Symbiogenesis – the hidden model of evolution

Have you ever considered that every organelle in your cell is alive, sentient and self-motivated? Or is of bacterial origin? Thinking about organelles as independent units of bacterial origin was a game changer for me.

The theory of endosymbiosis is widely accepted and understood to be how eukaryotic cells were formed. Mitochondria were an imposter bacteria which occupied ancient eukaryotic cells. This alien invader formed an alliance with the invaded internal ecosystem and over time began producing energy for the cell. If mitochondria were originally immigrant intruders making themselves at home in foreign cells, what’s the origin story for the other organelles?

I’ve been banging this drum for a while but it really is bacteria all the way down!

Let’s go through the evidence of organelles acting as independent players during their long historical timelines.


One of the only things we learned from school is that mitochondria are the powerhouse of the cell.

Do you remember mitochondria’s role in endosymbiosis?

Mitochondria were the first organelle to give us a clue about their outside or alien origin. Their small size and simple mechanism of dividing was enough to convince Paul Portier in 1918 that they were bacterial cells lodged inside animal and plant cells.

Stages of Mitochondrial Division, TEM | Science photos, Science ...
Stages of Mitochondrial division

Found in almost every nucleated cell, these membrane bound aliens provide the cell surrounding them with abundant energy derived from the oxygen of the air through a process called oxidative phosphorylation.

Because of mitochondria, all Earthly beings made of nucleated cells- which, includes us and all organisms except bacteria- have remarkably similar metabolisms.

Apart from plant and algae which use photosynthesis to generate their energy (in a process identical to cyanobacteria), all eukaryotic metabolism is fundamentally the same. 

We are extremely indebted to mitochondria for their specialised process of aerobic respiration. The reactions in mitochondria produce enough ATP for itself and the rest of the cell.

Examining cells through the lens of endosymbiosis

Widely accepted in the scientific community is endosymbiosis (proposed by Lynn Margulis) with symbiogenesis as the mechanism. Endosymbiosis is where a single-celled organism resides within another cell as part of a mutually beneficial relationship [1].

Prokaryotic vs. Eukaryotic

  • A nucleus is not present in prokaryotes.
  • Prokaryotes are usually single-celled organisms such as bacteria.
  • Eukaryotes contain a more complex composition of organelles (mitochondria in animal cells, chloroplasts in plants) which are organized into membrane bound compartments.
  • A cell can be considered as a collection of autonomous, self-sufficient bodies that only to a certain degree have lost their individuality.
  • Each exists in its own interests and represents special units of life also outside of the collection in which they are partners
  • Many of a cell’s organelles are not a result of differentiation but instead of a union or joining of units of life from outside the cell.
  • Prior to this incorporation they were autonomous and existed independently.
  • Therefore a multicellular organism can be considered as a result of “integration and differentiation” or
  • A collection of initially heterogeneous units into a union or composite of parts that could ensure the division of labour.

Bacterial empires – Selfish or Symbiotic?

Taken from the preface of Symbiogenesis: A New Principle of Evolution

Picture the earth 3 billion years ago. Life is autopoietic (fancy word describing a system capable of reproducing and maintaining itself), omnipotent and self-preserving. Life consists of bacteria flourishing and embracing the Earth in an aggregated film. How life came to be packaged or animated into self-organising lipid bubbles as cells is unknown, however we do know this bacterial empire contained the same universal genetic material that we share now. Every unit of life contains the universal genetic code of DNA or RNA embedded in it.

These bacteria have never left. They live in our gut, in symbiotic relationships with roots of plants (rhizobacteria, nitrogen-fixing bacteria), and as symbioses with other organisms constituting a new species.

Bacterial empires gave rise to the rest of life so how did they do it?

The classic Darwinian model proposes a world where only the fittest and strongest survive and reproduce, preserving their genetic material and lineage. This view focuses on the individual and their unique genetic qualities interacting and shaped by their environment. Darwinian evolution is true on many levels but it is not the only model to be considered.

The cooperation, altruism and parasitism of individual units of life is a massive piece of natural law which is often overlooked. As life forms we often are not acting alone, although the struggle may be on an individual level, the reality is we interact with, collaborate, share, act altruistically or take advantage of others.

This is glaringly obvious when we zoom in on the world of microbiology.

Perhaps it’s a stretch to consider bacteria as consciously altruistic. Their symbioisis can be chalked down to a form of commensalism.

  • Altrusim is a conscious, voluntary form of mutual assistance.
  • Pure commensalism is where one partner takes what the other does not need and vice versa.
  • Mutualism is a symbiosis based on mutual exploitation.
  • Parasitism is where one organism exploits another forcefully.
  • Domatism is the exploitation of one partner of another for shelter.

