TY - JOUR
T1 - Evolutionary stasis of a deep subsurface microbial lineage
AU - Becraft, Eric D.
AU - Lau Vetter, Maggie C.Y.
AU - Bezuidt, Oliver K.I.
AU - Brown, Julia M.
AU - Labonté, Jessica M.
AU - Kauneckaite-Griguole, Kotryna
AU - Salkauskaite, Ruta
AU - Alzbutas, Gediminas
AU - Sackett, Joshua D.
AU - Kruger, Brittany R.
AU - Kadnikov, Vitaly
AU - van Heerden, Esta
AU - Moser, Duane
AU - Ravin, Nikolai
AU - Onstott, Tullis
AU - Stepanauskas, Ramunas
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/10
Y1 - 2021/10
N2 - 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.
AB - 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.
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U2 - 10.1038/s41396-021-00965-3
DO - 10.1038/s41396-021-00965-3
M3 - Article
C2 - 33824425
AN - SCOPUS:85103621105
SN - 1751-7362
VL - 15
SP - 2830
EP - 2842
JO - ISME Journal
JF - ISME Journal
IS - 10
ER -