Introduction to Microbiology: Important Concepts and Terms

by Vincent Racaniello, PhD

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    00:02 Hello and welcome to Introduction to Microbiology. My learning goals for you include, you will be able to define a microbe, you'll understand the differences among archaeal, bacterial and eukaryotic microbes, you will appreciate that microbes are everywhere and outnumber all other living things, you'll know why microbes are essential for life and you'll appreciate how microbes shape the earth. Let's begin with the definition of a microbe. The word microbe has 'micro' in it, and that comes from 'microscope' and that's because what these are small organisms visible only under the microscope. The study of microbes is called microbiology.

    00:51 There are a number of different kinds of microbes that we're going to be talking about, and the first group is called the bacteria. Here is an electron micrograph, a high magnification image of a common bacteria that's in your intestine, E. coli, you can see that they're rod shaped, they are individual cells and they have a number of properties that we're going to be discussing, this is magnified about 100,000 times.

    01:18 Bacteria have a number of properties that distinguish them from the cells that are in you and I. For example, they don't have nuclei as do ourselves and they don't have membrane-bound organelles like mitochondria or chloroplasts which are found in plants. There are a lot of different shapes of bacteria, they include rods, spheres and spirals and a few others.

    01:47 There are many, many bacteria on earth; our estimate is about 5×10 to the 30th, that's a huge number, actually bigger than we can really comprehend. You may be used to about a billion which is a giga of something, well 10 to the 30th is a lot more than that.

    02:07 The bacteria can be found in every environment on earth, wherever you look, whether it be in soil, in the oceans, in rocks even, you can find bacteria.

    02:20 Another group of microbes that I'd like to tell you about are the archaea. When the archaea were first discovered, they looked like bacteria, they can occur as spheres or rods, and so scientists thought these must be bacteria, so they were classified along with them. These archaea lack nuclei and they also lack membrane-bound organelles like mitochondria and chloroplast and so it was thought these must be bacteria, but it turned out that we were wrong.

    02:53 The archaea are evolutionarily closer to eukaryotes, the cells within us, in you and I, these are eukaryotic cells, archaea resemble them more than they resemble bacteria. Archaea are often found in extreme environments and we like to call them extremophiles, because they love those extreme environments and here's one of them, this is a hot spring in Yellowstone National Park in the US where the waters are over 90°C, some of the archaea love to grow in these environments, it is truly amazing. One of the archaea that grows in such extreme environment is called pyrococcus furiosus, and I love this particular archaea. You can see it's an oval shaped cell with lots of what we call flagella at one end, and this is how these cells move around. But they are not always present in just extreme environments, some of the archaea live more normally, like we do, you can find them in soils, you can find them in oceans, you can find them in other wet areas like marshlands and they are also in us, in you and I, we contain archaea. You can find them in your colon, your large intestine, they are in your mouth and they are also found on your skin.

    04:20 The next group of microbes that I'd like to discuss with you are the eukaryotes.

    04:27 The eukaryotes of course are cells with nuclei and we're made of eukaryotes, as you are as well and there are several different kinds of eukaryotes that I'd like to discuss, they are all microbes, and the first is the fungi. Many of you are probably familiar with fungi as the mold that grows on your bread or perhaps on your fruit and they are really two kinds of fungi, the first type is what we call filamentous fungus and that's shown here. These are organisms made up of long strands called mycelia and these strands are made up of smaller parts called hyphae. And again this is the fungus that you might find on your moldy bread or your moldy fruit. The other kind of fungus that we know of, exists as single cells and these are the yeasts and on the left you can see a diagram of the single cell yeast and on the right is a photograph of them. A very famous yeast is called saccharomyces cerevisiae or baker’s yeast. So again these are unicellular fungi, as opposed to the filamentous fungi that we just talked about. Mushrooms are also fungi. Now these are not microbes of course, because you can see them with the naked eye, but mushrooms are really just made up of a lot of mycelia, a lot of those filamentous fungal particles put together to form a mushroom.

