Functional and genetic characterization of hydrocarbon biodegrader and exopolymer-producing clones from a petroleum reservoir metagenomic library

References

• Oliveira VM, Sette LD, Simioni KCM, Santos Neto EV. Bacterial diversity characterization in petroleum samples from Brazilian reservoirs. Braz J Microbiol. 2008;39:445–452.
   PubMed Web of Science ®Google Scholar
• Jing G, Xia LP, Wang L-Y, Liu J-F, Gu J-D, Mu B-Z. Diversity and distribution of sulfate-reducing bacteria in four petroleum reservoirs detected by using 16S rRNA and dsrAB genes. Int Biodeterior Biodegrad. 2013;76:58–66.
   Web of Science ®Google Scholar
• Hui L, Yang SH, Mu BZ, Rong ZF, Zhang J. Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oil field. FEMS Microbiol Ecol. 2007;60:74–84.
   PubMed Web of Science ®Google Scholar
• Cunha CD, Rosado AS, Sebastián GV, Seldin L, Von der Weid I. Oil biodegradation by Bacillus strains isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil. Appl Microbiol Biotechnol. 2006;73:949–959.
   PubMed Web of Science ®Google Scholar
• Churchill SA, Harper JP, Churchill PF. Isolation and characterization of a Mycobacterium species capable of degrading three- and four-ring aromatic and aliphatic hydrocarbons. Appl Microbiol Biotechnol. 1999;65:549–552.
   Web of Science ®Google Scholar
• Calvo C, Manzanera M, Silva-Castro GA, Uad I, González-López J. Review: application of bioemulsifiers in soil oil bioremediation processes. Future prospects Sci Total Environ. 2009;407:3634–3640.
   PubMed Web of Science ®Google Scholar
• Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM. Microbial biofilms. Annu Rev Microbiol. 1995;49:711–745.
   PubMed Web of Science ®Google Scholar
• Flemming H, Wingender J. The biofilm matrix. Nature. 2010;8:623–633.
   Web of Science ®Google Scholar
• Shreve GS, Inguva S, Gunnam S. Rhamnolipid biosurfactant enhancement of hexadecane biodegradation by Pseudomonas aeruginosa. Mol Mar Biol Biotechnol. 1995;4:331–337.
   PubMedGoogle Scholar
• Mulligan CN. Recent advances in the environmental applications of biosurfactants. Cur Opin Coll Inter Sci. 2009;14:372–378.
   Web of Science ®Google Scholar
• Ron EZ, Rosenberg E. Minireview: natural roles of biosurfactants. Environ Microbiol. 2001;3:229–236.
   PubMed Web of Science ®Google Scholar
• Sen R. Biotechnology in petroleum recovery: the microbial EOR progress in energy and combustion. Science. 2008;34:714–724.
   Web of Science ®Google Scholar
• Banat IB, Franzetti A, Gandolfi I, et al. Microbial biosurfactants production, applications and future potential. Appl Microbiol Biotechnol. 2010;87:427–444.
   PubMed Web of Science ®Google Scholar
• Silva RCFS, Almeida DG, Rufino RD, Luna JM, Santos VA, Sarubbo LA. Applications of biosurfactants in the petroleum industry and the remediation of oil spills. Int J Mol Sci. 2014;15:12523–12542.
   PubMed Web of Science ®Google Scholar
• Vasconcellos SP, Angolini CFF, Sierra-García IN, et al. Screening for hydrocarbon biodegraders in a metagenomic clone library derived from Brazilian petroleum reservoirs. Org Geochem. 2010;41:675–681.
   Web of Science ®Google Scholar
• Bodour AA, Drees KP, Maier RM. Distribution of biosurfactant-producing bacteria in undisturbed and contaminated arid Southwestern soils. Appl Environ Microbiol. 2003;69:3280–3287.
   PubMed Web of Science ®Google Scholar
• Bushnell LD, Haas HF. The utilization of certain hydrocarbons by microorganisms. J Bacteriol. 1941;415:653–673.
