Ultrastructural Insights into Microbial Life at the Hydrocarbon: Aqueous Environment Interface

  • Nassim Ataii
  • Tyne McHugh
  • Junha Song
  • Armaity Nasarabadi
  • Manfred Auer
Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)

Abstract

Despite the harmful effects observed when bacteria grow in a hydrocarbon-rich environment, some have been able to overcome the potential toxicity; however, specific interactions that operate at the hydrocarbon/aqueous interface remain unknown due to the difficulty of studying these interactions. Fortunately, there have been vast improvements in sample preparation such as the introduction of high-pressure freezing/freeze substitution (HPF/FS) which are able to preserve the ultrastructure while imaging. This process has been a gateway to a greater understanding of the ultrastructure of these interactions which could present deeper insight into the many processes that involve hydrocarbons. These processes include events such as catastrophic oil spills that give the opportunity to study the hydrocarbon/aqueous interface for the potential of utilizing new mechanisms in future disasters. This follows the possibility of reducing industrial oil souring by studying sulfate-producing bacterium, as well as furthering our understanding in biofuel production, where engineered microbes are used to produce hydrocarbon fuels.

References

  1. Abbasian F, Lockington R, Mallavarapu M, Naidu R (2015) A comprehensive review of aliphatic hydrocarbon biodegradation by bacteria. Appl Biochem Biotechnol 176(3):670–699.  https://doi.org/10.1007/s12010-015-1603-5CrossRefPubMedGoogle Scholar
  2. Andrews RE, Parks LW, Spence KD (1980) Some effects of douglas fir terpenes on certain microorganisms. Appl Environ Microbiol 40(2):301–304. http://www.ncbi.nlm.nih.gov/pubmed/16345609. Accessed 22 Aug 2017PubMedPubMedCentralGoogle Scholar
  3. Atlas RM (1981) Microbial degradation of petroleum hydrocarbons: an environmental perspective. Microbiol Rev 45(1):180–209. http://www.ncbi.nlm.nih.gov/pubmed/7012571. Accessed 22 Aug 2017PubMedPubMedCentralGoogle Scholar
  4. Baelum J, Borglin S, Chakraborty R et al (2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 14(9):2405–2416.  https://doi.org/10.1111/j.1462-2920.2012.02780.xCrossRefPubMedGoogle Scholar
  5. Cheville NF, Stasko J (2014) Techniques in electron microscopy of animal tissue. Veterinary Pathology, 51(1):28–41.  https://doi.org/10.1177/0300985813505114
  6. Chhabra et al (2011) Generalized schemes for high-throughput manipulation of Desulfovibrio vulgaris genome. Appl Environ Microbiol 77(221):7595-7604.  https://doi.org/10.1128/AEM.05495-11
  7. Das N, Chandran P (2011) Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol Res Int 2011:941810.  https://doi.org/10.4061/2011/941810PubMedGoogle Scholar
  8. De Smet MJ, Kingma J, Witholt B (1978) The effect of toluene on the structure and permeability of the outer and cytoplasmic membranes of Escherichia coli. Biochim Biophys Acta Biomembr 506(1):64–80.  https://doi.org/10.1016/0005-2736(78)90435-2CrossRefGoogle Scholar
  9. Dunlop MJ, Dossani ZY, Szmidt HL et al (2011) Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol 7:487.  https://doi.org/10.1038/msb.2011.21CrossRefPubMedPubMedCentralGoogle Scholar
  10. Gill CO, Ratledge C (1972) Effect of n-alkanes on the transport of glucose in Candida sp. strain 107. Biochem J 127(3):59P–60P. http://www.ncbi.nlm.nih.gov/pubmed/5076204. Accessed 22 Aug 2017CrossRefPubMedPubMedCentralGoogle Scholar
  11. Harrop AJ, Hocknult MD, Lilly MD (1989) Biotransformations in organic solvents: a difference between gram-positive and gram-negative bacteria. Biotechnol Lett 11:807–810. https://link.springer.com/content/pdf/10.1007/BF01026102.pdf. Accessed 22 Aug 2017CrossRefGoogle Scholar
  12. Hazen TC, Dubinsky EA, DeSantis TZ et al (2010) Deep-Sea oil plume enriches indigenous oil-degrading bacteria. Science 330(6001):204. http://science.sciencemag.org/content/330/6001/204. Accessed 22 Aug 2017CrossRefPubMedGoogle Scholar
  13. Heidelberg JF, Seshadri R, Haveman SA et al (2004) The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol 22(5):554–559.  https://doi.org/10.1038/nbt959CrossRefPubMedGoogle Scholar
