Transmembrane transport of polycyclic aromatic hydrocarbons by bacteria and functional regulation of membrane proteins

doi:10.1007/s11783-019-1188-2

摘要
图/表
参考文献
相关文章
多维度评价

全文: PDF(1873 KB) HTML
导出: BibTeX | EndNote | Reference Manager | ProCite | RefWorks

Abstract：

• Explaintheadsorption, uptake and transmembrane transport of PAHs by bacteria.

• Analyze functional regulation of membrane proteins inthe transmembrane transport.

• Proteomics technology such as iTRAQ labeling was used to access expressed proteins.

• Single cell analysis technology wereused to study the morphological structure.

In recent years, increasing research has been conducted on transmembrane transport processes and the mechanisms behind the microbial breakdown of polycyclic aromatic hydrocarbons (PAHs), including the role of membrane proteins in transmembrane transport and the mode of transmission. This article explains the adsorption, uptake and transmembrane transport of PAHs by bacteria, the regulation of membrane protein function during the transmembrane transport. There are three different regulation mechanisms for uptake, depending on the state and size of the oil droplets relative to the size of the microbial cells, which are (i) direct adhesion, (ii) emulsification and pseudosolubilization, and (iii) interfacial uptake. Furthermore, two main transmembrane transport modes are introduced, which are (i) active transport and (ii) passive uptake and active efflux mechanism. Meanwhile, introduce the proteomics and single cell analysis technology used to address these areas of research, such as Isobaric tags for relative and absolute quantitation (iTRAQ) technology and Nano Secondary ion mass spectrometry (Nano-SIMS). Additionally, analyze the changes in morphology and structure and the characteristics of microbial cell membranes in the process of transmembrane transport. Finally, recognize the microscopic mechanism of PAHs biodegradation in terms of cell and membrane proteins are of great theoretical and practical significance for understanding the factors that influence the efficient degradation of PAHs contaminants in soil and for remediating the PAHs contamination in this area with biotechnology.

Keywords Polycyclic aromatic hydrocarbons Transmembrane transport Adsorption and uptake of hydrocarbons Proteomics Functional regulation of membrane protein Single cell analysis technology

发布日期: 2019-10-31

	服务

	推荐给朋友
	免费邮件订阅
	RSS订阅
	作者相关文章

	Hongqi Wang
	Ruhan Jiang
	Dekang Kong
	Zili Liu
	Xiaoxiong Wu
	Jie Xu
	Yi Li

引用本文:

Hongqi Wang,Ruhan Jiang,Dekang Kong, et al. Transmembrane transport of polycyclic aromatic hydrocarbons by bacteria and functional regulation of membrane proteins[J]. Front. Environ. Sci. Eng., 2020, 14(1): 9.

网址:

https://journal.hep.com.cn/fese/EN/10.1007/s11783-019-1188-2 OR https://journal.hep.com.cn/fese/EN/Y2020/V14/I1/9

Fig.1 Scheme of mycelia fluoranthene biosorption, transport and release (Schamfuss et al., 2013).

Adsorption type	Microbial species	Hydrocarbons species	Parameters and results	References
Direct adhesion	Pseudomonas sp. M1	n-Hexadecane	The degradation was not significantly affected by 4 mM EDTA.	^{Goswami and Singh (1991)}
	Acinetobacter sp. CR	n-Heneicosane	Higher impeller speed resulted in both lower microbial growth and lower n-alkane degradation rate of the bacterium, although it increased the specific surface area of the oil, which was measured by a previously developed device. This result was due to the decreased number of cells adhering to the oil surface, i.e., intense agitation inhibited the adhesion of cells to the oil surface.	^{Hori et al. (2002)}
	Rhodococcus equi OU2	Hexadecane	The surfactant is unnecessary for hexadecane to be degraded by OU2	^{Bouchez-Naitali and Vandecasteele (2008)}
	Rhodococcus baikonurensis EN3	Diesel oil	Tergitol 15 S, APG, LAE 9 and Tween 80 were effective only to a small extent in the enhancement of the biodegradation of diesel oil, and SDS inhibited rather than stimulated the degradation of diesel oil.	^{Lee et al. (2006)}
Emulsification and pseudosolubilization	Pseudomonas sp. N1	n-Hexadecane	The degradation was strongly inhibited by the 4 mM EDTA.	^{Goswami and Singh (1991)}
	Pseudomonas aeruginosa GL1	Hexadecane	The surfactant is necessary for hexadecane to be degraded by GL1.	^{Bouchez-Naitali and Vandecasteele (2008)}
	Pseudomonas aeruginosa AT10	Total petroleum hydrocarbons, the group of isoprenoids from the aliphatic fraction and the alkylated PAHs from the aromatic fraction	The rhamnolipid MAT10 reduced the surface tension (cST) up to 26.8 mN/m and the interfacial tension (cIT) against hexadecane to 1 mN/m. The CMC of MAT10 was 150 mg/L.	^{Geddes et al. (2008)}
	Mixed consortia of Pseudomonas aeruginosa strain PG201, Rhodococcus sp. H131A, and a Pseudomonas strain which produced the rhamnolipid Dyna270	Hexadecane, dodecane, benzene, toluene, iso-octane, pristane (2,6,10,14-tetramethyl pentadecane), naphthalene, and phenanthrene	The rhamnolipid biosurfactants enhanced the rate of linear alkane biodegradation more than the biodegradation rate of the monoaromatics.	^{Inakollu et al. (2004)}
	Rhodococcus baikonurensis EN3	Diesel oil	These hydrocarbon solubilization studies for pure hydrocarbons and mixed hydrocarbon systems have indicated that the biosurfactant shows hydrocarbon specificity, with hydrocarbon substrate packed within the micelle core and is influenced by the size and shape of the hydrocarbon substrate in the mixed waste systems.	^{Lee et al. (2006)}
	Rhodococcus sp.	Pyrene	The experimental kinetic data were fitted well with a mathematical model showing PAHs uptake both from the interface and from the aqueous medium by a population consisting of adsorbed cells in dynamic equilibrium with cells in the aqueous medium; interfacial uptake was predominant in these experiments.	^{Bouchez et al. (1997)}
	Mycobacterium PYR-1	PAHs	Results showed that the agitation rate affected cell growth and PAH degradation rates, while the substrate concentration did not; these are two characteristics of systems that exhibit an interfacial uptake mechanism. Moreover, detailed examination using fluorescence microscopy revealed that, in addition to associating with the aqueous-organic interface, this bacterium exists exclusively on the organic side of the interface.	^{MacLeod and Daugulis (2005)}
	Candida lipolytica	Hexadecane	Interfacial tension between oil and water and Sauter mean drop size decreased as cultivation proceeded.	^{Nakahara et al. (1977)}
	Candida lipolytica NRRL Y-6795 Candida intermedia IF0 0761 Candida tropicalis ATCC 20336 Saccharomyces cerevisiae HANSEN IF0 0305	n-Decane	C. intermedia and C. tropicalis, which can utilize hydrocarbon, adhere well to hydrocarbon, but S. cerevisiae, which cannot utilize hydrocarbon, did not adhere.	^{Miura et al. (1977)}

Tab.1 Three different regulation mechanisms in the adsorption and uptake of hydrocarbons by bacteria

Fig.2 Schematic overview of the interactions between bacteria, soil, pollutants, and surfactants (^{Volkering et al., 1997}).

