Microbial Ecology

, Volume 67, Issue 3, pp 520–539 | Cite as

Metaproteomic Survey of Six Aquatic Habitats: Discovering the Identities of Microbial Populations Active in Biogeochemical Cycling

  • Buck T. Hanson
  • Ian Hewson
  • Eugene L. MadsenEmail author
Microbiology of Aquatic Systems


Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography–mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.


Synechococcus Glycine Betaine Prochlorococcus Marine Sample Stable Isotope Probe 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Funding to ELM was provided by NSF grant #DEB-0841999. Samples were collected by J. Brown on board the R/V Atlantis cruise AT15-16 (A. Knapp and D. Capone, Chief Scientists, supported by NSF OCE-0850801), on board the R/V Pelican on cruise EK1009 (C. Heil, Chief Scientist), and on board the R/V Hugh R. Sharp cruise 10702 (B. Crump, Chief Scientist, supported by NSF OCE-0961920). Collection of samples was supported on NSF OCE-0961894). Support for sample collection was also provided by NSF grants DEB 1028898 awarded to N. Hairston and I. Hewson, and OCE-1049670 awarded to M. Brietbart, K. Daly, and I. Hewson.

Supplementary material

248_2013_346_MOESM1_ESM.docx (1.7 mb)
ESM 1 (DOCX 1.71 MB)


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Buck T. Hanson
    • 1
  • Ian Hewson
    • 1
  • Eugene L. Madsen
    • 1
    Email author
  1. 1.Department of Microbiology, B57A Wing HallCornell UniversityIthacaUSA

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