Stable-isotope probing

Stable-isotope probing (SIP) is a technique in microbial ecology for tracing fluxes of nutrients in biogeochemical cycling by microorganisms. A substrate is enriched with a heavier stable isotope that is consumed by the organisms to be studied.[1][2] Biomarkers with the heavier isotopes incorporated into them can be separated from biomarkers containing the more naturally abundant lighter isotope by isopycnic centrifugation. For example, ¹³CO₂ can be used to find out which organisms are actively photosynthesizing or consuming new photosynthate. As the biomarker, DNA with ¹³C is then separated from DNA with ¹²C by centrifugation. Sequencing the DNA identifies which organisms were consuming existing carbohydrates and which were using carbohydrates more recently produced from photosynthesis.[3]

When DNA is the biomarker, SIP can be performed using isotopically labeled C, H, O, or N, though ¹³C is used most often. A weaker DNA buoyant density shift is observed when ¹⁵N- versus ¹³C-labeled substrates were used in pure culture. Conversely, a very strong buoyant density shift was observed when both labels were used.[4]