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What is a microbe? The word “microbe” refers to living organisms that are so small that we can't see them without the aid of magnification. The word combines “micro” and “bios” (small life). The word "microbe" most commonly refers to bacteria and archaea,the most ancient kind of life, but many organisms which are not bacteria are also invisible to our eyes. Some are microscopic fungi, such as yeasts and the hyphae of most fungi. Some are small multi-cellular animals such as nematode worms, rotifers, water bears and tiny mollusks such as daphnia and cyclops.

Microbes are hugely important. Most life on Earth is microbial. Biofilm scientists estimate that microbes weigh about one thousand times as much as all the macroscopic lives on earth.

Many one-celled organisms, invisible to us, are called Protists, mostly Algae and Protozoans. Many protists live in water, salt and fresh, and many live in soil. Protozoans are very small: one gram of soil will contain around 30,000 protozoans. One-cell algae? Even smaller. About 400,000 per gram of soil. Procaryotes, though are, incredibly, much tinier: That gram of soil will contain around 2.5 million bacteria and archaea.

For a gallery of eucaryote microbes, go here.

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Microcosm and Macrocosm

The biosphere of Earth contains at least two worlds, the microcosm (small invisible world) and the macrocosm (large visible world). Until a few hundred years ago, we didn't even know there was a micro-world of life. Now, we know it thrives everywhere
--on our skins, in our bodies, floating in the air, in the sunlit surface waters and in the muds in total dark miles below the ocean surface, and in every soil. Recently, scientists discovered bacteria thriving inside solid rock 2 kilometers deep.

Every macro-organism, plant, animal or fungus, is home to millions of micro-lives. A very few microbes do hurt us. Such hurtful microbes are called pathogens, and cause some of our most infectious diseases, such as cholera, diphtheria, and tuberculosis.

To find out why we call microbes germs, click here.

Most microbes, however, help macrolife survive. Procaryotes are the ancestors of all other life. As animal life developed, bacteria and archaea came along as working partners. We depend on them to digest our food, create oxygen, supply us with vitamins and amino acids, as well as the more taste-based uses: to make yogurt, chocolate, cheese, beer, and wine, and also, oddly, to supply us with antibiotics. Recently, microbes are being used to clean up pollution, in a process called bioremediation.

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Procaryote Domain

There are two primary kinds of life on Earth.They are distinguished by the kind of cell they have. Every organism is made of cells, tiny parts that carry out independent functions. The basic work of life is done inside cells--converting food into power (metabolism); and exchanging gases (respiration). Most cells reproduce themselves.

Procaryotes are the first and largest domain of life. They are all microbes.

The other domain are the Eucaryotes. Their cells look very different from procaryote cells, but are connected by inheritance. Many eucaryotes, the protists, are microbes, but even more are multicellular organisms that we know as plants, fungi, and animals.
We explore eucaryote-type cells here.

Some basics of Procaryotes

Procaryotes are of two distinct kinds, which look alike but differ chemically:

Bacteria, also called Eubacteria, discovered in the mid 1800s

Archaea, also called Archaeobacteria, discovered in the late 1900s

Cells of both kinds of Procaryotes have similar structures:

adapted from Ken Todar

A cell envelope or capsule (outer surface layer; cell wall; cell membranes) separates the organism from its environment. The outer layer may produce slime, which helps the cell afhere to surfaces and create biofilms. The outer layer also protects the cell from toxins.The cell wall is semi-permeable. It contains sensors that tell the cell about chemicals it wants to block and those it may let in. Using this ability, it can absorb compounds from outside, which is how it eats.

Often projecting out of the cell envelope are flagella, whip-like structures which allow the cell to swim. Shorter hairlike structures called pili help bacteria adhere to surfaces.

Inside the procaryote cell wall there are usually no membranes.


1) Photosynthetic bacteria (cyanobacteria) have chlorophyl organelles surrounded by a cell membrane

2) Nitrifying bacteria have energy-making organelles surrounded by a cell membrane.

There is no cell nucleus in procaryote cells.

The rest of the interior is cytoplasm that contains:

• a large chromosome of DNA, the genetic instructions that are inherited when the cell reproduces by division and budding. This DNA looks like a tangle of string.

• smaller circles of DNA called plasmids, active in gene transfer

• Many granules of RNA called ribosomes.

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Why Are Procaryotes Important?

Procaryotes are the ancestors of all other life on Earth

• Procaryotes are the living roots of the tree of life. Macro-life cannot stay alive without ongoing procaryote support.

• Archaea and bacteria had the planet to themselves for 2.5 billion years. In that huge span of time, Archaea and bacteria created the environment that makes today's life possible, and eventually, through symbiogenesis, they began today's eucaryote organisms.

• Cyanobacteria invented photosynthesis, and for more than 1,000 million years added oxygen to the atmosphere, where there had been none.

• Archaea and bacteria created most of the metal deposits that we mine.

• Bacteria (along with fungi) decompose (disassemble) dead plants and animals. Without this disassembly, nutrient pools would dry up, for no cycling would take place. Without raw materials, new life could not survive. No death, no life.

• Bacteria and Archaea take nitrogen from air and transform it into chemicals that plants must have to grow. Without nitrogen-fixing, no plants, no animals, no macrosphere of life.

• Bacteria and Archaea live in symbiosis with every kind of macro-life. They were there right from the beginning, and evolved with macro-life kinds. Among other things, they live in every insect gut; they digest cellulose for every grazing animal and for termites; they provide amino acids to cockroaches and aphids; they live in every vertebrate gut, where they provide digestion services, often provide vitamins, and sometimes offer essential amino acids.

