Articles | Volume 22, issue 5
https://doi.org/10.5194/bg-22-1321-2025
© 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/bg-22-1321-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
10 Mar 2025
Research article |
| 10 Mar 2025
| 10 Mar 2025
Animal burrowing at cold seep ecotones boosts productivity by linking macromolecule turnover with chemosynthesis and nutrient cycling
Maxim Rubin-Blum
CORRESPONDING AUTHOR
Charney School of Marine Sciences (CSMS), University of Haifa, Haifa, Israel
Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
Eyal Rahav
Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
Guy Sisma-Ventura
Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
Yana Yudkovski
Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
Zoya Harbuzov
Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
Or M. Bialik
Charney School of Marine Sciences (CSMS), University of Haifa, Haifa, Israel
Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
Institute of Geology and Palaeontology, University of Münster, Münster, Germany
Oded Ezra
Charney School of Marine Sciences (CSMS), University of Haifa, Haifa, Israel
Anneleen Foubert
Department of Geosciences, University of Fribourg, Fribourg, Switzerland
Barak Herut
Charney School of Marine Sciences (CSMS), University of Haifa, Haifa, Israel
Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
currently at: Faculty of Marine Sciences, Ruppin Academic Center, Mikhmoret, Israel
Yizhaq Makovsky
Charney School of Marine Sciences (CSMS), University of Haifa, Haifa, Israel
Related authors
Tom Reich, Natalia Belkin, Guy Sisma-Ventura, Hagar Hauzer, Maxim Rubin-Blum, Ilana Berman-Frank, and Eyal Rahav
EGUsphere, https://doi.org/10.5194/egusphere-2025-1445, https://doi.org/10.5194/egusphere-2025-1445, 2025
Short summary
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.
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
Short summary
Short summary
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
Short summary
Short summary
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.
Tamar Guy-Haim, Maxim Rubin-Blum, Eyal Rahav, Natalia Belkin, Jacob Silverman, and Guy Sisma-Ventura
Biogeosciences, 17, 5489–5511, https://doi.org/10.5194/bg-17-5489-2020, https://doi.org/10.5194/bg-17-5489-2020, 2020
Short summary
Short summary
The availability of nutrients in oligotrophic marine ecosystems is limited. Following jellyfish blooms, large die-off events result in the release of high amounts of nutrients to the water column and sediment. Our study assessed the decomposition effects of an infamous invasive jellyfish in the ultra-oligotrophic Eastern Mediterranean Sea. We found that jellyfish decomposition favored heterotrophic bacteria and altered biogeochemical fluxes, further impoverishing this nutrient-poor ecosystem.
Natalie M. Mahowald, Longlei Li, Julius Vira, Marje Prank, Douglas S. Hamilton, Hitoshi Matsui, Ron L. Miller, P. Louis Lu, Ezgi Akyuz, Daphne Meidan, Peter Hess, Heikki Lihavainen, Christine Wiedinmyer, Jenny Hand, Maria Grazia Alaimo, Célia Alves, Andres Alastuey, Paulo Artaxo, Africa Barreto, Francisco Barraza, Silvia Becagli, Giulia Calzolai, Shankararaman Chellam, Ying Chen, Patrick Chuang, David D. Cohen, Cristina Colombi, Evangelia Diapouli, Gaetano Dongarra, Konstantinos Eleftheriadis, Johann Engelbrecht, Corinne Galy-Lacaux, Cassandra Gaston, Dario Gomez, Yenny González Ramos, Roy M. Harrison, Chris Heyes, Barak Herut, Philip Hopke, Christoph Hüglin, Maria Kanakidou, Zsofia Kertesz, Zbigniew Klimont, Katriina Kyllönen, Fabrice Lambert, Xiaohong Liu, Remi Losno, Franco Lucarelli, Willy Maenhaut, Beatrice Marticorena, Randall V. Martin, Nikolaos Mihalopoulos, Yasser Morera-Gómez, Adina Paytan, Joseph Prospero, Sergio Rodríguez, Patricia Smichowski, Daniela Varrica, Brenna Walsh, Crystal L. Weagle, and Xi Zhao
Atmos. Chem. Phys., 25, 4665–4702, https://doi.org/10.5194/acp-25-4665-2025, https://doi.org/10.5194/acp-25-4665-2025, 2025
Short summary
Short summary
Aerosol particles are an important part of the Earth system, but their concentrations are spatially and temporally heterogeneous, as well as being variable in size and composition. Here, we present a new compilation of PM2.5 and PM10 aerosol observations, focusing on the spatial variability across different observational stations, including composition, and demonstrate a method for comparing the data sets to model output.
Tom Reich, Natalia Belkin, Guy Sisma-Ventura, Hagar Hauzer, Maxim Rubin-Blum, Ilana Berman-Frank, and Eyal Rahav
EGUsphere, https://doi.org/10.5194/egusphere-2025-1445, https://doi.org/10.5194/egusphere-2025-1445, 2025
Short summary
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.
Anneleen Foubert, Derek Keir, Balemwal Atnafu, Tesfaye Kidane, and the ADD-ON Workshop Consortium
Sci. Dril., 33, 207–218, https://doi.org/10.5194/sd-33-207-2024, https://doi.org/10.5194/sd-33-207-2024, 2024
Short summary
Short summary
The Dallol area (northern Afar, Ethiopia) is the ideal field lab to study the birth of a future ocean. The ADD-ON workshop brought together scientists from different disciplines, government agencies, local universities, and communities to plan a scientific drilling into the Dallol deep subsurface. This drilling will provide unique archives to resolve questions related to rift processes, seismic and volcanic activity, climate change, the deep biosphere, geothermal energy, and water resources.
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
Short summary
Short summary
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.
Montserrat Alonso-Garcia, Jesus Reolid, Francisco J. Jimenez-Espejo, Or M. Bialik, Carlos A. Alvarez Zarikian, Juan Carlos Laya, Igor Carrasquiera, Luigi Jovane, John J. G. Reijmer, Gregor P. Eberli, and Christian Betzler
Clim. Past, 20, 547–571, https://doi.org/10.5194/cp-20-547-2024, https://doi.org/10.5194/cp-20-547-2024, 2024
Short summary
Short summary
The Maldives Inner Sea (northern Indian Ocean) offers an excellent study site to explore the impact of climate and sea-level changes on carbonate platforms. The sediments from International Ocean Discovery Program (IODP) Site U1467 have been studied to determine the drivers of carbonate production in the atolls over the last 1.3 million years. Even though sea level is important, the intensity of the summer monsoon and the Indian Ocean dipole probably modulated the production at the atolls.
