Short-term stable isotope probing of proteins reveals taxa incorporating inorganic carbon in a hot spring microbial mat

Laurey Steinke, Gordon W. Slysz, Mary S. Lipton, Christian Klatt, James J. Moran, Margie F. Romine, Jason M. Wood, Gordon Anderson, Donald A. Bryant, David M. Ward

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation.

Original languageEnglish (US)
Article number1829
JournalApplied and environmental microbiology
Issue number7
StatePublished - Mar 1 2020


  • Geochemistry
  • Inorganic carbon uptake
  • Metaproteomics
  • Microbial mat
  • Mushroom spring
  • Phototrophy
  • Stable isotope probing
  • Stable isotope signature
  • Stromatolite

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology


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