Publications (since 2000)

2013

Enav, H., Mandel-Gutfreund, Y. and Béjà, O. Metagenomic analysis suggests viral induced shift of host metabolism toward nucleotide biosynthesis. submitted

Sabehi, G., and Béjà, O. Preparation of BAC libraries from marine microbial populations. Methods Enzymol. submitted

Philosof, A., and Béjà, O. (2013) Bacterial, archaeal and viral-like rhodopsins from the Red Sea. Environ. Microbiol. Rep. 5, 475-482.

Béjà, O., Pinhassi, J. and Spudich, J.L. Proteorhodopsins: widespread microbial light-driven proton pumps. In: Levin S.A. (ed.) Encyclopedia of Biodiversity 6, 280-285.

Finkel, O.M., Béjà, O., and Belkin, S. (2013) Global abundance of microbial rhodopsins. ISME J. 7, 448-451.

2012

Mazor, Y., Greenberg, I., Toporik, H., Béjà, O., and Nelson, N. (2012) The evolution of PSI in light of phage encoded reaction centers. Phil. Trans. R. Soc. B. 367, 3400-3405.

Bodaker, I., Suzuki, M.T., Oren, O., and Béjà, O. (2012) Dead Sea rhodopsins revisited. Environ. Microbiol. Rep. 4, 617-621. 

Béjà, O., Fridman, S., and Glaser, F. (2012) Viral clones from the GOS expedition with an unusual photosystem-I gene cassette organization. ISME J. 6, 1617-1620. Supplementary Information

Atamna-Ismaeel, N., Finkel, O.M., Glaser, F., von Mering, C., Vorholt, J.A., Koblizek, M., Belkin, S., and Béjà, O. (2012) Bacterial anoxygenic photosynthesis on plant leaf surfaces. Environ. Microbiol. Rep. 4, 209-216.

Feingersch, R., Philosof, A., Mejuch, T.,  Glaser, F., Alalouf, O., Shoham, Y. and Béjà, O. (2012) Potential for phosphite and phosphonate utilization by Prochlorococcus.  ISME J. 6, 827-834.

Enav, H., Béjà, O., and Mandel-Gutfreund, Y. (2012) Cyanophage tRNAs may play a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts. ISME J. 6, 619-628. 

Atamna-Ismaeel, N., Finkel, O.M., Glaser, F., Sharon, I., Schneider, R., Post, A.F., Spudich, J.L., von Mering, C., Vorholt, J.A., Iluz, D., Béjà, O. and  Belkin, S. (2012) Microbial rhodopsins on leaf surfaces of terrestrial plants. Environ. Microbiol. 14, 140-146. Special Issue: Omics Driven Microbial Ecology

See also Science Editor's Choice on this work

2011

Philosof, A., Battchikova, N., Aro, E.-M., and Béjà, O. (2011) Marine cyanophages: Tinkering with the electron transport chain. ISME J. 5, 1568-1570.

Sharon, I., Battchikova, N., Aro, E.-M., Giglione, C., Meinnel, T., Glaser, F., Pinter, R.Y., Breitbart, M., Rohwer, F., and Béjà, O. (2011) Comparative metagenomics of microbial traits within oceanic viral communities. ISME J. 5, 1178-1190.
Check also the accompanying VirMic website  

Yogev, T., Rahav, E., Bar Zeev, E., Aharonovich, D., Stambler, N., Kress, N., Béjà, O., Mulholland, M., Herut, B., and Berman-Frank, I. (2011) Is dinitrogen fixation significant in the Levantine Basin, East Mediterranean Sea? Environ. Microbiol. 13, 854-871.
See also Michael Krom's Highlight paper

Alperovitch*, A., Sharon*, I., Rohwer, F., Aro, E.M., Milo, R., Nelson, N., and Béjà, O. (2011) Reconstructing a puzzle: Existence of cyanophages containing both photosystem-I & photosystem-II gene-suites inferred from oceanic metagenomic datasets. Environ. Microbiol.  13, 24-32. 
*equal contribution

2010

Koh, Y.E., Atamna-Ismaeel, N., Andrew R. Martin, A.R., Cowie, R.O.M., Béjà, O. Davy, S.K., and Ryan, K.G. (2010) Proteorhodopsin-bearing bacteria in Antarctic sea ice. Appl. Environ. Microbiol. 76, 5918-5925.

