Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface

PLoS One. 2013;8(3):e57819. doi: 10.1371/journal.pone.0057819. Epub 2013 Mar 5.


While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux through Geobacter respiratory pathways, and the synthesis of anapleurotic four carbon compounds from acetyl-CoA via pyruvate ferredoxin oxidoreductase activity. Across a 40-day period where Fe(III) reduction was occurring, fluctuations in protein expression reflected changes in anabolic versus catabolic reactions, with increased levels of biosynthesis occurring soon after acetate arrival in the aquifer. In addition, localized shifts in nutrient limitation were inferred based on expression of nitrogenase enzymes and phosphate uptake proteins. These temporal data offer the first example of differing microbial protein expression associated with changing geochemical conditions in a subsurface environment.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biomass
  • Carbon / chemistry
  • Environment
  • Gene Expression Regulation, Bacterial*
  • Geobacter / metabolism*
  • Geobacter / physiology*
  • Groundwater
  • Humic Substances
  • Iron / chemistry
  • Oxidation-Reduction
  • Phosphates / chemistry
  • Plankton / metabolism
  • Proteomics
  • RNA, Ribosomal, 16S / metabolism
  • Tandem Mass Spectrometry
  • Uranium / chemistry
  • Vanadium / chemistry
  • Water Microbiology*


  • Humic Substances
  • Phosphates
  • RNA, Ribosomal, 16S
  • Vanadium
  • Uranium
  • Carbon
  • Iron

Grants and funding

This research was funded by the United States Department of Energy, Office of Science, Environmental Remediation Science Program through the Integrated Field Research Challenge Site at Rifle, Colorado, under contract number DE-AC05-76RL01830 to Pacific Northwest National Laboratory. (http://science.energy.gov/ber/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.