Fig.3 Uptake of PAHs by Mycobacterium PYR-1 exanimated using fluorescence microscopy (^{MacLeod and Daugulis, 2005}).

Fig.4 Effect of different inhibitors on the trans-membrane transport of ¹⁴C-fluoranthene by Rhodococcus sp. BAP-1 was added as an inhibitors at 0 min (a) and 5 min (b) (^{Li et al., 2014}).

Type of transport	Microbial species	Hydrocarbon species	Features and conclusions	References
Active transport	Pseudomonas putida	Toluene	The results show that the efflux system in P. putida S12 is specific for organic solvents and does not export antibiotics or other known substrates of multidrug-resistant pumps.	^{Isken and De Bont (2000)}
	Pseudomonas putida KT2442	Toluene	Solute molecules are transported across the cell membrane by consuming energy of an inverse concentration gradient with the participation of pump proteins.	^{Fukumori et al. (1998)}
	Pseudomonas putida DOT-T1E	1,2,4-[C-14] Trichlorobenzene, toluene, xylenes, benzene	The concentration of organic molecules at the cell membrane increased with the addition of energy inhibitors.	^{Ramos et al. (1998)}
	Pseudomonas sp. DG17	Octadecane	Addition of the energy inhibitor NaN₃ inhibited the uptake of ¹⁴C-octadecane by Pseudomonas sp. DG17.	^{Hua and Wang (2014)}
	Rhodococcus sp. BAP-1	Fluoranthene	Demonstrated that the mechanism for fluoranthene travel across the cell membrane of Rhodococcus sp. BAP-1 requires energy	^{Li et al. (2014)}
Passive uptake and active efflux mechanism	Mixed microbial consortium Yersinia enterocolitica, Pseudomonas aeruginosa, Serratia liquefaciens, Pseudomonas fluorescens	Phenol	This study was carried out to understand the effect of varying sublethal concentrations of phenol on isolated individual bacterial cultures.	^{Sharma et al. (2002)}
Assisted diffusion of ingestible material and an active efflux mechanism	Pseudomonas fluorescens LP6a	Phenanthrene	The mechanism of transport of PAHs by Pseudomonas fluorescens LP6a, a PAM-degrading bacterium, was studied by inhibiting membrane transport and measuring the resulting change in cellular uptake. The data were consistent with the presence of two conflicting transport mechanisms: uptake by passive diffusion and an energy-driven efflux system to transport PAHs out of the cell.	^{Bugg et al. (2000)}

Tab.2 Passive and active transmembrane transport of hydrocarbons by bacteria

Fig.5 Structural features of TodX, TbuX, and FadL [TodX (left), TbuX (center), FadL (right)] (^{Ramos-González et al., 2002}).

Fig.6 Structural features of OmpW (^{Hong et al., 2006}).

Fig.7 Functional analysis of differentially expressed proteins in every cluster (Wang et al., 2019).

Fig.8 The number of upregulated and downregulated proteins in different KEGG-identified pathways (Wang et al., 2019).

Specific technology	Microbial species	Substances that interact with cells	Features and conclusions	References
iTRAQ	Streptococcus suis	Erythromycin	Seventy-nine differentially expressed proteins were identified in sub-MIC erythromycin inhibiting planktonic cell. Several cell surface proteins, as well as those involved in quorum-sensing, were found to be implicated in biofilm formation.	^{Zhao et al. (2015)}
	Rice suspension cells	Pathogenic bacteria of bacterial blight (Xanthomonas oryzae pv. oryzae).	Proteomics analysis of rice PM can be applied to identify potential PM components involved in the rice defense response to microbes.	^{Chen et al. (2007)}
	Resistance to fusarium	Pathogenic bacteria of head blight (FHB)	The first report of the application of proteomic techniques in studying the interaction between a series of barley genotypes representing various levels of resistance to FHB and the F. graminearum pathogen. The induced plant defense responses following fungal infection were diverse among resistant, intermediate and susceptible barley genotypes.	^{Geddes et al. (2008)}
	Madam Vinous’ sweet orange plants	Pathogenic bacteria of citrus Huanglongbing (HLB)	iTRAQ technology has been used to in identified 20 proteins and 10 differentially expressed proteins. These proteins may be good candidates for biomarkers to identify HLB-diseased plants prior to the expression of typical symptoms. However, similar changes in protein expression may be caused by other abiotic stresses, such as wounding and pathogen infections other than those induced by CLas.	^{Fan et al. (2011)}
	Abomasal mucosa	Nematode, Hemonchus contorts	The study identified and quantified more than 4400 unique proteins, of which 158 proteins showed>1.5-fold difference between resistant and susceptible sheep. Trefoil factor 2, a member of RAS oncogene family (RAP1A) and ring finger protein 126 were among the proteins found to be highly abundant in the abomasal surface of resistant sheep, whereas adenosine deaminase and the gastrokine-3-like precursor were found at higher levels in susceptible sheep.	^{Nagaraj et al. (2012)}
	E. chaffeensis	Tick-borne rickettsial pathogen, Ehrlichia chaffeensis	The study documents the impact of mutations on the global expression of pathogen protein and the influence of protein abundance on attenuation of mutations and protection of vertebrate host against infection.	^{Kondethimmanahalli et al. (2019)}
	Rubrivivax benzoatilyticus JA2	Glucose	The present study deciphered the molecular/metabolic events associated with glucose-grown cells of strain JA2 and unraveled how a carbon source modulates metabolic phenotypes. Proteomic profiling revealed extensive metabolic remodeling in the glucose-grown cells wherein signal transduction, selective transcription, DNA repair, protein transport and quality control processes were upregulated to cope with the changing milieu. Proteins involved in DNA replication, translation, electron transport, photosynthetic machinery were downregulated, possibly to conserve energy.	^{Gupta et al. (2019)}
	Clostridium difficile	Metronidazole	This study provided an in-depth proteomic analysis of a stable, metronidazole-resistant C. difficile isolate. The results suggested that a multifactorial response may be associated with high level metronidazole resistance in C. difficile, including the possible roles in altered iron metabolism and/or DNA repair.	^{Chong et al. (2014)}
1-DE/LC-MS/MS	Novosphingobium pentaromativorans US6-1	PAHs	1-DE/LC-MS/MS analysis of N. pentaromativorans US6-1 cultured in the presence of different PAHs and monocyclic aromatic hydrocarbons (MAHs) identified approximately 1,000 and 1,400 proteins, respectively.	^{Yun et al. (2014)}
2-DE	Cyanobacterium Anabaena PD-1	Polychlorobiphenyl	Twenty-five upregulated proteins were identified using 2-DE coupled with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). These proteins were involved in (i) PCB degradation, (ii) transport processes, (iii) energetic metabolism, (iv) electron transport, (v) general stress response, (vi) carbon metabolism, and (vii) nitrogen reductase.	^{Zhang et al. (2014)}

