Genomic and transcriptomic characterization revealed key adaptive mechanisms of Marinobacter hydrocarbonoclasticus NI9 for proliferation and degradation of jet fuel

International Biodeterioration & Biodegradation - Tập 175 - Trang 105502 - 2022
Thusitha S. Gunasekera1, Loryn L. Bowen2, Osman Radwan2, Richard C. Striebich2, Oscar N. Ruiz1
1Fuels and Energy Branch, Aerospace Systems Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, 45433, USA
2University of Dayton Research Institute, University of Dayton, Dayton, OH, 45469, USA

Tài liệu tham khảo

Aktas, 2013, Effects of oxygen on biodegradation of fuels in a corroding environment, Int. Biodeterior. Biodegrad., 81, 114, 10.1016/j.ibiod.2012.05.006 Brezna, 2006, Molecular characterization of cytochrome P450 genes in the polycyclic aromatic hydrocarbon degrading Mycobacterium vanbaalenii PYR-1, Appl. Microbiol. Biotechnol., 71, 522, 10.1007/s00253-005-0190-8 Brown, 2010, Community dynamics and phylogenetics of bacteria fouling Jet A and JP-8 aviation fuel, Int. Biodeterior. Biodegrad., 64, 253, 10.1016/j.ibiod.2010.01.008 Branchu, 2017, Impact of temperature on Marinobacter hydrocarbonoclasticus SP17 morphology and biofilm structure during growth on alkanes, Microbiology (Read.), 163, 669, 10.1099/mic.0.000466 Camacho, 2009, BLAST+: architecture and applications, BMC Bioinf., 10, 421, 10.1186/1471-2105-10-421 Dewangan, 2018, Adhesion of M. Hydrocarbonoclasticus to surfactant-decorated dodecane droplets, Langmuir: ACS J. Surf. Colloids, 34, 14012, 10.1021/acs.langmuir.8b02071 Dong, 2012, Characterization of two long-chain fatty acid CoA ligases in the Gram-positive bacterium Geobacillus thermodenitrificans NG80-2, Microbiol. Res., 167, 602, 10.1016/j.micres.2012.05.001 Dobin, 2015, Mapping RNA-seq reads with STAR, Curr. Protoc. Bioinform., 51, 11.14.1, 10.1002/0471250953.bi1114s51 Dunlop, 2011, Engineering microbial biofuel tolerance and export using efflux pumps, Mol. Syst. Biol., 7, 487, 10.1038/msb.2011.21 Duran, 2016, Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment, FEMS Microbiol. Rev., 40, 814, 10.1093/femsre/fuw031 Ennouri, 2017, The extracellular matrix of the oleolytic biofilms of Marinobacter hydrocarbonoclasticus comprises cytoplasmic proteins and T2SS effectors that promote growth on hydrocarbons and lipids, Environ. Microbiol., 19, 159, 10.1111/1462-2920.13547 Fang, 2013, Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution, BMC Genom., 14, 450, 10.1186/1471-2164-14-450 Fillet, 2012, Transcriptional control of the main aromatic hydrocarbon efflux pump in Pseudomonas, Environ. Microbiol. Rep., 4, 158, 10.1111/j.1758-2229.2011.00255.x Galperin, 2015, Expanded microbial genome coverage and improved protein family annotation in the COG database, Nucleic Acids Res., 43, D261, 10.1093/nar/gku1223 Gauthier, 1992, M. hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium, Int. J. Syst. Bacteriol., 42, 568, 10.1099/00207713-42-4-568 Grady, 2017, A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes, BMC Genom., 18, 334, 10.1186/s12864-017-3708-4 Gunasekera, 2022, Leveraging bioinformatics to elucidate the genetic and physiological adaptation of Pseudomonas aeruginosa to hydrocarbon-rich jet fuel, 249 Gunasekera, 2017, Transcriptomic analyses elucidate adaptive differences of closely related