Abstract
Hydrocarbons have been part of the biosphere for millions of years, and a diverse group of prokaryotes has evolved to use them as a source of carbon and energy. To date, the vast majority of formally defined genera are eubacterial, in 7 of the 24 major phyla currently formally recognized by taxonomists (Tree of Life, http://tolweb.org/Eubacteria. Accessed 1 Sept 2017, 2017); principally in the Actinobacteria, the Bacteroidetes, the Firmicutes, and the Proteobacteria. Some Cyanobacteria have been shown to degrade hydrocarbons on a limited scale, but whether this is of any ecological significance remains to be seen – it is likely that all aerobic organisms show some basal metabolism of hydrocarbons by nonspecific oxygenases, and similar “universal” metabolism may occur in anaerobes. This chapter focuses on the now quite large number of named microbial genera where there is reasonably convincing evidence for hydrocarbon metabolism. We have found more than 320 genera of Eubacteria, and 12 genera of Archaea. Molecular methods are revealing a vastly greater diversity of currently uncultured organisms – Hug et al. (Nat Microbiol 1:16048, 2016) claim 92 named bacterial phyla, many with almost totally unknown physiology – and it seems reasonable to believe that the catalog of genera reported here will be substantially expanded in the future.
This is a preview of subscription content, log in via an institution.
References
Abbasian F, Lockington R, Megharaj M, Naidu R (2016) A review on the genetics of aliphatic and aromatic hydrocarbon degradation. Appl Biochem Biotechnol 178:224–250
Abed RMM, Köster J (2005) The direct role of aerobic heterotrophic bacteria associated with cyanobacteria in the degradation of oil compounds. Int Biodeter Biodegr 55:29–37
Abed RM, Al-Kharusi S, Prigent S, Headley T (2014) Diversity, distribution and hydrocarbon biodegradation capabilities of microbial communities in oil-contaminated cyanobacterial mats from a constructed wetland. PLoS One 9:e114570
Acuña Alvarez L, Exton DA, Suggett DJ, Timmis KN, McGenity TJ (2009) Characterization of marine isoprene-degrading communities. Environ Microbiol 11:3280–3291
Adachi K, Katsuta A, Matsuda S, Peng X, Misawa N, Shizuri Y, Kroppenstedt RM, Yokota A, Kasai H (2007) Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae. Int J Syst Evol Microbiol 57:297–301
Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S (2017) The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J. https://doi.org/10.1038/ismej.2017.122
Akyon B, Stachler E, Wei N, Bibby K (2015) Microbial mats as a biological treatment approach for saline wastewaters: the case of produced water from hydraulic fracturing. Environ Sci Technol 49:6172–6180
Al-Awadhi H, Sulaiman RHD, Mahmoud HM, Radwan SS (2007) Alkaliphilic and halophilic hydrocarbon-utilizing bacteria from Kuwaiti coasts of the Arabian Gulf. Appl Microbiol Biotechnol 77:183–186
Al-Awadhi H, Al-Mailem D, Dashti N, Khanafer M, Radwan S (2012) Indigenous hydrocarbon-utilizing bacterioflora in oil-polluted habitats in Kuwait, two decades after the greatest man-made oil spill. Arch Microbiol 194:689–705
Al-Hasan RH, Al-Bader DA, Sorkhoh SS, Radwan NA (1998) Evidence for n-alkane consumption and oxidation by filamentous cyanobacteria from oil-contaminated coasts of the Arabian Gulf. Mar Biol 130:521–527
Allen EE, Banfield JF (2005) Community genomics in microbial ecology and evolution. Nat Rev Microbiol 3:480–498
Al-Mailem DM, Sorkhoh NA, Al-Awadhi H, Eliyas M, Radwan SS (2010) Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles 14:321–328
Al-Mailem DM, Eliyas M, Radwan S (2014a) Enhanced bioremediation of oil-polluted, hypersaline, coastal areas in Kuwait via vitamin-fertilization. Environ Sci Pollut Res 21:3386–3394
Al-Mailem DM, Kansour MK, Radwan SS (2014b) Hydrocarbonoclastic biofilms based on sewage microorganisms and their application in hydrocarbon removal in liquid wastes. Can J Microbiol 60:477–486
Al-Mueini R, Al-Dalali M, Al-Amri IS, Patzelt H (2007) Hydrocarbon degradation at high salinity by a novel extremely halophilic actinomycete. Environ Chem 4:5–7
Almutairi A (2015) Prauserella soli sp. nov., isolated from crude oil-contaminated soil. Int J Syst Evol Microbiol 65:3060–3065
Al-Saleh E, Drobiova H, Obuekwe C (2009) Predominant culturable crude oil-degrading bacteria in the coast of Kuwait. Int Biodeter Biodegr 63:400–406
Al-Wahaib D, Al-Bader D, Abdou DK, Eliyas M, Radwan SS (2016) Consistent occurrence of hydrocarbonoclastic Marinobacter strains in various cultures of picocyanobacteria from the Arabian gulf: promising associations for biodegradation of marine oil pollution. J Mol Microbiol Biotechnol 26:261–268
Anan’ina LN, Plotnikova EG, Gavrish EY, Demakov VA, Evtushenko LI (2007) Salinicola socius, gen. nov., sp. nov., a moderately halophilic bacterium from a naphthalene-utilizing microbial association. Microbiology 76:324–330
Ang LI, Yuanyuan QU, Jiti ZH, Min GO (2009) Isolation and characteristics of a novel biphenyl-degrading bacterial strain, Dyella ginsengisoli LA-4. J Environ Sci 21:211–217
Austin B, Calomiris JJ, Walker JD, Colwell RR (1977) Numerical taxonomy and ecology of petroleum-degrading bacteria. Appl Environ Microbiol 34:60–68
Bacosa HP, Inoue C (2015) Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan. J Hazard Mater 283:689–697
Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK (2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 14:2405–2416
Barabas G, Vargha G, Szabo IM, Penyige A, Damjanovich S, Szollosi J, Matko J, Hirano T, Matyus A, Szabo I (2001) n-Alkane uptake and utilisation by Streptomyces strains. Antonie Van Leeuwenhoek 79:269–276
Bergey (2012) Taxonomic outlines of the Prokaryotes. Bergey’s manual of systematic bacteriology. http://www.bergeys.org. Accessed 1 Oct 2017
Bergey’s Manual of Systematics of Archaea and Bacteria (2017) Last updated on 27th March 2017. http://onlinelibrary.wiley.com/store/10.1002/9781118960608/asset/homepages/Taxonomic_Outline_080516.pdf?v=1&s=3142d10f69e6b4c26967830534de161f32dd9be2. Accessed 5 June 2017
Bisht S, Pandey P, Sood A, Sharma S, Bisht NS (2010) Biodegradation of naphthalene and anthracene by chemo-tactically active rhizobacteria of Populus deltoides. Braz J Microbiol 41:922–930
Bodour AA, Wang J, Brusseau ML, Maier RM (2003) Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system. Environ Microbiol 5:888–895
Bodrossy L, Holmes EM, Holmes AJ, Kovacs KL, Murrell JC (1997) Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, Methylocaldum gen. nov. Arch Microbiol 168:493–503
Bogan BW, Sullivan WR, Kayser KJ, Derr KD, Aldrich HC, Paterek JC (2003) Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils. Int J Syst Evol Microbiol 53:1389–1395
Bordenave S, Goñi-Urriza M, Vilette C, Blanchard S, Caumette P, Duran R (2008) Diversity of ring-hydroxylating dioxygenases in pristine and oil contaminated microbial mats at genomic and transcriptomic levels. Environ Microbiol 10:3201–3211
Bossert I, Bartha R (1984) The fate of petroleum in soil ecosystems. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 435–473
Bourguignon N, Isaac P, Alvarez H, Amoroso MJ, Ferrero MA (2014) Enhanced polyaromatic hydrocarbon degradation by adapted cultures of actinomycete strains. J Basic Microbiol 54:1288–1294
Bowman J (2006) The methanotrophs – the families Methylococcaceae and Methylocystaceae. In: Dworkin MM, Schleifer KH, Rosenberg E, Falkow S (eds) The prokaryotes: a handbook on the biology of bacteria, Vol. 5: Proteobacteria: alpha and beta subclass. Springer, New York, pp 266–289
Bowman JP, Sly LI, Nichols PD, Hayward AC (1993) Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the Group I methanotrophs. Int J Syst Bacteriol 43:735–753