    06:00 And these mushrooms actually have a way of growing that's quite unusual, the mycelium grows under the ground and the mushroom sprouts from above the ground. Now fungi are what we call heterotrophs, they have to acquire their nutrition from outside sources, they can't make any of their nutrients. And so fungi often grow in nature, in soil or on rotting plants and the mycelium grows and absorbs nutrients, and the mycelium grows bigger and bigger and on the surface the only thing that you can see are the mushrooms sprouting up, these are actually the reproductive forms of the fungus. Now the fungal cell wall is quite different from the cell wall that's in plants or bacteria or even in us. There is a cell membrane as you can see here, which is a typical lipid bilayer, but above the cell membrane is a layer of chitin. Chitin, which is shown on the left of the slide, is a polymer of sugars, in particular N-acetylglucosamine.

    07:04 Above the chitin is a layer of sugars called beta glucans and on the very top of the cell wall is another glycoprotein which consists of mostly mannose linked to protein. So these are very different cell walls from the other organisms on earth. So that brings us to the other kinds of eukaryotic microbes I'd like to tell you about, there are several that we won't touch upon, there are slime molds for example which are considered microbes, there are microscopic algae and then there are protozoa. Collectively we call these last three protists. And I just want to focus on the protozoa because we'll be talking about those in some detail.

    07:46 The protozoas are a diverse group of unicellular eukaryotes. That means they consist of just one cell. And a very famous one is the Paramecium, which is a protozoan with cilia on it, it has tiny hair-like extrusions around the surface. You may know Paramecium because when you were in school, you may have looked at a drop of pond water and seeing these very tiny protozoans swimming around. It's often studied in schools because it's safe. Many human pathogens happen to be protozoans, for example as shown in this photograph, there are flagellated protozoans that cause human disease, the Trypanosoma, the agents of sleeping sickness. Amoeba are also protozoa and some of these are known to cause human diseases, for example the Entamoeba shown in this photograph which are agents of diarrheal disease. There are ciliated protozoan parasites also; this one is called Balantidium, which in humans can cause gastrointestinal disease. And finally some of the protozoas called Apicomplexa can cause human disease and these include the very well-known Plasmodium, the agents of malaria, and Toxoplasma, the agents of toxoplasmosis.

    09:04 Let's take a look at the timeline of evolution on earth, because it turns out that microbes are incredibly ancient. We think that the Earth formed about four and a half billion years ago.

    09:18 And about 4 billion years ago, life began. We're not really sure what that life looked like, we don't have any experimental evidence for it, but many scientists think that it composed of small nucleic acids replicating in the waters of earth. About three and a half billion years ago, the first bacteria evolved, these were photosynthetic bacteria that could take sunlight and make energy from it, but these were not oxygenic bacteria, in other words they didn't make oxygen, so up to that point there was no oxygen on the earth. About two and a half billion years ago, two and a half to 3 billion years ago, the photosynthetic cyanobacteria emerged on earth. These were oxygenic, these bacteria actually produced the first oxygen on earth. And because of that, then about two and a quarter billion years ago, the aerobic bacteria arose. Those are the bacteria that can use oxygen to grow. Unicellular eukaryotes arose about 2 billion years ago, a little less than a billion years ago, the multicellular eukaryotes arose, like jellyfish and then plants and animals about 1 and a half billion years ago.

    10:40 The hominids, which include humans, chimpanzees and the apes and so forth, are arosed about 14 million years ago and humans only a 150,000 years ago. So microbes are truly ancient.

    10:57 We classify living things by using what we call phylogenetic trees and sometimes we call them the tree of life. And the purpose of these trees is to show how organisms are related.

    11:09 So let's take a look at these microbes that we've talked about and put them on the tree of life. First we will start with the bacteria, they're all shown here and the way this tree is organized, it shows you the relationships with the different bacteria, so the further apart they are, the more distant. All the bacteria are related as you can see, but different kinds of bacteria obviously have differences among each other. Now let's put onto this the eukaryotic microbes and other eukaryotes that we've talked about. Here we include the protozoa, the algae, plants, animals and fungi, you can see they form a separate branch on the tree of life. They are more related to each other, than they are to the bacteria.

