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Hydrocarbon-Degrading Microbes as Sources of New Biocatalysts

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Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes

Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

Abstract

Petroleum hydrocarbons, including those discharged to the marine environment, are metabolized through different catabolic pathways by a number of microorganisms. Each hydrocarbon-degrading microorganism produces interesting enzymes for degrading alkanes and/or aromatic compounds that allow them to be used as sources of carbon and energy, and thus, these microbes occupy hydrocarbon-rich ecological niches. Their diversity and hydrocarbon-degrading metabolic abilities have been extensively examined in multiple environmental and phylogenetic contexts. Genes encoding enzymes involved in degradation, such as alkane hydroxylases and other monooxygenases, P450 cytochromes, rubredoxin reductases, and ferredoxin reductases, have been examined by genome analysis, and a number of them have been successfully cloned, expressed, purified, and their activities confirmed. However, in these microorganisms, the accumulated information regarding other types of enzymes, particularly those most used at industrial level, is limited. Here, we compile information about the accumulated enzymatic knowledge of obligate marine hydrocarbonoclastic bacteria (OMHCB), key players in bioremediation of hydrocarbons in contaminated marine ecosystems. We focused on bacteria of the genera Cycloclasticus, Alcanivorax, Oleispira, Thalassolituus, and Oleiphilus. Enzymatic data of these representative OMHCB members are restricted to enzymes of the class hydroxylases, cytochrome P450, dioxygenases, synthases, dehalogenases, ligases, and mostly for hydrolases with a typical α/β hydrolase fold. Despite the limited information reported, the available data suggest that these organisms may be important sources of industrial biocatalysts, the analysis of which may deserve deeper investigation. Comparative information is provided regarding the occurrence of key biotechnologically relevant ester-hydrolases in the genomes of OMHCB and suggesting which of the OMHCB may potentially have higher promise as a source of biocatalysts. We also discuss how the properties of these enzymes could be biologicallly important for these bacteria, as some of them can convert a broad range of compounds.

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References

  • Alcaide M, Tornés J, Stogios PJ, Xu X, Gertler C, Di Leo R, Bargiela R, Lafraya A, Guazzaroni ME, López-Cortés N, Chernikova TN, Golyshina OV, Nechitaylo TY, Plumeier I, Pieper DH, Yakimov MM, Savchenko A, Golyshin PN, Ferrer M (2013) Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the α/β hydrolase family. Biochem J 454:157–166

    Article  CAS  Google Scholar 

  • Arpigny JL, Jaeger KE (1999) Bacterial lipolytic enzymes: classification and properties. Biochem J 343:177–183

    Article  CAS  Google Scholar 

  • Barbato M, Mapelli F, Chouaia B, Crotti E, Daffonchio D, Borin S (2015) Draft genome sequence of the hydrocarbon-degrading bacterium Alcanivorax dieselolei KS-293 isolated from surface seawater in the Eastern Mediterranean Sea. Genome Announc 3:e01424–e01415

    Article  Google Scholar 

  • Bargiela R, Mapelli F, Rojo D, Chouaia B, Tornés J, Borin S, Richter M, Del Pozo MV, Cappello S, Gertler C, Genovese M, Denaro R, Martínez-Martínez M, Fodelianakis S, Amer RA, Bigazzi D, Han X, Chen J, Chernikova TN, Golyshina OV, Mahjoubi M, Jaouanil A, Benzha F, Magagnini M, Hussein E, Al-Horani F, Cherif A, Blaghen M, Abdel-Fattah YR, Kalogerakis N, Barbas C, Malkawi HI, Golyshin PN, Yakimov MM, Daffonchio D, Ferrer M (2015) Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature. Sci Rep 5:11651

    Article  CAS  Google Scholar 

  • Bargiela R, Yakimov MM, Golyshin PN, Ferrer M (2017) Distribution of hydrocarbon degradation pathways in the sea. In: TJ MG, Timmis KN, Nogales B (eds) Consequences of microbial interactions with hydrocarbons, oils, and lipids: production of fuels and chemicals. Springer International Publishing, Cham, pp 1–23

    Google Scholar 

  • Biely P, Puls J, Schneider H (1985) Acetylxylan esterases in fungal cellulolytic systems. FEMS Lett 186:80–84