There are a number of potential scenarios whereby a chance viable symbiosis could be allowed to flourish.

Lynn Margulis

Saúde no Solo: Lynn Margulis, das bactérias à Symbiogênese ...

Lynn Margulis was the main scientist perpetuating the theory of symbiogenesis. Lynn was an outstanding evolutionary microbiologist whose voice was boldly calling for an alternative model of evolution and she dedicated her life to uncovering them.

After being exposed to Lynn Margulis through Connor Habib’s podcast interview recorded not long before her passing, Lynn’s passion and knowledge for microbiology and evolution drove me to further investigate her body of work. I was quickly captivated with her ideas on symbiogenesis as a mechanism for evolution. Her body of published work is large but I was spurred into reading Microcosmos – 4 million Years of Bacterial Evolution and Symbiogenesis: A New Principle of Evolution.

The fascinating thing about Symbiogenesis: A New Principle of Evolution is that it was written in 1917 by the Russian biologist Boris Kozo-Polyansky but only saw the light in 2010 after Lynn Margulis found a translator, co-edited and published it.

What is symbiogenesis?

You’re probably asking what is symbiogenesis?

It it widely accepted in experimental biology that hereditary change occurs through recombination and mutation. Evidence shows that symbiogenesis forms the basis for this process. It is described as:

  1. Combination of 2 or more heterogeneous organisms into a composite organism.
  2. This gives rise to a new form which is more complex in structure than each of its partners taken separately.
  3. The new composite organism is composed of two or more genomes to produce a “symbioma” (Guerrero and Margulis 2010).
  4. The interaction of the components of such an organism system determines:
    1. Movement of these components within a system
    2. Extinction of some components
    3. Modification of their features

All of the above results in changes in the characteristics of the entire system.

Boris Kozo-Polyansky (1890-1957)

Lynn Margulis, des bactéries à la symbiogenèse - 13e ...

Boris Kozo-Polyansky was the Russian biologist who dreamed up the principle of symbiogenesis as a mechanism for evolution in 1915. Mind you, this was before electron microscopy was invented and before the differences between prokaryotic (bacterial) and eurkaryotic (nucleated, animal) cells had been explicitly defined. Let’s call him KP for short. KP, clearly an interesting character and brilliant mind, incredibly demonstrated the symbiotic origin of cells with nuclei.

Back then, the organelles he was examining through his microscope would be murky compared to the resolution we have now. The chloroplasts and mitochondria would have been barely distinguishable from another. Yet he classified chloroplasts and mitochondria as former bacteria and claimed they were “symbiotic microorganisms”

What an incredible perspective for a young man (early twenties) living in the back a*** of Russia (the town of Voronezh, an agricultural center, was known as “blackearth” Russia), to view the cells of animals and plants (eukaryotes) as a pool of cohabiting organelles that were once free-living bacteria or “bioblasts” that became microbial symbionts. After decades of neglect, ridicule, and intellectual abuse, his ideas are now held to be correct by virtually all biologists.

KP outlines numerous examples some of which I’ll outline where microorganisms work and live together in a number of ways for mutual benefit. 

Life before cells

KP wrote that life preceded cells by:

  • Bioblasts – unit of living matter without cytoplasm or traditional cellular structures (nucleus). By itself it constitutes a living organism e.g. mitochondria. Free-living bacteria. Bioblasts have been described as “the aliens with permanent residence in our cells”.
  • Cytodes – flagellated cells using a tail for locomotion (spermatazoa).
  • Oxygenic photosynthesisers (then known as cyanophyceae, now known as cyanobacteria/ blue-green algae).

Parts of a whole

KP noticed that if cyanophyceae were eaten by non-photosynthesising organisms, some were incorporated and not digested. The union of cyanophyceae into the predator cell would endow the eater whether animal, fungus, protist the remarkable function of photosynthesis.

He saw first hand the power of symbiogenesis in the positive evolution of chloroplasts in plants and algae as well as the acquisition of photosynthesis by sponges, coral animals, and the fungi that become lichens. 

By the combination and union of life forms, KP discovered how new functionality and species could arise suddenly and not gradually. In a matter of generations, species could adapt a new functionality rather than over millions of years. He postulated this is how green sponges, green slugs and green medusoids were formed. 


There are numerous examples of mobile, autonomous organelles exiting and entering the cells where they are residing independently. 

