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Stable Isotope Probing

Microbial ecologists presently use the term, Stable Isotope Probing (SIP), to refer to various techniques based on isotopic labeling of microbial biomarkers used for microbial identification (usually 13C), followed by analysis of labeled biomarkers to identify the organisms assimilating substrate. Though SIP is not the only tool that allows such analysis it is particularly well-suited for soils and biodegradation research. Typical biomarkers include phospholipid fatty acids, DNA, and RNA, with nucleic acid SIP generally the most informative due to the extensive 16S rRNA database (>120,000 sequences) available for searching. DNA-and RNA-based SIP are accomplished with the same basic protocol. A community is exposed to a labeled, then a sample is extracted to recover nucleic acids and nucleic acids are separated by density gradient centrifugation and the heavy fractions ultimately are sequenced for identification. An increase in the Buoyant Density (BD) of enriched nucleic acids is considered evidence the sequence came from an active degrader. The DNA-SIP method has been applied to assimilation of numerous substrates, such as naphthalene phenol, methanol, methane, propionate, methyl bromide, methyl chloride, pentachlorophenol, ammonium, and 2,4-D. Obviously, SIP methods are subject to the weaknesses of molecular methods (nucleic acid recovery, PCR bias, etc.) and incubation time may result in crossfeeding if too long or insufficient labeling if too short.
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Last date updated on July, 2014

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