    CAS  Google Scholar 

  • Blum DL, Li X, Chen H, Ljungdahl LG (1999) Characterization of an acetyl xylan esterase from anaerobic fungus Orpinomyces sp. strain PC-2. Appl Environ Microbiol 65:3990–3995

    CAS  PubMed  PubMed Central  Google Scholar 

  • Boll M, Löffler C, Morris BEL, Kung JW (2014) Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes. Environ Microbiol 16:612–627

    Article  CAS  Google Scholar 

  • Cappello S, Caruso G, Zampino D, Monticelli LS, Maimone G, Denaro R, Tripodo B, Troussellier M, Yakimov MM, Giuliano L (2007) Microbial community dynamics during assays of harbour oil spill bioremediation: a microscale simulation study. J Appl Microbiol 102:184–194

    Article  CAS  Google Scholar 

  • Christov LP, Prior BA (1993) Esterases of xylan-degrading microorganisms: production, properties, and significance. Enzyme Microb Technol 15:460–475

    Article  CAS  Google Scholar 

  • Coscolín C, Martínez-Martínez M, Chow J, Bargiela R, García-Moyano A, Bjerga GEK, Bollinger A, Stokke R, Steen IH, Golyshina OV, Yakimov MM, Jaeger K-E, Yakunin AF, Streit WR, Golyshin PN, Ferrer M (2018) Relationships between substrate promiscuity and chiral selectivity of esterases from phylogenetically and environmentally diverse microorganisms. Catalysts 8:10

    Article  Google Scholar 

  • Cui Z, Xu G, Li Q, Gao W, Zheng L (2013) Genome sequence of the pyrene- and fluoranthene-degrading bacterium Cycloclasticus sp. strain PY97M. Genome Announc 1:e00536–e00513

    PubMed  PubMed Central  Google Scholar 

  • Díaz E, Jiménez JI, Nogales J (2013) Aerobic degradation of aromatic compounds. Curr Opin Biotechnol 24:431–442

    Article  Google Scholar 

  • Distaso MA, Tran H, Ferrer M, Golyshin PN (2017) Metagenomic mining of enzyme diversity. In: TJ MG, Timmis KN, Nogales B (eds) Consequences of microbial interactions with hydrocarbons, oils, and lipids: production of fuels and chemicals. Springer International Publishing, Cham, pp 1–25, 1–23

    Google Scholar 

  • Dong C, Chen X, Xie Y, Lai Q, Shao Z (2014) Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean. Stand Genomic Sci 9:893–901

    Article  Google Scholar 

  • Dyksterhouse SE, Gray JP, Herwig RP, Lara JC, Staley JT (1995) Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int J Syst Bacteriol 45:116–123

    Article  CAS  Google Scholar 

  • Ferrer M, Chernikova TN, Yakimov MM, Golyshin PN, Timmis KN (2003) Chaperonins govern growth of Escherichia coli at low temperatures. Nat Biotechnol 21:1266–1267

    Article  CAS  Google Scholar 

  • Ferrer M, Bargiela R, Martínez-Martínez M, Mir J, Koch R, Golyshina OV, Golyshin PN (2015) Biodiversity for biocatalysis: a review of the α/β-hydrolase fold superfamily of ester-hydrolases-lipases discovered in metagenomes. Biocatal Biotransformation 33:235–249

    Article  CAS  Google Scholar 

  • Fu X, Lai Q, Dong C, Wang W, Shao Z (2018) Complete genome sequence of Alcanivorax xenomutans P40, an alkane-degrading bacterium isolated from deep seawater. Mar Genomics 38:1–4

    Article  Google Scholar 

  • GESAMP (2007) Estimates of oil entering the marine environment from sea-based activities. Journal series GESAM reports and studies, vol 75. IMO Publisher, London, 96 pp

    Google Scholar 

  • Golyshin PN, Chernikova TN, Abraham W-R, Lünsdorf H, Timmis KN, Yakimov MM (2002) Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 52:901–911

