How prehistoric plants and microbes solved Earth's nitrogen crisis eons before synthetic fertilizers
For billions of years, life on Earth faced a paradoxical crisis: surrounded by an atmosphere rich in nitrogen, organisms were starving for lack of it.
This essential building block of DNA and proteins was locked away in an unusable form, creating a major barrier to life's expansion. The solution emerged from some of nature's most ancient partnerships—collaborations between plants and microbes that would shape our planet's future. Recent discoveries have revealed that these biological nitrogen-fixing relationships are far older and more sophisticated than scientists ever imagined.
Nitrogen is fundamental to all known life, forming crucial components of DNA, RNA, and proteins. Yet most organisms cannot access the abundant nitrogen that makes up 78% of our atmosphere. The reason lies in chemistry: atmospheric nitrogen consists of two atoms triply bonded together (N₂), creating one of the strongest chemical bonds in nature 1 .
Breaking this bond requires enormous energy. In nature, only lightning strikes, volcanic activity, and meteor impacts could convert atmospheric nitrogen into usable forms before life found a way . This severely limited the amount of nitrogen available to early life, creating what scientists consider the primary limitation to plant growth in most ecosystems even today 1 .
DNA & RNA
Proteins
Energy Transfer
Nitrogen is a fundamental component of all living organisms, yet atmospheric nitrogen (N₂) is chemically inert and inaccessible to most life forms.
The breakthrough came when certain microbes evolved nitrogenase, an enzyme complex capable of breaking nitrogen's powerful bonds. This enzyme allowed them to convert atmospheric nitrogen into ammonia, a form other organisms could utilize 4 . This process, called biological nitrogen fixation, required staggering amounts of energy—16 molecules of ATP for each nitrogen molecule fixed, compared to just 3 ATP molecules to fix carbon dioxide through photosynthesis 1 .
The earliest evidence of biological nitrogen fixation comes from 3.8-billion-year-old rocks in the Isua Supracrustal Belt in Greenland . Scientists analyzing nitrogen levels in these ancient formations found concentrations that could not be explained by non-biological processes alone.
"When I developed a model of abiotic nitrogen processes that could have played a role in early Earth, the results showed that such abiotic processes alone could not explain the nitrogen levels seen in the Isua rocks," said Eva Stüeken, a researcher with the NASA Astrobiology Institute. "Under abiotic conditions, it is impossible to accumulate so much nitrogen in sediments. Life, on the other hand, can easily accumulate so much nitrogen" .
This finding pushed back the evidence of life's involvement in the nitrogen cycle to before 3.8 billion years ago, suggesting nitrogen-fixing organisms were among Earth's earliest life forms.
Elevated nitrogen levels in Isua Supracrustal Belt rocks
Earliest potential evidence of biological nitrogen fixation
Evolution of symbiotic nitrogen fixation in plants 7
Major expansion of nitrogen-fixing plants during high CO₂ period
Discovery of nitroplast organelle 9
First confirmed nitrogen-fixing organelle in a eukaryotic cell
For billions of years, nitrogen fixation remained exclusively the domain of bacteria and archaea. Then, around 100 million years ago, during the late Cretaceous period, a revolutionary development occurred: plants began forming symbiotic relationships with nitrogen-fixing bacteria 7 .
This era featured atmospheric CO₂ levels approximately four times higher than present concentrations 7 . In this carbon-rich environment, plants could better afford the enormous energy expense of nitrogen fixation. Multiple plant families independently evolved the ability to host nitrogen-fixing bacteria in specialized root structures called nodules 1 .
The evolution of this symbiosis occurred through a process of convergent evolution, where similar traits develop independently in different lineages. Researchers from the Florida Museum of Natural History found that chemical receptors plants use to recognize nitrogen-fixing bacteria evolved independently at least three separate times 1 .
"Beans are in other ways not a burdensome crop to the ground, they even seem to manure it...wherefore the people of Macedonia and Thessaly turn over the ground when it is in flower,"
— Theophrastus (350-287 B.C.) 1
This quote shows how ancient farmers recognized this beneficial relationship long before the science was understood.
