Articles | Volume 21, issue 6
https://doi.org/10.5194/os-21-3055-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/os-21-3055-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
19 Nov 2025
Research article |
| 19 Nov 2025
| 19 Nov 2025
Contribution of dark inorganic carbon fixation to bacterial carbon demand in the oligotrophic Southeastern Mediterranean Sea
Tom Reich
CORRESPONDING AUTHOR
National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
Natalia Belkin
National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
Guy Sisma-Ventura
National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
Hagar Hauzer
National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
Maxim Rubin-Blum
National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
Ilana Berman-Frank
CORRESPONDING AUTHOR
Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
Department of Earth and Environmental Science, Ben-Gurion University of the Negev, Beer Sheva, Israel
Institute of Marine Science, University of California, Santa Cruz, CA, USA
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Eyal Rahav and Adina Paytan
EGUsphere, https://doi.org/10.5194/egusphere-2026-2917, https://doi.org/10.5194/egusphere-2026-2917, 2026
This preprint is open for discussion and under review for Ocean Science (OS).
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To understand how ocean warming may alter carbon storage, we examined seasonal carbon cycling in the northern Red Sea over five months. As summer warming intensified water-column stratification and reduced nutrient supply, carbon fixation by microscopic algae declined, while a larger fraction of newly produced carbon was released as dissolved material and rapidly respired by bacteria. This near-surface recycling may reduce carbon transfer to depth and weaken ocean carbon storage.
Elad Albagly and Eyal Rahav
EGUsphere, https://doi.org/10.5194/egusphere-2026-934, https://doi.org/10.5194/egusphere-2026-934, 2026
This preprint is open for discussion and under review for Biogeosciences (BG).
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Photosynthetic microbes form the base of ocean food webs, yet their size is often assumed to be constant. We show that in the nutrient-poor water Eastern Mediterranean Sea, these microbes become larger with depth and vary from coast to open sea. These subtle size shifts change how much carbon they store, meaning common methods can underestimate ocean carbon stocks. Accounting for size improves estimates and strengthens predictions of how stratified oceans function under climate change.
Eyal Rahav, Scott D. Wankel, and Adina Paytan
EGUsphere, https://doi.org/10.5194/egusphere-2026-855, https://doi.org/10.5194/egusphere-2026-855, 2026
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Microbes in the sunlit waters of the nitrogen-poor northern Red Sea transform ammonia into other forms of nitrogen, a process once thought to be almost absent in surface waters. We found that this activity does occur, but at very low rates. Additionally, these microbes contribute only a small share to carbon production, yet they recycle nitrogen and influence how scientists estimate ocean productivity in a warming world.
Maxim Rubin-Blum, Eyal Rahav, Guy Sisma-Ventura, Yana Yudkovski, Zoya Harbuzov, Or M. Bialik, Oded Ezra, Anneleen Foubert, Barak Herut, and Yizhaq Makovsky
Biogeosciences, 22, 1321–1340, https://doi.org/10.5194/bg-22-1321-2025, https://doi.org/10.5194/bg-22-1321-2025, 2025
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Chemotones, transition zones in chemosynthetic ecosystems, alter geochemical cycles and biodiversity. We studied seep chemotones, which are heavily burrowed by ghost shrimp. To investigate if burrowing affects habitat functionality, we surveyed the seafloor with deep-sea vehicles, analyzed sediment, and explored microbial communities in burrows. We found chemosynthetic biofilms, linking them to macromolecule turnover and nutrient cycling. This process may play a crucial role in deep-sea cycles.
Nir Haim, Vika Grigorieva, Rotem Soffer, Boaz Mayzel, Timor Katz, Ronen Alkalay, Eli Biton, Ayah Lazar, Hezi Gildor, Ilana Berman-Frank, Yishai Weinstein, Barak Herut, and Yaron Toledo
Earth Syst. Sci. Data, 16, 2659–2668, https://doi.org/10.5194/essd-16-2659-2024, https://doi.org/10.5194/essd-16-2659-2024, 2024
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This paper outlines the process of creating an open-access surface wave dataset, drawing from deep-sea research station observations located 50 km off the coast of Israel. The discussion covers the wave monitoring procedure, from instrument configuration to wave field retrieval, and aspects of quality assurance. The dataset presented spans over 5 years, offering uncommon in situ wave measurements in the deep sea, and addresses the existing gap in wave information within the region.