Tab.3 Proteomics technology

GO	Protein sources	Interference factors	Protein functions	References
Cellular components	Synechocystis sp. PCC 6803	Butanol	Cytoplasm, cytoplasmic part, protein transport, establishment of protein localization and protein localization.	^{Tian et al., (2013)}
	Fillets treated by microwave thawing (MT)	Magnetic nanoparticles plus microwave exposure	Membrane, membrane par, cell, cell part, organelle, organelle part.	^{Cao et al. (2019)}
	Vibrio parahemolyticus ATCC 17802	Food preservative and low temperature	Cell outer membrane.	^{Zhong et al. (2018)}
	Cotton Roots and Leaves	Salt stress	Cell, cell part, intracellular part, intracellular organelle, organelle-related components.	^{Chen et al. (2016)}
	Aspergillus flavus	Water activity	Cell, cell part, extracellular region, extracellular region part.	^{Zhang et al. (2015)}
	Rhodococcus sp. BAP-1	Fluoranthene	Cell, macromolecular complex, membrane.	^{Wang et al. (2019)}
Molecular functions	Synechocystis sp. PCC 6803	Butanol	Ribonucleoprotein complex, macromolecular complex, structural molecule activity, RNA binding, nucleic acid binding, gene expression and macromolecule metabolic processes.	^{Tian et al. 2013)}
	Fillets treated by microwave thawing (MT)	Magnetic nanoparticles plus microwave	Binding, catalytic activity, transporter activity.	^{Cao et al. 2019)}
	Vibrio parahemolyticus ATCC 17802	Food preservative and low temperature	Siderophore transmembrane transporter activity, receptor activity, iron ion binding, receptor activity.	^{Zhong et al. (2018)}
	Rice (Oryza sativa) Embryogenesis	–	Metabolic enzymes, binding (protein binding and nucleotide binding), transporters.	^{Zi et al. (2013)}
	Aspergillus flavus	Water activity	Catalytic activity, binding, molecular transducer activity, nucleic acid binding transcription factor activity, nutrient reservoir activity, receptor activity, structural molecule activity.	^{Zhang et al. (2015)}
	Rhodococcus sp. BAP-1	Fluoranthene	Catalytic activity, binding followed by transporter activity.	^{Wang et al. (2019)}
Biological processes	Synechocystis sp. PCC 6803	Butanol	Inorganic cation transmembrane transporter activity, hydrogen ion transmembrane transporter activity, monovalent inorganic cation transmembrane transporter activity, intracellular protein transport.	^{Tian et al. (2013)}
	Fillets treated by microwave thawing (MT)	Magnetic nanoparticles plus microwave	Biological regulation, cellular processes, regulation biological processes, response to stimuli and signaling, metabolic processes, developmental processes.	^{Cao et al. (2019)}
	Vibrio parahemolyticus ATCC 17802	Food preservative and low temperature	Choline transport, iron ion transport and homeostasis.	^{Zhong et al. (2018)}
	Rice (Oryza sativa) Embryogenesis	–	Proteins that participate in metabolism and respond to stimuli.	^{Zi et al. (2013)}
	The resurrection plant Xerophyta viscosa	Dehydration stress	Cellular processes, binding.	^{Abdalla and Rafudeen (2012)}
	Cotton Roots and Leaves	Salt stress	Metabolic processes, organic substance metabolic processes, primary metabolic processes, cellular metabolic processes.	^{Chen et al. (2016)}
	Aspergillus flavus	Water activity	Metabolic processes, cellular processes, single-organism processes.	^{Zhang et al. (2015)}
	Rhodococcus sp. BAP-1	Fluoranthene	Metabolic processes, cellular processes, single-organism processes.	^{Wang et al. (2019)}

Tab.4 Functional classification of the combination of differentially expressed proteins based on GO

Fig.9 High resolution Nano-SIMS images of cultured BDG-3 (^{Su et al., 2016}).

Specific technology	Microbial species	Features and conclusions	References
FISH	?	FISH not only enables the detection of culturable microorganisms but also yet-to-be cultured (so-called unculturable) organisms and can therefore help in understanding complex microbial communities. In this review, methodological aspects, as well as problems and pitfalls of FISH, are discussed in an examination of past, present and future applications.	^{Moter and Göbel (2000})
	Marine bacteria	FISH with horseradish peroxidase (HRP)-labeled oligonucleotide probes and tyramide signal amplification, also known as catalyzed reporter deposition (CARD), is currently not generally applicable to heterotrophic bacteria in marine samples. The enhanced fluorescence intensities and signal-to-background ratios make CARD-FISH superior to FISH with directly labeled oligonucleotides for the staining of bacteria with low rRNA content in the marine environment.”	(^{Pernthaler et al. (2002)}
	Bacterial populations in human feces	FISH with group-specific 16S rRNA-targeted oligonucleotide probes. The combination of the two Bacteroides-specific probes detected a mean of 5.4 × 10¹⁰ cells·g^?¹ (dry weight) in feces; the Clostridium coccoides-Eubacterium rectale group-specific probe detected a mean of 7.2 × 10¹⁰ cells·g^?¹ (dry weight) in feces. The Clostridium histolyicum, Clostridium lituseburense, and Streptococcus-Lactococcus group-specific probes detected only numbers ranging from 1 × 10⁷ to 7 × 10⁸ cells·g^?¹ (dry weight) in feces.	^{Franks et al. (1998})
Nano-SIMS	E. coli	E. coli exposed to food-grade TiO₂ showed some internalization of TiO₂ (7% of cells), as observed with high-resolution nano secondary ion mass spectrometry (nano-SIMS) chemical imaging.	^{Radziwill-Bienkowska et al. (2018)}
	Spleen cells	Nano-SIMS makes it possible to both capture images of and quantify molecules labeled with stable or radioactive isotopes within subcellular compartments.	^{Lechene et al.(2006)}
	Individual bacteria within eukaryotic host cells	In this study, with multi-isotope imaging mass spectrometry we directly captured images and measured nitrogen fixation by individual bacteria within eukaryotic host cells and demonstrated that fixed nitrogen is used for host metabolism.	^{Lechene et al. (2007)}
	E. coli	E. coli in water were treated with OD radicals, and D atom incorporation into cells was visualized using time-of-flight SIMS and nano-SIMS. The results show that D atoms from NTPJ reach the cytoplasm of E. coli in H₂O, indicating the usefulness of this OD-tracking method for the study of radical interactions within living cells.	^{Lee et al. (2014)}
	Paracoccus sp. strain HPD-2	Nano-SIMS results provided a direct evidence for the contribution of hematite to the formation of iron ions inside of HPD-2 cell, which resulted in the prominent generation of ROS (including EPFRs) that has been demonstrated to be able to affect cells.	^{Gan et al. (2018)}

