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How Does Life Work?

Biosphere Community

Eucaryote Domain:
The Four Kingdoms

The Biosphere Community
Serial Symbiogenesis
The Eucaryote Cell
Eucaryote Microbes
Gene Transfer in Eucaryotes
"Lower and Higher" Nonsense
The Communal Tree of Life
Four Kingdoms of Eucaryotes









The Biosphere Community

"Biosphere" is a term from the science of ecology. The word "ecology" shares meaning with the Greek words for hearth and household.
Ecology is the study of Earth's Household. All living organisms are members of this Household, this huge interdependent Community, that has continued to diversify and develop new ways of living ever since the Microcosm began.


The Biosphere began when Earth was young, with procaryote cells of archaea and bacteria, founders of the Microbial Domain of life. Toward the end of 2.5 Billion years of being the quiet but flourishing owners of the planet, the Procaryotes developed a new kind of larger cell, the kind of cell now in the human body, called a eucaryote cell. Procaryote cells began merging in a process called Symbiogenesis, and after a period of trying out various mergers, one sequence of combining began to work well. This was the Eucaryote Protist cell, which over time led to the Macrocosm of living organisms that are visible to human eyes. For example, we now know that green algae are the direct ancestors of plants.


So, what is this wonderful new kind of cell that mergers of procaryotes created? How did they create it, again?



Serial Symbiogenesis is a sequence of symbioses that over a very long time, resulted in the Eucaryote cell, several billion of which cells are you. That long name? "Serial" just means "in a sequence." Science requires the use of precise language. We don't know the exact sequence of these symbioses, and we are not yet sure of which parts of the eucaryote cell are the results of bacterial symbiosis. But the symbiotic origin of two cell structures is entirely clear. They are mitochondria and chloroplasts. All eucaryote cells contain mitochondria, which are the power plants of each cell. They make respiration possible, without which the cell dies. All photosynthesis is done by cells containing chloroplasts in plants, green algae, and cyanobacteria.

A mitochondrion by electron microscope,
image by Genomics Digital Lab
Chloroplasts packing living plant cells

Both chloroplasts and mitochondria have their own DNA, separate from the cell's nucleus. This gave microbiologists the first clues toward symbiogenesis.

The mitochondria scenario is this: In the procaryote world, every cell must eat. A small bacterium invades a larger bacteriun to eat its insides. The larger bacterium tries to kill and eat the invader. They both survive, and become partners. The invader knows how to make energy very efficiently, and learns to share that energy with its large host, which, in turn, learns to feed the intruder. It's a win/win result.

The chloroplast scenario is similar, but perhaps less antagonistic. One sunny day a cyanobacterium is engulfed by a larger, predatory bacterium. The cyanobacterium is full of chloroplasts, which keep photosynthesizing, making food, which is promptly eaten by the predator, which doesn't eat the little green cell inside it because it is being fed by it anyway. The two cells become partners, cyano providing food and predator supplying safety and access to light. Win/win.

Biologist Lynne Margulis, who is largely responsible for the general acceptance of endosymbiosis, thinks that there were other players in this sequential game of partners. One would be a spirochete bacterium (which wiggle all the time to move about) attaching itself to a non-mobile bacterium, giving it the ability to move, Another possible symbiotic event may have been the cell nucleus originating as a separate bacterium. The origin of centrioles is an open question.

As you can see in the photo above, plant cells have lots of chloroplasts. Animal cells have lots of mitochondria, from a few up to two thousand. But there is some evidence that they all connect up and act together.

The Eucaryote Cell

Under the microscope, Ithe eucaryote cell looks very different from a bacterial cell. It is much larger, and much more complex.

The cell shown is a one-celled protozoan, a mobile other-feeder. This cell has a large spherical nucleus that contains most of the cell's genes and is surrounded by a membrane. Several other kinds of membraned organelles can be seen in the cytoplasm. One kind are mitochondria, small granular-looking organelles within membranes that are relict survivors of bacterial symbionts. They are the cell's power plants. All eucaryote cells have at least one mitochondrian; some animal cells have 2,000.There are many kinds of other organelles in these complex cells, and some, such as centrioles and the nucleus itself, may be the result of bacteria symbiosis.

