Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities

Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing methods lack the ability to measure low levels of isotope incorporation and comprehensively resolve the microorganisms and metabolic pathways involved. We present here an approach to quantify both (i) the extent of ¹⁵N incorporation in thousands of proteins and (ii) the relative abundances of ¹⁵N protein isotopologues in shotgun proteomics samples. This method was used to quantify the time-dependent degree of ¹⁵N incorporation into a model chemoautotrophic microbial community in an organism- and protein-specific manner. The results suggest migration of selected microorganisms, especially heterotrophic archaea, from established communities into regrowing communities. The method can be applied to many other stable isotope probing applications involving mixed microbial communities.