   Google Scholar
• Widdel F, Boetius A, Rabus R. Anaerobic biodegradation of hydrocarbons including methane. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors. The prokaryotes. New York: Springer; 2006. p. 1028–1049.
   Google Scholar
• Klock J-H, Wieland A, Seifert R, Michaelis W. Extracellular polymeric substances (EPS) from cyanobacterial mats: characterisation and isolation method optimisation. Mar Biol. 2007;152:1077–1085.
   Web of Science ®Google Scholar
• Vasconcellos SP, Wieland A, Klock J, et al. Potential for hydrocarbon biodegradation and production of extracellular polymeric substances (EPS) of aerobic bacteria isolated from a Brazilian petroleum reservoir. W J Microbiol Biotechnol. 2011;27:1513–1518.
   PubMed Web of Science ®Google Scholar
• Desai JD, Banat IM. Microbial production of surfactants and their commercial potential. Microbiol Molec Biol Rev. 1997;61:47–64.
   PubMed Web of Science ®Google Scholar
• Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007;17:377–386.
   PubMed Web of Science ®Google Scholar
• Meyer F, Paarmann D, D’Souza M, et al. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:611–386.
   Web of Science ®Google Scholar
• Tatusov RL, Natale DA, Garkavtsev IV, et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acid Res. 2001;29:22–28.
   PubMed Web of Science ®Google Scholar
• Sierra-García IN, Alvarez JC, Vasconcellos SP, Souza AP, Santos Neto EV, Oliveira VM. New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. Plos One. 2014;9:1–13.
   Web of Science ®Google Scholar
• Dellagnezze BM. Bioprospection of genes related to the synthesis of biosurfactants from anaerobic microbial communities of petroleum reservoirs [Master thesis]. Universidade Estadual de Campinas; 2010.
   Google Scholar
• Eboigbodin KE, Biggs CA. Characterization of the extracellular polymeric substances produced by Escherichia coli using infrared spectroscopic, proteomic, and aggregation studies. Biomacromol. 2008;9:686–695.
   PubMed Web of Science ®Google Scholar
• Vaz DA, Gudina EJ, Alameda EJ, Teixeira JÁ, Rodrigues LR. Performance of a biosurfactant produced by a Bacillus subtilis strain isolated from crude oil samples as compared to commercial chemical surfactants. Colloids Surf B Biointerfaces. 2012;89:167–174.
   PubMed Web of Science ®Google Scholar
• Bento FM, Camargo FAO, Okeke BC, Frankenberger WT. Comparative bioremediation of soils contaminated with diesel oil by natural attenuation, biostimulation and bioaugmentation. Bior Technol. 2005;96:1049–1055.
   PubMed Web of Science ®Google Scholar
• Bacosa H, Suto K, Inoue C. Preferential degradation of aromatic hydrocarbons in kerosene by a microbial consortium. Int Biodeterior Biodegradation. 2010;64:702–710.
   Web of Science ®Google Scholar
• Van Hamme JD, Singh A, Ward OP. Physiological aspects. Part 1 in a series of papers devoted to surfactants in microbiology and biotechnology. Biotechnol Adv. 2006;24:604–620.
   PubMed Web of Science ®Google Scholar
• Falatko DM, Novak JT. Effects of biologically produced surfactants on the mobility and biodegradation of petroleum hydrocarbons. Water Environ Res. 1992;64:163–169.
   Web of Science ®Google Scholar
• Suenaga H, Koyama Y, Miyakoshi M, et al. Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J. 2009;3:1335–1348.
   PubMed Web of Science ®Google Scholar
• Dos Santos HF, Cury JC, do Carmo FL, et al. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. Plos One. 2011;6:1–8.
   Web of Science ®Google Scholar
• Militon C, Boucher D, Vachelard C, et al. Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil. FEMS Microbiol Ecol. 2010;74:669–681.
   PubMed Web of Science ®Google Scholar
• Kloer DP, Hagel C, Heider J, Schulz GE. Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum. Structure. 2006;14:1377–1388.