strains of Pseudomonas aeruginosa in fuel, Appl. Environ. Microbiol., 83, 10.1128/AEM.03249-16 Gunasekera, 2013, Transcriptional profiling suggests that multiple metabolic adaptations are required for effective proliferation of Pseudomonas aeruginosa in jet fuel, Environ. Sci. Technol., 47, 13449, 10.1021/es403163k Gunasekera, 2018, Draft genome sequence of achromobacter spanius strain 6, a soil bacterium isolated from a hydrocarbon-degrading microcosm, Microbiol. Resourc. Announ., 7, 10.1128/MRA.01124-18 Heider, 1998, Anaerobic bacterial metabolism of hydrocarbons, FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Rev., 22, 459 Kanehisa, 2000, KEGG: kyoto encyclopedia of genes and genomes, Nucleic Acids Res., 28, 27, 10.1093/nar/28.1.27 Kostka, 2011, Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater horizon oil spill, Appl. Environ. Microbiol., 77, 7962, 10.1128/AEM.05402-11 Krohn, 2021, Deep (Meta) genomics and (Meta)transcriptome analyses of fungal and bacteria consortia from aircraft tanks and kerosene identify key genes in fuel and tank corrosion, Front. Microbiol., 12, 10.3389/fmicb.2021.722259 Lee, 2014, Issues for storing plant-based alternative fuels in marine environments, Bioelectrochemistry, 97, 145, 10.1016/j.bioelechem.2013.12.003 Li, 1995, A toluene-tolerant mutant of Pseudomonas aeruginosa lacking the outer membrane protein F, Biosci. Biotechnol. Biochem., 59, 2358, 10.1271/bbb.59.2358 Li, 1998, Role of the multidrug efflux systems of Pseudomonas aeruginosa in organic solvent tolerance, J. Bacteriol., 180, 2987, 10.1128/JB.180.11.2987-2991.1998 Li, 1999, Organic solvent-tolerant mutants of Pseudomonas aeruginosa display multiple antibiotic resistance, Can. J. Microbiol., 45, 18, 10.1139/w98-127 Martin, 1991, The case for iron, Limnol. Oceanogr., 36, 1793, 10.4319/lo.1991.36.8.1793 McCarthy, 2012, Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation, Nucleic Acids Res., 40, 4288, 10.1093/nar/gks042 Mounier, 2014, The marine bacterium M.hydrocarbonoclasticus SP17 degrades a wide range of lipids and hydrocarbons through the formation of oleolytic biofilms with distinct gene expression profiles, FEMS Microbiol. Ecol., 90, 816, 10.1111/1574-6941.12439 Mounier, 2018, AupA and AupB are outer and inner membrane proteins involved in alkane uptake in M. Hydrocarbonoclasticus SP17, mBio, 9, 10.1128/mBio.00520-18 Neethu, 2019, Oil-spill triggered shift in indigenous microbial structure and functional dynamics in different marine environmental matrices, Sci. Rep., 9, 1354, 10.1038/s41598-018-37903-x Neher, 2009, Pseudomonas fluorescens ompW: plasmid localization and requirement for naphthalene uptake, Can. J. Microbiol., 55, 553, 10.1139/W09-002 Paliy, 2007, Growth of E. coli BL21 in minimal media with different gluconeogenic carbon sources and salt contents, Appl. Microbiol. Biotechnol., 73, 1169, 10.1007/s00253-006-0554-8 Passman, 2001, Oxygenated gasoline biodeterioration and its control in laboratory microcosm, Int. Biodeterior. Biodegrad., 47, 95, 10.1016/S0964-8305(00)00080-9 Ramos, 2002, Mechanisms of solvent tolerance in Gram negative bacteria, Annu. Rev. Microbiol., 56, 743, 10.1146/annurev.micro.56.012302.161038 Ramos, 2015, Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida, FEMS Microbiol. Rev., 39, 555, 10.1093/femsre/fuv006 