Figure 1.
Phyloecological cluster tree of Archaea.
A. The cluster tree was built with average linkage of distances based on correlation metric by using the 5-features subset. Cut-off distance for the formation of clusters was 1.0. The tree is divided into three main phyloecological clusters. The first cluster (highlighted in yellow) is comprised of hyperthermophilic species, non-halophilic or halotolerant, and aerobic hyperthermoacidophiles. The members of the second cluster (highlighted in blue) are halophilic and extremely halophilic Archaea, growing in the various temperature ranges (mesophilic, thermophilic or hyperthermophilic values), and conditions of neutral pH or alkaliphilic. The third cluster (highlighted in red) contains mesophilic (mostly methanogens) and thermoacidophilic Archaea, non-halophiles or halotolerant. B. Leaves of the tree display names of phyla for each species from A.
Table 1.
Abundances of environmental phenotypes within the clusters.
Figure 2.
Heat map visualization of archaeal proteomic properties across phyloecological clusters.
In this heat map, the rows correspond to each species and the columns correspond to the proteomic features; therefore, each row depicts the subset of 5 proteomic features per given archaeon. Normalized values of each feature are associated with the colors in the heat map as shown on the legend on the left side. The cluster tree was built with correlation metric and average linkage, same as in Fig. 1. Three main phyloecological clusters are highlighted with three different colors of the branches (yellow: hyperthermophiles and hyperthermoacidophiles; blue: halophiles and extreme halophiles; red: mesophilic methanogens and thermoacidophiles).
Figure 3.
Assessing predictive power of phyloecological clustering.
We added five new species to the dataset and preformed hierarchical clustering with the established parameters. The new species became a part of the clusters defined with similar environmental conditions as it is found in their respective niches. One archaeon joined the “red” cluster with other mesophilic methanogens; two species merged with the members of halophilic ”blue” cluster; and two hyperthermoacidophilic organisms became members of the corresponding “yellow” cluster.