Natalie M. Mahowald, Longlei Li, Julius Vira, Marje Prank, Douglas S. Hamilton, Hitoshi Matsui, Ron L. Miller, Louis Lu, Ezgi Akyuz, Daphne Meidan, Peter Hess, Heikki Lihavainen, Christine Wiedinmyer, Jenny Hand, Maria Grazia Alaimo, Célia Alves, Andres Alastuey, Paulo Artaxo, Africa Barreto, Francisco Barraza, Silvia Becagli, Giulia Calzolai, Shankarararman Chellam, Ying Chen, Patrick Chuang, David D. Cohen, Cristina Colombi, Evangelia Diapouli, Gaetano Dongarra, Konstantinos Eleftheriadis, Corinne Galy-Lacaux, Cassandra Gaston, Dario Gomez, Yenny González Ramos, Hannele Hakola, Roy M. Harrison, Chris Heyes, Barak Herut, Philip Hopke, Christoph Hüglin, Maria Kanakidou, Zsofia Kertesz, Zbiginiw Klimont, Katriina Kyllönen, Fabrice Lambert, Xiaohong Liu, Remi Losno, Franco Lucarelli, Willy Maenhaut, Beatrice Marticorena, Randall V. Martin, Nikolaos Mihalopoulos, Yasser Morera-Gomez, Adina Paytan, Joseph Prospero, Sergio Rodríguez, Patricia Smichowski, Daniela Varrica, Brenna Walsh, Crystal Weagle, and Xi Zhao
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2024-1, https://doi.org/10.5194/essd-2024-1, 2024
Preprint withdrawn
Short summary
Short summary
Aerosol particles can interact with incoming solar radiation and outgoing long wave radiation, change cloud properties, affect photochemistry, impact surface air quality, and when deposited impact surface albedo of snow and ice, and modulate carbon dioxide uptake by the land and ocean. Here we present a new compilation of aerosol observations including composition, a methodology for comparing the datasets to model output, and show the implications of these results using one model.
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
Short summary
Short summary
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.
Valentina Beccari, Ahuva Almogi-Labin, Daniela Basso, Giuliana Panieri, Yizhaq Makovsky, Irka Hajdas, and Silvia Spezzaferri
J. Micropalaeontol., 42, 13–29, https://doi.org/10.5194/jm-42-13-2023, https://doi.org/10.5194/jm-42-13-2023, 2023
Short summary
Short summary
Planktonic gastropods (pteropods and heteropods) have been investigated in cores collected in the eastern Mediterranean along the Israeli coast in coral, pockmark, and channel areas. The sediment spans the last 5300 years. Our study reveals that neglecting the smaller fraction (> 63 µm) may result in a misinterpretation of the palaeoceanography. The presence of tropical and subtropical species reveals that the eastern Mediterranean acted as a refugium for these organisms.
Robin Fentimen, Eline Feenstra, Andres Rüggeberg, Efraim Hall, Valentin Rime, Torsten Vennemann, Irka Hajdas, Antonietta Rosso, David Van Rooij, Thierry Adatte, Hendrik Vogel, Norbert Frank, and Anneleen Foubert
Clim. Past, 18, 1915–1945, https://doi.org/10.5194/cp-18-1915-2022, https://doi.org/10.5194/cp-18-1915-2022, 2022
Short summary
Short summary
The investigation of a 9 m long sediment core recovered at ca. 300 m water depth demonstrates that cold-water coral mound build-up within the East Melilla Coral Province (southeastern Alboran Sea) took place during both interglacial and glacial periods. Based on the combination of different analytical methods (e.g. radiometric dating, micropaleontology), we propose that corals never thrived but rather developed under stressful environmental conditions.
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
Short summary
Short summary
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
Short summary
Short summary
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.
Jean-Philippe Blouet, Patrice Imbert, Sutieng Ho, Andreas Wetzel, and Anneleen Foubert
Solid Earth, 12, 2439–2466, https://doi.org/10.5194/se-12-2439-2021, https://doi.org/10.5194/se-12-2439-2021, 2021
Short summary
Short summary
Biochemical reactions related to hydrocarbon seepage are known to induce carbonates in marine sediments. Seep carbonates may act as seals and force lateral deviations of rising hydrocarbons. However, crustacean burrows may act as efficient vertical fluid channels allowing hydrocarbons to pass through upward, thereby allowing the vertical growth of carbonate stacks over time. This mechanism may explain the origin of carbonate columns in marine sediments throughout hydrocarbon provinces worldwide.
Tamar Guy-Haim, Maxim Rubin-Blum, Eyal Rahav, Natalia Belkin, Jacob Silverman, and Guy Sisma-Ventura
Biogeosciences, 17, 5489–5511, https://doi.org/10.5194/bg-17-5489-2020, https://doi.org/10.5194/bg-17-5489-2020, 2020
Short summary
Short summary
The availability of nutrients in oligotrophic marine ecosystems is limited. Following jellyfish blooms, large die-off events result in the release of high amounts of nutrients to the water column and sediment. Our study assessed the decomposition effects of an infamous invasive jellyfish in the ultra-oligotrophic Eastern Mediterranean Sea. We found that jellyfish decomposition favored heterotrophic bacteria and altered biogeochemical fluxes, further impoverishing this nutrient-poor ecosystem.
Cited articles
Abed-Navandi, D., Koller, H., and Dworschak, P. C.: Nutritional ecology of thalassinidean shrimps constructing burrows with debris chambers: The distribution and use of macronutrients and micronutrients, Mar. Biol. Res., 1, 202–215, https://doi.org/10.1080/17451000510019123, 2005.
