Metabolic biochemical models of N2 fixation for sulfide oxidizers, methanogens, and methanotrophs

Abstract

Dinitrogen (N₂) fixation provides bioavailable nitrogen to the biosphere. However, in some habitats (e.g., sediments), the metabolic pathways of organisms carrying out N₂ fixation are unclear. We present metabolic models representing various chemotrophic N₂ 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 N₂ fixers. Our results demonstrate that all modeled organisms fix sufficient N₂ for growth. Aerobic organisms allocate more electrons to N₂ fixation and growth, yielding more biomass and fixing more N₂, while methanogens using acetate and organisms using sulfate allocate fewer electrons. This work can be applied to investigate the depth distribution of N₂ fixers based on nutrient availability, complementing field measurements of biogeochemical processes and microbial communities.IMPORTANCEN₂ fixation is an important process in the global N cycle. Researchers have developed models for heterotrophic and photoautotrophic N₂ fixers, but there is a lack of modeling studies on chemoautotrophic N₂ fixers. Here, we built nine biochemical models for different chemoautotrophic N₂ fixers by combining different types of half-chemical reactions. We include three sulfide oxidizers using different electron acceptors (O₂, NO₃^-, and Fe³⁺), contributing to the sulfur, nitrogen, and iron cycles in the sediment. We have two methanogens using different substrates (H₂ and acetate) and four methanotrophs using different electron acceptors (O₂, NO₃^-, Fe³⁺, and SO₄^2-). By modeling these methane producers and users in the sediment and their N₂-fixing metabolic pathways, our work can provide insight for future carbon cycle studies. This study outlines various metabolic pathways that can facilitate N₂ fixation, with implications for where in the environment they might occur.

Keywords: CFM-CNF; N2 fixation; biochemical model; electron allocation; energy; methanogens; methanotrophs; sediment; sulfide oxidizers.