Bowman JP, McCammon SA, Skerratt JH (1997) Methylosphaera hansonii gen. nov., sp. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes. Microbiology 143:1451–1459
Bradley PM, Landmeyer JE, Chapelle FH (2001) Widespread potential for microbial MTBE degradation in surface-water sediments. Environ Sci Technol 35:658–662
Brenner K, You L, Arnold FH (2008) Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol 26:483–489
Brito EMS, Guyoneaud R, Goñi-Urriza M, Ranchou-Peyruse A, Verbaere A, Crapez MAC, Wasserman JCA, Duran R (2006) Characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in Guanabara Bay, Brazil. Res Microbiol 157:752–762
Brzostowicz PC, Walters DM, Jackson RE, Halsey KH, Ni H, Rouvière PE (2005) Proposed involvement of a soluble methane monooxygenase homologue in the cyclohexane-dependent growth of a new Brachymonas species. Environ Microbiol 7:179–190
Buzoleva LS, Bogatyrenko EA, Repina MA, Belkova NL (2017) Oil-oxidizing activity of bacteria isolated from south Sakhalin coastal waters. Microbiology 86:338–345
Campbell BJ, Engel AS, Porter ML, Takai K (2006) The versatile ε-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4:458–468
Cao B, Ma T, Ren Y, Ren Y, Li G, Li P, Guo X, Ding P, Feng L (2011) Complete genome sequence of Pusillimonas sp. T7-7, a cold-tolerant diesel oil-degrading bacterium isolated from the Bohai Sea in China. J Bacteriol 193:4021–4022
Cao Y, Chastain RA, Eloe EA, Nogi Y, Kato C, Bartlett DH (2014) Novel psychropiezophilic Oceanospirillales species Profundimonas piezophila gen. nov., sp. nov., isolated from the deep-sea environment of the Puerto Rico Trench. Appl Environ Microbiol 80:54–60
Cerniglia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351–368
Cerniglia CE, Gibson GT, Van Baalen C (1979) Algal oxidation of aromatic hydrocarbons; formation of 1-naphthol from naphthalene by Agmenellum quadruplicatum strain PR-6. Biochem Biophys Res Commun 88:50–58
Chaillan F, Le Flèche A, Bury E, Phantavong Y, Grimont P, Saliot A, Oudot J (2004) Identification and biodegradation potential of tropical aerobic hydrocarbon-degrading microorganisms. Res Microbiol 155:587–595
Chaineau CH, Morel J, Dupont J, Bury E, Oudot J (1999) Comparison of the fuel oil biodegradation potential of hydrocarbon-assimilating microorganisms isolated from a temperate agricultural soil. Sci Total Environ 227:237–247
Chronopoulou P-M, Fahy A, Coulon F, Paissé S, Goñi-Urriza MS, Peperzak L, Acuña-Alvarez L, McKew BA, Lawson T, Timmis KN, Duran R, Underwood GJC, McGenity TJ (2013) Impact of a simulated oil spill on benthic phototrophs and nitrogen-fixing bacteria. Environ Microbiol 15:241–252
Chung WK, King GM (2001) Isolation, characterization, and polyaromatic hydrocarbon degradation potential of aerobic bacteria from marine macrofaunal burrow sediments and description of Lutibacterium anuloederans gen. nov., sp. nov., and Cycloclasticus spirillensus sp. nov. Appl Environ Microbiol 67:5585–5592
Coates JD, Bhupathiraju VK, Achenbach LA, McInerney MJ, Lovley DR (2001a) Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers. Int J Syst Evol Microbiol 51:581–588
Coates JD, Chakraborty R, Lack JG, O’Connor SM, Cole KA, Bender KS, Achenbach LA (2001b) Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411:1039–1043
Cohen Y (2002) Bioremediation of oil by marine microbial mats. Int Microbiol 5:189–193
Cohn F (1873) Memoirs: on a new alga, Crenothrix polyspora (Cohn) from the well-water of Breslau. Q J Microsc Sci 2:163–168
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145
Corteselli EM, Aitken MD, Singleton DR (2017a) Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds. Int J Syst Evol Microbiol 67:311–318
Corteselli EM, Aitken MD, Singleton DR (2017b) Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov. Int J Syst Evol Microbiol 67:925–931
Cravo-Laureau C, Matheron R, Cayol JL, Joulian C, Hirschler-Rea A (2004) Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 54:77–83
Cravo-Laureau C, Labat C, Joulian C, Matheron R, Hirschler-Réa A (2007) Desulfatiferula olefinivorans gen. nov., sp. nov., a long-chain n-alkene-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 57:2699–2702
Crisafi F, Giuliano L, Yakimov MM, Azzaro M, Denaro R (2016) Isolation and degradation potential of a cold-adapted oil/PAH-degrading marine bacterial consortium from Kongsfjorden (Arctic region). Rend Lincei 27:261–270
Dai X, Wang Y, Wang B, Liu S, Zhou Y (2005) Planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of Planococcus psychrophilus and Planococcus alkanoclasticus to Planomicrobium as Planomicrobium psychrophilum comb. nov. and Planomicrobium alkanoclasticum comb. nov. Int J Syst Evol Microbiol 55:699–702
Darwin CR, Wallace AR (1858) On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection. Zool J Linnean Soc 3:45–62
Dashti N, Khanafer M, El-Nemr I, Sorkhoh N, Ali N, Radwan S (2009) The potential of oil-utilizing bacterial consortia associated with legume root nodules for cleaning oily soils. Chemosphere 74:1354–1359
Dashti N, Ali N, Eliyas M, Khanafer M, Sorkhoh NA, Radwan SS (2015) Most hydrocarbonoclastic bacteria in the total environment are diazotrophic, which highlights their value in the bioremediation of hydrocarbon contaminants. Microbes Environ 30:70–75
Davidova IA, Duncan KE, Choi OK, Suflita JM (2006) Desulfoglaeba alkanexedens gen. nov., sp. nov., an n-alkane-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 56:2737–2742
Davis JB, Yarbrough HF (1966) Anaerobic oxidation of hydrocarbons by Desulfovibrio desulfuricans. Chem Geol 1:137–144
Dedysh SN, Liesack W, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Bares AM, Panikov NS, Tiedje JM (2000) Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int J Syst Evol Microbiol 50:955–969
Dedysh SN, Khmelenina VN, Suzina N, Trotsenko YA, Semrau JD, Liesack W, Tiedje JM (2002) Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. Int J Syst Evol Microbiol 52:251–261
Deutzmann JS, Hoppert M, Schink B (2014) Characterization and phylogeny of a novel methanotroph, Methyloglobulus morosus gen. nov., sp. nov. Syst Appl Microbiol 37:165–169
Dixit VS, Pant A (2000) Hydrocarbon degradation and protease production by Nocardiopsis sp. NCIM 5124. Lett Appl Microbiol 30:67–69
Dobzhansky T (1937) Genetics and the origin of species. Columbia University Press, New York
Dore SY, Clancy QE, Rylee SM, Kulpa CF (2003) Naphthalene-utilizing and mercury-resistant bacteria isolated from an acidic environment. Appl Microbiol Biotechnol 63:194–199
DSMZ (2017) The German collection of microorganisms and cell cultures. http://www.dsmz.de/. Accessed 1 Oct 2017
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
Engelhardt MA, Daly K, Swannell RPJ, Head IM (2001) Isolation and characterization of a novel hydrocarbon-degrading, gram-positive bacterium, isolated from intertidal beach sediment, and description of Planococcus alkanoclasticus sp. nov. J Appl Microbiol 90:237–247
Erdoğmuş SF, Mutlu B, Korcan SE, Güven K, Konuk M (2013) Aromatic hydrocarbon degradation by halophilic archaea isolated from Çamaltı Saltern, Turkey. Water Air Soil Pollut 224:1449
Eriksson S, Ankner T, Abrahamsson K, Hallbeck L (2005) Propylphenols are metabolites in the anaerobic biodegradation of propylbenzene under iron-reducing conditions. Biodegradation 16:253–263
Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, Schreiber F, Dutilh BE, Zedelius J, De Beer D, Gloerich J (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543–548
Euzéby JP (2017) List of Prokaryotic names with Standing in Nomenclature. http://www.bacterio.net/ Accessed 1 Oct 2017