Aller, R. C.: Transport and reaction in the bioirrigated zone, in: The Benthic Boundary Layer: Transport Processes and Biogeochemistry, edited by: Boudreau, B. P. and Jorgensen, B. B., Oxford University Press, https://doi.org/10.1093/oso/9780195118810.003.0011, 269–301, 2001.
Alves, J. I., Visser, M., Arantes, A. L., Nijsse, B., Plugge, C. M., Alves, M. M., Stams, A. J. M., and Sousa, D. Z.: Effect of sulfate on carbon monoxide conversion by a thermophilic syngas-fermenting culture dominated by a Desulfofundulus species, Front. Microbiol., 11, 588468, https://doi.org/10.3389/fmicb.2020.588468, 2020.
Amon, D. J., Gobin, J., Van Dover, C. L., Levin, L. A., Marsh, L., and Raineault, N. A.: Characterization of methane-seep communities in a deep-sea area designated for oil and natural gas exploitation off Ttrinidad and Tobago, Front. Mar. Sci., 4, 342, https://doi.org/10.3389/fmars.2017.00342, 2017.
Anantharaman, K., Hausmann, B., Jungbluth, S. P., Kantor, R. S., Lavy, A., Warren, L. A., Rappé, M. S., Pester, M., Loy, A., Thomas, B. C., and Banfield, J. F.: Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle, ISME J., 12, 1715–1728, https://doi.org/10.1038/s41396-018-0078-0, 2018.
Andersen, K. S., Kirkegaard, R. H., Karst, S. M., and Albertsen, M.: ampvis2: an R package to analyse and visualise 16S rRNA amplicon data, bioRxiv, 299537, https://doi.org/10.1101/299537, 2018.
Appel, J., Phunpruch, S., Steinmüller, K., and Schulz, R.: The bidirectional hydrogenase of Synechocystis sp. PCC 6803 works as an electron valve during photosynthesis, Arch. Microbiol., 173, 333–338, https://doi.org/10.1007/s002030000139, 2000.
Apprill, A., Mcnally, S., Parsons, R., and Weber, L.: Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton, Aquat. Microb. Ecol., 75, 129–137, https://doi.org/10.3354/ame01753, 2015.
Ashford, O. S., Guan, S., Capone, D., Rigney, K., Rowley, K., Orphan, V., Mullin, S. W., Dawson, K. S., Cortés, J., Rouse, G. W., Mendoza, G. F., Lee, R. W., Cordes, E. E., and Levin, L. A.: A chemosynthetic ecotone – “chemotone” – in the sediments surrounding deep-sea methane seeps, Limnol. Oceanogr., 66, 1687–1702, https://doi.org/10.1002/lno.11713, 2021.
Astall, C. M., Taylor, A. C., and Atkinson, R. J. A.: Behavioural and physiological implications of a burrow-dwelling lifestyle for two species of upogebiid mud-shrimp (Crustacea: Thalassinidea), Estuar. Coast. Shelf S., 44, 155–168, https://doi.org/10.1006/ecss.1996.0207, 1997.
Åström, E. K. L., Bluhm, B. A., and Rasmussen, T. L.: Chemosynthetic and photosynthetic trophic support from cold seeps in Arctic benthic communities, Front. Mar. Sci., 9, 1–19, https://doi.org/10.3389/fmars.2022.910558, 2022.
Bai, S., Xu, H. and Peng, X.: Microbial communities of the hydrothermal scaly-foot snails from kairei and longqi vent fields, Front. Mar. Sci., 8, 764000, https://doi.org/10.3389/fmars.2021.764000, 2021.
Barnum, T. P., Figueroa, I. A., Carlström, C. I., Lucas, L. N., Engelbrektson, A. L., and Coates, J. D.: Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities, ISME J., 12, 1568–1581, https://doi.org/10.1038/s41396-018-0081-5, 2018.
Basso, D., Beccari, V., Almogi-Labin, A., Hyams-Kaphzan, O., Weissman, A., Makovsky, Y., Rüggeberg, A., and Spezzaferri, S.: Macro- and micro-fauna from cold seeps in the Palmahim Disturbance (Israeli off-shore), with description of Waisiuconcha corsellii n.sp. (Bivalvia, Vesicomyidae), Deep.-Sea Res. Pt. II, 171, 104723, https://doi.org/10.1016/j.dsr2.2019.104723, 2020.
Bayon, G., Loncke, L., Dupré, S., Caprais, J.-C., Ducassou, E., Duperron, S., Etoubleau, J., Foucher, J.-P. J.-P., Fouquet, Y., Gontharet, S., Henderson, G. M., Huguen, C., Klaucke, I., Mascle, J., Migeon, S., Olu-Le Roy, K., Ondreas, H., Pierre, C., Sibuet, M., Stadnitskaia, A., and Woodside, J.: Multi-disciplinary investigation of fluid seepage on an unstable margin: The case of the Central Nile deep sea fan, Mar. Geol., 261, 92–104, https://doi.org/10.1016/j.margeo.2008.10.008, 2009.
Beccari, V., Basso, D., Spezzaferri, S., Rüggeberg, A., Neuman, A., and Makovsky, Y.: Preliminary video-spatial analysis of cold seep bivalve beds at the base of the continental slope of Israel (Palmahim Disturbance), Deep.-Sea Res. Pt. II, 171, 104664, https://doi.org/10.1016/j.dsr2.2019.104664, 2020.
Blouet, J.-P., Imbert, P., Ho, S., Wetzel, A., and Foubert, A.: What makes seep carbonates ignore self-sealing and grow vertically: the role of burrowing decapod crustaceans, Solid Earth, 12, 2439–2466, https://doi.org/10.5194/se-12-2439-2021, 2021.
Boetius, A. and Wenzhöfer, F.: Seafloor oxygen consumption fuelled by methane from cold seeps, Nat. Geosci., 6, 725–734, https://doi.org/10.1038/ngeo1926, 2013.
Burgdorf, T., Lenz, O., Buhrke, T., Van Der Linden, E., Jones, A. K., Albracht, S. P. J., and Friedrich, B.: [NiFe]-hydrogenases of Ralstonia eutropha H16: Modular enzymes for oxygen-tolerant biological hydrogen oxidation, J. Mol. Microb. Biotech., 10, 181–196, https://doi.org/10.1159/000091564, 2006.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., and Holmes, S. P.: DADA2: High-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581–583, https://doi.org/10.1038/nmeth.3869, 2016.
