Seminar Stable isotopes in Microbiology: from activity to function

Microbial communities are extraordinarily diverse, but identifying which microorganisms are active
and determining what they are actually doing remains a major challenge in microbiology. Stable
isotopes provide a powerful set of tools to move beyond measurements of microbial presence or
abundance and directly trace biological processes. In this seminar, I will introduce the principles of
stable isotope tracing and illustrate how different isotopes can be used to investigate microbial
activity, growth and metabolism. Examples will include the use of 13C and 15N to follow substrate
utilization and elemental transformations, 18O incorporation into DNA to quantify microbial growth,
and deuterated water as a tracer of microbial biosynthesis. I will also discuss stable isotope probing
approaches that combine isotope incorporation with biomarkers or molecular techniques to identify
the organisms responsible for particular processes. Most examples will come from soil microbial
ecology, where complex and highly diverse communities provide an ideal testing ground for these
approaches, but the underlying concepts are broadly applicable across microbial systems.
Particular attention will be given to how isotope approaches can complement sequencing and other
omics techniques, allowing microbial identity to be linked to activity and function. Finally, I will
discuss some of the methodological challenges, assumptions and opportunities associated with
these approaches.