Tab.5 Single cell analysis technology—FISH and Nano-SIMS

1	K O Abdalla, M S Rafudeen (2012). Analysis of the nuclear proteome of the resurrection plant Xerophyta viscosa in response to dehydration stress using iTRAQ with 2DLC and tandem mass spectrometry. Journal of Proteomics, 75(8): 2361–2374 https://doi.org/10.1016/j.jprot.2012.02.006 pmid: 22361341
2	M Abouseoud, A Yataghene, A Amrane, R Maachi (2010). Effect of pH and salinity on the emulsifying capacity and naphthalene solubility of a biosurfactant produced by Pseudomonas fluorescens. Journal of Hazardous Materials, 180(1-3): 131–136 https://doi.org/10.1016/j.jhazmat.2010.04.003 pmid: 20430520
3	M S Almén, K J V Nordström, R Fredriksson, H B Schiöth (2009). Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biology, 7(1): 1–14 https://doi.org/10.1186/1741-7007-7-50 pmid: 19678920
4	Z Aspridou, A Balomenos, P Tsakanikas, E Manolakos, K Koutsoumanis (2019). Heterogeneity of single cell inactivation: Assessment of the individual cell time to death and implications in population behavior. Food Microbiology, 80: 85–92 https://doi.org/10.1016/j.fm.2018.12.011 pmid: 30704600
5	A S Azevedo, C Almeida, B Pereira, P Madureira, J Wengel, N F Azevedo (2015). Detection and discrimination of biofilm populations using locked nucleic acid/2'-O-methyl-RNA fluorescence in situ hybridization (LNA/2'OMe-FISH). Biochemical Engineering Journal, 104: 64–73 https://doi.org/10.1016/j.bej.2015.04.024
6	V Bansal, K H Kim (2015). Review of PAH contamination in food products and their health hazards. Environment International, 84: 26–38 https://doi.org/10.1016/j.envint.2015.06.016 pmid: 26203892
7	J N Bateman, B Speer, L Feduik, R A Hartline (1986). Naphthalene association and uptake in Pseudomonas putida. Journal of Bacteriology, 166(1): 155–161 https://doi.org/10.1128/jb.166.1.155-161.1986 pmid: 3957866
8	L F Bautista, R Sanz, M C Molina, N Gonzalez, D Sanchez (2009). Effect of different non-ionic surfactants on the biodegradation of PAHs by diverse aerobic bacteria. International Biodeterioration & Biodegradation, 63(7): 913–922 https://doi.org/10.1016/j.ibiod.2009.06.013
9	E Borbás, B Sinkó, O Tsinman, K Tsinman, É Kiserdei, B Démuth, A Balogh, B Bodák, A Domokos, G Dargó, G T Balogh, Z K Nagy (2016). Investigation and Mathematical Description of the Real Driving Force of Passive Transport of Drug Molecules from Supersaturated Solutions. Molecular Pharmaceutics, 13(11): 3816–3826 https://doi.org/10.1021/acs.molpharmaceut.6b00613 pmid: 27611057
10	M Bouchez, D Blanchet, J P Vandecasteele (1997). An interfacial uptake mechanism for the degradation of pyrene by a Rhodococcus strain. Microbiology, 143(4): 1087–1093 https://doi.org/10.1099/00221287-143-4-1087
11	M Bouchez Naïtali, H Rakatozafy, R Marchal, J Y Leveau, J P Vandecasteele (1999). Diversity of bacterial strains degrading hexadecane in relation to the mode of substrate uptake. Journal of Applied Microbiology, 86(3): 421–428 https://doi.org/10.1046/j.1365-2672.1999.00678.x pmid: 10196747
12	M Bouchez-Naïtali, J P Vandecasteele (2008). Biosurfactants, an help in the biodegradation of hexadecane? The case of Rhodococcus and Pseudomonas strains. World Journal of Microbiology & Biotechnology, 24(9): 1901–1907 https://doi.org/10.1007/s11274-008-9691-9
13	D A P Bramwell, S Laha (2000). Effects of surfactant addition on the biomineralization and microbial toxicity of phenanthrene. Biodegradation, 11(4): 263–277
14	T Bugg, J M Foght, M A Pickard, M R Gray (2000). Uptake and active efflux of polycyclic aromatic hydrocarbons by Pseudomonas fluorescens LP6a. Applied and Environmental Microbiology, 66(12): 5387–5392 https://doi.org/10.1128/AEM.66.12.5387-5392.2000 pmid: 11097918
15	T P Call, M K Akhtar, F Baganz, C Grant (2016). Modulating the import of medium-chain alkanes in E. coli through tuned expression of FadL. Journal of Biological Engineering, 10(1): 5 https://doi.org/10.1186/s13036-016-0026-3 pmid: 27053948
16	M Cao, A Cao, Y Li, W Wang, Y Wang, L Cai (2019). Effects of magnetic nanoparticles plus microwave on the thawing of largemouth bass (Micropterus salmoides) fillets based on iTRAQ quantitative proteomics. Food Chemistry, 286: 506–514 https://doi.org/10.1016/j.foodchem.2019.02.051 pmid: 30827639
17	B Chen, J Ding (2012). Biosorption and biodegradation of phenanthrene and pyrene in sterilized and unsterilized soil slurry systems stimulated by Phanerochaete chrysosporium. Journal of Hazardous Materials, 229-230: 159–169 https://doi.org/10.1016/j.jhazmat.2012.05.090 pmid: 22709850
18	B Chen, Y Wang, D Hu (2010). Biosorption and biodegradation of polycyclic aromatic hydrocarbons in aqueous solutions by a consortium of white-rot fungi. Journal of Hazardous Materials, 179(1-3): 845–851 https://doi.org/10.1016/j.jhazmat.2010.03.082 pmid: 20381959
19	F Chen, Y Yuan, Q Li, Z He (2007). Proteomic analysis of rice plasma membrane reveals proteins involved in early defense response to bacterial blight. Proteomics, 7(9): 1529–1539 https://doi.org/10.1002/pmic.200500765 pmid: 17407182
20	T Chen, L Zhang, H Shang, S Liu, J Peng, W Gong, Y Shi, S Zhang, J Li, J Gong, Q Ge, A Liu, H Ma, X Zhao, Y Yuan (2016). iTRAQ-based quantitative proteomic analysis of cotton roots and leaves reveals pathways associated with salt stress. PLoS One, 11(2): 1–15 https://doi.org/10.1371/journal.pone.0148487 pmid: 26841024
21	P M Chong, T Lynch, S McCorrister, P Kibsey, M Miller, D Gravel, G R Westmacott, M R Mulvey, Canadian Nosocomial Infection Surveillance Program (CNISP) (2014). Proteomic analysis of a NAP1 Clostridium difficile clinical isolate resistant to metronidazole. PLoS One, 9(1): 1–10 https://doi.org/10.1371/journal.pone.0082622 pmid: 24400070
22	J Chunyun, L Peijun, L Xiaojun, T Peidong, L Wan, G Zongqiang (2011). Degradation of pyrene in soils by extracellular polymeric substances (EPS) extracted from liquid cultures. Process Biochemistry, 46(8): 1627–1631
23	R W Eaton (1994). Organization and evolution of naphthalene catabolic pathways: Sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. Journal of Bacteriology, 176(24): 7757–7762 https://doi.org/10.1128/jb.176.24.7757-7762.1994 pmid: 8002605
24	D A Edwards, Z Liu, R G Luthy (1992). Interactions between nonionic surfactant monomers, hydrophobic organic-compounds and soil. Water Science and Technology, 26(1-2): 147–158 https://doi.org/10.2166/wst.1992.0395
