Ecology & Evolutionary Processes
microbial ecologists and evolutionary biologists seek to understand the dynamic processes that explain microbial variation across scales, from cells to populations, communities, and ecosystems. Mathematical modeling of natural systems and lab-based mesocosms allow us to predict and test the stability of ecosystems in response to disturbances and social interactions. Experimental evolution using model bacteria, yeast, and unicellular algae illuminates the evolution of complex traits such as multicellularity and the trade-offs that constrain adaptation. Genomic analyses and metabolic profiling inform us of the diversity and function of microbial communities that drive the geochemical cycles sustaining life on the planet, including the effects of climate change on these processes. Project themes may include:
- deciphering mechanisms that allow bacterial aggregates to form in conditions mimicking an ecological niche
- characterizing of novel microbial species involved in oil bioremediation by 16S rRNA and whole-genome sequencing
- investigating the impacts of climate drivers (warming and elevated atmospheric CO2) on microbial diversity and community composition in a salt marsh.
- studying the role of early multicellular life cycles on the subsequent dynamics of multicellular adaptation
Cellular and Molecular Mechanisms
Cellular and molecular microbiologists study the structure, function, intracellular pathways, and formation of microorganisms; biological processes at cellular scale; and the macromolecular components that define them. DNA integrity and maintenance in the face of environmental assault and damage is essential to life. Pathways for repairing DNA damage and protein misfolding are commonly studied in microbes as a means to prevent mutation and disease processes. Unraveling signal transduction pathways, such as quorum sensing, that microbes use to sense and respond to extracellular chemical molecules and cues is an active research area because these pathways trigger a myriad of complex processes and are often targets for drug development. Finally, the molecular scaffolds derived from microbial natural products form the basis of most drugs and hold promise for the development of novel biotechnologies. Project themes may include:
- using of metabolomics to investigate the prevalence of antimicrobial compounds in field corals
- experimentally evolving bacteria to resist antimicrobial antagonism by the Type VI “nano-harpoon”
- analyzing yeast mutants with increased frequency of DNA break repair by transcript RNA
Synthetic Biology and Biophysics
Synthetic microbiology seeks to understand microbes from first principles and to develop and apply their molecular parts to solve unanswered problems. The physical laws responsible for behaviors such as collective swarming, cooperation, and conflict, and the creation of synthetic cells, help us understand how living systems differ from non-living systems. Determination of molecular architecture and dynamics of individual microbes and microbial populations with customized genetic circuitry has allowed the development of cellular and cell-free biosensors. Fabricated cells and microbial communities may also be harnessed for industrial chemical production and bioremediation of industrial waste, with applications in engineering microbiomes to contribute to biodiversity conservation. Project themes may include:
- making hybrid cells with living and artificial parts to ask how cellular organelles function together.
- engineering alternate cooperative-communications in regulatory protein scaffold to develop a new tool for synthetic biology.
- developing experimental evolution approaches to test if bacteria can evolve multicellular groups in response to selection for large cell size