    CAS  PubMed  Google Scholar 

  • Golyshin PN, Martins Dos Santos VA, Kaiser O, Ferrer M, Sabirova YS, Lünsdorf H, Chernikova TN, Golyshina OV, Yakimov MM, Pühler A, Timmis KN (2003) Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems. J Biotechnol 106:215–220

    Article  CAS  Google Scholar 

  • Golyshin PN, Werner J, Chernikova TN, Tran H, Ferrer M, Yakimov MM, Teeling H, Golyshina OV, MAMBA Scientific Consortium (2013) Genome sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T). Genome Announc 1:e0014113

    Article  Google Scholar 

  • Gomila M, Mulet M, Lalucat J, García-Valdés E (2017) Draft genome sequence of the marine bacterium Pseudomonas aestusnigri VGXO14 T. Genome Announc 5:e00765–e00717

    PubMed  PubMed Central  Google Scholar 

  • Goral AM, Tkaczuk KL, Chruszcz M, Kagan O, Savchenko A, Minor W (2012) Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica. J Struct Funct Genomics 13:27–36

    Article  CAS  Google Scholar 

  • Grohman K, Mitchell PJ, Himmel ME, Sale BE, Schroeder HA (1989) The role of ester groups in resistance of plant cell wall polysaccharides to enzymatic hydrolysis. Appl Biochem Biotechnol 20:45–61

    Article  Google Scholar 

  • Gutierrez T (2017) Aerobic hydrocarbon-degrading Gammaproteobacteria – Porticoccus. In: McGenity TJ, Prince R (eds) Handbook of hydrocarbon and lipid microbiology, vol 6. Springer, Heidelberg, Germany

    Google Scholar 

  • Gutierrez T, Green DH, Whitman WB, Nichols PD, Semple KT, Aitken MD (2012) Algiphilus aromaticivorans gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov. Int J Syst Evol Microbiol 62:2743–2749

    Article  CAS  Google Scholar 

  • Gutierrez T, Singleton DR, Berry D, Yang T, Aitken MD, Teske A (2013) Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP. ISME J 7:2091–2104

    Article  CAS  Google Scholar 

  • Gutierrez T, Thompson HF, Angelova A, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T (2015a) Genome sequence of Polycyclovorans algicola strain TG408, an obligate polycyclic aromatic hydrocarbon-degrading bacterium associated with marine eukaryotic phytoplankton. Genome Announc 3:e00207–e00215

    PubMed  PubMed Central  Google Scholar 

  • Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T (2015b) Genome sequence of Porticoccus hydrocarbonoclasticus strain MCTG13d, an obligate polycyclic aromatic hydrocarbon-degrading bacterium associated with Marine eukaryotic phytoplankton. Genome Announc 3:e00672–e00615

    PubMed  PubMed Central  Google Scholar 

  • Hajighasemi M, Nocek BP, Tchigvintsev A, Brown G, Flick R, Xu X, Cui H, Hai T, Joachimiak A, Golyshin PN, Savchenko A, Edwards EA, Yakunin AF (2016) Biochemical and structural insights into enzymatic depolymerization of polylactic acid and other polyesters by microbial carboxylester-hydrolases. Biomacromolecules 17:2027–2039

    Article  CAS  Google Scholar 

  • Hara A, Baik SH, Syutsubo K, Misawa N, Smits TH, van Beilen JB, Harayama S (2004) Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2. Environ Microbiol 6:191–197

    Article  CAS  Google Scholar 

  • Harayama S, Kasai Y, Hara A (2004) Microbial communities in oil-contaminated seawater. Curr Opin Biotechnol 15:205–214

    Article  CAS  Google Scholar 

  • Head IM, Jones DM, Röling WF (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4(3):173–182

    Article  CAS  Google Scholar 

  • Joye SB, Kleindienst S, Gilbert JA, Handley KM, Weisenhorn P, Overholt WA, Kostka JE (2016) Responses of microbial communities to hydro-carbon exposures. Oceanography 23:136–149

    Article  Google Scholar 

  • Jung E, Park BG, Ahsan MM, Kim J, Yun H, Choi KY, Kim BG (2016) Production of ω-hydroxy palmitic acid using CYP153A35 and comparison of cytochrome P450 electron transfer system in vivo. Appl Microbiol Biotechnol 100:10375–10384

