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Introduction to the Isolation and Cultivation of Microbes Involved in the Hydrocarbon Cycle

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Hydrocarbon and Lipid Microbiology Protocols

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Abstract

Our knowledge of the uncultivated microbial majority is driving innovative approaches to cultivation, alongside novel cultivation-independent methods, to better understand microbial ecophysiology, biochemistry, and evolution. Biotechnological applications also provide a major impetus for obtaining microbial cultures, particularly in the field of hydrocarbon and lipid cycling, which address important societal challenges, including: biofuel production, anaerobic digestion, bioplastic synthesis, and mitigating the effects of diverse hydrocarbon pollutants and climate-active gases. This chapter provides a brief overview of cultivation strategies, focussing on those approaches that are most relevant to hydrocarbon cycling. The areas covered include: sample handling, strategies for delivery of carbon and energy sources and terminal electron acceptors, consideration of the physicochemical environment, supply of metabolites and undefined environmental components, assays for microbes, and preservation of cultures.

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References

  1. McGenity TJ, Oren A (2012) Hypersaline environments. In: Bell EM (ed) Life at extremes: environments, organisms and strategies for survival. CAB International, Wallingford, pp 402–437

    Chapter  Google Scholar 

  2. 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  PubMed  Google Scholar 

  3. Yakimov MM, Golyshin PN, Lang S, Moore ERB, 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

    Article  CAS  PubMed  Google Scholar 

  4. He X, McLean JS, Edlund A, Yooseph S, Hall AP, Liu SY et al (2015) Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc Natl Acad Sci U S A 112:244–249

    Article  CAS  PubMed  Google Scholar 

  5. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Sabirova J (2010) Polyhydroxyalkanoates produced by hydrocarbon-degrading bacteria. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 2981–2994

    Chapter  Google Scholar 

  7. Overmann J (2013) Principles of enrichment, isolation, cultivation, and preservation of prokaryotes. In: Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin/Heidelberg, pp 149–207

    Chapter  Google Scholar 

  8. Tanner RS (2007) Cultivation of bacteria and fungi. In: Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (eds) Manual of environmental microbiology, 3rd edn. ASM, Washington, pp 69–78. doi 10.1128/9781555815882.ch6

  9. Morales M, Le Borgne S (2014) Protocols for the isolation and preliminary characterization of bacteria for biodesulfurization and biodenitrogenation of petroleum-derived fuels. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_41

  10. Müller AL, de Rezende JR, Hubert CRJ, Kjeldsen KU, Lagkouvardos I, Berry D, Jørgensen BB, Loy A (2013) Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents. ISME J 8:1153–1165

    Article  PubMed  PubMed Central  Google Scholar 

  11. Horikoshi K (1999) Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 63:735–750

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Priscu JC, Achberger AM, Cahoon JE, Christner BC, Edwards RL, Jones WL et al (2013) A microbiologically clean strategy for access to the Whillans Ice Stream subglacial environment. Antarct Sci 25:637–647

    Article  Google Scholar 

  13. Gramain A, Chong Díaz G, Demergasso C, Lowenstein TK, McGenity TJ (2011) Archaeal diversity along a subterranean salt core from the Salar Grande (Chile). Environ Microbiol 13:2105–2121

    Article  PubMed  Google Scholar 

  14. Tsesmetzis N, Maguire MJ, Head IM, Lomans BP(2016) Protocols for investigating the microbial communities of oil and gas reservoirs. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi:10.1007/8623_2016_212

  15. Callaghan AV, Wawrik B (2014) Protocols for investigating the microbiology of coal-bed produced waters. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_32

  16. Cragg BA, Bale SJ, Parkes RJ (1992) A novel method for the transport and long-term storage of cultures and samples in an anaerobic atmosphere. Lett Appl Microbiol 15:125–128

    Article  Google Scholar 

  17. Foght JM, Siddique T, Gieg LM (2014) Protocols for handling, storing and cultivating oil sands tailings ponds materials for microbial and molecular biological study. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_26

  18. Kieft TL (2014) Sampling the subsurface. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_27

  19. Gutierrez T (2014) Cultivating aerobic hydrocarbon-degrading microbes from micro-algae. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_1

  20. Coulon F, Chronoupolou P-M, Fahy A, Païssé S, Goñi-Urriza MS, Peperzak L, Acuña-Alvarez L, McKew BA, Brussard C, Underwood GJC, Timmis KN, Duran R, McGenity TJ (2012) Central role of dynamic tidal biofilms dominated by aerobic hydrocarbonoclastic bacteria and diatoms in the biodegradation of hydrocarbons in coastal mudflats. Appl Environ Microbiol 78:3638–3648

