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The hydrogen, methane and ammonia biosphere on early Earth
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  • Published: 18 March 2026

The hydrogen, methane and ammonia biosphere on early Earth

  • Hiroshi Ohmoto1,2 &
  • James Gregory Ferry3 

Scientific Reports , Article number:  (2026) Cite this article

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Subjects

  • Biochemistry
  • Biogeochemistry
  • Biological techniques
  • Chemical biology
  • Environmental sciences
  • Evolution
  • Microbiology
  • Chemical origin of life
  • Planetary science
  • Solid Earth sciences

Abstract

Current paradigms for the origin and evolutions of life and the environment on early Earth have been based on the premises that carbon dioxide (CO2) and nitrogen gas (N2) were the principal constituents of the atmosphere and the sources of carbon and nitrogen for organisms today. Based on thermodynamic analyses of the redox state of the Hadean (4.56-4.0 Ga) mantle, the atmospheric compositions during the magma-ocean stage, and the effects of submarine hydrothermal fluids on the atmosphere of the ocean-covered Late-Hadean Earth, we suggest that life evolved sometime during 4.50–3.9 Ga under a reducing atmosphere, rich in hydrogen (H2), methane (CH4), and ammonia (NH3), but very poor in CO2, which was similar to today’s atmosphere on Jupiter. The ocean water was alkaline (pH = 10 ± 1) and poor in Fe2− and S2−. CH4 and NH3 were the principal sources for carbon nitrogen and energy of the first organisms, greenhouse gases, and the UV shield on early Earth. The first organisms on Earth were possibly aerobic phototrophic methanotrophs, either oxygenic and/or anoxygenic. They evolved in micro-aerobic environments, which were created by the photodissociation of H2O on the surfaces of photocatalytic minerals (e.g., rutile (TiO2), pyrrhotite (FeS)) that accumulated in shallow water bodies on tropical islands. The enzymes for oxygenic Photosystem II (PSII) and PSI may also have evolved in the Late-Hadean microaerobic environments, facilitating the appearance of cyanobacteria. The symbiotic relationships between CO2-generating methanotrophs and the CH4-generating, H2-oxidizing methanogens and cyanobacteria characterized the first biosphere. Plate tectonics has played a key role in the transformation of the H2-CH4–NH3-rich to CO2-N2-rich atmosphere and biosphere by ~ 3.9 Ga because of the increased oxidation of the mantle, caused by the continuous subduction of the oxidized and hydrated oceanic crust into the mantle. Our study suggests that the search for life in the universe should be directed toward planets with a H2-CH4--NH3-rich atmosphere, as well as to those with a CO2–N2-rich atmosphere.

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Data availability

All data generated and analyzed during this study are included in this published article and its supplementary information files.

References

  1. Allegre, C. J., Manhés, G. M. & Göpel, C. The age of the Earth. Geochim. Cosmochim. Acta 39, 1445–1456 (1995).

    Google Scholar 

  2. Barboni, M. et al. Early formation of the Moon 4.51 billion years ago. Sci. Adv. 3, e1602365 (2017).

    Google Scholar 

  3. Valley, J. W. et al. Hadean age for a post-magma ocean zircon confirmed by atom-probe tomography. Nat. Geosci. 7, 219–223 (2014).

    Google Scholar 

  4. Rosing, M. & Frei, R. U-rich Archaean sea-floor sediments from Greenland – Indications of > 3700 Ma oxygenic photosynthesis. Earth Planet. Sci. Lets. 217, 237–244 (2004).

    Google Scholar 

  5. Frei, R. & Polat, A. Source heterogeneity for the major components of ~ 3.7 Ga banded iron formations (Isua Greenstone Belt, Western Greenland): Tracing the nature of interacting water masses in BIF formation. ESPL 253, 266–281 (2007).

    Google Scholar 

  6. Tashiro, T. et al. Early trace of life from 3.95 Ga sedimentary rocks in Labrador, Canada. Nature 549, 516–518 (2017).

    Google Scholar 

  7. Mojzisis, S. J. et al. Evidence for life on Earth before 3,800 million years ago. Nature 384, 55–59 (1996).

    Google Scholar 

  8. Schidlowski, M. Carbon isotopes as biogeochemical recorders of life over 3.8 Ga of Earth history: Evolution of a concept. Precamb. Res. 106, 117–234 (2001).

    Google Scholar 

  9. Des Marais, D. J. Isotopic evolution of the biogeochemical carbon cycle during the Precambrian. In Stable Isotope Geochemistry, J. Valley, D. R. Cole, eds. Review in Mineralogy and Geochemistry Vol. 43, 555–578 (2001).

  10. Holland, H. D. The Chemical Evolution of the Atmosphere and Ocean (Princeton Univ. Press, 1984).

    Google Scholar 

  11. Oparin, A. I. The Origin of Life on Earth (Academic Press, 1957).

    Google Scholar 

  12. Miller, S. L. & Urey, H. C. Organic compound synthesis on the primitive Earth. Science 130, 245–251 (1959).

    Google Scholar 

  13. Kasting, J. F. Earth’s early atmosphere. Science 259, 920–926 (1993).

    Google Scholar 

  14. Canfield, D. E., Rosing, M. T. & Bjerrum, C. Early anaerobic metabolisms. Phil Trans. R Soc. B. 361, 1819–1836 (2006).

    Google Scholar 

  15. Farquhar, J., Zerkle, A. L. & Bekker, A. Geologic and geochemical constraints on Earth’s early atmosphere. In The Atmosphere-History (ed. Farquhar, J.) Vol. 6 Treatise on Geochemistry 2nd Ed. (eds. Holland, H.D. & Turekian, K.) 91–138 (Elsevier, 2014).

  16. Lyons, T. W., Reinhard, C. T. & Planesky, N. J. The rise of oxygen in Earth’s early ocean and atmosphere. Nature 506, 307–315 (2014).

    Google Scholar 

  17. Martin, W., Baross, J., Kelley, D. & Russell, M. J. Hydrothermal vents and the origin of life. Nat. Rev. Microbiol. 6, 805–814 (2008).

    Google Scholar 

  18. Sleep, N. H., Bird, D. K. & Pope, E. C. Serpentinite and the dawn of life. Philos. T R Soc. B. 366, 2857–2860 (2011).

    Google Scholar 

  19. Zahnle, K. Z., Lupu, R. & Catling, D. C. Creation and evolution of impact-generated reduced atmosphere of early Earth. Plan. Sci. J. 1, 1–21 (2020).

    Google Scholar 

  20. Delano, J. W. Redox history of the Earth’s interior since ~ 3,900 Ma: implications for prebiotic molecules. Orig Life Evol. Biosphere. 31, 311–341 (2001).

    Google Scholar 

  21. Ohmoto, H. A seawater-sulfate origin for early Earth’s volcanic sulfur. Nat. Geosci. 13, 576–583 (2020).

    Google Scholar 

  22. Symonds, R. B., Rose, W. I. & Bluth, G. J. S. Volcanic-gas studies: Methods, results, and applications. In Volatiles in Magmas, M. R. Carroll, J. R. Halloway eds. Review in Mineralogy. Vol. 30, 1–66 (1994).

  23. Miyazaki, Y. & Korenaga, J. A wet heterogeneous mantle creates a habitable world in the Hadean. Nature 603, 86–90, 90A–90M (2022).

  24. Wood, B. J., Walter, M. L. & Wade, J. Accretion of the Earth and segregation of its core. Nature 441, 825–833 (2006).

    Google Scholar 

  25. Righter, K., Herd, C. D. & Boujibar, A. Redox processes in early Earth accretion and in terrestrial bodies. Elements 16, 161–166 (2020).

    Google Scholar 

  26. Stagno, V. & Fei, Y. The redox boundaries of Earth’s interior. Elements 16, 167–172 (2020).

    Google Scholar 

  27. Korenaga, J. Crustal evolution and mantle dynamics through Earth history. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 376, 1–35 (2018).

    Google Scholar 

  28. Ohmoto, H. Formation of volcanogenic massive sulfide deposits: The Kuroko perspective. Ore Geol. Rev. 10, 135–177 (1996).

    Google Scholar 

  29. Trainer, M. G. et al. Organic haze on Titan and the early Earth. Proc. Natl. Acad. Sci. U. S. A. 103, 18035–18042 (2006).

    Google Scholar 

  30. Sander, R. Compilation of Henry’s law constants (version 4.0) for water as solvent. Atmos. Chem. Phys. 15, 4399–4981 (2015).

    Google Scholar 

  31. Atreya, S. K., Mahaffy, P. R., Miemann, H. B., Wong, M. H. & Owen, T. C. Composition and origin of the atmosphere of Jupiter -an update, and implications for the extrasolar giant planets. Planet. Space Sci. 51, 105–112 (2003).

    Google Scholar 

  32. NASA Space Math (Gov). The composition of Planetary atmosphere. http://spacemath.gsfc.nasa.gov%3Eastrob.

  33. Ohmoto, H., Watanabe, Y. & Kumazawa, K. Evidence for massive siderite beds for a CO2-rich atmosphere before ~ 1.8 billion years ago. Nature 429, 395–399 (2004).

    Google Scholar 

  34. Kelley, D. S. et al. A serpentine–hosted ecosystem: The Lost City hydrothermal field. Science 307, 1428–1434 (2005).

    Google Scholar 

  35. Marques, J. M. et al. Origins of high pH mineral waters from ultramafic rocks, Central Portugal. App Geochem. 23, 3278–3289 (2008).

    Google Scholar 

  36. Konn, C. et al. Hydrocarbons and oxidized organic compounds in hydrothermal fluids from rainbow and Lost City ultramafic-hosted vents. Chem. Geol. 258, 299–314 (2009).

    Google Scholar 

  37. Klein, F., Grozeva, N. G. & Seewald, J. S. Abiotic methane synthesis and serpentine in olivine-hosted fluid inclusions. PNAS 116, 17669 (2019).

    Google Scholar 

  38. Giampouras, M. et al. Geochemistry and mineralogy of serpentinization-driven hyperalkaline springs in the Ronda peridotites. Lithos 350–351, 1–22 (2019).

    Google Scholar 

  39. Stumm, W. & Morgan, J. J. (eds) Aquatic Chemistry. 3rd. (Wiley, 1996).

  40. Trainer, M. G. Atmospheric prebiotic chemistry and organic haze. Curr. Org. Chem. 17, 1710–1723 (2013).

    Google Scholar 

  41. Madgan, M. T., Marinko, J. M. & Parker, J. Brock Biology of Microorganisms Ninthe Edition (Prentice Hall, 2000).

    Google Scholar 

  42. Levin, L. A. et al. Hydrothermal vents and methane seeps: Rethinking the sphere of influence. Front. Mar. Sci. 3, 1–23 (2016).

    Google Scholar 

  43. Ward, L. et al. Phototrophic methane oxidation in a member of the Chloroflexi phylum. biorxiv 531582 (2019).

  44. Miroshnikov, K. K., Belova, S. E. & Dedysh, S. N. Genomic determinants of phototrophy in methanotrophic Alphaproteobacteria. Microbiology 88, 548–555 (2019).

    Google Scholar 

  45. Oshkin, I. Y., amiroshnikov, K. K., Grouzdev, D. S. & Dedysh, S. N. Pan-genome-based analysis as a framework for demarcating two closely related methanotroph genera Methlococystis and Metholosinus. Microorganisms 8, 8,768 (2020).

    Google Scholar 

  46. Cerbin, S. et al. Methane-derived carbon as a driver for cyanobacterial growth. Front. Miscrobiol. 13, 837198. https://doi.org/10.3389/fmicb.2023.837198 (2023).

    Google Scholar 

  47. Dumont, M. G. Community-level analysis: key genes of aerobic methane oxidation. Environmental microbiology, Leadbetter (Elsevier Academic, 2005). 0-12-182802-6, 978-0-12-182802-8.

  48. Navarro, R. M., del Valle, F., de la Villario, J. A., Alvarez-Galvan, M. C. & Fierro, J. L. G. Photocatalytic water splitting under visible light: Concept and catalysts development. Adv. Chem. Eng. 36, 111–143 (2009).

    Google Scholar 

  49. Ismail, A. A. & Bahnemann, D. W. Photochemical splitting for hydrogen production by photocatalysys: A review. Solar Energy Mater. Solar Cells. 128, 85–101 (2014).

    Google Scholar 

  50. Xing, J., Fang, W. Q. & Zhao, H. J. Inorganic photocatalysts for overall water splitting. Chem. Asian J. 7, 642–657 (2012).

    Google Scholar 

  51. Tachibana, Y., Vayssieres, L. & Durrant, J. R. Artificial photosynthesis for solar water-splitting. Nat. Photonics. 6, 511–518 (2012). \.

    Google Scholar 

  52. Kasem, K. K. & Dahn, M. Photodissociation of water using colloidal nanoparticles of doped titanium (IV) oxide semiconductors for hydrogen production. Curr. Sci. 99, 1068–1073 (2010).

    Google Scholar 

  53. Yan, Z. et al. Respiration-driven methanotrophic growth of diverse marine methanogens. Proc. Natl. Acad. Sci. U. S. A. 120, e2303179120 (2023).

    Google Scholar 

  54. Bahcall, J. N. & Pinsonneault, M. H. Standard solar models, with and without helium diffusion, and the solar neutrino problem. Rev. Mod. Phys. 64, 885–926 (1992).

    Google Scholar 

  55. Feulner, G. The young Sun problem. Rev. Geophys. 50, RG2006 (2012).

    Google Scholar 

  56. Canuto, V. M., Levine, J. S., Augutsson, T. R. & Imhoff, C. L. UV radiation from the young Sun and oxygen and ozone levels in the prebiological palaeatmosphere. Nature 296, 816–821 (1982).

