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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)

 
Mira Rosenberg (Lab Manager)
Ultramicroscopy

 
Alon Philosof (Ph.D. student)
Marine microbial metagenomics

 
Hagay Enav
(joint Ph.D. student with Prof. Yael Mandel-Gutfreund)
Phage-bacteria
co-evolution

 
Svetlana Fridman
(joint Ph.D. student with Prof. Debbie Lindell)
Viral photosynthesis


Shay Kirzner (Postdoctoral Fellow)
Viral photosynthesis


 
Shirley Larom (Postdoctoral Fellow)
Viral photosynthesis


Onit Alalouf (Postdoctoral Fellow)
Viral photosynthesis

 
Gur Hevroni (M.Sc. student)
Viral photosynthesis

 
Sheila Roitman (M.Sc. student)
Viral photosynthesis


 
Alina Pushkarev
(Ph.D. student)

Metagenomics of biomass degradation


Jose Flores
(Ph.D. student)

Biofuels


Alumni
Aia Oz
Keren Limor
Sima Usvyatsov
Shani Tzachor

Dr. Gazalah Sabehi
Dr. Gil Zeidner
Dr. Rina Anati
Dr. Natalya Yutin
Dr. Baruch Karniol
Dr. Dikla Man-Aharonovich

Dr. Itai Sharon
Dr. Nof Atamna-Ismaeel
Dr. Ariella Alperovitch-Lavy
Dr. Roi Feingersch
Dr. Idan Bodaker
Dr. Yoni Sher





Publications (since 2000)

2014

Sher, Y., Pushkarev, A. et al. High-throughput functional metagenomic screen for glycoside hydrolases from freshwater, marine and hypersaline environments. in preparation
 
Hevroni, G.,
Enav, H., Glaser, F., Rohwer, F., and Beja, O. Diversity of viral photosystem-I psaA genes. in preparation

  Beja O. and Lanyi, J.K. Nature's toolkit for microbial rhodopsin ion pumps. Proc. Natl. Acad. Sci. USA doi/10.1073/pnas.1405093111. 


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.
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.

2009

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.

2008

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.

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 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.

2005

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. 

2004

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. 


2003

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. 


2002

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. 



2001

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.

2000

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


Research Trip to Eilat Cave diving in Mexico Research Trip to Spain










Oren A. 2006 HUJI
BTR survey to Jordan 2005 BTR Jordan July 2005 Dead Sea cruise 2006




Dead Sea cruise 2007 Kinneret cruise 2007 Mediterranean Sea 2009






Eilat cruise 2010 Eilat cruise February 2011
Eilat Cruise June 2012



Last updated April 2014

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