Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea

Abstract

Marine ammonia-oxidizing archaea (AOA) play an important role in the global nitrogen cycle by obtaining energy for biomass production from CO2 via oxidation of ammonium. The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1, which represents the globally distributed AOA in the ocean, provided an opportunity for uncovering the contributions of those AOA to carbon and nitrogen cycles in ocean. Although several ammonia oxidation pathways have been proposed for SCM1, little is known about its ATP production efficiency. Here, based on the published genome of Nitrosopumilus maritimus SCM1, a genome-scale metabolic model named NmrFL413 was reconstructed. Based on the model NmrFL413, the estimated ATP/NH4+ yield (0.149–0.276 ATP/NH4+) is tenfold lower than the calculated theoretical yield of the proposed ammonia oxidation pathways in marine AOA (1.5–1.75 ATP/NH4+), indicating a low energy production efficiency of SCM1. Our model also suggested the minor contribution of marine AOA to carbon cycle comparing with their significant contribution to nitrogen cycle in the ocean.Electronic supplementary materialThe online version of this article (10.1186/s13568-018-0635-y) contains supplementary material, which is available to authorized users.

Carbon content, carbon fixation yield and dissolved organic carbon release from diverse marine nitrifiers

“…DIC fixation yields of two Nitrosopumilus strains were recently reported to be up to 10 times higher (0.18–1.2, Meador et al 2020 ) compared to values in our study and previously published values of N. adriaticus NF5 (0.1, Bayer et al 2019 c ) and a Nitrosarchaeum enrichment culture (0.1, Berg et al 2014 ). However, such high values would require unrealistically high ATP yields (up to 2.4 mol ATP per mole NH 3 oxidized) compared to reported estimates of 0.15–0.28 ATP/NH 3 (mol/mol) (Li et al 2018 ).…”

Carbon content, carbon fixation yield and dissolved organic carbon release from diverse marine nitrifiers

“…However, such high values would require unrealistically high ATP yields (up to 2.4 moles ATP per mole NH3 oxidized) compared to reported estimates of 0.15-0.28 ATP/NH3 (mol/ mol) (Li et al 2018). times higher DIC fixation yields of NOB compared to incubations conducted until late exponential growth (when NO2was completely oxidized) (Fig.…”

Cultivo e estudo de diversidade e distribuição de arqueias oxidantes de amônia em ambientes marinhos

“…Essa via é mais efetivamente energética para fixação de carbono em comparação com o ciclo de Calvin-Benson, encontrado na maioria da bactéria quimiolitotróficas, cianobactérias e outras arqueias. (KÖNNEKE et al, 2014;BARBOSA;GOMEZ;TORRES, 2018;LI et al, 2018b).…”