A big difference between most eucaryote cells and the much smaller procaryote cells is the way they transfer genes, or DNA inheritance. Procaryotes use horizontal gene transfer of plasmids, as described here . Procaryotes also use binary fission (division) to reproduce. Each split "half" is a genetic duplicate of its parent cell. Division is often incredibly fast.

We often think of eucaryotes as multicellular macro-organisms, visible to us. The fact is that many eucaryotes are micro-organisms, invisible to us without magnification. Many of these micobes are one-celled, but many, such as rotifers and nematodes, are multicelled.

A Sampling of Eucaryote Microbes

yeast cells budding, fungus, 5 to 10 µm
volvox, colonial protozoan,
"sun animalcule"
© Wim van Egmond

amoeba, protozoan
© Wim van Egmond

"bell animalcule," protozoan, aquatic
© Wim van Egmond
rotifer, multicellular,
© Wim van Egmond
trichonympha, protozoan, symbiont in termite gut
© Wim van Egmond
stentor, protozoan,
netrium,diatom, alga,
daphnia, crustacean,
visible in water as speck
© Wim van Egmond
water bear, tardigrade,
just below visibility
ostracod, crustacean, visible in water as speck
© Wim van Egmond

Gene Transfer in Eucaryotes

Some protist one-celled eucaryotes apparently can transfer genes horizontally, but this is not the case with multi-cellular organisms. However, many protists also reproduce asexually/non-sexually, by division, which can be very fast. Some algae reproduce so fast at times that they cause huge planktonic blooms off coastlines and color the ocean green.

Eucaryotes had to invent sex as a way to transmit genes down to the next generation. Gene transfer from parent to child is called vertical gene transfer, and it is much slower than the procaryote method. It takes a generation to transfer genes.

Living organisms are classified by science into their different kinds, by relationship, into larger and more inclusive groups, until you reach Kingdoms, very large groups, but at the very top are two Domains based on cell type, the Procaryote Domain of bacteria and archaea, and the Eucaryote Domain, which includes Four Kingdoms of eucaryotic life.

The Procaryote Domain, the eldest organisms, are the roots of the Tree of Life, and the Eucaryotes are often represented as the branching trunk above ground. This may be a useful way to suggest heritage, but it has an unfortunate side-effect.

"Lower" and "Higher" Nonsense

People often get the idea that the more recently an organism has leafed-out on the Tree, the more superior it is to the organisms that have emerged before. Humans only recently appeared on the Tree, of course, perhaps a million years ago. According to these notions, bacteria and archaea are primitive and simple and less worthy than more "advanced" life. Ditto for anything that is small, especially if it crawls. In this fallacious mindset, higher animals and lower animals are all that exists. We humans have long proclaimed ourselves the pinnacle of creation, and keep coming up with ways to decide, without blushing, that we in our glory are the reason the whole universe exists. (Google the Strong Anthropic Principle)

Earth Household deserves better from us. More and more, we discover that in nature cooperation is probably more powerful than competition in the relationships within ecosystems. It is past time that we recognized our kinships in Earth Household, and past time that we in the so-called developed nations, stopped regarding all living beings (including people) as resources to be used as we like, as if Earth could be owned.

We macro-organisms, so enormous compared to tiny procaryotes, cannot live without their help. Procaryotes have always facilitated success for the eucaryotes they invented, and they always included themselves inside each leaf that emerged to take the sun on the increasingly complex and diverse Tree of Life.

Consider that procaryote cells have been evolving for four billion years, that's four thousand million years, and that they are fluid, changing organisms. They are not lower, simple, static, out-of-date organisms. Instead,they have become 'streamlined' for maximal flexibility. Procaryotes have developed a great diversity of metabolisms, have invented every life strategy there is, and since they are so small, they have an almost infinite number of ecological niches where they can make a living.

When mulicellular eucaryotes such animals and plants become highly specialized within one niche, environmental change may render them extinct quickly, because they can adapt only slowly, through vertical gene inheritance in sexual generations. Bacteria, in contrast, can adapt quickly to any change, for two reasons, horizontal gene transfer and incredibly fast reproduction.