    11:52 And finally let's add the archaea, they are in green here and you can see that they too form a separate branch on this tree of life. So the three groups of eukaryotic and bacterial and archaea microbes that we've talked about, all arose from a common ancestor billions of years ago and over time they have diverged and become very different.

    12:15 Now microbiology, the study of microbes is a relatively recent science. Humans didn't always think there were very small things in the world that could be only seen with a microscope.

    12:26 We thought everything that we could see was all that there was. It took a Dutch lens maker Antonie Van Leeuwenhoek to actually see the first microbe. He made the first microscope which is shown here and he took pond water, he took his own fluids and he looked at them under this microscope. And he was amazed to see that there were tiny organisms swimming around. About 100 years later, Louis Pasteur working in France, made a science out of microbiology.

    13:00 He showed that microbes, like bacteria, could grow in a liquid broth, but that they were not spontaneously generated. One of the prevalent thoughts at this time was that life arose spontaneously; Louis Pasteur put an end to that theory. He also found that microbes were responsible for the processes that gave us wine and cheese and bread. And finally Robert Koch, working in Germany, showed that some microbes could cause animal and human diseases.

    13:37 So these were the origins of microbiology and you can see that it's a relatively recent science.

    13:45 Now why do we care about microbes? There are lots of reasons that they're very important.

    13:51 To quote John Ingraham, “They are our progenitors, our inventors and our keepers”. We evolved from microbes and today without them, we couldn't survive. They are everywhere in us and on us, not just humans, but in animals as well, they're all over the earth, you can find them in soil, you can find them in hot springs, they're at the bottom of the ocean, they're on mountaintops, they're in the air, they're even inside of rocks and you can find them kilometers below the surface of the earth. Only microbes can take nitrogen gas from the air and convert it into a chemical that can be used by other lifeforms to grow, that's called fixing nitrogen and many plants have bacteria growing in their roots so that they can acquire the nitrogen that they need to grow. Only bacteria can degrade cellulose, which is a big component of plants. And by degrading the cellulose, they release carbon that other living things can use. If it weren't for the bacteria, the plants would just die and lie on the floor of the forest and never be recycled, so bacteria are very important for recycling nutrients in our ecosystems. Now bacteria live all over us as well as within us as well. They're in our intestines, they're in our stomachs, they're everywhere, they're on our skin and this diagram shows you all the different kinds of bacteria that are located in different parts of our skin alone. And the different colors on the pie charts show you the different colonies or communities of bacteria that are found, from your eyes, to your hands, to your feet. All of these bacteria have a function, they're beneficial for us, we call this our microbiom. And in fact the number of bacteria in us outnumber the number of human cells in us. It's safe to say that without microbes, other organisms on earth would not exist.

    16:00 Now as I said before, microbes are very good in surviving extremes, let's explore this a little bit. Some microbes can survive enough radiation that would kill humans thousands of times over. They can survive five megarads of gamma radiation. They can survive pressures that would easily crush a car, 8,000 atmospheres. They grow at extremes, they can grow anywhere from pH 0, extremely acid, to pH 11, extremely alkaline. They can grow at temperature extremes, from incredibly cold to incredibly hot, 121°C. They can grow at high pressures and they can grow in high salt. Many bacteria and archaea grow in lakes that are very very salty. We use this extreme nature of bacteria in our own daily life. For example, the polymerase chain reaction is a reaction that's widely used in biotechnology, in forensics and in research to detect very small amounts of DNA. This procedure requires incubation at high temperatures and the only reason we can do this is, is because of a bacterium that was isolated from the hotsprings in Yellowstone National Park, that has an enzyme that will survive high temperatures. If you wash your clothes in hot water, you have the bacteria to thank for that. Laundry detergents have within them an enzyme called the hydrolase, that is isolated from the thermophilic bacteria. And these are just two examples of the many ways that we take advantage of the extremophiles out there in the microworld. Microbes are also metabolic wizards, they invented photosynthesis. This is the process by which sunlight is converted into energy, and microbes were the first on earth to do that. Many microbes get energy from the chemical bonds in inorganic compounds, such as hydrogen, reduced iron and sulfides, way more than any other lifeform on earth does, and these are reactions in which no light is needed, so the bacteria can grow in dark places, in caves or even within rocks, using inorganic compounds to get energy. You may be aware at the bottom of the ocean, there are communities called vents, deep-sea vents. And these are areas where hot water is shooting out from the center of the earth. And around these events, is an incredible array of life of different sorts, but also there are bacteria and they are able to make organic compounds down there in the dark that all of these other animals can use. Microbes have shaped our earth in many different ways; half of the oxygen that you are breathing today is produced by bacteria. Plants decay because of the microbes that are present in soil, if it weren't for the microbes, the plants would never decay and that carbon would never be recycled.

    19:15 Microbes are the only significant source of nitrogen on the earth; this is essential for plants to grow and microbes take the nitrogen gas from the atmosphere and convert it to chemicals that plants can use. Humans know how to do this, we make fertilizer for example, but microbes are essential for plants to grow. If microbial activities on the planet were stopped, the plants would run out of nitrogen in a week, and we wouldn't be able to make enough fertilizer to make up the difference.

    19:48 You may be aware of a scientific experiment done a number of years ago called BioLab 2.

    19:54 This was a lab built in the desert of Arizona, a few humans were put into this, plants were put into this and the idea was that the humans would be self-sufficient; they would grow all of the food that they would need and dispose of it as well. Well this experiment failed because we didn't put the right bacteria in the soil to generate the compounds that the humans needed to survive. So given water, microbes can break down anything and we use this for remediation. So for example, if there is an oil spill in the ocean due to a tanker breaking or a broken pipeline, we can add bacteria which will then degrade the oil.

    20:36 Microbes also shape the physical earth that we live on, the caves that you are familiar with, with open caverns and the stalactites and stalagmites growing from the walls, these are produced by microbial activity. Microbes actually produce sulfuric acid which plays a role in eroding away the stone. The limestone that makes up so many caves is actually a microbial product. A microbe called a coccolithophore makes about one and a half million tons of calcite each year and that goes towards building these caves. If you look up into the sky and happen to see a cloud today, that cloud is a product of microbial activity. Marine algae, together with bacteria, produce a compound called dimethyl sulfide. They make about 50 million tons of this a year. This goes up into the atmosphere where it turns into sulfate, and that in turn attracts water, and that forms clouds. I'll bet you didn't know that.

    21:45 There are other reasons why we care about microbes of course and that is because some of them make us sick, and there are diseases caused by bacteria like Staphylococci and Pseudomonas, some of which are shown here. There are protozoan parasitic diseases caused by Entamoeba, Giardia and Plasmodium. There are fungal diseases caused by Histoplasma and Candid. And of course all of these microbes that we've talked about have their viruses.

    22:19 And there are also viruses that infect humans that cause disease such as HIV, poliovirus and influenza. But it turns out that the organisms that cause disease are a small fraction of all those that are out there, most of them are in fact beneficial. Many microbes live in a close relationship with another organism. We call that a symbiotic relationship, and when both the microbe and the other organism benefits, we call it a mutualistic symbiotic relationship. An example is the bacteria in our intestines, we provide those trillions of bacteria with a place to live and some nutrients and in turn they give us nutrients in exchange, they help our immune system develop, and they provide countless other benefits as well. We can take this mutualism a step further. Some organisms, in some organisms the bacteria not just live in them, but they actually live inside of their cells and this is called Endosymbiosis. It's very common in insects, and this picture shows an insect cell that's full of vesicles of bacteria growing in them. This is not at all harmful; in fact it's beneficial for the insect. I'll give you an example of an endosymbiosis and this takes place in the aphid, a common insect that lives off of plants. The aphid drinks the sap of plants in order to live and that's all that the aphid drinks, however, sap is made largely of sugars and animals cannot live on sugars alone. Within the aphid, and in fact within the cells of the aphid, is a bacteria called buchnera aphidicola and that bacteria takes the sugars that the aphid eats and converts them to other compounds like amino acids, so the aphid can grow. So the bacteria gets a place to live and gets sugars and in turn the aphid gets to grow.

