Our projects

A Living Atlas of California’s Belowground Microbial Biodiversity

Soils are the most biodiverse habitats on Earth. A single gram of soil can contain up to 10,000 unique bacterial taxa. About 500 of these taxa are abundant and ubiquitous in soils globally. Only ~50% of the cosmopolitan soil bacteria have been studied in any detail. And extensive physiological and genomic data only exist for a few model soil organisms. In a project supported by the California Institute for Biodiversity, we’ll apply high throughput cultivation approaches to diverse soils collected in California. The goal of the project is to isolate new microbes from soils collected across California and preserve them in perpetuity, akin to a seed bank, for future utility in a changing world.

Systems biology of death cheating sediment microbes (Simons Foundation)

Microbes in sediments are key mediators of global nutrient cycles and long-term carbon sequestration. Yet, most of these microbes are not actively dividing due to the limited supply of energy-yielding growth substrates, such that in situ growth rates approach zero. These microbes cheat death by maintaining basal metabolic activity, but are confined to extremely slow growth states that are physiologically distinct from exponentially growing, dormant, or stationary-phase cells. In a key knowledge gap, there is a poor understanding of how active but slow growing subseafloor cells interact with neighboring microbes and their surrounding environment. In part, this knowledge gap persists because of the technical challenges associated with acquiring and studying samples from the deep biosphere, including the reproducible cultivation of deep biosphere microbes in the laboratory. In a project supported by the Simons Foundation, we apply a systems microbial ecology-based approach to advance our understanding of the types of ecological interactions in the deep biosphere and how they are regulated at low growth rates.

RNA STABILITY IN DESICCATED CELLS (National Science Foundation)

Dryland soils are home to complex microbiomes that mediate processes crucial to human and planetary health, including water sustainability, soil fertility, food security, biodiversity, and variability in atmospheric CO2 concentrations. Soil microbes persist in dry soil by entering desiccation-induced microbial dormancy. The mechanisms that influence the transitions to and from desiccation-induced dormancy are poorly understood. As part of an NSF CAREER award, this project investigates how different groups of bacteria tackle the problem of surviving desiccation with an emphasis on understanding the fate of intracellular RNA. The soil bacteria that will be investigated are abundant mediators of soil carbon cycling and agricultural health in drylands. Thus, studying the mechanisms of desiccation tolerance in soil bacteria can influence decisions about how to prevent or rehabilitate degraded dryland ecosystems. The project aims to attract, train, and retain undergraduates that are historically excluded in STEM fields as part of a larger vision to build a diverse American STEM workforce. The research aims will be conducted by students conducting authentic course-based research on drought—a topic of global and local importance. A mentorship training program will educate graduate students in effective mentorship and provide them with authentic mentorship experience.

Microbial contributions to arsenic transformations in the gut (National Institute of EnvironMEtal Health ScienceS)

Gut microbial communities transform inorganic arsenic to a variety of organoarsenicals with varying toxicities. However, it is unclear whether these biotransformations are mediated by individual taxa, or are an emergent community-level property. As part of the NIEHS Superfund Research Program, we are using molecular data to inform function-based high throughput cultivation murine fecal communities to facilitate the design of synthetic microbial communities. We are investigating the capacity of these synthetic communities to biotransform arsenic both in culture and in germ-free mice.

Arizona Culture Collection (AZCC)

We love isolating new microbes in the laboratory! We initiated the AZCC in 2017. This collection is comprised of microbial cultures (currently comprised of Bacteria & Archaea) that we’ve isolated from sites around the world, with a central focus on the American West. Every culture we isolate is cryopreserved for potential future use. Such culture collections will almost certainly have utility in a changing world. When browsing NCBI, strains we isolate and identify are appended with an AZCC strain number. These strains are available upon request. When requesting, keep in mind that some isolates are difficult to culture so we reserve the right to limit the number of strains requested at once. Also, while we do our best to ensure viability after cryopreservation, not all strains ‘wake up’ after being frozen and we have limited amounts of each isolate.