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.[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]

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  1. ^ Dumont MG, Murrell JC (June 2005). "Stable isotope probing - linking microbial identity to function". Nature Reviews. Microbiology. 3 (6): 499–504. doi:10.1038/nrmicro1162. PMID 15886694. S2CID 24051877.
  2. ^ Neufeld JD, Dumont MG, Vohra J, Murrell JC (April 2007). "Methodological considerations for the use of stable isotope probing in microbial ecology". Microbial Ecology. 53 (3): 435–42. doi:10.1007/s00248-006-9125-x. PMID 17072677. S2CID 9417066.
  3. ^ Radajewski S, Ineson P, Parekh NR, Murrell JC (February 2000). "Stable-isotope probing as a tool in microbial ecology". Nature. 403 (6770): 646–9. doi:10.1038/35001054. PMID 10688198. S2CID 4395764.
  4. ^ Cupples AM, Shaffer EA, Chee-Sanford JC, Sims GK (2007). "DNA buoyant density shifts during 15N-DNA stable isotope probing". Microbiological Research. 162 (4): 328–34. doi:10.1016/j.micres.2006.01.016. PMID 16563712.

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