 DeLong, E.F., and Béjà, O. (2010) The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times.  PLoS Biol. 8, e1000359.
This article is featured in PLoS Hubs: Biodiversity  

Man-Aharonovich*, D., Philosof*, A., Kirkup, B.C., Le Gall, F., Yogev, T., Berman-Frank, I., Polz, M.F., Vaulot, D., and Béjà, O. (2010) Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts. ISME J. 4, 1044-1052. 
*equal contribution

Corrigendum: Atamna-Ismaeel, N., et al. (2010) Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems. ISME J. 4, 462.
Correction to: ISME J.  (2008) 2, 656-662.

Bodaker*, I.,  Sharon*, I., Suzuki, M.T., Feingersch, R., Shmoish, M., Andreishcheva, E., Sogin, M.L., Rosenberg, M., Maguire, M.E., Belkin, S., Oren, O., and Béjà, O. (2010) Comparative community genomics in the Dead Sea, an increasingly extreme environment. ISME J. 4 , 399-407. 
*equal contribution

Feingersch, R., Suzuki, M.T., Shmoish, M., Sharon, I., Sabehi, G., Partensky, F., and Béjà, O. (2010) Microbial community genomics in eastern Mediterranean Sea surface waters. ISME J. 4, 78-87. 

Mano, A., Tuller, T., Béjà, O., and Pinter, R.Y. (2010) Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. BMC Bioinformatics 11, S38.

2009

Bodaker, I., Béjà, O., Sharon, I., Feingersch, R., Rosenberg, M., Oren, A., Hindiyeh, M.Y., and Malkawi, H.I. (2009) Archaeal diversity in the Dead Sea: microbial survival under increasingly harsh conditions. Natural Resources and Environmental Issues V5, Article 25.

Philosof, A., Sabehi, G., and Béjà, O. (2009) Comparative analysis of actinobacterial genomic fragments from Lake Kinneret.  Environ. Microbiol. 11, 3189-3200. 

Sharon*, I., Alperovitch*, A., Rohwer, F., Haynes, M., Glaser, F., Atamna-Ismaeel, N., Pinter, R.Y., Partensky, F., Koonin, E.V., Wolf Y.I., Nelson, N. and Béjà, O. (2009) Photosystem-I gene cassettes are present in marine virus genomes. Nature 461, 258-262.   Supplementary Information
*equal contribution

Yutin, N., Suzuki, M.T., Rosenberg, M., Rotem, D., Madigan, M.T., Süling, J.,  Imhoff, J.F., and Béjà, O. (2009) BchY-based degenerate primers target all types of anoxygenic photosynthetic bacteria in a single PCR reaction. Appl. Environ. Microbiol. 75, 7556-7559.   Supplementary Material

Feingersch, R., and Béjà, O. (2009) Bias in assessments of marine SAR11 biodiversity in environmental fosmid & BAC libraries? ISME J. 3, 1117-1119. 

Tzahor*, S., Man-Aharonovich*, D., Kirkup, B.C., Yogev, T., Berman-Frank, I., Polz, M., Béjà, O., and Mandel-Gutfreund, Y. (2009) A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment.  BMC Genomics 10:229.
*equal contribution

Loy, A., Duller, S., Baranyi, C., Mußmann, M., Ott, J., Sharon, I., Béjà, O., Le Paslier, D., Dahl, C., and Wagner, M. (2009) Reverse dissimilatory sulfite reductase and other Dsr Proteins in sulfur-oxidizing bacteria: evolutionary history and suitability as phylogenetic markers. Environ. Microbiol.  11, 289-299.

2008

Yutin, N., Béjà, O., and Suzuki, M.T.  The use of denaturing gradient gel electrophoresis with fully degenerate pufM primers to monitor aerobic anoxygenic phototrophic assemblages. Limnol. Oceanogr. Methods  6, 427-440.

Bar Zeev, E., Yogev, T., Man-Aharonovich, D., Kress, N., Herut, B., Béjà, O. and Berman-Frank, I. (2008) Seasonal dynamics of the endosymbiotic, nitrogen-fixing cyanobacterium Richelia intracellularis in the eastern Mediterranean Sea. ISME J. 2, 911-923.

Atamna-Ismaeel, N., Sabehi, G., Sharon, I., Witzel, K-P., Labrenz, M., Jürgens, K., Barkay, T., Stomp, M., Huisman, J., and Béjà, O. (2008) Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems. ISME J.  2, 656-662.
Corrigendum ISME J.  (2010) 4, 462.