Cambon-Bonavita, M.-A., Aubé, J., Cueff-Gauchard, V., and Reveillaud, J.: Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria, Microbiome, 9, 87, https://doi.org/10.1186/s40168-021-01045-6, 2021.
Campbell, A., Gdanetz, K., Schmidt, A. W., and Schmidt, T. M.: H2 generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers, Microbiome, 11, 133, https://doi.org/10.1186/s40168-023-01565-3, 2023.
Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., and Parks, D. H.: GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database, Bioinformatics, 36, 1925–1927, https://doi.org/10.1093/bioinformatics/btz848, 2020.
Chen, Y.-J. J., Leung, P. M., Wood, J. L., Bay, S. K., Hugenholtz, P., Kessler, A. J., Shelley, G., Waite, D. W., Franks, A. E., Cook, P. L. M. M., and Greening, C.: Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem, ISME J., 15, 2986–3004, https://doi.org/10.1038/s41396-021-00988-w, 2021.
Cheng, J., Li, H., Zhang, J., Ding, L., Ye, Q., and Lin, R.: Enhanced dark hydrogen fermentation of Enterobacter aerogenes/HoxEFUYH with carbon cloth, Int. J. Hydrogen Energ., 44, 3560–3568, https://doi.org/10.1016/j.ijhydene.2018.12.080, 2019.
Chklovski, A., Parks, D. H., Woodcroft, B. J., Tyson, G. W., Chkolovski, A., Parks, D. H., Woodcroft, B. J., Tyson, G. W., Chklovski, A., Parks, D. H., Woodcroft, B. J., and Tyson, G. W.: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning, Nat. Methods, 20, 1203–1212, https://doi.org/10.1038/s41592-023-01940-w, 2023.
Coelho, V., Cooper, R., and de Almeida Rodrigues, S.: Burrow morphology and behavior of the mud shrimp Upogebia omissa (Decapoda:Thalassinidea:Upogebiidae), Mar. Ecol. Prog. Ser., 200, 229–240, https://doi.org/10.3354/meps200229, 2000.
Coleman, D. and Ballard, R.: A highly concentrated region of cold hydrocarbon seeps in the southeastern Mediterranean Sea, Geo-Mar. Lett., 21, 162–167, https://doi.org/10.1007/s003670100079, 2001.
Coleman, D. F., Austin Jr., J. A., Ben-Avraham, Z., Makovsky, Y., and Tchernov, D.: Seafloor pockmarks, deepwater corals, and cold seeps along the continental margin of Israel, Oceanography, 25, 40–41, 2012.
Coleman, D. F. D., Austin Jr., J. A., Ben-Avraham, Z., Ballard, R. D., Austin, J. A., Ben-Avraham, Z., and Ballard, R. D.: Exploring the continental margin of Israel: “Telepresence” at work, EOS T. Am. Geophys. Un., 92, 81–82, https://doi.org/10.1029/2011EO100002, 2011.
Dittmer, J., Bredon, M., Moumen, B., Raimond, M., Grève, P., and Bouchon, D.: The terrestrial isopod symbiont `Candidatus Hepatincola porcellionum' is a potential nutrient scavenger related to Holosporales symbionts of protists, ISME Commun., 3, 18, https://doi.org/10.1038/s43705-023-00224-w, 2023.
Drake, H. L.: Acetogenesis, Acetogenic Bacteria, and the Acetyl-CoA “Wood/Ljungdahl” Pathway: Past and Current Perspectives, in: Acetogenesis, edited by: Drake, H. L., Springer US, Boston, MA, https://doi.org/10.1007/978-1-4615-1777-1_1, 3–60, 1994.
Dworschak, P. C., Koller, H., and Abed-Navandi, D.: Burrow structure, burrowing and feeding behaviour of Corallianassa longiventris and Pestarella tyrrhena (Crustacea, Thalassinidea, Callianassidae), Mar. Biol., 148, 1369–1382, https://doi.org/10.1007/s00227-005-0161-8, 2006.
Fang, J., Jiang, W., Meng, S., He, W., Wang, G., Guo, E., and Yan, Y.: Polychaete bioturbation alters the taxonomic structure, co-occurrence network, and functional groups of bacterial communities in the intertidal flat, Microb. Ecol., 86, 112–126, https://doi.org/10.1007/s00248-022-02036-2, 2023.
Fang, Y., Liu, J., Yang, J., Wu, G., Hua, Z., Dong, H., Hedlund, B. P., Baker, B. J., and Jiang, H.: Compositional and metabolic responses of autotrophic microbial community to salinity in lacustrine environments, edited by: Mackelprang, R., mSystems, 7, e0033522, https://doi.org/10.1128/msystems.00335-22, 2022.
Fernández-Gómez, B., Richter, M., Schüler, M., Pinhassi, J., Acinas, S. G., González, J. M., and Pedrós-Alió, C.: Ecology of marine bacteroidetes: A comparative genomics approach, ISME J., 7, 1026–1037, https://doi.org/10.1038/ismej.2012.169, 2013.
Finster, K.: Microbiological disproportionation of inorganic sulfur compounds, J. Sulfur Chem., 29, 281–292, https://doi.org/10.1080/17415990802105770, 2008.
Finster, K. W., Kjeldsen, K. U., Kube, M., Reinhardt, R., Mussmann, M., Amann, R., and Schreiber, L.: Complete genome sequence of desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds, Stand. Genomic Sci., 8, 58–68, https://doi.org/10.4056/sigs.3777412, 2013.
Flood, B. E., Fliss, P., Jones, D. S., Dick, G. J., Jain, S., Kaster, A.-K., Winkel, M., Mußmann, M., and Bailey, J.: Single-cell (meta-)genomics of a dimorphic Candidatus Thiomargarita nelsonii reveals genomic plasticity, Front. Microbiol., 7, 603, https://doi.org/10.3389/fmicb.2016.00603, 2016.
