Evolutionary patterns of archaea predominant in acidic environment

Abstract

Background: Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called "alphabet-plasmas", and collectively dubbed "E-plasma", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.

Results: Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the "E-plasma" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of "E-plasma", which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.

Conclusions: This study has analysed the metagenome-assembled genome of "E-plasma", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.

Keywords: Acid mine drainage (AMD); Acidophilic archaea; Microbial dark matter; Mine-impacted environments; Parys Mountain; Thermoplasmatales.

Fig. 1

Phylogenetic tree based on 122 proteins from Thermoplasmatota archaea as per GTDB dataset. The tree was calculated using GTDB-Tk program to locate the genome within the Ca. Thermoplasmatota phylum, using the phylum Ca. Poseidoniia as the outgroup. Bootstrap results shown with open (< 80) and closed (> 80) circles. Parys Mt “E-plasma” bin is placed exactly next to the Iron Mt “E-plasma” genome GCA_000496135.1, within the order Thermoplasmatales. Colours used to distinguish between different archaeal clades

Fig. 2

Functional categories of genes in four genomes. For the analysis were used genomes of both “E-plasma” variants (Parys Mt, UK and Iron Mt, USA) and of C. divulgatum strains PM4 and S5. Relative abundances of genes in genomes are shown according to functional arCOGs categories, %. Assignments are based on the results of psi-blast against arCOGs database using the pangenomic sequences returned by Roary v3.12.0. The relative abundance of arCOGs per genomes of both “E-plasma” are shown in blue colours, while Cuniculiplasma genomes are shown in red colours

Fig. 3

Metabolic reconstruction of selected pathways (Sulfate reduction and Glyoxylate shunt) for “E-plasma” and Cuniculiplasma divulgatum. Presence of relevant genes in both genomes are shown in green colour. Presence of encoding genes, only present in “E-plasma” shown in blue colour and the absence of genes in both genomes (“E-plasma” and Cuniculipasma divulgatum) shown in black colour. Steps including more than one reaction shown as dashed arrows

Fig. 4

Thermoplasmatales phylogenetic tree based on 122 concatenated protein sequences in combination with other data. 122 concatenated protein sequences combined with: G + C mol%, Genome size (Mbp) and Coding sequences (x1000). Bootstrap results shown with open (< 80) and closed (> 80) circles

Fig. 5

Unrooted core protein families-based phylogenetic tree of Thermoplasmatales illustrating gene gains/losses. Bootstrap values are shown as open (< 80) and closed (> 80) circles. Total numbers of modifications (sums of gains, losses, reductions and expansions) are shown with lines of different thickness and colour (see the code in the top right corner of the figure). At each node, the numbers of genes present in ancestors (grey), gene gains (green) and losses (red) are shown. Bars of similar colours below those numbers represent relative proportions vs. the maximum number of genes among all ancestors, e.g. 1.854 genes present and 795 gene gains in Cuniculiplasma ancestor, or 856 gene losses, shown for “I-plasma” ancestor

Fig. 6

The census of proteins from metabolism-related subcategories of arCOGs in “E-plasma”-Cuniculiplasma core protein families. Bar sizes of 100% correspond to maximal numbers of each gene along the genomes and ancestors included in the branch. Bold labels correspond to proteins encoded by an operon, or multidomain complexes. For each protein, grey bars represent the number of genes in a genome. Overlapping grey bars of sizes corresponding to the percentage of present gene numbers to gains (light green) or expansions (dark green). Bars opposing the grey bars show relative numbers of losses in that genome for each gene. CA, the Common Ancestor of the “E-plasma”-Cuniculiplasma branch (the Node 9 in Fig. 4; LTCA, Last Thermoplasmatales Common Ancestor)

Fig. 7

The pangenome of the Ferroplasma-Acidiplasma-Picrophilus—”I-plasma” cluster. The plot was drawn using metabolism related census of subcategories of arCOGs. Bars 100% the total number of modifications for each gene along the genomes/ancestors included in the branch. Bold labels indicate proteins encoded by an operon, or multidomain complexes. Grey bars show genes present in the genome. Gains are shown as light green, expansions as dark green, the gene losses are shown as red bars. CA, the Common Ancestor of the Ferroplasma-Acidiplasma-Picrophilus-”I-plasma” cluster. Please note that the organism/genome represented by each outer circle is not considered as a descendant of the neighbouring organism/genome, represented by inner circle