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Genovese M, Denaro R, Russo D, Crisafi F, Santisi S, Cappello S, Giuliano L, Yakimov MM (2015) Cultivation and preservation of hydrocarbonoclastic microorganisms, particularly Cycloclasticus species. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi:10.1007/8623_2015_167

  22. Chronopoulou P-M, Sanni GO, Silas-Olu DI, van der Meer JR, Brussaard CPD, Timmis KN, McGenity TJ (2015) Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea. Microb Biotechnol 8:434–447

    Article  CAS  PubMed  Google Scholar 

  23. Redmond MC, Valentine DL (2011) Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proc Natl Acad Sci U S A 109:20292–20297

    Article  PubMed  PubMed Central  Google Scholar 

  24. Murrell JC (2010) The aerobic methane oxidizing bacteria (Methanotrophs). In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 1953–1966

    Chapter  Google Scholar 

  25. Dedysh SN, Dunfield PF (2014) Cultivation of methanotrophs. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_14

  26. Kelly DP, Ardley JK, Wood AP (2014) Cultivation of methylotrophs. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_4

  27. Crombie AT, Murrell JC (2014) Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature 510:148–151

    Article  CAS  PubMed  Google Scholar 

  28. Acuña Alvarez L, Exton DA, Suggett DJ, Timmis KN, McGenity TJ (2009) Characterization of marine isoprene-degrading communities. Environ Microbiol 11:3280–3291

    Article  Google Scholar 

  29. Rosenberg E (2006) Hydrocarbon-oxidizing bacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 564–577

    Chapter  Google Scholar 

  30. Horowitz A, Gutnick D, Rosenberg E (1975) Sequential growth of bacteria on crude oil. Appl Microbiol 30:10–19

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Zamir SM, Tavassoli T, Shojaosadati SA (2015) Protocol for isolation, screening and cultivation of asphaltene-degrading microorganisms. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi:10.1007/8623_2015_163

  32. Whitby C (2010) Microbial naphthenic acid degradation. Adv Appl Microbiol 70:93–125

    Article  CAS  PubMed  Google Scholar 

  33. Aeppli C, Carmichael CA, Nelson RK, Lemkau KL, Graham WM, Redmond MC, Valentine D, Reddy CM (2012) Oil weathering after the Deepwater Horizon disaster led to the formation of oxygenated residues. Environ Sci Technol 46:87–99

    Article  Google Scholar 

  34. King TL, Robinson B, Boufadel M, Lee K (2014) Flume tank studies to elucidate the fate and behavior of diluted bitumen spilled at sea. Mar Pollut Bull 83:32–37

    Article  CAS  PubMed  Google Scholar 

  35. Demeter MA, Lemire JA, Yue G, Ceri H, Turner RJ (2015) Culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation. Front Microbiol 6:936

    Article  PubMed  PubMed Central  Google Scholar 

  36. Johnson RJ, Smith BE, Sutton PA, McGenity TJ, Rowland SJ, Whitby C (2011) Microbial biodegradation of aromatic alkanoic naphthenic acids is affected by the degree of alkyl side chain branching. ISME J 5:486–496

    Article  CAS  PubMed  Google Scholar 

  37. Katayama T, Kamagata Y (2015) Cultivation of methanogens. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_141

  38. Duong VT, Bao B, Schenk PM (2015) Oleaginous microalgae isolation and screening for lipid productivity using a standard protocol. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi:10.1007/8623_2015_181

  39. Morin N, Crutz-Le Coq A-M, Rossignol T, Nicaud JM (2014) Protocols for monitoring growth and lipid accumulation in oleaginous yeasts. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_40

  40. Fahy A, Ball AS, Lethbridge G, McGenity TJ, Timmis KN (2008) High concentrations of benzene can favour Gram-positive microorganisms in groundwaters from a contaminated aquifer. FEMS Microbiol Ecol 65:526–533

    Article  CAS  PubMed  Google Scholar 

  41. Singh AK, Sherry A, Gray ND, Jones DM, Bowler BFJ, Head IM (2014) Kinetic parameters for nutrient enhanced crude oil biodegradation in intertidal marine sediments. Front Microbiol 5:160

    Article  PubMed  PubMed Central  Google Scholar 

  42. Bucheli-Witschel M, Egli T (2010) Growth of hydrocarbon-degrading bacteria in continuous culture. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 3530–3541

