A geological timescale for bacterial evolution and oxygen adaptation

Creators: Davín, Adrián A.^{1, 2, 3}; Woodcroft, Ben J.⁴; Soo, Rochelle M.¹; Morel, Benoit^{5, 6}; Murali, Ranjani⁷; Schrempf, Dominik^{2, 8}; Clark, James W.^{9, 10}; Álvarez-Carretero, Sandra⁹; Boussau, Bastien¹¹; Moody, Edmund R. R.⁹; Szánthó, Lénárd L.^{2, 12, 13}; Richy, Etienne⁹; Pisani, Davide⁹; Hemp, James¹⁴; Fischer, Woodward⁷; Donoghue, Philip C. J.⁹; Spang, Anja^{15, 16}; Hugenholtz, Philip¹; Williams, Tom A.⁹; Szöllősi, Gergely J.^{2, 8, 12, 13}

1. University of Queensland
2. Eötvös Loránd University
3. University of Tokyo
4. Translational Research Institute
5. Heidelberg Institute for Theoretical Studies
6. Karlsruhe Institute of Technology
7. California Institute of Technology
8. Hungarian Academy of Sciences
9. University of Bristol
10. University of Bath
11. Biometry and Evolutionary Biology Laboratory
12. Centre for Ecological Research
13. Okinawa Institute of Science and Technology
14. Metrodora Institute, West Valley City, UT, USA.
15. Royal Netherlands Institute for Sea Research
16. University of Amsterdam

Abstract

Microbial life has dominated Earth's history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE). We combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial time tree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Phanerozoic. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, in the cyanobacterial ancestor, aerobic metabolism likely predated the GOE, which may have facilitated the evolution of oxygenic photosynthesis.

Copyright and License

© 2025 the authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original US government works. https://www.science.org/about/science-licenses-journal-article-reuse.

Acknowledgement

We thank J. A. Palacios for providing R scripts to compute the D2 distance for ranked trees. We are grateful for the help and support provided by the Scientific Computing and Data Analysis section of Core Facilities at OIST.

Funding

This work was funded by the following: European Research Council (ERC) grant 714774 “GENECLOCKS” (to A.A.D., L.L.S., D.S., and G.J.S.) under the European Union’s Horizon 2020 research and innovation program; ERC grant 947317” ASymbEL” (to A.S.) under the European Union’s Horizon 2020 research and innovation program; Gordon and Betty Moore Foundation grant GBMF9741 (to T.A.W., A.S., P.C.J.D., and G.J.S.); Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative grant GBMF9346 (to A.S.); Moore–Simons Project on the Origin of the Eukaryotic Cell, Simons Foundation 735929LPI grant 735929LP (to A.S.); Royal Society University Research Fellowship (to T.A.W.); John Templeton Foundation grant 62220 (to E.R.R.M., D.P., P.C.J.D., and T.A.W.); Leverhulme Trust Research Fellowship grant RF-2022-167 (to P.C.J.D.); Biotechnology and Biological Sciences Research Council grants BB/T012773/1 and BB/Y003624/1 (to P.C.J.D.); Australian Research Council (ARC) Future Fellowship grant FT210100521 (to B.J.W.); ARC Discovery Project grant DP230101171 (to B.J.W.); ARC Discovery Early Career Researcher Award grant DE190100008 (to R.M.S.); ARC Laureate Fellowship grant FL150100038 (to A.A.D. and P.H.); ARC Discovery Project grant DP220100900 (to A.A.D. and P.H.).

Data Availability

All data used are described in detail in the SM and available in the figshare repository associated with the submission (92). All code used is described in detail in the SM and available either openly on github or other relevant public repository, as indicated, or included in the figshare repository (92) associated with the submission in the case of more specialized scripts.

Conflict of Interest

R.M. is currently affiliated with Dept Life Sciences, University of Nevada, Las Vegas. All other authors declare no other competing interests.

Supplemental Material

Materials and Methods; Supplementary Text; Figs. S1 to S39; Tables S1 to S8; References (96–221) (PDF)

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