Eukaryogenesis Exposed: The Collapse of Endosymbiotic Theory

Claim: The article by Mironov, A et al. from 2021 claims that all eukaryotic cells possess either Golgi complexes or remnants thereof, along with a minimal set of proteins essential for intracellular transport. The authors propose that the ER and Golgi complex evolved together, with their development closely linked to the emergence of intracellular transport mechanisms. This suggests that even the simplest eukaryotes retain fundamental aspects of the ER-Golgi system, highlighting its essential role in eukaryotic cell evolution. 1

Response: The ER and its complex components, including the ERAD system, smooth and rough ER, and ER-mitochondria contact sites, present significant challenges to evolutionary explanations. The interdependence of these structures, their irreducible complexity, and the absence of viable intermediate forms make gradual evolutionary processes unlikely. Recent studies have revealed unexpected levels of complexity in these systems, further complicating evolutionary scenarios. The simultaneous development of multiple complex components, such as protein translocation mechanisms and specialized membrane structures, seems implausible through step-wise evolutionary processes. These observations suggest that the origin of the ER and its associated systems can hardly be explained by unguided evolutionary mechanisms.

Claim: The paper by Vesteg and Krajčovič (2008) 2 presents a hypothesis for the origin of eukaryotic cells, suggesting that the endoplasmic reticulum (ER) and nuclear membranes evolved from the inner membrane of a pre-karyotic ancestor. This ancestor, which might have been a remnant of the pre-cellular world, could have harbored α-proteobacteria as parasitic entities in its intermembrane space. The paper proposes that the eukaryotic cytoplasm corresponds to the pre-karyote's periplasm, while the nucleoplasm is derived from the pre-karyote's cytoplasm. The model implies that mitochondria's ancestors were parasitic α-proteobacteria infecting the pre-karyotic intermembrane space, analogous to Bdellovibrio's infection of Gram-negative bacteria's periplasm.

Response:  The scientific paper posits a novel hypothesis on the supposed evolution of eukaryotic cells, particularly focusing on the origin of the endoplasmic reticulum (ER) and nuclear membranes. This hypothesis suggests that these structures derived from the inner membrane of a pre-karyotic ancestor, which harbored α-proteobacteria as parasitic entities in its intermembrane space. However, several critical aspects of this hypothesis warrant a thorough examination to highlight its limitations and the inherent challenges in explaining such complex evolutionary processes. Firstly, the development of the ER would necessitate the formation of a membrane-bound compartment capable of protein and lipid synthesis, along with the establishment of complex systems for protein folding, quality control, and transport. Additionally, the nuclear envelope would require a double-membrane structure with nuclear pore complexes to regulate nucleo-cytoplasmic transport, alongside mechanisms for DNA replication, transcription, and repair. Such an ensemble of features is exceedingly complex and raises questions about the feasibility of their simultaneous evolution under primitive conditions. The paper's hypothesis faces significant deficits in explaining the evolutionary origin of these structures. The idea that the eukaryotic cytoplasm and nucleoplasm could have originated from the pre-karyote's periplasm and cytoplasm, respectively, lacks direct empirical support and detailed mechanistic insights. The interdependencies of the ER and nuclear envelope with other cell structures, such as the cytoskeleton and mitochondria, further complicate the evolutionary narrative. These interdependencies necessitate highly coordinated changes across multiple cellular components, making the evolutionary explanations highly complex and speculative. Moreover, the suggestion that intermediate forms or precursors of these structures could be functional and subject to natural selection is problematic. Intermediate forms of the ER or nuclear envelope without full functionality would likely be non-viable, as partial structures could disrupt cellular homeostasis and fail to confer any selective advantage. This raises doubts about the gradualistic evolutionary model proposed in the paper. Persistent lacunae in the explanations include the lack of detailed pathways for the transition from parasitic α-proteobacteria within a pre-karyote to fully integrated mitochondria and the absence of concrete evidence supporting the proposed membrane derivations. The hypothesis also does not adequately address the origin of the complex machinery required for ER and nuclear envelope functions, such as signal recognition particles, translocons, and nuclear pore complexes. Critically evaluating this hypothesis highlights the need for a more comprehensive understanding of the supposed evolutionary mechanisms underlying the emergence of eukaryotic cellular complexity. While the paper presents a thought provoking model, its speculative nature and the substantial gaps in mechanistic explanations underscore the challenges in reconstructing the evolutionary history of such cellular structures. Future research should aim to provide more concrete evidence and detailed mechanistic insights to support or refute such hypotheses.

References: 

1. Mironov, A. A., Banin, V. V., Sesorova, I. S., Dolgikh, V. V., Luini, A., & Beznoussenko, G. V. (2021). Evolution of the Endoplasmic Reticulum and the Golgi Complex, in Eukaryotic Membranes and Cytoskeleton, pp 61–72. Link

2. Vesteg, M., & Krajčovič, J. (2008). Origin of eukaryotic cells as a symbiosis of parasitic α-proteobacteria in the periplasm of two-membrane-bounded sexual pre-karyotes. Communicative & Integrative Biology, 1(1), 104-113. Link. (This paper proposes a novel hypothesis for the origin of eukaryotic cells, suggesting a symbiosis between parasitic α-proteobacteria and a two-membrane-bounded sexual pre-karyote.) Link

Claim: The scientific paper by Mowbrey, K., & Dacks, J. B. (2009) 1  presents a view of the supposed evolutionary history of the Golgi body across eukaryotes. It claims that the ancestral eukaryote possessed a stacked Golgi body, with at least eight independent instances of Golgi unstacking occurring throughout eukaryotic history. The paper argues that even organisms previously thought to lack Golgi bodies likely possess some form of the organelle, based on molecular evolutionary, genomic, and cell biological evidence. It proposes that the absence of visible Golgi stacks in some unicellular eukaryotes is due to secondary loss or modification rather than primitive absence. The authors suggest that phylogenetic analysis places these "Golgi-lacking" organisms within clades of organisms possessing stacked Golgi bodies, supporting the idea of secondary loss or modification rather than ancestral absence.

Response: The scientific paper presents a view that faces several challenges when subjected to scrutiny. The evolution of the Golgi body from prokaryotic precursors would require multiple, highly specific developments to occur simultaneously. These requirements include the formation of a complex membrane system, the development of specialized protein sorting and modification machinery, the evolution of vesicle trafficking pathways, the emergence of mechanisms for maintaining Golgi structure and polarity, and the creation of a system for Golgi inheritance during cell division. The simultaneous completion of these requirements in primitive conditions poses a significant challenge to the evolutionary hypothesis. The Golgi body is a complex organelle that performs multiple essential functions in eukaryotic cells. Its emergence would necessitate the concurrent development of numerous interdependent systems, each of which is complex in its own right. The probability of all these systems evolving simultaneously through random mutations and natural selection is exceedingly low.

