Publications

2024

• Sher, D., Segrè, D and Follows, M. (2024). Some common quantitative principles of metabolism at multiple scales. Nature Microbiology, 9, 1940–1953 . https://doi.org/10.1038/s41564-024-01764-0 

• Sher, D, George, E. E., Wietz, M., Gifford, S., Zoccaratto, L., Weissberg, O., Koedooder, C.,Valliya Khaladi, W. B.#, Malisano Barreto Filho, M., Mireles, R., Malavin, S., Liddor Naim, M.,  Idan, T., Shrivastava, V., Itelson, L., Sade, D., Abu Hamoud, A.,  Soussan, Y.,  Barak, N., Karp, P. and Moore, L. (2024). Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126. Submitted and available on BioRxiv (https://doi.org/10.1101/2023.12.13.571488)
  
  
  

• Barak, N., Brekhman, V., Aharonovich, D., Lotan, T. and Sher, D. (2024). Jellyfish blooms Through the Microbial Lens: Temporal Changes, Cross-Species and Jellyfish-Water Comparisons. Submitted and available on BioRxiv: https://doi.org/10.1101/2024.05.23.595640 

• Malul, D., Berman, H., Solodoch, A., Tal, O., Barak, N., Mizrahi, G., Berenshtein, I., Toledo, Y., Lotan, T., Sher, D., Shavit, U. and Lehahn, Y. (2024). Directional swimming patterns in jellyfish aggregations. Current Biology 34, 1-6. https://doi.org/10.1016/j.cub.2024.07.038

• Givati, S., Forchielli, E., Aharonovich, D., Barak, N., Weissberg, O., Belkin, N., Rahav, E., Segrè, D. and Sher, D. (2024). Diversity in the Utilization of Different Molecular Classes of Dissolved Organic Matter by Heterotrophic Marine Bacteria. Applied and Environmental Microbiology e00256-24. https://doi.org/10.1128/aem.00256-24

• Omta, A. W., Liefer, J. D., Finkel, Z. V., Irwin, A. J, Sher, D and Follows, M. J. (2024). A model of time-dependent macromolecular and elemental composition of phytoplankton. Journal of Theoretical Biology 592, 111883, https://doi.org/10.1016/j.jtbi.2024.111883

2023

• Tal Ben-Ezra, Tom Reich, Anat  Tsemel, Ilana Berman-Frank, Yoav Lehahn, Y, Daniel Sher, Yair Suari, Mike D. Krom,  (2023). Nutrient dynamics across the Israeli coastal shelf: An unusual oligotrophic coastal system. Continental Shelf Research, 266 https://doi.org/10.1016/j.csr.2023.105103

• Falk Eigemann, Eyal Rahav, Hans-Peter Grossart, Dikla Aharonovich, Maren Voss and Daniel Sher (2023). Phytoplankton Producer Species and Transformation of Released Compounds over Time Define Bacterial Communities following Phytoplankton Dissolved Organic Matter Pulses. Applied and Environmental Microbiology 26;89(7):e0053923. doi: 10.1128/aem.00539-23
  
  
  

• Noga Barak, Edouard Fadeev, Vera  Brekhman, Dikla Aharonovich, Tamar Lotan and Daniel Sher D (2023). Selecting 16S rRNA Primers for Microbiome Analysis in a Host–Microbe System: The Case of the Jellyfish Rhopilema nomadica. Microorganisms 11(4), 955. https://doi.org/10.3390/microorganisms11040955 . 

• Shira Givati, Xinyu Yang, Daniel Sher. and Eyal  Rahav (2023). Testing the Growth Rate and Temperature Compensation Hypotheses in Marine Bacterioplankton. Environmental Microbiology,  https://doi.org/10.1111/1462-2920.16346.

• Orna Schweitzer-Natan,. Maya Ofek-Lalzar., Daniel Sher and Assaf Sukenik, (2023). The microbial community spatially varies during a Microcystis bloom event in Lake Kinneret. Freshwater Biology 68 (2), 349-363.  https://doi.org/10.1111/fwb.14030

• Edouard Fadeev, Cécile Carpaneto Bastos, Jennifer H Hennenfeind, Steven J Biller, Daniel Sher, Matthias Wietz and Gerhard J Herndl  (2023). Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle. microLife 4. https://doi.org/10.1093/femsml/uqac025

• Osnat Weissberg, Dikla Aharonovich and Daniel Sher,  (2023). Phototroph-heterotroph interactions during growth and long-term starvation across Prochlorococcus and Alteromonas diversity. The ISME Journal, https://doi.org/10.1038/s41396-022-01330-8

2022

• Zhen Wu*, Dikla Aharonovich*, Dalit Roth-Rosenberg, Osnat Weissberg, Tal Luzzatto-Knaan, Angela Vogts, Luca Zoccarato, Falk Eigemann, Hans-Peter Grossart,Maren Voss and Daniel Sher (2022). Single-cell measurements and modelling reveal substantial  organic carbon acquisition by Prochlorococcus in the oceans. Nature Microbiology, https://doi.org/10.1038/s41564-022-01250-5.

