Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS
- Author(s)
- Xavier Mayali, Peter K. Weber, Erin Nuccio, Jory Lietard, Mark Somoza, Steven J. Blazewicz, Jennifer Pett-Ridge
- Abstract
Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes (13C, 15N, and 18O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass spectrometer (SIMS) to determine the relative isotope incorporation of the rRNA at each probe location. Using a maskless array synthesizer (MAS), we synthesize multiple unique sequences to target hundreds of taxa at the ribosomal operational taxonomic unit (OTU) level on an array surface, and then analyze it with a NanoSIMS 50, using its high-spatial resolution imaging capability to generate isotope ratios for individual probes. The Chip-SIP method has been used in diverse systems, including surface marine and estuarine water, rhizosphere, and peat soils, to quantify taxon-specific relative incorporation of different substrates in complex microbial communities. Depending on the hypothesis and experimental design, Chip-SIP allows the user to compare the same community incorporating different substrates, different communities incorporating the same substrate(s), or quantify how a community responds to treatment effects, such as temperature or nutrient concentrations.
- Organisation(s)
- Department of Inorganic Chemistry
- External organisation(s)
- Lawrence Livermore National Laboratory
- Volume
- 2046
- Pages
- 71-87
- No. of pages
- 17
- DOI
- https://doi.org/10.1007/978-1-4939-9721-3_6
- Publication date
- 08-2019
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 104004 Chemical biology, 106022 Microbiology
- Keywords
- ASJC Scopus subject areas
- Molecular Biology, Genetics
- Sustainable Development Goals
- SDG 14 - Life Below Water
- Portal url
- https://ucrisportal.univie.ac.at/en/publications/f6c015be-f440-4839-ae53-d4a93f1efaf1