Skip to main content

Electron Microscopy Protocols for the Study of Hydrocarbon-Producing and Hydrocarbon-Decomposing Microbes: Classical and Advanced Methods

  • Protocol
  • First Online:
Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

One of the fascinating areas of hydrocarbon microbiology biology is the quest for an ultratstructural understanding of (macro)-molecular mechanisms underlying the degradation, synthesis, and intracellular storage of hydrocarbons, which due to their hydrophobic characteristics continuously threaten the integrity of biological membranes. Here we review classical and novel advanced electron microscopy approaches, including correlative light and electron microscopy that in combination with genetics and biochemical experimentation can be utilized to study such hydrocarbon–cell interactions.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Ladygina N, Deyukhina EG, Veinshtein MB (2006) A review on microbial synthesis of hydrocarbons. Process Biochem 41:1001–1014

    Article  CAS  Google Scholar 

  2. Head I, Aitken C, Gray N et al (2010) Hydrocarbon degradation in petroleum reservoirs. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg

    Google Scholar 

  3. Sierra-Garcia I, de Oliveira V (2013) Microbial hydrocarbon degradation: efforts to understand biodegradation in petroleum reservoirs. In: Chamy R (ed) Biodegradation – engineering and technology. InTech, ISBN: 978-953-51-1153-5, doi:10.5772/55920

  4. Wenger L, Davis C, Isaksen G 2002 Multiple controls on petroleum biodegradation and impact on oil quality. In: Society for petroleum engineers (SPE) reservoir evaluation and engineering, pp 375–383

    Google Scholar 

  5. Roling W, Head I, Larter S (2003) The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects. Res Microbiol 154:321–328

    Article  CAS  PubMed  Google Scholar 

  6. Atlas R, Bartha R (1993) Microbial ecology - fundamentals and applications. Benjamin-Cummings, Redwood City

    Google Scholar 

  7. Atlas R (1981) Microbial degradation of petroleum hydrocarbons: an environmental perspective. Microbiol Rev 45(1):180–209

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Van Hamme J, Singh A, Ward O (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67(4):503–549

    Article  PubMed  PubMed Central  Google Scholar 

  9. Muthuswamy S, Binupriya A, Baik S, Yun S (2008) Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium isolated from hydrocarbon contaminated areas. Clean 36(1):92–96

    Google Scholar 

  10. Martins L, Piexoto R (2012) Biodegradation of petroleum hydrocarbons in hypersaline environments. Braz J Microbiol 43(3):865–872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Hazen T, Dubinsky E, De Santis T, Andersen G et al (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330(6001):204–208

    Article  CAS  PubMed  Google Scholar 

  12. Baelum J, Borglin S, Chakraborty R, Fortney J et al (2012) Deep-sea bacteria enriched by oil and dispersant from the deepwater horizon spill. Environ Microbiol 14(9):2405–2416

    Article  CAS  PubMed  Google Scholar 

  13. Biological Agents. http://www2.epa.gov/emergency-response/biological-agents. Accessed 24 Nov 2014

  14. Kostka J, Prakash O, Overholt W, Green S et al (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(22):7962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Scott C, Finnerty W (1976) A comparative analysis of the ultrastructure of hydrocarbon – oxidizing microorganisms. J Gen Microbiol 94:342–350

    Article  CAS  PubMed  Google Scholar 

  16. Pinzon N, Aukema K, Gralnick J et al (2011) Nile red detection of bacterial hydrocarbons and ketones in a high throughput format. MBio 2(4):e00109-11. doi:10.1128/mBio.00109-11

    Article  PubMed  PubMed Central  Google Scholar 

  17. Singer M, Tyler S, Finnerty W (1985) Growth of Acinetobacter sp. strain HO1-N on n-hexadecanol: physiological and ultrastructural characteristics. J Bacteriol 162(1):162

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Alvarez H, Steinbuchel A (2002) Triacylglycerols in prokaryotic microorganisms. Appl Microbiol Biotechnol 60:367–376

    Article  CAS  PubMed  Google Scholar 

  19. Waltermann M, Steinbuchel A (2005) Neutral lipid bodies in prokaryotes: recent insights into structure, formation and relationship to eukaryotic lipid depots. J Bacteriol 187(11):3607

    Article  PubMed  PubMed Central  Google Scholar 

  20. Marin M, Pedregosa A, Laborda F (1996) Emulsifier production and microscopical study of emulsions and biofilms formed by the hydrocarbon-utilizing bacteria Acinetobacter calcoaceticus MM5. Appl Microbiol Biotechnol 44:660–667

    Article  CAS  Google Scholar 

  21. Waltermann M, Hinz A, Robenek H et al (2005) Mechanism of lipid body formation in prokaryotes: how bacteria fatten up. Mol Microbiol 55(3):750–763

