Articles | Volume 19, issue 23
https://doi.org/10.5194/bg-19-5401-2022
© Author(s) 2022. 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-19-5401-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Controls on the relative abundances and rates of nitrifying microorganisms in the ocean
Emily J. Zakem
CORRESPONDING AUTHOR
Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
Barbara Bayer
Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
Wei Qin
Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
Alyson E. Santoro
Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
Yao Zhang
State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
Naomi M. Levine
Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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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
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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.
Travis Mellett, Justine Albers, Alyson Santoro, Pascal Salaun, Joseph Resing, Wenhao Wang, Alistar Lough, Alessandro Tagliabue, Maeve Lohan, Randelle Bundy, and Kristen Buck
EGUsphere, https://doi.org/10.5194/egusphere-2025-1798, https://doi.org/10.5194/egusphere-2025-1798, 2025
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Hydrothermal plumes of iron have been observed to persist in the deep ocean, but the exact mechanisms that contribute to the long-range transport of iron is not well defined. We collected plume waters from three different vent systems along the mid-Atlantic Ridge and monitored the temporal evolution of the physical and chemical forms of iron and its interaction with organic matter over time to learn about the mechanisms that control its dispersion.
Colleen L. Hoffman, Patrick J. Monreal, Justine B. Albers, Alastair J. M. Lough, Alyson E. Santoro, Travis Mellett, Kristen N. Buck, Alessandro Tagliabue, Maeve C. Lohan, Joseph A. Resing, and Randelle M. Bundy
Biogeosciences, 21, 5233–5246, https://doi.org/10.5194/bg-21-5233-2024, https://doi.org/10.5194/bg-21-5233-2024, 2024
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Hydrothermally derived iron can be transported kilometers away from deep-sea vents, representing a significant flux of vital micronutrients to the ocean. However, the mechanisms that support the stabilization of dissolved iron remain elusive. Using electrochemical, spectrometry, and genomic methods, we demonstrated that strong ligands exert an important control on iron in plumes, and high-affinity iron-binding siderophores were identified in several hydrothermal plume samples for the first time.
Weiyi Tang, Bess B. Ward, Michael Beman, Laura Bristow, Darren Clark, Sarah Fawcett, Claudia Frey, François Fripiat, Gerhard J. Herndl, Mhlangabezi Mdutyana, Fabien Paulot, Xuefeng Peng, Alyson E. Santoro, Takuhei Shiozaki, Eva Sintes, Charles Stock, Xin Sun, Xianhui S. Wan, Min N. Xu, and Yao Zhang
Earth Syst. Sci. Data, 15, 5039–5077, https://doi.org/10.5194/essd-15-5039-2023, https://doi.org/10.5194/essd-15-5039-2023, 2023
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Nitrification and nitrifiers play an important role in marine nitrogen and carbon cycles by converting ammonium to nitrite and nitrate. Nitrification could affect microbial community structure, marine productivity, and the production of nitrous oxide – a powerful greenhouse gas. We introduce the newly constructed database of nitrification and nitrifiers in the marine water column and guide future research efforts in field observations and model development of nitrification.
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.
Xiaofeng Dai, Mingming Chen, Xianhui Wan, Ehui Tan, Jialing Zeng, Nengwang Chen, Shuh-Ji Kao, and Yao Zhang
Biogeosciences, 19, 3757–3773, https://doi.org/10.5194/bg-19-3757-2022, https://doi.org/10.5194/bg-19-3757-2022, 2022
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This study revealed the distinct distribution patterns of six key microbial functional genes and transcripts related to N2O sources and sinks in four estuaries spanning the Chinese coastline, which were significantly constrained by nitrogen and oxygen concentrations, salinity, temperature, and pH. The community structure of the nosZ clade II was distinctly different from those in the soil and marine OMZs. Denitrification may principally control the N2O emissions patterns across the estuaries.