Eyheraguibel B, Traikia M, Fontanella S, Sancelme M, Bonhomme S, Fromageot D, Lemaire J, Lauranson G, Lacoste J, Delort AM (2017) Characterization of oxidized oligomers from polyethylene films by mass spectrometry and NMR spectroscopy before and after biodegradation by a Rhodococcus rhodochrous strain. Chemosphere 184:366–374
Fahy A, Ball AS, Lethbridge G, Timmis KN, McGenity TJ (2008) Isolation of alkali-tolerant benzene-degrading bacteria from a contaminated aquifer. Lett Appl Microbiol 47:60–66
Fang T, Wang H, Huang Y, Zhou H, Dong P (2015) Oleiagrimonas soli gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield. Int J Syst Evol Microbiol 65:1666–1671
Farkas M, Táncsics A, Kriszt B, Benedek T, Tóth EM, Kéki Z, Veres PG, Szoboszlay S (2015) Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm. Int J Syst Evol Microbiol 65:274–279
Federhen S (2014) Type material in the NCBI taxonomy database. Nucleic Acids Res 43:D1086–D1098
Feitkenhauer H, Müller R, Märkl H (2003) Degradation of polycyclic aromatic hydrocarbons and long chain alkanes at 60–70°C by Thermus and Bacillus spp. Biodegradation 14:367–372
Feng TC, Cui CZ, Dong F, Feng YY, Liu YD, Yang XM (2012) Phenanthrene biodegradation by halophilic Martelella sp. AD-3. J Appl Microbiol 113:779–789
Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, Pedrós-Alió C (2013) Ecology of marine bacteroidetes: a comparative genomics approach. ISME J 7:1026–1037
Floodgate GD (1984) The fate of petroleum in marine ecosystems. In: Atlas RM (ed) Petroleum microbiology. Macmillan, New York, pp 355–397
Francisco ÉC, Franco TT, Wagner R, Jacob-Lopes E (2014) Assessment of different carbohydrates as exogenous carbon source in cultivation of cyanobacteria. Bioprocess Biosyst Eng 37:1497–1505
Friedrich MM, Lipski A (2008) Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov., hexane-degrading bacteria isolated from a hexane-treated biofilter. Int J Syst Evol Microbiol 58:2324–2329
Frindte K, Maarastawi SA, Lipski A, Hamacher J, Knief C (2017) Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai. Int J Syst Evol Microbiol 67:4507–4514
Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3:722–732
Gamila HA, Ibrahim MBM, El-Ghafar HH (2003) The role of cyanobacterial isolated strains in the biodegradation of crude oil. Int J Environ Stud 60:435–444
Gauthier M, Lafay B, Christen R, Fernandez L, Acquaviva M, Bonin P, Bertrand JC (1992) Marinobacter hydrocarbonoclasticus gen. nov. sp. nov., a new extreme halotolerant hydrocarbon-degrading marine bacterium. Int J Syst Bacteriol 42:568–576
Gauthier E, Deziel E, Villemur R, Juteau P, Lepine F, Beaudet R (2003) Initial characterization of new bacteria degrading high-molecular weight polycyclic aromatic hydrocarbons isolated from a 2-year enrichment in a two-liquid-phase culture system. J Appl Microbiol 94:301–311
Gentile G, Bonasera V, D’Amico C, Giuliano L, Yakimov MM (2003) Shewanella sp. GA-22, a psychrophilic hydrocarbonoclastic Antarctic bacterium producing polyunsaturated fatty acids. J Appl Microbiol 95:1124–1133
Gest H (1999) Bacterial classification and taxonomy: a “primer” for the new millennium. Microbiol Today 26:70–71
Gest H (2008) Unknowledgeables promote “unculturables”. Microbe 3:499
Geymonat E, Ferrando L, Tarlera SE (2011) Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field. Int J Syst Evol Microbiol 61:2568–2572
Gieg LM, Fowler SJ, Berdugo-Clavijo C (2014) Syntrophic biodegradation of hydrocarbon contaminants. Curr Opin Biotechnol 27:21–29
Godheja J, Shekhar SK, Satyanarayan GN, Singh SP, Modi DR (2017) Antibiotic and heavy metal tolerance of some indigenous bacteria isolated from petroleum contaminated soil sediments with a study of their aromatic hydrocarbon degradation potential. Int J Curr Microbiol Appl Sci 6:194–211
Golyshin PN, Chernikova TN, Abraham WR, Lunsdorf 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
Gradova NB, Gornova IB, Eddaudi R, Salina RN (2003) Use of bacteria of the genus Azotobacter for bioremediation of oil-contaminated soils. Appl Biochem Microbiol 39:279–281
Gray ND, Sherry A, Grant RJ, Rowan AK, Hubert CRJ, Callbeck CM, Aitken CM, Jones DM, Adams JJ, Larter SR, Head IM (2011) The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes. Environ Microbiol 13:2957–2975
Green DH, Echavarri-Bravo V, Brennan D, Hart MC (2015) Bacterial diversity associated with the coccolithophorid algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii. Biomed Res Int 2015:194540
Gutierrez T, Green DH, Whitman WB, Nichols PD, Semple KT, Aitken MD (2012a) 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
Gutierrez T, Nichols PD, Whitman WB, Aitken MD (2012b) Porticoccus hydrocarbonoclasticus sp. nov., an aromatic hydrocarbon-degrading bacterium identified in laboratory cultures of marine phytoplankton. Appl Environ Microbiol 78:628–637
Gutierrez T, Green DH, Nichols PD, Whitman WB, Semple KT, Aitken MD (2013) Polycyclovorans algicola gen. nov., sp. nov., an aromatic-hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton. Appl Environ Microbiol 79:205–214
Gutierrez T, Rhodes G, Mishamandani S, Berry D, Whitman WB, Nichols PD, Semple KT, Aitken MD (2014) Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp. and description of Arenibacter algicola sp. nov., an aromatic hydrocarbon-degrading bacterium. Appl Environ Microbiol 80:618–628
Hadad D, Geresh S, Sivan A (2005) Biodegradation of polyethylene by the thermophilic bacterium Brevibacillus borstelensis. J Appl Microbiol 98:1093–1100
Halden RU, Halden BG, Dwyer DF (1999) Removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin from soils inoculated with Sphingomonas sp. strain RW1. Appl Environ Microbiol 65:2246–2249
Hamamura N, Arp DJ (2000) Isolation and characterization of alkane-utilizing Nocardioides sp. strain CF8. Microbiol Lett 186:21–26
Hamann C, Hegemann J, Hildebrandt A (1999) Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett 173:255–263
Harms G, Zengler K, Rabus R, Aeckersberg F, Minz D, Rossello-Mora R, Widdel F (1999) Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria. Appl Environ Microbiol 65:999–1004
Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K (2007) Characterization of diverse hydrocarbon-degrading bacteria isolated from Indonesian seawater. Microbes Environ 22:412–415
Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K (2008) Tranquillimonas alkanivorans gen. nov., sp. nov., an alkane-degrading bacterium isolated from Semarang Port in Indonesia. Int J Syst Evol Microbiol 58:2118–2121
Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K (2009a) Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia. Int J Syst Evol Microbiol 59:388–391
Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K (2009b) Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia. Int J Syst Evol Microbiol 59:392–396
Hassanshahian M, Ahmadinejad M, Tebyanian H, Kariminik A (2013) Isolation and characterization of alkane degrading bacteria from petroleum reservoir waste water in Iran (Kerman and Tehran provenances). Mar Pollut Bull 73:300–305
Hays SG, Patrick WG, Ziesack M, Oxman N, Silver PA (2015) Better together: engineering and application of microbial symbioses. Curr Opin Biotechnol 36:40–49
Hazen TC, Prince RC, Mahmoudi N (2016) Marine oil biodegradation. Environ Sci Technol 50:2121–2129
Hedlund BP, Staley JT (2001) Vibrio cyclotrophicus sp. nov., a polycyclic aromatic hydrocarbon (PAH)-degrading marine bacterium. Int J Syst Evol Microbiol 51:61–66
Hedlund BP, Geiselbrecht AD, Bair TJ, Staley JT (1999) Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Appl Environ Microbiol 65:251–259