Frank, H., Rahav, E., and Bar-Zeev, E.: Short-term effects of SWRO desalination brine on benthic heterotrophic microbial communities, Desalination, 417, 52–59, https://doi.org/10.1016/j.desal.2017.04.031, 2017.
Gadol, O., Tibor, G., ten Brink, U., Hall, J. K., Groves-Gidney, G., Bar-Am, G., Hübscher, C., and Makovsky, Y.: Semi-automated bathymetric spectral decomposition delineates the impact of mass wasting on the morphological evolution of the continental slope, offshore Israel, Basin Res., 32, 1166–1193, https://doi.org/10.1111/bre.12420, 2020.
Garfunkel, Z., Arad, A., and Almagor, G.: The Palmahim disturbance and its regional setting, Geol. Surv. Isr. Bull., 56, 1979.
Gavriilidou, A., Gutleben, J., Versluis, D., Forgiarini, F., Van Passel, M. W. J., Ingham, C. J., Smidt, H., and Sipkema, D.: Comparative genomic analysis of Flavobacteriaceae: Insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis, BMC Genomics, 21, 569, https://doi.org/10.1186/s12864-020-06971-7, 2020.
Gibson, G. R., Macfarlane, G. T., and Cummings, J. H.: Sulphate reducing bacteria and hydrogen metabolism in the human large intestine, Gut, 34, 437–439, https://doi.org/10.1136/gut.34.4.437, 1993.
Gilbertson, W. W., Solan, M., and Prosser, J. I.: Differential effects of microorganism-invertebrate interactions on benthic nitrogen cycling, FEMS Microbiol. Ecol., 82, 11–22, https://doi.org/10.1111/j.1574-6941.2012.01400.x, 2012.
Glöckner, F. O., Yilmaz, P., Quast, C., Gerken, J., Beccati, A., Ciuprina, A., Bruns, G., Yarza, P., Peplies, J., Westram, R., and Ludwig, W.: 25 years of serving the community with ribosomal RNA gene reference databases and tools, J. Biotechnol., 261, 169–176, https://doi.org/10.1016/j.jbiotec.2017.06.1198, 2017.
Glud, R. N., Thamdrup, B., Stahl, H., Wenzhoefer, F., Glud, A., Nomaki, H., Oguri, K., Revsbech, N. P., and Kitazatoe, H.: Nitrogen cycling in a deep ocean margin sediment (Sagami Bay, Japan), Limnol. Oceanogr., 54, 723–734, https://doi.org/10.4319/lo.2009.54.3.0723, 2009.
Grondin, J. M., Tamura, K., Déjean, G., Abbott, D. W., and Brumer, H.: Polysaccharide utilization loci: Fueling microbial communities, J. Bacteriol., 199, https://doi.org/10.1128/JB.00860-16, 2017.
Gutekunst, K., Chen, X., Schreiber, K., Kaspar, U., Makam, S., and Appel, J.: The bidirectional NiFe-hydrogenase in Synechocystis sp. PCC 6803 Is reduced by flavodoxin and ferredoxin and is essential under mixotrophic, nitrate-limiting conditions, J. Biol. Chem., 289, 1930–1937, https://doi.org/10.1074/jbc.M113.526376, 2014.
Gvirtzman, Z., Reshef, M., Buch-Leviatan, O., Groves-Gidney, G., Karcz, Z., Makovsky, Y., and Ben-Avraham, Z.: Bathymetry of the Levant basin: interaction of salt-tectonics and surficial mass movements, Mar. Geol., 360, 25–39, https://doi.org/10.1016/j.margeo.2014.12.001, 2015.
Hembree, D. I.: Burrows and ichnofabric produced by centipedes: modern and ancient examples, Palaios, 34, 468–489, https://doi.org/10.2110/palo.2019.059, 2019.
Herut, B., Rubin-Blum, M., Sisma-Ventura, G., Jacobson, Y., Bialik, O. M., Ozer, T., Lawal, M. A., Giladi, A., Kanari, M., Antler, G., and Makovsky, Y.: Discovery and chemical composition of the eastmost deep-sea anoxic brine pools in the Eastern Mediterranean Sea, Front. Mar. Sci., 9, 1040681, https://doi.org/10.3389/fmars.2022.1040681, 2022.
Hui, M., Wang, A., Cheng, J., and Sha, Z.: Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts, PeerJ, 10, e13758, https://doi.org/10.7717/peerj.13758, 2022.
Ionescu, D. and Bizic, M.: Giant Bacteria, in: Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, https://doi.org/10.1002/9780470015902.a0020371.pub2, 2019.
Joye, S. B.: The geology and biogeochemistry of hydrocarbon seeps, Annu. Rev. Earth Pl. Sc., 48, 205–231, https://doi.org/10.1146/annurev-earth-063016-020052, 2020.
Jumars, P. A., Dorgan, K. M., Mayer, L. M., Boudreau, B. P., and Johnson, B. D.: Material constraints on infaunal lifestyles. May the persistent and strong forces be with you, in: Trace Fossils. Concepts, Problems, Prospects, Elsevier Science, https://doi.org/10.1016/B978-044452949-7/50152-2, 442–457, 2007.
Kang, D. D., Froula, J., Egan, R., and Wang, Z.: MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities, PeerJ, 3, e1165, https://doi.org/10.7717/peerj.1165, 2015.
Kieser, S., Brown, J., Zdobnov, E. M., Trajkovski, M., and McCue, L. A.: ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data, BMC Bioinformatics, 21, 257, https://doi.org/10.1186/s12859-020-03585-4, 2020.
Knaust, D.: Siphonichnidae (new ichnofamily) attributed to the burrowing activity of bivalves: Ichnotaxonomy, behaviour and palaeoenvironmental implications, Earth-Sci. Rev., 150, 497–519, https://doi.org/10.1016/j.earscirev.2015.07.014, 2015.
Knittel, K. and Boetius, A.: Anaerobic oxidation of methane: progress with an unknown process, Annu. Rev. Microbiol., 63, 311–34, https://doi.org/10.1146/annurev.micro.61.080706.093130, 2009.
