,541(7637):331-338.
[118]	Rinke C, Schwientek P, Sczyrba A, et al. Insights into the phylogeny and coding potential of microbial dark matter[J]. Nature, 2013,499(7459):431-437.
[119]	Gross A, Schoendube J, Zimmermann S, et al. Technologies for Single-Cell Isolation[J]. International Journal of Molecular Sciences, 2015,16(8):16897-16919.
[120]	Shembekar N, Chaipan C, Utharala R, et al. Droplet-based microfluidics in drug discovery, transcriptomics and high-throughput molecular genetics[J]. Lab on a Chip, 2016,16(8):1314-1331.
[121]	Li R, Zhou M, Yue C, et al. Multiple single cell screening and DNA MDA amplification chip for oncogenic mutation profiling[J]. Lab on a Chip, 2018,18(5):723-734.
[122]	Macaulay I C, Ponting C P, Voet T. Single-Cell Multiomics:Multiple Measurements from Single Cells[J]. Trends in Genetics, 2017, 33(2):155-168.
[123]	Chen S, Yin H, Chang J, et al. Physiology and bioprocess of single cell of Stenotrophomonas maltophilia in bioremediation of co-existed benzo a pyrene and copper[J]. Journal of Hazardous Materials, 2017,321:9-17.
[124]	Croxton A N, Wikfors G H. The use of flow cytometric applications to measure the effects of PAHs on growth, membrane integrity, and relative lipid content of the benthic diatom, Nitzschia brevirostris [J]. Marine Pollution Bulletin, 2015,91(1):160-165.
[125]	Zhang D, Berry J P, Zhu D, et al. Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community[J]. Isme Journal, 2015,9(3):603-614.
[126]	Ghahremani M, Aslani A, Hosseinnia M, et al. Direct and indirect measurement of the magnetocaloric effect in bulk and nanostructured Ni-Mn-In Heusler alloy[J]. AIP Advances, 2018,8(5):056426.
[127]	Tzitzios V K. Chemical synthesis of L10Fe-Pt-Ni alloy nanoparticles[J]. AIP Advances, 2018,8(5):056210.
[128]	Paul T, Basu S, Sarkar K. SPION-mediated soil DNA extraction and comparative analysis with conventional and commercial kit-based protocol[J]. 3Biotech, 2014,4(6):669-677.
[129]	Kamat V, Pandey S, Paknikar K, et al. A facile one-step method for cell lysis and DNA extraction of waterborne pathogens using a microchip[J]. Biosensors and Bioelectronics, 2018,99:62-69.
[130]	Wang J, Ali Z, Si J, et al. Simultaneous Extraction of DNA and RNA from Hepatocellular Carcinoma (Hep G2) Based on Silica-Coated Magnetic Nanoparticles[J]. Journal of Nanoscience and Nanotechnology, 2017,17(1):802-806.
[131]	Tang Y, Zou J, Chao M, et al. Highly Sensitive and Rapid Detection of Pseudomonas aeruginosa Based on Magnetic Enrichment and Magnetic Separation[J]. Theranostics, 2013,3(2):85-92.
[132]	Zhang S, Gao H, Bao G. Physical Principles of Nanoparticle Cellular Endocytosis[J]. Acs Nano, 2015,9(9):8655-8671.
[133]	Zhang D, Fakhrullin R F, Ozmen M, et al. Functionalization of whole-cell bacterial reporters with magnetic nanoparticles[J]. Microbial Biotechnology, 2011,4(1):89-97.
[134]	Wang X, Zhao X, Li H, et al. Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation[J]. Research in Microbiology, 2016,167(9/10):731-744.