Articles | Volume 23, issue 15
https://doi.org/10.5194/bg-23-5571-2026
© Author(s) 2026. 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-23-5571-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
The Ni cycle in the Southern Ocean: insights from Ni concentrations, isotopes and metagenomics
LEGOS (CNRS/CNES/IRD/UT3), University of Toulouse, Toulouse, 31400, France
Department of Earth and Planetary Sciences, Institute of Geochemistry and Petrology, ETH Zurich, 8092 Zurich, Switzerland
Emile Faure
CORRESPONDING AUTHOR
Station Biologique de Roscoff, CNRS/Sorbonne University, Roscoff, 29680, France
Univ Brest, CNRS, IFREMER, BEEP, Plouzané, 29280, France
BRIDGE, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK
Ricardo Zamora
Department of Earth and Planetary Sciences, Institute of Geochemistry and Petrology, ETH Zurich, 8092 Zurich, Switzerland
Corey Archer
Department of Earth and Planetary Sciences, Institute of Geochemistry and Petrology, ETH Zurich, 8092 Zurich, Switzerland
Matthias Sieber
Department of Earth and Planetary Sciences, Institute of Geochemistry and Petrology, ETH Zurich, 8092 Zurich, Switzerland
College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA
Michael Ellwood
Research School of Earth Sciences, Australian National University, Canberra, 2601, Australia
Christel Hassler
Institute of Earth Sciences, University of Lausanne, 1015 Lausanne, Switzerland
School of Architecture, Civil & Environmental Engineering, Alpine and Polar Environmental Research Center, EPFL, 1951 Sion, Switzerland
Yajuan Lin
Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX 78412, USA
Division of Earth and Climate Sciences, Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
CNRS, Univ Brest, IRD, Ifremer, LEMAR, Plouzané, 29280, France
Nicolas Cassar
Division of Earth and Climate Sciences, Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
CNRS, Univ Brest, IRD, Ifremer, LEMAR, Plouzané, 29280, France
Lois Maignien
Univ Brest, CNRS, IFREMER, BEEP, Plouzané, 29280, France
Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
Derek Vance
Department of Earth and Planetary Sciences, Institute of Geochemistry and Petrology, ETH Zurich, 8092 Zurich, Switzerland
Related authors
Natasha René van Horsten, Hélène Planquette, Géraldine Sarthou, Thomas James Ryan-Keogh, Nolwenn Lemaitre, Thato Nicholas Mtshali, Alakendra Roychoudhury, and Eva Bucciarelli
Biogeosciences, 19, 3209–3224, https://doi.org/10.5194/bg-19-3209-2022, https://doi.org/10.5194/bg-19-3209-2022, 2022
Short summary
Short summary
The remineralisation proxy, barite, was measured along 30°E in the southern Indian Ocean during early austral winter. To our knowledge this is the first reported Southern Ocean winter study. Concentrations throughout the water column were comparable to observations during spring to autumn. By linking satellite primary production to this proxy a possible annual timescale is proposed. These findings also suggest possible carbon remineralisation from satellite data on a basin scale.
Guanghui Chen, Insa Rapp, Matthias Sieber, Eric P. Achterberg, Tim J. Conway, Martha Gledhill, Mark J. Hopwood, and Ruifang C. Xie
EGUsphere, https://doi.org/10.5194/egusphere-2026-3486, https://doi.org/10.5194/egusphere-2026-3486, 2026
This preprint is open for discussion and under review for Biogeosciences (BG).
Short summary
Short summary
Iron (Fe) is an essential micronutrient for marine organisms. In the Peruvian oxygen minimum zone, controversies exist regarding mechanisms governing temporal Fe supply. Here, we demonstrate that El Niño modulated Peru-Chile Undercurrent intensification is key influencing the variations in sediment-derived shelf-to-slope Fe plume in Peruvian anoxic waters. In contrast, we show that organic ligand complexation and authigenic Fe formation control Fe biogeochemistry in offshore anoxic waters.
Ming Cheng, Nicola Maher, and Michael J. Ellwood
Biogeosciences, 22, 7269–7291, https://doi.org/10.5194/bg-22-7269-2025, https://doi.org/10.5194/bg-22-7269-2025, 2025
Short summary
Short summary
The Southern Ocean helps regulate Earth’s climate by cycling nutrients and carbon. We studied how well 14 modern climate models represent key ocean properties, such as plant growth, nutrients, and carbon particles. By comparing model results with real-world observations, we found large differences in model performance. Some models captured certain features better than others. Our findings can guide future improvements in ocean and climate predictions.
