Stable-isotope probing

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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. Biomarkers with the heavier isotope 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.[1]

When DNA is the biomarker, SIP theoretically can be performed using isotopically labeled C, H, O or N, though 13C is used most often. Cupples et al. (2007) demonstrated a weaker DNA buoyant density shift in 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.[2]

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  1. ^ Radajewski, Stefan; Ineson, Philip; Parekh, Nisha R.; Murrell, Colin (2000). "Stable-isotope probing as a tool in microbial ecology". Nature. 403 (6770): 646–649. doi:10.1038/35001054. PMID 10688198.
  2. ^ Cupples, A.M., E.A. Shaffer, J.C. Chee-Sanford, and G.K. Sims. 2007. DNA buoyant density shifts during 15N DNA stable isotope probing. Microbiological Res. 162:328-334.