Kormas, K. A. and Meziti, A.: The microbial communities of the East Mediterranean Sea mud volcanoes and pockmarks, in: Marine Hydrocarbon Seeps: Microbiology and Biogeochemistry of a Global Marine Habitat, edited by: Teske, A. P. and Carvalho, V., Springer Nature Switzerland, https://doi.org/10.1007/978-3-030-34827-4_7, 143–148, 2020.
Kristensen, E. and Kostka, J. E.: Macrofaunal burrows and irrigation in marine sediment: Microbiological and biogeochemical interactions, in: Interactions Between Macro- and Microorganisms in Marine Sediments, edited by: Kristensen, E., Haese, R. R., and Kostka, J. E., AGU, Washington, DC, US, https://doi.org/10.1029/60CE08, 125–157, 2005.
Laverock, B., Smith, C. J., Tait, K., Osborn, A. M., Widdicombe, S., and Gilbert, J. A.: Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments, ISME J., 4, 1531–1544, https://doi.org/10.1038/ismej.2010.86, 2010.
Lawal, M. A., Bialik, O. M., Lazar, M., Waldmann, N. D., Foubert, A., and Makovsky, Y.: Modes of gas migration and seepage on the salt-rooted Palmahim Disturbance, southeastern Mediterranean, Mar. Petrol. Geol., 153, 106256, https://doi.org/10.1016/j.marpetgeo.2023.106256, 2023.
Levin, L. A. and Sibuet, M.: Understanding continental margin biodiversity: A new imperative, Ann. Rev. Mar. Sci., 4, 79–112, https://doi.org/10.1146/annurev-marine-120709-142714, 2012.
Levin, L. A., Baco, A. R., Bowden, D. A., Colaco, A., Cordes, E. E., Cunha, M. R., Demopoulos, A. W. J., Gobin, J., Grupe, B. M., Le, J., Metaxas, A., Netburn, A. N., Rouse, G. W., Thurber, A. R., Tunnicliffe, V., Van Dover, C. L., Vanreusel, A., and Watling, L.: Hydrothermal vents and methane seeps: rethinking the sphere of influence, Front. Mar. Sci., 3, 72, https://doi.org/10.3389/fmars.2016.00072, 2016.
Makovsky, Y., Rüggeberg, A., Bialik, O., Foubert, A., Almogi-Labin, A., Alter, Y., Bampas, V., Basso, D., Feenstra, E., and Fentimen, R.: South East Mediterranean SEEP Carbonate, R/V Aegaeo Cruise, EuroFLEETS2 SEMSEEP, R/V Aegaeo Cruise EuroFLEETS2 SEMSEEP, https://drive.google.com/file/d/16WKBpPIibT8eqYcDlc2SHhkBKntcT2CT/view?usp=sharing (last access: 6 March 2025), 2017.
Martens, E. C., Chiang, H. C., and Gordon, J. I.: Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont, Cell Host Microbe, 4, 447–457, https://doi.org/10.1016/j.chom.2008.09.007, 2008.
Martens, E. C., Koropatkin, N. M., Smith, T. J., and Gordon, J. I.: Complex glycan catabolism by the human gut microbiota: The bacteroidetes sus-like paradigm, J. Biol. Chem., 284, 24673–24677, https://doi.org/10.1074/jbc.R109.022848, 2009.
Martin, M.: Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, 17, 10–12, https://doi.org/10.14806/ej.17.1.200, 2011.
Mavropoulou, A. M., Vervatis, V., and Sofianos, S.: Dissolved oxygen variability in the Mediterranean Sea, J. Marine Syst., 208, 103348, https://doi.org/10.1016/j.jmarsys.2020.103348, 2020.
Mayer, M., Schaffner, L., and Kemp, W.: Nitrification potentials of benthic macrofaunal tubes and burrow walls:effects of sediment NH4+ and animal irrigation behavior, Mar. Ecol. Prog. Ser., 121, 157–169, https://doi.org/10.3354/meps121157, 1995.
McMurdie, P. J. and Holmes, S.: phyloseq: An R Package for reproducible interactive analysis and graphics of microbiome census data, edited by: Watson, M., PLoS One, 8, e61217, https://doi.org/10.1371/journal.pone.0061217, 2013.
Meile, C. and Van Cappellen, P.: Global estimates of enhanced solute transport in marine sediments, Limnol. Oceanogr., 48, 777–786, https://doi.org/10.4319/lo.2003.48.2.0777, 2003.
Mohr, W., Großkopf, T., Wallace, D. W. R., and LaRoche, J.: Methodological underestimation of oceanic nitrogen fixation rates, PLoS One, 5, e12583, https://doi.org/10.1371/journal.pone.0012583, 2010.
Molari, M., Hassenrueck, C., Laso-pérez, R., Wegener, G., Offre, P., Scilipoti, S., and Boetius, A.: A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes, Nat. Microbiol., 8, 651–665, https://doi.org/10.1038/s41564-023-01342-w, 2023.
Mulholland, M. R., Bernhardt, P. W., Heil, C. A., Bronk, D. A., and Neil, J. M. O.: Nitrogen fixation and release of fixed nitrogen by Trichodesmium spp. in the Gulf of Mexico, Limnol. Oceanogr., 51, 1762–1776, https://doi.org/10.4319/lo.2006.51.4.1762, 2006.
Ndeh, D. and Gilbert, H. J.: Biochemistry of complex glycan depolymerisation by the human gut microbiota, FEMS Microbiol. Rev., 42, 146–164, https://doi.org/10.1093/femsre/fuy002, 2018.
Nielsen, O., Gribsholt, B., Kristensen, E., and Revsbech, N.: Microscale distribution of oxygen and nitrate in sediment inhabited by Nereis diversicolor: spatial patterns and estimated reaction rates, Aquat. Microb. Ecol., 34, 23–32, https://doi.org/10.3354/ame034023, 2004.
Olm, M. R., Brown, C. T., Brooks, B., and Banfield, J. F.: DRep: A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication, ISME J., 11, 2864–2868, https://doi.org/10.1038/ismej.2017.126, 2017.
