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Early fossil eukaryotes were benthic aerobes

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Abstract

The evolution of the eukaryotic cell paved the way for the emergence of all complex life on Earth. Despite its significance, the environmental context of early eukaryote evolution is largely unknown1,2. Here we use the geological record to reconstruct the habitats of the oldest known fossil eukaryotes, approximately 1.75–1.4 billion years old. Our integrated palaeontological, sedimentological and geochemical analyses show that although fossil eukaryotes are found in samples deposited in a range of environments from coastal to offshore, they are almost entirely restricted to those from settings with oxygenated bottom waters. This distribution suggests these organisms were aerobes (obligate, facultative and/or microaerophilic) and, given their size and morphological complexity, probably possessed mitochondria. Furthermore, their near absence from otherwise fossiliferous anoxic samples suggests a benthic habit, as planktonic eukaryotes would be expected to be present in both oxic and anoxic samples. We propose that eukaryotes were largely restricted to oxic benthic habitats for much of the Proterozoic eon, only expanding into planktonic habitats during the Neoproterozoic era (1–0.54 billion years ago). This late ecological expansion could account for the mismatch between the appearance of eukaryotic body fossils and molecular biomarkers3 and explain the stepwise increase in eukaryote diversity during the Neoproterozoic era4.

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Fig. 1: Stratigraphic columns, data and map.
The alternative text for this image may have been generated using AI.
Fig. 2: Representative fossils.
The alternative text for this image may have been generated using AI.
Fig. 3: Fossil distributions by sample redox state and depositional setting.
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Fig. 4: Proposed model of habitat occupation through time.
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Data availability

All data from this study are included in the Extended Data and Supplementary Information. Supplementary data tables are also available through Dryad at https://doi.org/10.5061/dryad.1vhhmgr8n (ref. 69).

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Acknowledgements

We thank K. Gibson for sample collection; D. Stacey for help in organizing and facilitating sampling of these cores; S. Wang for helpful discussion of statistical methods; T. H. Bui and A. Poirier for assistance with laboratory work; and D. Mills for discussions. M.A.L., L.A.R., S.M.P. and G.P.H. disclose support from Moore–Simons Project on the Origin of the Eukaryotic Cell, Simons Foundation (735933LPI; https://doi.org/10.46714/735933LPI). G.P.H. discloses support from a Natural Sciences and Engineering Council of Canada (Discovery Grant). L.A.R. discloses support from the Palaeontological Association (PA-RG201902) and the American Philosophical Society Lewis and Clark Fund for Exploration and Field Research in Astrobiology. L.A.R. and S.M.P disclose support from the National Aeronautics and Space Administration Exobiology Program (80NSSC25K7872). M.W. declares no relevant funding.

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Author notes

  1. Maxwell A. Lechte

    Present address: School of Geosciences, The University of Sydney, Sydney, New South Wales, Australia

  2. These authors contributed equally: Maxwell A. Lechte, Leigh Anne Riedman

Authors and Affiliations

  1. Department of Earth and Planetary Sciences/Geotop, McGill University, Montreal, Quebec, Canada

    Maxwell A. Lechte, Galen P. Halverson & Margaret Whelan

  2. Department of Earth Science, University of California, Santa Barbara, Santa Barbara, CA, USA

    Leigh Anne Riedman & Susannah M. Porter

  3. Earth Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA

    Leigh Anne Riedman

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Contributions

S.M.P., G.P.H., L.A.R. and M.A.L. designed the project. L.A.R. planned and conducted sampling. M.A.L. and M.W. contributed geochemical data, L.A.R. contributed palaeontological data, S.M.P conducted statistical analyses and M.A.L. and G.P.H. contributed sedimentological interpretations. M.A.L. and L.A.R. developed the first draft; S.M.P. and G.P.H. contributed to editing and writing of subsequent drafts.

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Correspondence to Maxwell A. Lechte or Leigh Anne Riedman.

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Extended data figures and tables

Extended Data Fig. 1 Geochemical scatter plots.

Redox proxy data from a, the Tawallah Group, b, the McArthur and Limbunya groups, and c, the Roper, Bullita and Tijunna Groups. Data are coloured according to their interpreted redox conditions (interpretation based holistically on the overall geochemical context). Symbol shape corresponds to the interpreted depositional environment. Faded colours represent data from the published literature and Northern Territory Geological Survey core sampling reports. Iron speciation data show the ratio of highly reactive iron to total iron (FeHR/FeT) and the ratio of pyrite iron to highly reactive iron (Fepy/FeHR). Trace element (V, Mo and U) enrichments are shown as a mass ratio normalised to Al content (in μg g−1 / %), with the dashed line boxes representing the values characteristic of sediments deposited in modern oxic or euxinic basins (see ref. 63; Supplementary Information).

Extended Data Fig. 2 Geochemical box-and-whisker plots.

Data showing FeT/Al ratios, TOC content, Corg/P ratios and trace element enrichment factors (XEF) for V, Cr, Mo and U (see ref. 62; Supplementary Information). These are subdivided into categories based on their interpreted redox setting and depositional environment, from a, coastal, b, lagoonal / restricted, c, shoreface, and d, offshore settings. For all plots, n values represent the total number of samples for each category for which the relevant data are available. The boxes represent the interquartile range, with the horizontal line indicating the median, while the whiskers represent 1.5 times the interquartile range and circles indicate outliers (datapoints that lie outside the range of the whiskers).

