Dr. Stephanie A. Eichorst

Soils represent habitats with unpredictable conditions for microorganisms, often confronting them with suboptimal conditions for growth. As such, up to 80% of soil microorganisms are assumed to be in a state of non-growth or ‘dormancy’ – a state with low metabolic activity enabling long-term persistence. In many soil systems, microorganisms alter between ‘dormant’ and active states, presumably as a means of survival. It is believed that the state of ‘dormancy’ helps to maintain the extensive biodiversity in soils, with estimates ranging from 1,000- 1,000,000 species per gram of soil. Atmospheric gas oxidation, such as molecular hydrogen, has been proposed as a means to generate energy during periods of carbon limitation. It is believed to be a widespread survival strategy that contributes to bacterial persistence. Using a combination of genomics, transcriptomics, growth-based experiments, enzyme kinetics and molecular analyses, we are exploring this physiology in model organisms and in temperate and desert soils.

One aspect of my research is to investigate the active participants in microbial processes at the single-cell level to confirm their activity and to gain additional information at this scale. As such, we are developing pipelines and are optimizing tools that permit the analysis of our targeted processes down to the single-cell level, such as FISH, NanoSIMS and Raman microspectroscopy combined with stable isotope tracers (such as ¹³C, ¹⁵N and D) in complex systems, such as soil. 

Some of our developments have been highlighted by the Joint Genome Institute, Science Highlights: A Single-Cell Pipeline for Soil Samples.