Microbial evolution : the view from the acidophiles 2 . 1

Acidophilic organisms have provided a highly fertile ground for research into microbial evolution. Their low-biodiversity communities have allowed for extensivemetagenomic, metatranscriptomic, and metaproteomic analysis [1]. A wealth of data from comparative genomics of closely related strains is beginning to reveal the evolutionary processes that allow for genotypic change, and how they relate to selective pressures. In the last decade it has become evident that the genetic diversity available in bacterial communities is vast and in constant flow. DNA is constantly mobilized by plasmids and phage, and recombination occurs at high rates. Recent studies in acidophiles have described not only the type of events that are taking place, but also to begin to make a quantitative assessment of their predominance and rates. The acidophiles have been mainly studied in two scenarios. The first one, acid mine drainage (AMD) environments, are areas in which organisms rely on chemoautotrophic production mainly based on iron and sulphur oxidation. In addition to very low pH, there are often high concentrations of heavy metals such as iron, zinc or arsenic [1–3]. Well-characterized examples of these environments include the Río Tinto in Southern Spain [4] and Iron Mountain in California, USA [5]. The main actors of these studies have been Leptospirillum (Nitrospira), Acidithiobacillus (Gammaproteobacteria) and Ferroplasma (Archaea, Thermoplasmata). The second scenario is the volcanic springs or “mudpots” generated by geothermal activity, inwhich, in addition to extreme acidity, organisms must contend with temperatures that can reach 80 °C. These environments are dominated by thermoacidophilic Archaea and themain actor of evolutionary studies has been the genus Sulfolobus (Crenarchaeota). Although it had been assumed that extremely acidic environments could prove hostile or limit DNA exchange, there is no evidence that mechanisms of gene transfer or genomic change are different from those operating in other less-extreme habitats. Numerous phage, plasmids, andmobile elements have been described in association with acidophilic communities or as part of the genomes of acidophiles, as well as mechanisms for DNA uptake, DNA secretion, or CRISPR (clusters of regularly interspaced short palindromic repeats) defense systems [see reviews in6–9]. Indeed, phage are abundant and diverse in all environments where acidophilic prokaryotes have been found. For example, the optimal growth conditions of the Sulfolobus turreted icosahedral virus (STIV) are pH 3.3 and 80 °C [10]. There is some evidence, however, that DNA exchange among acidophilic organisms, even when not closely related phy-