Extended Data Fig. 3 Ambiguous taxa plate.

a, Leiosphaeridia crassa. Drill core DD90VRB1, depth 419.52 m. b, L. tenuissima. DD90VRB1, 413.7 m. c, L. minutissima. DD90VRB1, 419.52 m. d, L. jacutica. DD90VRB1, 413.7 m. e, Pterospermopsimorpha sp. DD90VRB1, 413.7 m. f, Navifusa majensis. DD90VRB1, 413.7 m. g, Navifusa majensis. DD90VRB1, 413.7 m. h, Pterospermopsimorpha sp. 99VRNTGSDD2, 323.2 m. i, Cucumiforma vanavaria. 99VRNTGSDD2, 225.12 m. j, Squamosphaera colonialica. 99VRNTGSDD2, 92.8 m. k, Simia sp. 99VRNTGSDD2, 91.35 m. l, Germinosphaera sp. 99VRNTGSDD2, 319.08 m. m, Simia sp. 99VRNTGSDD2, 82.1 m. n, Schizofusa sinica. GSD7, 546.07 m. o, Unnamed tube- note tubular process with visible circular junction (arrow), GSD7, 640.55 m. p, Unnamed tube. GSD7, 640.55 m. q, Plicatidium latum. 99VRNTGSDD2, 122.27 m. Scale bar is 20 µm for all. Images in d–g reproduced from ref. 17 (CC BY 4.0).

Extended Data Fig. 4 Prokaryotes plate.

a, Synsphaeridium sp. 99VRNTGSDD2, 94.7 m. b, Eomicrocystis sp. GSD7, 687.35 m. c, Eomicrocystis sp. MCDD0005, 516.86 m. d, Synsphaeridium sp. 99VRNTGSDD2, 94.7 m. e, Oscilliatoriopsis obtusa. DD90VRB1, 413.7 m. f, Synsphaeridium sp. Broughton-1, 168.1 m. f, L. jacutica. 99VRNTGSDD2, 323.2 m. g, Tortunema patomica. DD90VRB1, 417.4 m. h, Siphonophycus typicum. 99VRNTGSDD2, 225.23 m. i, Siphonophycus typicum. 99VRNTGSDD2, 225.78 m. Scale bar is 20 µm for all. Images in e and g reproduced from ref. 17 (CC BY 4.0).

Extended Data Fig. 5 Fossil distribution bar charts.

Fossil distributions by sample redox state and depositional setting for selected individual eukaryote (a–g) and prokaryote (h–j) taxa. Bars show percent of fossiliferous samples bearing that taxon according to sample redox state (left hand panels; n = number of fossiliferous samples of that redox state) and depositional setting and redox state (right hand panels; n = number of fossiliferous samples of that depositional setting). Asterisk indicates the association of Siphonophycus sp. with oxic samples is statistically significant (two-sided Fisher’s exact test, p = 0.030). Note that the small sample sizes for each individual eukaryotic species mean that statistical comparisons are not robust. However, nearly every eukaryotic species is restricted to oxic samples. See Supplementary Table 1 for fossil occurrence data and details of statistical analyses.

Extended Data Fig. 6 Fossils from anoxic samples.

All are from ferruginous samples, except for f which is from a euxinic sample. a, L. minutissima. DD90VRB2, 182.19 m. b, L. minutissima. DD90VRB2, 182.19 m. c, Eomicrocystis sp. GSD7, 687.35 m. d, Unnamed tube form. GSD7, 687.35 m. e, L. jacutica. DD90VRB2, 182.19 m. f, L. crassa. McA5, 266.02 m. g, L. crassa. DD90VRB2, 253.9 m. h, Eomicrocystis sp. MCDD0005, 516.86 m. i, L. tenuissima. GSD7, 696.46 m. j, Pterospermopsimorpha sp. MCDD0005, 516.86 m. k, Pterospermopsimorpha sp. DD90VRB2, 253.9 m. l, Satka favosa. DD90VRB1, 157.9 m. m, Satka favosa. DD90VRB2, 149.97 m. n–p, Jixiania lineata fragments. MCDD0005, 539.4 m. Scale bar is 20 µm for all. Image in m reproduced from ref. 17 (CC BY 4.0).

Extended Data Fig. 7 Expected fossil assemblages of different hypothetical ecosystem scenarios.

a, Scenario with eukaryotes restricted to oxic habitats. If eukaryotes were planktonic, we would expect eukaryote fossils in sedimentary rock samples deposited in environments with oxic or anoxic bottom waters, as planktonic aerobes could have lived in the oxygenated surface waters. However, if all eukaryotes were benthic, then only rare, transported eukaryote fossils would be present in anoxic samples. b, Scenario with eukaryotes restricted to anoxic habitats. Regardless of whether eukaryotes were planktonic or benthic, we would expect to near-exclusively find eukaryote fossils in anoxic samples. c, Scenario with eukaryotes in oxic and anoxic habitats. In this scenario, we would expect to find eukaryote fossils in comparable abundances in oxic and anoxic samples, though the diversity and taxa may vary.

Supplementary information

Supplementary Information (download PDF )

Supplementary Discussion, Supplementary Figs. 1–8 and Supplementary References.

Reporting Summary (download PDF )

Supplementary Table 1 (download XLSX )

Composite data table. Palaeontological, geochemical and sedimentological data for each drill core sample; matrices for statistical analyses of various taxonomic groups

Supplementary Table 2 (download XLSX )

Table of taxa. Listing of eukaryotic and prokaryotic taxa and those of ambiguous affinity accompanied by descriptions and references for affinity.

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Lechte, M.A., Riedman, L.A., Porter, S.M. et al. Early fossil eukaryotes were benthic aerobes. Nature (2026). https://doi.org/10.1038/s41586-026-10533-4

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