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.
Soil is 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 diversity. We have developed the infrastructure to culture and work with ultraoligotrophic soil cultures with a goal of obtaining high quality genomic DNA for long-read sequencing, and metabolomes from poorly studied groups of abundant soil bacteria.
Illuminating subsurface microbial diversity 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. In collaboration with the Joint Genome Institute, isolates from high-throughput cultivation experiments will have genomes, transcriptomes and metabolomes analyzed under a variety of growth conditions.