Uncovering the link between bacterial growth and secondary metabolite dynamics in soil biocrusts

Bacterial secondary metabolites are highly valuable to humanity as antimicrobials. However, the antimicrobial discovery rate has been lagging behind rapid resistance development.

Our lack of knowledge about when and why different taxa produce secondary metabolites is a major source of difficulty in the discovery process.

Studies on Actinomycetes in batch culture have shown that secondary metabolites tend to be produced in stationary phase, but evidence suggests that production dynamics are different in other phyla as well as in situ.

The goal of this project is to understand how in situ and in vitro SM production dynamics relate to growth rate and transcriptomic changes in soil bacteria.

To achieve this, I will conduct a time-series rewetting experiment on a Negev desert biocrust as a model system of soil with reduced diversity.

I will apply quantitative stable isotope probing metagenomics and metatranscriptomics to each timepoint to obtain a specific growth rate and expression profile for each metagenome-assembled genome. I will supplement the in situ data with in vitro expression studies in isolates.

Together, this will allow me to assess how growth rate & phase, expression of other pathways, and the soil environment impact secondary metabolite biosynthetic gene cluster expression.

The results of this project will give unprecedented insights into the dynamics of secondary metabolite production, challenge long-held assumptions, and ultimately lead to improved discovery pipelines.