A needle in a haystack: How to study active organisms in complex environments with stable isotopes and metagenomics

“Who is there?” and “What are they doing?” are the main questions microbial ecology attempts to answer. The “who” part is relatively easy to address with marker gene surveys and metagenomics. “What” is a bit trickier, as genomic potential does not necessarily imply function and activity, and culture-dependent studies do not take into account interactions within a microbial community.

Stable isotope probing (SIP) is a method that attempts to link those two questions through addition of an isotopically labeled substrate and tracking the label into organisms within the community. In the last 2 decades SIP has been combined with marker gene surveys to detect taxa that incorporate the labeled substrate.

With metagenomics yields increasing as price decreases, it now becomes achievable to replace marker genes with metagenomes as the SIP companion analysis. We will discuss the exciting new questions that can be asked using metagenomic-SIP as well as methodological precision and robustness.

Speaker:

Dr. Ella Sieradzki
Postdoctoral Researcher
University of California, Berkeley

Ella Sieradzki is a microbial ecologist who worked in a variety of environments from marine sponges through seawater and soil. She did her PhD at the University of Southern California with Prof. Jed Fuhrman on the role of marine bacteria and viruses in light harvesting mechanisms and degradation of oil using ‘omics and stable isotope probing. She is currently a postdoc working with Prof. Mary Firestone and Prof. Jill Banfield using the same methods to track the activity of nitrogen cycling and growth and infection rates of bacteria, archaea and viruses associated with plant roots.