    Google Scholar 

  57. Lee, K., Nam, W. S. & Han, G. Y. Photocatalytic water-splitting in alkaline solution using redox mediator. 1: Parameter study. Int. J. of Hydrogen Energy 29, 1343–1347 (2004).

    Google Scholar 

  58. Hameed, A., Gondai, M. A. & Yamani, Z. H. Significance of pH measurements in photocatalytic splitting of water using 355 nm UV laser. J. of Molecular Catalysis A. Chemical 227, 241–246 (2005).

    Google Scholar 

  59. Taylor, C. E. Methane conversion via photocatalytic reactions. Catal. Today 84, 9–15 (2003).

    Google Scholar 

  60. Yang, W., Zhou, H. & Cicek, N. Treatment of organic micropollutants in water and wastewater by UV-based processes: A critical literature review. Crit. Rev. Environ. Sci. Technol. B44, 1443–1476 (2013).

    Google Scholar 

  61. Ogura, K. & Kataoka, M. Photochemical conversion of methane. J. Mol. Catal. 43, 371–379 (1988).

    Google Scholar 

  62. Dunn, W., Aikawa, Y. & Bard, A. l. Heterogeneous photosynthetic production of amino acids at Pt/TiO2 suspension by near ultraviolet light. J. Chem. Soc. 183, 6893–6898 (1981).

    Google Scholar 

  63. Ponnamperuma, C., Lemmon, R. M. & Mariner, R. Formation of adenine by electron irradiation of methane, ammonia, and water. Proc. Natl. Acad. Sci. U. S. A. 49, 737–740 (1963).

    Google Scholar 

  64. Barber, J. Photosynthetic energy conversion: Natural and artificial. Chem. Soc. Rev. 38, 185–196 (2009).

    Google Scholar 

  65. Hedges, B. & Kumar, S. The Timetree of Life (Oxford Univ. Press, 2009).

    Google Scholar 

  66. Hamilton, T. L., Bryant, D. & Macalady, J. L. The role of biology in planetary evolution: Cyanobacterial primary production in low-oxygen Proterozoic oceans. Environ. Microbiol. 18, 325–340 (2016).

    Google Scholar 

  67. Fisher, W. W., Hemp, J. & Johnson, J. E. Evolution of oxygenic photosynthesis. Annu. Rev. Earth Planet. Sci. 44, 647–83 (2016).

    Google Scholar 

  68. Cardona, T., Sanchez-Baracald, P., Rutherford, A. W. & Larkum, A. W. Early Archean origin of Photosystem II. Geobiology 17, 127–150 (2019).

    Google Scholar 

  69. Cardona, T. Thinking twice about the evolution of photosynthesis. Open Biol. 9, 180246 (2019).

    Google Scholar 

  70. Kato, Y., Kano, T. & Kunugiza, K. Negative Ce anomaly in the Indian banded iron formations: Evidence for the emergence of oxygenated deep-sea at 2.9–2.7 Ga. Resour. Geol. 52, 101–110 (2002).

    Google Scholar 

  71. Ohmoto, H. Evidence in pre-2.2 Ga paleosol for the early evolution of atmospheric oxygen and terrestrial biota. Geology 24, 1135–1138 (1996).

    Google Scholar 

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Acknowledgements

We wish to thank B. Hedges, D. Bryant, T. Cardona, T. Kakegawa, P. Knauth, L. Kump, S. Ono, S. Poulson, A. Sicree, K. Spangler, Y. Watanabe and A. Whitfield for discussions and comments on an earlier manuscript.

Author information

Authors and Affiliations

  1. Department of Geosciences, The Pennsylvania State University, University Park, PA, 16802, USA

    Hiroshi Ohmoto

  2. Faculty of Science, Tohoku University, Sendai, 980, Japan

    Hiroshi Ohmoto

  3. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA

    James Gregory Ferry

Authors
  1. Hiroshi Ohmoto
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  2. James Gregory Ferry
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HO & JGF conceived the primary concepts, and wrote the manuscript. HO constructed all figures with inputs from JGF.

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Correspondence to Hiroshi Ohmoto or James Gregory Ferry.

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Ohmoto, H., Ferry, J.G. The hydrogen, methane and ammonia biosphere on early Earth. Sci Rep (2026). https://doi.org/10.1038/s41598-026-43917-7

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  • Received: 31 July 2024

  • Accepted: 09 March 2026

  • Published: 18 March 2026

  • DOI: https://doi.org/10.1038/s41598-026-43917-7

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Keywords

  • Origin and evolutions of life
  • Methane and ammonia rich early atmosphere
  • Photocatalysis
  • Methanotrophs
  • Photosystem II
  • Cyanobacteria
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