The PDF file includes:

• Section S1. Network representations of catalyzed biochemical reaction
• Section S2. Topological measures
• Fig. S1. Percentage of nodes in the LCC of a network versus the size of its LCC.
• Fig. S2. Reaction knockout for unipartite networks.
• Fig. S3. Additional network measures for individuals and ecosystems show universal scaling across levels.
• Fig. S4. Scaling of bipartite network structure for individuals and ecosystems.
• Fig. S5. Additional network measures for randomly sampled individuals and randomly sampled reactions.
• Fig. S6. Scaling of bipartite network structure for randomly sampled individuals and randomly sampled reactions.
• Fig. S7. Distributions of network sizes for each domain and across levels of organization.
• Fig. S8. Biochemical diversity and network topology measures for parsed datasets.
• Fig. S9. Biochemical diversity and network topology measures for domain-weighted frequency-sampled random reaction networks.
• Table S1. Percentage of networks in each dataset with x% of nodes in the LCC.
• Table S2. Distinguishability of individuals and ecosystems, and ecosystems and random genome networks.
• Legends for data files S1 to S2C
• References (73–75)

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Other Supplementary Material for this manuscript includes the following:

• Data file S1 (.csv format). Scaling parameters for topological measures with 95% confidence intervals.
• Data file S2A (.csv format). Summary of measured network properties, by domain.
• Data file S2B (.csv format). Summary of measured network properties, by levels (parsed data only).
• Data file S2C (.csv format). Summary of measured network properties, by levels (parsed data excluded).