Spirogyra algae, light micrograph - Stock Image - B302/0323 ...
Spirogyra algae

In some species of the filamentous green alga Spirogyra, the organelle that was thought to be its regular nucleus is in fact an entire cell itself, with its own membrane, cytoplasm, and a real nucleus inside (Famintsyn [1907, 1912]). This cell is an autonomous unicellular organism, which lives symbiotically in Spirogyra’s cell (Famintsyn [1907, 1912]). These types of nuclei are also present in some gregarines, radiolarians, and rhizopods.

An example of symbiosis between an orchid and a fungus accounts for some unusual nucleus behaviour. KP wrote how:

The fungal mycorrhiza occupies a number of cells of the orchid. As it grows it begins to fill, in a globular shape, almost the entire cell, meanwhile, the nucleus becomes compressed in the center. Then the nucleus makes its way, wiggling, to the closest cell wall. It moves actively, resembling an amoeba, and on its way breaks into pieces, each piece independently making their way to the cells of the orchid wall. Next to the orchid wall, the fungal nuclei restores its original integrity and “obtains a certain, almost mysterious acting force” [Burgeff 1909]. The outlines of mycorrhiza become less definite, its hyphae fuse and turn into shapeless masses and are slowly digested.

I tried to conceptualize the nuclei moving from the hyphae to the orchid’s cell wall by drawing some diagrams. The text describing this process unfortunately didn’t elaborate what the fungal nucleus does upon migrating to the orchid cell wall. We can only presume it continues living autonomously inside the orchid cell. What intrigues me most is how the nucleus fragments and then reassembles itself! The self-preserving fungal nucleus jumps ship abandoning the mycorrhizal cell in sub-optimal conditions to colonize a different species. That’s one smart nucleus.

Nucleus Stickers | Redbubble

A number of other examples documenting the “migration” of nuclei exist.

It is not uncommon for nuclei to leave the cell they were residing in and crawl into a new cell or number of cells.

When a binucleate cell is formed in rust fungi, a nucleus crawls into the neighbouring cell of the same hypha and also into a cell of another hypha if the cell lies close enough. The nucleus squeezes itself into a very narrow cell wall pore. A nucleus that leaves its cell does not return, it lives from then on in an alien cell. The abandoned cell slowly loses its cytoplasm and empties. Another example is during apogamy (asexual reproduction) in ferns. 

KP notes that “the nucleus cannot be considered absolutely necessary for life as numerous non-nucleated organisms have exceptional vitality”. Cells with nuclei artificially removed stay alive for a shorter amount of time but cell respiration, responding to stimuli, photosynthesis and other cell functions carry on as normal. 

These examples portray the bacterial nature of the nucleus.


Illustration credit

Hands down one of my favourite organelles is the trusted chloroplast! Without chloroplasts we could not survive.

The green plastids we call chloroplasts present in plants and green seaweed are larger and more obviously resemble bacteria than mitochondria.

  • Plastids also have their own DNA and messenger RNA.
  • Their ribosomes are the same size as those in bacteria.
  • Like mitochondria, they have a double membrane separating them from the rest of the cell.
  • Plastids divide by splitting directly in two like bacteria.
  • Their DNA, RNA and proteins are very similar to that of cyanobacteria.

Plastids exist in one form or another in all plant cells. Colourless plastids are non-photosynthetic and their function is mysterious. Perhaps their presence represents an ancient alliance between organelles that once served an important function inside the plant cell.

Difference between algae and plastids

  • Algae are eukaryotic aquatic photosynthetic organisms.
  • Although cyanobacteria are often called “blue-green” algae they prokaryotic so are often excluded from the algae taxonomy.
  • Plastids are double-membrane bound organelles containing chlorophyll for photosynthesis and exist inside eukaryotic organisms.

Chlorophyll organelles in animal cells

Cienkowski (1871) was the first to notice that yellow organelles of Radiolaria (unicellular animals or protoctists) can also live outside of the host cell. These yellow organelles had all the structural characteristics previously ascribed to plastids. He noted these “organelles” did not emerge from the cytoplasm and they had to be inherited or acquired from outside.

Radiolarians | SpringerLink

Several other researchers around this time concluded these independent chlorophyll organisms lead a symbiotic existence inside animal bodies (G. Entz [1881], Brandt [1881-1883], Geddes [1882], Hamann[1882], etc.). These chlorophyll organelles were later identified as unicellular algae.

In all true plants (excluding fungi and some colorless flowering plants), chlorophyll is packaged inside the chloroplast organelle.

Prochloron – a missing symbiotic link between plants and bacteria

Related image
Prochloron - an overview | ScienceDirect Topics

In the late 1950s, Ralph Lewin, a marine biologist of the Scripps Institute of Oceanography in California, discovered an obscure green bacterium dotted at various locations along the sun belt of the Pacific Ocean – California, Singapore and the Palau Islands. Calling it Prochloron, it is found growing on sea squirts, a marine animal. Some sea squirt larvae even contain pouches of Prochloron to ensure symbiotic association with the next generation.

