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 t..., All codes were written in the Wolfram Language platform using Mathematica 12., , # Hierarchical Structure within the Nnetwork Directory

```
yourdirectory/Nnetwork
│
├── Data
│ ├── DfG0.csv
│ ├── N_reactions.csv
│ ├── N_reactions_not_half.csv
│ └── REDOXlist
│ ├── REDOXlist.csv
│ ├── REDOXlist_Text.csv
│ ├── REDOXlist_kdef.csv
│ ├── divdata_all.csv
│ └── edges_all.csv
│
├── Programs
│ ├── 0_Make_Redox_reaction_List.nb
│ ├── 1_Preparation.nb
│ ├── 2_err_response.nb
│ ├── 3_time_constrained_response.nb
│ ├── 4_SS_export.nb
│ ├── 5_SS_visualize.nb
│ ├── Fig_2a.nb
│ ├── Fig_3b.nb
│ ├── Fig_S2.nb
│ ├── Fig_S3.nb
│ ├── Functions_X.nb
│ ├── Functions_1.nb
│ ├── Functions_2.nb
│ └── Functions_3.nb
│
└── Results
└── kdef_XX
└── Iin_YY
└── p_ZZ
```

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# Description of Each Directory and File

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## Data

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All CSV files in this directory are used as input data. These files are processed by `../Programs/0_Make_Redox_reaction_List.nb`.

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#### N\_reaction...