Kagan, J., Sharon, I., Béjà, O., and Kuhn, J. (2008) The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization. Genome Biol. 9, R20

Massana, R., Karniol, B., Pommier, T., Bodaker, I., and Béjà, O. (2008) Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate. Environ. Microbiol. 10, 1335–1343.

Béjà, O., and Suzuki, M.T. Photoheterotrophic marine prokaryotes. In Microbial Ecology of the Oceans 131-157. Kirchman, D.L. (ed). New York: John Wiley & Sons, Inc.

2007

Sharon*, I., Tzahor*, S., Williamson*, S., Shmoish, M., Man-Aharonovich, D., Rusch, D.B., Yooseph, S., Zeidner, G., Golden, S.S., Mackey, S.R., Adir, N., Weingart, U., Horn, D., Venter, J.C, Mandel-Gutfreund, Y., and Béjà, O. (2007) Viral photosynthetic reaction center genes and transcripts in the marine environment. ISME J. 1, 492-501.   Supplementary information
*equal contribution

See also a series of papers on the Global Ocean Sampling Expedition published in PLoS Biology

Man-Aharonovich, D., Kress, N., Bar Zeev, E., Berman-Frank, I., and Béjà, O. (2007) Molecular ecology of nifH genes and transcripts in Eastern Mediterranean Sea. Environ. Microbiol.  9, 2354-2363. 

Yutin, N., Suzuki, M.T., Teeling, H., Weber, M., Venter, J.C., Rusch, D. and Béjà, O. (2007) Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes. Environ. Microbiol. 9, 1464-1475. Supplementary materials

Sabehi*, G., Kirkup*, B.C., Rosenberg, M., Stambler, N., Polz, M.F., and Béjà, O. (2007) Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas. ISME J. 1, 48-55.
Supplementary materials
*equal contribution

See also Nature Reviews in Microbiology Research Highlights on this work

Suzuki, M.T., and Béjà, O. (2007) An elusive marine photosynthetic bacterium is finally unveiled. Proc. Natl. Acad. Sci. USA 104, 2561–2562. 

Sabehi, G., and Béjà, O. (2007) BAC libraries construction from marine microbial assemblages. Molecular Microbial Ecology Manual 1863-1879.

2005

Yutin, N., Suzuki, M.T., and Béjà, O. (2005) Novel primers reveal a wider diversity among marine aerobic anoxygenic phototrohs. Appl. Environ. Microbiol. 71, 8958-8962. Supplemental online materials

Zeidner, G., and Béjà, O. (2005) Community-level analysis of phototrophy: psbA gene diversity. Methods Enzymol. 397, 372-380. 

Yutin, N., and Béjà, O. (2005) Putative novel photosynthetic reaction center organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from environmental genomics & metagenomics.  Environ. Microbiol. 7, 2027-2033. 

Sabehi*, G., Loy*, A., Jung, K.H., Partha, R., Spudich, J.L., Isaacson, T., Hirschberg, J., Wagner, M., and Béjà, O. (2005) New insights into metabolic properties of marine bacteria encoding proteorhodopsins.  PLoS Biol. 3, e173.   
*equal contribution

 Zeidner, G., Bielawski, J.P., Shmoish, M., Scanlan, D.J., Sabehi, G., and Béjà, O. (2005) Potential photosynthesis gene recombination between Prochlorococcus & Synechococcus via viral intermediates. Environ. Microbiol.  7, 1505-1513. 

Oz, A., Sabehi, G., Koblízek, M., Massana, R., and Béjà, O. (2005) Roseobacter-like bacteria in Red and Mediterranean Sea aerobic anoxygenic photosynthetic populations.  Appl. Environ. Microbiol. 71, 344-353. 

2004

Suzuki, M.T., Preston, C.M., Béjà, O., de la Torre, R.J., Steward, G, and DeLong, E.F. (2004) Quantitative phylogenetic screening of ribosomal RNA gene-containing clones in Bacterial Artificial Chromosome (BAC) libraries from different depths in Monterey Bay.  Microbial Ecol.  48, 473-488. 

Bielawski, J. P., Dunn, K.A., Sabehi, G., and Béjà, O. (2004) Darwinian adaptation of proteorhodopsin to different light intensities in the environment.  Proc. Natl. Acad. Sci. USA 141, 14824–14829.  