Zhibo Shao, Yangchun Xu, Hua Wang, Weicheng Luo, Lice Wang, Yuhong Huang, Nona Sheila R. Agawin, Ayaz Ahmed, Mar Benavides, Mikkel Bentzon-Tilia, Ilana Berman-Frank, Hugo Berthelot, Isabelle C. Biegala, Mariana B. Bif, Antonio Bode, Sophie Bonnet, Deborah A. Bronk, Mark V. Brown, Lisa Campbell, Douglas G. Capone, Edward J. Carpenter, Nicolas Cassar, Bonnie X. Chang, Dreux Chappell, Yuh-ling Lee Chen, Matthew J. Church, Francisco M. Cornejo-Castillo, Amália Maria Sacilotto Detoni, Scott C. Doney, Cecile Dupouy, Marta Estrada, Camila Fernandez, Bieito Fernández-Castro, Debany Fonseca-Batista, Rachel A. Foster, Ken Furuya, Nicole Garcia, Kanji Goto, Jesús Gago, Mary R. Gradoville, M. Robert Hamersley, Britt A. Henke, Cora Hörstmann, Amal Jayakumar, Zhibing Jiang, Shuh-Ji Kao, David M. Karl, Leila R. Kittu, Angela N. Knapp, Sanjeev Kumar, Julie LaRoche, Hongbin Liu, Jiaxing Liu, Caroline Lory, Carolin R. Löscher, Emilio Marañón, Lauren F. Messer, Matthew M. Mills, Wiebke Mohr, Pia H. Moisander, Claire Mahaffey, Robert Moore, Beatriz Mouriño-Carballido, Margaret R. Mulholland, Shin-ichiro Nakaoka, Joseph A. Needoba, Eric J. Raes, Eyal Rahav, Teodoro Ramírez-Cárdenas, Christian Furbo Reeder, Lasse Riemann, Virginie Riou, Julie C. Robidart, Vedula V. S. S. Sarma, Takuya Sato, Himanshu Saxena, Corday Selden, Justin R. Seymour, Dalin Shi, Takuhei Shiozaki, Arvind Singh, Rachel E. Sipler, Jun Sun, Koji Suzuki, Kazutaka Takahashi, Yehui Tan, Weiyi Tang, Jean-Éric Tremblay, Kendra Turk-Kubo, Zuozhu Wen, Angelicque E. White, Samuel T. Wilson, Takashi Yoshida, Jonathan P. Zehr, Run Zhang, Yao Zhang, and Ya-Wei Luo
Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023, https://doi.org/10.5194/essd-15-3673-2023, 2023
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N2 fixation by marine diazotrophs is an important bioavailable N source to the global ocean. This updated global oceanic diazotroph database increases the number of in situ measurements of N2 fixation rates, diazotrophic cell abundances, and nifH gene copy abundances by 184 %, 86 %, and 809 %, respectively. Using the updated database, the global marine N2 fixation rate is estimated at 223 ± 30 Tg N yr−1, which triplicates that using the original database.
Natalia Belkin, Tamar Guy-Haim, Maxim Rubin-Blum, Ayah Lazar, Guy Sisma-Ventura, Rainer Kiko, Arseniy R. Morov, Tal Ozer, Isaac Gertman, Barak Herut, and Eyal Rahav
Ocean Sci., 18, 693–715, https://doi.org/10.5194/os-18-693-2022, https://doi.org/10.5194/os-18-693-2022, 2022
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We studied how distinct water circulations that elevate (cyclone) or descend (anticyclone) water from the upper ocean affect the biomass, activity and diversity of planktonic microorganisms in the impoverished eastern Mediterranean. We show that cyclonic and anticyclonic eddies differ in their community composition and production. Moreover, the anticyclone may be a potential bio-invasion and dispersal vector, while the cyclone may serve as a thermal refugee for native species.
Hanni Vigderovich, Werner Eckert, Michal Elul, Maxim Rubin-Blum, Marcus Elvert, and Orit Sivan
Biogeosciences, 19, 2313–2331, https://doi.org/10.5194/bg-19-2313-2022, https://doi.org/10.5194/bg-19-2313-2022, 2022
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Anaerobic oxidation of methane (AOM) is one of the major processes limiting the release of the greenhouse gas methane from natural environments. Here we show that significant AOM exists in the methane zone of lake sediments in natural conditions and even after long-term (ca. 18 months) anaerobic slurry incubations with two stages. Methanogens were most likely responsible for oxidizing the methane, and humic substances and iron oxides are likely electron acceptors to support this oxidation.
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Short summary
Dark carbon fixation by chemoautotrophs take a vital part in marine primary productivity. Measured rates can be seen all the way down to the dark layers of the ocean and integrated in our study site come close to the magnitude of photosynthesis. It can also explain about ~ 35 % of the missing organic carbon supply needed by deep microbial communities. By using oceanographic observations and analysis this paper highlights the significant of this overlooked parameter.
Dark carbon fixation by chemoautotrophs take a vital part in marine primary productivity....