Brandon M. Stephens, Montserrat Roca-Martí, Amy E. Maas, Vinícius J. Amaral, Samantha Clevenger, Shawnee Traylor, Claudia R. Benitez-Nelson, Philip W. Boyd, Ken O. Buesseler, Craig A. Carlson, Nicolas Cassar, Margaret Estapa, Andrea J. Fassbender, Yibin Huang, Phoebe J. Lam, Olivier Marchal, Susanne Menden-Deuer, Nicola L. Paul, Alyson E. Santoro, David A. Siegel, and David P. Nicholson
Biogeosciences, 22, 3301–3328, https://doi.org/10.5194/bg-22-3301-2025, https://doi.org/10.5194/bg-22-3301-2025, 2025
Short summary
Short summary
The ocean’s mesopelagic zone (MZ) plays a crucial role in the global carbon cycle. This study combines new and previously published measurements of organic carbon supply and demand collected in August 2018 in the MZ of the subarctic North Pacific Ocean. Supply was insufficient to meet demand in August, but supply entering into the MZ in the spring of 2018 could have met the August demand. Results suggest observations over seasonal timescales may help to close MZ carbon budgets.
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.
Natasha René van Horsten, Hélène Planquette, Géraldine Sarthou, Thomas James Ryan-Keogh, Nolwenn Lemaitre, Thato Nicholas Mtshali, Alakendra Roychoudhury, and Eva Bucciarelli
Biogeosciences, 19, 3209–3224, https://doi.org/10.5194/bg-19-3209-2022, https://doi.org/10.5194/bg-19-3209-2022, 2022
Short summary
Short summary
The remineralisation proxy, barite, was measured along 30°E in the southern Indian Ocean during early austral winter. To our knowledge this is the first reported Southern Ocean winter study. Concentrations throughout the water column were comparable to observations during spring to autumn. By linking satellite primary production to this proxy a possible annual timescale is proposed. These findings also suggest possible carbon remineralisation from satellite data on a basin scale.
Cited articles
Alonso-Sáez, L., Waller, A. S., Mende, D. R., Bakker, K., Farnelid, H., Yager, P. L., Lovejoy, C., Tremblay, J. É., Potvin, M., Heinrich, F., Estrada, M., Riemann, L., Bork, P., Pedrós-Alió, C., and Bertilssona, S.: Role for urea in nitrification by polar marine Archaea, P. Natl. Acad. Sci. USA, 109, 17989–17994, https://doi.org/10.1073/pnas.1201914109, 2012.
Antoine, D., Thomalla, S., Berliner, D., Little, H., Moutier, W., Olivier-Morgan, A., Robinson, C., Ryan-Keogh, T., and Schuback, N.: Phytoplankton pigment concentrations of seawater sampled during the Antarctic Circumnavigation Expedition (ACE) during the Austral Summer of 2016/2017, Zenodo, https://doi.org/10.5281/ZENODO.3816726, 2020.
Aramaki, T., Blanc-Mathieu, R., Endo, H., Ohkubo, K., Kanehisa, M., Goto, S., and Ogata, H.: KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold, Bioinformatics, 36, 2251–2252, https://doi.org/10.1093/bioinformatics/btz859, 2020.
Archer, C., Vance, D., Milne, A., and Lohan, M. C.: The oceanic biogeochemistry of nickel and its isotopes: New data from the South Atlantic and the Southern Ocean biogeochemical divide, Earth Planet. Sc. Lett., 535, 116118, https://doi.org/10.1016/j.epsl.2020.116118, 2020.
Benoit, G., Peterlongo, P., Mariadassou, M., Drezen, E., Schbath, S., Lavenier, D., and Lemaitre, C.: Multiple comparative metagenomics using multiset k-mer counting, PeerJ Comput. Sci., 2016, 1–25, https://doi.org/10.7717/peerj-cs.94, 2016.
Bian, X., Yang, S. C., Raad, R. J., Odendahl, C. E., Lanning, N. T., Sieber, M., Huang, K. F., Fitzsimmons, J. N., Conway, T. M., and John, S. G.: Distribution and Cycling of Nickel and Nickel Isotopes in the Pacific Ocean, Geophys. Res. Lett., 51, e2024GL111115, https://doi.org/10.1029/2024GL111115, 2024.