The Communal Tree of Life

The realm of recent life on Earth is incredibly diverse. Until human impact began to cause extinctions, there were probably more species alive than ever before. Life exerts a pressure to expand and elaborate, and to let no ecological niche go unfilled.

Imagine the entire biosphere as a single gigantic tree of life. Surrounding and nourishing the roots are Earth’s generous conditions for life: liquid water,reasonable temperatures, a good mix of elements, dissolved from Earth’s rocks, which readily form organic compounds.

Every life--in the ocean, wetlands, rivers; in the sky, in caves; in forest and grassland, mountain and city and desert--is one leaf on that great Tree.

A Tree of Life Timeline:

4 billion years ago: The roots of the Tree are the eldest, the procaryote single-celled organisms that began things, bacteria and archea. They have spent 2+ billion years elaborating possibilities.
1.6 billion years ago: First Eucaryote cells, leading to algae and protozoa. The trunk of life's tree are Protists, eucaryote single celled organisms which led to the first multicellular organisms.From the first few progenitor species of algae and protozoans, the next 1.7 billion years saw an incredible flowering of protist species. The trunk is strong in its diversity, able to respond flexibly to new environmental challenges.
0.6 billion years ago: Here the tree begins to branch, and then those branches branch. Once it begins branching, it becomes a wildly growing tree that branches and branches endlessly, each leaf of each twig of each branch a new life, often a new form of life.

Once the tree began to branch it never stopped. Speciation continues every day. Many leaves have fallen (gone extinct) during the wild growth of this incredible tree; probably 95% of all leaves that ever greened on Life’s tree have fallen away.

We know that there were five great extinction events when the Tree lost many of its leaves. But the roots were never in danger of collapse. After a great extinction, the number of leaves on the Tree are reduced, but they increase, often by leaps and bounds, until the Tree is again full and round. There is great biodiiversity again, but its community membership will have changed. New species have emerged to fill the spaces left by the extinct.

Right now there are probably some 100 million species of living organisms on Earth. And they are each unique, different from all the other species. In diversity is resilience.

Explore these fundamental kinds of leaves on life's tree.

The Four Kingdoms of Eucaryotes

click names to explore pages

Size and Pattern
Typical Cell

mostly microscopic

Termite gut ciliate symbiote

microscopic, unicellular and
macroscopic, multicellular


microscopic, unicellular, some colonies


bindweed leaf

from fern prothallis to redwoods and sequoias

Typical, showing adjacent cell walls

Turkey Tail
microscopic hyphae,
mycelium, fruit.
Cells have many nuclei.

Yeast cell

Treefrog, Hyla versicolor

microscopic springtails and nematodes to
macroscopic blue whales

Typical, showing many mitochondria


Explore Further in Biosphere

Biosphere: Introduction
Biosphere as Place: Introduction
Biosphere as Ocean: Life Zones
Biosphere as Ocean Floor: Benthic Biomes One
Biosphere as Ocean Floor: Benthic Biomes Two
Biosphere on Land: Terrestrial Biomes
Biosphere on Land: Anthropogenic Biomes
Biosphere as Process: Introduction
Biosphere Process: Floating Continents, Tectonic Plates
Biosphere Process: Photosynthesis
Biosphere Process: Life Helps Make Earth's Crust
Biosphere Process:
Rock Cycle--Marriage of Water and Rock
Biosphere Process: Marriage of Wind and Water
Biosphere Process: Gas Exchange
Biosphere as An Expression of Spirit
The Ecological Function of Art
The Earth Goddess
The Tree of Life
The Green Man
Earth Art
Biosphere as Community
Biosphere Microcosm: Bacteria and Archaea
The Procaryote Domain
Biosphere Microcosm: Germs
Biosphere Community: The Eucaryote Domain
Biosphere Community: Protists 1: Algae
  Biosphere Community: Protists 2: Protozoa
Biosphere Community: Plants: What's New?
Biosphere Community: Plant Diversity--Major Groups
Biosphere Community: Plant Defense
Biosphere Community: Plant Pollination
Biosphere Community: Plant Seed Dispersal
Biosphere Community: Kingdom Animals
Biosphere Community: Kingdom Fungi
Biosphere Community: Six Great Extinctions
Return to Ecology Index