A) Map of the coring locations within the Plum Island Estuary Long Term Ecological Research (PIE LTER) site and B) Details of core sampling and the bioinformatic approach used to identify metabolic complementarity among co-occurring MAGs within the sediment layers.

The tree at the center of the display shows the phylogenetic relationship among all MAGs.

The innermost ring is a histogram the single copy gene completion estimate (range = 0-100%), followed by redundancy (range = 0-10%), total length of the genome (range = 0-7.6Mbp). The “Depth proportion” ring shows the proportion of the total reads mapped to a MAG from each depth. The outermost ring shows the phylum level taxonomy as a color bar with matching text. Arrows are positioned adjacent to phyla names with split positions in the tree.

Summary of redundant genome recovery per sample.

The line plot at the top of the figure (dark gray and black) shows how many genomes were grouped into the dereplicated genome cluster. The second layer from the top represents the phylum level classification for the representative MAG in the cluster. The heat map layers show the proportion of samples where a MAG in the dereplicated genome cluster was recovered. The key indicating how many of the same MAGs (identified by dRep) were collected per depth is shown on the right. The MAGs are organized according to the phylogenetic reconstruction outlined in the methods section. The phylum color key is shown at the bottom of the figure and the gray triangles above the phylum color align with the heatmap.

A.) The random matrix theory derived co-occurrence network, based on MAG relative abundance. The point size (genome size), color (phylum), and shape (module) are used to describe each MAG in the network. All connections are significant and positive. Ellipses are used to clarify the modules. B) The NMDS ordination of MAGs included in the network based on KEGG functional potential. Both panels show the same ordination, with the left panel colors indicating the phylum classification and right, the module assignment. The key adjacent to panel A applies to the colors used for taxa and modules shown in panel B.

Bubble plots for the cumulative phylum level relative abundance of MAGs contained in each of the network modules.

Relative abundance (size of the bubble) indicates the percentage of reads mapped to the MAGs glommed at the phylum level relative to the number of reads mapped to the sample. The colors for each phylum are congruent across all four panels. The box-whisker relative abundance plots nested within each box describe the relative abundance of MAGs in the module at each depth.

A) The submodule of tightly correlated MAGs with connectivity among the four subsurface modules. The shape in the network indicates module origin of each MAG, the size represents the number of genes in the MAG, and the color is used for taxonomic classification. Gray lines connecting the MAGs represent significant positive correlations. B.) Bubble plot of relative abundance for MAG phylum level relative abundance within the vertical profile of the sediment. The color of the bubble is based on the phylum classification and matches the color in panel A. C) Select functional annotation for all MAGs in the network. Functional potential of each MAG in the network is described as presence (black bar) or absence (gray bar) for each function. Major functional categories are shown on the left of the panel, and the taxonomic classification of each MAG is shown at the top. MAGs are organized according to presence-absence of the genes in the display and the hierarchical clustering tree is displayed at the bottom of the panel.