The Science of Everything Podcast - Episode 112: Introduction to Microbiology

Episode Date: October 31, 2020

An overview of the field of microbiology, beginning with a brief history of the discipline, and then proceeding through a summary of the structure and function of various microbial life forms, including protists, yeasts, bacteria, archaea, viruses, and prions. The episode concludes with a discussion of microbial growth and methods to reduce it. Recommended pre-listening is Episode 10: The Cell.   If you enjoyed the podcast please consider supporting the show by making a paypal donation or becoming a patreon supporter. https://www.patreon.com/jamesfodor https://www.paypal.me/ScienceofEverything

You're listening to The Science of Everything podcast episode 112. Introduction to Microbiology. I'm your host, James Fodor. In this episode, we're going to give an overview of the field of microbiology. So this is going to be a fairly survey-level discussion. So I'm going to talk about the different types of organisms that are studied in microbiology, including protists, yeasts, bacteria, and archaea, viruses, and preons. With a little bit of discussion at the end about microbiology.

growth and efforts to control microbial growth. Recommended pre-listening for this episode is episode 10, an introduction to the cell, just for a bit of background on some of the cell biology topics that will come up. But I do emphasize that this episode is going to be only a fairly cursory discussion. The idea is to give an overview of the different, of the sort of diversity of organisms that come under the sort of umbrella of microbiology, not to dive into any of the details too much, and perhaps we'll be able to do that in some future episodes. So, without further ado, let's make a start.

And I want to start before diving in and talking about the different organisms. I want to just briefly discuss some of the history of the field of microbiology. Because throughout most of human history, people didn't know about microbes. There were some ideas from ancient world, including ancient India, especially associated with the Jain tradition, that there were microbiotic or tiny forms of life that couldn't be observed with the human eye, but existed kind of everywhere. But these were really pre-scientific ideas that people just sort of came up with.

that there was no empirical evidence in favor of this. The first real evidence for the existence of microscopic life forms came with the work in the late 17th century of Antonine Van Loynhoek, probably mispronounced that name, but this was a Dutch scientist who was, I think, the first, or at least among the first, to use a microscope to observe bacteria and is considered the father of microbiology as a result of this. However, because of the limitations of microscopes at the time, he wasn't able to say very much about the nature of these microbes other than that they existed and that he found them in lots of different places. And so the field of microbiology didn't really progress for over a century until sort of the

19th century. And critical here was the work of Louis Pasteur, who you're probably familiar with from the word pasteurization, which is derives from his name. What he was interested in doing is investigating the notion of spontaneous generation. Now, this was an idea that had existed for centuries that organisms or, well, life forms would spontaneously arise from, like, rotting organic matter or just in a stagnant pool of water or something like that. Like flies, for example, thought to spontaneously generate and then emerge from organic material

if it was left for long enough. And Louis Pasteur is accredited as being the one who definitively refuted spontaneous generation, although there had been a number of experiments before that with people who were skeptical about this idea. But what he was able to do is show that boiling a broth of water, so that we're going, water with organic matter in it. Boiling the broth of water was able to ensure that no microorganisms grew within the broth and therefore no flies or other bacteria or cloudiness was observed in the medium. Now people had done this before. People knew that boiling water prevented things from growing

in it, but the contention was whether this was because it killed the organisms that existed within the water or whether boiling the water changed it in some way such that life couldn't grow in it. And this was a little bit difficult to determine, of course, because if you then exposed, it was known that if you expose the boiling water to, you know, the air afterwards, then things would grow in it. But this could be because life was then able to get to the water, or because the contact with the air was able to somehow change the water back. Of course, we now know that, you know, boiling the water doesn't do anything to the water if it's then allowed to condense back. All it does is kill any life that exists in it. But, of course, this wasn't

understood at the time. So what Pustua did, and his unique contribution, was that he designed these very elaborately shaped glass bottles, essentially, that had these ends that allowed them to be still exposed to the air, so they weren't sealed tight, which is the difference between previous ones, but also they were sufficiently, had sufficiently long necks or curved necks such that no dust particles were able to get in there. And so because of that, he was able to show that it wasn't the fact that the water was changed that prevented things from growing in the solution after boiling, because he had it still exposed to the air. Instead, it was the fact that dust particles carried spores that then allowed microorganisms to grow in the broth after it was boiled. And so by

