Unique genes from the consortium involved in copper bioleaching with the smallest CIB values.

<p>Unique genes from the consortium involved in copper bioleaching with the smallest CIB values.</p

Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium

<div><p>The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine.</p></div

Hierarchical clustering of 10 biomining bacteria according to CIB values grouped by COG category.

<p><b>A.</b> Conserved genes, <b>B.</b> Unique genes. For each strain, the mean value of CIB was calculated for genes (both conserved and unique) within each COG category. The strains were then hierarchically clustered using average linkage with the Pearson product correlation coefficient measuring the distance between the vectors of mean CIB per COG category. The color bar ranges from green (low CIB, 0.0) to red (high CIB, 0.5).</p

List of genes from the consortium with lower CIB values compared to its non-consortium counterpart.

<p>List of genes from the consortium with lower CIB values compared to its non-consortium counterpart.</p

Average value of CIB for genes belonging to the consortium biomining species and the selected comparison groups under study.

<p>Each value is the average CIB calculated over all the species from each independent group classified according to COG category. The asterisks mark the four COG categories for which the greatest difference was observed between the mean CIB for the consortium and the mean CIB for the 2014 COG database.</p

Origins of biomining strains under study.

<p>Origins of biomining strains under study.</p

Average value of CIB for genes belonging to ten strains of bacteria (consortium and non-consortium) and the COG database binned by gene length in bases.

<p>Each bin contains genes from <i>ℓ</i>-499 to <i>ℓ</i> bases in length, where <i>ℓ</i> can be read off the x-axis. The y-axis indicates the mean value of CIB for genes belonging to the bin indicated on the x-axis. Bacterial strains belonging to the same species are plotted using the same point shape. Strains belonging to the biomining consortium are distinguished by filled points linked by solid lines while non-consortium strains are hollow points linked by dotted lines. The average CIB values for the 2014 COG database are plotted as crosses linked by a red solid line.</p

Percent identity and divergence score matrix of the 100 concatenated gene nucleotide sequence.

a<p>The numbers in italics (upper left) are the percent identity and divergence scores of the CA strains.</p>b<p>The numbers in bold are the percent identity and divergence scores of the hybrid strain.</p>c<p>The numbers in regular text (down right) are the percent identity and divergence scores of the HA strains.</p

Molecular clock/time of divergence estimates based on sSNP analysis within and between clades.

<p>Molecular clock/time of divergence estimates based on sSNP analysis within and between clades.</p

Position of the 100 genes analyzed on the TX16 (DO) chromosome.

<p>The chromosomal map of the <i>Enterococcus faecium</i> genome of the endocarditis isolate TX16, commonly referred to as DO. The arrows represent the 100 genes chosen for clade and SNP analysis and their position on the chromosome. The red arrows depict genes transcribed in the forward orientations, and blue arrows depict genes transcribed in the reverse orientation. The general location of a few subset of the 100 genes are labeled.</p