Hedlund BP, Dodsworth JA, Murugapiran SK, Rinke C, Woyke T (2014) Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles 18:865–875
Hernandez-Raquet G, Budzinski H, Caumette P, Dabert P, Le Ménach K, Muyzer G, Duran R (2006) Molecular diversity studies of bacterial communities of oil polluted microbial mats from the Etang de Berre (France). FEMS Microbiol Ecol 58:550–562
Hess A, Zarda B, Hahn D, Haner A, Stax D, Hohener P, Zeyer J (1997) In situ analysis of denitrifying toluene- and m-xylene-degrading bacteria in a diesel fuel-contaminated laboratory aquifer column. Appl Environ Microbiol 63:2136–2141
Heyer J, Berger U, Hardt M, Dunfield PF (2005) Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea. Int J Syst Evol Microbiol 55:1817–1826
Higashioka Y, Kojima H, Watanabe M, Fukui M (2013) Desulfatitalea tepidiphila gen. nov., sp. nov., a sulfate-reducing bacterium isolated from tidal flat sediment. Int J Syst Evol Microbiol 63:761–765
Hirayama H, Fuse H, Abe M, Miyazaki M, Nakamura T, Nunoura T, Furushima Y, Yamamoto H, Takai K (2013) Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments. Int J Syst Evol Microbiol 63:1073–1082
Hirayama H, Abe M, Miyazaki M, Nunoura T, Furushima Y, Yamamoto H, Takai K (2014) Methylomarinovum caldicuralii gen. nov., sp. nov., a moderately thermophilic methanotroph isolated from a shallow submarine hydrothermal system, and proposal of the family Methylothermaceae fam. nov. Int J Syst Evol Microbiol 64:989–999
Hoefman S, van der Ha D, Iguchi H, Yurimoto H, Sakai Y, Boon N, Vandamme P, Heylen K, De Vos P (2014) Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water. Int J Syst Evol Microbiol 64:2100–2107
Hou S, Makarova KS, Saw JH, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M (2008) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3:26
Hristova KR, Schmidt R, Chakicherla AY, Legler TC, Wu J, Chain PS, Scow KM, Kane SR (2007) Comparative transcriptome analysis of Methylibium petroleiphilum pm1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Appl Environ Microbiol 73:7347–7357
Hu YT, Zhou PJ, Zhou YG, Liu ZH, Liu SJ (2004) Saccharothrix xinjiangensis sp. nov., a pyrene-degrading actinomycete isolated from Tianchi Lake, Xinjiang, China. Int J Syst Evol Microbiol 54:2091–2094
Hu P, Dubinsky EA, Probst AJ, Wang J, Sieber CM, Tom LM, Gardinali PR, Banfield JF, Atlas RM, Andersen GL (2017) Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proc Natl Acad Sci USA 114:7432–7437
Huang Y, Zeng Y, Feng H, Wu Y, Xu X (2015) Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus. Int J Syst Evol Microbiol 65:1531–1536
Hubert CR, Oldenburg TB, Fustic M, Gray ND, Larter SR, Penn K, Rowan AK, Seshadri R, Sherry A, Swainsbury R, Voordouw G, Voordouw JK, Head IM (2012) Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil. Environ Microbiol 14:387–404
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y (2016) A new view of the tree of life. Nat Microbiol 1:16048
Ibacache-Quiroga C, Ojeda J, Espinoza-Vergara G, Olivero P, Cuellar M, Dinamarca MA (2013) The hydrocarbon-degrading marine bacterium Cobetia sp. strain MM1IDA2H-1 produces a biosurfactant that interferes with quorum sensing of fish pathogens by signal hijacking. Microb Biotechnol 6:394–405
Iguchi H, Yurimoto H, Sakai Y (2011) Methylovulum miyakonense gen. nov., sp. nov., a type I methanotroph isolated from forest soil. Int J Syst Evol Microbiol 61:810–815
Iida T, Mukouzaka Y, Nakamura K, Kudol T (2003) Plasmid-borne genes code for an angular dioxygenase involved in dibenzofuran degradation by Terrabacter sp. Strain YK3. Appl Environ Microbiol 68:3716–3723
Ilori MO, Amund D, Robinson CK (2000) Ultrastructure of two oil-degrading bacteria isolated from the tropical soil environment. Folia Microbiol 45:259–262
Iwabuchi N, Sunairi M, Urai M, Itoh C, Anzai H, Nakajima M, Harayama S (2002) Extracellular polysaccharides of Rhodococcus rhodochrous S-2 stimulate the degradation of aromatic components in crude oil by indigenous marine bacteria. Appl Environ Microbiol 68:2337–2343
Iwaki H, Yamamoto T, Hasegawa Y (2018) Isolation of marine xylene-utilizing bacteria and characterization of Halioxenophilus aromaticivorans gen. nov., sp. nov. and its xylene degradation gene cluster. FEMS Microbiol Lett 365(7):fny042
Jahromi H, Fazaelipoor MH, Ayatollahi S, Niazi A (2014) Asphaltenes biodegradation under shaking and static conditions. Fuel 117:230–235
Jeon CO, Park W, Ghiorse WC, Madsen EL (2004) Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment. Int J Syst Evol Microbiol 54:93–97
Jeong HI, Jin HM, Jeon CO (2015) Confluentimicrobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from sea-tidal-flat sediment, and emended description of the genus Confluentimicrobium Park et al. 2015. Int J Syst Evol Microbiol 65:4191–4195
Jeong HI, Jin HM, Jeon CO (2016) Complete genome sequence of Sphingorhabdus sp. M41, a versatile hydrocarbon degrader, isolated from crude oil-contaminated costal sediment. J Biotechnol 227:41–42
Jin HM, Im Jeong H, Jeon CO (2015) Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013. Int J Syst Evol Microbiol 65:1550–1555
Juhasz AL, Stanley GA, Britz ML (2000) Microbial degradation and detoxification of high molecular weight polycyclic aromatic hydrocarbons by Stenotrophomonas maltophilia strain VUN 10,003. Lett Appl Microbiol 30:396–401
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, pp 21–132
Jurelevicius D, Alvarez VM, Marques JM, de Sousa Lima LRF, de Almeida Dias F, Seldin L (2013) Bacterial community response to petroleum hydrocarbon amendments in freshwater, marine, and hypersaline water-containing microcosms. Appl Environ Microbiol 79:5927–5935
Juteau P, Larocque R, Rho D, LeDuy A (1999) Analysis of the relative abundance of different types of bacteria capable of toluene degradation in a compost biofilter. Appl Microbiol Biotechnol 52:863–868
Kaiser RI, Parker DS, Mebel AM (2015) Reaction dynamics in astrochemistry: low-temperature pathways to polycyclic aromatic hydrocarbons in the interstellar medium. Annu Rev Phys Chem 66:43–67
Kalyuzhnaya MG, De Marco P, Bowerman S, Pacheco CC, Lara JC, Lidstrom ME, Chistoserdova L (2006) Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates. Int J Syst Evol Microbiol 56:2517–2522
Kalyuzhnaya MG, Khmelenina V, Eshinimaev B, Sorokin D, Fuse H, Lidstrom M, Trotsenko Y (2008) Classification of halo(alkali)philic and halo(alkali)tolerant methanotrophs provisionally assigned to the genera Methylomicrobium and Methylobacter and emended description of the genus Methylomicrobium. Int J Syst Evol Microbiol 58:591–596
Kämpfer P, Denger K, Cook AM, Lee ST, Jäckel U, Denner EB, Busse HJ (2006) Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov. Int J Syst Evol Microbiol 56:815–819
Kanaly RA, Harayama S (2000) Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria. J Bacteriol 182:2059–2067
Kanaly RA, Harayama S, Watanabe K (2002) Rhodanobacter sp. strain BPC1 in a benzo[a]pyrene-mineralizing bacterial consortium. Appl Environ Microbiol 68:5826–5833
Kanamori T, Rashid N, Morikawa M, Atomi H, Imanaka T (2002) Oleomonas sagaranensis gen. nov., sp. nov., represents a novel genus in the alpha-proteobacteria. FEMS Microbiol Lett 217:255–261
Kebbouche-Gana S, Gana ML, Khemili S, Fazouane-Naimi F, Bouanane NA, Penninckx M, Hacene H (2009) Isolation and characterization of halophilic Archaea able to produce biosurfactants. J Ind Microbiol Biotechnol 36:727–738
Kertesz MA, Kawasaki A (2009) Hydrocarbon-degrading sphingomonads – Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg, pp 1693–1705
Khalifa A, Lee CG, Ogiso T, Ueno C, Dianou D, Demachi T, Katayama A, Asakawa S (2015) Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere. Int J Syst Evol Microbiol 65:3527–3534
