top of page

Microbial Diversity, Metabolic Potential, and Roles in Biogeochemical Cycling in the Terrestrial Subsurface

The terrestrial subsurface is an untapped reservoir of diverse microbial life with far-reaching implications for global biogeochemical cycling, environmental science, biotechnology, and policy development. Our research aims to unravel the microbial diversity, metabolic potential, and roles in biogeochemical cycling in the terrestrial subsurface, with a focus on previously uncharacterized archaeal bacteria candidate phyla and mobile genetic elements.

Our approach integrates advanced methodologies from microbiology, genomics, bioinformatics, and geochemistry. We employ comprehensive cultivation-independent identification techniques to profile microbial communities in diverse subsurface environments, such as aquifers, caves, deep-sea sediments, vernal pools in Lake County, California, and deep-subsurface groundwater at Alum Rock Park. By leveraging high-throughput DNA sequencing and advanced bioinformatics methods, we can reconstruct hundreds to thousands of genomes, providing unprecedented insight into the composition and metabolic potential of these hidden microbial ecosystems.


Many subsurface microorganisms belong to novel bacterial phyla without cultivated representatives, making our research invaluable for shedding light on the ecological roles of these enigmatic organisms in biogeochemical cycling. We predict their metabolic capacities using functional omics methods and test these predictions through field experiments and collaborations with other researchers.

Our research is conducted as part of a large LBNL-led initiative in an aquifer adjacent to the Colorado River, Rifle, USA. Other team members use our metabolic predictions as inputs for modeling efforts, further elucidating the complex interplay between subsurface microbial communities and the environment. Additionally, our work expands to system study sites, including a vernal pool located in Lake County, California, and deep-subsurface groundwater at Alum Rock Park.

Key Objectives:

Characterize the microbial diversity in the terrestrial subsurface, with an emphasis on identifying novel archaeal bacteria candidate phyla and mobile genetic elements.
Investigate the metabolic potential of subsurface microorganisms using functional omics methods and field experiments across diverse system study sites.
Assess the ecological roles of subsurface microorganisms in biogeochemical cycling, including their contributions to carbon, nitrogen, hydrogen, oxygen, metal, and sulfur cycles in various environments.
By combining cutting-edge techniques and interdisciplinary collaborations, our research is expanding our understanding of the terrestrial subsurface's hidden world. This work not only advances our knowledge of Earth's microbial diversity and ecology but also inspires novel ideas and applications for harnessing the potential of these unique microbial ecosystems.

bottom of page