Abstract
The large datasets generated in the immense complex field of hydrocarbon and lipid microbiology cannot be addressed and understood without computer-assisted analysis. Key components in computer-assisted analysis are bioinformatics, databases, statistics, and mathematical modeling. Computer-assisted analysis contributes to the entire scientific process: experimental design, data analysis, data storage, and utilization of these stored data. A wide range of relevant protocols are presented in this volume: protocols dealing with subjects that are also popular in other research areas and protocols addressing important topics specific for hydrocarbon and lipid microbiology. The basics of a major open-source programming language, Python, will be introduced.
†Deceased, September 25, 2015
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References
Head IM, Jones DM, Röling WFM (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4:173–182
Prince RC (2005) The microbiology of marine oil spill bioremediation. In: Ollivier B, Magot M (eds) Petroleum microbiology. American Society for Microbiology Press, Washington DC, pp 317–336
Schneiker S, dos Santos V, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Puhler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorholter FJ, Weidner S, Kaiser O, Golyshin PN (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24:997–1004
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
Röling WFM, Milner MG, Jones DM, Fratepietro F, Swannell RPJ, Daniel F, Head IM (2004) Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil. Appl Environ Microbiol 70:2603–2613
Prosser JI (2010) Replicate or lie. Environ Microbiol 12:1806–1810
Mason OU, Hazen TC, Borglin S, Chain PSG, Dubinsky EA, Fortney JL, Han J, Holman HYN, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe SG, Woyke T, Zhou JH, Rubin EM, Jansson JK (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to deepwater horizon oil spill. ISME J 6:1715–1727
Lu ZM, Deng Y, Van Nostrand JD, He ZL, Voordeckers J, Zhou AF, Lee YJ, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D’Haeseleer P, Hazen TC, Zhou JZ (2012) Microbial gene functions enriched in the deepwater horizon deep-sea oil plume. ISME J 6:451–460
Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D’Haeseleer P, Holman HYN, Osman S, Lu ZM, Van Nostrand JD, Deng Y, Zhou JZ, Mason OU (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330:204–208
Röling WFM, van Bodegom PM (2014) Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example. Front Microbiol 5
Quinn G, Keough M (2002) Experimental design and data analysis for biologists. Cambridge University Press, Cambridge
Legendre P, Legendre L (1998) Numerical ecology. Elsevier Science, Amsterdam
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Röling, W.F.M. (2015). Introduction to Computer-Assisted Analysis in Hydrocarbon and Lipid Microbiology. In: McGenity, T., Timmis, K., Nogales Fernández, B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_86
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DOI: https://doi.org/10.1007/8623_2015_86
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