Khelifi N, Grossi V, Hamdi M, Dolla A, Tholozan JL, Ollivier B, Hirschler-Réa A (2010) Anaerobic oxidation of fatty acids and alkenes by the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus. Appl Environ Microbiol 76:3057–3060
Khomenkov VG, Shevelev AB, Zhukov VG, Kurlovich AE, Zagustina NA, Popov VO (2005) Application of molecular systematics to study of bacterial cultures consuming volatile organic compounds. Appl Biochem Microbiol 41:154–161
Kim MK, Schubert K, Im WT, Kim KH, Lee ST, Overmann J (2007) Sphingomonas kaistensis sp. nov., a novel alphaproteobacterium containing pufLM genes. Int J Syst Evol Microbiol 57:1527–1534
Kim JM, Le NT, Chung BS, Park JH, Bae JW, Madsen EL, Jeon CO (2008) Influence of soil components on the biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BD-a59. Appl Environ Microbiol 74:7313–7320
Kim SJ, Park SJ, Cha IT, Min D, Kim JS, Chung WH, Chae JC, Jeon CO, Rhee SK (2014a) Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis. Environ Microbiol 16:189–204
Kim SJ, Park SJ, Jung MY, Kim JG, Madsen EL, Rhee SK (2014b) An uncultivated nitrate-reducing member of the genus Herminiimonas degrades toluene. Appl Environ Microbiol 80:3233–3243
Kim SH, Kim JG, Jung MY, Kim SJ, Gwak JH, Yu WJ, Roh SW, Kim YH, Rhee SK (2018) Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater. Int J Syst Evol Microbiol 68:2258–2264
Klankeo P, Nopcharoenkul W, Pinyakong O (2009) Two novel pyrene-degrading Diaphorobacter sp. and Pseudoxanthomonas sp. isolated from soil. J Biosci Bioeng 108:488–495
Kleindienst S, Herbst FA, Stagars M, von Netzer F, von Bergen M, Seifert J, Peplies J, Amann R, Musat F, Lueders T, Knittel K (2014) Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps. ISME J 8:2029–2044
Knief C (2015) Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front Microbiol 6:1346
Kodama Y, Stiknowati LI, Ueki A, Ueki K, Watanabe K (2008) Thalassospira tepidiphila sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from seawater. Int J Syst Evol Microbiol 58:711–715
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
Kuever J, Rainey FA, Widdel F (2005) Family Desulfohalobiaceae. In: Garrity GM (ed) Bergey’s manual of systematic bacteriology, vol 2, 2nd edn. Springer, New York, pp 948–955
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Kummer C, Schumann P, Stackebrandt E (1999) Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int J Syst Bacteriol 49:1513–1522
Kunapuli U, Jahn MK, Lueders T, Geyer R, Heipieper HJ, Meckenstock RU (2010) Desulfitobacterium aromaticivorans sp. nov. and Geobacter toluenoxydans sp. nov., iron-reducing bacteria capable of anaerobic degradation of monoaromatic hydrocarbons. Int J Syst Evol Microbiol 60:686–695
Kuppusamy S, Thavamani P, Megharaj M, Lee YB, Naidu R (2016) Kinetics of PAH degradation by a new acid-metal-tolerant Trabulsiella isolated from the MGP site soil and identification of its potential to fix nitrogen and solubilize phosphorous (sic). J Hazard Mater 307:99–107
Kwon KK, Lee HS, Yang SY, Kim SJ (2005) Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the “Alphaproteobacteria”. Int J Syst Evol Microbiol 55:2033–2037
Kwon KK, Lee HS, Jung HB, Kang JH, Kim SJ (2006) Yeosuana aromativorans gen. nov., sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae, isolated from estuarine sediment of the South Sea, Korea. Int J Syst Evol Microbiol 56:727–732
Lai Q, Yuan J, Wu C, Shao Z (2009) Oceanibaculum indicum gen. nov., sp. nov., isolated from deep seawater of the Indian Ocean. Int J Syst Evol Microbiol 59:1733–1737
Lai Q, Cao J, Yuan J, Li F, Shao Z (2014) Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int J Syst Evol Microbiol 64:4160–4167
LaRoe SL, Wang B, Han JI (2010) Isolation and characterization of a novel polycyclic aromatic hydrocarbon–degrading bacterium, Sphingopyxis sp. strain M2R2, capable of passive spreading motility through soil. Environ Eng Sci 27:505–512
Lavania M, Cheema S, Sarma PM, Mandal AK, Lal B (2012) Biodegradation of asphalt by Garciaella petrolearia TERIG02 for viscosity reduction of heavy oil. Biodegradation 23:15–24
Le Petit J, Bertrand JC, N’Guyen MH, Tagger S (1975) On the taxonomy and physiology of bacteria utilizing hydrocarbons in the sea. Ann Microbiol (Paris) 126:367–380
Lee Y, Jeon CO (2018) Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil. Int J Syst Evol Microbiol 68:1251–1257
Lee DW, Lee H, Kwon BO, Khim JS, Yim UH, Park H, Park B, Choi IG, Kim BS, Kim JJ (2018) Zobellella maritima sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium, isolated from beach sediment. Int J Syst Evol Microbiol 68:2279–2284
Leys NMEJ, Ryngaert A, Bastiaens L, Verstraete W, Top EM, Springael D (2004) Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl Environ Microbiol 70:1944–1955
Li H, Liu YH, Luo N, Zhang XY, Luan TG, Hu JM, Wang ZY, Wu PC, Chen MJ, Lu JQ (2006) Biodegradation of benzene and its derivatives by a psychrotolerant and moderately haloalkaliphilic Planococcus sp. strain ZD22. Res Microbiol 157:629–636
Li G, He Z, An T, Zeng X, Sheng G, Fu J (2008) Comparative study of the elimination of toluene vapours in twin biotrickling filters using two microorganisms Bacillus cereus S1 and S2. J Chem Technol Biotechnol 83:1019–1028
Lin WC, Coppi MV, Lovley DR (2004) Geobacter sulfurreducens can grow with oxygen as a terminal electron acceptor. Appl Environ Microbiol 74:2525–2528
Lipus D, Vikram A, Ross D, Bain D, Gulliver D, Hammack R, Bibby K (2017) Predominance and metabolic potential of Halanaerobium in produced water from hydraulically fractured Marcellus Shale wells. Appl Environ Microbiol 83:e02659–e02616. https://doi.org/10.1128/AEM.02659-16.
Lo Giudice A, Casella P, Caruso C, Mangano S, Bruni V, De Domenico M, Michaud L (2010) Occurrence and characterization of psychrotolerant hydrocarbon-oxidizing bacteria from surface seawater along the Victoria Land coast (Antarctica). Polar Biol 33:929–943
Lo N, Kim KH, Baek K, Jia B, Jeon CO (2015) Aestuariicella hydrocarbonica gen. nov., sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from a sea tidal flat. Int J Syst Evol Microbiol 65:1935–1940
Luo C, Xie S, Sun W, Li X, Cupples AM (2009) Identification of a novel toluene-degrading bacterium from the candidate phylum TM7, as determined by DNA stable isotope probing. Appl Environ Microbiol 75:4644–4647
Ma Y, Wang L, Shao Z (2006) Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer. Environ Microbiol 8:455–465
Maciel H, Mathis H, Lopes Ferreira N, Lyew D, Guiot S, Monot F, Greer C, Fayolle-Guichard F (2008) Use of Mycobacterium austroafricanum IFP 2012 in a MTBE-degrading bioreactor. J Mol Microbiol Biotechnol 15:190–198
Maeda R, Nagashima H, Zulkharnain AB, Iwata K, Omori T (2009) Isolation and characterization of a car gene cluster from the naphthalene, phenanthrene, and carbazole-degrading marine isolate Lysobacter sp. strain OC7. Curr Microbiol 59:154–159
Maneerat S, Bamba T, Harada K, Kobayashi A, Yamada H, Kawai F (2006) A novel crude oil emulsifier excreted in the culture supernatant of a marine bacterium, Myroides sp. strain SM1. Appl Microbiol Biotechnol 70:254–259
Margesin R, Spröer C, Schumann P, Schinner F (2003) Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 53:1291–1296
Martínez I, Mohamed ME, Santos VE, García JL, García-Ochoa F, Díaz E (2017) Metabolic and process engineering for biodesulfurization in Gram-negative bacteria. J Biotechnol 262:47
McGenity TJ (2016) An introduction to cultivation of hydrocarbon-cycling microbes. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols: isolation and cultivation. Springer, Berlin. https://doi.org/10.1007/8623_2015_177.
