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Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) show minimal genome evolution across continents, suggesting ancient separation. Their highly conserved genomes point to efficient DNA repair mechanisms, challenging typical microbial evolution models.

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Area of Science:

  • Microbiology
  • Evolutionary Biology
  • Genomics

Background:

  • Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) are found globally in deep subsurface environments.
  • Understanding microbial evolution in isolated environments is crucial for subsurface ecosystem modeling.

Purpose of the Study:

  • To investigate the evolutionary divergence of Candidatus Desulforudis audaxviator (CDA) populations across different continents.
  • To constrain models of microbial evolution in the deep subsurface.

Main Methods:

  • Single-cell genomics was employed to analyze 126 partial genomes from Africa, North America, and Eurasia.
  • Complete genomes from isolates and metagenome-assembled genomes were also analyzed.
  • Comparative genomic analyses focused on average nucleotide identity, single nucleotide polymorphisms (SNPs), prophages, and CRISPRs.

Main Results:

  • CDA genomes from three continents exhibited >99.2% average nucleotide identity and conserved genetic elements.
  • Low SNP frequencies and near-perfectly conserved prophages and CRISPRs were observed.
  • Analysis ruled out sample cross-contamination, recent dispersal, and strong purifying selection as explanations.

Conclusions:

  • CDA populations have undergone minimal evolution since their physical separation, potentially dating back to the breakup of Pangea.
  • High-fidelity DNA replication and repair mechanisms are the likely cause of CDA's conserved genome.
  • CDA's evolutionary stasis contrasts sharply with model organisms that adapt rapidly.