25	D A Edwards, Z B Liu, R G Luthy (1994). Experimental-data and modeling for surfactant micelles, hocs, and soil. Journal of Environmental Engineering, 120(1): 23–41 https://doi.org/10.1061/(ASCE)0733-9372(1994)120:1(23)
26	J Fan, C Chen, Q Yu, R H Brlansky, Z G Li, F G Gmitter Jr (2011). Comparative iTRAQ proteome and transcriptome analyses of sweet orange infected by “Candidatus Liberibacter asiaticus”. Physiologia Plantarum, 143(3): 235–245 https://doi.org/10.1111/j.1399-3054.2011.01502.x pmid: 21838733
27	K J Foster, S J Miklavcic (2016). Modeling Root Zone Effects on Preferred Pathways for the Passive Transport of Ions and Water in Plant Roots. Frontiers in plant science, 7: 914 https://doi.org/10.3389/fpls.2016.00914 pmid: 27446144
28	A H Franks, H J M Harmsen, G C Raangs, G J Jansen, F Schut, G W Welling (1998). Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Applied and Environmental Microbiology, 64(9): 3336–3345 pmid: 9726880
29	F Fukumori, H Hirayama, H Takami, A Inoue, K Horikoshi (1998). Isolation and transposon mutagenesis of a Pseudomonas putida KT2442 toluene-resistant variant: involvement of an efflux system in solvent resistance. Extremophiles, 2(4): 395–400 https://doi.org/10.1007/s007920050084 pmid: 9827328
30	S Furuno, K Päzolt, C Rabe, T R Neu, H Harms, L Y Wick (2010). Fungal mycelia allow chemotactic dispersal of polycyclic aromatic hydrocarbon-degrading bacteria in water-unsaturated systems. Environmental Microbiology, 12(6): 1391–1398 pmid: 19691501
31	S Gan, E V Lau, H K Ng (2009). Remediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Journal of Hazardous Materials, 172(2-3): 532–549 https://doi.org/10.1016/j.jhazmat.2009.07.118 pmid: 19700241
32	X Gan, Y Teng, L Zhao, W Ren, W Chen, J Hao, P Christie, Y Luo (2018). Influencing mechanisms of hematite on benzo(a)pyrene degradation by the PAH-degrading bacterium Paracoccus sp. Strain HPD-2: insight from benzo(a)pyrene bioaccessibility and bacteria activity. Journal of Hazardous Materials, 359: 348–355 https://doi.org/10.1016/j.jhazmat.2018.07.070 pmid: 30048949
33	D Gao, X Huang, Y J C R I B Tao (2015). A critical review of NanoSIMS in analysis of microbial metabolic activities at single-cell level. Critical Reviews in Biotechnology, 36(5): 1
34	F Gao, F Nan, J Feng, J Lv, Q Liu, S J R B Xie (2016). Identification and characterization of microRNAs in Eucheuma denticulatum by high-throughput sequencing and bioinformatics analysis. RNA biology, 13(3): 343–352
35	M García-Junco, E De Olmedo, J J Ortega-Calvo (2001). Bioavailability of solid and non-aqueous phase liquid (NAPL)-dissolved phenanthrene to the biosurfactant-producing bacterium Pseudomonas aeruginosa 19SJ. Environmental Microbiology, 3(9): 561–569 https://doi.org/10.1046/j.1462-2920.2001.00223.x pmid: 11683866
36	J Geddes, F Eudes, A Laroche, L B Selinger (2008). Differential expression of proteins in response to the interaction between the pathogen Fusarium graminearum and its host, Hordeum vulgare. Proteomics, 8(3): 545–554 https://doi.org/10.1002/pmic.200700115 pmid: 18232057
37	P Goswami, H D Singh (1991). Different modes of hydrocarbon uptake by two Pseudomonas species. Biotechnology and Bioengineering, 37(1): 1–11 https://doi.org/10.1002/bit.260370103 pmid: 18597301
38	P C Goswami, H D Singh, S D Bhagat, J N Baruah (1983). Mode of uptake of insoluble solid substrates by microorganisms. I: Sterol uptake by an arthrobacter species. Biotechnology and Bioengineering, 25(12): 2929–2943 https://doi.org/10.1002/bit.260251210 pmid: 18548628
39	D Gupta, M Mohammed, L P Mekala, S Chintalapati, V R Chintalapati (2019). iTRAQ-based quantitative proteomics reveals insights into metabolic and molecular responses of glucose-grown cells of Rubrivivax benzoatilyticus JA2. Journal of Proteomics, 194: 49–59 https://doi.org/10.1016/j.jprot.2018.12.027 pmid: 30597313
40	E M Hearn, D R Patel, B van den Berg (2008). Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation. Proceedings of the National Academy of Sciences of the United States of America, 105(25): 8601–8606 https://doi.org/10.1073/pnas.0801264105 pmid: 18559855
41	H Hong, D R Patel, L K Tamm, B van den Berg (2006). The outer membrane protein OmpW forms an eight-stranded -barrel with a hydrophobic channel. The Journal of biological chemistry, 281(11): 7568–7577 https://doi.org/10.1074/jbc.M512365200 pmid: 16414958
42	K Hori, Y Matsuzaki, Y Tanji, H Unno (2002). Effect of dispersing oil phase on the biodegradability of a solid alkane dissolved in non-biodegradable oil. Applied Microbiology and Biotechnology, 59(4-5): 574–579 https://doi.org/10.1007/s00253-002-1021-9 pmid: 12172628
43	F Hua, H Wang (2012). Uptake modes of octadecane by Pseudomonas sp. DG17 and synthesis of biosurfactant. Journal of Applied Microbiology, 112(1): 25–37 https://doi.org/10.1111/j.1365-2672.2011.05178.x pmid: 22008053
44	F Hua, H Q Wang (2014). Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms. Biotechnology, Biotechnological Equipment, 28(2): 165–175 https://doi.org/10.1080/13102818.2014.906136 pmid: 26740752
45	S Inakollu, H C Hung, G S Shreve (2004). Biosurfactant enhancement of microbial degradation of various structural classes of hydrocarbon in mixed waste systems. Environmental Engineering Science, 21(4): 463–469 https://doi.org/10.1089/1092875041358467
46	S Isken, J A De Bont (2000). The solvent efflux system of Pseudomonas putida S12 is not involved in antibiotic resistance. Applied Microbiology and Biotechnology, 54(5): 711–714 https://doi.org/10.1007/s002530000453 pmid: 11131400
47	C Y Jia, P J Li, X J Li, P D Tai, W Liu, Z Q Gong (2011). Degradation of pyrene in soils by extracellular polymeric substances (EPS) extracted from liquid cultures. Process Biochemistry, 46(8): 1627–1631 https://doi.org/10.1016/j.procbio.2011.05.005
48	A P Jonsson, T L Östberg (2011). The effects of carbon sources and micronutrients in whey and fermented whey on the kinetics of phenanthrene biodegradation in diesel contaminated soil. Journal of Hazardous Materials, 192(3): 1171–1177 https://doi.org/10.1016/j.jhazmat.2011.06.024 pmid: 21741168
49	H Y Kahng, A M Byrne, R H Olsen, J J Kukor (2000). Characterization and role of tbuX in utilization of toluene by Ralstonia pickettii PKO1. Journal of Bacteriology, 182(5): 1232–1242 https://doi.org/10.1128/JB.182.5.1232-1242.2000 pmid: 10671442