McGenity TJ, Folwell BD, McKew BA, Sanni GO (2012) Marine crude-oil biodegradation: a central role for interspecies interactions. Aquat Biosyst 8:10
Melcher RJ, Apitz SE, Hemmingsen BB (2002) Impact of irradiation and polycyclic aromatic hydrocarbon spiking on microbial populations in marine sediment for future aging and biodegradability studies. Appl Environ Microbiol 68:2858–2868
Meyer S, Moser R, Neef A, Stahl U, Kampfer P (1999) Differential detection of key enzymes of polyaromatic-hydrocarbon-degrading bacteria using PCR and gene probes. Microbiology 145:1731–1741
Mikolasch A, Hammer E, Schauer F (2003) Synthesis of imidazol-2-yl amino acids by using cells from alkane-oxidizing bacteria. Appl Environ Microbiol 69:1670–1679
Mohanty G, Mukherji S (2008) Biodegradation rate of diesel range n-alkanes by bacterial cultures Exiguobacterium aurantiacum and Burkholderia cepacia. Int Biodeter Biodegr 61:240–250
Mohebali G, Ball AS (2008) Biocatalytic desulfurization (BDS) of petrodiesel fuels. Microbiology 154:2169–2183
Morasch B, Schink B, Tebbe CC, Meckenstock RU (2004) Degradation of o-xylene and m-xylene by a novel sulfate-reducer belonging to the genus Desulfotomaculum. Arch Microbiol 181:407–417
Morris JJ, Kirkegaard R, Szul MJ, Johnson ZI, Zinser ER (2008) Facilitation of robust growth of Prochlorococcus colonies and dilute liquid cultures by “helper” heterotrophic bacteria. Appl Environ Microbiol 74:4530–4534
Mor R, Sivan A (2008) Biofilm formation and partial biodegradation of polystyrene by the actinomycete Rhodococcus ruber. Biodegradation 19:851–858
Muangchinda C, Pansri R, Wongwongsee W, Pinyakong O (2013) Assessment of polycyclic aromatic hydrocarbon biodegradation potential in mangrove sediment from Don Hoi Lot, Samut Songkram Province, Thailand. J Appl Microbiol 114:1311–1324
Muratova A, Pozdnyakova N, Makarov O, Baboshin M, Baskunov B, Myasoedova N, Golovleva L, Turkovskaya O (2014) Degradation of phenanthrene by the rhizobacterium Ensifer meliloti. Biodegradation 25:787–795
Musat F, Harder J, Widdel F (2006) Study of nitrogen fixation in microbial communities of oil-contaminated marine sediment microcosms. Environ Microbiol 8:1834–1843
Nagashima H, Zulkharnain AB, Maeda R, Fuse H, Iwata K, Omori T (2010) Cloning and nucleotide sequences of carbazole degradation genes from marine bacterium Neptuniibacter sp. strain CAR-SF. Curr Microbiol 61:50–56
Nakatsu CH, Hristova K, Hanada S, Meng X-Y, Hanson JR, Scow KM, Kamagata Y (2006) Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. Int J Syst Evol Microbiol 56:983–989
Narro ML, Cerniglia CE, Van Baalen C, Gibson DT (1992) Metabolism of phenanthrene by the marine cyanobacterium Agmenellum quadruplicatum PR-6. Appl Environ Microbiol 58:1351–1359
Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE, Gupta RS (2015) A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie Van Leeuwenhoek 107:467–485
Naysim LO, Kang HJ, Jeon CO (2014) Zhongshania aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from marine sediment, and transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov. Int J Syst Evol Microbiol 64:3768–3774
Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA, Ivanova AE, Lysenko AM, Petrunyaka VV, Osipov GA, Belyaev SS, Ivanov MV (2001) Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int J Syst Evol Microbiol 51:433–446
NCBI (2017) The National Center for biological information. https://www.ncbi.nlm.nih.gov/taxonomy. Accessed 1 Oct 2017
Nie Y, Tang YQ, Li Y, Chi CQ, Cai M, Wu XL (2012) The genome sequence of Polymorphum gilvum SL003B-26A1T reveals its genetic basis for crude oil degradation and adaptation to the saline soil. PLoS One 7:e31261
Nie Y, Fang H, Li Y, Chi CQ, Tang YQ, Wu XL (2013) The genome of the moderate halophile Amycolicicoccus subflavus DQS3-9A1T reveals four alkane hydroxylation systems and provides some clues on the genetic basis for its adaptation to a petroleum environment. PLoS One 8:e70986
Ntougias S, Melidis P, Navrozidou E, Tzegkas F (2015) Diversity and efficiency of anthracene-degrading bacteria isolated from a denitrifying activated sludge system treating municipal wastewater. Int Biodeter Biodegr 97:151–158
Obuekwe CO, Al-Jadi ZK, Al-Saleh ES (2009) Hydrocarbon degradation in relation to cell-surface hydrophobicity among bacterial hydrocarbon degraders from petroleum-contaminated Kuwait desert environment. Int Biodeter Biodegr 63:273–279
Odokumal LO, Dickson AA (2003) Bioremediation of a crude oil polluted tropical rain forest soil. Glob J Environ Sci 2:29–40
Okai M, Kihara I, Yokoyama Y, Ishida M, Urano N (2015a) Isolation and characterization of benzo[a]pyrene-degrading bacteria from the Tokyo Bay area and Tama River in Japan. FEMS Microbiol Lett 362(18):fnv143
Okai M, Watanabe A, Ishida M, Urano N (2015b) Draft genome sequence of a benzo[a]pyrene-degrading bacterium, Olleya sp. strain ITB9. Genome Announc 3:e01328–e01315
Okpokwasili GC, Okorie BB (1988) Biodeterioration potentials of microorganisms isolated from car engine lubricating oil. Tribol Int 21:215–220
Ommedal H, Torsvik T (2007) Desulfotignum toluenicum sp. nov., a novel toluene-degrading, sulphate-reducing bacterium isolated from an oil-reservoir model column. Int J Syst Evol Microbiol 57:2865–2869
Oren A (2017) Aerobic hydrocarbon-degrading Archaea. In: TJ MG (ed) Taxonomy, genomics and ecophysiology of hydrocarbon-degrading microbes, handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg. https://doi.org/10.1007/978-3-319-60053-6_5-1
Ortiz de Montellano PR (2009) Hydrocarbon hydroxylation by cytochrome P450 enzymes. Chem Rev 110:932–948
Ozaki S, Kishimoto N, Fujita T (2006) Isolation and phylogenetic characterization of microbial consortia able to degrade aromatic hydrocarbons at high rates. Microbes Environ 21:44–52
Padden AN, Rainey FA, Kelly DP, Wood AP (1997) Xanthobacter tagetidis sp. nov., an organism associated with Tagetes species and able to grow on substituted thiophenes. Int J Syst Bacteriol 47:394–401
Palleroni NJ, Port AM, Chang HK, Zylstra GJ (2004) Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the γ-Proteobacteria active in alkane and aromatic hydrocarbon degradation. Int J Syst Evol Microbiol 54:1203–1207
Pal R, Bhasin VK, Lal R (2006) Proposal to reclassify [Sphingomonas] xenophaga Stolz et al. 2000 and [Sphingomonas] taejonensis Lee et al. 2001 as Sphingobium xenophagum comb. nov. and Sphingopyxis taejonensis comb. nov., respectively. Int J Syst Evol Microbiol 56:667–670
Pal S, Kundu A, Banerjee TD, Mohapatra B, Roy A, Manna R, Sar P, Kazy SK (2017) Genome analysis of crude oil degrading Franconibacter pulveris strain DJ34 revealed its genetic basis for hydrocarbon degradation and survival in oil contaminated environment. Genomics 109:374–382
Parales RE, Ditty JL, Harwood CS (2000) Toluene-degrading bacteria are chemotactic towards the environmental pollutants benzene, toluene, and trichloroethylene. Appl Environ Microbiol 66:4098–4104
Peressutti SR, Alvarez HM, Pucci OH (2003) Dynamics of hydrocarbon-degrading bacteriocenosis of an experimental oil pollution in Patagonian soil. Int Biodeter Biodegr 52:21–30
Pham VD, Hnatow LL, Zhang S, Fallon RD, Jackson SC, Tomb JF, DeLong EF, Keeler SJ (2009) Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. Environ Microbiol 11:176–187
Pinyakong O, Tiangda K, Iwata K, Omori T (2012) Isolation of novel phenanthrene-degrading bacteria from seawater and the influence of its physical factors on the degradation of phenanthrene. Sci Asia 38:36–43
Pirnik MP, Atlas RM, Bartha R (1974) Hydrocarbon metabolism by Brevibacterium erythrogenes: normal and branched alkanes. J Bacteriol 119:868–878
Plotnikova EG, Rybkina DO, Anan’ina LN, Yastrebova OV, Demakov VA (2006) Characteristics of microorganisms isolated from technogenic soils of the Kama region. Rus J Ecol 37:233–240
Popa O, Landan G, Dagan T (2017) Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. ISME J 11:543–544
Posman KM, DeRito CM, Madsen EL (2017) Benzene degradation by a Variovorax species within a coal tar-contaminated groundwater microbial community. Appl Environ Microbiol 83:e02658–e02616
Postec A, Ollivier B, Fardeau ML (2017) Objection to the proposition of the new genus Abyssivirga. Int J Syst Evol Microbiol 67:174
