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Oded Beja, Ph.D.
Professor, Faculty of Biology,
Technion-Israel Institute of Technology, 
Haifa 32000,  Israel

Ph.D., 1998, Weizmann Institute of Science

Office: (972)-4-8293961
Lab: (972)-4-8293410
Fax: (972)-4-8225153

Environmental Genomics is a new emerging field that enables us to look at parts of the ocean that were, until recently, masked to us. With present estimates suggesting that >99% of the microorganisms in most environments are not amenable to growth in pure culture, thus very little is known about their physiology and roles in the ocean. These organisms can, however, be categorized into phylotypes according to their ribosomal RNA (rRNA) genes, which can be amplified directly from environmental DNA extracts, cloned, and sequenced. Although this approach has provided information on the identity and distribution of microbial species, rRNA gene sequences alone do not reveal the physiology, biochemistry, or ecological function of uncultivated microorganisms. This problem can be now bypassed by accessing the genomes of these microorganisms and identifying protein coding genes and biochemical pathways that will shed some light on their physiological properties and ecological function.

To illuminate the role of microorganisms in the open seas, the lab is exploring the metabolism of planktonic microbes using novel molecular biology techniques, along with functional genomics and bioinformatics.  The lab is now focusing on photosynthesis genes found in viruses that infect cyanobacteria and on developing different functional metagenomic screens.

Integrative Ecological Genomics, Roscoff June 2011

Oded Beja
(Principal Investigator)

Mira Rosenberg (Lab Manager)

Dr. Shirley Larom (Postdoctoral Fellow)
Viral photosynthesis

Sheila Roitman (Ph.D. student)
Viral photosynthesis

Gur Hevroni (Ph.D. student)
Viral photosynthesis

Dr. Svetlana Fridman 

Viral photosynthesis

Alina Pushkarev  (Ph.D. student)
Metagenomics of biomass degradation

Jose Flores
(Ph.D. student)

Dr. Alon Philosof
Marine microbial metagenomics

Dr. Hagay Enav


Dr. Onit Alalouf (Postdoctoral Fellow)
Viral photosynthesis

Dr. Faris Salama  (Postdoctoral Fellow)
Viral photosynthesis

Dr. Andrey Rozenberg  (Postdoctoral Fellow)
Viral photosynthesis

Dr. Ofir Tal Protein specialist

Alumni (current position)
Aia Oz
Dr. Keren Limor (Cambridge, UK)
Dr. Sima Usvyatsov (U. New Brunswick, Canada)
Shani Tzachor (Open U.)

Dr. Gazalah Sabehi (Faculty of Biology, Technion)
Dr. Gil Zeidner (Noble Energy, Technion)
Dr. Rina Anati
Dr. Natalya Yutin (NCBI, NLM, NIH)
Dr. Baruch Karniol (Volcani Center)
Dr. Dikla Man-Aharonovich
(School of Marine Science, U. Haifa)
Dr. Itai Sharon (Principle Investigator, MIGAL-Galilee Research Institute)
Dr. Nof Atamna-Ismaeel (Israel 'Master Chef' 2014 winner)
Dr. Ariella Alperovitch-Lavy (Faculty of Medicine, Technion)
Dr. Roi Feingersch (GeneSort)
Dr. Idan Bodaker (I.M.S.- Industrial Measurement Systems)
Dr. Yoni Sher (UC Berkeley, California)
Dr. Shay Kirzner (Technion Life Sciences and Engineering Infrastructure Unit)

Publications (since 2000)

Pushkarev, A., Sher, Y., Feingersh, R., Alalouf, O., Shoham, Y.  and Beja O. High-throughput functional metagenomic screen for glycoside hydrolases from freshwater, marine and hypersaline environments. in preparation
Philosof, A.,
and Beja, O. A day in a life in the Red Sea: A viral (and phage) perspective. in preparation

Fridman, S. et al. Isolation of a novel widespread marine cyanophage carrying both photosystems-I and II genes. in preparation


Yaniv, K., Golberg, K., Kramarsky-Winter, E., Marks, R., Pushkarev, A., Beja, O., and Kushmaro, A. Functional marine metagenomic screening for anti-quorum sensing and anti-biofilm activity. Biofouling http://dx.doi.org/10.1080/08927014.2016.1253684

Pinhassi, J., DeLong, E.F., Beja, O., Gonzalez, J.M., and Pedros-Alio, C. (2016) Marine bacterial and archaeal ion-pumping rhodopsins: genetic diversity, physiology and ecology. Microbiol. & Mol. Biol. Rev. 80, 929-954.

Ledermann, B., Beja, O., and Frankenberg-Dinkel, N. (2016) New biosynthetic pathway for pink pigments from uncultured oceanic viruses. Environ. Microbiol. accepted manuscript online. DOI: 10.111/1462-2920.13290.