50	T Kanbayashi, H Miyafuji (2016). Microscopic characterization of tension wood cell walls of Japanese beech (Fagus crenata) treated with ionic liquids. Micron (Oxford, England: 1993), 88: 24–29 https://doi.org/10.1016/j.micron.2016.05.007 pmid: 27285953
51	Y Kasai, J Inoue, S Harayama (2001). The TOL plasmid pWW0 xylN gene product from Pseudomonas putida is involved in m-xylene uptake. Journal of Bacteriology, 183(22): 6662–6666 https://doi.org/10.1128/JB.183.22.6662-6666.2001 pmid: 11673437
52	L Ke, L Luo, P Wang, T Luan, N F Y Tam (2010). Effects of metals on biosorption and biodegradation of mixed polycyclic aromatic hydrocarbons by a freshwater green alga Selenastrum capricornutum. Bioresource Technology, 101(18): 6950–6972 https://doi.org/10.1016/j.biortech.2010.04.011 pmid: 20435470
53	C Kondethimmanahalli, H Liu, R R Ganta (2019). Proteome Analysis Revealed Changes in Protein Expression Patterns Caused by Mutations in Ehrlichia chaffeensis. Frontiers in Cellular and Infection Microbiology, 9: 58 https://doi.org/10.3389/fcimb.2019.00058 pmid: 30937288
54	S Kumar, T Verma, R Mukherjee, F Ariese, K Somasundaram, S Umapathy (2016). Raman and infra-red microspectroscopy: towards quantitative evaluation for clinical research by ratiometric analysis. Chemical Society Reviews, 45(7): 1879–1900 https://doi.org/10.1039/C5CS00540J pmid: 26497386
55	C C Lai, Y C Huang, Y H Wei, J S Chang (2009). Biosurfactant-enhanced removal of total petroleum hydrocarbons from contaminated soil. Journal of Hazardous Materials, 167(1/3): 609–614 https://doi.org/10.1016/j.jhazmat.2009.01.017 pmid: 19217712
56	C Lechene, F Hillion, G McMahon, D Benson, A M Kleinfeld, J P Kampf, D Distel, Y Luyten, J Bonventre, D Hentschel, K M Park, S Ito, M Schwartz, G Benichou, G Slodzian (2006). High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry. Journal of Biology, 5(6): 20 https://doi.org/10.1186/jbiol42 pmid: 17010211
57	C P Lechene, Y Luyten, G McMahon, D L Distel (2007). Quantitative imaging of nitrogen fixation by individual bacteria within animal cells. Science, 317(5844): 1563–1566 https://doi.org/10.1126/science.1145557 pmid: 17872448
58	C B Lee, Y H Na, T E Hong, E H Choi, H S Uhm, K Y Baik, G Kwon (2014). Evidence of radicals created by plasma in bacteria in water. Applied Physics Letters, 105(7): 073702 https://doi.org/10.1063/1.4893565
59	M Lee, M K Kim, I Singleton, M Goodfellow, S T Lee (2006). Enhanced biodegradation of diesel oil by a newly identified Rhodococcus baikonurensis EN3 in the presence of mycolic acid. Journal of Applied Microbiology, 100(2): 325–333 https://doi.org/10.1111/j.1365-2672.2005.02756.x pmid: 16430509
60	B W Lepore, M Indic, H Pham, E M Hearn, D R Patel, B van den Berg (2011). Ligand-gated diffusion across the bacterial outer membrane. Proceedings of the National Academy of Sciences of the United States of America, 108(25): 10121–10126 https://doi.org/10.1073/pnas.1018532108 pmid: 21593406
61	W Li, L Wen, C Li, R Chen, Z Ye, J Zhao, J Pan (2016). Contribution of the outer membrane protein OmpW in Escherichia coli to complement resistance from binding to factor H. Microbial Pathogenesis, 98: 57–62 https://doi.org/10.1016/j.micpath.2016.06.024 pmid: 27364548
62	Y Li, H Wang, F Hua, M Su, Y Zhao (2014). Trans-membrane transport of fluoranthene by Rhodococcus sp. BAP-1 and optimization of uptake process. Bioresource Technology, 155(155C): 213–219 https://doi.org/10.1016/j.biortech.2013.12.117 pmid: 24457306
63	J Ling, Y F Jiang, Y S Wang, J D Dong, Y Y Zhang, Y Z Zhang (2015). Responses of bacterial communities in seagrass sediments to polycyclic aromatic hydrocarbon-induced stress. Ecotoxicology (London, England), 24(7-8): 1517–1528 https://doi.org/10.1007/s10646-015-1493-x pmid: 26048240
64	S Liu, C Guo, Z Dang, X Liang (2017). Comparative proteomics reveal the mechanism of Tween80 enhanced phenanthrene biodegradation by Sphingomonas sp. GY2B. Ecotoxicology and Environmental Safety, 137: 256–264 https://doi.org/10.1016/j.ecoenv.2016.12.015 pmid: 27984820
65	Y F Lu, M Lu (2015). Remediation of PAH-contaminated soil by the combination of tall fescue, arbuscular mycorrhizal fungus and epigeic earthworms. Journal of Hazardous Materials, 285: 535–541 https://doi.org/10.1016/j.jhazmat.2014.07.021 pmid: 25534968
66	C T MacLeod, A J Daugulis (2005). Interfacial effects in a two-phase partitioning bioreactor: Degradation of polycyclic aromatic hydrocarbons (PAHs) by a hydrophobic Mycobacterium. Process Biochemistry, 40(5): 1799–1805 https://doi.org/10.1016/j.procbio.2004.06.042
67	A M Martorana, S Motta, P Sperandeo, P Mauri, A Polissi (2016). Bacterial Cell Wall Homeostasis: Methods and Protocols. Hong H J, ed. New York: Springer, 57–70
68	C Militon, R Jézéquel, F Gilbert, Y Corsellis, L Sylvi, C Cravo-Laureau, R Duran, P Cuny (2015). Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes. Environmental Science and Pollution Research International, 22(20): 15260–15272 https://doi.org/10.1007/s11356-015-4510-y pmid: 25997808
69	Y Miura, M Okazaki, S I Hamada, S I Murakawa, R Yugen (1977). Assimilation of liquid hydrocarbon by microorganisms. I. Mechanism of hydrocarbon uptake. Biotechnology and Bioengineering, 19(5): 701–714 https://doi.org/10.1002/bit.260190507 pmid: 322743
70	N Miyata, K Iwahori, J M Foght, M R Gray (2004). Saturable, energy-dependent uptake of phenanthrene in aqueous phase by Mycobacterium sp. strain RJGII-135. Applied and Environmental Microbiology, 70(1): 363–369 https://doi.org/10.1128/AEM.70.1.363-369.2004 pmid: 14711664
71	A Moter, U B Göbel (2000). Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. Journal of Microbiological Methods, 41(2): 85–112 https://doi.org/10.1016/S0167-7012(00)00152-4 pmid: 10991623
72	H Mulder, A M Breure, J G Van Andel, J T C Grotenhuis, W H Rulkens (1998). Influence of hydrodynamic conditions on naphthalene dissolution and subsequent biodegradation. Biotechnology and Bioengineering, 57(2): 145–154 https://doi.org/10.1002/(SICI)1097-0290(19980120)57:2<145::AID-BIT3>3.0.CO;2-N pmid: 10099189
73	R V V S N Murthy, J S Arora, B V S J I J Kumar O a R (2015). Comparative proteome analysis of Brucella abortus under different growth conditions by two dimensional electrophoresis. International Journal of Advanced Research, 3(2): 795–800