The scientific paper's explanations for the evolutionary origin of the Golgi body exhibit several deficits. The proposed stepwise evolution of Golgi proteins fails to account for the irreducible complexity of the Golgi system. The Golgi's functions are dependent on the coordinated action of multiple proteins and lipids, and the absence of any one component would render the entire system non-functional. The paper does not adequately address how these interdependent components could have evolved gradually while maintaining functionality at each step. The Golgi body's interdependencies with other cell structures further complicate evolutionary explanations. The Golgi is intimately connected with the endoplasmic reticulum, the plasma membrane, and various vesicular transport systems. It plays crucial roles in protein modification, lipid metabolism, and cellular secretion. The evolution of the Golgi would need to be coordinated with the evolution of these other cellular components, adding layers of complexity to an already improbable scenario. The hypothesis that intermediate forms or precursors of the Golgi were functional and selected for by natural processes is problematic. A partially formed Golgi would likely be a detriment to cellular function rather than a benefit. The energy cost of maintaining such a structure without its full functionality would likely result in negative selection pressure. Persistent lacunae in the paper's explanations include the origin of the Golgi's unique membrane composition, the evolution of its complex morphology, and the development of its protein-lipid interactions. The paper also fails to provide a convincing mechanism for the supposed transition from prokaryotic to eukaryotic cellular organization, a fundamental step in the hypothesized evolution of the Golgi body. The evolutionary hypothesis presented in the paper has significant limitations. It relies heavily on sequence homology and phylogenetic analysis, which can be misleading when applied to ancient evolutionary events. The assumption that similarity implies common ancestry does not account for the possibility of convergent evolution or common design. Furthermore, the paper's reliance on the concept of a Last Eukaryotic Common Ancestor (LECA) is speculative and not supported by direct evidence. The scientific paper's claims regarding the supposed evolution of the Golgi body face substantial challenges when critically examined. The complexity and interdependence of the Golgi system, combined with the lack of plausible intermediate forms and the requirement for simultaneous development of multiple components, cast doubt on the proposed evolutionary scenario.

1. Mowbrey, K., & Dacks, J. B. (2009). Evolution and diversity of the Golgi body. FEBS letters, 583(23), 3738-3745. Link. (This review examines the evolutionary history and diversity of the Golgi body across eukaryotes, discussing its presence in various lineages and proposing scenarios for its evolution.)

Where Did Eukaryotic Cells Come From?
https://www.youtube.com/watch?v=4LhBZ2H5SwM&t=1s

Claims: 

Life on Earth emerged at least three and a half billion years ago as prokaryotes. These are simple unicellular organisms. They have a membrane on the outside and cellular machinery inside, all mixed together, touching, and sharing the same environment. This worked, certainly. Life chugged along this way for nearly half of the history of life on Earth.

But then, 1.8 billion years ago, something remarkable happened. Something that led to a tremendous shift in the scope and complexity of life. Something we should all be grateful for because, without that leap, we would not exist. Cells started to... contain cells.

This isn't generally how it's talked about in science class. There you hear that Eukaryotes have "membrane-bound organelles." These are areas of the cell that are separated from the rest of the cytoplasm by membranes, just as the cell itself is separated from the rest of the universe by its membrane. It turns out, different activities require different conditions, and these cells within cells allow for those different conditions. That, in short, is the secret of Eukaryotic success.

But how did it happen? Well, over decades of study, we have determined something shockingly peculiar. Something so odd that it makes us kind of mad that we now discuss it as if it isn't the miracle it is. 1.8 billion years ago, a cell consumed another cell... but then it didn't digest it... it let it reproduce inside of it, and they lived together, and, over time, became the same organism. Or did they?

This is what we call "Endosymbiotic Theory." Mitochondria appeared when the consumed cell was adapted to live in an oxygen-rich environment, and chloroplasts appeared when the swallowed cell was photosynthetic. This idea was deeply controversial when it was first proposed, but as data have continued to come in, endosymbiotic theory has been able to explain more and more about the realities we find. For example, chloroplasts have their own DNA, which they use to create the proteins required for their function.

As we dive deeper into the microcosmos, it just becomes obvious that this happens. This is Paramecium bursaria, a single-celled protozoan that has several hundred algal cells from the genus Chlorella living in its own cytoplasm, making it green. The algae live inside Paramecium bursaria, providing it with fuel in the form of sugar and other substances produced via photosynthesis. And Paramecium bursaria provides protection for the algae from algae eaters and viruses.

P. bursaria is regarded as a predatory protozoan; it feeds on bacteria, small organisms, and, yes, algae. Because of that, it's often thought that the algae in it are temporary symbionts engulfed by Paramecium bursaria's feeding behavior. But in fact, while many other protozoa acquire algae in that manner for temporary use, that is not the case for P. bursaria; its symbionts are continuously inherited from generation to generation through cell division.

The symbiotic Chlorella guide the Paramecium to well-lit areas, so they can photosynthesize more efficiently. The mutual relationship is extremely beneficial for the Paramecium. Even when the Chlorella-containing Paramecium cells are put in nutrition-free saline solution, they can survive for more than 3 months, while cells that didn't have Chlorella died within a week!

This is another single-celled organism with endosymbiotic algae; it's a testate amoeba. A kind of amoeba that builds itself a shell. This species, like some kind of sculptural artist, pulls bits and pieces of mineral from its environment to create these amazing-looking homes. You can see the amoeba extending from the opening of the shell and you can see the green algae in its cytoplasm. Just like Paramecium bursaria, the algae use sunlight to produce food, sharing it with the amoeba while the amoeba provides protection.

Some unicellular organisms don't need oxygen for growth; indeed, the presence of free oxygen can affect them negatively or even kill them. These organisms are known as anaerobes. Such as this one, Metopus. It is an anaerobic ciliate we find in pond sediment, and it has an endosymbiotic relationship with methanogenic archaea.

Now we haven't talked much on this channel about archaea, but they are the third domain of life, along with bacteria and eukaryotes and, like bacteria, they are prokaryotic. We can't wait to do our episode on them someday soon.

Many of the single-celled eukaryotes living in anaerobic environments contain symbiotic prokaryotes; some of these prokaryotes are methanogens, meaning they can use free hydrogen to generate energy and methane. The advantages of having these symbionts are not fully understood, but while Metopus can live without the symbionts, they grow faster when they have them.

Endosymbiosis occurs in multicellular organisms as well. This is a freshwater relative of jellyfish and sea anemones, Hydra! It's simply stuffed full of algal endosymbionts. We collected this Hydra from a nearby pond and cultured it in our aquarium. The benefits provided by the symbiotic relationship here have been well documented, with scientists actually tracking how carbon moves from the environment, into the algae, and then into the hydra. Studies have shown that up to 69% of the caloric requirements of the hydra is satisfied by its algal symbionts. Nice.

So, we see, some organisms temporarily pull in symbionts, others pass them from generation to generation. Some can survive without them, and some cannot. When we look at the algal cells in P. bursaria, we're forced to ask if those cells are part of the organism, or if they're simply cells of one species living in the cells of another. If that's the case, it's worth asking whether the mitochondria in you are you at all, or if they are just another extremely successful species of prokaryote that is particularly reliant on its host cell.

As we look deeper and deeper down, the line between organisms is harder and harder to find. Which is why, if you think hard enough, you might begin to feel like our cells are more than just ourselves.

Thank you for coming on this journey with us as we explore the unseen world that surrounds... and inhabits us.

Journey to the Microcosmos is produced by Complexly, which produces over a dozen shows on YouTube, including SciShow. And we wanted to let you know that the SciShow team has just put out a really interesting new episode.

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Responses

1. Complexity of Eukaryotic Cells:
  - Issue: The transition from prokaryotic to eukaryotic cells involves numerous innovations and modifications that are highly complex. The idea of a gradual transformation is difficult to reconcile with the complex structures and functions observed in eukaryotic cells. The leap in complexity is too vast to be accounted for by small, incremental changes over time.

2. Challenges to Gradual Evolution:
  - Issue: The simultaneous evolution of multiple interdependent components in eukaryotic cells presents a significant challenge. The interdependencies observed suggest that these components must have arisen together to function properly. The likelihood of such coordinated changes occurring through gradual processes is highly improbable.

3. Nuclear Envelope Evolution:
  - Issue: The origin of the nuclear envelope and its integral components, such as nuclear pores, is difficult to explain through gradual evolutionary mechanisms. The complexity and specificity of these structures imply that they could not have evolved step by step without compromising cellular function.

