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

Sarah M. Sowell, Paul E. Abraham, Manesh Shah, Nathan C. Verberkmoes, Daniel P. Smith, Douglas F. Barofsky, Stephen J. Giovannoni

Research output: Contribution to journalArticlepeer-review

133 Scopus citations

Abstract

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 m 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.

Original languageEnglish
Pages (from-to)856-865
Number of pages10
JournalISME Journal
Volume5
Issue number5
DOIs
StatePublished - May 2011

Funding

We thank the crew of the Elaka and Joshua Kitner for their help in sample collection, and Francis Chan for data and discussions about oceanographic conditions. This work was supported in part by a Marine Microbiology Initiative Investigator Award from the Gordon and Betty Moore Foundation. Additional sponsorship was received from the US Department of Energy under contract DE-AC05-00OR22725 with Oak Ridge National Laboratory, managed and operated by UT-Battelle, LLC.

FundersFunder number
U.S. Department of EnergyDE-AC05-00OR22725
Gordon and Betty Moore Foundation
Oak Ridge National Laboratory

    Keywords

    • OM43 clade
    • metaproteomics; marine plankton

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