5N – Microbes & micro organisms

Supporting article N: Understanding a little more by getting some order amongst the trillions of creatures in the category: Microbes or micro organisms.




Over the years there have been different ways of grouping the living things on Earth. Some scientists have used something called a Phenetic System that uses phenotypic similarities. Phenotypic means “physical.” Scientists compared what animals looked like, not their genetics. Also, organisms were grouped according to their similarities. For example, a dolphin could be more like a fish than you, because they swim and have fins. But in reality, they are mammals and have more similarities to you than to any fish.

As an aside, there is something called genotypic similarities that are genetic in nature, like the number of chromosomes you have.

Scientists also used a Cladistic System when they used phylogenic similarities. The phylogenic system uses evolutionary similarities to group organisms. So birds might be related to dinosaurs, which are reptiles, because scientists think that birds evolved from early dinosaurs.

The Littlest Organisms
Let’s study the wee ones of the world known as the microbes or the microorganisms. If you spend your life studying them, you would be a microbiologist. These are the smallest of the small and the simplest of the simple. Some of them, like viruses, may not even be alive as we currently define life.

What is a Microbe (micro-organism)?
What makes a microbe? We suppose you need a microscope to see them. That’s about it. There is a huge variety of creatures in this section. They can work alone or in colonies. They can help you or hurt you. Most important fact is that they make up the largest number of living organisms on the planet. It helps to be that small. It’s not millions, billions, or trillions. There are trillions of trillions of trillions of microbes around the Earth. Maybe more.

Calling all Microscopes
As with all of science, discovery in biology is a huge thing. While microbes like bacteria, fungi, some algae, and protozoa have always existed, scientists did not always know they were there. They may have seen a mushroom here or there, but there were hundreds of thousands of species to be discovered.

It took one invention to change the way we see the world of microbes – the microscope. In 1673, Anton von Leeuwenhoek put a couple of lenses together and was able to see a completely new world. He made the first microscope. It wasn’t that impressive, but it started a whole history of exploration. More important to us, scientists were eventually able to discover the cause and cure of many diseases.

Too Many to Count, Too Small to Find
We’ll give the big overview on the variety of microorganisms here. There is no simple explanation of a microbe besides the fact that they are small. The list goes on. Just remember that there is a lot of variety going on here.

They can be heterotrophic or autotrophic. These two terms mean they either eat other things (hetero) or make food for themselves (auto). Think about it this way: plants are autotrophic and animals are heterotrophic.

They can be solitary or colonial. A protozoan like an amoeba might spend its whole life alone, cruising through the water. Others, like fungi, work together in colonies to help each other survive.

They can reproduce sexually or asexually. Sometimes the DNA of two microbes mixes and a new one is created (sexual reproduction). Sometimes a microbe splits into two identical pieces by itself (asexual reproduction).


Prokaryotes – Cells that have no nuclleus

If you’re looking to learn about cells with a nucleus, this is the wrong place. Prokaryotes do not have an organized nucleus. Their DNA is kind of floating around the cell. It’s clumped up, but not inside of a nucleus. If you want to learn about cells with a nucleus, look for information on eukaryotes. And, once again, a prokaryote is a single cell or organisms that does NOT have organized nuclei.


You can’t, but they can. What can you do without a nucleus? You can do a whole lot. Most prokaryotes are bacteria and bacteria can do amazing things. Although they are very simple organisms, they are found everywhere on the planet. Some scientists even think that they may be found on other planets (maybe even Mars). Some places you can find bacteria every day are in your intestines, a cup of natural yogurt, or a bakery. Prokaryotes are the simplest of simple organisms. Here’s the checklist.

(1) Prokaryotes have no organized nucleus. Like we said, the DNA is clumped in an area but there is no organized nucleus with a membrane.

(2) Prokaryotes do not usually have any organelles. They will probably have ribosomes inside of their cells, but ribosomes are not technically considered organelles. No chloroplasts. No mitochondria. No nucleus. Not much at all.

(3) Prokaryotes are very small. Because they don’t have all of the normal cell machinery, they are limited in size. As always in biology, there are exceptions, but generally, prokaryotes are very small (compared to other cells). Mind you, compared to a virus they are big, but next to an amoeba, tiny.

(4) Prokaryotes don’t have mitosis or meiosis like other cells. Scientists don’t really have a good way of describing how they duplicate, but it’s not through normal means. Check out the bacteria tutorial to get an idea.



This is the place to learn about cells with a nucleus and all sorts of organelles. Eukaryotes are what you think of when you think of a classic “cell.” There are cells without organized nuclei or organelles that are called prokaryotes, but not on this page.

The possibilities are endless. Eukaryotes are cells that can do anything. They are the cells that have helped organisms advance to new levels of specialization beyond imagination. You wouldn’t be here if eukaryotic cells did not exist. What makes a eukaryotic cell? Let’s watch.

(1) Eukaryotic cells have an organized nucleus with a nuclear envelope. They have a “brain” for the cell. They have a discreet area where they keep their DNA. It is also said that they have a “true nucleus.” Can we say it any other way?

(2) Eukaryotic cells usually have organelles. They might have mitochondria, maybe a chloroplast, or some endoplasmic reticulum. They have parts that work to make the cell a self-sufficient organism.

(3) Although limited in size by the physics of diffusion, eukaryotic cells can get very large. There are even some extreme examples called plasmodial slime molds that can be a meter wide. The cell is multinucleated (many nuclei) and it gets huge. Generally, eukaryotic cells are a couple hundred times the size of a prokaryotic cell.

(4) Eukaryotic cells have extra stuff going on and extra parts attached. Since they have organelles and organized DNA they are able to create parts. One example is the flagellum (a tail-like structure to help it move). They could also create cilia (little hairs that help scoot the cell through the water). In the invertebrate section, we talk about nematocysts that are cells with little harpoons for catching prey. The list is endless.


We’re starting with the smallest of the small here. Some scientists argue that viruses are not even living things. We suppose it’s easier to give you a list of what they can’t do as opposed to what they can. What viruses can’t do:
(1) They can’t reproduce on their own. They need to infect or invade a host cell. That host cell will do all the work to duplicate the virus.
(2) They don’t respond to anything. You can poke them or set up barriers, it doesn’t matter. They either function or they are destroyed.
(3) They don’t really have any working parts. While there some advanced viruses that seem fancy, viruses don’t have any of the parts you would normally think of when you think of a cell. They have no nuclei, mitochondria, or ribosomes. Some viruses do not even have cytoplasm.

We’ve already established what viruses aren’t. Let’s talk about what they are. Every virus has a few basic parts. The most important part is a small piece of DNA or RNA (never both). That strand of nucleic acid is considered the core of the virus. The second big part is a protein coat to protect the nucleic acid. That coat is called the capsid. The capsid protects the core but also helps the virus infect new cells. Some viruses have another coat or shell called the envelope. The envelope is made of lipids and proteins in the way a regular cell membrane is structured. The envelope can help a virus get into systems unnoticed and help them invade new host cells.

As you go on to study more biology, you’ll see many virus types. There are three basic shapes.
1) First there are helical virions. They are set up like a tube. The protein coat winds up like a garden hose around the core.
2) Next comes the polyhedral shape. This shape group includes the classic virus shape that looks like a dodecahedron. A dodecahedron is a geometric shape with twelve (12) sides. These viruses have many facets and a seemingly hard shell of capsomeres (pieces of a capsid). There is a variation of the polyhedral called globular. Globular shapes are basically polyhedral virions inside of a spherical (like a ball) envelope.
3) Last is the complex virus shape. You may have seen this one in books with the geometric head and long legs.

There are things out there even smaller than viruses. The two that scientists have discovered are called prions and viroids. A prion is (as far as we know) just a protein. Prions are proteins that can invade cells and somehow direct their own duplication, making more of the isolated proteins. Viroids are a little different in that they are just RNA. Scientists have even discovered that they are responsible for some diseases.


Bacteria are the simplest of creatures that are considered alive. Bacteria are everywhere. They are in the bread you eat, the soil that plants grow in, and even inside of you. They are very simple cells that fall under the heading prokaryotic. That word means they do not have an organized nucleus. Bacteria are small single cells whose whole purpose in life is to replicate.

Okay. So we’ve told you they don’t have an organized nucleus. True. They do have DNA. It is grouped in an area called the nucleoid. They have cell membranes like other cells and even a protective cell wall. Mind you, their cell wall is not like the one in a plant. It’s a special kind that bacteria have for protection. They don’t have any organelles, just ribosomes. (These are all characteristics of prokaryotes if you remember.)

Very small. Very, very small. You might have seen pictures of some bacteria. Since we don’t know what you have seen, we’ll tell you there are three basic shapes. Spherical bacteria are in the shape of little spheres or balls. They usually form chains of cells like a row of circles. Rod shaped bacteria are look like the E. coli living in your intestine. You can imagine a bunch of bacteria that look like hot dogs. They can make chains like a set of linked sausages. Spiral shaped bacteria twist a little. Think about balloon animals for these shapes. It’s like a balloon animal in the shape of a corkscrew.

All sorts of things. Sorry to be so vague, but they do just about everything. Some help plants absorb nitrogen (N) from the soil. Some cause diseases like botulism. Some bacteria even live inside the stomachs of cows to help them break down cellulose. Cows on their own can digest grass and plants about as well as we do. They don’t get many nutrients out of the plants and can’t break down the cellulose. With those super bacteria, the cellulose can be broken down into sugars and then release all of the energy they need. Imagine if scientists could develop bacteria to live inside of us that would break down plants. That would be something. We could eat grass and leaves all day long.



Protozoa are also known as protists. These are the bad boys of the microbe world (bad meaning “advanced”). Protists are eukaryotes with special structures that may be the base organisms of multicellular organisms. Meaning: they have structures that can be seen in advanced creatures and those structures are not seen anywhere else in the microbe world. You will also find the funkiest microbes in this category, such as the plasmodial slime molds. Actually, we just like saying “plasmodial”. Mmmmm… Plasmodial.

Let’s start with the fun ones. Slime molds are not molds like a fungus. They sometimes act like a fungus, but they aren’t. They are actually independent organisms. There are two big kinds of slime molds, cellular and acellular. Cellular slime molds are actually thousands of individual cells that team up and work together. They specialize for a short time and some do the eating, some work on reproduction, and some build special structures. When they are at the food source, they find it more efficient to work together.

Acellular slime molds might also be called plasmodial slime molds. Plasmodial slime molds are actually one cell. They can be huge, a couple of feet across, but still only one cell. They are able to grow so large because the one cell is multinucleated. That word means the cell has several nuclei inside. The plasmodial slime molds ooze across the ground of forests digesting everything they can. When it comes time to reproduce, they release all sorts of spores (like a fungus).

Amoebas are easier to describe. You may have even seen these in your classrooms. They are small-single celled organisms that ooze from place to place. They reach out with one part of the cell, a structure called a pseudopod. They don’t really have a shape because they are constantly on the move, hunting down food and eating by a process called phagocytosis. They wrap themselves around the food and absorb it into their body for digestion.

The next protists are called flagellates because they move with a specialized tail called a flagellum. They live in water and the water inside of dirt. The flagella whip around like a not-so-coordinated fish tail. When it whips, the protist scoots along though the water. They do not do well in dry areas. They need that liquid environment to move. Remember when we said that protists have specialized structures you can see in animals? Sponges are a great example of where you will see flagella in action.

While a flagellum is a long tail structure, cilia are short little hairs. The classic example of a ciliate protist is a Paramecium. They are the very complex protists that have little hairs all over their body. The hairs flap and push the organism through the water. They can even hunt down food and attack them with a structure called a trichocyst. Instead of surrounding their prey like an amoeba, they take in the food through an oral groove (a protist version of a mouth). They even have a way of getting rid of the food through an anal pore. They might not seem like much to you, but the structures are very advanced for a single-celled creature. They were the first creatures to have them.

Last, we’ll talk about the parasites of the protist world. Not all protists go about their life eating little bits of food in a pond. Some, called sporozoans, are nasty little parasites. These protists, like all parasites, cannot live on their own, and they harm the host organism over time. A disease called malaria is caused by one example of a sporozoan protist.

Look into our eyes. Look deep into our eyes. There are no such things as molds. All molds are actually fungi. That’s a bunch of fungus. This surprised us when we first learned about it. We always heard about mold in the shower or mold on the bread. Mold is actually a type of fungus. It has a shape called a zygote to be exact. While yeasts are single celled fungi, molds are multicellular fungi. Bread takes one kind of fungus (yeast) to make it rise. If you leave the bread out, another type of fungus comes in (bread mold) to break it down. It’s not amazing, but it’s true!

Let’s look at Club Fungi first. Mushrooms! Everyone knows about these fungi. So what is a mushroom or a puffball? Bunches of strands living underground are called hyphae (pronounced hi-fah). Those strands are the basic fungus in action, decomposing leaves, or rotting bark on the ground. When it’s time to reproduce, they develop a stalk and cap. The mushroom that you see popping out of the ground. It’s only one part of the fungus. On the bottom of that cap are a set of gills that have little clubs with fungus spores.

We already talked a little about mold. That is only one example of the Zygote Fungi. These have hyphae-like mushrooms but they reproduce in a different way. When it’s time to make more fungi, they create a stalk and release something called zygospores (thus the name zygote). When your bread gets old and green or black, you are seeing a type of zygote fungus in action. If you wait long enough, you will see the stalks develop and the zygotes released.

Let’s finish up by looking at Sac Fungi, simple, single celled fungi. Yeast is used to make several types of food for humans. We need yeast to make breads. We also use them to make alcohol. It’s a whole process called fermentation. Sugars are broken down in an environment without oxygen. It’s called anaerobic fermentation. And voila, alcohol. Even though they are single celled, you may find them in colonies. They reproduce very quickly and hang out together. It takes a lot of them (because they are so small) to get a lot of work done.


Lichens are special organisms. They are actually two types of organisms in one. Scientists still debate on whether both organisms are helped by teaming up. You’re here to get the facts and might be saying, “What are the two organisms? Tell us now.” Ahhh, the excitement of learning.

It’s all about a fungus and some algae. That’s it. Lichen is two organisms working together. When you read about fungi we talked about hyphae. Hyphae are strands of the fungi that form a mesh as they grow. In lichen are actually cells of algae living between those strands. The two organisms work together. The fungus acts as a protector from the environment and loss of moisture. The algae go about their business of photosynthesis and creating food. The fungus uses the energy and the algae are protected and can survive.

So? Why does all of this matter? Why does this help the two organisms survive and multiply? Lichens can live in places that many organisms cannot. Lichens can even live on the side of a rock. That’s it. They don’t need soil. Slowly the fungus can break down the minerals in the rock. The algae provide energy. They are a self-sufficient team. Scientists may call that team a composite organism. They are both able to be in places they could not go alone. It’s an advantage for their survival.

Are we killing off the lichens of the world? In some places, yes. Indirectly we may be killing many species of lichen. In the same way that air and water pollution are killing off many species of amphibians, lichens are very delicate organisms. Changes in the levels of poisons and toxins hurt the relationship that the fungi and algae have. Always remember, even if the fungi can survive the poisons, if you hurt the algae, the whole organism will die. They are dependent on each other.


With such a variety of microscopic organisms, it’s bound to happen that there are some that help the world. There will also be some that hurt the world. We will cover those in another section. We’re going to cover a few of the good ones here.

There are bacteria that go through a process called fixing nitrogen. These bacteria, living in the roots of plants, actually help them absorb nitrogen from the surrounding soil. The nitrogen is very important for the growth of the plant, and these little bacteria give them an advantage for survival.

