Fig 1.
A graphical outline of the hypothesis, methods and results of this study.
Fig 2.
Case examples illustrating different scenarios for MAG-V9 OTU match scenarios, results for the “rho” proportionality metrics (see the detailed description of each scenario in the text).
Results for Spearman’s correlation are shown in S10 Fig in S1 File. A: The proportionality of the 10 best V9 OTU matches within two taxonomic subsets, for each MAG. Proportionality values of V9 OTUs paired with MAGs are shown on the vertical axis, and the rank of the match on the horizontal axis (log scale). Colours represent the rank of the V9 OTU taxonomic subset (from higher to lower rank: supergroup, taxogroup 1, taxogroup 2, taxogroup 3, or genus). Different groups have different taxonomic levels represented, depending on the resolution of the taxonomic assignments of the V9 OTUs in the group (see S1 Table in S1 File). The filled ribbons represent the mean +/- standard deviation of proportionality obtained for the shuffled datasets of a given taxonomic subset (negative controls). Lines for the MAGs highlighted in a given scenario are indicated with large points (two lines for each highlighted MAG: one for each taxonomic subset). B: The number of MAGs potentially matching a given V9 OTU. The top 10 best-ranked MAG-V9 OTU matches within the two lowest-ranked taxonomic subsets are represented as tiles. The horizontal axis represents V9 OTUs included in the taxonomic subset, the vertical axis shows MAGs, and each individual tile thus corresponds to a given MAG-V9 OTU pair. The fill colour of each tile shows the proportionality value of the match (the scale may differ among subfigures). This plot illustrates the uniqueness of each match: if several MAGs match the same V9 OTU, several tiles will be present at the same coordinate on the horizontal axis, across different points on the vertical axis and vice versa. The rank of the V9 OTU taxonomic subset presented is indicated at the top of each plot. MAGs in candidate matches from panel A are highlighted with orange dashes. Phylogenetic trees on the left of each plot represent the genetic relatedness of MAGs in each taxonomic subset, with tree topology and branch lengths from the RNA-polymerase multigene phylogeny of [15]. C: Relative abundances across stations for MAGs and V9 OTUs from candidate pairs. Each line represents a smoothed relative abundance of a single feature (either a MAG or a V9 OTU) from candidate matches. Samples on each plot are ranked based on the abundance of the MAG. Different colours represent different MAGs and V9 OTUs.
Fig 3.
Classification of MAGs into MAG/OTU match scenarios.
The taxonomic relationship (based on UniEuk; [52]) among groups of input MAGs is displayed on the left. Columns indicate: the number of MAGs in each input group, the number of OTUs in the lower-rank and second-lower-rank taxonomic subsets against which MAGs were searched for potential matches, and the distribution of MAG/OTU matches into 4 possible scenarios. Only the MAG/OTU matches meeting the criteria described in the text are included (as such, the number of classified MAGs may be lower than the total number of MAGs in a group). Within each scenario, matches are divided by confidence: high, medium, low and very low probability of being a true match.