Cited articles
Armstrong, R. A.: Grazing limitation and nutrient limitation in marine
ecosystems: Steady state solutions of an ecosystem model with multiple food
chains, Limnol. Oceanogr., 39, 597–608,
https://doi.org/10.4319/lo.1994.39.3.0597, 1994. a
Babbin, A. R., Buchwald, C., Morel, F. M., Wankel, S. D., and Ward, B. B.:
Nitrite oxidation exceeds reduction and fixed nitrogen loss in anoxic
Pacific waters, Mar. Chem., 224, 103814, https://doi.org/10.1016/j.marchem.2020.103814,
2020. a, b
Baltar, F. and Herndl, G. J.: Ideas and perspectives: Is dark carbon fixation relevant for oceanic primary production estimates?, Biogeosciences, 16, 3793–3799, https://doi.org/10.5194/bg-16-3793-2019, 2019. a
Bayer, B., Vojvoda, J., Reinthaler, T., Reyes, C., Pinto, M., and Herndl,
G. J.: Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp.
nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the
class Nitrososphaeria, Int. J. Syst. Evol. Microb., 69, 1892–1902, https://doi.org/10.1099/ijsem.0.003360, 2019. a
Bayer, B., Saito, M. A., McIlvin, M. R., Lücker, S., Moran, D. M.,
Lankiewicz, T. S., Dupont, C. L., and Santoro, A. E.: Metabolic versatility
of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic
response to oxygen-limited conditions, ISME J., 15, 1025–1039,
https://doi.org/10.1038/s41396-020-00828-3, 2020. a, b
Beman, J. M., Leilei Shih, J., and Popp, B. N.: Nitrite oxidation in the
upper water column and oxygen minimum zone of the eastern tropical North
Pacific Ocean., ISME J., 7, 2192–205, https://doi.org/10.1038/ismej.2013.96,
2013. a
Berg, C., Listmann, L., Vandieken, V., Vogts, A., and Jürgens, K.:
Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a
pelagic redox gradient in the Baltic Sea, Front. Microbiol., 5, 786,
https://doi.org/10.3389/fmicb.2014.00786, 2015. a
Clayton, S., Dutkiewicz, S., Jahn, O., and Follows, M. J.: Dispersal, eddies,
and the diversity of marine phytoplankton, Limnol. Oceanogr., 3, 182–197, https://doi.org/10.1215/21573689-2373515, 2013. a
Dutkiewicz, S., Follows, M. J., and Bragg, J. G.: Modeling the coupling of
ocean ecology and biogeochemistry, Global Biogeochem. Cy., 23, 1–15,
https://doi.org/10.1029/2008GB003405, 2009. a
Dutkiewicz, S., Hickman, A. E., Jahn, O., Gregg, W. W., Mouw, C. B., and Follows, M. J.: Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model, Biogeosciences, 12, 4447–4481, https://doi.org/10.5194/bg-12-4447-2015, 2015a. a, b
Dutkiewicz, S., Morris, J. J., Follows, M. J., Scott, J., Levitan, O., Dyhrman,
S. T., and Berman-Frank, I.: Impact of ocean acidification on the structure
of future phytoplankton communities, Nat. Clim. Change, 5, 1002–1006,
https://doi.org/10.1038/nclimate2722, 2015b. a, b
Dutkiewicz, S., Hickman, A. E., Jahn, O., Henson, S., Beaulieu, C., and Monier,
E.: Ocean colour signature of climate change, Nat. Commun., 10,
578, https://doi.org/10.1038/s41467-019-08457-x, 2019. a
Follows, M. J., Dutkiewicz, S., Grant, S., and Chisholm, S. W.: Emergent
biogeography of microbial communities in a model ocean, Science, 315,
1843–1846, https://doi.org/10.1126/science.1138544, 2007. a
Füssel, J., Lam, P., Lavik, G., Jensen, M. M., Holtappels, M.,
Günter, M., and Kuypers, M. M. M.: Nitrite oxidation in the Namibian
oxygen minimum zone, ISME J., 6, 1200–1209, https://doi.org/10.1038/ismej.2011.178,
2012. a, b
Füssel, J., Lücker, S., Yilmaz, P., Nowka, B., van Kessel, M. A.