  14. Hunter RC, Beveridge TJ (2005) High-resolution visualization of Pseudomonas aeruginosa PAO1 biofilms by freeze-substitution transmission electron microscopy. J Bacteriol.  https://doi.org/10.1128/JB.187.22.7619-7630.2005
  15. Jhamb K, Auer M (2015) Electron microscopy protocols for the study of hydrocarbon-producing and hydrocarbon-decomposing microbes: classical and advanced methods. In: Springer, Berlin/Heidelberg, Hydrocarbon and Lipid Microbiology Protocols, pp 5–28.  https://doi.org/10.1007/8623_2015_96
  16. Lamendella R, Strutt S, Borglin S et al (2014) Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Front Microbiol 5:130.  https://doi.org/10.3389/fmicb.2014.00130CrossRefPubMedPubMedCentralGoogle Scholar
  17. Leahy JG, Colwell RR (1990) Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54(3):305–315. http://www.ncbi.nlm.nih.gov/pubmed/2215423. Accessed 22 Aug 2017PubMedPubMedCentralGoogle Scholar
  18. Lee SK, Chou H, Ham TS, Lee TS, Keasling JD (2008) Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr Opin Biotechnol 19(6):556–563.  https://doi.org/10.1016/j.copbio.2008.10.014CrossRefPubMedGoogle Scholar
  19. Leffler WL (2008) Petroleum refining in nontechnical language. PennWell, TulsaGoogle Scholar
  20. Liamleam W, Annachhatre AP (2007) Electron donors for biological sulfate reduction. Biotechnol Adv 25(5):452–463.  https://doi.org/10.1016/j.biotechadv.2007.05.002CrossRefPubMedGoogle Scholar
  21. Marchant, Banat (2015) Protocols for measuring biosurfactant production in microbial cultures. In: Hydrocarbon and lipid microbiology protocols – Springer protocols handbooks.  https://doi.org/10.1007/8623
  22. Matias VRF, Al-Amoudi A, Dubochet J, Beveridge TJ (2003) Cryo-transmission electron microscopy of frozen-hydrated sections of Escherichia coli and Pseudomonas aeruginosa cryo-transmission electron microscopy of frozen-hydrated sections of Escherichia coli and Pseudomonas aeruginosa. J Bacteriol.  https://doi.org/10.1128/JB.185.20.6112
  23. McDonald KL, Zalpuri R (1997) Electron Microscope Lab. Methods generic processing protocol. University of California, Berkeley, unpublished. http://em-lab.berkeley.edu/EML/protocols/pgeneric.php
  24. McDonald Z. Electron Microscope Lab, 26 Giannini Hall, University of California, Berkeley, unpublishedGoogle Scholar
  25. McDonald KL, Auer M (2006) High-pressure freezing, cellular tomography, and structural cell biology. Biotechniques.  https://doi.org/10.2144/000112226
  26. McDonald KL, Morphew M, Verkade P, Müller-Reichert T (2007) Recent advances in high-pressure freezing: equipment- and specimen-loading methods. In: Electron microscopy: methods and protocols. Springer, Microscope Laboratory, University of California, Berkeley. https://doi.org/10.1007/978-1-59745-294-6_8
  27. Muyzer G, Stams AJM (2008) The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol.  https://doi.org/10.1038/nrmicro1892
  28. Palsdottir H, Remis JP, Schaudinn C et al (2009) Three-dimensional macromolecular organization of cryofixed Myxococcus xanthus biofilms as revealed by electron microscopic tomography. J Bacteriol.  https://doi.org/10.1128/JB.01333-08
  29. Ratcliffe RM (2017) Successful bioaugmentation with microbes. http://bioremediate.com/hydrocarbon.html. Accessed 25 Aug 2017
  30. Sauer K, Camper AK, Ehrlich GD, Costerton JW, Davies DG (2002) Pseudomonas aeruginosa. J Bacteriol.  https://doi.org/10.1128/JB.184.4.1140
  31. Sikkema J, De Bontt J, Poolmann B (1994) Interactions of cyclic hydrocarbons with biological membranes*. J Biol Chem 269(11):8022–8028. http://www.jbc.org/content/269/11/8022.full.pdf. Accessed 22 Aug 2017PubMedGoogle Scholar
  32. Varjani SJ (2017) Microbial degradation of petroleum hydrocarbons. Bioresour Technol 223:277–286.  https://doi.org/10.1016/j.biortech.2016.10.037CrossRefPubMedGoogle Scholar
  33. Zehr JP (2010) Microbes in Earth’s aqueous environments. Front Microbiol 1:4.  https://doi.org/10.3389/fmicb.2010.00004CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Nassim Ataii
    • 1
  • Tyne McHugh
    • 1
  • Junha Song
    • 1
  • Armaity Nasarabadi
    • 1
  • Manfred Auer
    • 1
  1. 1.Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyUSA

Personalised recommendations