## Supplementary Tables
**Supplementary Table 1.** Assembly group description, sample inclusion, and basic assembly statistics.
**Supplementary Table 2.** TOPAZ Eukaryotic MAG taxonomy, genomic characteristics (e.g., total length, GC content, N50, number of predicted proteins), and estimated completeness and contamination.
**Supplementary Table 3.** TOPAZ Prokaryotic MAG taxonomy as estimated by GTDB, dataset indication (non-redundant representatives (NR), total size, and estimated completeness and contamination.
**Supplementary Table 4.** TOPAZ Prokaryotic MAG summary of recovered MAGs across phyla. Total counts are shown for all MAGs (All), the non-redundant subset of MAGs (AllNR), and the high-quality, non-redundant MAGs (HQNR).
**Supplementary Table 5.** Vita selected KOs and their associated heterotrophy, phototrophy, and mixotrophy ratios as described in equations 1-4.
**Supplementary Table 6.** Eukaryotic TOPAZ MAG predicted trophic status and heterotrophy index (H-index).
**Supplementary Table 7.** Network analysis community composition.
**Supplementary Table 8.** Eukaryotic cluster groups derived from average nucleotide identity clustering of eukaryotic TOPAZ MAGs with the Delmont eukaryotic MAGs (Delmont et al. 2022) based on an ANI cutoff of 99%.
**Supplementary Table 9.** Environmental correlations with network derived communities.
## Supplementary Datasets
**Supplementary Dataset 1**. Reference transcriptomes used in the construction and testing of the trophic model. The manually annotated trophic status and details, relevant reference literature, and taxonomic information are noted. Additionally, a presence/absence matrix is provided for all eukaryotic KEGG ids considered here.
**Supplementary Dataset 2.** KEGG presence and absence for the TOPAZ eukaryotic MAGs, as was used in the trophic model.
**Supplementary Dataset 3.** Pfam presence and absence across the TOPAZ eukaryotic MAGs.
**Supplementary Dataset 4.** Burns model (Burns et al. 2018) predicted prototrophy, photosynthetic ability, and phagocytosis for the TOPAZ eukaryotic MAGs.
