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]

See also

• Stable isotope labeling by amino acids in cell culture

References

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.

Further reading

• Berry D, Loy A (December 2018). "Stable-Isotope Probing of Human and Animal Microbiome Function". Trends in Microbiology. 26 (12): 999–1007. doi:10.1016/j.tim.2018.06.004. PMC 6249988. PMID 30001854.
• Egert M, Weis S, Schnell S (October 2018). "RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions". Methods. San Diego, Calif. 149: 25–30. doi:10.1016/j.ymeth.2018.05.022. PMID 29857194.
• Jiang B, Jin N, Xing Y, Su Y, Zhang D (November 2018). "Unraveling uncultivable pesticide degraders via stable isotope probing (SIP)" (PDF). Critical Reviews in Biotechnology. 38 (7): 1025–1048. doi:10.1080/07388551.2018.1427697. PMID 29385846. S2CID 1218065.
• Wegener G, Kellermann MY, Elvert M (October 2016). "Tracking activity and function of microorganisms by stable isotope probing of membrane lipids". Current Opinion in Biotechnology. 41: 43–52. doi:10.1016/j.copbio.2016.04.022. PMID 27179643.