Bruland, K. W.: Oceanographic distributions of cadmium, zinc, nickel, and copper in the North Pacific, Earth Planet. Sc. Lett., 47, 176–198, https://doi.org/10.1016/0012-821X(80)90035-7, 1980.
Cameron, V. and Vance, D.: Heavy nickel isotope compositions in rivers and the oceans, Geochim. Cosmochim. Acta, 128, 195–211, https://doi.org/10.1016/j.gca.2013.12.007, 2014.
Cammack, R., Fernandez, V. M., and Hatchikian, E. C.: Nickel-Iron Hydrogenase, Methods Enzymol., 243, 43–68, https://doi.org/10.1016/0076-6879(94)43007-1, 1994.
Cavagna, A. J., Fripiat, F., Elskens, M., Mangion, P., Chirurgien, L., Closset, I., Lasbleiz, M., Florez-Leiva, L., Cardinal, D., Leblanc, K., Fernandez, C., Lefèvre, D., Oriol, L., Blain, S., Quéguiner, B., and Dehairs, F.: Production regime and associated N cycling in the vicinity of Kerguelen Island, Southern Ocean, Biogeosciences, 12, 6515–6528, https://doi.org/10.5194/bg-12-6515-2015, 2015.
Chen, C.-C., Rodriguez, I. B., Chen, Y.-L. L., Zehr, J. P., Chen, Y.-R., Hsu, S.-T. D., Yang, S.-C., and Ho, T.-Y.: Nickel superoxide dismutase protects nitrogen fixation in Trichodesmium, Limnol. Oceanogr. Lett., 7, 363–371, https://doi.org/10.1002/lol2.10263, 2022.
Chiu, C. F., Archer, C., Vance, D., de Souza, G. F., Ellwood, M. J., and Janssen, D. J.: Elucidating the role of biogenic and authigenic phases in marine cycling of nickel with paired dissolved and particulate nickel isotopes, Earth Planet. Sc. Lett., 681, 119934, https://doi.org/10.1016/j.epsl.2026.119934, 2026.
Christians, S. and Kaltwasser, H.: Nickel-content of urease from Bacillus pasteurii, Arch. Microbiol., 145, 51–55, https://doi.org/10.1007/BF00413026, 1986.
Conover, R. J., Mumm, N., Bruecker, P., and MacKenzie, S.: Sources of urea in arctic seas: seasonal fast ice?, Mar. Ecol. Prog. Ser., 179, 55–69, https://doi.org/10.3354/meps179055, 1999.
Cutter, G., Casciotti, K., Croot, P., Geibert, W., Heimbürger, L.-E., Lohan, M., Planquette, H., and Van De Flierdt, T.: Sampling and the sample-handling protocoles for GEOTRACES cruises, 1–178, https://epic.awi.de/id/eprint/51363/1/Cookbook.pdf (last access: 21 July 2023), 2017.
Dehairs, F., Fripiat, F., Cavagna, A. J., Trull, T. W., Fernandez, C., Davies, D., Roukaerts, A., Fonseca Batista, D., Planchon, F., and Elskens, M.: Nitrogen cycling in the Southern Ocean Kerguelen Plateau area: Evidence for significant surface nitrification from nitrate isotopic compositions, Biogeosciences, 12, 1459–1482, https://doi.org/10.5194/bg-12-1459-2015, 2015.
de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Wincker, P., and Karsenti, E.: Eukaryotic plankton diversity in the sunlit ocean, Science, 348, 1–12, https://doi.org/10.1126/science.1261605, 2015.
Doré, H., Guyet, U., Leconte, J., Farrant, G. K., Alric, B., Ratin, M., Ostrowski, M., Ferrieux, M., Brillet-Guéguen, L., Hoebeke, M., Siltanen, J., Le Corguillé, G., Corre, E., Wincker, P., Scanlan, D. J., Eveillard, D., Partensky, F., and Garczarek, L.: Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies, ISME J., 17, 720–732, https://doi.org/10.1038/s41396-023-01386-0, 2023.
Dupont, C. L., Neupane, K., Shearer, J., and Palenik, B.: Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases, Environ. Microbiol., 10, 1831–1843, https://doi.org/10.1111/j.1462-2920.2008.01604.x, 2008a.
Dupont, C. L., Barbeau, K., and Palenik, B.: Ni uptake and limitation in marine Synechococcus strains., Appl. Environ. Microbiol., 74, 23–31, https://doi.org/10.1128/AEM.01007-07, 2008b.