Sabehi, G., Béjà O., Preston, C. M., Suzuki, M. T., and DeLong, E.F. (2004) Different SAR86 subgroups harbour divergent proteorhodopsins. Environ. Microbiol. 6, 903-910. 

Béjà, O. (2004) To BAC or not to BAC: Marine Ecogenomics .  Curr. Opin. Biotech. 15, 187-190.   

Man-Aharonovich, D., Sabehi, G., Sineshchekov O.A., Spudich, E.N., Spudich, J.L., and Béjà, O.  (2004) Characterization of RS29, a blue-green proteorhodopsin variant from the Red Sea. Photochem. Photobiol. Sci.  3, 459-462.   

Zeidner, G., and Béjà, O.  (2004) The use of DGGE analyses to explore eastern Mediterranean and Red Sea marine picophytoplankton assemblages. Environ. Microbiol.  6, 528-534. 

2003

Koblizek M., Béjà, O., Bidigare R.R., Christensen S., Benitez-Nelson B., Vetriani C., Kolber M.K., Falkowski P.G., Kolber Z.S.  (2003) Isolation and Characterization of Erythrobacter sp. Strains from the Upper Ocean.  Arch. Microbiol. 180, 327-338.

de la Torre, R.J., Christianson, L., Béjà, O., Suzuki, M.T., Karl, D., Heidelberg, J.F., and DeLong, E.F. (2003) Proteorhodopsin genes are widely distributed among divergent bacterial taxa. Proc. Natl. Acad. Sci. USA 100, 12830-12835.

Sabehi, G., Massana, R., Bielawski J.P., Rosenberg M., Delong, E.F., and Béjà, O. (2003) Novel Proteorhodopsin Variants from the Mediterranean and Red Seas. Environ. Microbiol. 5, 842-849.

   Man, D., Wang, W., Sabehi, G., Aravind, L., Post, A.F., Massana, R., Spudich, E.N., Spudich, J.L., and Béjà, O. (2003) Diversification and spectral tuning in marine proteorhodopsins.  EMBO J. 22, 1725-1731. 

Zeidner, G., Preston, C.M., DeLong, E.F., Massana, R., Post, A.F., Scanlan, D.J., and Béjà, O. (2003) Molecular diversity among marine picophytoplankton as revealed by psbA analyses. Environ. Microbiol. 5, 212-216. 


2002

Béjà, O. ,  Suzuki, M.T., Heidelberg, J.F., Nelson, W.C., Preston, C.M., Hamada, T., Eisen, J.A., Fraser, C.M. and DeLong, E.F. (2002).  Unsuspected diversity among marine aerobic anoxygenic phototrophs.  Nature 415, 630-633 .
See also news feature and news and views articles on this work

Béjà, O. ,  Koonin, E.V., Aravind, L., Taylor, L.T., Seitz, H., Stein, J.L., Bensen, D.C., Feldman, R.A., Swanson, R.V. and DeLong, E.F. (2002).  Comparative genomic analysis of archaeal genotypic variants in a single population, and in two different oceanic provinces. Appl. Environ. Microbiol. 68, 335-345. 

2001

Béjà, O. , Spudich, E.N., Spudich, J.L., Leclerc, M., and DeLong, E.F. (2001).  Proteorhodopsin Phototrophy in the Ocean.  Nature 411 , 786-789 .  

Suzuki, M.T.,  Béjà, O., Taylor, L.T., and DeLong, E.F. (2001).  Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton.  Environ. Microbiol. 3, 323-331.

2000

Béjà, O. , Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, C., Jovanovich, S. B., Gates, C.M., Feldman, R.A., Spudich, J.L., Spudich, E.N., and DeLong, E.F. (2000).  Bacterial Rhodopsin: Evidence For a New Type of Phototrophy in the Sea. Science 289, 1902-1906 .   
See also Science comment  and Aparna Sreenivasan's Science Note

Béjà, O. , Suzuki, M.T., Koonin, E.V., Aravind, L., Hadd, A., Nguyen, L.P., Villacorta, R., Amjadi, M., Garrigues, C., Jovanovich, S.B., Feldman, R.A., and DeLong, E.F. (2000).  Construction and Analysis of Bacterial Artificial Chromosome libraries from a marine microbial assemblage. Environ. Microbiol . 2, 516-529.