Research

Phentotypic heterogeneity in microbial populations

phenotype_fig_dancingMicrobes are, admittedly, relatively simple organisms: single cells, small genomes. We often assume that two microbial cells that have the same genome will behave in the same way if they’re in the same environment. But in reality, microbial populations are capable of generating surprising complexity even in when they’re composed of genetically identical individuals. This is sometimes due to interactions with each other or with the environment, but sometimes it’s simply stochastic! I’m curious about how this diversity– even the stochastic kind– can make a population better adapted to its environment. In the lab, I’ve been investigating phenotypic heterogeneity in tolerance to the toxin formaldehyde in populations of Methylobacterium extorquens. And with colleagues from the SFI Complex Systems Summer School, I’m using agent-based modeling to investigate when and how phenotypic heterogeneity can evolve in a microbial population. You can read more about the surprising “individuality” of bacterial cells in a blog post I wrote in 2017, and in this recent article in Quanta Magazine, which features my work and the work of many others.

Microbial ecology and evolution from the perspective of functional traits
vanillin_vanillate_Methylobacterium

The Methylobacterium are a group of plant-associated alphaproteobacteria that we think make a great system for studying microbial diversity. They’re best-known for the model organism M. extorquens, a pink leaf-dweller that has long been studied for its ability to live solely on single-carbon compounds such as methanol. However, members of this genus are found all over the plant, are capable of metabolizing diverse growth substrates, and many play a role in promoting plant growth. I recently completed an investigation into the metabolism of lignin-derived aromatic compounds in Methylobacterium. I’m also currently part of a multi-institution research project using this genus to study the relationship between functional diversity and phylogenetic diversity in microbes, and how diverse microbial communities assemble on the plant host. This research is the basis for Methylothon, a project that brings microbial ecology into high school classrooms.

Thriving and surviving in desert soils

BadwaterBasin2019Microbial life is everywhere on earth. Even in the places that are so dry, hot, and sun-stressed that they are at the limit of what we consider habitable, we still find evidence of microbial communities. But how many of the microbes we find in desert soils are truly active and growing in those dry and stressful conditions, and how many are just waiting it out to do most of their growing during the rare events that bring resources (for instance, the seasonal rain in Death Valley)? And how many never belonged there in the first place, but left their DNA behind for us to find? With colleagues from the Boundaries of Life Initiative, I’m studying how microbial communities in soils from Death Valley National Park change in response to a rain event, with a special emphasis on methods that allow us to distinguish living, growing cells from those that are living but not growing, and those that are not living at all.   [photo credit: Brittany Baker]

Nitrogen-cycling microbes in San Francisco Bay—diversity, ecology, biogeography
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The nitrogen cycle is a critically important process in estuaries (as it is everywhere!), and estuarine sediment is a hotbed for dentrification—the microbial transformation of nitrate (a dissolved form of nitrogen that many organisms can make use of) to dinitrogen gas (78% of our atmosphere, and relatively inert). For my PhD thesis, I took on an extensive survey, using quantitative PCR and next-generation sequencing, of the diversity and abundance of denitrifying bacteria in San Francisco Bay sediments. I followed communities as they changed over the seasons in several sites along the salinity gradient from the Delta to the Central Bay. Read more about the project here.