   PubMed Web of Science ®Google Scholar
• Wöhlbrand L, Wilkes H, Halder T, Rabus R. Anaerobic degradation of p-ethylphenol by ‘Aromatoleum aromaticum’ strain EbN1: pathway, regulation, and involved proteins. J Bacteriol. 2008;190:5699–5709.
   PubMed Web of Science ®Google Scholar
• Płociniczak MP, Płaza GA, Piotrowska-seget Z, Cameotra SS. Environmental applications of biosurfactants: recent advances. Int J Mol Sci. 2011;12:633–654.
   PubMed Web of Science ®Google Scholar
• Mnif S, Chamkha M, Labat M, Sayadi S. Simultaneous hydrocarbon biodegradation and biosurfactant production by oilfield-selected bacteria. J Appl Microbiol. 2011;111:525–536.
   PubMed Web of Science ®Google Scholar
• Perfumo A, Smyth TJP, Marchant R, Banat IM. Production and roles of biosurfactants and bioemulsifiers in accessing hydrophobic substrates. In: Timmis KN, McGenity TJ, van der Meer JR, de Lorenzo V, editor. Handbook of hydrocarbon and lipid microbiology. Berlin: Springer-Verlag; 2010. p. 1501–1512.
   Google Scholar
• Déziel E, Lépine F, Dennie D, Boismenu D, Mamer OA, Villemur R. Liquid chromatography/mass spectrometry analysis of mixtures of rhamnolipids produced by Pseudomonas aeruginosa strain 57RP grown on mannitol or naphthalene. Biochim Biophys Acta. 1999;1440:244–252.
   PubMed Web of Science ®Google Scholar
• Fraser GM, Hughes C. Swarming motility. Cur Opin Microbiol. 1999;2:630–635.
   PubMed Web of Science ®Google Scholar
• Chrzanowski L, Lawniczak L, Czaczyk K. Why do microorganisms produce rhamnolipids? W J Microbiol Biotechnol. 2012;28:401–419.
   PubMed Web of Science ®Google Scholar
• Van Hamme JD, Singh A, Ward OP. Recent advances in petroleum microbiology. Microbiol Mol Biol Rev. 2003;67:503–549.
   PubMed Web of Science ®Google Scholar
• Nie Y, Tang Y, Li Y, Chi C, Cai M, Wu X. The genome sequence of Polymorphum gilvum SL003B- 26A1 T reveals its genetic basis for crude oil degradation and adaptation to the saline soil. Plos One. 2012;7:1–6.
   Web of Science ®Google Scholar
• Nie M, Yin X, Ren C, Wang Y, Xu F, Shen Q. Novel rhamnolipid biosurfactants produced by a polycyclic aromatic hydrocarbon-degrading bacterium Pseudomonas aeruginosa strain NY3. Biotechnol Adv. 2010;28:635–643.
   PubMed Web of Science ®Google Scholar
• Fetzner S. Enzymes involved in the aerobic bacterial degradation of N-heteroaromatic compounds: molybdenum hydroxylases and ring-opening 2,4-dioxygenases. Naturwissenschaften. 2000;87:59–69.
   PubMed Web of Science ®Google Scholar
• Díaz E, Ferrández AF, Prieto MAA, García JL. Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev. 2001;65:523–569.
   PubMed Web of Science ®Google Scholar
• Breinig S, Schiltz E, Fuchs G. Genes involved in anaerobic metabolism of phenol in the bacterium Thauera aromatica. J Bacteriol. 2000;182:5849–5863.
   PubMed Web of Science ®Google Scholar
• DiDonato Jr RJ, Young ND, Butler JE, et al. Genome sequence of the deltaproteobacterial strain naphS2 and analysis of differential gene expression during anaerobic growth on naphthalene. Plos One. 2010;5:e14072–11.
   PubMed Web of Science ®Google Scholar
• Kube M, Beck A, Meyerdierks A, Amann R, Reinhardt R, Rabus R. A catabolic gene cluster for anaerobic benzoate degradation in methanotrophic microbial Black Sea mats. Syst Appl Microbiol. 2005;28:287–294.
   PubMed Web of Science ®Google Scholar