H. J., Bourceau, P., Hach, P. F., Littmann, S., Berg, J., Spieck, E., Daims,
H., Kuypers, M. M. M., and Lam, P.: Adaptability as the key to success for
the ubiquitous marine nitrite oxidizer Nitrococcus, Sci. Adv., 3,
e1700807, https://doi.org/10.1126/sciadv.1700807, 2017. a, b
Gruber, N.: The Marine Nitrogen Cycle: Overview and Challenges, in: Nitrogen
in the Marine Environment, edited by: Capone, D. G., Bronk, D. A., Mulholland,
M. R., and Carpenter, E. J., chap. 1, 1–50, Academic Press, 2nd edn.,
2008. a
Henson, S. A., Sanders, R., Madsen, E., Morris, P. J., Le Moigne, F., and
Quartly, G. D.: A reduced estimate of the strength of the ocean's biological
carbon pump, Geophys. Res. Lett., 38, L04606, https://doi.org/10.1029/2011GL046735,
2011. a, b
Horak, R. E. a., Qin, W., Schauer, A. J., Armbrust, E. V., Ingalls, A. E.,
Moffett, J. W., Stahl, D. a., and Devol, A. H.: Ammonia oxidation kinetics
and temperature sensitivity of a natural marine community dominated by
Archaea., ISME J., 7, 2023–33, https://doi.org/10.1038/ismej.2013.75, 2013. a
Karner, M. B., Delong, E. F., and Karl, D. M.: Archaeal dominance in the
mesopelagic zone of the Pacific Ocean, Nature, 409, 507–510,
https://doi.org/10.1038/35054051, 2001. a
Kirchman, D. L.: Uptake and Regeneration of Inorganic Nutrients by Marine
Heterotrophic Bacteria, in: Microbial Ecology of the Oceans, edited by:
Kirchman, D. L., Wiley-Liss, Inc, 261–288, 2000. a
Kitzinger, K., Marchant, H. K., Bristow, L. A., Herbold, C. W., Padilla, C. C.,
Kidane, A. T., Littmann, S., Daims, H., Pjevac, P., Stewart, F. J., Wagner,
M., and Kuypers, M. M.: Single cell analyses reveal contrasting life
strategies of the two main nitrifiers in the ocean, Nat. Commun.,
11, 767, https://doi.org/10.1038/s41467-020-14542-3, 2020. a, b, c, d, e
Koch, H., Galushko, A., Albertsen, M., Schintlmeister, A., Gruber-Dorninger,
C., Lücker, S., Pelletier, E., Le Paslier, D., Spieck, E., Richter,
A., Nielsen, P. H., Wagner, M., and Daims, H.: Microbial metabolism: Growth
of nitrite-oxidizing bacteria by aerobic hydrogen oxidation, Science, 345,
1052–1054, https://doi.org/10.1126/science.1256985, 2014. a, b
Koch, H., Lücker, S., Albertsen, M., Kitzinger, K., Herbold, C., Spieck,
E., Nielsen, P. H., Wagner, M., and Daims, H.: Expanded metabolic
versatility of ubiquitous nitrite-oxidizing bacteria from the genus
Nitrospira., P. Natl. Acad. Sci. USA, 112, 11371–11376, https://doi.org/10.1073/pnas.1506533112, 2015. a, b
Könneke, M., Bernhard, A. E., De La Torre, J. R., Walker, C. B.,
Waterbury, J. B., and Stahl, D. A.: Isolation of an autotrophic
ammonia-oxidizing marine archaeon, Nature, 437, 543–546,
https://doi.org/10.1038/nature03911, 2005. a
Kwiecinski, J. V. and Babbin, A. R.: A High-Resolution Atlas of the Eastern
Tropical Pacific Oxygen Deficient Zones, Global Biogeochem. Cy., 35,
https://doi.org/10.1029/2021GB007001, 2021. a
Laperriere, S. M., Morando, M., Capone, D. G., Gunderson, T., Smith, J. M., and
Santoro, A. E.: Nitrification and nitrous oxide dynamics in the Southern
California Bight, Limnol. Oceanogr., 66, 1–14,
https://doi.org/10.1002/lno.11667, 2020. a