Dupont, C. L., Buck, K. N., Palenik, B., and Barbeau, K.: Nickel utilization in phytoplankton assemblages from contrasting oceanic regimes, Deep-Sea Res. Pt. I, 57, 553–566, https://doi.org/10.1016/j.dsr.2009.12.014, 2010.
Egleston, E. S. and Morel, M. M.: Nickel limitation and zinc toxicity in a urea-grown diatom, Limnol. Oceanogr., 53, 2462–2471, https://doi.org/10.4319/lo.2008.53.6.2462, 2008.
Eren, A. M., Vineis, J. H., Morrison, H. G., and Sogin, M. L.: A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology, PLoS One, 8, e66643, https://doi.org/10.1371/journal.pone.0066643, 2013.
Eren, A. M., Esen, O. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., and Delmont, T. O.: Anvi'o: An advanced analysis and visualization platformfor 'omics data, PeerJ, 3, 1–29, https://doi.org/10.7717/peerj.1319, 2015.
Faure, E.: EmileFaure/Nickel_Omics, Zenodo [computer software], https://doi.org/10.5281/zenodo.21646714, 2026.
Faure, E., Pommellec, J., Noel, C., Cormier, A., Delpech, L.-M., Eren, M., Fernandez-Guerra, A., Chiara, V., Fourquez, M., Houssais, M.-N., Corinne, D. S., Frederick, G., Perdereau, A., Labadie, K., Guyet, U., Wincker, P., Poulain, J., Hassler, C., Lin, Y., Cassar, N., and Maignien, L.: Southern Ocean Reference Gene Catalogs, Zenodo [data set], https://doi.org/10.5281/zenodo.14181291, 2024.
Faure, E., Pommellec, J., Noel, C., Cormier, A., Delpech, L.-M., Eren, M., Fernandez-Guerra, A., Vanni, C., Fourquez, M., Houssais, M.-N., Da Silva, C., Gavory, F., Perdereau, A., Labadie, K., Wincker, P., Poulain, J., Hassler, C., Lin, Y., Cassar, N., and Maignien, L.: Water mass specific genes dominate the Southern Ocean microbiome, Nat. Commun., 17, 2025, https://doi.org/10.1038/s41467-026-69584-w, 2026a.
Faure, E., Lemaitre, N., Zamora, R., Archer, C., Sieber, M., Ellwood, M. et al.: Biological impacts on the nickel cycle in the Southern Ocean, figshare [data set], https://doi.org/10.6084/m9.figshare.29127848.v1, 2026b.
Fawcett, S. and Forrer, H.: Particulate organic carbon concentration in seawater profiles collected on board the R/V Akademik Tryoshnikov in the Southern Ocean during the austral summer of 2016/2017 as part of the Antarctic Circumnavigation Expedition (ACE), Zenodo, https://doi.org/10.5281/zenodo.3706710, 2020.
Fouilland, E., Gosselin, M., Rivkin, R. B., Vasseur, C., and Mostajir, B.: Nitrogen uptake by heterotrophic bacteria and phytoplankton in Arctic surface waters, J. Plankton Res., 29, 369–376, https://doi.org/10.1093/plankt/fbm022, 2007.
Fourquez, M., Janssen, D. J., Conway, T. M., Cabanes, D., Ellwood, M. J., Sieber, M., Trimborn, S., and Hassler, C.: Chasing iron bioavailability in the Southern Ocean: Insights from Phaeocystis antarctica and iron speciation, Sci. Adv., 9, eadf9696, https://doi.org/10.1126/sciadv.adf9696, 2023.
Fripiat, F., Elskens, M., Trull, T. W., Blain, S., Cavagna, A. J., Fernandez, C., Fonseca Batista, D., Planchon, F., Raimbault, P., Roukaerts, A., and Dehairs, F.: Significant mixed layer nitrification in natural iron-fertilized bloom of the Southern Ocean, Global Biogeochem. Cy., 29, https://doi.org/10.1002/2014GB005051, 2015.
GEOTRACES Intermediate Data Product Group: The GEOTRACES Intermediate Data Product 2025 (IDP2025), NERC EDS British Oceanographic Data Centre NOC [data set], https://doi.org/10.5285/42c92148-8d03-8be6-e063-7086abc09f0c, 2025.
Greening, C., Biswas, A., Carere, C. R., Jackson, C. J., Taylor, M. C., Stott, M. B., Cook, G. M., and Morales, S. E.: Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival, ISME J., 10, 761–777, https://doi.org/10.1038/ismej.2015.153, 2016.
