04 Jul 2022
04 Jul 2022
Status: this preprint is currently under review for the journal BG.

Controls on the relative abundances and rates of nitrifying microorganisms in the ocean

Emily J. Zakem1,2, Barbara Bayer3, Wei Qin4, Alyson Santoro5, Yao Zhang6, and Naomi M. Levine2 Emily J. Zakem et al.
  • 1Department of Global Ecology, Carnegie Institution for Science, Stanford, CA USA
  • 2Department of Biological Sciences, University of Southern California, Los Angeles, CA USA
  • 3Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
  • 4Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK USA
  • 5Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
  • 6State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China

Abstract. Nitrification controls the oxidation state of bioavailable nitrogen. Distinct clades of chemoautotrophic microorganisms – predominantly, ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) – regulate the two steps of nitrification in the ocean, but explanations for their observed relative abundances and nitrification rates remain incomplete, and their contributions to the global marine carbon cycle via carbon fixation remain unresolved. Using a mechanistic microbial ecosystem model with nitrifying functional types, we derive simple expressions for the controls on AOA and NOB in the deep, oxygenated open ocean. The relative yields, loss rates, and cell quotas of AOA and NOB control their relative abundances, though we do not need to invoke a difference in loss rates to explain the observed relative abundances. The supply of ammonium, not the traits of AOA or NOB, controls the relatively equal ammonia- and nitrite-oxidation rates at steady state. The relative yields of AOA and NOB alone set their relative bulk carbon fixation rates in the water column. The quantitative relationships are consistent with multiple in situ datasets. In a complex global ecosystem model, nitrification emerges dynamically across diverse ocean environments, and ammonia and nitrite oxidation and their associated carbon fixation rates are decoupled due to physical transport and complex ecological interactions in some environments. Nevertheless, the simple expressions capture global patterns to first order. The model provides a mechanistically estimated upper bound on global chemoautotrophic carbon fixation of 0.2–0.5 Pg C yr-1, which is on the low end of the wide range of previous estimates. Modeled carbon fixation by NOB (about 0.1 Pg C yr-1) is substantially lower than by AOA (0.2–0.3 Pg C yr-1), predominantly reflecting the relative yields. The simple expressions derived here can be used to quantify the biogeochemical impacts of additional metabolic pathways (i.e. mixotrophy) of nitrifying clades and to identify alternative carbon-fixing metabolisms in the deep ocean.

Emily J. Zakem et al.

Status: open (until 15 Aug 2022)

Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse
  • RC1: 'Comment on bg-2022-139', Anonymous Referee #1, 01 Aug 2022 reply
  • RC2: 'Comment on bg-2022-139', Christopher Somes, 04 Aug 2022 reply

Emily J. Zakem et al.

Emily J. Zakem et al.


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Short summary
We use a microbial ecosystem model to quantitatively explain the 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.