Molecular Microbial Ecology Lab

Our mission is to conduct whatever sound scientific research necessary in order to better understand how individual microbes function as part of communities, and how microbial functions scale to ecosystem functions. Our most frequently used tools include molecular characterization (DNA, RNA, lipids and protein sequencing), physiological measurements (CO2 and trace gas production, biomass measures, cell counts), and bioinformatics (statistical analysis and modeling). We strive to apply the right tool to answer the question at hand, and learn new techniques or build new tools when necessary.

About research in the DeAngelis lab: Our work concerns soil microbes and their interactions with the environment. Microbes are extremely diverse and are involved in all of earth’s biogeochemical cycles. Specifically, we are interested in understanding how climate change affects soil microbial communities, and then applying results towards modeling and predicting microbial feedbacks to climate and improving biofuels.

I am formally trained in microbiology with extensive experience in microbial ecology. I received my PhD in Microbiology from UC Berkeley, co-advised by Drs. Mary Firestone and Steven Lindow. During this time, I began work investigating the interactions in the rhizosphere between plants and the microbial communities that live and grow around their roots. My works showed a correlation between signals associated with bacterial group behavior, called quorum sensing, and extracellular enzymes important for nutrient exchange and availability in the rhizosphere.

During my postdoctoral work at UC Berkeley, LBNL and the Joint BioEnergy Institute, I investigated microbial communities and key bacterial isolates both for their role in decomposition as well as to improve lignocellulosic biofuels production. We hypothesized that the fast rates of decomposition and anaerobic conditions of tropical forest soils would be conducive to discovery of enzymes well-suited for imporoving lignocellulosic biofuels. This work involved the use of cultivation along with genomic and metagenomic investigation of communities to understand and harness natural mechanisms of microbial breakdown of plant materials.

As an assistant professor, my research incorporates controlled field and laboratory studies using known organisms and wild cultivated isolates. My work is balanced between experimental and computational approaches to understand what microbes do in soils.

Microbes interact with their environment as individuals, yet live in diverse communities whose functions can impact climate on a large, ecosystem scale. Our research seeks to bridge these scales by asking the questions such as: How is microbial community structure and function integrated over environment and time? What interactions with other organisms and viruses control microbial activity? What are the trade-offs in examining natural versus controlled, laboratory systems? With these questions in mind, we are using interdisciplinary techniques to begin understanding the microbial effects of carbon storage dynamics in terrestrial ecosystems.