Sea squirt | tunicate | Britannica
Sea squirt

Because of its large size and grass-green colour, Prochloron was assumed to be a green algae. Shockingly, under the scrutiny of a TEM, its identity as an enormous bacterium was revealed!

Some interesting revelations of Prochloron’s identity are:

  • Without its bacterial cell wall and preference for living outside sea squirts instead of inside them it would basically be a chloroplast.
  • It contains both chlorophyll A and B, being significantly more similar to plants metabolically than cyanobacteria which only have chlorophyll A.
  • It combines the physiology of a plant with the structure of a bacterium.
Micro Organisms in the Ocean. Homework Read p What are the most ...
Interesting slideshare on marine microorganisms

Prochloron provides a missing clue of symbiosis in the timeline of bacteria evolving into plants. Prochloron’s ancient ancestors were likely engulfed by single-celled protists and those who survived, endowed the newly occupied cell photosynthesizing metabolism. Today plants bend towards light to keep their fussy hitchhikers alive.

Lynn Margulis eloquently describing Prochloron:

As you look around at the world of nature you cannot fail to see the tremendous success of Prochloron’s descendants: jungles, gardens, house plants, and grassy hills, all of them
testify to the success of plastids. Eaten, but not digested, they have insinuated themselves into every corner of the world, hitchhiking as part of a cooperative partnership called the eukaryotic cell.

The new eukaryotes had diversified: some now had two basic ways of generating ATP-respiration and photosynthesis. Those that were also able to swim were virtually unstoppable as they took over compatible environments farther and farther afield. It is no wonder that in forms such as algae and phytoplankton, they began to dominate the oceans and other wet places of the world. Indeed, they continued to evolve to the point that they left the water, took over the land, and eventually became the primeval plants of the macrocosm.

The big picture

So we’ve seen mobile mitochondria and nuclei. Bacteria resembling chloroplasts existing symbiotically outside of plants. How does that influence evolution?

  • The movement of nuclei between species permits the transfer of new genetic information and potentially new functionality.
  • The premise of a foreign nucleus bringing new information quickly to the taken over cell allowing quick inheritance of new functionality in an alternative way to the Darwinian model of inheritance.
  • The engulfing or takeover of ancient bacteria to a foreign cell can bring drastic new processes of metabolism, aerobic in the case of mitochondria and photosynthesis in the case of chloroplasts or plastids.
  • The process of bacteria being engulfed by another organism is a refreshing spin on the age-old tale of differentiation through mutation.

Symbiogenesis is quite a glaring omission from Darwin’s natural selection. Thinking laterally and holistically, with a wide angle taking into account that no individual organism acts alone, how an organism can engulf or be incorporated into another one to both organisms advantage is speedy evolutionary progress.

We still don’t know where life originated from but we do know that the oldest progenitor life form we can trace was microbial in origin. Why had we distanced our thinking so much to not consider that even the constituents of our cells and cytoplasm – organelles – are conscious, self-motivated units of life that happened to strike an optimal scenario where each individual constituent can thrive but also be of benefit to the whole?

This realisation has been paradigm shifting for me. I always considered a cell or a neuron as a whole entity working toward a common goal of protein production or neurotransmission etc, but another likely scenario is that each organelle in a cell is independently alive and working toward its own goal which happens to be collaborating with the wider constituents of the entire cell. It’s incredible that even when you distill life down to its very minutia, examining the cell as a series of parts rather than a whole, its core units are independently intelligent! I wonder if many molecular biologists possess an animistic viewpoint for a cell’s organelles and components. Maybe I am just late to the party?


  1. Endosymbiosis – an overview
  2. Margulis, Lynn, and Dorion Sagan. Microcosmos: Four billion years of microbial evolution. Univ of California Press, 1997. Microcosmos
  3. Kozo-Poli︠a︡nskiĭ, Boris Mikhaĭlovich, and Peter H. Raven. Symbiogenesis: a new principle of evolution. Harvard University Press, 2010. Symbiogenesis: A New Principle of Evolution
  4. Aanen, Duur K., and Paul Eggleton. “Symbiogenesis: Beyond the endosymbiosis theory?.” Journal of theoretical biology 434 (2017): 99-103.
  5. Cover photo art


  1. beetleypete

    Phew, this takes me back to trying to study Biology at school. I didn’t understand it that well even then.
    Many thanks for following my blog, which is appreciated.
    Best wishes, Pete.


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