* equal contribution
†M.J. Follows and D. Sher are co-corresponding authors.

News and Views in Nature Microbiology: https://doi.org/10.1038/s41564-022-01251-4 

• Elena Forchielli, Daniel Sher and Daniel Segrè (2022). Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategies. mSystems, In Press . Available on BioRxiv: https://doi.org/10.1101/2022.01.07.475430

• Al Ashhab, A., Marmen, S., Schweitzer-Natan, O., Bolotin, E., Patil, H., Viner-Mozzini, D., Aharonovich, D.#, Hershberg, R., Minz, D., Carmeli, Sh., Cytryn, E., Sukenik, A and Sher, D. (2022). Freshwater microbial metagenomes sampled across water body types, space and time in Israel. Scientific Dat. 9, Article number: 652. https://doi.org/10.1038/s41597-022-01749-w
  
  
  

• Matthias Wietz, Mario López-Pérez, Daniel Sher, Steve Biller and Francisco Rodriguez-Valera (2022). Microbe Profile: Alteromonas macleodii - A widespread, fast-responding, “interactive” marine bacterium. Microbiology, In press. 

• Sabine Keuter, Jacob  Silverman, Guy Sisma-Ventura, Juntao Yu, Anat Tsemel, Michael Krom, Tal Ben-Ezra, Daniel Sher, Tom Reich, Gil Koplovitz and Miguel Frada (2022). Seasonal patterns and impact of living coccolithophores in the ultra-oligotrophic Levantine basin, the south-eastern section of the Mediterranean Sea. Marine Micropaleontology 175, 102153. https://doi.org/10.1016/j.marmicro.2022.102153 

• Tom Reich., Tal Be Ezra., Natalya Belkin, Anat Tsemel, Dikla Aharonovich, Dalit Roth-Rosenberg, Shira Givati, Or Bialik, Barak Herut, Ilana  Berman-Frank, Miguel Frada, Michael D. Krom, Yoav Lehahn, Eyal Rahav and Daniel Sher, D. (2022). A year in the life of the Eastern Mediterranean: Monthly dynamics of phytoplankton and bacterioplankton in an ultra-oligotrophic sea. Deep Sea Research Part I: Oceanographic Research Papers, 182, 103720. https://doi.org/10.1016/j.dsr.2022.103720

• Falk Eigemann, Eyal Rahav, Hans-Peter Grossart, Dikla Aharonovich, Daniel Sher, Angela Vogts and Maren Voss (2022). Phytoplankton exudates provide full nutrition to a subset of accompanying heterotrophic bacteria via carbon, nitrogen and phosphorus allocation. Environmental Microbiology, 24(5), 2467-2483. . https://doi.org/10.1111/1462-2920.15933

• Luca Zoccarato, Daniel Sher, Takeshi Miki, Daniel Segrè and Hans-Peter Grossart, (2022). Comparative whole-genome approach to identify traits underlying microbial interactions. Communication Biology, 5, 276. https://doi.org/10.1038/s42003-022-03184-4

2021

• Dalit Roth-Rosenberg, Markus Haber, Joshua Goldford, Maya Lalzar, Dikla Aharonovich, Ashraf Al-Ashhab, Yoav Lehahn, Michael D. Krom, Daniel Segrè, Laura Steindler and Daniel Sher (2021). Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental factors. Environmental Microbiology, 23(8), 4295-4308. https://doi.org/10.1111/1462-2920.15611 

• Dalit Roth-Rosenberg, Dikla Aharonovich, Anne Willem Omta, Michael J. Follows and Daniel Sher (2021). Dynamic macromolecular composition and high exudation rates in Prochlorococcus. Limnology and Oceanography, https://doi.org/10.1002/lno.11720 

• Shany Ofaim, Snorre Sulheim, Eivind Almaas, Daniel Sher and Daniel Segrè. (2021). Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus. Frontiers in Genetics, 9 Feb 2021, https://doi.org/10.3389/fgene.2021.586293
  
  

• Sarit Avrani and Daniel Sher. (2021). Viruses – agents of change in the oceans. Frontiers for Young Minds, 9:569372. doi: 10.3389/frym.2021.569372
  
  