Litchman, E., Klausmeier, C. A., Schofield, O. M., and Falkowski, P. G.: The
role of functional traits and trade-offs in structuring phytoplankton
communities: scaling from cellular to ecosystem level., Ecol. Lett., 10,
1170–1181, https://doi.org/10.1111/j.1461-0248.2007.01117.x, 2007. a, b, c
Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R., and Stahl,
D. A.: Ammonia oxidation kinetics determine niche separation of nitrifying
Archaea and Bacteria., Nature, 461, 976–979, https://doi.org/10.1038/nature08465, 2009. a, b
Middelburg, J. J.: Chemoautotrophy in the ocean, Geophys. Res. Lett., 38, L24604, https://doi.org/10.1029/2011GL049725, 2011. a
Newell, S. E., Fawcett, S. E., and Ward, B. B.: Depth distribution of ammonia
oxidation rates and ammonia-oxidizer community composition in the Sargasso
Sea, Limnol. Oceanogr., 58, 1491–1500,
https://doi.org/10.4319/lo.2013.58.4.1491, 2013. a, b
Pachiadaki, M. G., Sintes, E., Bergauer, K., Brown, J. M., Record, N. R., Swan,
B. K., Mathyer, M. E., Hallam, S. J., Lopez-Garcia, P., Takaki, Y., Nunoura,
T., Woyke, T., Herndl, G. J., and Stepanauskas, R.: Major role of
nitrite-oxidizing bacteria in dark ocean carbon fixation, Science, 358,
1046–1051, 2017. a, b, c, d
Paulmier, A. and Ruiz-Pino, D.: Oxygen minimum zones (OMZs) in the modern
ocean, Prog. Oceanogr., 80, 113–128,
https://doi.org/10.1016/j.pocean.2008.08.001, 2009. a
Qin, W., Amin, S. a., Martens-Habbena, W., Walker, C. B., Urakawa, H., Devol,
a. H., Ingalls, a. E., Moffett, J. W., Armbrust, E. V., and Stahl, D. a.:
Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and
wide ecotypic variation, P. Natl. Acad. Sci. USA,
111, 12504–12509, https://doi.org/10.1073/pnas.1324115111, 2014. a
Rittman, B. E. and McCarty, P. L.: Environmental Biotechnology: Principles and
Applications, McGraw-Hill, ISBN 1259002888, 9781259002885, 2001. a
Saito, M. A., McIlvin, M. R., Moran, D. M., Santoro, A. E., Dupont, C. L.,
Rafter, P. A., Saunders, J. K., Kaul, D., Lamborg, C. H., Westley, M.,
Valois, F., and Waterbury, J. B.: Abundant nitrite-oxidizing metalloenzymes
in the mesopelagic zone of the tropical Pacific Ocean, Nat. Geosci.,
13, 355–362, https://doi.org/10.1038/s41561-020-0565-6, 2020. a, b
Santoro, A. E. and Casciotti, K. L.: Enrichment and characterization of
ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and
stable isotope fractionation, ISME J., 5, 1796–808,
https://doi.org/10.1038/ismej.2011.58, 2011. a, b
Santoro, A. E., Casciotti, K. L., and Francis, C. A.: Activity, abundance and
diversity of nitrifying archaea and bacteria in the central California
Current., Environ. Microbiol., 12, 1989–2006,
https://doi.org/10.1111/j.1462-2920.2010.02205.x, 2010. a, b, c
Santoro, A. E., Saito, M. A., Goepfert, T. J., Lamborg, C. H., Dupont, C. L.,
and Ditullio, G. R.: Thaumarchaeal ecotype distributions across the
equatorial Pacific Ocean and their potential roles in nitrification and
sinking flux attenuation, Limnol. Oceanogr., 62, 1984–2003,
https://doi.org/10.1002/lno.10547, 2017. a
Santoro, A. E., Richter, R. A., and Dupont, C. L.: Planktonic marine archaea,
Annu. Rev. Mar. Sci., 11, 131–158,