Procaryotes are the living foundation of life as it exists; as life evolved and diversified and found every possible place and way to live, procaryotes were always present, and are today.

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Procaryote Reproduction

Bacteria and archaea reproduce by doubling in an asexual (non-sexual) process called binary fission. First the large DNA molecule makes a copy of itself, then the two DNA molecules separate as the cell doubles in size, then the cell capsule pinches in at the center like a tightening belt as new cell membrane and wall are created, until finally the belt tightens all the way, and the two new cells become separate, genetically identical organisms. If food is abundant, this reproduction is extremely fast, numbers growing exponentially until the food is exhausted or local environment changes for the worse. In that case, the bacteria begin to die.

bacteria growing fast on human skin--that's a hair
close look at rod bacteria dividing fast
staphlococcus expands like a cluster of grapes

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Procaryote Survival Spores

Many bacteria and archaea can survive and spread as a kind of spore, a tough resistant packaged version of the cell created inside the original bacterium in response to damaging local conditions, such as lack of water.

These are not like moss or fern spores, which are methods of reproduction. Procaryote spores are methods of cell survival. They are dormant and can survive for centuries in this condition. They float in air invisibly, until they encounter a good place to grow (food, water, warmth), then expand and resume growth.

Biofilms and Microbial Mats:
Procaryote Living Arrangements

Outside of the laboratory, 90% of procaryotes live in large communities called biofilms. A "film" to humans is a metropolis to bacteria. Most moist surfaces on Earth are covered in biofilms. Water tends to flow, which is a necessity for biofilms. The outside capsule of bacteria is usually sticky. A biofilm begins when a few cells floating downstream attach to a surface, then more, then even more, attaching on top of each other like floors in an apartment building. If there are nutrients in the water, the bacteria multiply rapidly. Bacteria can sense when they are with lots of others (quorum sensing), and when they do, they secrete a kind of sticky gel that envelops the whole biofilm. But, as in an apartment building, they leave lots of corridors and elevator shafts so water and nutrients can be supplied throughout the biofilm.

The most familiar biofilms grow on people's teeth. They are 300-500 cells thick, which tells you how small bacteria are and how fast they reproduce. Tooth films are made by streptococcus mutans bacteria, which grow a protein "glue" on their capsules that stick them to teeth. They then use sucrose (sugar) for food and to make a gummy matrix that holds their biofilm together. They can chemically break down that gum for food, which makes lactic acid which attacks enamel and creates plaque.

Biofilms often contain many kinds of bacteria and archaea. Some biofilms also include such eucaryotes as algae and yeasts.

The gel coatings on biofilms protect the colony from dangers such as antibiotics. Even if poisons kill top layers of the film, they tend not to penetrate lower levels.

When biofilms become really thick, they are often called microbial mats. When procaryotes were the only life for 2 billion years, such mats grew almost forever, becoming columns with bottom layers dead but stuck together and tops still alive, with populations in the trillions. Eventually, many such "tall" mats fossilized and are called stromatolites. Some still live in shallows off Australia.

A few examples of biofilms and microbial mats

biofilm on medical catheter
biofilm on human
intestinal villi
biofilm in methane reactor Image credit Henry Aldrich

puddle bottom biofilm
the color is algae,
dark bits bacteria

microbial mat on sand in a slow stream.
oxygen bubbles from algae
microbial mat on pebble in
fast creek, including algae
microbial mat on rock at cold seep in deep ocean
living stromatolite,
Australian shallows
fossil stromatolite, showing layers of life

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The Big Difference: Horizontal Gene Transfer

Macro-life can only transfer genes vertically, that is, from parents to child, through sexual reproduction. It's called inheritance.

Procartotes can do something that eucaryotes cannot. They can do horizontal gene transfer. This is a difference of enormous importance. Archaea and bacteria can transfer packets of genes called plasmids from one to another, side-by-side, in a process called conjugation.

When bacteria and archaea acquire a new capability that may be generally useful, they can transfer a plasmid containing that ability to each other. In other words, procaryotes can change their own genomes very rapidly, which means that they can evolve much more rapidly than macrolife.

For example, many bacteria that now show worldwide resistance to antibiotic drugs were not resistant 20 years ago. This means that bacteria worldwide have swapped genes that conferred resistance for each of the drugs that no longer are effective. Evolution in action. Worldwide. Think about that, and procaryote size.

Recombinant DNA processes hailed in genetic laboratories as breakthrough achievements of human science are really copies of everyday bacterial interaction.

Because very different body-types of bacteria and archaea conjugate with each other, the concept of species is not very useful to use with procaryotes, because they are always changing. It may be more functional to think of all bacteria as belonging to one earthwide species with varying but always shifting genomes. Microbiologists and taxonomists are debating this question now.

An odd thing: although archaea and bacteria are chemically quite different, they have conjugated across kinds to swap genes. This suggests, that on a practical level, it may be more useful to think of both procaryote domains, bacteria and archaea, as simply Procaryotes, a single domain of life.

There is growing evidence that some one-celled protists do transfer genes horizontally, even though they are eucaryotes.Sponge colonies have also transferred genes horizontally. It seems that living organisms try every strategy possible to survive, and often succeed in ways that violate the rules that humans infer from observation. Life remains mysterious.


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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



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