• Zhen Wu, Stephanie Dutkiewicz, Oliver Jahn, Daniel Sher, Angelicque E. White and Michael J. Follows (2021). Modeling Photosynthesis and Exudation in Subtropical Oceans. Global Biogeochemical Cycles, 35, e2021GB0069. https://doi.org/10.1029/2021GB006941
  
  

• Tal Ben Ezra, Michael D. Krom, Anat Tsemel, Ilana Berman-Frank, Barak Herut, Yoav Lehahn, Eyal Rahav, Tom Reich, Tron F. Thingstad, and Daniel Sher, (2021). Seasonal Nutrient Dynamics in the P depleted Eastern Mediterranean Sea. Deep Sea Research I, 176, 103607. https://doi.org/10.1016/j.dsr.2021.103607 

• Praher, D., Zimmermann, B., Dnyansagar, R., Miller, D.J., Moya, A., Modepalli, V., Fridrich, A., Sher, D., Friis-Møller, L., Sundberg, P., Fôret, S., Ashby, R., Moran, Y and Technau, U. (2021). Conservation and turnover of miRNAs and their highly complementary targets in early branching animals. Proceedings of the Royal Society B 288: 20203169. https://doi.org/10.1098/rspb.2020.3169
  
  

• Marmen, S., Fadeev, E., Al-Ashhab, A., Benet-Perelberg, A., Naor, A, Patil, H.J., Cytryn, E., Viner-Mozzini, Y., Sukenik, A., Lalzar, M and Daniel Sher (2021). Seasonal dynamics are the major driver of microbial diversity and composition in intensive freshwater aquaculture. Frontiers in Microbiology, 24 June 2021 | https://doi.org/10.3389/fmicb.2021.679743 

• Drake, J.L.*, Malik, A.*, Popovits, Y.*, Yosef, O., Shemesh, E., Stolarski, J., Tchernov, D., Sher, D and Mass, T. (2021). Physiological and transcriptomic variability indicative of differences in key functions within a single coral colony. Frontiers in Marine Sciences 30 June 2021 https://doi.org/10.3389/fmars.2021.685876
  * Equal contribution

2020

• Dalit Roth-Rosenberg, Dikla Aharonovich, Tal Luzzatto-Knaan, Angela Vogts, Luca Zoccarato, Falk Eigemann, Noam Nago, Hans-Peter Grossart, Maren Voss and Daniel Sher (2020) Prochlorococcus rely on microbial interactions rather than on chlorotic resting stages to survive long-term stress. mBio, 11(4), e01846-20,   https://doi.org/10.1128/mBio.01846-20

• Oshra Yosef, Yotam Popovits, Assaf Malik, Maya Ofek-Lalzer, Tali Mass and Daniel Sher (2020). A tentacle for every occasion: comparing the hunting tentacles and sweeper tentacles, used for territorial competition, in the coral Galaxea fascicularis.   BMC Genomics 21, article 548, https://doi.org/10.1186/s12864-020-06952-w

• Luca Zoccarato, Daniel Sher, Takeshi Miki, Daniel Segrè and Hans-Peter Grossart (2020).  Comparative whole-genome approach to identify traits underlying microbial interactions. Under review, Deposited on BioRxiv: doi: https://doi.org/10.1101/2020.06.30.179929

• Hemant J. Patil, Joao Gatica, Avihai Zolti, Ayana Benet-Perelberg, Alon Naor, Barak Dror, Ashraf Al Ashhab, Sophi Marman, Nur A. Hasan, Rita R. Colwell, Daniel Sher, Dror Minz and Eddie Cytryn (2020). Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment. Microorganisms 8, 1984. https://doi.org/10.3390/microorganisms8121984 

• Markus Haber, Dalit Roth-Rosenberg, Maya Lalzar, Ilia Burgsdorf, Kumar Saurav, Regina Lionheart, Yoav Lehahn, Dikla Aharonovich, Daniel Sher, Michael D. Krom and Laura Steindler (2020). Microbial communities in an ultra-oligotrophic sea are more affected by season than by distance from shore. Under review, Deposited on BioRxiv: https://doi.org/10.1101/2020.04.17.044305 

• Anne Willem Omta; David Talmy; Keisuke Inomura; Andrew J Irwin; Zoe V Finkel; Daniel Sher; Justin D Liefer; Michael J Follows (2020). Quantifying nutrient throughput and DOM production by algae in continuous culture. Journal of Theoretical Biology, 494, 110214. https://doi.org/10.1016/j.jtbi.2020.110214 

• Sophi Marmen, Lior Blank, Ashraf Al-Ashhab, Assaf Malik, Lars Ganzert, Maya Lalzar, Hans-Peter Grossart and Daniel Sher (2020).  The role of land use types and water chemical properties in structuring the microbiome of a connected lakes system. Frontiers in Microbiology 11/89, 12 February 2020  doi.org/10.3389/fmicb.2020.00089