74	S H Nagaraj, H C Harsha, A Reverter, M L Colgrave, R Sharma, N Andronicos, P Hunt, M Menzies, M S Lees, N R Sekhar, A Pandey, A Ingham (2012). Proteomic analysis of the abomasal mucosal response following infection by the nematode, Haemonchus contortus, in genetically resistant and susceptible sheep. Journal of Proteomics, 75(7): 2141–2152 https://doi.org/10.1016/j.jprot.2012.01.016 pmid: 22285630
75	T Nakahara, L E Erickson, J R Gutierrez (1977). Characteristics of hydrocarbon uptake in cultures with two liquid phases. Biotechnology and Bioengineering, 19(1): 9–25 https://doi.org/10.1002/bit.260190103 pmid: 843616
76	V J Orphan, C H House, K U Hinrichs, K D McKeegan, E F DeLong (2001). Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science, 293(5529): 484–487 https://doi.org/10.1126/science.1061338 pmid: 11463914
77	X L Pan, J Liu, W J Song, D Y Zhang (2012). Biosorption of Cu(II) to extracellular polymeric substances (EPS) from Synechoeystis sp.: A fluorescence quenching study. Frontiers of Environmental Science & Engineering, 6(4): 493–497 https://doi.org/10.1007/s11783-012-0416-9
78	X T Peng, Z X Guo, C H House, S Chen, K W Ta (2016). SIMS and NanoSIMS analyses of well-preserved microfossils imply oxygen-producing photosynthesis in the Mesoproterozoic anoxic ocean. Chemical Geology, 441: 24–34 https://doi.org/10.1016/j.chemgeo.2016.08.011
79	A Pernthaler, J Pernthaler, R Amann (2002). Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Applied and Environmental Microbiology, 68(6): 3094–3101 https://doi.org/10.1128/AEM.68.6.3094-3101.2002 pmid: 12039771
80	F Polak, M Urik, P Matus (2019). Low molecular weight organic acids in soil environment. Chemické Listy, 113: 307–314
81	J M Radziwill-Bienkowska, P Talbot, J B J Kamphuis, V Robert, C Cartier, I Fourquaux, E Lentzen, J N Audinot, F Jamme, M Réfrégiers, J K Bardowski, P Langella, M Kowalczyk, E Houdeau, M Thomas, M Mercier-Bonin (2018). Toxicity of Food-Grade TiO2 to commensal intestinal and transient food-borne bacteria: New Insights using nano-SIMS and synchrotron UV fluorescence imaging. Frontiers in Microbiology, 9: 794 https://doi.org/10.3389/fmicb.2018.00794 pmid: 29740421
82	J L Ramos, E Duque, P Godoy, A Segura (1998). Efflux pumps involved in toluene tolerance in Pseudomonas putida DOT-T1E. Journal of Bacteriology, 180(13): 3323–3329 pmid: 9642183
83	M I Ramos-González, M Olson, A A Gatenby, G Mosqueda, M Manzanera, M J Campos, S Víchez, J L Ramos (2002). Cross-regulation between a novel two-component signal transduction system for catabolism of toluene in Pseudomonas mendocina and the TodST system from Pseudomonas putida. Journal of Bacteriology, 184(24): 7062–7067 https://doi.org/10.1128/JB.184.24.7062-7067.2002 pmid: 12446657
84	E Rosenberg (1993). Exploiting microbial growth on hydrocarbons:New markets. Trends in Biotechnology, 11(10): 419–424 https://doi.org/10.1016/0167-7799(93)90005-T
85	M Rosenberg, D Gutnick, E Rosenberg (1980). Adherence of bacteria to hydrocarbons: A simple method for measuring cell-surface hydrophobicity. FEMS Microbiology Letters, 9(1): 29–33 https://doi.org/10.1111/j.1574-6968.1980.tb05599.x
86	P L Ross, Y N Huang, J N Marchese, B Williamson, K Parker, S Hattan, N Khainovski, S Pillai, S Dey, S Daniels, S Purkayastha, P Juhasz, S Martin, M Bartlet-Jones, F He, A Jacobson, D J Pappin (2004). Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Molecular & cellular proteomics: MCP, 3(12): 1154–1169 https://doi.org/10.1074/mcp.M400129-MCP200 pmid: 15385600
87	S Schamfuss, T R Neu, J R van der Meer, R Tecon, H Harms, L Y Wick (2013). Impact of mycelia on the accessibility of fluorene to PAH-degrading bacteria. Environmental Science & Technology, 47(13): 6908–6915 https://doi.org/10.1021/es304378d pmid: 23452287
88	A Sharma, D Kachroo, R Kumar (2002). Time dependent influx and efflux of phenol by immobilized microbial consortium. Environmental Monitoring and Assessment, 76(2): 195–211 https://doi.org/10.1023/A:1015532030347 pmid: 12108592
89	J M Stapleton, J R Mihelcic, D R Lueking (1994). Adsorption and desorption-kinetics of pyrene onto a great lakes sediment. Journal of Great Lakes Research, 20(3): 561–568 https://doi.org/10.1016/S0380-1330(94)71172-2
90	W T Stringfellow, L Alvarez-Cohen (1999). Evaluating the relationship between the sorption of PAHs to bacterial biomass and biodegradation. Water Research, 33(11): 2535–2544 https://doi.org/10.1016/S0043-1354(98)00497-7
91	G Stucki, M Alexander (1987). Role of dissolution rate and solubility in biodegradation of aromatic compounds. Applied and Environmental Microbiology, 53(2): 292–297 pmid: 3566268
92	M Su, Y Li, H Wang, S Diao, M Wang (2016). Subcellular imaging and metabolic analysis of isotopically labeled carbon compounds in biological sample: An ion microprobe (Nano SIMS) study. Journal of Beijing Normal University (Nature and Science), 52(2): 223–227
93	B Suszek-Łopatka, B Maliszewska-Kordybach, A Klimkowicz-Pawlas, B Smreczak (2016). Influence of temperature on phenanthrene toxicity towards nitrifying bacteria in three soils with different properties. Environmental pollution, 216: 911–918 https://doi.org/10.1016/j.envpol.2016.06.066 pmid: 27394082
94	M N Taha, M B Krawinkel, G E Morlock (2015). High-performance thin-layer chromatography linked with (bio)assays and mass spectrometry: A suited method for discovery and quantification of bioactive components? Exemplarily shown for turmeric and milk thistle extracts. Journal of Chromatography. A, 1394: 137–147 https://doi.org/10.1016/j.chroma.2015.03.029 pmid: 25846263
95	M C Tejeda-Agredano, S Gallego, J Vila, M Grifoll, J J Ortega-Calvo, M Cantos (2013). Influence of the sunflower rhizosphere on the biodegradation of PAHs in soil. Soil Biology & Biochemistry, 57: 830–840 https://doi.org/10.1016/j.soilbio.2012.08.008
96	J M Thomas, J R Yordy, J A Amador, M Alexander (1986). Rates of dissolution and biodegradation of water-insoluble organic compounds. Applied and Environmental Microbiology, 52(2): 290–296 pmid: 3092736
97	W Tian, J Zhao, Y Zhou, K Qiao, X Jin, Q Liu (2017). Effects of root exudates on gel-beads/reeds combination remediation of high molecular weight polycyclic aromatic hydrocarbons. Ecotoxicology and Environmental Safety, 135: 158–164 https://doi.org/10.1016/j.ecoenv.2016.09.021 pmid: 27736675
98	X Tian, L Chen, J Wang, J Qiao, W Zhang (2013). Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol. Journal of Proteomics, 78: 326–345 https://doi.org/10.1016/j.jprot.2012.10.002 pmid: 23079071
