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In a broad sense, molecular ecology is the study of ecological processes based on the analysis of biomolecules, particularly DNA, RNA, and proteins, using the techniques of molecular biology.
Molecular ecology at CBL is focused on microbes and aquatic environments in three subareas: phylogenetics and evolution, biodiversity, and biogeochemistry. In phylogenetics and evolution, gene and protein sequences are used to infer the degree of relatedness between different organisms and to trace their evolutionary histories. For the study of biodiversity, the presence of microorganisms with inconspicuous morphological traits or traits that are hard to recover by cultivation is assessed by determining the presence of their genes in the environment.
In the subarea of biogeochemistry, ecogenomics targets microorganisms that have potential environmental importance, but for which there is little information about their metabolic potential. Target organisms may be cultured or uncultured ones, and attempts to uncover their metabolic potential are made through genome sequencing.
With this information, quantitative assays can be developed for the measurement of the activity of key players in ecosystems, seeking to uncover their roles in the global cycles of major elements.