Metabolic biochemical models of N fixation for sulfide oxidizers, methanogens, and methanotrophs
Document Type
Article
Publication Date
9-8-2025
Abstract
Dinitrogen (N) fixation provides bioavailable nitrogen to the biosphere. However, in some habitats (e.g., sediments), the metabolic pathways of organisms carrying out N fixation are unclear. We present metabolic models representing various chemotrophic N fixers, which simulate potential pathways of electron transport and energy flow, resulting in predictions of whole-cell stoichiometries. By balancing mass, electrons, and energy for metabolic half-reactions, we quantify the electron usage for nine N fixers. Our results demonstrate that all modeled organisms fix sufficient N for growth. Aerobic organisms allocate more electrons to N fixation and growth, yielding more biomass and fixing more N, while methanogens using acetate and organisms using sulfate allocate fewer electrons. This work can be applied to investigate the depth distribution of N fixers based on nutrient availability, complementing field measurements of biogeochemical processes and microbial communities.IMPORTANCEN fixation is an important process in the global N cycle. Researchers have developed models for heterotrophic and photoautotrophic N fixers, but there is a lack of modeling studies on chemoautotrophic N fixers. Here, we built nine biochemical models for different chemoautotrophic N fixers by combining different types of half-chemical reactions. We include three sulfide oxidizers using different electron acceptors (O, NO, and Fe), contributing to the sulfur, nitrogen, and iron cycles in the sediment. We have two methanogens using different substrates (H and acetate) and four methanotrophs using different electron acceptors (O, NO, Fe, and SO). By modeling these methane producers and users in the sediment and their N-fixing metabolic pathways, our work can provide insight for future carbon cycle studies. This study outlines various metabolic pathways that can facilitate N fixation, with implications for where in the environment they might occur.
Publication Title
mSystems
Recommended Citation
Gao, M.,
Berberich, M. E.,
Brown, R.,
Costello, D. M.,
Cotner, J. B.,
Damashek, J.,
Kittu, L. R.,
Pastor, A.,
Fulweiler, R. W.,
Scott, J. T.,
Marcarelli, A. M.,
&
Inomura, K.
(2025).
Metabolic biochemical models of N fixation for sulfide oxidizers, methanogens, and methanotrophs.
mSystems, e0074825.
http://doi.org/10.1128/msystems.00748-25
Retrieved from: https://digitalcommons.mtu.edu/michigantech-p2/2052