99	J B van Beilen, G Eggink, H Enequist, R Bos, B Witholt (1992). DNA sequence determination and functional characterization of the OCT-plasmid-encoded alkJKL genes of Pseudomonas oleovorans. Molecular Microbiology, 6(21): 3121–3136 https://doi.org/10.1111/j.1365-2958.1992.tb01769.x pmid: 1453953
100	B van den Berg, P N Black, W M Clemons Jr, T A Rapoport (2004). Crystal structure of the long-chain fatty acid transporter FadL. Science, 304(5676): 1506–1509 https://doi.org/10.1126/science.1097524 pmid: 15178802
101	N Vedovato, D C Gadsby (2014). Route, mechanism, and implications of proton import during Na+/K+ exchange by native Na+/K+-ATPase pumps. The Journal of general physiology, 143(4): 449–464 https://doi.org/10.1085/jgp.201311148 pmid: 24688018
102	F Volkering, A M Breure, W H Rulkens (1997). Microbiological aspects of surfactant use for biological soil remediation. Biodegradation, 8(6): 401–417 https://doi.org/10.1023/A:1008291130109 pmid: 15765586
103	F Volkering, A M Breure, J G van Andel, W H Rulkens (1995). Influence of nonionic surfactants on bioavailability and biodegradation of polycyclic aromatic hydrocarbons. Applied and Environmental Microbiology, 61(5): 1699–1705 pmid: 16535016
104	H Wang, Y Yang, J Xu, D Kong, Y Li (2019). iTRAQ-based comparative proteomic analysis of differentially expressed proteins in Rhodococcus sp. BAP-1 induced by fluoranthene. Ecotoxicology and Environmental Safety, 169: 282–291 https://doi.org/10.1016/j.ecoenv.2018.11.022 pmid: 30458394
105	X D Wang, M Zhou, X R Meng, L Wang, D X Huang (2016). Effect of protein on PVDF ultrafiltration membrane fouling behavior under different pH conditions: interface adhesion force and XDLVO theory analysis. Frontiers of Environmental Science & Engineering, 10(4): 12 https://doi.org/10.1007/s11783-016-0855-9
106	Y Wang, L Fang, L Lin, T Luan, N F Y Tam (2014). Effects of low molecular-weight organic acids and dehydrogenase activity in rhizosphere sediments of mangrove plants on phytoremediation of polycyclic aromatic hydrocarbons. Chemosphere, 99: 152–159 https://doi.org/10.1016/j.chemosphere.2013.10.054 pmid: 24287262
107	Y Wang, M Rawlings, D T Gibson, D Labbé, H Bergeron, R Brousseau, P C K Lau (1995). Identification of a membrane protein and a truncated LysR-type regulator associated with the toluene degradation pathway in Pseudomonas putida F1. Molecular & general genetics: MGG, 246(5): 570–579 https://doi.org/10.1007/BF00298963 pmid: 7535376
108	C C West, J H Harwell (1992). Surfactants and subsurface remediation. Environmental Science & Technology, 26(12): 2324–2330 https://doi.org/10.1021/es00036a002
109	S Westgate, G Bell, P J Halling (1995). Kinetics of uptake of organic liquid substrates by microbial cells: A method to distinguish interfacial contact and mass-transfer mechanisms. Biotechnology Letters, 17(10): 1013–1018 https://doi.org/10.1007/BF00143092
110	L Wu, X Lin, F Wang, D Ye, X Xiao, S Wang, X Peng (2006). OmpW and OmpV are required for NaCl regulation in Photobacterium damsela. Journal of Proteome Research, 5(9): 2250–2257 https://doi.org/10.1021/pr060046c pmid: 16944937
111	L Xiao, X Qu, D Zhu (2007). Biosorption of nonpolar hydrophobic organic compounds to Escherichia coli facilitated by metal and proton surface binding. Environmental Science & Technology, 41(8): 2750–2755 https://doi.org/10.1021/es062343o pmid: 17533834
112	N Xiao, R Liu, C X Jin, Y Y Dai (2015). Efficiency of five ornamental plant species in the phytoremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Ecological Engineering, 75: 384–391 https://doi.org/10.1016/j.ecoleng.2014.12.008
113	Y Xu, G D Sun, J H Jin, Y Liu, M Luo, Z P Zhong, Z P Liu (2014). Successful bioremediation of an aged and heavily contaminated soil using a microbial/plant combination strategy. Journal of Hazardous Materials, 264: 430–438 https://doi.org/10.1016/j.jhazmat.2013.10.071 pmid: 24321347
114	X M Yin, X Liang, R Zhang, L Yu, G H Xu, Q S Zhou, X H Zhan (2015). Impact of phenanthrene exposure on activities of nitrate reductase, phosphoenolpyruvate carboxylase, vacuolar H+-pyrophosphatase and plasma membrane H+-ATPase in roots of soybean, wheat and carrot. Environmental and Experimental Botany, 113: 59–66 https://doi.org/10.1016/j.envexpbot.2015.02.001
115	S H Yun, C W Choi, S Y Lee, Y G Lee, J Kwon, S H Leem, Y H Chung, H Y Kahng, S J Kim, K K Kwon, S I Kim (2014). Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1. PLoS One, 9(3): e90812 https://doi.org/10.1371/journal.pone.0090812 pmid: 24608660
116	F Zhang, H Zhong, X Han, Z Guo, W Yang, Y Liu, K Yang, Z Zhuang, S Wang (2015). Proteomic profile of Aspergillus flavus in response to water activity. Fungal Biology, 119(2-3): 114–124 https://doi.org/10.1016/j.funbio.2014.11.005 pmid: 25749363
117	H Zhang, X Jiang, W Xiao, L Lu (2014). Proteomic strategy for the analysis of the polychlorobiphenyl-degrading cyanobacterium Anabaena PD-1 exposed to Aroclor 1254. PLoS One, 9(3): 1–10 https://doi.org/10.1371/journal.pone.0091162 pmid: 24618583
118	Y P Zhang, F Wang, X S Zhu, J Zeng, Q G Zhao, X Jiang (2015). Extracellular polymeric substances govern the development of biofilm and mass transfer of polycyclic aromatic hydrocarbons for improved biodegradation. Bioresource Technology, 193: 274–280 https://doi.org/10.1016/j.biortech.2015.06.110 pmid: 26141288
119	Y L Zhao, Y H Zhou, J Q Chen, Q Y Huang, Q Han, B Liu, G D Cheng, Y H Li (2015). Quantitative proteomic analysis of sub-MIC erythromycin inhibiting biofilm formation of S. suis in vitro. Journal of Proteomics, 116: 1–14 https://doi.org/10.1016/j.jprot.2014.12.019 pmid: 25579403
120	Q P Zhong, J Tian, J Wang, X Fang, Z L Liao (2018). iTRAQ-based proteomic analysis of the viable but nonculturable state of Vibrio parahaemolyticus ATCC 17802 induced by food preservative and low temperature. Food Control, 85: 369–375 https://doi.org/10.1016/j.foodcont.2017.10.011
121	J Zhou, K Wang, S Xu, J Wu, P Liu, G Du, J Li, J Chen (2015). Identification of membrane proteins associated with phenylpropanoid tolerance and transport in Escherichia coli BL21. Journal of Proteomics, 113: 15–28 https://doi.org/10.1016/j.jprot.2014.09.012 pmid: 25277045
122	J Zi, J Zhang, Q Wang, B Zhou, J Zhong, C Zhang, X Qiu, B Wen, S Zhang, X Fu, L Lin, S Liu (2013). Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis. PLoS One, 8(9): e74229 https://doi.org/10.1371/journal.pone.0074229 pmid: 24058531

No related articles found!

Viewed

Full text

Abstract

Cited

Shared

Discussed