4. Nuclear Pore Complexes (NPCs):
   - Issue: The evolution of NPCs, which are composed of numerous proteins, from simpler prokaryotic systems lacks a clear, plausible pathway. The complex design and assembly of NPCs make it hard to envision how they could have evolved incrementally without each intermediate step being fully functional and advantageous. 

   This critique is not an argument from ignorance because it is based on specific, well-documented challenges and gaps in the current evolutionary explanations. An argument from ignorance would claim that because we do not currently understand a process, it must be false. Instead, this issue points out that:

   - The highly specific and integrated nature of NPCs means that each component must work together seamlessly for the complex to function.
   - Current evolutionary models do not provide detailed, step-by-step pathways showing how each of these components could evolve gradually while remaining functional and advantageous at every stage.
   - The absence of intermediate forms or precursors in both the fossil record and modern biology raises legitimate questions about the feasibility of incremental evolutionary processes.

   Therefore, this critique highlights specific, evidence-based concerns about the explanatory power of current evolutionary models rather than relying on a lack of explanation as proof of impossibility.

5. Lack of Intermediate Forms:
   - Issue: The absence of clear evolutionary intermediates between prokaryotes and eukaryotes in the fossil record is a major concern. The fossil record does not provide the gradual transition expected by evolutionary theory, leaving a significant gap in the evidence for how such complex cells arose. 

   Furthermore, if evolution were true, we would and should expect to see many different transitional forms existing today, exhibiting various degrees of complexity between prokaryotic and eukaryotic cells. These forms should be observable not just in ancient records but in contemporary life as well. Instead, we observe a clear boundary between prokaryotes and eukaryotes. There are no living organisms that straddle this divide in a way that would suggest a gradual evolutionary transition. This stark separation challenges the notion of a smooth, continuous evolutionary process and raises significant questions about the adequacy of current evolutionary models to explain the origin of complex cellular structures. The complete absence of these transitional forms, both in the fossil record and in modern ecosystems, suggests that the evolutionary pathway from prokaryotes to eukaryotes is not well-supported as it is often portrayed.

6. Limitations of Endosymbiotic Theory:
  - Issue: Endosymbiotic theory primarily addresses the origin of mitochondria and chloroplasts but fails to account for the majority of eukaryotic innovations. This leaves many aspects of eukaryotic cell complexity unexplained by current evolutionary models. The integration of multiple theories still does not provide a comprehensive explanation for the emergence of such sophisticated cellular structures.

Problems: 

1. Lack of intermediate forms: There is a scarcity of observable intermediate stages between prokaryotes and eukaryotes, making it difficult to trace the proposed evolutionary pathway.
2. Complexity of eukaryotic features: The sudden appearance of complex eukaryotic features, such as the nucleus, endoplasmic reticulum, and Golgi apparatus, is challenging to explain through gradual evolutionary processes.
3. Membrane differences: The composition of eukaryotic membranes differs significantly from those of both bacteria and archaea, raising questions about the origin of these unique membrane structures.
4. Nuclear pore complexes: The intricate structure and function of nuclear pore complexes, composed of multiple proteins, presents a challenge for step-wise evolutionary explanations.
5. Mitochondrial protein import: The complex machinery for importing proteins into mitochondria appears to be an all-or-nothing system, difficult to explain through gradual evolution.
6. Endoplasmic reticulum origin: The evolution of the endoplasmic reticulum and its connection to the nuclear envelope is not adequately explained by the endosymbiotic theory.
7. Golgi apparatus complexity: The origin and evolution of the Golgi apparatus, with its unique structure and functions, is not well-addressed by the endosymbiotic theory.
8. Cytoskeleton evolution: The eukaryotic cytoskeleton, including microtubules and microfilaments, differs significantly from prokaryotic counterparts, raising questions about its evolutionary origin.
9. Eukaryotic gene content: Many eukaryotic genes have no clear prokaryotic homologs, challenging the idea of a simple merger between prokaryotic genomes.
10. Mitochondrial genome reduction: The extensive reduction of the mitochondrial genome is difficult to explain solely through the endosymbiotic theory.
11. Timing of mitochondrial acquisition: There is ongoing debate about whether mitochondria were acquired early or late in eukaryotic evolution, complicating the endosymbiotic narrative.
12. Origin of meiosis and sex: The evolution of meiosis and sexual reproduction in eukaryotes is not adequately explained by endosymbiosis.
13. Peroxisome origin: The origin of peroxisomes and their relationship to other organelles is not well-explained by the endosymbiotic theory.
14. Nucleus evolution: The formation of the nucleus and its complex regulatory systems presents significant challenges to gradual evolutionary models.
15. Endomembrane system: The origin and evolution of the complex endomembrane system in eukaryotes is not fully addressed by the endosymbiotic theory.
16. Eukaryotic-specific protein domains: Many protein domains found in eukaryotes have no prokaryotic counterparts, raising questions about their evolutionary origin.
17. Mitochondrial division machinery: The complex machinery for mitochondrial division in eukaryotes differs significantly from bacterial cell division systems.


7. Call for Reevaluation:
  - Issue: The complexity and interdependence of eukaryotic structures necessitate a reevaluation of the proposed evolutionary mechanisms. The current body of evidence challenges the adequacy of gradual evolutionary processes to fully account for the origin of eukaryotic cells. Alternative explanations should be considered to address these significant gaps and inconsistencies.

Conclusion

The evolutionary explanations for the origin of eukaryotic cells face substantial challenges given the complexity and intricate design of these cells. The gaps in the fossil record, the improbability of simultaneous co-evolution of interdependent components, and the limitations of existing theories highlight the need for a critical reassessment of how such advanced cellular structures could have arisen.

Evolution of Eukaryotes- How & Why Endosymbiosis Occurred & When First Eukaryotes Evolved | GEO GIRL
https://www.youtube.com/watch?v=yIIQFy_Zsp8

Claims: 

What Defines Eukaryotes?

We humans are biologically eukaryotes, meaning we're multicellular organisms composed of eukaryotic cells rather than prokaryotic cells. But when did eukaryotic cells evolve, and how? The evolution of eukaryotes began with what I'm calling "Pac-Man prokaryotes," but before we discuss that, let's talk about what eukaryotes are and how they differ from prokaryotes.

It's important to remember that the origin of multicellular life like ourselves is not the same as the origin of eukaryotes. Eukaryotes are not defined by multicellularity; single-celled eukaryotes evolved first and still survive today, including protozoans, algae, and fungi. Multicellular life, in which these single-celled eukaryotic organisms evolved into complex forms, came about later. Today, we'll focus on the evolution of eukaryotic cells - the single-cell eukaryotes that preceded multicellularity.

In terms of differences between eukaryotes and prokaryotes:

1. Eukaryotes have a membrane-bound nucleus that stores chromosomes.
2. They possess a cytoskeleton, which allows them to change shape and was crucial in their evolution.
3. Their cell membrane is stiffened by molecules called sterols, which are absent in prokaryotes and serve as important biomarkers in the rock record.
4. Eukaryotes contain organelles like mitochondria and chloroplasts, which are not present in prokaryotes.
5. They have a larger genome than prokaryotes.

How did eukaryotes evolve?

Endosymbiosis

Lynn Margulis proposed the endosymbiosis theory around 1970 to explain how eukaryotic cells evolved. This theory suggests that one prokaryote engulfed another, and the engulfed prokaryote eventually became one of the organelles in the host cell, which then became a eukaryote. Initially met with skepticism, this theory is now widely accepted due to substantial evidence.

