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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




People
 
Oded Beja
(Principal Investigator)


 
Dr. Shirley Larom (Lab Manager)
Viral photosynthesis

 
Mira Rosenberg (ex Lab Manager)
Ultramicroscopy

 
 
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)
Biofuels

 
Dr. Svetlana Fridman 

Viral photosynthesis

 
Dr. Alon Philosof
Marine microbial metagenomics



Dr. Hagay Enav

Phage-bacteria
co-evolution


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

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    

Roitman S.,
Hornung, E.,
Flores-Uribe, J., Sharon, I., Feussner, I., and Beja, O. Cyanophage-encoded xxxx xxxxxxx. in preparation

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

Fridman, S.,
Flores-Uribe, J., Larom, S., Liran, O., Yacoby, I., Salama, F., Bailleul, B., Rappaport, F., Alalouf, O., 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. in preparation

2017

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

2016

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.

2015

 
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

2014

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.

2013

Sabehi
, 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.

2012

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

2011

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

2010

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.