Roles of obligate oligotrophic bacteria from arid unclaimed mine tailings sites

Microbes are crucial for plant establishment and soil health in arid and semiarid unclaimed mine tailings sites. Although we know such sites can be extremely low in organic carbon and other nutrients, we don’t really understand the role of oligotrophic microbes in these microbial communities. As part of this project, we are cultivating abundant oligotrophs from mine tailings sites and integrating the information derived from these cultures with ongoing molecular characterization of the microbial communities inhabiting mine tailings sites.



High-Throughput Culturing and Metabolomics of Microbial Dark Matter in Soil and Dust

Soil and dust samples are among the most complex of all environmental samples, often containing thousands of uncultivated microbial taxa, for which we have limited or no genomic or metabolic information.  Oligotrophic microbes – those microbes that thrive in conditions where the effective nutrient availability is low – are likely a major component of uncultivated microbial “dark matter.” As part of this project we are developing the infrastructure to culture and work with oligotrophic cultures with a goal of obtaining high quality genomic DNA for long-read sequencing, and metabolomes from low-density limited-volume cultures.  



Illuminating subsurface microbial dark matter in the Catalina-Jemez Critical Zone Observatory

Oligotrophic microbes are likely a major component of nutrient poor soils deep in the soil profile. In collaboration with JCVI, we are profiling the microbial communities from three distinct soil depth profiles in the Catalina-Jemez CZO. Isolates from concomitant high-throughput cultivation experiments will have genomes sequenced.