Abstract
Acidithiobacillus ferrivorans is an acidophile that often occurs in low temperature acid mine drainage, e.g., that located at high altitude. Being able to inhabit the extreme environment, the bacterium must possess strategies to copy with the survival stress. Nonetheless, information on the strategies is in demand. Here, genomic and transcriptomic assays were performed to illuminate the adaptation mechanisms of an A. ferrivorans strain YL15, to the alpine acid mine drainage environment in Yulong copper mine in southwest China. Genomic analysis revealed that strain has a gene repertoire for metal-resistance, e.g., genes coding for the mer operon and a variety of transporters/efflux proteins, and for low pH adaptation, such as genes for hopanoid-synthesis and the sodium:proton antiporter. Genes for various DNA repair enzymes and synthesis of UV-absorbing mycosporine-like amino acids precursor indicated hypothetical UV radiation—resistance mechanisms in strain YL15. In addition, it has two types of the acquired immune system–type III-B and type I-F CRISPR/Cas modules against invasion of foreign genetic elements. RNA-seq based analysis uncovered that strain YL15 uses a set of mechanisms to adapt to low temperature. Genes involved in protein synthesis, transmembrane transport, energy metabolism and chemotaxis showed increased levels of RNA transcripts. Furthermore, a bacterioferritin Dps gene had higher RNA transcript counts at 6°C, possibly implicated in protecting DNA against oxidative stress at low temperature. The study represents the first to comprehensively unveil the adaptation mechanisms of an acidophilic bacterium to the acid mine drainage in alpine regions.
Highlights
Acid mine drainage as a typical extreme environment is associated with metal or coal mines and derelict mines
Christel et al [9] found that when using potassium tetrathionate as an energy source, the A. ferrivorans strain SS3 had little RNA transcript response related to cold stress and it was concluded that the strain is adapted to growth at 8 ̊C
We presented here the adaptation-related gene repertoire of an A. ferrivorans strain YL15 isolated from acid mine drainage in an alpine copper mine, using genomic and transcriptomic methods
Summary
Acid mine drainage as a typical extreme environment is associated with metal or coal mines and derelict mines. The elevated RNA transcript levels of cellular components of the transcriptional machinery at low temperature, together with the induction of genes involved in the transcriptional processes by cold, demonstrated that transcriptional regulation is central to cold adaptation in strain YL15. Numerous ABC transporter-associated genes were identified in the genome of strain YL15, 4 of which showed increased number of RNA transcript counts in the cold.
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