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.
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References
Ladygina N, Deyukhina EG, Veinshtein MB (2006) A review on microbial synthesis of hydrocarbons. Process Biochem 41:1001–1014
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
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
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
Roling W, Head I, Larter S (2003) The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects. Res Microbiol 154:321–328
Atlas R, Bartha R (1993) Microbial ecology - fundamentals and applications. Benjamin-Cummings, Redwood City
Atlas R (1981) Microbial degradation of petroleum hydrocarbons: an environmental perspective. Microbiol Rev 45(1):180–209
Van Hamme J, Singh A, Ward O (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67(4):503–549
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
Martins L, Piexoto R (2012) Biodegradation of petroleum hydrocarbons in hypersaline environments. Braz J Microbiol 43(3):865–872
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
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
Biological Agents. http://www2.epa.gov/emergency-response/biological-agents. Accessed 24 Nov 2014
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
Scott C, Finnerty W (1976) A comparative analysis of the ultrastructure of hydrocarbon – oxidizing microorganisms. J Gen Microbiol 94:342–350
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
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
Alvarez H, Steinbuchel A (2002) Triacylglycerols in prokaryotic microorganisms. Appl Microbiol Biotechnol 60:367–376
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
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
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
Meng X, Yang J, Xu X, Zhang L, Nie Q, Xian M (2009) Biodiesel production from oleaginous microorganisms. Renew Energy 34:1–5
U.S. Bioenergy Statistics. http://www.ers.usda.gov/data-products/us-bioenergy-statistics. Accessed 10 Oct 2014
Shi S, Valle-Rodriguez J, Siewers V, Nielsen J (2011) Prospects for microbial biodiesel production. Biotechnol J 6:277–285
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
Davies S, Whittenbury R (1970) Fine structure of methane and other hydrocarbon-utilizing bacteria. J Gen Microbiol 61:227–232
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
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
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
Osumi M (2012) Visualization of yeast cells by electron microscopy. J Electron Microsc 61(6):343–365
Li Z (ed) (2002) Industrial application of electron microscopy. CRC Press, Boca Raton, p 362
Wigglesworth V (1975) Lipid staining for the electron microscope: a new method. J Cell Sci 19:425–437
Trent J (1984) Ruthenium tetraoxide staining of polymers: new preparative methods for electron microscopy. Macromolecules 17:2930–2931
Khandpur A, Macosko C, Bates F (1995) Transmission electron microscopy of saturated hydrocarbon block copolymers. J Polym Sci B Polym Phys 33:247–252
Richter H, Sleytr U (1971) Fettextraction bei −78°C: nachweis im Gefrieratzbild. Z Naturforsch 26b:470–473
Meyer H, Winkelmann H (1970) Die Darstellung von lipiden bei der gefrieratzpraparation und ihre beziehung zur strukturanalyse biologischer membranen. Exp Pathol 4:47–59
Moor H, Muhlethaler K (1963) Fine structure in frozen etched yeast cells. J Cell Biol 17:609–628
Meyer H, Richter W (2001) Freeze-fracture studies on lipids and membranes. Micron 32:615–644
Scott C, Finnerty W (1976) Characterization of intracytoplasmic hydrocarbon inclusions from the hydrocarbon-oxidizing Acinetobacter Species HO1-N. J Bacteriol 127(1):481–489
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
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
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
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
Robenek H, Severs N (2008) Recent advances in freeze-fracture electron microscopy: the replica immunolabeling technique. Biol Proced Online 10:9–19
Scott C, Makula S, Finnerty W (1976) Isolation and characterization of membranes from a hydrocarbon-oxidizing Acinetobacter sp. J Bacteriol 127(1):469–480
Kellenberger E, Johansen R, Maeder M, Bohrmann B et al (1992) Artefacts and morphological changes during chemical fixation. J Microsc 168:181–201
Mc Donald K, Auer M (2006) High-pressure freezing, cellular tomography, and structural cell biology. Biotechniques 41(2):137, 139, 141
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
Dubochet J (1995) High-pressure freezing for cryoelectron microscopy. Trends Cell Biol 5(9):366–368
Hurbain I, Sachse M (2011) The future is cold: cryo-preparation methods for transmission electron microscopy of cells. Biol Cell 103:405–420
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
Al-Amoudi A, Chang J, Leforestier A, McDowall A et al (2004) Cryo –electron microscopy of vitreous section. EMBO J 23(18):3583–3588
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
Thomson N, Channon K, Mokhtar N, Staniewicz L et al (2011) Imaging internal features of whole, unfixed bacteria. Scanning 33(2):59–68
(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
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
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
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
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
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
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
Mc Donald K, Webb R (2011) Freeze substitution in 3 hours or less. J Microsc 243(3):227–233
Reynolds ES (1963) The use of lead citrate at high pH as an electron-opaque stain for electron microscopy. J Cell Biol 17:208
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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
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DOI: https://doi.org/10.1007/8623_2015_96
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