New High Throughput Approaches for Culturing Soil Microbes from Shallow Subsurface Soils

Abstract

The majority of soil microbial biodiversity is uncultured in the laboratory. In part, the inability to cultivate many microbial lineages may be because these uncultured microbes are oligotrophic and do not grow on typical high-nutrient growth media. While there are several microbial cultivation methods designed to isolate microbes inhabiting oligotrophic marine environments, these methods are challenging to implement in soil. My thesis research directly addresses the need for new microbial cultivation methods for soil oligotrophs. I developed a cell separation protocol to extract viable microbes from shallow subsurface soils and used the extracted cells for high-throughput dilution-to-extinction. We reported the impacts of substrate concentration on culturability of microbes inhabiting a shallow subsurface soil in a conifer forest in Tucson, AZ. Substrate concentration significantly influenced the culturability of Actinobacteria from these locations. Our results indicate that the dilution-to-extinction method, combined with the optimized method for separating viable cells from soil, is suitable for the isolation of oligotrophic microbes from shallow subsurface soils.