Why might these prokaryotes have engulfed one another, and how was it beneficial?

1. The engulfed prokaryote benefited from protection and a source of carbon and nutrients provided by the host cell.
2. The host cell benefited from extra ATP produced by the engulfed cell.
3. Over time, they became interdependent, and the engulfed cell within the host cell became the host cell's mitochondrion.
4. A similar process occurred for other organelles like the chloroplast.

The Hydrogen Hypothesis

This hypothesis proposes a step-by-step explanation for how endosymbiosis might have occurred:

1. Hydrogen became limited for anaerobic bacteria like methanogens, which use hydrogen as an electron donor to reduce carbon dioxide to methane.
2. These methanogens needed another hydrogen source and became closely associated with fermenting bacteria.
3. The archaea evolved a cytoskeleton to alter their cell shape, increasing surface area to maximize contact with the hydrogen-producing bacteria.
4. Eventually, the bacterium was fully engulfed by the host archaea.
5. Gene transfer between the bacteria and archaea allowed the host to meet both its carbon and energy needs, as well as those of its engulfed symbiont cell, heterotrophically.
6. The host evolved into a chemoheterotroph, using glucose as a source of reduced organic carbon and gaining more energy from its metabolic processes.
7. The symbiont evolved into the mitochondrion, leading to an increase in size and complexity of the host cell.

Evidence for Mitochondria & Chloroplast Origins

The evidence supporting the endosymbiotic origin of mitochondria and chloroplasts includes:

1. They have distinct DNA and RNA from the host cell.
2. They possess their own membranes.
3. They make their own proteins.
4. Chloroplasts share many traits with cyanobacteria and perform oxygenic photosynthesis, unique to cyanobacteria.
5. Mitochondria and chloroplasts have their own reproductive mechanisms.
6. They are susceptible to antibiotics.

Nucleus or Mitochondria First?

While the most phylogenetically ancient eukaryotes lack mitochondria and many other organelles, recent studies suggest that these amitochondriates likely once possessed mitochondria and lost them through evolutionary changes. This implies that mitochondria probably evolved prior to nuclei, which is consistent with the energy requirements needed for increased cellular complexity. However, this is still debated.

When Eukaryotes Evolved

The timeline for eukaryotic evolution includes:

- 2.7 billion years ago: Earliest potential evidence of eukaryotes (steranes in rock record)
- 2.1 billion years ago: More unequivocal evidence (algae fossils)
- 1.8 to 1.5 billion years ago: Oldest acritarch fossils
- 1.2 billion years ago: Multicellular red algae
- 700 to 550 million years ago: Significant increase in biodiversity (Neoproterozoic)

Why Low Diversity Until ~600 Ma?

Several factors contributed to the apparent low diversity before the Neoproterozoic:

1. Lack of hard parts for preservation
2. Limited rock record from earlier periods
3. Lack of habitable environments due to anoxic deep oceans
4. Snowball Earth events decreasing habitable environments
5. Lower oxygen levels limiting energy yields

Why High Diversity After ~600 Ma?

The increase in diversity during and after the Neoproterozoic can be attributed to:

1. Termination of Snowball Earth events, creating more habitable environments
2. Higher oxygen levels and more habitable environments
3. Changes in ocean chemistry allowing for skeleton formation
4. Stromatolite grazing, clearing seafloor area for other organisms
5. Evolution of advanced predators driving the development of protective skeletons

For more information on related topics, you can check out videos on the Cambrian Explosion and when life moved to land, as well as a historical geology playlist.

Responses: 

Complexity of Eukaryotic Cells

GEO GIRL Claim:  
Eukaryotes evolved through endosymbiosis, where one prokaryote engulfed another, leading to the formation of organelles like mitochondria and chloroplasts.

Refutation:  
"Eukaryogenesis Exposed" argues that the complexity of eukaryotic cells, which includes the development of membrane-bound organelles, a complex cytoskeleton, and sophisticated gene regulation mechanisms, cannot be adequately explained by the endosymbiotic theory alone. The simultaneous evolution of multiple interdependent components in eukaryotic cells presents a significant challenge to the gradual evolutionary explanations proposed by the endosymbiotic theory.

Evolution of the Nuclear Envelope

GEO GIRL Claim:  
The endosymbiotic theory primarily explains the origin of mitochondria and chloroplasts, suggesting a gradual process of engulfment and integration of prokaryotic cells into a host cell.

Refutation:  
"Eukaryogenesis Exposed" emphasizes that models for the origin of the nuclear envelope, such as the "inside-out" model proposed by Baum and Baum (2014), face significant challenges. These include:

1. Transition from Archaeal to Eukaryotic Membrane Composition  
The inside-out model suggests that the nuclear envelope evolved from the invagination of the plasma membrane in an archaeal ancestor. However, the membrane composition of archaea is fundamentally different from that of eukaryotes. Archaea have membranes made of isoprenoid ethers, whereas eukaryotic membranes are composed of fatty acid esters. This significant biochemical difference poses a challenge for the model, as it requires a complex and unlikely transition in membrane chemistry.

2. Formation of Endomembrane Structures  
The eukaryotic cell's endomembrane system, which includes the endoplasmic reticulum, Golgi apparatus, and vesicles, is highly complex and interconnected. The inside-out model must explain how such an intricate system could evolve from simple invaginations of the plasma membrane. The coordination and integration of multiple membrane-bound compartments with specific functions are not easily accounted for by gradual evolutionary processes.

3. Nuclear Pore Complexes (NPCs)  
The nuclear envelope contains nuclear pore complexes (NPCs), which are large protein structures that regulate the transport of molecules between the nucleus and the cytoplasm. NPCs are composed of about 30 different proteins, known as nucleoporins, which must assemble correctly to function. The evolution of such a complex and highly specific structure is challenging to explain, as it would require the simultaneous development of multiple interacting components.

4. Spatial and Temporal Coordination  
The formation of the nuclear envelope involves precise spatial and temporal coordination during cell division. In eukaryotic cells, the nuclear envelope disassembles and reassembles during mitosis, a process that is tightly regulated. The inside-out model must account for the evolution of these regulatory mechanisms, which are absent in prokaryotes and require sophisticated control systems.

5. Genetic and Molecular Evidence  
Comparative genomic studies reveal significant differences between the genes and molecular machinery involved in membrane dynamics and nuclear envelope formation in archaea and eukaryotes. These differences suggest that the origin of the nuclear envelope cannot be easily traced back to a simple prokaryotic ancestor, as would be expected if the inside-out model were accurate.

The "inside-out" model and similar evolutionary explanations for the origin of the nuclear envelope face substantial challenges in explaining the biochemical, structural, and regulatory complexities involved. These challenges highlight significant gaps in our understanding and suggest that alternative models or additional mechanisms may be necessary to fully explain the origin of the nuclear envelope.

Nuclear Pore Complexes (NPCs)

GEO GIRL Claim:  
The engulfed prokaryote provided benefits like extra ATP, eventually leading to the development of mitochondria and other organelles.

Refutation:  
The book highlights the complexity of nuclear pore complexes (NPCs), which are composed of approximately 30 different proteins present in multiple copies. The evolution of such a complex structure from prokaryotic precursors would require the simultaneous development of several key components. This level of complexity is difficult to explain through gradual evolutionary processes, as posited by the endosymbiotic theory.

Lack of Intermediate Forms

GEO GIRL Claim:  
The timeline for eukaryotic evolution includes evidence from 2.7 billion years ago (steranes in rock record) to more unequivocal evidence around 2.1 billion years ago (algae fossils).

Refutation:  
"Eukaryogenesis Exposed" points out the absence of clear evolutionary intermediates between prokaryotes and eukaryotes in both the fossil record and extant species. This lack of intermediate forms complicates our understanding of the transition and challenges the gradual evolutionary model proposed by the endosymbiotic theory.

Limitations of Endosymbiotic Theory

GEO GIRL Claim:  
Lynn Margulis's endosymbiotic theory, initially met with skepticism, is now widely accepted due to substantial evidence.

Refutation:  
"Eukaryogenesis Exposed" argues that it fails to account for the majority of eukaryotic innovations. The theory does not sufficiently explain the complexity and interdependence of eukaryotic structures, necessitating a reevaluation of current evolutionary models.

Call for Reevaluation

GEO GIRL Claim:  
The evolution of eukaryotes is explained by endosymbiosis, supported by substantial evidence such as distinct DNA and RNA in mitochondria and chloroplasts, and their own reproductive mechanisms.

Refutation:  
"Eukaryogenesis Exposed" calls for considering non-gradual mechanisms and exploring alternative explanations for the origin of essential eukaryotic features. The book suggests that the complexity and interdependence of eukaryotic structures cannot be fully explained by the endosymbiotic theory alone, urging further research and consideration of alternative models.

While the GEO GIRL video presents the endosymbiotic theory as a well-supported explanation for the evolution of eukaryotic cells, "Eukaryogenesis Exposed" provides a critical examination of this theory, highlighting significant challenges and gaps in the current understanding.

A bacterium has evolved into a new cellular structure inside algae

A brief summary:

1. A new cellular structure called a "nitroplast" has been discovered in a single-celled alga called Braarudosphaera bigelowii.
2. The nitroplast evolved from a nitrogen-fixing bacterium (UCYN-A) that has become an organelle within the algal cell.
3. This is only the fourth known case of a free-living bacterium evolving into an organelle in eukaryotic cells, the other three supposedly being mitochondria, chloroplasts, and chromatophores.
4. The research was conducted by Tyler Coale and colleagues at the University of California, Santa Cruz.
5. The study used soft X-ray tomography to observe how UCYN-A divides in sync with the algal cell, with each daughter cell inheriting one UCYN-A.
6. About half of the proteins in UCYN-A come from the algal host, indicating a high level of integration.
7. The nitroplast represents a new way for eukaryotic cells to fix nitrogen, a function previously thought to be exclusive to prokaryotes.
8. This discovery could have implications for understanding how to integrate nitrogen fixation into crop plants.
9. The document provides more detailed scientific background and context, including information about endosymbiosis, the evolution of organelles, and the importance of nitrogen fixation in biology.
10. It also includes additional perspectives from other scientists and more detailed explanations of the research methods and findings.

1. Evolutionary divergence:
- Around 91 million years ago, in the late Cretaceous period, the ancestral free-living cyanobacterium that would become UCYN-A entered into a symbiotic relationship with a prymnesiophyte algae.
- This initial symbiosis then diverged into at least two distinct lineages - UCYN-A1 and UCYN-A2 - each associating with a different but closely related prymnesiophyte host.

2. Genome reduction:
- As the symbiosis became more intimate, the UCYN-A genome underwent extensive reduction, losing many genes and pathways that became unnecessary in the symbiotic lifestyle.
- This included the loss of genes for photosystem II, carbon fixation via the Calvin cycle, and the tricarboxylic acid cycle.

3. Metabolic integration:
- The UCYN-A symbionts became specialized for nitrogen fixation, with the nitrogen fixation (nif) genes being among the most highly expressed.
- Energy production pathways (ATP synthase, cytochrome b6f, photosystem I) became tightly coupled to nitrogen fixation to provide the necessary ATP and reducing power.

4. Physical integration:
- UCYN-A cells became physically incorporated into their host cells.
- UCYN-A1 typically exists as 1-2 cells per host cell.
- UCYN-A2 forms a "symbiosome-like" structure with 3-10 cells inside the B. bigelowii host.

5. Partner fidelity:
- Each UCYN-A lineage developed strict specificity for its particular host species.
- This partner fidelity likely drove further co-evolution and specialization of each symbiotic pair.

6. Metabolic exchange:
- A mutualistic relationship developed where UCYN-A provides fixed nitrogen to the host, while the host likely provides fixed carbon and other nutrients to UCYN-A.

7. Gene expression adaptation:
- The UCYN-A gene expression became streamlined, with a strong focus on nitrogen fixation and associated energy production.

This merging represents a remarkable example of  a supposed evolutionary transition from free-living organisms to obligate symbionts, with extensive metabolic and genomic integration between the partners. The process resulted in highly specialized nitrogen-fixing "organelles" within the prymnesiophyte hosts.

The endosymbiotic event described in the case of UCYN-A and Braarudosphaera bigelowii is fundamentally different from the proposed prokaryote-to-eukaryote transition in the endosymbiotic theory. 

1. Pre-existing complexity:
   - In the UCYN-A case, the host organism (B. bigelowii) is already a complex eukaryotic alga.
   - The endosymbiotic theory for eukaryote origin proposes a transition from simple prokaryotes to complex eukaryotes, which is a much larger evolutionary leap.

2. Lack of intermediate forms:
   - There is a lack of observable intermediate stages between prokaryotes and eukaryotes which is a major problem with the endosymbiotic theory.
   - The UCYN-A case doesn't address this issue, as it involves two already distinct and complex organisms.

3. Complexity of eukaryotic features:
   - The appearance of complex eukaryotic features is a challenge for the endosymbiotic theory. Here's a list of the main innovations found in eukaryotes that are not present in prokaryotes:

a. Nucleus
   - Nuclear envelope with double membrane
   - Nuclear pore complexes
   - Chromosomes organized with histones

b. Endomembrane system
   - Endoplasmic reticulum (rough and smooth)
   - Golgi apparatus
   - Lysosomes
   - Vesicular transport system

c. Complex organelles
   - Mitochondria
   - Chloroplasts (in plants and algae)
   - Peroxisomes

e. Cytoskeleton
   - Microfilaments (actin)
   - Intermediate filaments
   - Microtubules
   - Centrosomes and centrioles

f. Cell division mechanisms
   - Mitosis with a spindle apparatus
   - Meiosis and sexual reproduction

g. Membrane-bound compartments
   - Vacuoles
   - Specialized vesicles

h. Complex gene regulation
   - Introns and exons
   - Alternative splicing
   - Epigenetic modifications

i. Linear chromosomes with telomeres
j. Larger cell size (typically 10-100 times larger than prokaryotes)
k. Complex cell signaling pathways
l. Cytoplasmic streaming
m. Phagocytosis and other complex forms of endocytosis
n. Flagella and cilia with "9+2" microtubule structure
o. Extracellular matrix production
p. Cell specialization and differentiation in multicellular organisms
q. Complex cell cycle regulation with checkpoints
r. Sophisticated DNA repair mechanisms
s. Membrane-bound cell surface receptors
t. Diverse membrane lipid composition
u. Ability to form complex multicellular organisms with specialized tissues and organs

These eukaryotic innovations represent a significant leap in cellular complexity compared to prokaryotes, and their sudden appearance poses a challenge for gradual evolutionary explanations, including the endosymbiotic theory.

   - The UCYN-A event doesn't explain the origin of these complex features (nucleus, ER, Golgi, etc.) as they already exist in the host alga.

4. Membrane differences:
   - There is a significant difference between eukaryotic and prokaryotic membranes.
   - The UCYN-A case doesn't address this fundamental difference in cellular architecture.

5. Nuclear pore complexes and other eukaryote-specific structures:
   - The origin of complex structures like nuclear pore complexes is not explained by the UCYN-A event.
   - These structures already exist in the host alga, so this symbiosis doesn't shed light on their evolutionary origin.

