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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)

Dr. Shirley Larom (Lab Manager)
Viral photosynthesis

Mira Rosenberg (ex Lab Manager)

Sheila Roitman (Ph.D. student)
Viral photosynthesis

Gur Hevroni (Ph.D. student)
Viral photosynthesis

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

Jose Flores
(Ph.D. student)

Dr. Svetlana Fridman 

Viral photosynthesis

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

Flores-Uribe, J., et al. A novel uncultured marine cyanophage lineage and a possible connection to cyanobacterial prophages. in preparation

Pushkarev, A., Jung, K.-H., and Beja O. The use of chimeric proteorhodopsins for the development of a lab curriculum in marine microbiology. in preparation

Enav, H., Kirzner, S., Avrani, S., Lindell, D., Mandel-Gutfreund, Y., and Beja, O. Adaptation of a wide host-range cyanophage to multiple hosts. in preparation    

Philosof, A., et al. A day in a life in the Red Sea: A viral (and phage) perspective. in preparation


Roitman, S.,
Hornung, E., Flores-Uribe, J., Sharon, I., Feussner, I., and Beja, O. Cyanophage-encoded lipid-desaturases: oceanic distribution, diversity and function.
bioRxiv 109157; doi: https://doi.org/10.1101/109157

Fridman, S.
Flores-Uribe, J., Larom, S., Alalouf, O., Liran, O., Yacoby, I., Salama, F., Bailleul, B., Rappaport, F., Ziv, T., Sharon, I., Philosof, A., Dupont, C.L., Cornejo-Castillo, F.M., Sanchez, P., Acinas, S.G., Rohwer, F., Lindell, D. and Beja, O. A novel myovirus encoding both photosystem-I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells. submitted

Philosof, A.,
Yutin, N.,
Flores-Uribe, J., Sharon, I., Koonin, E.V., and Beja, O. Novel abundant oceanic viruses of the uncultured Marine Group II Euryarchaeota identified by genome-centric metagenomics. bioRxiv 101196; doi: https://doi.org/10.1101/101196


Yaniv, K., Golberg, K., Kramarsky-Winter, E., Marks, R., Pushkarev, A., Beja, O., and Kushmaro, A. (2016) Functional marine metagenomic screening for anti-quorum sensing and anti-biofilm activity. Biofouling 33, 1-13.

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. 18, 4337-4347.

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