    Article  PubMed  Google Scholar 

  22. Meng X, Yang J, Xu X, Zhang L, Nie Q, Xian M (2009) Biodiesel production from oleaginous microorganisms. Renew Energy 34:1–5

    Article  Google Scholar 

  23. U.S. Bioenergy Statistics. http://www.ers.usda.gov/data-products/us-bioenergy-statistics. Accessed 10 Oct 2014

  24. Shi S, Valle-Rodriguez J, Siewers V, Nielsen J (2011) Prospects for microbial biodiesel production. Biotechnol J 6:277–285

    Article  CAS  PubMed  Google Scholar 

  25. Suzuki R, Ito N, Uno Y, Nishii I et al (2013) Transformation of lipid bodies related to hydrocarbon accumulation in a green alga, Botryococcus braunii (Race B). PLoS One 8(12), e81626. doi:10.1371/journal.pone.0081626

    Article  PubMed  PubMed Central  Google Scholar 

  26. Davies S, Whittenbury R (1970) Fine structure of methane and other hydrocarbon-utilizing bacteria. J Gen Microbiol 61:227–232

    Article  CAS  PubMed  Google Scholar 

  27. Kennedy R, Finnerty W, Sudarsanan K, Young R (1974) Microbial assimilation of hydrocarbons. I. The fine-structure of a hydrocarbon oxidizing Acinetobacter sp. Arch Microbiol 102:75–83

    Article  Google Scholar 

  28. Alvarez H, Mayer F, Fabritius D, Steinbüchel A (1996) Formation of intracytoplasmic lipid inclusions by Rhodococcus opacus strain PD630. Arch Microbiol 165(6):377–386

    Article  CAS  PubMed  Google Scholar 

  29. Diestra E, Esteve I, Burnat M, Maldonado J, Sole A (2007) Isolation and characterization of a heterotrophic bacterium able to grow in different environmental stress conditions, including crude oil and heavy metals. In: Méndez-Vilas A (ed) Communicating current research and educational topics and trends in applied microbiology. Formex, Badajoz

    Google Scholar 

  30. Osumi M (2012) Visualization of yeast cells by electron microscopy. J Electron Microsc 61(6):343–365

    Article  CAS  Google Scholar 

  31. Li Z (ed) (2002) Industrial application of electron microscopy. CRC Press, Boca Raton, p 362

    Google Scholar 

  32. Wigglesworth V (1975) Lipid staining for the electron microscope: a new method. J Cell Sci 19:425–437

    CAS  PubMed  Google Scholar 

  33. Trent J (1984) Ruthenium tetraoxide staining of polymers: new preparative methods for electron microscopy. Macromolecules 17:2930–2931

    Article  CAS  Google Scholar 

  34. Khandpur A, Macosko C, Bates F (1995) Transmission electron microscopy of saturated hydrocarbon block copolymers. J Polym Sci B Polym Phys 33:247–252

    Article  CAS  Google Scholar 

  35. Richter H, Sleytr U (1971) Fettextraction bei −78°C: nachweis im Gefrieratzbild. Z Naturforsch 26b:470–473

    Google Scholar 

  36. Meyer H, Winkelmann H (1970) Die Darstellung von lipiden bei der gefrieratzpraparation und ihre beziehung zur strukturanalyse biologischer membranen. Exp Pathol 4:47–59

    CAS  Google Scholar 

  37. Moor H, Muhlethaler K (1963) Fine structure in frozen etched yeast cells. J Cell Biol 17:609–628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Meyer H, Richter W (2001) Freeze-fracture studies on lipids and membranes. Micron 32:615–644

    Article  CAS  PubMed  Google Scholar 

  39. Scott C, Finnerty W (1976) Characterization of intracytoplasmic hydrocarbon inclusions from the hydrocarbon-oxidizing Acinetobacter Species HO1-N. J Bacteriol 127(1):481–489

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Ishige T, Tani A, Takabe K, Kawasaki K et al (2002) Wax ester production from n-Alkanes by Acinetobacter sp. strain M-1: ultrastructure of cellular inclusions and role of acyl coenzyme A reductase. Appl Environ Microbiol 68(3):1192–1195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Bleck C, Merz A, Gutierrez M, Alther P et al (2010) Comparison of different methods for thin section EM analysis of Mycobacterium smegmatis. J Microsc 237:23–28

    Article  CAS  PubMed  Google Scholar 

  42. Fujimoto K (1995) Freeze-fracture replica electron microscopy combined with SDS digestion for cytochemical labeling of integral membrane proteins - application to the immunogold labeling of intercellular junctional complexes. J Cell Sci 108:3443–3449

    CAS  PubMed  Google Scholar 

  43. Severs N (1995) Freeze-fracture cytochemistry: an explanatory survey of methods. In: Severs N, Shotton D (eds) Rapid freezing, freeze fracture, and deep etching. Wiley-Liss, New York, pp 173–208