Prakash O, Lal R (2006) Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov. Int J Syst Evol Microbiol 56:2147–2152
Prantera MT, Drozdowicz A, Leite SG, Rosado AS (2002) Degradation of gasoline aromatic hydrocarbons by two N2-fixing soil bacteria. Biotechnol Lett 24:85–89
Prince RC (2000) Biodegradation of methyl tertiary-butyl ether (MTBE) and other fuel oxygenates. Crit Rev Microbiol 26:163–178
Prince RC, Parkerton TF, Lee C (2007) The primary aerobic biodegradation of gasoline hydrocarbons. Environ Sci Technol 41:3316–3321
Rabus R, Nordhaus R, Ludwig W, Widdel F (1993) Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. Appl Environ Microbiol 59:1441–1451
Rabus R, Boll M, Heider J, Meckenstock RU, Buckel W, Einsle O, Ermler U, Golding BT, Gunsalus RP, Kroneck PM, Krüger M (2016) Anaerobic microbial degradation of hydrocarbons: from enzymatic reactions to the environment. J Mol Microbiol Biotechnol 26:5–28
Radwan SS, Al-Hasan RH, Ali N, Salamah S, Khanafer M (2005) Oil-consuming microbial consortia floating in the Arabian Gulf. Int Biodeter Biodegr 56:28–33
Raghukumar C, Vipparty V, David JJ, Chandramohan D (2001) Degradation of crude oil by marine cyanobacteria. Appl Microbiol Biotechnol 57:433–436
Rahalkar M, Bussmann I, Schink B (2007) Methylosoma difficile gen. nov., sp. nov., a novel methanotroph enriched by gradient cultivation from littoral sediment of Lake Constance. Int J Syst Evol Microbiol 57:1073–1080
Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633
RDP (2016) Ribosomal database project. http://rdp.cme.msu.edu/. Accessed 1 Oct 2017
Ritter S (2005) Gasoline. Chem Eng News 83(8):37
Robertson WJ, Bowman JP, Franzmann PD, Mee BJ (2001) Desulfosporosinus meridiei sp. nov., a spore-forming sulfate-reducing bacterium isolated from gasoline-contaminated groundwater. Int J Syst Evol Microbiol 51:133–140
Rochman FF, Sheremet A, Tamas I, Saidi-Mehrabad A, Kim JJ, Dong X, Sensen CW, Gieg LM, Dunfield PF (2017) Benzene and naphthalene degrading bacterial communities in an oil sands tailings pond. Front Microbiol 8:1845
Rodrigo-Torres L, Pujalte MJ, Arahal DR (2017) Draft genome sequence of Thalassobius gelatinovorus CECT 4357T, a roseobacter with the potential ability to degrade polycyclic aromatic hydrocarbons. Gene Reports 9:32–36
Rodríguez-Blanco A, Vetion G, Escande ML, Delille D, Ghiglione JF (2010) Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 60:504–509
Röling WFM, Couto de Brito IR, Swannell RPJ, Head IM (2004) Response of Archaeal communities in beach sediments to spilled oil and bioremediation. Appl Environ Microbiol 70:2614–2620
Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67
Roy I, Shukla SK, Mishra AK (1988) n-Dodecane as a substrate for nitrogen fixation by an alkane-utilizing Azospirillum sp. Curr Microbiol 16:303–309
Saadoun I, al-Akhras MA, Abu-Ashour J (1999) Bacterial degradation of hydrocarbons as evidenced by respirometric analysis. Microbios 100:19–25
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Salamanca D, Engesser KH (2014) Isolation and characterization of two novel strains capable of using cyclohexane as carbon source. Environ Sci Pollut Res 21:12757–12766
Sánchez O, Diestra E, Esteve I, Mas J (2005) Molecular characterization of an oil-degrading cyanobacterial consortium. Microb Ecol 50:580–588
Santo M, Weitsman R, Sivan A (2013) The role of the copper-binding enzyme–laccase–in the biodegradation of polyethylene by the actinomycete Rhodococcus ruber. Int Biodeter Biodegr 84:204–210
Sarma PM, Bhattacharya D, Krishnan S, Lal B (2004) Degradation of polycyclic aromatic hydrocarbons by a newly discovered enteric bacterium, Leclercia adecarboxylata. Appl Environ Microbiol 70:3163–3166
Sauret C, Séverin T, Vétion G, Guigue C, Goutx M, Pujo-Pay M, Conan P, Fagervold SK, Ghiglione JF (2014) ‘Rare biosphere’ bacteria as key phenanthrene degraders in coastal seawaters. Environ Pollut 194:246–253
Schink B (1985) Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus. Arch Microbiol 142:295–301
Schleheck D, Tindall BJ, Rosselló-Mora R, Cook AM (2004) Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. Int J Syst Evol Microbiol 54:1489–1497
Schouw A, Eide TL, Stokke R, Pedersen RB, Steen IH, Bødtker G (2016) Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica. Int J Syst Evol Microbiol 66:1724–1734
Selim SA, El-Alfy SM, Hagagy NI, Hassanin AA, Khattab RM, El-Meleigy ES, Aziz MH, Maugeri TL (2012) Oil-biodegradation and biosurfactant production by haloalkaliphilic Archaea isolated from Soda Lakes of the Wadi An Natrun, Egypt. J Pure Appl Microbiol 6:1011–1020
Selvaratnam C, Thevarajoo S, Ee R, Chan KG, Bennett JP, Goh KM, Chong CS (2016) Genome sequence of Roseivirga sp. strain D-25 and its potential applications from the genomic aspect. Mar Genomics 28:29–31
Sepic E, Bricelj M, Leskovsek H (1997) Biodegradation studies of polyaromatic hydrocarbons in aqueous media. J Appl Microbiol 83:561–568
Shao R, Lai Q, Liu X, Sun F, Du Y, Li G, Shao Z (2014) Zunongwangia atlantica sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 64:16–20
Shetty AR, de Gannes V, Obi CC, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H (2015) Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Stand Genomic Sci 10:55
Shi T, Fredrickson JK, Balkwill DL (2001) Biodegradation of polycyclic aromatic hydrocarbons by Sphingomonas strains isolated from the terrestrial subsurface. J Ind Microbiol Biotechnol 26:283–289
Shinoda Y, Sakai Y, Uenishi H, Uchihashi Y, Hiraishi A, Yukawa H, Yurimoto H, Kato N (2004) Aerobic and anaerobic toluene degradation by a newly isolated denitrifying bacterium, Thauera sp. Strain DNT-1. Appl Environ Microbiol 70:1385–1392
Shinoda Y, Akagi J, Uchihashi Y, Hiraishi A, Yukawa H, Yurimoto H, Sakai Y, Kato N (2005) Anaerobic degradation of aromatic compounds by Magnetospirillum strains: isolation and degradation genes. Biosci Biotechnol Biochem 69:1483–1491
Simarro R, González N, Bautista LF, Molina MC (2013) Assessment of the efficiency of in situ bioremediation techniques in a creosote polluted soil: change in bacterial community. J Hazard Mater 262:158–167
Solano-Serena F, Marchal R, Casarégola S, Vasnier C, Lebeault JM, Vandecasteele JP (2000) A Mycobacterium strain with extended capacities for degradation of gasoline hydrocarbons. Appl Environ Microbiol 66:2392–2399
Solano-Serena F, Marchal R, Heiss S, Vandecasteele JP (2004) Degradation of isooctane by Mycobacterium austroafricanum IFP 2173: growth and catabolic pathway. J Appl Microbiol 97:629–639
Song M, Luo C, Jiang L, Zhang D, Wang Y, Zhang G (2015) Identification of benzo[a]pyrene-metabolizing bacteria in forest soils by using DNA-based stable-isotope probing. Appl Environ Microbiol 81:7368–7376
Soucy SM, Huang J, Gogarten JP (2015) Horizontal gene transfer: building the web of life. Nat Rev Genet 16:472–482
Spang A, Caceres EF, Ettema TJ (2017) Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357:eaaf3883
Spring S, Scheuner C, Göker M, Klenk H-P (2015) A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 6:281
Stoecker K, Bendinger B, Schöning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M (2006) Cohn’s Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc Natl Acad Sci USA 103:2363–2367
Stucki G, Alexander M (1987) Role of dissolution rate and solubility in biodegradation of aromatic compounds. Appl Environ Microbiol 53:292–297
Surovtseva EG, Ivoilov VS, Beliaev SS (1999) Physiologo-biochemical properties of a strain of Beijerinckia mobilis 1phi Phn + − a degrader of polycyclic aromatic hydrocarbons. Microbiology 68:845–850
Szabó I, Szoboszlay S, Kriszt B, Háhn J, Harkai P, Baka E, Táncsics A, Kaszab E, Privler Z, Kukolya J (2011) Olivibacter oleidegradans sp. nov., a hydrocarbon-degrading bacterium isolated from a biofilter clean-up facility on a hydrocarbon-contaminated site. Int J Syst Evol Microbiol 61:2861–2865
Szoboszlay S, Atzél B, Kukolya J, Tóth EM, Márialigeti K, Schumann P, Kriszt B (2008) Chryseobacterium hungaricum sp. nov., isolated from hydrocarbon-contaminated soil. Int J Syst Evol Microbiol 58:2748–2754
Tavormina PL, Hatzenpichler R, McGlynn S, Chadwick G, Dawson KS, Connon SA, Orphan VJ (2015) Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the ‘deep sea-1’ clade of marine methanotrophs. Int J Syst Evol Microbiol 65:251–259
Teramoto M, Ohuchi M, Hatmanti A, Darmayati Y, Widyastuti Y, Harayama S, Fukunaga Y (2011) Oleibacter marinus gen. nov., sp. nov., a bacterium that degrades petroleum aliphatic hydrocarbons in a tropical marine environment. Int J Syst Evol Microbiol 61:375–380
Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL (2015) Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 197:359–370
Tourova TP, Sokolova DS, Semenova EM, Shumkova ES, Korshunova AV, Babich TL, Poltaraus AB, Nazina TN (2016) Detection of n-alkane biodegradation genes alkB and ladA in thermophilic hydrocarbon-oxidizing bacteria of the genera Aeribacillus and Geobacillus. Microbiology 85:693–707
Trautwein K, Kühner S, Wöhlbrand L, Halder T, Kuchta K, Steinbüchel A, Rabus R (2008) Solvent stress response of the denitrifying bacterium “Aromatoleum aromaticum” strain EbN1. Appl Environ Microbiol 74:2267–2274
Tsubota J, Eshinimaev BT, Khmelenina VN, Trotsenko YA (2005) Methylothermus thermalis gen. nov., sp. nov., a novel moderately thermophilic obligate methanotroph from a hot spring in Japan. Int J Syst Evol Microbiol 55:1877–1884
Tzintzun-Camacho O, Loera O, Ramírez-Saad HC, Gutiérrez-Rojas M (2012) Comparison of mechanisms of hexadecane uptake among pure and mixed cultures derived from a bacterial consortium. Int Biodeter Biodegr 70:1–7
Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T (2013) Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 31:154–165
Valentine DL, Reddy CM (2015) Latent hydrocarbons from cyanobacteria. Proc Natl Acad Sci USA 112:13434–13435
van Teeseling MCF, Pol A, Harhangi HR, van der Zwart S, Jetten MSM, Op den Camp HJM, van Niftrik L (2014) Expanding the verrucomicrobial methanotrophic world: description of three novel species of Methylacidimicrobium gen. nov. Appl Environ Microbiol 80:6782–6791
Vandenbroucke M, Largeau C (2007) Kerogen origin, evolution and structure. Org Geochem 38:719–833
Viggor S, Jõesaar M, Vedler E, Kiiker R, Pärnpuu L, Heinaru A (2015) Occurrence of diverse alkane hydroxylase alkB genes in indigenous oil-degrading bacteria of Baltic Sea surface water. Mar Pollut Bull 101:507–516
Vigliotta G, Nutricati E, Carata E, Tredici SM, De Stefano M, Pontieri P, Massardo DR, Prati MV, De Bellis L, Alifano P (2007) Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic gamma-Proteobacterium. Appl Environ Microbiol 73:3556–3565
Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P (2017) Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 8:682
Wang YN, Cai H, Chi CQ, Lu AH, Lin XG, Jiang ZF, Wu XL (2007) Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium. Int J Syst Evol Microbiol 57:1222–1226
Wang L, Wang W, Lai Q, Shao Z (2010) Gene diversity of CYP153A and AlkB alkane hydroxylases in oil-degrading bacteria isolated from the Atlantic Ocean. Environ Microbiol 12:1230–1242
Wang X, Jin D, Zhou L, Wu L, An W, Zhao L (2014a) Draft genome sequence of Advenella kashmirensis strain W13003, a polycyclic aromatic hydrocarbon-degrading bacterium. Genome Announc 2:e00003–e00014
Wang W, Zhong R, Shan D, Shao Z (2014b) Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow sea, China. Appl Microbiol Biotechnol 98:7253–7269
Wang Z, Yang C, Parrott JL, Frank RA, Yang Z, Brown CE, Hollebone BP, Landriault M, Fieldhouse B, Liu Y, Zhang G (2014c) Forensic source differentiation of petrogenic, pyrogenic, and biogenic hydrocarbons in Canadian oil sands environmental samples. J Hazard Mater 271:166–177
Wawrik B, Marks CR, Davidova IA, McInerney MJ, Pruitt S, Duncan KE, Suflita JM, Callaghan AV (2016) Methanogenic paraffin degradation proceeds via alkane addition to fumarate by ‘Smithella’ spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens. Environ Microbiol 18:2604–2619
Weelink SAB, Tan NCG, ten Broeke H, Kieboom C, Van Doesburg W, van Langenhoff AAM, Gerritse J, Junca H, Stams AJM (2008) Isolation and characterization of Alicycliphilus denitrificans strain bc, which grows on benzene with chlorate as the electron acceptor. Appl Environ Microbiol 74:6672–6681
Weelink SA, van Doesburg W, Saia FT, Rijpstra WI, Roling WF, Smidt H, Stams AJ (2009) A strictly anaerobic betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as an electron acceptor. FEMS Microbiol Ecol 70:243–253
Willumsen P, Karlson U, Stackebrandt E, Kroppenstedt RM (2001) Mycobacterium frederiksbergense sp. nov., a novel polycyclic aromatic hydrocarbon-degrading Mycobacterium species. Int J Syst Evol Microbiol 51:1715–1722
Wise MG, McArthur JV, Shimkets LJ (2001) Methylosarcina fibrata gen. nov., sp. nov. and Methylosarcina quisquiliarum sp. nov., novel type I methanotrophs. Int J Syst Evol Microbiol 51:611–621
Wittich RM, Wolff P (2007) Growth of the genetically engineered strain Cupriavidus necator RW112 with chlorobenzoates and technical chlorobiphenyls. Microbiology 153:186–195
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Xie S, Sun W, Luo C, Cupples AM (2010) Stable isotope probing identifies novel m-xylene degraders in soil microcosms from contaminated and uncontaminated sites. Water Air Soil Pollut 212:113–122
Xie S, Sun W, Luo C, Cupples AM (2011) Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing. Biodegradation 22:71–81
Xu HX, Wu HY, Qiu YP, Shi XQ, He GH, Zhang JF, Wu JC (2011) Degradation of fluoranthene by a newly isolated strain of Herbaspirillum chlorophenolicum from activated sludge. Biodegradation 22:335–345
Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lunsdorf 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
Yakimov MM, Giuliano L, Gentile G, Crisafi E, Chernikova TN, Abraham WR, 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
Yakimov MM, Giuliano L, Denaro R, Crisafi E, Chernikova TN, Abraham WR, Luensdorf 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
Yakimov MM, Timmis KN, Golyshin PN (2007) Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 18:257–266
Yamazoe A, Yagi O, Oyaizu H (2004) Degradation of polycyclic aromatic hydrocarbons by a newly isolated dibenzofuran-utilizing Janibacter sp. strain YY-1. Appl Microbiol Biotechnol 65:211–218
Yang J, Yang Y, Wu WM, Zhao J, Jiang L (2014) Evidence of polyethylene biodegradation by bacterial strains from the guts of plastic-eating waxworms. Environ Sci Technol 48:13776–13784
Yumoto I, Nakamura A, Iwata H, Kojima K, Kusumoto K, Nodasaka Y, Matsuyama H (2002) Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons. Int J Syst Evol Microbiol 52:85–90
Yuste L, Corbella ME, Turiegano MJ, Karlson U, Puyet A, Rojo F (2000) Characterization of bacterial strains able to grow on high molecular mass residues from crude oil processing. FEMS Microbiol Ecol 32:69–75
Zarilla KA, Perry JJ (1984) Thermoleophilum album gen. nov. and sp. nov., a bacterium obligate for thermophily and n-alkane substrates. Arch Microbiol 137:286–290
Zengler K, Heider J, Roselló-Mora R, Widdel F (1999) Phototrophic utilization of toluene under anoxic conditions by a new strain of Blastochloris sulfoviridis. Arch Microbiol 172:204–212
Zhang S, Wang Q, Xie S (2012) Stable isotope probing identifies anthracene degraders under methanogenic conditions. Biodegradation 23:221–230
Zhang S, Sun C, Xie J, Wei H, Hu Z, Wang H (2018) Defluviimonas pyrenivorans sp. nov., a novel bacterium capable of degrading polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 68:957–961
Zhao JK, Li XM, Zhang MJ, Jin J, Jiang CY, Liu SJ (2013) Parapedobacter pyrenivorans sp. nov., isolated from a pyrene-degrading microbial enrichment, and emended description of the genus Parapedobacter. Int J Syst Evol Microbiol 63:3994–3999
Zhao D, Kumar S, Zhou J, Wang R, Li M, Xiang H (2017) Isolation and complete genome sequence of Halorientalis hydrocarbonoclasticus sp. nov., a hydrocarbon-degrading haloarchaeon. Extremophiles 21:1081–1090
ZoBell CE (1946) Action of microörganisms on hydrocarbons. Bacteriol Rev 10:1–49
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Switzerland AG
About this entry
Cite this entry
Prince, R.C., Amande, T.J., McGenity, T.J. (2018). Prokaryotic Hydrocarbon Degraders. 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_15-1
Download citation
DOI: https://doi.org/10.1007/978-3-319-60053-6_15-1
Received:
Accepted:
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-60053-6
Online ISBN: 978-3-319-60053-6
eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences