Southern Ocean’s Weakened Carbon Pump Helped Fuel Earth’s Hottest Climate in 65 Million Years

Around 50 million years ago, during the Early Eocene Climatic Optimum (roughly 53- 49 million years ago), Earth was in its warmest climate of the past 65 million years (since the dinosaur extinction).

Global temperatures were more than 10°C higher than today, and atmospheric CO₂ reached about 1,600 ppm.

The biological carbon pump is a key natural process in the ocean that transfers carbon from the surface waters (and ultimately the atmosphere) into the deep ocean, where it can remain sequestered for hundreds to thousands of years.

Illustration of a sunlit ocean with marine particles and microscopic organisms beneath a mountainous island, titled “Southern Ocean’s Weakened Carbon Pump Helped Fuel Earth’s Hottest Climate in 65 Million Years.”
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Around 50 million years ago, during the Early Eocene Climatic Optimum (roughly 53- 49 million years ago), Earth was in its warmest climate of the past 65 million years (since the dinosaur extinction).

Global temperatures were more than 10°C higher than today, and atmospheric CO₂ reached about 1,600 ppm. Volcanic sources alone do not fully explain the sustained high CO₂; an international team (led by the Max Planck Institute for Chemistry, with key contributions from Université libre de Bruxelles researchers including François Fripiat) identified a major role for the Southern Ocean.

Key Mechanism: Weakened Biological Carbon Pump

The biological carbon pump is the process by which phytoplankton (algae) take up CO₂ in surface waters as they grow. When they die, some of that carbon sinks into the deep ocean, where it can stay sequestered for centuries to millennia, helping keep atmospheric CO₂ lower.

Researchers analyzed nitrogen isotopes (δ¹⁵N) preserved in the organic matter inside fossil shells of foraminifera (tiny single- celled marine organisms) from Ocean Drilling Program sediment cores at four Southern Ocean sites.

These isotopes record how completely phytoplankton used available nutrients (especially nitrate) in surface waters. Higher surface nitrate (less complete utilization) signals a less efficient pump.⁠

At the peak of Eocene warmth, Southern Ocean phytoplankton used roughly 40% less of the available nutrients than in cooler periods before and after.

This made the biological pump less efficient, so less carbon was transferred to the deep ocean and more CO₂ could accumulate in (or be released to) the atmosphere.⁠

Impact on Atmospheric CO₂

Using a numerical ocean- atmosphere model, the team quantified the effect:

  • The 40% reduction in nutrient utilization alone raised CO₂ from ~700 ppm to ~900 ppm.
  • Including warming and seawater-chemistry feedback, levels rose to about 1,100 ppm.
  • This accounts for at least half of the roughly 800 ppm CO₂ increase during the period.⁠

Eocene seawater had lower buffering capacity (due to lower pH and higher calcium ion concentrations) than today’s ocean, so changes in the biological pump had a stronger effect on atmospheric CO₂.

Why the High CO₂ Persisted for Millions of Years

Earth’s natural “thermostat”– chemical weathering of silicate rocks that removes CO₂ from the atmosphere, was less effective.

Before major mountain ranges such as the Alps and Himalayas rose (mainly 50- 30 million years ago), continents were relatively flat and deeply weathered, offering less fresh rock for weathering.

With this slowdown, extra CO₂ released from the ocean could stay in the atmosphere much longer, allowing Southern Ocean processes to influence climate over millions of years (rather than just the millennial scales seen in ice-age cycles).

Broader Context and Implications

This Southern Ocean feedback (warming → reduced biological pump efficiency → more atmospheric CO₂ → further warming) also operated during Pleistocene interglacials. Its appearance under very different boundary conditions (a hot greenhouse world lasting millions of years) points to a robust mechanism.

Researchers are examining whether it played a similar role in other sustained warm periods.⁠

The study was published in Nature Geoscience (2026) under the title “Elevated early Eocene atmospheric CO₂ tied to reduced Southern Ocean biological pump efficiency” (DOI: 10.1038/s41561-026-02142-7).

The team included scientists from ULB, UC Santa Cruz, University of Ferrara, Utrecht University, and several other institutions.