    Google Scholar 

  43. Aburto A, Fahy A, Coulon F, Lethbridge G, Ball AS, Timmis KN, McGenity TJ (2009) Mixed aerobic and anaerobic microbial communities in benzene-contaminated groundwater. J Appl Microbiol 107:317–328

    Article  Google Scholar 

  44. Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70:4748–4755

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Terrisse F, Duran R, Vitte I, Cravo-Laureau C (2015) Simulation of anoxic–oxic oscillations in crude oil-degrading bioreactors. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_43

  46. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS (1979) Methanogens: reevaluation of a unique biological group. Microbiol Rev 43:260–296

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Barnum TP, Coates JD (2016) Enrichment and isolation of chloroxyanion-respiring hydrocarbon oxidizers. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi:10.1007/8623_2016_194

  48. Widdel F (2016) Cultivation of anaerobic microorganisms with hydrocarbons as growth substrates. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi:10.1007/8623_2015_186

  49. Widdel F, Bak F (1992) Gram-negative mesophilic sulfate-reducing bacteria. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K-H (eds) The prokaryotes, vol 4, 2nd edn. Springer, New York, pp 3352–3378

    Chapter  Google Scholar 

  50. Heider J, Schühle K (2013) Anaerobic biodegradation of hydrocarbons including methane. In: Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin/Heidelberg, pp 605–634

    Chapter  Google Scholar 

  51. Widdel F, Musat F (2010) Diversity and common principles in enzymatic activation of hydrocarbons. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 983–1009

    Google Scholar 

  52. Widdel F, Kinttel K, Galushko A (2010) Anaerobic hydrocarbon-degrading microorganisms: an overview. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 1997–2021

    Chapter  Google Scholar 

  53. Williamson AJ, Coates JD (2016) Enrichment and isolation of metal respiring hydrocarbon oxidizers. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks doi: 10.1007/8623_2016_198

  54. Ettwig KF, Speth DR, Reimann J, Wu ML, Jetten MSM, Keltjens JT (2012) Bacterial oxygen production in the dark. Front Microbiol 3:273

    Article  PubMed  PubMed Central  Google Scholar 

  55. Kaye JZ, Baross JA (2004) Synchronous effects of temperature, hydrostatic pressure, and salinity on growth, phospholipid profiles, and protein patterns of four Halomonas species isolated from deep-sea hydrothermal-vent and sea surface environments. Appl Environ Microbiol 70:6220–6229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Tasumi E, Yanagawa K, Miyazaki J, Takai K (2015) In vitro high-pressure incubation and activity measurement of deep-sea methanogenic archaea. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_111

  57. Coulon F, McKew BA, Osborn AM, McGenity TJ, Timmis KN (2007) Effects of temperature and biostimulation on oil-degrading microbial communities in temperate estuarine waters. Environ Microbiol 9:177–186

    Article  CAS  PubMed  Google Scholar 

  58. Nakagawa S, Takai K (2006) The isolation of thermophiles from deep-sea hydrothermal environments. In: Rainey FA, Oren A (eds) Methods in microbiology, volume 35, extremophiles. Elsevier, Amsterdam, pp 55–91

    Chapter  Google Scholar 

  59. Russell NJ, Cowan DA (2006) Handling of psychrophilic microorganisms. In: Rainey FA, Oren A (eds) Methods in microbiology, volume 35, extremophiles. Elsevier, Amsterdam, pp 371–393

    Chapter  Google Scholar 

  60. Lo Giudice A, Rizzo C (2015) Protocols for investigating hydrocarbon-oxidizing bacterial communities in polar seas and ice. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi:10.1007/8623_2015_147

  61. Thrash JC, Weckhorst JL, Pitre DM (2015) Cultivating fastidious microbes. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_67

  62. Zengler K, Behrendt L (2014) Protocols for high throughput isolation and cultivation. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_38

  63. Bagi A, Pampanin DM, Brakstad OG, Kommedal R (2013) Estimation of hydrocarbon biodegradation rates in marine environments: a critical review of the Q10 approach. Mar Environ Res 89:83–90

    Article  CAS  PubMed  Google Scholar 

  64. Yayanos AA (1986) Evolutional and ecological implications of the properties of deep-sea barophilic bacteria. Proc Natl Acad Sci U S A 83:9542–9546

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Tamburini C, Boutrif M, Garel M, Colwell RR, Deming JW (2013) Prokaryotic responses to hydrostatic pressure in the ocean – a review. Environ Microbiol 15:1262–1274