6. Mitochondrial protein import and genome reduction:
   - While the UCYN-A case shows some genome reduction and protein import, it doesn't address the extensive mitochondrial genome reduction and complex protein import systems seen in eukaryotes.

7. Origin of other organelles:
   - The UCYN-A event doesn't explain the origin of other eukaryotic organelles like the endoplasmic reticulum, Golgi apparatus, or peroxisomes.

8. Cytoskeleton evolution:
   - There are significant differences between eukaryotic and prokaryotic cytoskeletons.
   - The UCYN-A case doesn't address this fundamental aspect of eukaryotic cell structure.

9. Eukaryotic gene content:
   - Many eukaryotic genes have no clear prokaryotic homologs, which isn't explained by the UCYN-A event.

10. Mitochondrial-nuclear interdependence:
    - There is complex interdependence between mitochondria and the nucleus in eukaryotes.
    - While the UCYN-A case shows some integration, it doesn't approach the level of interdependence seen in eukaryotic cells with mitochondria.

11. Irreducible complexity:
    - Many eukaryotic systems exhibit irreducible complexity.
    - The UCYN-A event, occurring between two already complex organisms, doesn't address how these systems could have evolved gradually.

While the UCYN-A and B. bigelowii symbiosis is an interesting example of ongoing endosymbiosis, it occurs between two already complex organisms and doesn't address the fundamental challenges posed to the endosymbiotic theory for eukaryote origin. The pre-existence of eukaryotic complexity in this case means it cannot serve as a model for the proposed prokaryote-to-eukaryote transition.



A bacterium has evolved into a new cellular structure inside algae
A once-independent bacterium has evolved into an organelle that provides nitrogen to algal cells – an event so rare that there are only three other known cases

Michael Le Page 11 April 2024

https://www.newscientist.com/article/2426468-a-bacterium-has-evolved-into-a-new-cellular-structure-inside-algae/

In the 3.5 billion years since life first evolved on Earth, it was thought that once-free-living bacteria had merged with other organisms on just three occasions, making this an exceedingly rare evolutionary event. Now, a fourth example has been found, in a single-celled alga common in the oceans. These algae were thought to “fix” nitrogen – convert atmospheric nitrogen into useable ammonia – with the help of a bacterium. Tyler Coale at the University of California, Santa Cruz, and his colleagues have now shown that this bacterium has evolved into a new cellular structure, or organelle. It is the first known nitrogen-fixing organelle, or nitroplast, says Coale, and could be the key to the success of these algae. “It appears to be a successful strategy for them,” he says. “These are very widespread algae. We find them all over the world’s oceans.”

Read more Evolution is evolving: 13 ways we must rethink the theory of nature It is quite common for one species to live inside the cells of another in a mutually beneficial relationship called endosymbiosis. For instance, cells in the roots of legumes such as peas host nitrogen-fixing bacteria. The success of cockroaches is partly due to endosymbiotic bacteria that produce essential nutrients. Some cells even host multiple endosymbionts. While endosymbiotic relationships can become very close, in almost all cases, the organisms remain distinct. For example, legumes acquire their root bacteria from the soil. And while the cockroach bacteria are passed down in eggs, they live in specialised cells, not in every cell.

But in three cases, endosymbionts have merged with their hosts to become a fundamental part of them. Energy-producing mitochondria arose from the merger of a bacterium with another simple cell, forming the complex cells that gave rise to animals, plants and fungi. Plants arose when a cyanobacterium combined with a complex cell to form the chloroplast, the organelle that carries out photosynthesis. And around 60 million years ago, another cyanobacterium merged with an amoeba, forming a different photosynthetic organelle called a chromatophore, found only in a few species of Paulinella. It has been suspected for more than a decade that a cyanobacterium known as UCYN-A living within the single-celled alga Braarudosphaera bigelowii has become an organelle. However, studying the partnership was difficult until team member Kyoko Hagino at Kochi University in Japan found ways of keeping B. bigelowii alive in the lab. This allowed the team to use a technique called soft X-ray tomography to watch what happens as the algal cells divide. From this, it was discovered that UCYN-A divides in concert with the algal cell, with each daughter cell inheriting one UCYN-A. “We did not know how this association was maintained before this,” says Coale.

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The team also found that around half of the 2000 or so different proteins inside UCYN-A come from the algal host, rather than being made within UCYN-A. Many of the imported proteins help UCYN-A fix nitrogen, says Coale. “I think it is being souped up by the algal cell to produce more nitrogen than it needs for itself.” There also seems to be a specialized system for delivering proteins to UCYN-A, as there is for other organelles. All the imported proteins have an extra section thought to be an “address label” marking them for delivery to UCYN-A. There is no universally accepted definition of an organelle, says Jeff Elhai at Virginia Commonwealth University, but many biologists regard coordinated division and the importing of proteins as key. “Both boxes are checked by Coale,” says Elhai. “Even to the semantic purists, UCYN-A must be counted as an organelle, joining mitochondria, chloroplasts and chromatophores.” The manufacture and use of nitrogen fertilizers is a major source of greenhouse gas emissions as well as an expense for farmers. So there is a lot of interest in modifying crop plants so they can fix their own nitrogen as legumes do. One way to achieve this would be to equip their cells with nitroplasts and Elhai has put together a proposal for how this could be done. But UCYN-A isn’t a good starting point because it is far too dependent on B. bigelowii, he says. Instead, Elhai envisages starting with cyanobacteria that have only just started down the road to becoming nitroplasts and don’t rely on imported proteins, so they could be easily added to a wide range of crop plants. Nevertheless, Elhai agrees with Coale that studying B. bigelowii could help us understand how to integrate nitrogen fixation into a plant cell.

The Nitroplast Revealed: A Nitrogen-fixing Organelle In A Marine Alga April 20, 2024 2

Evolution and function of the nitroplast – Multiple organelles in eukaryotic cells, including mitochondria, chloroplasts, and nitroplasts, evolved from the integration of endosymbiotic bacteria. In Braarudosphaera bigelowii, the chloroplast fixes inorganic carbon to produce glucose, which feeds the respiratory chain in mitochondria that produces adenosine triphosphate (ATP), which in turn fuels nitrogen fixation in the nitroplast. Glucose, ammonia, and ATP generated by the organelles, together with externally incorporated compounds (phosphorous, mineral nutrients, and vitamins), are the building blocks for cell metabolism, resulting in cell growth and division. 

A nitrogen-fixing bacterial endosymbiont of marine algae is evolving into a nitrogen-fixing organelle, or nitroplast, according to a new study, thereby expanding a function that was thought to be exclusively carried out by prokaryotic cells to eukaryotes. Eukaryotic cells are remarkably complex and contain various organelles, which are specialized structures within a living cell that have specific biological functions. Two organelles, mitochondria and chloroplasts, play a key role in energy metabolism and photosynthesis, respectively, and likely evolved from the integration of endosymbiotic bacteria to the eukaryotic cell.

The robust volumetric relationship between partners of a marine planktonic nitrogen-fixing symbiosis reflects predictable, balanced, and quantitative interdependencies among CO2 fixation, respiration, and N2 fixation that maximize synchronized growth rate. Biological nitrogen (N2) fixation, the conversion of atmospheric N2 gas to biologically available ammonia, is a key metabolic process that maintains the fertility of aquatic and terrestrial systems. N2 fixation in eukaryotes is only known to exist through diverse symbiotic partnerships with prokaryotic microbes capable of N2 fixation. However, the nature of these symbiotic relationships is poorly understood, and, to date, a N2-fixing organelle in eukaryotic cells has yet to be described. Tyler Coale and colleagues investigated the interactions between Candidatus Atelocyanobacterium thalassa, or UCYN-A, a metabolically streamlined N2-fixing cyanobacterium. which is a known endosymbiont of the unicellular marine algae Braarudosphaera bigelowii.