    Article  CAS  Google Scholar 

  • Kadri T, Rouissi T, Magdouli S, Brar SK, Hegde K, Khiari Z, Daghrir R, Lauzon JM (2018) Production and characterization of novel hydrocarbon degrading enzymes from Alcanivorax borkumensis. Int J Biol Macromol 112:230–240

    Article  CAS  Google Scholar 

  • Kasai Y, Kishira H, Harayama S (2002) Bacteria belonging to the genus Cycloclasticus play a primary role in the degradation of aromatic hydrocarbons released in a marine environment. Appl Environ Microbiol 68:5625–5633

    Article  CAS  Google Scholar 

  • Kasai Y, Shindo K, Harayama S, Misawa N (2003) Molecular characterization and substrate preference of a polycyclic aromatic hydrocarbon dioxygenase from Cycloclasticus sp. strain A5. Appl Environ Microbiol 69:6688–6697

    Article  CAS  Google Scholar 

  • Kimes NE, Callaghan AV, Aktas DF, Smith WL, Sunner J, Golding B, Drozdowska M, Morris PJ (2013) Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill. Front Microbiol 4:50

    Article  Google Scholar 

  • Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M (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 77:7962–7974

    Article  CAS  Google Scholar 

  • Kube M, Chernikova TN, Al-Ramahi Y, Beloqui A, Lopez-Cortez N, Guazzaroni ME, Heipieper HJ, Klages S, Kotsyurbenko OR, Langer I, Nechitaylo TY, Lünsdorf H, Fernández M, Juárez S, Ciordia S, Singer A, Kagan O, Egorova O, Petit PA, Stogios P, Kim Y, Tchigvintsev A, Flick R, Denaro R, Genovese M, Albar JP, Reva ON, Martínez-Gomariz M, Tran H, Ferrer M, Savchenko A, Yakunin AF, Yakimov MM, Golyshina OV, Reinhardt R, Golyshin PN (2013) Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. Nat Commun 4:2156

    Article  Google Scholar 

  • Lai Q, Shao Z (2012a) Genome sequence of an alkane-degrading bacterium, Alcanivorax pacificus type strain W11-5, isolated from deep sea sediment. J Bacteriol 194:6936

    Article  CAS  Google Scholar 

  • Lai Q, Shao Z (2012b) Genome sequence of the alkane-degrading bacterium Alcanivorax hongdengensis type strain A-11-3. J Bacteriol 194:6972

    Article  CAS  Google Scholar 

  • Lai Q, Li W, Shao Z (2012a) Complete genome sequence of Alcanivorax dieselolei type strain B5. J Bacteriol 194:6674

    Article  CAS  Google Scholar 

  • Lai Q, Li W, Wang B, Yu Z, Shao Z (2012b) Complete genome sequence of the pyrene-degrading bacterium Cycloclasticus sp. strain P1. J Bacteriol 194:6677

    Article  CAS  Google Scholar 

  • Li A, Shao Z (2014) Biochemical characterization of a haloalkane dehalogenase DadB from Alcanivorax dieselolei B-5. PLoS One 9:e89144

    Article  Google Scholar 

  • Liu Z, Liu J (2013) Evaluating bacterial community structures in oil collected from the sea surface and sediment in the northern Gulf of Mexico after the Deepwater Horizon oil spill. Microbiology 2:492–504

    CAS  Google Scholar 

  • Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee Y-J, Mason OU, Dubinky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D’haeseller P, Hazen TC, Zhou J (2011) Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J 6:451–460

    Article  Google Scholar 

  • Luan X, Cui Z, Gao W, Li Q, Yin X, Zheng L (2014) Genome sequence of the petroleum hydrocarbon-degrading bacterium Alcanivorax sp. strain 97CO-5. Genome Announc 2:e01277–e01214

    Article  Google Scholar 

  • Manilla-Pérez E, Lange AB, Hetzler S, Steinbüchel A (2010) Occurrence, production, and export of lipophilic compounds by hydrocarbonoclastic marine bacteria and their potential use to produce bulk chemicals from hydrocarbons. Appl Microbiol Biotechnol 86:1693–1706