    Article  CAS  PubMed  Google Scholar 

  66. Smedile F, La Cono V, Genovese M, Ruggeri G, Denaro R, Crisafi F, Giuliano L, Yakimov MM (2016) High pressure cultivation of hydrocarbonoclastic aerobic bacteria. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi 10.1007/8623_2016_208

  67. Kato C (2006) Handling of piezophilic microorganisms. In: Rainey FA, Oren A (eds) Methods in microbiology, volume 35 extremophiles. Elsevier, Amsterdam, pp 733–741

    Chapter  Google Scholar 

  68. Bartscht K, Cypionka H, Overmann J (1999) Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community. FEMS Microbiol Ecol 28:249–259

    Article  CAS  Google Scholar 

  69. Röling WFM (2010) Hydrocarbon-degradation by acidophilic microorganisms. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 1923–1930

    Chapter  Google Scholar 

  70. McGenity TJ, Whitby C, Fahy A (2010) Alkaliphilic hydrocarbon degraders. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 1931–1937

    Chapter  Google Scholar 

  71. Dedysh SN (2011) Cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps. Front Microbiol 2:184

    Article  PubMed  PubMed Central  Google Scholar 

  72. Zengler K, Heider J, Rossello-Mora R, Widdel F (1999) Phototrophic utilization of toluene under anoxic conditions by a new strain Blastochloris sulfoviridis. Arch Microbiol 172:204–212

    Article  CAS  PubMed  Google Scholar 

  73. Lea-Smith DJ, Biller SJ, Davey MP, Cotton CAR, Perez Sepulveda BM, Turchyn AV et al (2015) Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle. Proc Natl Acad Sci U S A. doi:10.1073/pnas.1507274112

    PubMed  PubMed Central  Google Scholar 

  74. McGenity TJ, Folwell BD, McKew BA, Sanni GO (2012) Marine crude-oil biodegradation: a central role for interspecies interactions. Aquatic Biosystems 8:10. doi:10.1186/2046-9063-8-10

  75. McGenity TJ, Gramain A (2010) Isolation and characterization of halophilic hydrocarbon degraders. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 3848–3854

    Google Scholar 

  76. Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K, Tamaki H, Tanaka M, Nakatsu CH, Kamagata Y (2014) A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Appl Environ Microbiol 80:7659–7666

    Article  PubMed  PubMed Central  Google Scholar 

  77. Feng XM, Karlsson A, Svensson BH, Bertilsson S (2010) Impact of trace element addition on biogas production from food industrial waste – Linking process to microbial communities. FEMS Microbiol Ecol 74:226–240

    Article  CAS  PubMed  Google Scholar 

  78. Ünal B, Perry VR, Sheth M, Gomez-Alvarez V, Chin K-J, Nüsslein K (2012) Trace elements affect methanogenic activity and diversity in enrichments from subsurface coal bed produced water. Front Microbiol 3:175. doi:10.3389/fmicb.2012.00175

    Article  PubMed  PubMed Central  Google Scholar 

  79. Demeter MA, Lemire J, Golby S, Schwering M, Ceri H, Turner RJ (2015) Cultivation of environmental bacterial communities as multispecies biofilms. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_82

  80. Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl Environ Microbiol 67:411–419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Deguchi S (2011) Versatile solidified media for growth of extremophiles. In: Horikoshi K (ed) Extremophiles handbook. Springer, Tokyo, pp 737–751

    Chapter  Google Scholar 

  82. de Bruyn JC, Boogerd FC, Bos P, Kuenen JG (1990) Floating filters, a novel technique for isolation and enumeration of fastidious, acidophilic, iron-oxidizing, autotrophic bacteria. Appl Environ Microbiol 56:2891–2894

    PubMed  PubMed Central  Google Scholar 

  83. van Teeseling MC, Pol A, Harhangi HR, van der Zwart S, Jetten MS, Op den Camp HJ, van Niftrik L (2014) Expanding the verrucomicrobial methanotrophic world: description of three novel species of Methylacidimicrobium gen. nov. Appl Environ Microbiol 80:6782–6791

    Article  PubMed  PubMed Central  Google Scholar 

  84. Walker JD, Colwell RR (1976) Enumeration of petroleum-degrading microorganisms. Appl Environ Microbiol 31:198–207.

    Google Scholar 

  85. Prince RC, Butler JD, Bragin GE, Parkerton TF, Redman AD, Kelley BA, Letinski DJ (2016) Preparing the hydrocarbon/crude oil. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi:10.1007/8623_2016_220

  86. Wick LY, Otto S, Holliger C (2015) Two-phase cultivation techniques for hydrocarbon-degrading organisms. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_124

