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.
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.
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.
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)". Critical Reviews in Biotechnology. 38 (7): 1025–1048. doi:10.1080/07388551.2018.1427697. PMID 29385846.
• 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.