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Rojo, 2009, Degradation of alkanes by bacteria, Environ. Microbiol., 11, 2477, 10.1111/j.1462-2920.2009.01948.x Ruiz, 2016, Effect of conventional and alternative fuels on a marine bacterial community and the significance to bioremediation, Energy Fuel., 30, 434, 10.1021/acs.energyfuels.5b02439 Ruiz, 2021, Metagenomic characterization reveals complex association of soil hydrocarbon-degrading bacteria, Int. Biodeterior. Biodegrad., 157, 10.1016/j.ibiod.2020.105161 Sasaki, 2005, Purification of cytochrome P450 and ferredoxin, involved in bisphenol A degradation, from Sphingomonas sp. strain AO1, Appl. Environ. Microbiol., 71, 8024, 10.1128/AEM.71.12.8024-8030.2005 Sennhauser, 2009, Crystal structure of the multidrug exporter MexB from Pseudomonas aeruginosa, J. Mol. Biol., 29389, 134, 10.1016/j.jmb.2009.04.001 Silby, 2011, Pseudomonas genomes: diverse and adaptable, FEMS Microbiol Rev., 35, 652, 10.1111/j.1574-6976.2011.00269.x Smith, 2013, Alkane hydroxylase gene (alkB) phylotype composition and diversity in northern Gulf of Mexico bacterioplankton, Front. Microbiol., 4, 370e378, 10.3389/fmicb.2013.00370 Stamper, 2012, Depletion of lubricity improvers from hydrotreated renewable and ultralow-sulfur petroleum diesels by marine microbiota, Energy Fuel., 26, 6854, 10.1021/ef301158n Stamps, 2020, In situ linkage of fungal and bacterial proliferation to microbiologically influenced corrosion in B20 biodiesel storage tanks, Front. Microbiol., 11, 167, 10.3389/fmicb.2020.00167 Striebich, 2014, Characterization of the F-76 diesel and Jet A aviation fuel hydrocarbon degradation profiles of Pseudomonas aeruginosa and Marinobacter hydrocarbonoclasticus, Int. Biodeterior. Biodegrad., 93, 33, 10.1016/j.ibiod.2014.04.024 Suflita, 2012, Molecular tools to track bacteria responsible for fuel deterioration and microbiologically influenced corrosion, Biofouling, 28, 1003, 10.1080/08927014.2012.723695 Teh, 1973, Utilization of n-alkanes by Cladosporium resinae, Appl. Microbiol., 25, 454, 10.1128/am.25.3.454-457.1973 Toshchakov, 2017, The genome analysis of Oleiphilus messinensis ME102 (DSM 13489T) reveals backgrounds of its obligate alkane-devouring marine lifestyle, Mar. Genom., 36, 41, 10.1016/j.margen.2017.07.005 Touw, 2010, The crystal structure of OprG from Pseudomonas aeruginosa, a potential channel for transport of hydrophobic molecules across the outer membrane, PLoS One, 5, 10.1371/journal.pone.0015016 Vila, 2010, Microbial community structure of a heavy fuel oil-degrading marine consortium: linking microbial dynamics with polycyclic aromatic hydrocarbon utilization, FEMS Microbiol. Ecol., 73, 349 Valot, 2015, What it takes to Be a Pseudomonas aeruginosa? The core genome of the opportunistic pathogen updated, PLoS One, 10, 10.1371/journal.pone.0126468 Xue, 2015, Marine oil-degrading microorganisms and biodegradation process of petroleum hydrocarbon in marine environments: a review, Curr. Microbiol., 71, 220, 10.1007/s00284-015-0825-7 Yakimov, 2007, Obligate oil-degrading marine bacteria, Curr. Opin. Biotechnol., 18, 257, 10.1016/j.copbio.2007.04.006 Zenati, 2018, A non-toxic microbial surfactant from M.hydrocarbonoclasticus SdK644 for crude oil solubilization enhancement, Ecotoxicol. Environ. Saf., 154, 100, 10.1016/j.ecoenv.2018.02.032