Data and code from: Thermodynamics underpinning the microbial community-level nitrogen networks

Nitrogen species often serve as crucial electron donors or acceptors in
microbial catabolism, enabling the synthesis of adenosine triphosphate
(ATP). Although theoretically any nitrogen redox reactions could be an
energy source, it remains unclear why specific reactions are predominantly
utilized. This study evaluates energetically superior reactions from 988
theoretically plausible combinations involving 11 nitrogen species, oxygen
gas, hydrogen ion, and water. Our analysis of the similarity between this
model-based energetically superior network and the actual microbial
community-level nitrogen network, reconstructed as a combination of
enzymatic reactions, showed increased link overlap rates with
thermodynamic weighting on reaction rates. In particular, existing
microbial reactions involving solely nitrogen species and additionally
oxygen, such as anaerobic ammonia oxidation (ANAMMOX) and complete and
partial nitrification, were frequently identified as energetically
superior among the examined reactions. The alignment of these reactions
with thermodynamically favorable outcomes underscores the critical role of
thermodynamics not only in individual metabolic processes but also in
shaping the broader network interactions within ecosystems, consequently
affecting biodiversity and ecological functions.