Professor, Faculty of Biology,
Technion-Israel Institute of Technology, Haifa 32000, Israel
Ph.D., 1998, Weizmann Institute of Science
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.
Oded Beja (Principal Investigator)
Dr. Shirley Larom (Lab Manager)
Mira Rosenberg (ex Lab Manager)
Sheila Roitman (Ph.D. student)
Gur Hevroni (Ph.D. student)
Alina Pushkarev (Ph.D. student)
Metagenomics of biomass degradation
Jose Flores (Ph.D. student)
Dr. Svetlana Fridman
Dr. Alon Philosof
Marine microbial metagenomics
Dr. Hagay Enav
Dr. Onit Alalouf (Postdoctoral Fellow)
Dr. Faris Salama (Postdoctoral Fellow)
Dr. Andrey Rozenberg (Postdoctoral Fellow)
Omer Nadel (M.Sc. student)
Alumni (current position)
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
Enav, H., Kirzner, 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 viral (and phage) perspective. in preparation
Tal, O., Fridman, S., Roitman, S., and Beja, O. Trimer formation of photosystem-I is unfavored in infected Prochlorococcus cells upon intercalation of viral encoded photosystem-I proteins. in preparation
Pushkarev, A., et al. Discovery-oriented teaching: The use of chimeric proteorhodopsins for the development of a lab curriculum in marine microbiology and for the discovery of natural red-shifted proteorhodopsins. in preparation
Fridman, S., Flores-Uribe, J., Larom, S., Alalouf, O., Liran, O., Yacoby, I., Salama, F., Bailleul, B., Rappaport, F., Ziv, T., Sharon, I., Cornejo-Castillo, F.M., Philosof, A., Dupont, C.L., 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
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
Philosof, A., Yutin, N., Flores-Uribe, J., Sharon, I., Koonin, E.V., and Beja, O. Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota. Curr. Biol. 27, 1362-1368.
see also 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. Microbiol. 17, 5100-5108