Separation Of Viable Microbes From Soil Matrices

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 growth media. While there are several microbial cultivation methods designed for microbes inhabiting oligotrophic marine environments, these methods are challenging to implement in soil. This thesis describes the optimization of a NycodenzTM density-gradient centrifugation method to separate viable cells from soil that are suitable for cultivation approaches that target oligotrophic microbes. Here we show that microbial cells are present but differentially distributed throughout the density gradient and that the distribution of these cells in the density gradient is soil-specific. This suggests that density-gradient centrifugation might be useful to enrich for specific microbial populations. To test this hypothesis in future experiments, we will quantify the types and relative abundances or microbial taxa from individual fractions to determine if different microbial taxa localize at different fractions on the density gradient after centrifugation.