Gueguen, B. and Rouxel, O.: The Nickel isotope composition of the authigenic sink and the diagenetic flux in modern oceans, Chem. Geol., 563, 120050, https://doi.org/10.1016/j.chemgeo.2020.120050, 2021.
Guidi, L., Chaffron, S., Bittner, L., Eveillard, D., Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J. R., Coelho, L. P., Cesar, J., Espinoza, I., Malviya, S., Sunagawa, S., Dimier, C., Kandels-lewis, S., Picheral, M., and Poulain, J.: Plankton networks driving carbon export in the oligotrophic ocean, Nature, 532, 465–470, https://doi.org/10.1038/nature16942, 2016.
Hassler, C. and Ellwood, M.: Nutrient concentration in seawater samples, collected from the underway supply, CTD and trace metal rosettes in the Southern Ocean during the austral summer of 2016/2017, on board the Antarctic Circumnavigation Expedition (ACE), Zenodo, https://doi.org/10.5281/ZENODO.3923586, 2020.
Ho, T.: Nickel limitation of nitrogen fixation in Trichodesmium, Limnol. Oceanogr., 58, 112–120, https://doi.org/10.4319/lo.2013.58.1.0112, 2013.
Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., Von Mering, C., and Bork, P.: Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper, Mol. Biol. Evol., 34, 2115–2122, https://doi.org/10.1093/molbev/msx148, 2017.
Hyatt, D., Chen, G.-L., Locascio, P. F., Land, M. L., Larimer, F. W., and Hauser, L. J.: Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, 11, 119, https://doi.org/10.1186/1471-2105-11-119, 2010.
Janssen, D. J., Sieber, M., Ellwood, M. J., Conway, T. M., Barrett, P. M., Chen, X., de Souza, G. F., Hassler, C. S., and Jaccard, S. L.: Trace metal and nutrient dynamics across broad biogeochemical gradients in the Indian and Pacific sectors of the Southern Ocean, Mar. Chem., 221, 103773, https://doi.org/10.1016/j.marchem.2020.103773, 2020.
John, S. G., Kelly, R. L., Bian, X., Fu, F., Smith, M. I., Lanning, N. T., Liang, H., Pasquier, B., Seelen, E. A., Holzer, M., Wasylenki, L., Conway, T. M., Fitzsimmons, J. N., Hutchins, D. A., and Yang, S.: The biogeochemical balance of oceanic nickel cycling, Nat. Geosci., 15, 906–912, https://doi.org/10.1038/s41561-022-01045-7, 2022.
John, S. G., Liang, H., Pasquier, B., Holzer, M., and Silva, S.: Biogeochemical fluxes of nickel in the global oceans inferred from a diagnostic model, Global Biogeochem. Cy., 38, https://doi.org/10.1029/2023GB008018, 2024.
Kong, Y., Zhang, R., Blain, S., and Obernosterer, I.: Seasonal dynamics in microbial trace metals transporters during phytoplankton blooms in the Southern Ocean, Environ. Microbiol., 26, e16695, https://doi.org/10.1111/1462-2920.16695, 2024.
Langmead, B. and Salzberg, S. L.: Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357–359, https://doi.org/10.1038/nmeth.1923, 2012.
Laso-Pérez, R., Rivas-Santisteban, J., Fernandez-Gonzalez, N., Mundy, C. J., Tamames, J., and Pedrós-Alió, C.: Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation, mBio, 16, e0074925, https://doi.org/10.1128/mbio.00749-25, 2025.
Lemaitre, N., Du, J., de Souza, G. F., Archer, C., and Vance, D.: The essential bioactive role of nickel in the oceans: Evidence from nickel isotopes, Earth Planet. Sc. Lett., 584, 117513, https://doi.org/10.1016/j.epsl.2022.117513, 2022.
Levine, N. M. and Leles, S. G.: Marine plankton metabolisms revealed, Nat. Microbiol., 6, 147–148, https://doi.org/10.1038/s41564-020-00856-x, 2021.
Li, D., Liu, C. M., Luo, R., Sadakane, K., and Lam, T. W.: MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics, 31, 1674–1676, https://doi.org/10.1093/bioinformatics/btv033, 2015.
Li, H., Tuo, S., Lu, M., and Ho, T.: The effects of Ni availability on H2 production and N2 fixation in a model unicellular diazotroph: The expression of hydrogenase and nitrogenase, Limnol. Oceanogr., 9999, 1–11, https://doi.org/10.1002/lno.12151, 2022.
