Chapter 40 : Environmental Genomics of C Metabolism

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Facultative methylotrophs are capable of growth on multicarbon compounds, while obligate methylotrophs are not. Knowledge of the content and structure of the genomes of methylotrophic bacteria is instrumental for detecting C metabolism genes in the environment. Comparative analysis of methylotroph genomes, as well as the proteomic analyses, provides knowledge on the complement of the genes essential for C metabolism in the environment. The current knowledge of the methylotrophy modules, however, remains incomplete. While originally developed for detection of copper-containing membrane-bound methane monooxygenase (pMMO), this protocol may be adapted to detect other genes encoding key enzymes of C metabolism. Detection of specific groups is based on light scattering and/or autofluorescence. In the absence of natural autofluorescence, microbial cells can be differentiated by various types of fluorescence staining, using either immunofluorescent labeling or fluorescent in situ hybridization (FISH). The first is the prohibitive cost, and the second is the computational difficulty of assembling the large databases of random DNA sequences . The progress in environmental genomics will bring about new clues as to the possible means of cultivating microbes that have so far resisted cultivation. The field of environmental genomics is still in its infancy, and it is easy to predict that the future will be full of surprises.

Citation: Kalyuzhnaya M, Nercessian O, Lidstrom M, Chistoserdova L. 2007. Environmental Genomics of C Metabolism, p 488-496. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch40

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Reverse Transcriptase PCR
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The central role of formaldehyde in C metabolism. Genes routinely detected in environmental samples are shown (italic).

Citation: Kalyuzhnaya M, Nercessian O, Lidstrom M, Chistoserdova L. 2007. Environmental Genomics of C Metabolism, p 488-496. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch40
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Strategies for detecting C-metabolizing populations in the environment.

Citation: Kalyuzhnaya M, Nercessian O, Lidstrom M, Chistoserdova L. 2007. Environmental Genomics of C Metabolism, p 488-496. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch40
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Protocol for mRNA-targeting FISH-based cell sorting

Citation: Kalyuzhnaya M, Nercessian O, Lidstrom M, Chistoserdova L. 2007. Environmental Genomics of C Metabolism, p 488-496. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch40

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