Olu-Le Roy, K., Sibuet, M., Fiala-Médioni, A., Gofas, S., Salas, C., Mariotti, A., Foucher, J. P. J. P. J.-P. J. P., and Woodside, J.: Cold seep communities in the deep eastern Mediterranean Sea: composition, symbiosis and spatial distribution on mud volcanoes, Deep-Sea Res. Pt. I, 51, 1915–1936, https://doi.org/10.1016/j.dsr.2004.07.004, 2004.
Orsi, W. D.: Ecology and evolution of seafloor and subseafloor microbial communities, Nat. Rev. Microbiol., 16, 671–683, https://doi.org/10.1038/s41579-018-0046-8, 2018.
Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A. R., Xia, F., and Stevens, R.: The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Res., 42, D206–D214, https://doi.org/10.1093/nar/gkt1226, 2014.
Papaspyrou, S., Gregersen, T., Cox, R. P., Thessalou-Legaki, M., and Kristensen, E.: Sediment properties and bacterial community in burrows of the ghost shrimp Pestarella tyrrhena (Decapoda: Thalassinidea), Aquat. Microb. Ecol., 38, 181–190, https://doi.org/10.3354/ame038181, 2005.
Parada, A. E., Needham, D. M., and Fuhrman, J. A.: Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples, Environ. Microbiol., 18, 1403–1414, https://doi.org/10.1111/1462-2920.13023, 2016.
Petersen, J. M., Zielinski, F. U., Pape, T., Seifert, R., Moraru, C., Amann, R., Hourdez, S., Girguis, P. R., Wankel, S. D., Barbe, V., Pelletier, E., Fink, D., Borowski, C., Bach, W., and Dubilier, N.: Hydrogen is an energy source for hydrothermal vent symbioses, Nature, 476, 176–80, https://doi.org/10.1038/nature10325, 2011.
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., and Korobeynikov, A.: Using SPAdes de novo assembler, Curr. Protoc. Bioinforma., 70, e102, https://doi.org/10.1002/cpbi.102, 2020.
R Core Team: R: A Language and Environment for Statistical Computing, http://www.r-project.org/ (last access: 31 January 2024), 2024.
Rahav, E., Silverman, J., Raveh, O., Hazan, O., Rubin-Blum, M., Zeri, C., Gogou, A., Kralj, M., Pavlidou, A., and Kress, N.: The deep water of Eastern Mediterranean Sea is a hotspot for bacterial activity, Deep-Sea Res. Pt. II, 164, 135–143, https://doi.org/10.1016/j.dsr2.2019.03.004, 2019.
Reeves, A. R., D'Elia, J. N., Frias, J., and Salyers, A. A.: A Bacteroides thetaiotaomicron outer membrane protein that is essential for utilization of maltooligosaccharides and starch, J. Bacteriol., 178, 823–830, https://doi.org/10.1128/jb.178.3.823-830.1996, 1996.
Reineck, H.-E.: Sedimentgefüge im Bereich der südlichen Nordsee, Schweizerbart Science Publishers, Stuttgart, Germany, [online] http://www.schweizerbart.de//publications/detail/isbn/9783510612956/Abhandlungen%5C_d%5C_Senckenb%5C_Naturf%5C_Gesell (last access: 31 January 2024), 1963.
Ritt, B., Pierre, C., Gauthier, O., Wenzhöfer, F., Boetius, A., and Sarrazin, J.: Diversity and distribution of cold-seep fauna associated with different geological and environmental settings at mud volcanoes and pockmarks of the Nile Deep-Sea Fan, Mar. Biol., 158, 1187–1210, https://doi.org/10.1007/s00227-011-1679-6, 2011.
Roether, W. and Well, R.: Oxygen consumption in the Eastern Mediterranean, Deep-Sea Res. Pt. I,, 48, 1535–1551, https://doi.org/10.1016/S0967-0637(00)00102-3, 2001.
Rubin-Blum, M., Shemesh, E., Goodman-Tchernov, B., Coleman, D. F., Ben-Avraham, Z., and Tchernov, D.: Cold seep biogenic carbonate crust in the Levantine basin is inhabited by burrowing Phascolosoma aff. turnerae, a sipunculan worm hosting a distinctive microbiota, Deep-Sea Res. Pt. I, 90, 17–26, https://doi.org/10.1016/j.dsr.2014.04.014, 2014a.
Rubin-Blum, M., Antler, G., Turchyn, A. V., Tsadok, R., Goodman-Tchernov, B. N., Shemesh, E., Austin, J. A., Coleman, D. F., Makovsky, Y., Sivan, O., and Tchernov, D.: Hydrocarbon-related microbial processes in the deep sediments of the Eastern Mediterranean Levantine Basin, FEMS Microbiol. Ecol., 87, 780–796, https://doi.org/10.1111/1574-6941.12264, 2014b.
Rubin-Blum, M., Dubilier, N., and Kleiner, M.: Genetic evidence for two carbon fixation pathways (the Calvin–Benson–Bassham Cycle and the reverse tricarboxylic acid cycle) in symbiotic and free-living bacteria, edited by: Hallam, S. J., mSphere, 4, 00394–18, https://doi.org/10.1128/mSphere.00394-18, 2019.
Rubin-Blum, M., Sisma-Ventura, G., Yudkovski, Y., Belkin, N., Kanari, M., Herut, B., and Rahav, E.: Diversity, activity, and abundance of benthic microbes in the Southeastern Mediterranean Sea, FEMS Microbiol. Ecol., 98, fiac09, https://doi.org/10.1093/femsec/fiac009, 2022.
Rubin-Blum, M., Makovsky, Y., Rahav, E., Belkin, N., Antler, G., Sisma-Ventura, G., and Herut, B.: Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea, Mar. Environ. Res., 198, 106497, https://doi.org/10.1016/j.marenvres.2024.106497, 2024.
Ruff, S. E., Biddle, J. F., Teske, A. P., Knittel, K., Boetius, A., and Ramette, A.: Global dispersion and local diversification of the methane seep microbiome, P. Natl. Acad. Sci. USA, 112, 4015–4020, https://doi.org/10.1073/pnas.1421865112, 2015.