https://doi.org/10.1146/annurev-marine-121916-063141, 2019. a, b, c
Santoro, A. E., Buchwald, C., Knapp, A. N., Berelson, W. M., Capone, D. G., and
Casciotti, K. L.: Nitrification and Nitrous Oxide Production in the Offshore
Waters of the Eastern Tropical South Pacific, Global Biogeochem. Cy.,
35, 1–21, https://doi.org/10.1029/2020GB006716, 2021. a, b, c
Schlitzer, R.: Applying the adjoint method for biogeochemical modeling: Expot
of particulate matter in the World Ocean, Geophys. Monogr., 114,
107–124, https://doi.org/10.1029/GM114p0107, 2000. a, b
Séférian, R., Berthet, S., Yool, A., Palmiéri, J., Bopp, L.,
Tagliabue, A., Kwiatkowski, L., Aumont, O., Christian, J., Dunne, J., Gehlen,
M., Ilyina, T., John, J. G., Li, H., Long, M. C., Luo, J. Y., Nakano, H.,
Romanou, A., Schwinger, J., Stock, C., Santana-Falcón, Y., Takano, Y.,
Tjiputra, J., Tsujino, H., Watanabe, M., Wu, T., Wu, F., and Yamamoto, A.:
Tracking Improvement in Simulated Marine Biogeochemistry Between CMIP5 and
CMIP6, Current Climate Change Reports, 6, 95–119,
https://doi.org/10.1007/s40641-020-00160-0, 2020. a
Siegel, D., Buesseler, K., Doney, S., Sailley, S., Behrenfeld, M., and Boyd,
P.: Global assessment of ocean carbon export by combining satellite
observations and food-web models, Global Biogeochem. Cy., 28,
181–196, https://doi.org/10.1002/2013GB004743, 2014. a, b
Smith, J. M., Damashek, J., Chavez, F. P., and Francis, C. A.: Factors
influencing nitrification rates and the abundance and transcriptional
activity of ammonia-oxidizing microorganisms in the dark northeast Pacific
Ocean, Limnol. Oceanogr., 61, 596–609, https://doi.org/10.1002/lno.10235,
2016. a
Spieck, E., Keuter, S., Wenzel, T., Bock, E., and Ludwig, W.: Characterization
of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a
member of the newly proposed phylum “Nitrospinae”, Syst. Appl. Microbiol., 37, 170–176, https://doi.org/10.1016/j.syapm.2013.12.005, 2014. a
Stephens, B. M., Wankel, S. D., Beman, J. M., Rabines, A. J., Allen, A. E., and
Aluwihare, L. I.: Euphotic zone nitrification in the California Current
Ecosystem, Limnol. Oceanogr., 65, 790–806,
https://doi.org/10.1002/lno.11348, 2020. a
Sun, X., Ji, Q., Jayakumar, A., and Ward, B. B.: Dependence of nitrite
oxidation on nitrite and oxygen in low-oxygen seawater, Geophys. Res.
Lett., 44, 7883–7891, https://doi.org/10.1002/2017GL074355, 2017. a
Swan, B. K., Martinez-Garcia, M., Preston, C. M., Sczyrba, A., Woyke, T., Lamy,
D., Reinthaler, T., Poulton, N. J., Masland, E. D. P., Gomez, M. L.,
Sieracki, M. E., DeLong, E. F., Herndl, G. J., and Stepanauskas, R.:
Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the
dark ocean, Science, 333, 1296–1300, https://doi.org/10.1126/science.1203690, 2011. a
Verdy, A., Follows, M., and Flierl, G.: Optimal phytoplankton cell size in an
allometric model, Mar. Ecol. Prog. Ser., 379, 07909,
https://doi.org/10.3354/meps07909, 2009. a
Volk, T. and Hoffert, M. I.: Ocean carbon pumps: analysis of relative
strengths and efficiencies in ocean-driven atmospheric CO2 changes, in: The
carbon cycle and atmospheric CO2: Natural variations Archean to present.
