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abundance of elements in the DNA. For example, the difference in mass between O and O (two atomic mass units) is twice that between C and C (one atomic mass unit), so incorporation of O into DNA will cause a larger per atom density shift than will incorporation of C. Conversely, DNA contains nearly twice as many carbon atoms (11.25 per base, on average) as oxygen atoms (6 per base), so at equivalent labeling (e.g., 50 atom percent C or O), DNA labeled with O will be only slightly more dense than DNA fully labeled with C. Similarly, nitrogen is less abundant in DNA (3.75 atoms per base, on average), so a weaker DNA buoyant density shift is observed with N- versus C-labeled or O-labeled substrates. Larger buoyant density shifts are observed when multiple isotope tracers are used. Because density shifts as a predictable function of the change in mass caused by isotope assimilation, stable isotope probing can be modeled to estimate the amount of isotope incorporation, an approach called quantitative stable isotope probing (qSIP), which has been applied to microbial communities in soils, marine sediments, and decomposing leaves to compare rates of growth and substrate assimilation among different microbial taxa.
76:
When DNA is the biomarker, SIP can be performed using isotopically labeled C, H, O, or N, though C is used most often. The density shift is proportional to the change in density in the DNA, which depends on the difference in mass between the rare and common isotopes for a given element, and on the
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and which were using carbohydrates more recently produced from photosynthesis. SIP with O-labeled water can be used to find out which organisms are actively growing, because oxygen from water is incorporated into DNA (and RNA) during synthesis.
356:
Hungate, Bruce A.; Mau, Rebecca L.; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa A.; Marks, Jane C.; Morrissey, Ember M. (2015). Schloss, P. D. (ed.).
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Starr, Evan P.; Shi, Shengjing; Blazewicz, Steven J.; Koch, Benjamin J.; Probst, Alexander J.; Hungate, Bruce A.; Pett-Ridge, Jennifer; Firestone, Mary K.; Banfield, Jillian F. (2021).
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Neufeld JD, Dumont MG, Vohra J, Murrell JC (April 2007). "Methodological considerations for the use of stable isotope probing in microbial ecology".
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Hayer, Michaela; Schwartz, Egbert; Marks, Jane C.; Koch, Benjamin J.; Morrissey, Ember M.; Schuettenberg, Alexa A.; Hungate, Bruce A. (2016).
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with the heavier isotopes incorporated into them can be separated from biomarkers containing the more naturally abundant lighter isotope by
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Egert M, Weis S, Schnell S (October 2018). "RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions".
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791:
321:
Cupples AM, Shaffer EA, Chee-Sanford JC, Sims GK (2007). "DNA buoyant density shifts during 15N-DNA stable isotope probing".
548:"Identification of growing bacteria during litter decomposition in freshwater through quantitative stable isotope probing"
801:
424:"Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil"
199:
Radajewski S, Ineson P, Parekh NR, Murrell JC (February 2000). "Stable-isotope probing as a tool in microbial ecology".
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483:"Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O"
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Dumont MG, Murrell JC (June 2005). "Stable isotope probing - linking microbial identity to function".
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733:"Tracking activity and function of microorganisms by stable isotope probing of membrane lipids"
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Coskun, Ă–mer K.; Ă–zen, Volkan; Wankel, Scott D.; Orsi, William D. (2019).
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609:"Stable-Isotope Probing of Human and Animal Microbiome Function"
359:"Quantitative Microbial Ecology through Stable Isotope Probing"
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with C is then separated from DNA with C by centrifugation.
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the DNA identifies which organisms were consuming existing
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by microorganisms. A substrate is enriched with a heavier
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Jiang B, Jin N, Xing Y, Su Y, Zhang D (November 2018).
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Stable isotope labeling by amino acids in cell culture
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can be used to find out which organisms are actively
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731:Wegener G, Kellermann MY, Elvert M (October 2016).
60:or consuming new photosynthate. As the biomarker,
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696:Critical Reviews in Biotechnology
737:Current Opinion in Biotechnology
607:Berry D, Loy A (December 2018).
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708:10.1080/07388551.2018.1427697
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807:Microbial population biology
792:Molecular biology techniques
750:10.1016/j.copbio.2016.04.022
658:. San Diego, Calif.: 25–30.
335:10.1016/j.micres.2006.01.016
250:Schwartz E (February 2007).
107:Nature Reviews. Microbiology
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664:10.1016/j.ymeth.2018.05.022
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802:Environmental microbiology
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625:10.1016/j.tim.2018.06.004
507:10.1038/s41396-019-0373-4
170:10.1007/s00248-006-9125-x
441:10.1128/msphere.00085-21
323:Microbiological Research
45:isopycnic centrifugation
787:Microbiology techniques
573:10.1111/1758-2229.12475
613:Trends in Microbiology
33:biogeochemical cycling
27:for tracing uptake of
17:Stable-isotope probing
383:10.1128/AEM.02280-15
281:10.1128/AEM.02021-06
23:) is a technique in
564:2016EnvMR...8..975H
499:2019ISMEJ..13.1546C
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272:2007ApEnM..73.2541S
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162:2007MicEc..53..435N
119:10.1038/nrmicro1162
369:(21): 7570–7581.
150:Microbial Ecology
58:photosynthesizing
25:microbial ecology
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781:Categories
93:References
66:Sequencing
41:Biomarkers
743:: 43–52.
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391:0099-2240
29:nutrients
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127:15886694
81:See also
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652:Methods
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560:Bibcode
524:6776007
495:Bibcode
451:8550312
428:mSphere
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62:DNA
31:in
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