Ruff, S. E., Humez, P., de Angelis, I. H., Diao, M., Nightingale, M., Cho, S., Connors, L., Kuloyo, O. O., Seltzer, A., Bowman, S., Wankel, S. D., McClain, C. N., Mayer, B., and Strous, M.: Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems, Nat. Commun., 14, 3194, https://doi.org/10.1038/s41467-023-38523-4, 2023.
Santos Correa, S., Schultz, J., Lauersen, K. J., and Soares Rosado, A.: Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways, J. Adv. Res., 47, 75–92, https://doi.org/10.1016/j.jare.2022.07.011, 2022.
Seilacher, A.: Trace Fossil Analysis, Springer Berlin Heidelberg, Berlin, Heidelberg, Heidelberg, https://doi.org/10.1007/978-3-540-47226-1, 2007.
Sieber, C. M. K., Probst, A. J., Sharrar, A., Thomas, B. C., Hess, M., Tringe, S. G., and Banfield, J. F.: Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy, Nat. Microbiol., 3, 836–843, https://doi.org/10.1038/s41564-018-0171-1, 2018.
Simon, M. and Azam, F.: Protein content and protein synthesis rates of planktonic marine bacteria, Mar. Ecol. Prog. Ser., 51, 201–213, https://doi.org/10.3354/meps051201, 1989.
Sisma-Ventura, G., Bialik, O. M., Makovsky, Y., Rahav, E., Ozer, T., Kanari, M., Marmen, S., Belkin, N., Guy-Haim, T., Antler, G., Herut, B., and Rubin-Blum, M.: Cold seeps alter the near-bottom biogeochemistry in the ultraoligotrophic Southeastern Mediterranean Sea, Deep-Sea Res. Pt. I, 183, 103744, https://doi.org/10.1016/j.dsr.2022.103744, 2022.
Smith, D. C., Smith, D. C., Azam, F., and Azam, F.: A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine, Mar. Microb. Food Webs, 6, 107–114, 1992.
Stamhuis, E., Schreurs, C., and Videler, J.: Burrow architecture and turbative activity of the thalassinid shrimp Callianassa subterranea from the central North Sea, Mar. Ecol. Prog. Ser., 151, 155–163, https://doi.org/10.3354/meps151155, 1997.
Teske, A. and Carvalho, V. (Eds.): Marine hydrocarbon seeps: microbiology and biogeochemistry of a global marine habitat, Springer International Publishing, Cham, Switzerland, https://doi.org/10.1007/978-3-030-34827-4, 2020.
Thomas, F., Hehemann, J. H., Rebuffet, E., Czjzek, M., and Michel, G.: Environmental and gut Bacteroidetes: The food connection, Front. Microbiol., 2, 93, https://doi.org/10.3389/fmicb.2011.00093, 2011.
Trojan, D., Schreiber, L., Bjerg, J. T., Bøggild, A., Yang, T., Kjeldsen, K. U., and Schramm, A.: A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema, Syst. Appl. Microbiol., 39, 297–306, https://doi.org/10.1016/j.syapm.2016.05.006, 2016.
Trueman, E. R., Brand, A. R., and Davis, P.: The dynamics of burrowing of some common littoral bivalves, J. Exp. Biol., 44, 469–492, https://doi.org/10.1242/jeb.44.3.469, 1966.
Ward, L. M., Bertran, E., and Johnston, D. T.: Expanded genomic sampling refines current understanding of the distribution and evolution of sulfur metabolisms in the Desulfobulbales, Front. Microbiol., 12, 666052, https://doi.org/10.3389/fmicb.2021.666052, 2021.
Weidlich, R., Bialik, O. M., Rüggeberg, A., Grobéty, B., Vennemann, T., Neuman, A., Makovsky, Y., and Foubert, A.: Occurrence and genesis of cold‐seep authigenic carbonates from the South‐Eastern Mediterranean Sea, Depos. Rec., 9, 844–870, https://doi.org/10.1002/dep2.239, 2023.
Weiss, R. F.: The solubility of nitrogen, oxygen and argon in water and seawater, Deep. Res. Oceanogr. Abstr., 17, 721–735, https://doi.org/10.1016/0011-7471(70)90037-9, 1970.
Wolf, P. G., Biswas, A., Morales, S. E., Greening, C., and Gaskins, H. R.: H2 metabolism is widespread and diverse among human colonic microbes, Gut Microbes, 7, 235–245, https://doi.org/10.1080/19490976.2016.1182288, 2016.
Wu, Y.-W., Simmons, B. A., and Singer, S. W.: MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets, Bioinformatics, 32, 605–607, https://doi.org/10.1093/bioinformatics/btv638, 2015.
Xu, Z., Wang, M., Zhang, H., He, W., Cao, L., Lian, C., Zhong, Z., Wang, H., Fu, L., Zhang, X., and Li, C.: Metabolism interactions promote the overall functioning of the episymbiotic chemosynthetic community of Shinkaia crosnieri of cold seeps, mSystems, 7, e0032022, https://doi.org/10.1128/msystems.00320-22, 2022.
Zhang, C., Fang, Y. X., Yin, X., Lai, H., Kuang, Z., Zhang, T., Xu, X. P., Wegener, G., Wang, J. H., and Dong, X.: The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules, Microbiome, 11, 37, https://doi.org/10.1186/s40168-023-01482-5, 2023.
Zhou, Z., Tran, P. Q., Breister, A. M., Liu, Y., Kieft, K., Cowley, E. S., Karaoz, U., and Anantharaman, K.: METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks, Microbiome, 10, 33, https://doi.org/10.1186/s40168-021-01213-8, 2022.
Zoccarato, L., Sher, D., Miki, T., Segrè, D., and Grossart, H. P.: A comparative whole-genome approach identifies bacterial traits for marine microbial interactions, Commun. Biol., 5, 276, https://doi.org/10.1038/s42003-022-03184-4, 2022.
Zvi-Kedem, T., Vintila, S., Kleiner, M., Tchernov, D., and Rubin-Blum, M.: Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels, ISME Commun., 3, 48, https://doi.org/10.1038/s43705-023-00254-4, 2023.
Short summary
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.
Chemotones, transition zones in chemosynthetic ecosystems, alter geochemical cycles and...
Altmetrics
Final-revised paper
Preprint