Fig 1.
Taxonomic diversity features of U. gibba and related environments.
(A) Alpha diversity measurements for U. gibba’s trap (Ugt), its surroundings (Ugm), Plant-associated (Pa), Water (W), and Soil (S) microbiomes. We made use of both 16S rRNA gene (circles) fragment assignments and lowest common ancestor (LCA, squares). Both Ugt and Ugm shows the largest expected number of species (Chao1) of the compared environments, although Ugm is more diverse (Shannon) than Ugt, and Ugt is in a less dominated environment than Ugm (Simpson).
Fig 2.
Most abundant phyla assigned for U. gibba's trap.
U. gibba's trap (Ugt), its surroundings (Ugm), and other related microbiomes. Independently of the classification method used the most abundant phyla are: Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Cyanobacteria.
Fig 3.
Family diversity and fragment recruitment to 1434 reference pan-genomes.
The most abundant species are shown using an identity >90% of 6 frame translations for both reference and queries. In the bottom line of fragment recruitments, we can observe the consensus sequence comparing with the reference pan-genome.
Fig 4.
U. gibba's traps are a unique environment according to its taxonomic profile.
Correspondence analysis using both (A) 16S rRNA gene, and (B) Lowest Common Ancestor (LCA) profiles families. It can be seen that the U. gibba's traps (Ugt) is a unique environment, this is more evident in the LCA bi-plot, where it stands on its own quadrant. This distribution explains a total of 66.71% variance. The bi-plots show the closest families to the Ugt. (C) 16S rRNA gene clustering dendrogram (complete linkage) showing the similarity between the U. gibba microbiomes and the soil, water, and plant-associated ones. The surrounding U. gibba's environment (Ugm) is closer to water samples than it is to Ugt, and Ugt is on its own with a large branch length. Using the LCA approach a family level clustering (D) shows that Ugt and water-related samples cluster apart from all the related environments.
Fig 5.
Comparative functional genomics and the complement between U. gibba's genome, and its trap (Ugt).
(A) Venn diagram comparing the amount of shared genes between the plant's genome, Ugt, and Ugm (using KEGG orthologs). (B) A Heat-map showing the overall metabolic complement supplied by Ugt, note that most of this complement is shared with Ugm and only a subset is in greater abundance in Ugt. (C) A ternary plot in which each dot corresponds to a KEGG ortholog and its diameter is proportional to its abundance. This plot shows that most of the predicted gene functions are shared between Ugt and Ugm, whereas a minimal portion of genes are shared directly between Ugt, Ugm and the plant's genome. (D) Major functions coded by both U. gibba's trap (Ugt) and its medium (Ugm). The categories used correspond to level 1 of the SEED's hierarchy.
Fig 6.
The Ugt metagenome is quite unique, even with the predicted functional analysis.
A Non-Metric Dimensional Scaling (NMDS) bi-plot analysis is shown and using 11,891 annotated features from M5NR DB, where level 1 SEED's functional hierarchy is used to color the predicted genes. The analysis confirms the uniqueness of Ugt with other metagenomes, and shows that Ugm is functionally clustered apart from Ugm.