Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

Ni, Z.; Osborn, T.; Zhong, J.; Gonzalez, A.; Puzella, W.; Klos, A.; Le, B.; Leonetti, A.; Boden, J. S.; Stueeken, E. E.; Anderson, R. E.

doi:10.1101/2025.11.13.688358

bioRxiv · 10.1101/2025.11.13.688358

Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

Ni, Z.·Osborn, T.·Zhong, J.·Gonzalez, A.·Puzella, W.·Klos, A.·Le, B.·Leonetti, A.·Boden, J. S.·Stueeken, E. E.·Anderson, R. E.

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Abstract

The co-evolution of life and Earth has profoundly transformed global biogeochemical cycles over the past 3.5 billion years. These cycles, in turn, have dictated the availability of essential nutrients like phosphorus, nitrogen, and iron, thereby affecting primary productivity and the scale of the Earths biosphere. Despite the critical role of nutrient limitation in shaping the size and scope of the biosphere, significant uncertainties persist about which nutrients were globally limiting at various points in Earth history. Here, we use a phylogenomic approach to trace the origin and spread of genes associated with nutrient limitation over time. We show that genes associated with phosphorus limitation emerged relatively early in lifes history, whereas genes associated with nitrogen limitation emerged later, closer to the Great Oxidation Event. In terms of iron limitation, we present novel evidence that siderophores, compounds that facilitate iron uptake, may have arisen as early as the Archean. Overall, our results have important implications for understanding how the geosphere has influenced the scale and extent of life on Earth for the past 4 billion years.

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Ni, Z., Osborn, T., Zhong, J., Gonzalez, A., Puzella, W., Klos, A., Le, B., Leonetti, A., Boden, J. S., Stueeken, E. E., Anderson, R. E.. 2025-11-14. Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history. https://doi.org/10.1101/2025.11.13.688358

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