Note on modern relevance: Today’s CO₂ rise is far faster (roughly 10- 100 times) and driven by human fossil- fuel emissions, unlike these slow natural geological processes.

Polar map showing Antarctica, the 30°S and 60°S latitude lines, a green boundary, and four labeled colored markers: 1263A, 690B, 738B/C, and 762C.
Locations of EECO sites investigated in this study on a palaeogeographic reconstruction. Credit: Nature Geoscience (2026). DOI: 10.1038/s41561-026-02142-7

The biological carbon pump is a key natural process in the ocean that transfers carbon from the surface waters (and ultimately the atmosphere) into the deep ocean, where it can remain sequestered for hundreds to thousands of years.

How It Works (Step by Step)

  1. Uptake in Surface Waters (Photosynthesis)
    In the sunlit upper ocean (euphotic zone), phytoplankton (microscopic algae) use sunlight to convert dissolved carbon dioxide (CO₂) and nutrients (especially nitrate, phosphate, and iron) into organic matter through photosynthesis.
    Simplified reaction:CO2+H2O+nutrients→lightorganic matter+O2This lowers the concentration of dissolved CO₂ in surface waters, allowing more CO₂ from the atmosphere to dissolve into the ocean.
  2. Transfer Through the Food Web
    Some of the organic carbon is consumed by zooplankton and larger organisms. A portion is respired back to CO₂ in the surface layer, but another portion becomes particulate organic carbon (POC) in the form of dead cells, fecal pellets, and aggregates known as “marine snow.”
  3. Export to the Deep Ocean (Sinking)
    Gravity causes a fraction of this particulate organic carbon to sink out of the surface layer into the deep ocean. This downward flux is the core of the “pump.” Only a small percentage of the carbon fixed by photosynthesis typically reaches the deep sea; most is recycled in the upper ocean.
  4. Remineralization at Depth
    In the deep ocean, bacteria and other microbes break down (remineralize) the sinking organic matter, converting it back into dissolved inorganic carbon (CO₂ and related forms) and releasing the associated nutrients.
    Because deep waters are isolated from the atmosphere for long periods (centuries to millennia, depending on ocean circulation), this carbon remains sequestered until upwelling or deep mixing eventually returns it to the surface.

Soft- Tissue vs. Carbonate Pump

  • The main process described above is often called the soft- tissue pump (organic carbon).
  • There is also a carbonate pump, in which organisms that build calcium carbonate shells (e.g., some foraminifera and coccolithophores) remove alkalinity and can actually counteract some of the CO₂ drawdown, but the soft-tissue pump is the dominant carbon-sequestering mechanism.

Factors That Control Efficiency

The pump’s strength depends on:

  • How completely phytoplankton use available nutrients (nutrient utilization efficiency).
  • The fraction of organic matter that sinks rather than being recycled near the surface (export efficiency).
  • Ocean circulation, temperature, light, and nutrient supply (especially iron in high-nutrient, low- chlorophyll regions like the Southern Ocean).

A more efficient pump draws more CO₂ out of the atmosphere. A weaker pump leaves more CO₂ in surface waters (or allows more deep-ocean CO₂ to escape to the atmosphere), raising atmospheric levels.

Climate Relevance

Over glacial– interglacial cycles and longer timescales, changes in the biological carbon pump, particularly in the Southern Ocean, have significantly influenced atmospheric CO₂ concentrations.

In the Early Eocene Climatic Optimum study discussed previously, reduced nutrient utilization (about 40% lower) in the Southern Ocean weakened the pump and helped elevate atmospheric CO₂ by hundreds of parts per million, amplifying global warmth.

In short, the biological carbon pump acts as a biological “conveyor” that links surface productivity to long- term carbon storage in the deep ocean, playing a central role in regulating Earth’s climate.

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Elevated early Eocene atmospheric CO2 tied to reduced Southern Ocean biological pump efficiency

This paper investigates why atmospheric CO₂ reached extremely high levels (~1,600 ppm) during the Early Eocene Climatic Optimum (EECO; ~53–49 million years ago), one of the warmest intervals of the past 66 million years. The authors show that a weakening of the Southern Ocean’s biological carbon pump played a major role.