  87. van Hamme JD, Singh A, Ward OP (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67:503–549

    Article  PubMed  PubMed Central  Google Scholar 

  88. Kiyohara H, Nagao K, Yana K (1982) Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl Environ Microbiol 43:454–457

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Shuttleworth KL, Cerniglia CE (1997) Practical methods for the isolation of polycyclic aromatic hydrocarbon (PAH)-degrading microorganisms and the determination of PAH mineralization and biodegradation intermediates. In: Hurst CJ, Knudsen GR, McInerney MJ, Stetzenbach LD, Walter MV (eds) Manual of environmental microbiology. American Society for Microbiology, Washington, DC, pp 766–775

    Google Scholar 

  90. Bogart A, Hemmingsen B (1992) Enumeration of phenanthrene degrading bacteria by an overlay technique and its use in evaluation of petroleum contaminated sites. Appl Environ Microbiol 58:2579–2582

    Google Scholar 

  91. Alley JF, Brown LR (2000) Use of sublimation to prepare solid microbial media with water-insoluble substrates. Appl Environ Microbiol 66:439–442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Colwell RR, Walker JD, Nelson JD (1973) Microbial ecology and the problem of petroleum degradation in Chesapeake Bay. In: Ahearn DG, Myers SP (eds) The microbial degradation of oil pollutants. Louisiana State University, Baton Rouge, pp 185–197

    Google Scholar 

  93. Bastiaens L, Springael D, Wattiau P, Harms H, deWachter R, Verachtert H, Diels L (2000) Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl Environ Microbiol 66:1834–1843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

    Article  PubMed  Google Scholar 

  95. Stewart AJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Lagier J-C, Hugon P, Khelaifia S, Fournier P-E, La Scola B, Raoult D (2015) The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 28:237–264

    Article  PubMed  PubMed Central  Google Scholar 

  97. Ferrari BC, Binnerup SJ, Gillings M (2005) Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol 71:8714–8720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A et al (2010) Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl Environ Microbiol 76:2445–2450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Calvo C, Martinez-Checa F, Toledo FL, Porcel J, Quesada E (2002) Characteristics of bioemulsifiers synthesised in crude oil media by Halomonas eurihalina and their effectiveness in the isolation of bacteria able to grow in the presence of hydrocarbons. Appl Microbiol Biotechnol 60:347–351

    Article  CAS  PubMed  Google Scholar 

  100. Song Y, Li B, Qiu Y, Yin H (2015) Single bacteria studies using microfluidics. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_70

  101. Readman JW, Bayona JM, Albaigés J (2014) Protocols for the chemical analysis of hydrocarbons in petroleum oils and the assessment of environmental contamination. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_7

  102. Walters CC (2016) Protocols for GC-based methods of hydrocarbon analysis. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. doi 10.1007/8623_2015_190

  103. McKew BA, Smith CJ (2015) Real-time PCR approaches for analysis of hydrocarbon-degrading bacterial communities. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_64

  104. Schlosser D, Wick LY (2015) Cultivation of hydrocarbon-degrading fungi. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_97

  105. Beggah S, Van der Meer JR (2014) Protocol for inferring compound biodegradation at low concentrations from biomass measurements. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2014_20

  106. Emtiazi G, Mridamadian S, Habibi MH (2005) Instability of petroleum oil degradation by induction of mutation in 45kb and 60kb plasmids. Int J Environ Stud 62:467–472

    Article  CAS  Google Scholar 

  107. Vekeman B, Heylen K (2015) Preservation of microbial pure cultures and mixed communities. In: McGenity TJ, Timmis KN, Nogales B (eds) Hydrocarbon and lipid microbiology protocols. Springer protocols handbooks. Springer, Berlin. doi:10.1007/8623_2015_51

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Acknowledgements

I’d like to thank Dr Balbina Nogales, Dr Boyd McKew, Mr Gordon Murphy, Mr Tivkaa Amande, and Professor Ken Timmis for their useful comments on this chapter, and Dr Anne Fahy for information in Box 1.

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  1. University of Essex, Colchester, UK

    Terry J. McGenity

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  1. Terry J. McGenity
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Correspondence to Terry J. McGenity .

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Editors and Affiliations

  1. School of Biological Sciences, University of Essex, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

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McGenity, T.J. (2015). Introduction to the Isolation and Cultivation of Microbes Involved in the Hydrocarbon Cycle. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_177

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  • DOI: https://doi.org/10.1007/8623_2015_177

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-45178-6

  • Online ISBN: 978-3-662-45179-3

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