Introducing the "nitroplast" -- The first nitrogen-fixing organelle

In a remarkable scientific breakthrough, an international team of researchers has discovered the “nitroplast” — first known nitrogen-fixing organelle within a eukaryotic cell.

This finding challenges the long-held belief that only bacteria can convert atmospheric nitrogen into a biologically usable form.

The nitroplast organelle discovery marks the fourth instance of primary endosymbiosis in history, a process where a prokaryotic cell is engulfed by a eukaryotic cell and evolves into an organelle.

Significance of the nitroplast discovery

The discovery of the nitroplast was made by a team led by Tyler Coale, a postdoctoral scholar at UC Santa Cruz, and Jonathan Zehr, a distinguished professor of marine sciences at the same institution. The findings were published in two recent papers, showcasing the importance of their work.

“It’s very rare that organelles arise from these types of things. The first time we think it happened, it gave rise to all complex life,” Coale explained.

“Everything more complicated than a bacterial cell owes its existence to that event, referring to the origins of the mitochondria. A billion years ago or so, it happened again with the chloroplast, and that gave us plants,” he continued.

Breaking the nitrogen fixation paradigm

The path to discovering the nitroplast was a long and arduous one, spanning decades of research. In 1998, Zehr found a short DNA sequence of what appeared to be an unknown nitrogen-fixing cyanobacterium in Pacific Ocean seawater. He and his colleagues spent years studying the mystery organism, which they called UCYN-A.

Simultaneously, Kyoko Hagino, a paleontologist at Kochi University in Japan, was working tirelessly to culture a marine alga, which turned out to be the host organism for UCYN-A.

After more than 300 sampling expeditions and over a decade of work, Hagino successfully grew the alga in culture, enabling other researchers to study UCYN-A and its marine alga host together in the lab.

Nitroplast evolution from symbiosis to organelle

Initially, scientists considered UCYN-A an endosymbiont closely associated with an alga. However, the two recent papers suggest that UCYN-A has co-evolved with its host beyond symbiosis and now meets the criteria for an organelle.

In a paper published in Cell in March 2024, Zehr and colleagues demonstrated that the size ratio between UCYN-A and their algal hosts is similar across different species of the marine haptophyte algae Braarudosphaera bigelowii.

Their model showed that the growth of the host cell and UCYN-A are controlled by the exchange of nutrients, with their metabolisms linked. This synchronization in growth rates led the researchers to call UCYN-A “organelle-like.”

“That’s exactly what happens with organelles,” said Zehr. “If you look at the mitochondria and the chloroplast, it’s the same thing: they scale with the cell.”

Confirming the organelle status

To confidently classify UCYN-A as an organelle, the scientists needed to confirm additional lines of evidence. In the cover article of the journal Science, Zehr, Coale, Kendra Turk-Kubo, Wing Kwan Esther Mak, and collaborators showed that UCYN-A imports proteins from its host cells.

“That’s one of the hallmarks of something moving from an endosymbiont to an organelle,” said Zehr. “They start throwing away pieces of DNA, and their genomes get smaller and smaller, and they start depending on the mother cell for those gene products — or the protein itself — to be transported into the cell.”

Coale’s work on the proteomics for the study revealed that the host cell makes proteins and labels them with a specific amino acid sequence, signaling the cell to send them to the nitroplast.

The nitroplast then imports and uses these proteins, filling gaps in certain pathways within UCYN-A. “It’s kind of like this magical jigsaw puzzle that actually fits together and works,” said Zehr.

Implications for ocean ecosystems and agriculture

The discovery of the nitroplast provides new insights into ocean ecosystems. UCYN-A is globally important for its ability to fix nitrogen from the atmosphere, and researchers have found it in various locations, from the tropics to the Arctic Ocean, where it fixes a significant amount of nitrogen.

“It’s not just another player,” said Zehr.

The nitroplast also has the potential to revolutionize agriculture. The Haber-Bosch process, which synthesizes ammonia fertilizers from atmospheric nitrogen, allowed agriculture and the world population to take off in the early 20th century.

However, it also creates enormous amounts of carbon dioxide, accounting for about 1.4% of global emissions. Researchers have been trying to find a way to incorporate natural nitrogen fixation into agriculture for decades.

“This system is a new perspective on nitrogen fixation, and it might provide clues into how such an organelle could be engineered into crop plants,” said Coale.

Importance of nitroplasts and the nitrogen cycle

The nitrogen cycle, as discussed above, plays a crucial role in sustaining life on our planet. This biogeochemical cycle involves the continuous movement of nitrogen through the atmosphere, soil, and living organisms.

Understanding the nitrogen cycle helps us appreciate the delicate balance of ecosystems and the importance of maintaining this balance for the well-being of all life forms.

Stages of the nitrogen cycle

Nitrogen fixation

As mentioned previously, nitrogen fixation converts atmospheric nitrogen (N2) into biologically usable forms, such as ammonia (NH3) and nitrates (NO3-).

Lightning and certain bacteria, such as Rhizobium, perform this process naturally. Humans also contribute to nitrogen fixation through industrial processes like the Haber-Bosch process, which produces ammonia for fertilizers.

Assimilation

Plants absorb the biologically usable forms of nitrogen from the soil through their roots. They incorporate these nitrogen compounds into their tissues, creating amino acids, proteins, and other essential biomolecules. Animals obtain nitrogen by consuming plants or other animals that have already assimilated nitrogen.

Ammonification

When plants and animals die, decomposers like bacteria and fungi break down their tissues, releasing nitrogen in the form of ammonium (NH4+) into the soil. This process, called ammonification, makes nitrogen available for other organisms to use.

Nitrification

Nitrifying bacteria, such as Nitrosomonas and Nitrobacter, convert ammonium into nitrites (NO2-) and then nitrates (NO3-) through the process of nitrification. Plants readily absorb these nitrates from the soil.

Denitrification

Denitrifying bacteria, found in anaerobic conditions like waterlogged soils, convert nitrates back into atmospheric nitrogen gas (N2). This process, called denitrification, completes the nitrogen cycle by returning nitrogen to the atmosphere.

Human impact on the nitrogen cycle

Human activities, such as the excessive use of nitrogen-based fertilizers and the burning of fossil fuels, have significantly altered the nitrogen cycle.

These activities have led to an increased presence of nitrogen in the environment, causing problems like water pollution, soil acidification, and greenhouse gas emissions.

Sustainable agricultural practices and reduced reliance on fossil fuels can help mitigate these issues and restore balance to the nitrogen cycle.

By understanding the stages of the nitrogen cycle and the impact of human activities on this process, we can work towards maintaining the delicate balance of our ecosystems.

Protecting the nitrogen cycle is essential for ensuring the health and well-being of our planet and all its inhabitants.

Nitroplasts: Revolutionary discovery in eukaryotic cells

In summary, the discovery of the nitroplast is a milestone in the field of biology, challenging long-held beliefs and opening up new avenues for research.

While many questions about UCYN-A and its algal host remain unanswered, this finding is undoubtedly one for the textbooks.

As the first of its kind, the nitroplast provides a fresh perspective on organellogenesis and has the potential to impact both ocean ecosystems and agriculture.

The research team, led by Kendra Turk-Kubo, an assistant professor at UC Santa Cruz, will continue to investigate the intricacies of UCYN-A and its host, paving the way for further groundbreaking discoveries in the future.

The full study was published in the journal Science.

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