Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

ISME J. 2011 May;5(5):856-65. doi: 10.1038/ismej.2010.168. Epub 2010 Nov 11.


Metaproteomics is one of a suite of new approaches providing insights into the activities of microorganisms in natural environments. Proteins, the final products of gene expression, indicate cellular priorities, taking into account both transcriptional and posttranscriptional control mechanisms that control adaptive responses. Here, we report the proteomic composition of the < 1.2 μm fraction of a microbial community from Oregon coast summer surface waters, detected with two-dimensional liquid chromatography coupled with electrospray tandem mass spectrometry. Spectra corresponding to proteins involved in protein folding and biosynthesis, transport, and viral capsid structure were the most frequently detected. A total of 36% of all the detected proteins were best matches to the SAR11 clade, and other abundant coastal microbial clades were also well represented, including the Roseobacter clade (17%), oligotrophic marine gammaproteobacteria group (6%), OM43 clade (1%). Viral origins were attributed to 2.5% of proteins. In contrast to oligotrophic waters, phosphate transporters were not highly detected in this nutrient-rich system. However, transporters for amino acids, taurine, polyamines and glutamine synthetase were among the most highly detected proteins, supporting predictions that carbon and nitrogen are more limiting than phosphate in this environment. Intriguingly, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry.

Publication types

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

MeSH terms

  • Bacterial Proteins / analysis
  • Chromatography, High Pressure Liquid
  • Gammaproteobacteria / classification
  • Gammaproteobacteria / genetics
  • Gammaproteobacteria / metabolism*
  • Mass Spectrometry
  • Oceans and Seas
  • Oregon
  • Plankton / classification
  • Plankton / genetics
  • Plankton / metabolism*
  • Proteomics*
  • Roseobacter / classification
  • Roseobacter / genetics
  • Roseobacter / metabolism*
  • Seawater / microbiology*


  • Bacterial Proteins