    Google Scholar 

  44. Robenek H, Severs N (2008) Recent advances in freeze-fracture electron microscopy: the replica immunolabeling technique. Biol Proced Online 10:9–19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Scott C, Makula S, Finnerty W (1976) Isolation and characterization of membranes from a hydrocarbon-oxidizing Acinetobacter sp. J Bacteriol 127(1):469–480

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Kellenberger E, Johansen R, Maeder M, Bohrmann B et al (1992) Artefacts and morphological changes during chemical fixation. J Microsc 168:181–201

    Article  CAS  PubMed  Google Scholar 

  47. Mc Donald K, Auer M (2006) High-pressure freezing, cellular tomography, and structural cell biology. Biotechniques 41(2):137, 139, 141

    Google Scholar 

  48. Djaczenko W, Muller M, Benedetto A (1990) Ultra-rapid high pressure freezing in high resolution EM of cell-cell and cell-substrate interactions. Cell Biol Int Rep 14

    Google Scholar 

  49. Dubochet J (1995) High-pressure freezing for cryoelectron microscopy. Trends Cell Biol 5(9):366–368

    Article  CAS  PubMed  Google Scholar 

  50. Hurbain I, Sachse M (2011) The future is cold: cryo-preparation methods for transmission electron microscopy of cells. Biol Cell 103:405–420

    Article  PubMed  Google Scholar 

  51. Paul T, Beveridge T (1994) Preservation of surface lipids and determination of ultrastructure of Mycobacterium kansasii by freeze substitution. Infect Immun 62(5):1542–1550

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Al-Amoudi A, Chang J, Leforestier A, McDowall A et al (2004) Cryo –electron microscopy of vitreous section. EMBO J 23(18):3583–3588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Comolli L, Kundmann M, Downing K (2006) Characterization of intact subcellular bodies in whole bacteria by cryo-electron tomography and spectroscopic imaging. J Microsc 223:40–52

    Article  CAS  PubMed  Google Scholar 

  54. Thomson N, Channon K, Mokhtar N, Staniewicz L et al (2011) Imaging internal features of whole, unfixed bacteria. Scanning 33(2):59–68

    Article  CAS  PubMed  Google Scholar 

  55. (2010) Probes for lipids and membranes. In: The molecular probes® handbook: a guide to fluorescent probes and labeling technologies, 11th edn. http://www.lifetechnologies.com/us/en/home/references/molecular-probes-the-handbook/probes-for-lipids-and-membranes.html

  56. Chen W, Zhang C, Song L, Sommerfeld M, Hu Q (2009) A high throughput Nile red method for quantitative measurement of neutral lipids in microalgae. J Microbiol Methods 77:41–47

    Article  CAS  PubMed  Google Scholar 

  57. Elle I, Olsen L, Pultz D, Rødkær S, Færgeman N (2010) Something worth dyeing for: molecular tools for the dissection of lipid metabolism in Caenorhabditis elegans. FEBS Lett 584:2183–2193

    Article  CAS  PubMed  Google Scholar 

  58. Govender T, Ramanna L, Bux R (2012) BODIPY staining, an alternative to the Nile Red fluorescence method for the evaluation of intracellular lipids in microalgae. Bioresour Technol 114:507–511

    Article  CAS  PubMed  Google Scholar 

  59. Dantuma N, Pijnenburg M, Diederen J, Van der Horst D (1998) Electron microscopic visualization of receptor–mediated endocytosis of DiI–labeled lipoproteins by diaminobenzidine photoconversion. J Histochem Cytochem 46(9):1085–1089

    Article  CAS  PubMed  Google Scholar 

  60. Cortese K, Diaspro A, Taccheti C (2009) Advanced correlative light/electron microscopy: current methods and new developments using Tokuyasu cryosections. J Histochem Cytochem 57(12):1103–1112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Staubli W (1963) A new embedding technique for electron microscopy, combining a water soluble epoxy resin (Durcupan) with water insoluble Araldite. J Cell Biol 16:197–199

    Article  PubMed Central  Google Scholar 

  62. Mc Donald K, Webb R (2011) Freeze substitution in 3 hours or less. J Microsc 243(3):227–233

    Article  CAS  Google Scholar 

  63. Reynolds ES (1963) The use of lead citrate at high pH as an electron-opaque stain for electron microscopy. J Cell Biol 17:208

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Manfred Auer .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer-Verlag Berlin Heidelberg

About this protocol

Cite this protocol

Jhamb, K., Auer, M. (2015). Electron Microscopy Protocols for the Study of Hydrocarbon-Producing and Hydrocarbon-Decomposing Microbes: Classical and Advanced Methods. 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_96

Download citation

  • DOI: https://doi.org/10.1007/8623_2015_96

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-49132-4

  • Online ISBN: 978-3-662-49134-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics