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← Older revision		Revision as of 22:08, 26 April 2022
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	*[[Molecular Biological Tools - MBTs]]		*[[Molecular Biological Tools - MBTs]]
	*[[Quantitative Polymerase Chain Reaction (qPCR)]]		*[[Quantitative Polymerase Chain Reaction (qPCR)]]
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 '''Related Article(s):'''
 *[[Molecular Biological Tools - MBTs]]
 *[[Quantitative Polymerase Chain Reaction (qPCR)]]
-'''CONTRIBUTOR(S):''' [[Dora Ogles-Taggart]] and [[Dr. Brett Baldwin]]
 '''Key Resource(s):'''
 *[http://dx.doi.org/10.1007/s10532-011-9455-3 Identification of TBA-utilizing organisms in BioGAC reactors using <sup>13</sup>C-DNA SIP]<ref name ="Aslett2011"> Aslett, D., Haas, J., Hyman, M., 2011. Identification of tertiary butyl alcohol(TBA)-utilizing organisms in BioGAC reactors using <sup>13</sup>C-DNA stable isotope probing. Biodegradation, 22(5), 961-972. [http://dx.doi.org/10.1007/s10532-011-9455-3 doi:10.1007/s10532-011-9455-3]</ref>
-*[http://onlinelibrary.wiley.com/doi/10.1111/gwmr.12031/abstract Using DNA‐Stable Isotope Probing to Identify MTBE‐and TBA‐Degrading Microorganisms in Contaminated Groundwater]<ref name = "Key2013">Key, K.C., Sublette, K.L., Duncan, K., Mackay, D.M., Scow, K.M., Ogles, D., 2013. Using DNA‐Stable Isotope Probing to Identify MTBE‐and TBA‐Degrading Microorganisms in Contaminated Groundwater. Groundwater Monitoring & Remediation, 33(4), 57-68. [http://onlinelibrary.wiley.com/doi/10.1111/gwmr.12031/abstract doi:10.1111/gwmr.12031]</ref>
+*[http://dx.doi.org/10.1007/s10532-011-9455-3 Identification of TBA-utilizing organisms in BioGAC reactors using <sup>13</sup>C-DNA SIP]<ref name="Aslett2011"> Aslett, D., Haas, J., Hyman, M., 2011. Identification of tertiary butyl alcohol(TBA)-utilizing organisms in BioGAC reactors using <sup>13</sup>C-DNA stable isotope probing. Biodegradation, 22(5), 961-972. [http://dx.doi.org/10.1007/s10532-011-9455-3 doi:10.1007/s10532-011-9455-3]</ref>
 ==Introduction==
 Stable isotope probing (SIP) is used to conclusively determine whether in situ biodegradation of a contaminant is occurring. The “probe” is a synthesized version of the contaminant compound composed of the heavier stable isotope (e.g., <sup>13</sup>C, <sup>15</sup>N) rather than the more common light isotope of that element (e.g., <sup>12</sup>C, <sup>14</sup>N). The heavy isotope serves as the “label” to track the environmental fate of the contaminant and determine if biodegradation is occurring.
-SIP is used to conclusively determine if biodegradation of some common contaminants like petroleum hydrocarbons (e.g., [[wikipedia: BTX (chemistry) | BTEX]], [[Polycyclic Aromatic Hydrocarbons (PAHs) | polycyclic aromatic hydrocarbons (PAHs)]]) and oxygenates (e.g., [[wikipedia: Methyl tert-butyl ether | MTBE]], [[wikipedia: tert-Butyl alcohol | TBA]]) is occurring. Results are often used to evaluate the feasibility of [[Monitored Natural Attenuation (MNA)| monitored natural attenuation (MNA)]] as a site management strategy<ref>Busch‐Harris, J., Sublette, K., Roberts, K.P., Landrum, C., Peacock, A.D., Davis, G., Ogles, D., Holmes, W.E., Harris, D., Ota, C., Yang, X., 2008. Bio‐Traps Coupled with Molecular Biological Methods and Stable Isotope Probing Demonstrate the In Situ Biodegradation Potential of MTBE and TBA in Gasoline‐Contaminated Aquifers. Groundwater Monitoring & Remediation, 28(4), 47-62. [http://dx.doi.org/10.1111/j.1745-6592.2008.00216.x doi:10.1111/j.1745-6592.2008.00216.x]</ref><ref>Geyer, R., Peacock, A.D., Miltner, A., Richnow, H.H., White, D.C., Sublette, K.L., Kästner, M., 2005. In situ assessment of biodegradation potential using biotraps amended with <sup>13</sup>C-labeled benzene or toluene. Environmental Science & Technology, 39(13), 4983-4989. [http://dx.doi.org/10.1021/es048037x doi:10.1021/es048037x]</ref><ref>Key, K.C., Sublette, K.L., Johannes, T.W., Ogles, D., Baldwin, B., Biernacki, A., 2014. Assessing BTEX Biodegradation Potential at a Refinery Using Molecular Biological Tools. Groundwater Monitoring & Remediation, 34(1), 35-48. [http://onlinelibrary.wiley.com/doi/10.1111/gwmr.12037/abstract doi:10.1111/gwmr.12037]</ref><ref>Williams, N., Hyland, A., Mitchener, R., Sublette, K., Key, K.C., Davis, G., Ogles, D., Baldwin, B., Biernacki, A., 2013. Demonstrating the In Situ Biodegradation Potential of Phenol Using Bio‐Sep<sup>®</sup> Bio‐Traps<sup>®</sup> and Stable Isotope Probing. Remediation Journal, 23(1), 7-22. [http://onlinelibrary.wiley.com/doi/10.1002/rem.21335/abstract doi:10.1002/rem.21335]</ref>. Conclusive evidence of contaminant biodegradation increases stakeholder confidence that MNA is more than a “do nothing” alternative. While often performed to assess MNA, SIP can also be used to evaluate the feasibility and performance of [[Remediation Technologies | engineered bioremediation]] approaches. In research settings, SIP can also be used with DNA-based analyses to help identify the organisms involved in specific biodegradation processes<ref name ="Aslett2011" /><ref name = "Hatzinger2014">Hatzinger, P., Fuller, M., 2014. New approaches to evaluate the biological degradation of RDX in groundwater. Project ER-1607. Strategic Environmental Research Development Program, Arlington, VA. [https://www.serdp-estcp.org/Program-Areas/Environmental-Restoration/Contaminants-on-Ranges/Characterizing-Fate-and-Transport/ER-1607 ER-1607]</ref><ref name = "Key2013" />.
+SIP is used to conclusively determine if biodegradation of some common contaminants like petroleum hydrocarbons (e.g., [[wikipedia: BTX (chemistry) | BTEX]], [[Polycyclic Aromatic Hydrocarbons (PAHs) | polycyclic aromatic hydrocarbons (PAHs)]]) and oxygenates (e.g., [[wikipedia: Methyl tert-butyl ether | MTBE]], [[wikipedia: tert-Butyl alcohol | TBA]]) is occurring. Results are often used to evaluate the feasibility of [[Monitored Natural Attenuation (MNA)| monitored natural attenuation (MNA)]] as a site management strategy<ref>Busch‐Harris, J., Sublette, K., Roberts, K.P., Landrum, C., Peacock, A.D., Davis, G., Ogles, D., Holmes, W.E., Harris, D., Ota, C., Yang, X., 2008. Bio‐Traps Coupled with Molecular Biological Methods and Stable Isotope Probing Demonstrate the In Situ Biodegradation Potential of MTBE and TBA in Gasoline‐Contaminated Aquifers. Groundwater Monitoring & Remediation, 28(4), 47-62. [http://dx.doi.org/10.1111/j.1745-6592.2008.00216.x doi:10.1111/j.1745-6592.2008.00216.x]</ref><ref>Geyer, R., Peacock, A.D., Miltner, A., Richnow, H.H., White, D.C., Sublette, K.L., Kästner, M., 2005. In situ assessment of biodegradation potential using biotraps amended with <sup>13</sup>C-labeled benzene or toluene. Environmental Science & Technology, 39(13), 4983-4989. [http://dx.doi.org/10.1021/es048037x doi:10.1021/es048037x]</ref><ref>Key, K.C., Sublette, K.L., Johannes, T.W., Ogles, D., Baldwin, B., Biernacki, A., 2014. Assessing BTEX Biodegradation Potential at a Refinery Using Molecular Biological Tools. Groundwater Monitoring & Remediation, 34(1), 35-48. [http://onlinelibrary.wiley.com/doi/10.1111/gwmr.12037/abstract doi:10.1111/gwmr.12037]</ref><ref>Williams, N., Hyland, A., Mitchener, R., Sublette, K., Key, K.C., Davis, G., Ogles, D., Baldwin, B., Biernacki, A., 2013. Demonstrating the In Situ Biodegradation Potential of Phenol Using Bio‐Sep<sup>®</sup> Bio‐Traps<sup>®</sup> and Stable Isotope Probing. Remediation Journal, 23(1), 7-22. [http://onlinelibrary.wiley.com/doi/10.1002/rem.21335/abstract doi:10.1002/rem.21335]</ref>. Conclusive evidence of contaminant biodegradation increases stakeholder confidence that MNA is more than a “do nothing” alternative. While often performed to assess MNA, SIP can also be used to evaluate the feasibility and performance of [[Remediation Technologies | engineered bioremediation]] approaches. In research settings, SIP can also be used with DNA-based analyses to help identify the organisms involved in specific biodegradation processes<ref name="Aslett2011" /><ref name="Hatzinger2014">Hatzinger, P., Fuller, M., 2014. New approaches to evaluate the biological degradation of RDX in groundwater. Project ER-1607. Strategic Environmental Research Development Program, Arlington, VA. [https://www.serdp-estcp.org/Program-Areas/Environmental-Restoration/Contaminants-on-Ranges/Characterizing-Fate-and-Transport/ER-1607 ER-1607]</ref><ref name="Key2013" />.
 ==How Does SIP Work==
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 ==Advantages==
 *'''Conclusive''': SIP can provide conclusive evidence that in situ biodegradation of the contaminant is occurring.
@@ Line 40: / Line 45: @@
 ==Limitations==
 *'''Not applicable to all contaminants''': SIP is generally not appropriate for compounds that are used as terminal electron acceptors, such as [[wikipedia: Trichloroethylene | trichloroethylene (TCE)]] and other chlorinated ethenes, because the <sup>13</sup>C label is not incorporated into biomass or CO<sub>2 </sub> during this microbial process. Tools such as [[Compound Specific Isotope Analysis (CSIA) | compound-specific isotope analysis (CSIA)]] performed on the contaminant itself is more applicable for these compounds. For large or more complex compounds, synthesis of the <sup>13</sup>C-labeled compound can be expensive or simply not available.
@@ Line 45: / Line 51: @@
 ==Reporting SIP Results==
-SIP results are reported as <sup>13</sup>C/<sup>12</sup>C ratios in delta notation (δ<sup>13</sup>C) with units of parts per thousand (“per mil” ‰), where δ<sup>13</sup>C is defined as follows<ref name="LABSIE">Laboratory S.I.E. Overview of Stable Isotope Research. [http://sisbl.uga.edu/stable.html http://sisbl.uga.edu/stable.html]</ref><ref>USGS Fundamentals of Stable Isotope Geochemistry. [http://wwwrcamnl.wr.usgs.gov/isoig/res/funda.html USGS Resources on Isotopes]</ref>:
+SIP results are reported as <sup>13</sup>C/<sup>12</sup>C ratios in delta notation (δ<sup>13</sup>C) with units of parts per thousand (“per mil” ‰), where δ<sup>13</sup>C is defined as follows<ref name="LABSIE">Laboratory S.I.E. Overview of Stable Isotope Research. http://sisbl.uga.edu/stable.html</ref><ref>USGS Fundamentals of Stable Isotope Geochemistry. [http://wwwrcamnl.wr.usgs.gov/isoig/res/funda.html USGS Resources on Isotopes]</ref>:
 [[File:Ogles equ.JPG|center|400px]]
 ::Where:
-::R<sub>sample</sub> is the <sup>13</sup>C/<sup>12</sup>C ratio of the sample and
+::Where:
 ::R<sub>standard</sub> is the <sup>13</sup>C/<sup>12</sup>C ratio of the Vienna Pee Dee Belemnite (VPDB) standard.
 ==Background δ<sup>13</sup>C Values==
-The <sup>13</sup>C/<sup>12</sup>C ratio of the VPDB standard (1.1112328% <sup>13</sup>C) is greater than most other natural carbon-based substances<ref name="LABSIE"/>. Because R<sub>standard</sub> is typically larger than R<sub>sample </sub>, calculated δ<sup>13</sup>C values of most naturally-occurring materials will be negative values (0‰ to -110‰).
+The <sup>13</sup>C/<sup>12</sup>C ratio of the VPDB standard (1.1112328% <sup>13</sup>C) is greater than most other natural carbon-based substances<ref name="LABSIE" />. Because R<sub>standard</sub> is typically larger than R<sub>sample </sub>, calculated δ<sup>13</sup>C values of most naturally-occurring materials will be negative values (0‰ to -110‰).
 The isotopic composition of subsurface microorganisms and their metabolic products (e.g., CO<sub>2 </sub>) will directly reflect the isotopic composition of the compounds used as carbon and energy sources. Thus under natural conditions, background δ<sup>13</sup>C values for microbial biomass and DIC would be expected to be negative and are often between -20‰ and -30‰ <ref>Pelz, O., Chatzinotas, A., Zarda-Hess, A., Abraham, W.R., Zeyer, J., 2001. Tracing toluene-assimilating sulfate-reducing bacteria using <sup>13</sup>C-incorporation in fatty acids and whole-cell hybridization. FEMS Microbiology Ecology, 38(2-3), 123-131. [http://dx.doi.org/10.1111/j.1574-6941.2001.tb00890.x doi:10.1111/j.1574-6941.2001.tb00890.x]</ref>. In a SIP study, δ<sup>13</sup>C values for microbial biomass and DIC will be greater than these background levels if biodegradation is occurring because the contaminant degraders are utilizing <sup>13</sup>C from the synthesized contaminant as a carbon and energy source.
@@ Line 80: / Line 87: @@
 ==Summary==
-For contaminants that microbes can use as a carbon and energy source (Table 1), stable isotope probing (SIP) is a useful tool for conclusively determining whether in situ biodegradation is occurring. While SIP can aid in evaluating MNA at any site, SIP studies are particularly valuable at complex sites where stakeholders may be reluctant to accept MNA as a site management strategy. Definitive evidence of contaminant biodegradation increases stakeholder confidence that MNA is more than a “do nothing” alternative. At the remedy selection phase, SIP studies can also be performed as part of a pilot study to assess active bioremediation approaches. Greater <sup>13</sup>C incorporation into DIC and biomass in Bio-Traps<sup>®</sup> deployed in wells influenced by site activities (pilot study, injection area, system operation) relative to wells outside of the radius of influence strongly suggests that the remediation technology enhanced biodegradation. In research settings, SIP is used with DNA-based analyses to help identify the organisms involved in specific biodegradation processes<ref name ="Aslett2011"/><ref name = "Hatzinger2014"/><ref name = "Key2013"/>.
+For contaminants that microbes can use as a carbon and energy source (Table 1), stable isotope probing (SIP) is a useful tool for conclusively determining whether in situ biodegradation is occurring. While SIP can aid in evaluating MNA at any site, SIP studies are particularly valuable at complex sites where stakeholders may be reluctant to accept MNA as a site management strategy. Definitive evidence of contaminant biodegradation increases stakeholder confidence that MNA is more than a “do nothing” alternative. At the remedy selection phase, SIP studies can also be performed as part of a pilot study to assess active bioremediation approaches. Greater <sup>13</sup>C incorporation into DIC and biomass in Bio-Traps<sup>®</sup> deployed in wells influenced by site activities (pilot study, injection area, system operation) relative to wells outside of the radius of influence strongly suggests that the remediation technology enhanced biodegradation. In research settings, SIP is used with DNA-based analyses to help identify the organisms involved in specific biodegradation processes<ref name="Aslett2011" /><ref name="Hatzinger2014" /><ref name="Key2013" />.
 [[File:Table1 SIP Ogles.JPG|thumbnail|center|750px|Table 1. Examples of appropriate contaminants for SIP studies.]]
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 ==See Also==
 *[http://www.itrcweb.org/documents/team_emd/SIP_Fact_Sheet.pdf Stable Isotope Probing – Fact Sheet]<br />
 *[http://www.itrcweb.org/emd-2/Content/7%20stable%20isotope%20probing%20Sip.htm Stable Isotope Probing (SIP)]<br />
@@ Line 93: / Line 101: @@
 *[https://www.serdp-estcp.org/Program-Areas/Environmental-Restoration/Contaminants-on-Ranges/Characterizing-Fate-and-Transport/ER-1607/ER-1607 New Approaches to Evaluate the Biological Degradation of RDX in Groundwater ER-1607]<br />
 *[[Characterization, Assessment & Monitoring]]<br />
-*[https://www.coursera.org/learn/natural-attenuation-of-groundwater-contaminants/lecture/83aUM/stable-isotope-probing  Online Lecture Course - Stable Isotope Probing]
+*[https://www.coursera.org/learn/natural-attenuation-of-groundwater-contaminants/lecture/83aUM/stable-isotope-probing Online Lecture Course - Stable Isotope Probing]

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Stable Isotope Probing (SIP) - Revision history

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