    24:28 So I hope that you have learned today that you'll be able to define a microbe. I hope you'll understand the differences among archaea, bacterial and eukaryotic microbes. I hope you'll appreciate that microbes are everywhere on earth and that they outnumber every other living thing on our planet. I hope you'll know why microbes are essential for life and I hope you'll appreciate how microbes have shaped the earth.

    About the Lecture

    The lecture Introduction to Microbiology: Important Concepts and Terms by Vincent Racaniello, PhD is from the course Microbiology: Introduction. It contains the following chapters:

    • Introduction Microbiology
    • Fungi
    • Protozoa
    • The Concept of Microorganisms
    • Surviving the Extremes of Life
    • Metabolic Wizardry
    • Why Do We Care about Microbes?

    Included Quiz Questions

    1. Both human and bacterial cells can live and proliferate in the internal conditions of the human body.
    2. They both have membrane bound organelles such as mitochondria.
    3. They both have a prominent nucleus with a well established nuclear membrane.
    4. Both bacteria and human cells contain chloroplasts to provide essential nutrients.
    5. Both bacteria and human cells are exclusively rod shaped.
    1. Lungs
    2. Skin
    3. Colon
    4. Mouth
    5. GI tract
    1. They both lack nuclei and membrane bound organelles
    2. They are evolutionarily similar
    3. They colonize different environments
    4. They have symbiotic relationships with humans
    5. They lack a cell wall
    1. Phylogenetic trees
    2. Mannose-based glycoprotein
    3. Beta glucans
    4. Lipid bilayer
    5. Chitin
    1. Archaea
    2. FIlamentous
    3. Yeast
    4. Hyphae
    5. Mycelia
    1. Plasmodium
    2. Entamoeba
    3. Paramecium
    4. Typanosome
    5. Balantidium
    1. Slime mold
    2. Spirochetes
    3. Euryarchaeota
    4. Blue-green algae
    5. Planctomycetes
    1. Fix nitrogen
    2. Asexually reproduce
    3. Break down fructose
    4. Convert carbon dioxide to a usable chemical in the soil
    5. Stop the degradation of our ecosystem
    1. Pressures up to 8,000 atms
    2. pH of 14
    3. Temperatures of 0 degrees Kelvin
    4. 1000 megarads of gamma radiation
    5. 32 M of NaCl
    1. Many bacteria can derive energy from inorganic material
    2. Bacteria have developed light-independent photosynthesis
    3. Most bacteria can form spores that grow in times of harsh environmental factors
    4. Many bacteria can convert heat to energy
    5. Bacteria can use decayed organic material for energy instead of photosynthesis
    1. Sulfuric acid
    2. Carbon dioxide
    3. Inorganic material
    4. Sodium Chloride
    5. Oxygen
    1. Buchnera aphidicola
    2. Histoplasma
    3. Pseudomonas
    4. Giardia
    5. Staphylococci
    1. Microbes are classified into two main types: positive contributors and negative contributors.
    2. Microbes help to shape various parts of the physical Earth.
    3. Microbes live all over and within the human body.
    4. Microbes are exceptionally good at surviving extreme pH and temperature.
    5. Microbes outnumber every other living thing on the planet.

    Author of lecture Introduction to Microbiology: Important Concepts and Terms

     Vincent Racaniello, PhD

    Vincent Racaniello, PhD

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    Understood it all very well
    By Neuer P. on 11. January 2017 for Introduction to Microbiology: Important Concepts and Terms

    Understood it all very well. Easy to learn and the quiz in the end helps a lot too!

    Easy to understand
    By Yoga N. on 24. November 2016 for Introduction to Microbiology: Important Concepts and Terms

    As an "Bahasa Indonesia" speaker, English is not my mother language. This professor talks clearly and easy to understand. All basic information about microorganism is provided by this communicative video. I am really appreciate your explanation, Prof. Thank you very Much

    Thanks for the comprehensive …
    By Marissa D. on 20. May 2016 for Introduction to Microbiology: Important Concepts and Terms

    Thanks for the comprehensive basic introduction to microbiology.