    Article  Google Scholar 

  • Martínez-Martínez M, Lores I, Peña-García C, Bargiela R, Reyes-Duarte D, Guazzaroni ME, Peláez AI, Sánchez J, Ferrer M (2014) Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters. Microb Biotechnol 7:184–191

    Article  Google Scholar 

  • Martínez-Martínez M, Bargiela RM, Coscolín C, Navarro J, Golyshin PN, Ferrer M (2017) Functionalization and modification of hydrocarbon-like molecules guided by metagenomics: esterases and lipases from the α/β-hydrolase fold superfamily and transaminases as study cases. In: McGenity TJ, Timmis KN, Nogales B (eds) Consequences of microbial interactions with hydrocarbons, oils, and lipids: production of fuels and chemicals. Springer International Publishing, Cham, pp 1–21. 978-3-319-31421-1

    Google Scholar 

  • Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A, Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M, The Inmare Consortium (2018) Determinants and prediction of esterase substrate promiscuity patterns. ACS Chem Biol 13:225–234

    Article  Google Scholar 

  • Mason OU, Hazen TC, Borglin S, Chain PSG, Dubinsky EA, Fortney JL, Han J, Holman H-YN, Hultman J, Lamendella R, Mackelprag R, Malfatti S, Tom LM, Tringe SG, Woyke T, Zhou J, Rubin EM, Jansson JK (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 6:1715–1727

    Article  CAS  Google Scholar 

  • Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Baelum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Álvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK (2014) Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J 8:1464–1475

    Article  CAS  Google Scholar 

  • McGenity TJ, Folwell BD, McKew BA, Sanni GO (2012) Marine crude-oil biodegradation: a central role for interspecies interactions. Aquat Biosyst 8:10

    Article  Google Scholar 

  • Messina E, Denaro R, Crisafi F, Smedile F, Cappello S, Genovese M, Genovese L, Giuliano L, Russo D, Ferrer M, Golyshin PN, Yakimov MM (2016) Genome sequence of obligate marine polycyclic aromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME, isolated from petroleum deposits of the sunken tanker Amoco Milford Haven, Mediterranean Sea. Mar Genomics 25:11–13

    Article  Google Scholar 

  • Miri M, Bambai B, Tabandeh F, Sadeghizadeh M, Kamali N (2010) Production of a recombinant alkane hydroxylase (AlkB2) from Alcanivorax borkumensis. Biotechnol Lett 32:497–502

    Article  CAS  Google Scholar 

  • Misawa N, Nodate M, Otomatsu T, Shimizu K, Kaido C, Kikuta M, Ideno A, Ikenaga H, Ogawa J, Shimizu S, Shindo K (2011) Bioconversion of substituted naphthalenes and β-eudesmol with the cytochrome P450 BM3 variant F87V. Appl Microbiol Biotechnol 90:147–157

    Article  CAS  Google Scholar 

  • Miura T, Tsuchikane K, Numata M, Hashimoto M, Hosoyama A, Ohji S, Yamazoe A, Fujita N (2014) complete genome sequence of an alkane degrader, Alcanivorax sp. Strain NBRC 101098. Genome Announc 2:e00766–e00714

    Article  Google Scholar 

  • Naing SH, Parvez S, Pender-Cudlip M, Groves JT, Austin RN (2013) Substrate specificity and reaction mechanism of purified alkane hydroxylase from the hydrocarbonoclastic bacterium Alcanivorax borkumensis (AbAlkB). J Inorg Biochem 121:46–52

    Article  CAS  Google Scholar 

  • Nolte JC, Schürmann M, Schepers CL, Vogel E, Wübbeler JH, Steinbüchel A (2014) Novel characteristics of succinate coenzyme A (Succinate-CoA) ligases: conversion of malate to malyl-CoA and CoA-thioester formation of succinate analogues in vitro. Appl Environ Microbiol 80:166–176

    Article  CAS  Google Scholar 

  • Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW (2017) Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2:1533–1542

    Article  CAS  Google Scholar 

  • Prince RC, Amande TJ, McGenity TJ (2018) Prokaryotic hydrocarbon degraders. In: McGenity TJ (ed) Taxonomy, genomics and ecophysiology of hydrocarbon-degrading microbes: handbook of hydrocarbon and lipid microbiology, 2nd edn. Springer, Cham

