The dynamic genomes of acidophiles

The large-scale sequencing of microbial genomes and environmental samples in the last decade has revealed a huge amount of genetic diversity in natural populations. Extremophilic species in which the genomes of independently isolated strains have been sequenced often show a high variance in gene content as well as the pervasive effects of genomic rearrangements due to recombination. On the other hand, metagenomic studies have highlighted the dynamic complexity of bacterial populations and the action of mobile elements (plasmids, phage, and transposons) in shaping the genetic makeup of these organisms. Here we review the lessons gained from studies of the genomes, transcriptomes, and proteomes of acidophilic bacteria, with emphasis on what is known about the mechanisms that generate diversity and favor genetic exchange in acidic environments. Genome plasticity due to the combination of horizontal gene transfer (HGT) and the activity of mobile genetic elements (mobilome) could be essential during ecological specialization and adaptation to extreme environments