Chapman conference papers, 1984, edited by: Sundquist, E. T. and Broecker,
W. S., American Geophysical Union, 99–110, 1985. a
Ward, B. A., Dutkiewicz, S., Jahn, O., and Follows, M. J.: A size-structured
food-web model for the global ocean, Limnol. Oceanogr., 57,
1877–1891, https://doi.org/10.4319/lo.2012.57.6.1877, 2012. a, b, c
Ward, B. B.: Nitrogen transformations in the Southern California Bight, Deep
Sea Res., 34, 785–805,
https://doi.org/10.1016/0198-0149(87)90037-9, 1987. a, b
Ward, B. B.: Temporal variability in nitrification rates and related
biogeochemical factors in Monterey Bay, California, USA, Mar. Ecol.
Prog. Ser., 292, 97–109, https://doi.org/10.3354/meps292097, 2005. a
Watson, S. W. and Waterbury, J. B.: Characteristics of two marine nitrite
oxidizing bacteria, Nitrospina gracilis nov. gen. nov. sp. and Nitrococcus
mobilis nov. gen. nov. sp, Arch. Mikrobiol., 77, 203–230,
https://doi.org/10.1007/BF00408114, 1971. a
Wuchter, C., Abbas, B., Coolen, M. J. L., Herfort, L., Van, J., Timmers, P.,
Strous, M., Teira, E., Herndl, G. J., Middelburg, J. J., Schouten, S., and
Damsté, J. S. S.: Archaeal nitrification in the ocean, P. Natl. Acad. Sci. USA, 103, 12317–12322,
https://doi.org/10.1073/pnas.0600756103, 2006. a, b, c
Wunsch, C. and Heimbach, P.: Practical global oceanic state estimation,
Physica D, 230, 197–208, https://doi.org/10.1016/j.physd.2006.09.040, 2007. a
Yool, A., Martin, A. P., Fernandez, C., and Clark, D.: The significance of
nitrification for oceanic new production, Nature, 447, 999–1002,
https://doi.org/10.1038/nature05885, 2007.
a
Zakem, E. J.: eco-nitrify_Cfixation, https://doi.org/10.5281/zenodo.6384810, Zenodo [code], last access: 25 March 2022. a
Zakem, E. J., Al-Haj, A., Church, M. J., Van Dijken, G. L., Dutkiewicz, S.,
Foster, S. Q., Fulweiler, R. W., Mills, M. M., and Follows, M. J.:
Ecological control of nitrite in the upper ocean, Nat. Commun., 9,
1206, https://doi.org/10.1038/s41467-018-03553-w, 2018. a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x
Zakem, E. J., Mahadevan, A., Lauderdale, J. M., and Follows, M. J.: Stable
aerobic and anaerobic coexistence in anoxic marine zones, ISME J., 14,
288–301, https://doi.org/10.1038/s41396-019-0523-8, 2019. a
Zakem, E. J., Polz, M. F., and Follows, M. J.: Redox-informed models of global
biogeochemical cycles, Nat. Commun., 11, 5680,
https://doi.org/10.1038/s41467-020-19454-w, 2020. a
Zhang, Y., Qin, W., Hou, L., Zakem, E. J., Wan, X., Zhao, Z., Liu, L., Hunt,
K. A., Jiao, N., Kao, S.-J., Tang, K., Xie, X., Shen, J., Li, Y., Chen, M.,
Dai, X., Liu, C., Deng, W., Dai, M., Ingalls, A. E., Stahl, D. A., and
Herndl, G. J.: Nitrifier adaptation to low energy flux controls inventory of
reduced nitrogen in the dark ocean, P. Natl. Acad. Sci. USA, 117, 4823–4830, 2020. a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q
Short summary
We use a microbial ecosystem model to quantitatively explain the mechanisms controlling observed relative abundances and nitrification rates of ammonia- and nitrite-oxidizing microorganisms in the ocean. We also estimate how much global carbon fixation can be associated with chemoautotrophic nitrification. Our results improve our understanding of the controls on nitrification, laying the groundwork for more accurate predictions in global climate models.
We use a microbial ecosystem model to quantitatively explain the mechanisms controlling observed...
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