Functional Marker Gene Assays for Hydrocarbon Degrading Microbial Communities: Aerobic
In this chapter we discuss the state of the art on functional marker gene assays for aerobic hydrocarbon-degrading microbial communities, and the different approaches available to detect genes or activities associated with biodegradative processes in the
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troduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4291
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Knowledge and Gaps in the Microbial Ecology of Biodegradation . . . . . . . . . . . . . . 4292
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Approaches to Study the Microbial Ecology of Biodegradation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4293
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Key Catabolic Activities and Associated Gene Families in Bacterial Aerobic Hydrocarbon Degradation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4294
5 5.1 5.2 5.3 5.4 5.5
Sequence-Based Methods to Detect and to Assess Catabolic Functions: PCR-Based Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4294 DNA Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4295 Primer Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4297 Quantifying Functional Gene Copies in Contaminated Environments . . . . . . . . . . . . 4299 Resolving Sequence Complexity: PCR Clone Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4300 Genetic Fingerprinting Methods to Analyze Metabolic Gene Composition . . . . . . . 4300
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Hybridization-Based Detection of Functional Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4303
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Activity-Based Assays to Detect Functional Proteins or Gene Families Involved in Hydrocarbon Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4303 7.1 Metagenomics to Assess Catabolic Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4304 7.2 Genetic Traps to Catch Previously Hidden Biomineralization Genes and Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4305 7.3 Stable Isotope Probing (SIP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4305
K. N. Timmis (ed.), Handbook of Hydrocarbon and Lipid Microbiology, DOI 10.1007/978-3-540-77587-4_336, # Springer-Verlag Berlin Heidelberg, 2010
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Functional Marker Gene Assays for Hydrocarbon Degrading Microbial Communities
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Community Structure Insights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4306
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Future Perspectives to Assess Microbial Metabolic Functions in the Environment: Combination of Techniques and New Fields of Research . . . . . . . . . 4306
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Abstract: In this chapter we discuss the state of the art on functional marker gene assays for aerobic hydrocarbon-degrading microbial communities, and the different approaches available to
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