OUR RESEARCH

Microbial Ecology and Systems Biology Approaches

Microbial ecology is a discipline that studies the relationship microbes have with each other and with their environment. Pure culture studies are useful to learn about a process of interest that the microbe under study catalyzes; however, such studies are generally insufficient to understand how the microbe performs when embedded within a natural microbial community. The Löffler lab applies a Systems Biology Approach to understand the ecology of microorganisms of interest. We apply top-down (reductionist) approaches (e.g., enrichment and isolation) to separate system components, which are then studied in isolation to unravel mechanistic details of processes of interest. To explore the components’ functions in a natural community with dynamic interactions and interrelationships with other components of the system, we apply bottom-up (system science) approaches (e.g., metagenomics, metatranscriptomics, metaproteomics, metabolomics). This biphasic approach generates detailed mechanistic understanding and informs about the process in the context of the environment (i.e., in situ conditions). System science approaches can develop dynamic, systems-level understanding of organism and community function.

Reductionist approaches alone cannot reveal the dynamic interactions with other components of the system. For example, Dehalococcoides mccartyi (Dhc) strains catalyze key detoxification reactions but cannot synthesize essential growth factors (e.g., corrinoid) required to assemble functional reductive dehalogenase enzyme systems. Further, Dhc are limited to hydrogen as an electron donor, and depend on fermenting organisms to supply hydrogen. Hence, Dhc activity can not be predicted and manipulated without recognizing all interacting components and the system as a whole is understood.