Pushkarev, A., and Beja, O. (2016) Functional metagenomic screen reveals new and diverse microbial rhodopsins. ISME J. 10, 2331-2335


Roitman*, S., Flores-Uribe*, J., Philosof, A.
, Knowles, B., Rohwer, F., Ignacio-Espinoza, J.C., Sullivan, M.B., Cornejo-Castillo, F.M., Sanchez, P., Acinas, S.G., Dupont, C.L.,
and Beja, O. (2015) Closing the gaps on the viral photosystem-I psaDCAB gene organization. Environ. Microbiol17, 5100-5108 
*equal contribution

Hevroni*, G., Enav*, H., Rohwer, F., and Beja, O. (2015) Diversity of viral photosystem-I psaA genes. ISME J. 9, 1892-1898.
*equal contribution


Beja O. and Lanyi, J.K. (2014) Nature's toolkit for microbial rhodopsin ion pumps. Proc. Natl. Acad. Sci. USA 111, 6538-6539. 

Enav, H., Mandel-Gutfreund, Y., and
Beja, O. (2014) Comparative metagenomic analyses reveal viral induced shifts of host metabolism towards nucleotide biosynthesis.
Microbiome 2, 9.


, G., and Beja, O. (2013) Preparation of BAC libraries from marine microbial populations. Methods Enzymol. 531, 111-122.

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

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


Mazor, Y., Greenberg, I., Toporik, H., Beja, 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 Beja, O. (2012) Dead Sea rhodopsins revisited. Environ. Microbiol. Rep. 4, 617-621. 

Beja, 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 Beja, 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 Beja, O. (2012) Potential for phosphite and phosphonate utilization by Prochlorococcus.  ISME J. 6, 827-834.

Enav, H., Beja, 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., Beja, 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


Philosof, A., Battchikova, N., Aro, E.-M., and Beja, 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 Beja, 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., Beja, 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 Beja, 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


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

thumbnailOB.jpg DeLong, E.F., and Beja, 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 Beja, 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 Beja, 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 Beja, O. (2010) Microbial community genomics in eastern Mediterranean Sea surface waters. ISME J. 4, 78-87

Mano, A., Tuller, T., Beja, 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.


Bodaker, I., Beja, 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 Beja, 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 Beja, 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., Suling, J.,  Imhoff, J.F., and Beja, 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 Beja, 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., Beja, 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., Musmann, M., Ott, J., Sharon, I., Beja, 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.


Yutin, N., Beja, 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., Beja, 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., Jurgens, K., Barkay, T., Stomp, M., Huisman, J., and Beja, 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., Beja, 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 Beja, O. (2008) Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate. Environ. Microbiol. 10, 1335-1343.

Beja, 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.


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 Beja, 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 Beja, 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 Beja, 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 Beja, 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 Beja, O. (2007) An elusive marine photosynthetic bacterium is finally unveiled. Proc. Natl. Acad. Sci. USA 104, 2561-2562. 

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


Yutin, N., Suzuki, M.T., and Beja, 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 Beja, O. (2005) Community-level analysis of phototrophy: psbA gene diversity. Methods Enzymol. 397, 372-380. 

Yutin, N., and Beja, 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 Beja, 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 Beja, O. (2005) Potential photosynthesis gene recombination between Prochlorococcus & Synechococcus via viral intermediates. Environ. Microbiol.  7, 1505-1513. 

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


Suzuki, M.T., Preston, C.M.Beja, 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 Beja, O. (2004) Darwinian adaptation of proteorhodopsin to different light intensities in the environment.  Proc. Natl. Acad. Sci. USA 141, 14824-14829.  

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

Beja, 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 Beja, O.  (2004) Characterization of RS29, a blue-green proteorhodopsin variant from the Red Sea. Photochem. Photobiol. Sci.  3, 459-462.   

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


Koblizek M., Beja, 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., Beja, 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 Beja, 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 Beja, 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 Beja, O. (2003) Molecular diversity among marine picophytoplankton as revealed by psbA analyses. Environ. Microbiol. 5, 212-216. 


Beja, 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

Beja, 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. 


Beja, 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.,  Beja, 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.


Beja, 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

Beja, 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. 


Trips, Cruises & Events

Researcher's Night September 2014 Line Islands Expedition 2015 Seychelles 2016

Mediterranean Sea 2009 Eilat cruise 2010 Eilat cruise February 2011 Eilat Cruise June 2012

Oren A. 2006 HUJI

BTR Jordan July 2005 Dead Sea cruise 2006 Dead Sea cruise 2007 Kinneret cruise 2007

Research Trip to Eilat Cave diving in Mexico Research Trip to Spain BTR survey to Jordan 2005

Last updated September 2016

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