    Google Scholar 

  • Ron EZ, Rosenberg E (2014) Enhanced bioremediation of oil spills in the sea. Curr Opin Biotechnol 27:191–194

    Article  CAS  Google Scholar 

  • Sabirova JS, Ferrer M, Lünsdorf H, Wray V, Kalscheuer R, Steinbüchel A, Timmis KN, Golyshin PN (2006) Mutation in a “tesB-like” hydroxyacyl-coenzyme A-specific thioesterase gene causes hyperproduction of extracellular polyhydroxyalkanoates by Alcanivorax borkumensis SK2. J Bacteriol 188:8452–8459

    Article  CAS  Google Scholar 

  • Schneiker S, Martins dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24:997–1004

    Article  CAS  Google Scholar 

  • Shindo K, Tachibana A, Tanaka A, Toba S, Yuki E, Ozaki T, Kumano T, Nishiyama M, Misawa N, Kuzuyama T (2011) Production of novel antioxidative prenyl naphthalen-ols by combinational bioconversion with dioxygenase PhnA1A2A3A4 and prenyltransferase NphB or SCO7190. Biosci Biotechnol Biochem 75:505–510

    Article  CAS  Google Scholar 

  • Tchigvintsev A, Tran H, Popovic A, Kovacic F, Brown G, Flick R, Hajighasemi M, Egorova O, Somody JC, Tchigvintsev D, Khusnutdinova A, Chernikova TN, Golyshina OV, Yakimov MM, Savchenko A, Golyshin PN, Jaeger KE, Yakunin AF (2015) The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes. Appl Microbiol Biotechnol 99:2165–2178

    Article  CAS  Google Scholar 

  • Teimoori A, Ahmadian S, Madadkar-Sobhani A, Bambai B (2011) Rubredoxin reductase from Alcanivorax borkumensis: expression and characterization. Biotechnol Prog 27:1383–1389

    Article  CAS  Google Scholar 

  • Teimoori A, Ahmadian S, Madadkar-Sobhani A (2012) Biochemical characterization of two recombinant ferredoxin reductases from Alcanivorax borkumensis SK2. Biotechnol Appl Biochem 59:457–464

    Article  CAS  Google Scholar 

  • Toshchakov SV, Korzhenkov AA, Chernikova TN, Ferrer M, Golyshina OV, Yakimov MM, Golyshin PN (2017) The genome analysis of Oleiphilus messinensis ME102 (DSM 13489T) reveals backgrounds of its obligate alkane-devouring marine lifestyle. Mar Genomics 36:41–47

    Article  Google Scholar 

  • van Beilen JB, Marín MM, Smits TH, Röthlisberger M, Franchini AG, Witholt B, Rojo F (2004) Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ Microbiol 6:264–273

    Article  Google Scholar 

  • Wang W, Shao Z (2012) Diversity of flavin-binding monooxygenase genes (almA) in marine bacteria capable of degradation long-chain alkanes. FEMS Microbiol Ecol 80:523–533

    Article  CAS  Google Scholar 

  • Wong DW (2006) Feruloyl esterase: a key enzyme in biomass degradation. Appl Biochem Biotechnol 133:87–112

    Article  CAS  Google Scholar 

  • Yakimov MM, Golyshin PN, Lang S, Moore ERB, Abraham W-R, Lünsdorf H, Timmis KN (1998) Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int J Syst Bacteriol 48:339–348

    Article  CAS  Google Scholar 

  • Yakimov MM, Giuliano L, Gentile G, Crisafi E, Chernikova TN, Abraham W-R, Lünsdorf H, Timmis KN, Golyshin PN (2003) Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water. Int J Syst Evol Microbiol 53:779–785

    Article  CAS  Google Scholar 

  • Yakimov MM, Giuliano L, Denaro R, Crisafi E, Chernikova TN, Abraham W-R, Lünsdorf H, Timmis KN, Golyshin PN (2004) Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 54:141–148

    Article  CAS  Google Scholar 

  • Yakimov MM, Denaro R, Genovese M, Cappello S, D’Auria G, Chernikova TN, Timmis KN, Golyshin PN, Giluliano L (2005) Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Environ Microbiol 7:1426–1441