As we said, not all protists are bad for the world. In the bacteria section we already told you about a species that lives in the digestive system in cows. These bacteria help cows break down the cellulose in plants. Similar bacteria live in all sorts of grazing animals, helping them survive off plant material. Many ecosystems are based on creatures that are called herbivores.

Scientists have even discovered fungi that will help you battle bacterial diseases. So you get sick, the doctor looks at you and says you have a bacterial infection, maybe bronchitis. He prescribes an antibiotic to help you get better. Antibiotics are drugs designed to destroy bacteria by weakening their cell walls. When the bacterial cell walls are weak, your immune cells can go in and destroy the bacteria. Although there are many types now, one of the first antibiotics was called penicillin. It was developed from a fungus (a fungus named Penicillium found on an orange, to be exact).

With such a variety of microscopic organisms, it’s bound to happen that some do not help anything in the world. Some also help the world. We cover those in another section. We’re going to cover a few of the bad ones here.

Many species of bacteria cause disease in humans, animals, and even plants. Humans worry about bacteria that cause botulism (bacteria living in spaces without oxygen, such as cans), tetanus and E. coli. You should know that there are also some good forms of E. Coli living in your intestines. They help break down food and live a simple life (and yes, they make it smell down there). There are also E. Coli that can be passed to you from undercooked meat. These bad bacteria can make you very sick and even kill you.

We don’t know of any viruses that are good for the world. They are an important piece of evolution and natural selection. Weaker and older animals are more easily infected. Those organisms are removed from the population so that healthier animals can survive. But the virus life cycle, that of a parasite, only hurts the organisms. Some even destroy cells in order to reproduce. And don’t think you are the only one to get sick. Viruses attack plants and even bacteria. No organism is safe from damage. Examples of viruses include Rabies, Pneumonia, and Meningitis.

Humans are actually creating stronger bacteria and viruses by accident. The idea of natural selection is that weaker organisms are killed off and stronger ones survive and duplicate. Think about a bacterium for a moment. If you take antibiotics that kill bacteria, you get better.

However, because of variety, some bacteria may survive your medicine. Not enough bacteria survive to hurt you now, but they are there. If they eventually get someone sick, there is a chance that the antibiotics will not work again. You have incubated super bacteria! It’s happening all the time in hospitals. We are killing off the easy diseases but some mutant strains are surviving. We might not be able to cure people next time a bad disease infects people.


As with many things in life, humans need more than nature provides, not only to battle hazards in nature but also to battle things we have created ourselves. You’re asking, “What are these guys talking about?” Biotechnology! Scientists all over the world are experimenting with viruses, bacteria, and fungi for hundreds of reasons. Why mess around with these little creatures? They are the simplest of all organisms. They can also be the most deadly. That is reason enough to study them.

Scientists are working with microbes and the compounds they create to make new medicines to save our lives. You might be vaccinated for pox or the flu. Scientists have studied those viruses to see how they act. Then they came up with a way to teach your immune system to do battle. If you get sick at all, you will be able to fight off the infection. Labs are also developing drugs that help you fight infections after you get the disease. We already spoke about antibiotics. Labs are creating new and stronger antibiotics every day.

Although nobody likes to talk about it, humans have a history of using disease and compounds created by microbes in warfare. Labs were built to create chemical compounds that would kill people. They also isolate diseases (viruses) that could be released to infect entire populations of people. Most of the world has chosen not to develop diseases for use in war. They realized how dangerous and uncontrollable these diseases are. Once they are out, they might not be able to be stopped.

Let’s finish on a good note. Scientists are also working with microbes to help the environment. In reality, the environment did not need help; we’re just trying to lower the negative impact we have on the environment. Good examples are the bacteria that have developed to break down oil in the water. If a tanker leaked and oil began to get into the water, these bacteria could be released to break down the oil. The resulting compounds would not hurt the environment. Scientists are also working with bacteria and fungi to help breakdown garbage