Research Areas
Microbial communities are the engines of Earth's biogeochemical cycles and the hidden drivers of both resilience and vulnerability in the environments they inhabit. We study them not as static genetic inventories, but as dynamic, spatially organized systems whose behavior emerges from how individual cells interact with each other and with their physical surroundings. We build imaging and computational tools that enable visualization of these interactions across scales.
Unraveling the multiscale mechanisms driving the emergence and spread of antibiotic resistance in complex microbiomes
Image: Grace, Sarah
Environmental antimicrobial resistance (AMR) reservoirs are chemically and biologically complex, major gaps remain in resolving how ARGs spread within these microbial communities. This level of resolution is essential for characterizing wastewater samples and their highly heterogeneous genetic and metabolic contributions. Spatial context is also crucial, as the emergence of resistance mutations can be associated with the physical structure of the community (i.e. biofilms). The overarching goals are to establish the quantitative and imaging foundation for probing how antibiotic resistance is acquired and propagated in complex microbiomes, from single cells to whole communities. Our long-term goal is to understand how bacteria acquire and pass on antibiotic resistance in the complex environments they actually live: sewers, soils, the human gut, and to build the tools that make that process visible.
While metagenomics has catalogued the breadth of ARGs in wastewater and gut, three fundamental questions remain: which bacterial hosts carry these genes, what mechanisms enable their transfer, and are they actively conferring resistance?
We aim to integrate these complementary modalities into a unified view of AMR in natural microbiomes such as the human gut and wastewater. To this end we are developing integrated computational and spatial Raman microspectroscopy pipelines to quantify in-situ HGT with imaging modalities that enables direct visualization of host-MGE interactions at the single-cell level.
Natural microbial consortia for rare earth element bioaccumulation in geothermal waters
Image: Emma
Rare earth elements (REEs) are used in a variety of products such as medical imaging devices, batteries, and skincare products, among many others. Despite being called “rare,” REEs are abundant on Earth, but are rarely concentrated in mineral forms. This makes their recovery, through solvent- and catalyst-based extractions, costly, inefficient, and environmentally disastrous. New solutions for acquiring REE are needed.
Biology is one such alternative. Until 2012, REEs were thought to have no biological function. The discovery of lanthanide-dependent enzymes changed this. However, to-date, the majority of LDEs are studied in a handful of model organisms from temperate environments; little is known about their distribution across Earth systems. We seek to uncover the diversity of REE biology in geothermal waters (where REEs are often elevated) and investigate our hypothesis that, when REEs are more abundant, biology will leverage their capabilities in unique, currently undescribed ways.
Ultimately, exploring REE biology may provide direct benefits to society, including new techniques to concentrate and immobilize REEs, model organisms that can withstand toxicity and bioaccumulate REEs, and enzymes that may be adapted for industrial use. Approaches to sustainable REE biomining will require new organisms and enzymes that are well-suited for high-temperature, acidic, and/or geochemically complex feedstocks.
Our foundational work in this area is currently focused on:
1. Characterizing the geochemistry and geomicrobiology of geothermal waters
2. Spatially resolving and distinguishing modes of REE transport in geothermally relevant microorganisms
3. Developing genetically tractable, REE-bioaccumulating model organisms for eventual industrial deployment
By combining computational biology, mass spectroscopy, and microanalytical techniques, our work will enable mechanistic investigations into the structure and function of REE biology in nature and serve as a launchpad for industrial-scale biorecovery technologies in geothermal fluids and other REE-enriched supply streams.