Through subcellular images taken with soft X-ray tomography to visualize the algae’s cell morphology and division, Coale et al. observed a coordinated cell cycle in which endosymbiotic UCYN-A divided and is split evenly between daughter B. bigelowii cells, which is similar to the way chloroplast and mitochondria organelles are transmitted during cell division. Moreover, further proteomic and genomic analyses show that UCYN-A contains many proteins that are imported from the eukaryotic host cell’s nucleus, including those essential for cellular metabolism and control of the cell cycle. According to Coale et al., the findings suggest that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N2-fixing organelle. “The nitroplast represents a textbook case of a eukaryotic organelle that complements the energy, carbon, and nitrogen needs of the algal host and is another example of how ecology is the theater where evolution takes place,” writes Ramon Massana in a related Perspective.

The nitroplast: a nitrogen-fixing organelle
A bacterial endosymbiont of microalgae evolved to an organelle 3

By Ramon Massana

Eukaryotic cells are notably complex, including by having various organelles, which are membrane-bound structures with specific functions. Two of these organelles, mitochondria and chloroplasts, which function in respiration and photosynthesis, evolved from the integration of endosymbiotic bacteria into the eukaryotic cell (1). In marine systems, some nitrogen-fixing bacteria are endosymbionts of microalgae, such as UCYN-A, a cyanobacterial symbiont of the unicellular algae Braarudosphaera bigelowii (2). On page XXX of this issue, Coale et al. (3) demonstrate a close integration of this endosymbiont into the architecture and function of the host cell, which are characteristics of organelles. These findings show that UCYN-A has evolved from a symbiont to a eukaryotic organelle for nitrogen fixation, the nitroplast, thereby expanding a function that was thought to be exclusively carried out by prokaryotic cells to eukaryotic cells.

Biological nitrogen fixation, which reduces atmospheric dinitrogen gas (N₂) into bioavailable ammonia (NH₃), is crucial in the nitrogen biogeochemical cycle as the only path to incorporate the abundant dinitrogen gas into biomass. This process represents a main driver of fertilization for aquatic and terrestrial systems, and is continuously studied to increase crop yields in agriculture (4). To directly benefit from the resulting ammonia, many photosynthetic organisms, from terrestrial plants to microalgae, incorporate nitrogen-fixing endosymbionts (5). This is the case of B. bigelowii and relatives (belonging to the algal class Prymnesiophyceae) carrying the nitrogen-fixing UCYN-A cyanobacteria. The latter symbiont lacks the genes for photosynthesis, whereas it is suitable for performing oxygenic photosynthesis while involved in a stable partnership with the host, providing it with fixed nitrogen and receiving fixed carbon in return (6). This symbiosis is now known to be very stable, widespread in sunlit coastal and oceanic waters, and to play a crucial role in the nitrogen biogeochemical cycle (6). However, establishing stable cultures of B. bigelowii and UCYN-A have limited studies on this symbiosis. Coale et al. successfully grew B. bigelowii in culture, which enabled them to further probe its interactions with UCYN-A. Tridimensional subcellular images taken with soft X-ray tomography were used to follow the development of the nucleus, mitochondria, chloroplasts, and UCYN-A during the cell cycle. The data revealed a coordinated fiber of events for the replication and fission of these four components that show that UCYN-A is as integrated within the eukaryotic cell architecture as the other three organelles. These findings also suggest that UCYN-A division is tightly controlled by the host and that the symbiont is transmitted to daughter cells during cell division. Furthermore, proteomics and comparative genomics analyses showed that UCYN-A contains many proteins that are imported from the eukaryotic host. These proteins are encoded in the host nucleus, translated in the host cytoplasm, signaled for transport to the nitroplast and complement metabolic pathways that appear incomplete in the UCYN-A genome, such as those involved in the synthesis of some amino acids, nucleotides, or cofactors. The synchronized division and the import of essential eukaryotic proteins indicate that UCYN-A has evolved beyond endosymbiosis (7) and that it can be instead considered a eukaryotic organelle under the full control of the host. The nitroplast takes the name proposed years ago for analogous systems ( and denotes its role in nitrogen fixation and its cyanobacterial origin (by analogy to plastids, also derived from cyanobacteria).

Distinguishing an endosymbiont from an organelle can be challenging (9), and each reported endosymbiosis may appear at a different stage of a putative endosymbiont-organelle continuum. Nevertheless, the nitroplast cellular integration and dependency supports the view that the nitroplast of B. bigelowii can be added to the short list of endosymbiosis-derived organelles. The evolutionary history of the nitroplast is analogous to that of mitochondria and chloroplasts, including gene loss, coordinated division, and subjugation to the host. Besides the mitochondria, chloroplast and nitroplast, there are few additional cases of endosymbiosis-derived organelles (10), such as the chromatophore of the amoeba Paulinella. In addition, the spheroid bodies of rhopalodiid diatoms, which resemble UCYN-A in many ways, may represent another example of an evolving nitroplast (11). Nonetheless, it is still intriguing that so few endosymbiosis-derived organelles are known, emphasizing how difficult it is to achieve this transition (12).

The transitions from endosymbionts to the various organelles happened independently at different times of eukaryotic evolution, and this influences their taxonomic coverage. Mitochondria acquisition (thought to have occurred around 2 billion years ago) predates the origin of the eukaryotic cell and these organelles are found throughout the eukaryotic tree of life, with some cases of secondary loss or modification. The primary endosymbiosis that originated the chloroplast also occurred in ancient times (likely around 1.5 billion years ago) in the supergroup Archaeplastida. Chloroplasts were later transferred to other eukaryotic supergroups by secondary or tertiary endosymbiosis. The establishment of the nitroplast is more recent, about 100 million years ago (13), and this may explain why this organelle is taxonomically constrained to prymnesiophytes. Even within this narrow host range, this variant has coevolved, revealing a remarkable relationship between organelle size and host size in related species (14). Given enough time, the nitroplast might be transferred to other lineages through secondary endosymbiosis, securing nitrogen supply to distant eukaryotes.

The study from Coale et al. shows that a revived endosymbiont is actually the nitroplast organelle, an optimal adaptation of the microalgae to thrive in nitrogen-limited waters. Like photosynthesis, a prokaryotic innovation that was incorporated by endosymbiosis into the eukaryotic cell and is now considered a eukaryotic function, these authors propose the claim that nitrogen fixation is no longer an exclusive prokaryotic function and that eukaryotes can fix nitrogen using their nitroplast. The nitroplast represents a textbook case of an eukaryotic organelle that complements the energy, carbon and nitrogen needs of the algal host (see the figure) and another example of how ecology is the theatre where evolution takes place.

Incredible Discovery of an Entirely New Organelle That Fixes Nitrogen 4

When it comes to life, and specifically the individual cells that make up much of life like us, one of the more mysterious and difficult questions to answer regards the complexity inside the cell and how various structures formed over time. Over billions of years of evolution, animal cells and plant cells, specifically eukaryotic cells, developed a lot of complexity that relies on a concept known as endosymbiosis. This is a kind of symbiotic relationship between various types of organisms providing for each other and getting something back in return.