2019

• Orna Schweitzer-Natan, Maya Ofek-Lalzar, Daniel Sher and Assaf Sukenik (2019) Particle-Associated Microbial Community in a Subtropical Lake During Thermal Mixing and Phytoplankton Succession. Frontiers in Microbiology 13 September. https://doi.org/10.3389/fmicb.2019.02142 

2018

• Hanit Ben-Ari, Moran Paz and Daniel Sher (2018) The chemical armament of reef-building corals: inter- and intra-specific variation and the identification of an unusual actinoporin in Stylophora pistilata. Scientific Reports 8: 251. doi:10.1038/s41598-017-18355-1  

2017

• Omta, A.W., Talmy, D., Sher, D., Finkel, Z.V., Irwin, A.J. and Follows, M. J. (2017). Extracting phytoplankton physiological trains from batch and chemostat culture data. Limnology and Oceanography - Methods 15, 453–466 . https://doi.org/10.1002/lom3.10172 

• Grossowicz, M*., Roth-Rosenberg, D*., Aharonovich, D., Silverman, J., Follows, M.J. and Sher, D (2017). Prochlorococcus in the lab and in silico: the importance of representing exudation.  Limnology and Oceanography. doi: 10.1002/lno.10463

     *equal contribution

2016

• Dubinski V, Haber M, Lehahn Y, Saurav K, Burgsdorf I, Malik A, Sher D, Aharonovich D, Steindler L. (2016). Metagenomic analysis of phototrophic strategies reveals unusually high incidence of proteorhodopsin genes in the ultraoligotrophic Eastern Mediterranean Sea. Environmental Microbiology. doi:10.1111/1462-2920.13624 

• Aharonovich, D and Sher, D. (2016).  Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals. The ISME Journal 10, 2892-2906, doi:10.1038/ismej.2016.70

• Marmen, S., Aharonovich, D., Blank, L., Yacobi, Y.Z. and Sher, D. (2016). Distribution and habitat specificity of potentially-toxic Microcystis across climate, land and water use gradients. Frontiers in Microbiology., 15 March 2016, doi:10.3389/fmicb.2016.00271

• Fadeev, E., De Pascale, F., Vezzi, A., Hübner, S., Aharonovich, D and Sher, D. (2016). Why close a bacterial genome? The plasmid of Alteromonas macleodii HOT1A3 is a vector for inter-specific transfer of a flexible genomic island. Frontiers in Microbiology., 08 March 2016, doi:10.3389/fmicb.2016.00248

• Armoza-Zvuloni, R., Schneider, A., Sher, D. and Shaked, Y. (2016). Rapid Hydrogen Peroxide release from the coral Stylophora pistillata during feeding and in response to chemical and physical stimuli. Scientific Reports, 6, Article number: 21000 (2016), doi:10.1038/srep21000

2015

• Rachamim, T*., Morgenstern, D*., Aharonovich, D ., Brekhman, V., Lotan, T and Sher, D (2015).  The dynamically-evolving nematocyst content of an Anthozoan, a Scyphozoan and a Hydrozoan.  Molecular Biology and Evolution, 32 (3): 740-753.  doi: 10.1093/molbev/msu335 

    *equal contribution

2014

• Berube, PM., Biller, SJ., Kent, AG., Berta-Thompson, JW., Roggensack, SE, Roache-Johnson, KH., Ackerman, M., Moore, LJ., Meisel, JD., Sher, D., Thompson, LR., Campbell, L, Martiny, AC and Chisholm, SW (2014). Physiology and evolution of nitrate acquisition in Prochlorococcus. The ISME Journal, 9(5), 1195-1207. doi:10.1038/ismej.2014.211 

• Glasser E , Rachamim T , Aharonovich D and Sher D. (2014). Hydra actinoporin-like toxin-1, an unusual hemolysin from the nematocyst venom of Hydra magnipapillata which belongs to an extended gene family. Toxicon 91 103–113. doi: 10.1016/j.toxicon.2014.04.004. 

2013

• Nesher, N., Shapira, E., Sher, D., Moran, Y.,  Turchetti-Maia, A.L., Horowitz, M., Hochner, B. and Zlotkin, E. (2013). AdE-1, a new inotropic peptide from Aiptasia diaphana is similar to, yet distinct from, known anemone sodium channel toxins. Biochemical Journal, 451(1):81-90 doi: 10.1042/BJ20121623 

2012

• Rachamim, T and Sher, D. (2012). What hydra can teach us about chemical ecology – how a simple, soft organism survives in a hostile aqueous environment.  International Journal of Developmental Biology 56, 605 – 611 doi: 10.1387/ijdb.113474tr