Goal

• Summary of the methods used by SIP studies to ID isotope incorporators
  • focus on high throughput sequencing methods

'Heavy' window method

Anything found in the 'heavy' fraction is classified as an incorporator.

• Methanotrophic bacteria in warm geothermal spring sediments identified using stable-isotope probing

  • Christine E. Sharp, Azucena Martínez-Lorenzo, Allyson L. Brady, Stephen E. Grasby, Peter F. Dunfield
  • https://femsec.oxfordjournals.org/content/90/1/92
  • nucleotide: DNA
  • gradient: CsCl
  • isotope: 13CH4
  • marker: pmoA
  • sequencing: pyrosequencing
  • heavy window: 1.72-1.74

• Identification of Nitrogen-Incorporating Bacteria in Petroleum-Contaminated Arctic Soils by Using [15N]DNA-Based Stable Isotope Probing and Pyrosequencing

  • Terrence H. Bell1,2, Etienne Yergeau2, Christine Martineau1,2, David Juck2, Lyle G. Whyte1 and Charles W. Greer2
  • http://aem.asm.org/content/77/12/4163.full.pdf+html
  • nucleotide: DNA
  • gradient: CsCl
  • isotope: 15N-MAP
  • marker: 16S rRNA
  • sequencing: pyrosequencing
  • heavy window: 1.727-1.735

• Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing

  • CE Sharp, MB Stott, PF Dunfield
  • http://journal.frontiersin.org/article/10.3389/fmicb.2012.00303/abstract
  • nucleotide: DNA
  • gradient: CsCl
  • isotope: 13C-CH4 + 13CO2
  • marker: 16S rRNA
  • sequencing: pyrosequencing
  • heavy window: 1.73-1.75
  • light window: 1.69

• Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph

  • Carolina Grob,1† Martin Taubert, Alexandra M. Howat,1 Oliver J. Burns, Joanna L. Dixon,3 Hans H. Richnow,4, Nico Jehmlich,5 Martin von Bergen,5,6,7 Yin Chen8 and J. Colin Murrell1
  • http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12935/full
  • nucleotide: DNA
  • gradient: CsCl
  • isotope: 13C-methanol
  • marker: 16S rRNA
  • sequencing: pyrosequencing
  • heavy window: 1.725
  • light window: 1.7

• Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing

  • http://aem.asm.org/content/78/7/2316.full.pdf+html
  • nucleotide: DNA
  • gradient: CsCl
  • isotope: 13C-cellulose
  • marker: 16S rRNA
  • sequencing: clone library + Sanger
  • heavy window: ?!?!?!

• http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02501.x/epdf

  • nucleotide: DNA
  • gradient: CsCl
  • isotope: 13C-PAHs
  • marker: 16S rRNA
  • sequencing: clone library + Sanger
  • heavy window: ?!?!?!