Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have since been found in geographically widespread deep subsurface locations. In order to constrain models for subsurface microbial evolution, we compared CDA genomes from Africa, North America and Eurasia using single cell genomics. Unexpectedly, 126 partial single amplified genomes from the three continents, a complete genome from of an isolate from Eurasia, and metagenome-assembled genomes from Africa and Eurasia shared >99.2% average nucleotide identity, low frequency of SNP’s, and near-perfectly conserved prophages and CRISPRs. Our analyses reject sample cross-contamination, recent natural dispersal, and unusually strong purifying selection as likely explanations for these unexpected results. We therefore conclude that the analyzed CDA populations underwent only minimal evolution since their physical separation, potentially as far back as the breakup of Pangea between 165 and 55 Ma ago. High-fidelity DNA replication and repair mechanisms are the most plausible explanation for the highly conserved genome of CDA. CDA presents a stark contrast to the current model organisms in microbial evolutionary studies, which often develop adaptive traits over far shorter periods of time.

硫酸盐还原菌CandidatusDesulforudis audaxviator (CDA) 最初是在通过南非金矿进入的深层压裂液中发现的，此后在地理分布广泛的深层地下位置被发现。为了限制地下微生物进化的模型，我们使用单细胞基因组学比较了非洲、北美和欧亚大陆的 CDA 基因组。出乎意料的是，来自三大洲的 126 个部分单一扩增基因组、来自欧亚大陆分离物的完整基因组以及来自非洲和欧亚大陆的宏基因组组装基因组共享 >99.2% 的平均核苷酸同一性、低频率的 SNP 和近乎完美保守的噬菌体和 CRISPR。我们的分析拒绝将样本交叉污染、最近的自然扩散和异常强烈的净化选择作为对这些意外结果的可能解释。因此，我们得出结论，所分析的 CDA 种群自物理分离以来仅经历了最小的进化，可能追溯到 165 至 55 Ma 前盘古大陆的分裂。高保真 DNA 复制和修复机制是对 CDA 高度保守基因组最合理的解释。CDA 与微生物进化研究中的当前模型生物形成鲜明对比，后者通常在更短的时间内形成适应性特征。