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Chapter 40 : Environmental Genomics of C1 Metabolism
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 C1 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 C1 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 C1 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.
The central role of formaldehyde in C1 metabolism. Genes routinely detected in environmental samples are shown (italic).
Strategies for detecting C1-metabolizing populations in the environment.
Protocol for mRNA-targeting FISH-based cell sorting