The best example here is what you see in this video: mitochondria. Billions of years ago, mitochondria were most likely individual bacteria that were exceptional at producing energy, mostly in the form of a molecule known as ATP. Then, at some point, something happened and they essentially formed a symbiotic relationship with various cells, providing that extra energy to them and in return getting a lot of safety and essentially a house to live in (and possibly something else). So, over billions of years, modern cells evolved to use mitochondria as an essential organelle in pretty much every cell inside our body. There are over 80 trillion of them inside each of us, and basically almost every cell contains them. Something very similar happened to plant cells, specifically various algae and chloroplasts - another bacterium that was very good at photosynthesis became absorbed by various algae, with some eventually evolving into plants. Over billions of years, both mitochondria and chloroplasts became so specialized that they can't actually live outside of a typical cell. They require our cells for survival, and our cells even provide them with a lot of additional proteins in order to reproduce and copy themselves over many generations.

This process of ingestion of bacteria, where the whole cell and the ingested bacteria eventually become codependent, seems to have happened at least three times. The absorption of chloroplasts potentially was the first, with this beautiful picture of a typical moss showing us huge amounts of chloroplasts present in each of the cells. Then we had the absorption of mitochondria, which became essential for a lot of more complex life on the planet, basically responsible for producing a lot of energy but also for regulating many things in our body, making these organelles crucial for more complex life. More recently, researchers discovered the most recent such case from an organism known as Paulinella. This probably happened only 60 to maybe 100 million years ago, basically during the time of the dinosaurs, as opposed to billions of years ago when we believe mitochondria and chloroplasts became part of various cells. Approximately 60 million years ago, another cyanobacterium merged with an amoeba, forming a new organelle known as a chromatophore - essentially a completely separate photosynthetic organelle that seems to only exist in these specific organisms.

This idea of various specialized bacteria getting swallowed and merging with more complex cells, eventually becoming a part of them, seems to be a relatively common scenario in the evolution of complex life. This idea today is known as the Endosymbiotic Theory - basically, the process of ingesting bacteria in order to form this permanent relationship that then changes the cell and creates a new organism. Though mitochondria and chloroplasts still obviously have their own DNA, they're completely dependent on the cell they reside in. But so far, these examples only present us with two separate chemical reactions that life relies on: we have photosynthesis and we have the production of ATP, or the energy molecule. But we know that bacteria evolved to actually use a lot of other chemical reactions for survival on the planet. For example, something that plants rely on as well is the idea of nitrogen fixation. Plants need nitrogen for growth, and normally most plants get nitrogen by creating a kind of collaboration, or once again symbiosis, with nitrogen-fixing bacteria somewhere around the roots. This is sometimes referred to as the root microbiome, and it's kind of similar to what we have in our guts that essentially helps roots digest various types of matter and acquire different nutrients they need for growth.

But here, just like with our guts, the microbes don't live inside the cells; they basically live around the roots, forming their own communities. This type of bacterial symbiosis is extremely common. As I mentioned, we have something similar inside our guts, and pretty much most animals out there use bacteria for something to some extent. When it comes to nitrogen, it is a very crucial element, and it's actually kind of surprising that no life so far has developed an ability to basically integrate these bacteria into the cells, forming organelles kind of like mitochondria or chloroplasts. Or so we thought.

Transitioning into the actual topic that we're discussing today, it turns out something has done that. Researchers have just now discovered a new organism that seems to have nitrogen-fixing properties, and the organelle in this case is now going to be referred to as nitroplast. It fixates nitrogen, with all of this discovered in a single-cell algae known as Braarudosphaera bigelowii, and the cyanobacterium that seems to be present here, responsible for the fixation of nitrogen, is now referred to as UCYN-A.

The thing about the strange organism that possesses this organelle is that it's already kind of strange. It's essentially what's known as a coccolithophore. We actually discussed this in one of the previous videos (you can find it in the description), but in essence, these are some of the strangest looking organisms on the entire planet. They're all marine organisms; they essentially rely on oceans. They're also extremely successful and exist everywhere, and more importantly, they seem to form these unusual shield-like formations around the cell. It's not clear why; they're actually super diverse and do come in a lot of varieties and have definitely existed on the planet for over 100 million years. As a matter of fact, that previous video that I mentioned in the description talks about the ones that existed around the time dinosaurs perished. But despite their complexity and their overall numbers, we still barely know anything about them because they are super tiny and are also generally very different from a lot of other life. The organism we're discussing today looks like this: it contains unusual fivefold symmetry and contains 12 unusual pentagons forming a kind of dodecahedral structure, but only 10 micrometers in size. These organisms are also autotrophic; they basically feed themselves. By covering themselves with this calcium shell, they kind of protect themselves from possible hazards outside. This unusual shell is known as the coccosphere, although the real reason why the coccosphere exists is still unknown. It's actually one of the mysteries here.

Nevertheless, these organisms are super important because they capture a lot of calcium but also a lot of carbon. This is actually made out of calcium carbonate, and as a result, they form one of the biggest parts of the carbon cycle in the oceans, which is why so many scientists try to understand them a little bit better. This time, by using X-ray tomography and by watching these cells divide using individual frames, the researchers realized that as they divide, one of the unusual bacteria known as Atelocyanobacterium thalassa that lives inside of them seems to rely on a lot of genetic code and a lot of proteins from the whole cell. For example, they don't seem to have genes producing RuBisCO, which is usually essential, and they're also unable to fix carbon via photosynthesis. Yet the cell they live in can do all of this but just doesn't really have any nitrogen. So approximately 2,000 various proteins essential for this bacterium seem to come from the whole cell and not from the DNA inside. In other words, this is basically an actual organelle and not a bacterium anymore. And obviously, in return, it seems to fix nitrogen, allowing the whole cell to then use it for food.

So basically, this is the first ever known nitroplast. Instead of relying on some kind of a culture of bacteria like roots of plants, just like with mitochondria, this just became an organelle. Although obviously, it's not clear when all of this happened. But what's, I guess, more impressive is that this is not just like one or two examples here. We're actually talking about an extremely widespread organism pretty much found all over the planet, which basically means that this is a very successful evolutionary change that provides the host with some essential advantages. This is the fourth known organelle that used to be a bacteria. We have mitochondria, chloroplasts, chromatophores, and now nitroplasts. For actual plants, in other words, is there any way for us to replicate this and possibly genetically modify plants somehow in order to give them not just chloroplasts but also nitroplasts, which would then make them way more efficient at basically growing? But most importantly, it would suddenly make nitrogen fertilizers kind of useless. And since fertilizers are both expensive and generally are not very good for the environment, being able to somehow introduce nitroplasts into plants might actually change everything.

There's obviously no real way we can do this yet, but this unusual discovery could definitely present us with some options in the future. But because this is a super recent discovery, there's really not much else we know about this, and I'm sure there will be more discoveries in the next few months. And so, until then, or until we know something else, that's pretty much all I wanted to mention. Thank you for watching, subscribe, share this with someone who loves to learn about space and sciences, come back tomorrow to learn something else. Support this channel on Patreon, by joining Channel membership, or by buying the wonderful person t-shirt you can find in the description. Stay wonderful, I'll see you tomorrow, and as always, bye-bye.


This is a Braarudosphaera Bigelowii (Latin name) otherwise known as a coastal PhytoPlanktonic algae. It is so small that its diameter is just a couple of microns (the average cross-section of a human hair is 50 microns) Living geometry is truly amazing.

1. https://www.science.org/doi/10.1126/science.ado8571
2. https://astrobiology.com/2024/04/the-nitroplast-revealed-a-nitrogen-fixing-organelle-in-a-marine-alga.html
3. https://docs.google.com/viewerng/viewer?url=https://digital.csic.es/bitstream/10261/354070/3/Massana_2024_postprint.pdf
4. https://www.youtube.com/watch?v=eGkV_k8IcQ0