The team measured foraminifera-bound nitrogen isotopes (FB-δ¹⁵N) in fossil shells from four Ocean Drilling Program (ODP) sites:

  • Southern Ocean, high- latitude: Sites 690 and 738
  • Mid- latitude: Sites 1263 (Atlantic) and 762 (Indian Ocean)

Nitrogen isotopes track how completely phytoplankton consumed nitrate (NO₃⁻) in surface waters. Phytoplankton preferentially take up the lighter isotope (¹⁴N), so incomplete nutrient use leaves residual nitrate enriched in ¹⁵N. By comparing the Southern Ocean FB- δ¹⁵N stack with the mid- latitude stack (which approximates the deep-ocean nitrate δ¹⁵N baseline), they calculated changes in the degree of nutrient consumption (Δf).

Key Findings

  • During peak EECO warmth, Southern Ocean phytoplankton used ~40% less of the available nutrients than before or after.
  • This indicates higher surface nitrate concentrations and a less efficient biological carbon pump.
  • Less carbon was sequestered in the deep ocean, allowing more CO₂ to accumulate in (or be released to) the atmosphere.
  • The effect was amplified by the low seawater buffering capacity of the Eocene ocean (lower pH and higher Ca²⁺ concentrations).
  • Modeling shows this change alone can raise CO₂ from ~700 ppm to ~900- 1,100 ppm (accounting for warming and chemistry feedback), explaining at least half of the observed ~800 ppm rise during the EECO.

Supporting evidence includes reduced vertical δ¹³C gradients (indicating weaker global biological pump efficiency), reduced density stratification in the Southern Ocean, and other paleoceanographic indicators of enhanced deep-ocean ventilation.

Broader Implications

The same Southern Ocean feedback (warming → reduced nutrient utilization → weaker biological pump → higher atmospheric CO₂ → further warming) operated during Pleistocene interglacials, but here it is shown to have functioned under very different (much warmer and longer- lasting) conditions.

Low silicate- rock weatherability during the Eocene likely weakened Earth’s long- term CO₂ “thermostat”, allowing the elevated CO₂ to persist for millions of years.

The paper is led by researchers including Simone Moretti and Alfredo Martínez- García (Max Planck Institute for Chemistry), with contributions from François Fripiat (Université libre de Bruxelles) and others.

Journal: Nature Geoscience, Open access

DOI: 10.1038/s41561-026-02142-7

Provided: Université libre de Bruxelles

Published: 06 November 2026

Authors: Simone Moretti,
François Fripiat,
Mathis P. Hain,
Valeria Luciani,
Lucas Lourens,
Paul Borucki,
Lukas Gerber,
Tobias Agterhuis,
Laura Haynes,
Giulia Filippi,
Ralf Schiebel,
Gerald H. Haug,
Daniel M. Sigman &
Alfredo Martínez-García

Abstract

The Early Eocene Climatic Optimum (53 to 49 million years ago) was an interval in Earth’s history when reconstructed temperatures and atmospheric CO2 concentrations were among the highest of the Cenozoic Era (that is, the last 66 million years). The causes of the high CO2 levels remain unclear. CO2 changes over recent ice age cycles appear to be largely controlled by the biologically mediated build-up and release of carbon from the Southern Ocean, a process that might have also played a role earlier in the Cenozoic. Here we test this possibility with foraminifera-bound nitrogen isotope measurements. Our data show higher surface nitrate concentrations in the Southern Ocean, and thus a more inefficient biological sequestration of carbon during peak Early Eocene Climatic Optimum. The associated transfer of CO2 from the deep ocean to the atmosphere would have been amplified by the low seawater buffering capacity of the Eocene, due to the lower pH and high Ca ion concentration. Previously proposed low silicate rock weatherability during the Eocene may have weakened the weathering thermostat, allowing the reconstructed change in biological pump efficiency in the Southern Ocean to explain at least half of the atmospheric CO2 increase observed during the Early Eocene Climatic Optimum.