Li, W. and Godzik, A.: Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658–1659, https://doi.org/10.1093/bioinformatics/btl158, 2006.
Love, M. I., Huber, W., and Anders, S.: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 1–21, https://doi.org/10.1186/s13059-014-0550-8, 2014.
Lu, J., Rincon, N., Wood, D. E., Breitwieser, F. P., Pockrandt, C., Langmead, B., Salzberg, S. L., and Steinegger, M.: Metagenome analysis using the Kraken software suite, Nat. Protoc., 17, 2815–2839, https://doi.org/10.1038/s41596-022-00738-y, 2022.
Mackey, D. J., O'Sullivan, J. E., Watson, R. J., and Dal Pont, G.: Trace metals in the Western Pacific: temporal and spatial variability in the concentrations of Cd, Cu, Mn and Ni, Deep-Sea. Res. Pt. 1, 49, 2241–2259, https://doi.org/10.1016/S0967-0637(02)00124-3, 2002.
Middag, R., Baar, H. J. W. De, Bruland, K. W., and van Heuven, S. M. A. C.: The distribution of nickel in the west-Atlantic Ocean, its relationship with phosphate and a comparison to cadmium and zinc, Front. Mar. Sci., 7, 1–17, https://doi.org/10.3389/fmars.2020.00105, 2020.
Morel, F. M. M., Lam, P. J., and Saito, M. A.: Trace metal substitution in marine phytoplankton, Annu. Rev. Earth Planet. Sci., 48, 491–517, https://doi.org/10.1146/annurev-earth-053018-060108, 2020.
Oksanen, J., Simpson, G. L., Blanchet, G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Solymos, P., Henrey, M., Stevens, H., Szoecs, E., Wagner, H., Barbour, M., Bedward, M., Bolker, B., Borcard, D., Carvalho, G., Chirico, M., De Caceres, M., Durand, S., Beatriz, H., Evangelista, A., Firtz-John, R., Friendly, M., Furneaux, B., Hannigan, G., Hill, M. O., Lahti, L., McGlinn, D., Ouellette, M.-H., Ribeiro Cunha, E., Smith, T., Stier, A., Ter Braak, C. J. F., and Weedon, J.: vegan: Community Ecology Package, R package version 2.6-2, 2022.
Orsi, A. H., Whitworth III, T., and Nowlin, W. D.: On the meridional extent and fronts of the Antarctic Circumpolar Current, Deep-Sea Res. Pt. I, 42, 641–673, 1995.
Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P. A., and Hugenholtz, P.: GTDB: An ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucl. Acids Res., 50, D785–D794, https://doi.org/10.1093/nar/gkab776, 2022.
Pommellec, J., Maignien, L., and Faure, E.: Antarctic Circumnavigation Expedition ecogenomics – METAGENOMES, IFREMER [data set], https://doi.org/10.12770/9c786963-e6a5-4a1c-95f8-1c6ab8a52d2b, 2021.
Price, N. M. and Morel, F. M. M.: Colimitation of phytoplankton growth by nickel and nitrogen, Limnol. Oceanogr., 36, 1071–1077, https://doi.org/10.4319/lo.1991.36.6.1071, 1991.
Ragsdale, S. W.: Nickel-based enzyme systems, J. Biol. Chem., 284, 18571–18575, https://doi.org/10.1074/jbc.R900020200, 2009.
Rickli, J., Janssen, D. J., Hassler, C., Ellwood, M. J., and Jaccard, S. L.: Chromium biogeochemistry and stable isotope distribution in the Southern Ocean, Geochim. Cosmochim. Acta, 262, 188–206, https://doi.org/10.1016/j.gca.2019.07.033, 2019.
Robinson, C. M., Huot, Y., Schuback, N., Ryan-Keogh, T. J., Thomalla, S. J., and Antoine, D.: High latitude Southern Ocean phytoplankton have distinctive bio-optical properties, Opt. Express, 29, 21084–21112, https://doi.org/10.1364/oe.426737, 2021.