Biological nitrogen fixation occurs through the action of the nitrogenase enzyme complex, which contains unusual metal clusters in its active site 5 . The process follows this essential reaction:
N₂ + 8H⁺ + 8e⁻ + 16ATP → 2NH₃ + H₂ + 16ADP + 16Pi 5
This energy-intensive process explains why nitrogen-fixing organisms are so selective about when and where they perform it. The enzyme is also highly sensitive to oxygen, which presented a major challenge when oxygen began accumulating in Earth's atmosphere approximately 2.4 billion years ago 4 .
To understand why nitrogen fixation evolved when it did, researchers designed an innovative experiment comparing plant performance under ancient and modern atmospheric conditions 7 .
Scientists grew three species of nitrogen-fixing plants (Alnus species) and their non-fixing close relatives (Betula species) under two different CO₂ levels:
All plants were grown across a gradient of soil nitrogen availability, equivalent to 0, 10, 50, and 200 kg N ha⁻¹ year⁻¹ 7 .
The results revealed that under ancient CO₂ levels, nitrogen-fixing plants maintained competitive advantage over non-fixers at more than twice the soil nitrogen level compared to modern conditions. Specifically, the nitrogen level where both plant types performed equally well was:
The experiment also demonstrated that nitrogen-fixing plants could partially downregulate their energy-intensive fixation in response to increased soil nitrogen availability, reducing biomass allocation to nodules from 0.98% to 0.17% as nitrogen additions increased 7 .
| Condition | N Level Where Plant Types Perform Equally | Nodule Biomass Allocation at High N |
|---|---|---|
| Ancient CO₂ (1600 ppm) | 61 kg N ha⁻¹ year⁻¹ | Decreased to 0.17% |
| Modern CO₂ (400 ppm) | 27 kg N ha⁻¹ year⁻¹ | Decreased to 0.17% |
| Research Tool | Application |
|---|---|
| Nitrogen isotope analysis | Identifying biological vs. abiotic nitrogen fixation in ancient rocks |
| Soft X-ray tomography | Visualizing intracellular structures and organelle relationships 9 |
| Proteomic analysis | Determining protein origins and organelle integration 9 |
| Single-cell RNA sequencing | Mapping gene expression in different nodule cell types 6 |
In a groundbreaking 2024 discovery, scientists confirmed the first known nitrogen-fixing organelle, termed the "nitroplast," in the marine alga Braarudosphaera bigelowii 9 . This organelle evolved from a cyanobacterial endosymbiont (UCYN-A) that began integrating with the alga approximately 100 million years ago.
The nitroplast represents an intermediate stage in organelle evolution. It imports essential proteins from the host cell—including a redox protein called flavodoxin crucial for nitrogen fixation—and divides in synchrony with other host organelles 9 .
"This is a very interesting paper," said Verena Kreichbaumer, a plant cell biologist at Oxford Brookes University who was not involved in the study. "It's solid science based on a lot of controls" 9 .
Age: >1 billion years
Source: Purple bacterium
Function: Energy production
Age: >1 billion years
Source: Cyanobacterium
Function: Photosynthesis
Age: ~100 million years
Source: Cyanobacterium (UCYN-A)
Function: Nitrogen fixation
Age: ~100 million years
Source: Cyanobacterium
Function: Photosynthesis
Understanding ancient nitrogen fixation has profound implications for addressing modern challenges. With synthetic nitrogen fertilizer production consuming 1% of global energy expenditure annually and causing significant environmental pollution, researchers are looking to transfer natural nitrogen-fixing capabilities to crop plants 8 .
The discovery of the nitroplast suggests nitrogen-fixing organelles might be engineered into eukaryotic cells. As one research team noted, "Biological nitrogen fixation plays a crucial role in the global nitrogen cycle and holds significant potential for reducing the reliance on chemical fertilizers" 8 .
Transferring nitrogen-fixing capabilities to major cereal crops could revolutionize agriculture.
Reducing dependence on energy-intensive synthetic fertilizers.
Decreasing nitrogen pollution in waterways and reducing greenhouse gas emissions.
Studying these ancient biological partnerships continues to reveal nature's innovative solutions to fundamental challenges—solutions that may help build a more sustainable agricultural future.
From Earth's earliest microbes to modern laboratory discoveries, the story of nitrogen fixation demonstrates life's remarkable ability to overcome even the most daunting chemical barriers through collaboration and evolutionary innovation.