    Article  CAS  Google Scholar 

  • Yakimov MM, Timmis KN, Golyshin PN (2007) Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 18:257–266

    Article  CAS  Google Scholar 

  • Zhang S, Wu G, Liu Z, Shao Z, Liu Z (2014a) Characterization of EstB, a novel cold-active and organic solvent-tolerant esterase from marine microorganism Alcanivorax dieselolei B-5(T). Extremophiles 18:251–259

    Article  CAS  Google Scholar 

  • Zhang Y, Yi L, Lin Y, Zhang L, Shao Z, Liu Z (2014b) Characterization and site-directed mutagenesis of a novel class II 5-enopyruvylshikimate-3-phosphate (EPSP) synthase from the deep-sea bacterium Alcanivorax sp. L27. Enzym Microb Technol 63:64–70

    Article  CAS  Google Scholar 

  • Zhang H, Liu R, Wang M, Wang H, Gao Q, Hou Z, Gao D, Wang L (2016) Draft genome sequence of Alcanivorax sp. strain KX64203 isolated from deep-sea sediments of Iheya North, Okinawa Trough. Genome Announc 4:e00872–e00816

    PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This project received funding from the European Union’s Horizon 2020 research and innovation program [Blue Growth: Unlocking the potential of Seas and Oceans] under grant agreement no. [634486] (project acronym INMARE). This research was also supported by the grants PCIN-2014-107 (within ERA NET IB2 grant no. ERA-IB-14-030 - MetaCat), PCIN-2017-078 (within the ERA-MarineBiotech grant ProBone), BIO2014-54494-R, and BIO2017-85522-R from the Spanish Ministry of Economy, Industry and Competitiveness (actually, Ministry of Science, Innovation and Universities). P.N.G. gratefully acknowledges funding from the UK Biotechnology and Biological Sciences Research Council (grant no. BB/M029085/1). R.B. and P.N.G. acknowledge the support of the Supercomputing Wales project, which is part-funded by the European Regional Development Fund (ERDF) via Welsh Government. P.N.G. acknowledges the support of the Centre of Environmental Biotechnology Project funded by the European Regional Development Fund (ERDF) through Welsh Government. The authors gratefully acknowledge financial support provided by the European Regional Development Fund (ERDF). C. Coscolín thanks the Spanish Ministry of Economy, Industry and Competitiveness for a PhD fellowship (Grant BES-2015-073829).

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Authors and Affiliations

  1. Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain

    Cristina Coscolín, Mónica Martínez-Martínez, Sandra Alonso & Manuel Ferrer

  2. School of Natural Sciences, Bangor University, Bangor, UK

    Rafael Bargiela, Tatyana N. Chernikova, Tran Hai, Olga V. Golyshina & Peter N. Golyshin

  3. Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf and Forschungszentrum Jülich GmbH, Jülich, Germany

    Alexander Bollinger, Stephan Thies & Karl-Erich Jaeger

  4. Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, Messina, Italy

    Michail M. Yakimov

  5. Immanuel Kant Baltic Federal University, Kaliningrad, Russia

    Michail M. Yakimov

  6. Centre for Environmental Biotechnology, Bangor University, Bangor, UK

    Olga V. Golyshina & Peter N. Golyshin

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  1. Cristina Coscolín
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  2. Rafael Bargiela
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  4. Sandra Alonso
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  5. Alexander Bollinger
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  7. Tatyana N. Chernikova
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  8. Tran Hai
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  9. Olga V. Golyshina
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  10. Karl-Erich Jaeger
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  11. Michail M. Yakimov
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  12. Peter N. Golyshin
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  13. Manuel Ferrer
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Corresponding author

Correspondence to Manuel Ferrer .

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Editors and Affiliations

  1. University of Essex, School of Biological Sciences University of Essex, Colchester, Essex, UK

    Terry J. McGenity

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Coscolín, C. et al. (2018). Hydrocarbon-Degrading Microbes as Sources of New Biocatalysts. In: McGenity, T. (eds) Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-60053-6_13-1

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  • DOI: https://doi.org/10.1007/978-3-319-60053-6_13-1

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