Royo-Llonch, M., Sánchez, P., Ruiz-González, C., Salazar, G., Pedrós-Alió, C., Sebastián, M., Labadie, K., Paoli, L., M. Ibarbalz, F., Zinger, L., Churcheward, B., Babin, M., Bork, P., Boss, E., Cochrane, G., de Vargas, C., Gorsky, G., Grimsley, N., Guidi, L., Hingamp, P., Iudicone, D., Jaillon, O., Kandels, S., Not, F., Ogata, H., Pesant, S., Poulton, N., Raes, J., Sardet, C., Speich, S., Setmmann, L., Sullivan, M. B., Chaffron, S., Eveillard, D., Karsenti, E., Sunagawa, S., Wincker, P., Karp-Boss, L., Bowler, C., and Acinas, S. G.: Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean, Nat. Microbiol., 6, 1561–1574, https://doi.org/10.1038/s41564-021-00979-9, 2021.
Sarmiento, J. L., Gruber, N., Brzezinski, M. A., and Dunne, J. P.: High-latitude controls of thermocline nutrients and low latitude biological productivity, Nature, 427, 56–60, https://doi.org/10.1038/nature10605, 2004.
Sclater, F. R., Boyle, E., and Edmond, J. M.: On the marine geochemistry of nickel, Earth Planet. Sc. Lett., 31, 119–128, https://doi.org/10.1016/0012-821X(76)90103-5, 1976.
Sieber, M., Conway, T. M., de Souza, G. F., Hassler, C. S., Ellwood, M. J., and Vance, D.: High-resolution Cd isotope systematics in multiple zones of the Southern Ocean from the Antarctic Circumnavigation Expedition, Earth Planet. Sc. Lett., 527, 115799, https://doi.org/10.1016/j.epsl.2019.115799, 2019.
Sieber, M., Conway, T. M., de Souza, G. F., Hassler, C. S., Ellwood, M. J., and Vance, D.: Cycling of zinc and its isotopes across multiple zones of the Southern Ocean: Insights from the Antarctic Circumnavigation Expedition, Geochim. Cosmochim. Acta, 268, 310–324, https://doi.org/10.1016/j.gca.2019.09.039, 2020.
Sieber, M., Conway, T. M., de Souza, G. F., Hassler, C. S., Ellwood, M. J., and Vance, D.: Isotopic fingerprinting of biogeochemical processes and iron sources in the iron-limited surface Southern Ocean, Earth Planet. Sc. Lett., 567, 116967, https://doi.org/10.1016/j.epsl.2021.116967, 2021.
Sohrin, Y., Urushihara, S., Nakatsuka, S., Kono, T., Higo, E., Minami, T., Norisuye, K., and Umetani, S.: Multielemental determination of GEOTRACES key trace metals in seawater by ICPMS after preconcentration using an ethylenediaminetriacetic acid chelating resin, Anal. Chem., 80, 6267–6273, https://doi.org/10.1021/ac800500f, 2008.
Stanke, M., Steinkamp, R., Waack, S., and Morgenstern, B.: AUGUSTUS: A web server for gene finding in eukaryotes, Nucl. Acids Res., 32, 309–312, https://doi.org/10.1093/nar/gkh379, 2004.
Stirnimann, L., Bornman, T. G., Forrer, H. J., Mirkin, J., Ryan-Keogh, T. J., Flynn, R. F., Dorrington, R. A., Verheye, H. M., and Fawcett, S. E.: A Circum-Antarctic plankton isoscape: carbon export potential across the summertime Southern Ocean, Global Biogeochem. Cy., 38, e2023GB007808, https://doi.org/10.1029/2023GB007808, 2024.
Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., Cornejo-Castillo, F. M., Costea, P. I., Cruaud, C., D'Ovidio, F., Engelen, S., Ferrera, I., Gasol, J. M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B. T., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Pesant, S., Speich, S., Stemmann, L., Sullivan, M. B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S. G., and Bork, P.: Structure and function of the global ocean microbiome, Science, 348, 1–10, https://doi.org/10.1126/science.1261359, 2015.
Sutherland, K. M., Ward, L. M., Colombero, C. R., and Johnston, D. T.: Inter-domain horizontal gene transfer of nickel-binding superoxide dismutase, Geobiology, 19, 450–459, https://doi.org/10.1111/gbi.12448, 2021.
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., and the UniProt Consortium: UniRef clusters: A comprehensive and scalable alternative for improving sequence similarity searches, Bioinformatics, 31, 926–932, https://doi.org/10.1093/bioinformatics/btu739, 2015.
Takano, S., Tanimizu, M., Hirata, T., Shin, K.-C., Fukami, Y., Suzuki, K., and Sohrin, Y.: A simple and rapid method for isotopic analysis of nickel, copper, and zinc in seawater using chelating extraction and anion exchange, Anal. Chim. Acta, 967, 1–11, https://doi.org/10.1016/j.aca.2017.03.010, 2017.
