Nature 438, 82-85 (3 November 2005) | doi:10.1038/nature04032; Received 29 November 2004; Accepted 11 July 2005

Proteorhodopsin in the ubiquitous marine bacterium SAR11

Stephen J. Giovannoni1, Lisa Bibbs4, Jang-Cheon Cho1,5, Martha D. Stapels2,5, Russell Desiderio3, Kevin L. Vergin1, Michael S. Rappé1,5, Samuel Laney3, Lawrence J. Wilhelm1, H. James Tripp1, Eric J. Mathur4 & Douglas F. Barofsky2

  1. Department of Microbiology,
  2. Department of Chemistry, and
  3. College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon 97331, USA
  4. Diversa Corporation, 4955 Directors Place, San Diego, California 92121-1609, USA
  5. †Present addresses: Department of Oceanography, 5N541, Inha University Younghyun-dong, Nam-Gu, Incheon 402-751, Korea (J.-C.C.); Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, USA (M.D.S.); Hawaii Institute of Marine Biology, SOEST, University of Hawaii, PO Box 1346, Kaneohe, Hawaii 96744, USA (M.S.R.)

Correspondence to: Stephen J. Giovannoni1 Correspondence and requests for materials should be addressed to S.J.G. (Email: steve.giovannoni@oregonstate.edu). The HTCC1062 proteorhodopsin gene sequence has been deposited in GenBank under accession number CP000084.

Proteorhodopsins are light-dependent proton pumps that are predicted to have an important role in the ecology of the oceans by supplying energy for microbial metabolism1, 2. Proteorhodopsin genes were first discovered through the cloning and sequencing of large genomic DNA fragments from seawater1. They were later shown to be widely distributed, phylogenetically diverse, and active in the oceans3, 4, 5, 6, 7. Proteorhodopsin genes have not been found in cultured bacteria, and on the basis of environmental sequence data, it has not yet been possible to reconstruct the genomes of uncultured bacterial strains that have proteorhodopsin genes. Although the metabolic effect of proteorhodopsins is uncertain, they are thought to function in cells for which the primary mode of metabolism is the heterotrophic assimilation of dissolved organic carbon. Here we report that SAR11 strain HTCC1062 ('Pelagibacter ubique')8, the first cultivated member of the extraordinarily abundant SAR11 clade, expresses a proteorhodopsin gene when cultured in autoclaved seawater and in its natural environment, the ocean. The Pelagibacter proteorhodopsin functions as a light-dependent proton pump. The gene is expressed by cells grown in either diurnal light or in darkness, and there is no difference between the growth rates or cell yields of cultures grown in light or darkness.