Tan, S., Hu, X., Yin, P., and Zhao, L.: Photosynthetic inhibition and oxidative stress to the toxic Phaeocystis globosa caused by a diketopiperazine isolated from products of algicidal bacterium metabolism, J. Microbiol., 54, 364–375, https://doi.org/10.1007/s12275-016-6012-0, 2016.
Tortell, P., Maldonado, M., and Price, N.: The role of heterotrophic bacteria in iron-limited ocean ecosystems, Nature, 383, 330–332, https://doi.org/10.1038/383330a0, 1996.
Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., Kottmann, R., Mitchell, A., Sanchez, P., Siren, K., Steinegger, M., Glöckner, F. O., and Fernandez-Guerra, A.: Unifying the known and unknown microbial coding sequence space, Elife, 11, 1–60, https://doi.org/10.7554/eLife.67667, 2022.
Vernette, C., Lecubin, J., Sánchez, P., Acinas, S. G., Babin, M., Bork, P., Boss, E., Bowler, C., Cochrane, G., De Vargas, C., Gorsky, G., Guidi, L., Grimsley, N., Hingamp1, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Karp-Boss, L., Karsenti, E., Not, F., Ogata, H., Poulton, N., Pesant, S., Sardet, C., Speich, S., Stemmann, L., Sullivan, M. B., Sunagawa, S., Wincker, P., Sunagawa, S., Delmont, T. O., Pelletier, E., Pelletier, E., Hingamp, P., and Lescot, M.: The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes, Nucl. Acids Res., 50, W516–W526, https://doi.org/10.1093/nar/gkac420, 2022.
Wang, R. M., Archer, C., Bowie, A. R., and Vance, D.: Zinc and nickel isotopes in seawater from the Indian Sector of the Southern Ocean: The impact of natural iron fertilization versus Southern Ocean hydrography and biogeochemistry, Chem. Geol., 511, 452–464, https://doi.org/10.1016/j.chemgeo.2018.09.010, 2019.
White, R. A., Callister, S. J., Moore, R. J., Baker, E. S., and Jansson, J. K.: The past, present and future of microbiome analyses, Nat. Protocols, 11, 2049–2053, https://doi.org/10.1038/nprot.2016.148, 2016.
Yang, S., Kelly, R. L., Bian, X., Conway, T. M., Huang, K., Ho, T., Neibauer, J. A., Keil, R. G., Moffett, J. W., and John, S. G.: Lack of redox cycling for nickel in the water column of the Eastern tropical north pacific oxygen deficient zone: Insight from dissolved and particulate nickel isotopes, Geochim. Cosmochim. Acta, 309, 235–250, https://doi.org/10.1016/j.gca.2021.07.004, 2021.
Yang, S. C., Hawco, N. J., Pinedo-González, P., Bian, X., Huang, K.-F., Zhang, R., and John, S. G.: A new purification method for Ni and Cu stable isotopes in seawater provides evidence for widespread Ni isotope fractionation by phytoplankton in the North Pacific, Chem. Geol., 547, 119662, https://doi.org/10.1016/j.chemgeo.2020.119662, 2020.
Youn, H.-D., Kim, E.-J., Roe, J.-H., Hah, Y. C., and Kang, S.-O.: A novel nickel-containing superoxide dismutase from Streptomyces spp, Biochem. J., 318, 889–896, https://doi.org/10.1042/bj3180889, 1996.
Zecher, K., Hayes, K. R., and Philipp, B.: Evidence of interdomain ammonium cross-feeding from methylamine- and glycine betaine-degrading Rhodobacteraceae to Diatoms as a widespread Interaction in the Marine phycosphere, Front. Microbiol., 11, 1–15, https://doi.org/10.3389/fmicb.2020.533894, 2020.
Short summary
Nickel (Ni) is a micronutrient used by microorganisms in key metabolic processes. In the Southern Ocean, we observe heavy Ni isotope compositions in surface waters from lower latitudes and near the Mertz Glacier. Combined with metagenomics, we show that isotope variation may be due preferential uptake of Ni by microorganisms using Ni-SOD and Urease enzymes. This demonstrates how marine microbiology can influence the chemistry of the ocean.
Nickel (Ni) is a micronutrient used by microorganisms in key metabolic processes. In the...
Altmetrics
Final-revised paper
Preprint