shaping the necks of the glass vessels in a way that dust particles couldn't get into the broth, he was able to prevent that from happening. So this was the experiment, there was a series of experiments that he used to definitively refute spontaneous generation, which supported the germ theory of disease, the theory that many types of diseases are caused by small microscopic organisms that grow in an organism. The germ theory of disease and microbiology generally received a lot of further support with the work of Robert Koch, who lived in the late 19th century,

and he established specifically that microorganisms can and do cause disease. He did this by manipulating the blood of cattle that was infected with anthrax, and particularly the bacteria that were found in that blood. He found that he could transmit anthrax from one animal to another by taking a sample of the blood from an infected animal and injecting into a healthy one. He also found that he could grow the bacteria in a nutrient broth, inject not the blood, but the broth with the bacteria growing in it

into a healthy animal and cause the disease. And he developed a set of postulates that are still used in medicine today called Cox postulates that are used to establish whether a given pathogen is the cause of a specific disease. So this was established by the end of the 19th century, and by the early 20th century with the work of Paul Ehrlich, for example, the first antibiotics were developed that were able to treat bacterial infections. And penicillin, which is a group of antibiotics, was discovered in 1928 by Alexander Fleming, and it began to be used during World War II to treat infections, and then more widely alongside other antibiotics following World War II. So that's a brief history of the field of microbiology, just to give a bit of an overview of where these ideas come from. so they're fairly recent in the scheme of things.

Now let's go through and talk about the different types of life forms that are found within the general field of microbiology. It's important to understand that microbiology is just defined in terms of the size of the organisms it discovered, its studies, not in terms of their evolutionary relationship or anything like that. So almost all life that exists on Earth is microscopic, and the earliest forms of life being single-celled organisms were also microscopic. And so there's a very diverse range of life forms that are studied here. they can be grouped into different, I'll just say categories, because they're not necessarily taxonomic relationships, but they can be grouped into different categories based on the key

differentiating characteristics of those forms, and also the manner in which they potentially cause disease, which is often one of the major reasons we're interested in them. And so the way I've set this out, which is fairly standard, is what we're going to do is we're going to start with the largest organisms, purely in terms of size, but also complexity, and then move to the smaller, simpler ones. So we'll start with protists and then move to yeasts, then we'll talk about bacteria and archaea, and finish with the subcellular organisms. So let's start with protists. Now, protist is a bit of an old-fashioned term, but I'm going to use it here just because

I don't want to get distracted by the details of the taxonomic relationships, and it can get rather confusing, because I just want to talk about the basic types of organisms that exist in some of their key properties. So a protist is, technically speaking, any eukaryotic organisms. that is not an animal plant or a fungus. Remember, a eukaryote is an organism whose cells contain a nucleus and generally other organelles as well. So eukaryotes are more complicated, more recently evolved types of organisms, and they're distinct from prokaryotes, which are evolutionarily older, more simple organisms that don't have a nucleus and that don't have cellular organelles and so forth.

We'll get to prokaryotes later, but bacteria and archaea are prokaryotes. Protists, though, are not prokaryotes. They're eukaryotes, so they're more complicated cells, they're also physically larger. But notice that it's defined in a weird way because all eukaryotes are evolutionary related to each other, but protists don't form a clade. So a clade is, and I talked about this in previous episodes where we looked at the diversity of animals, but a clade is a group of all of the organisms that descend from a single common ancestor. So protists do descend from a single common ancestor, the last eukaryotic common ancestor. But the group protest doesn't include all of the descendants of that common ancestor because the descendants of that common

ancestor also include animals, plants, and fungi. So this is why a protest is a bit of an old-fashioned group. It's defined kind of functionally and morphologically, not in terms of evolutionary relationships. But nevertheless, I think it's still useful for getting an understanding of the types of organisms that exist. So essentially, most eukaryotes, just in terms of the number of organisms, are protists. So most of the small, single-celled organisms, there's many different types of them, and they're very diverse. We're just going to lump them all together and call them protists for the purpose here, because they all protists fit under the rubric of microbiology, whereas, of course, animals, plants, and most fungi don't, because they're larger and

multicellular. So because they're extremely diverse, there's a very diverse range of reproductive, metabolic, and other functions across protists. So again, the only distinguishing feature, really, of protest is that they're eukaryotic and single-celled. So of course, they're small, larger than prokaryotes. Just to give you an idea, so protists are about the same. So protists are about the size as other eukaryotic cells, so particularly animal cells. So as a rough rule of thumb, you can think of a protist cell as being maybe 10 micrometers across, whereas a prokaryate cell is about a tenths the size of that, so about one micrometer. And then when we go to viruses, it's another factor of 10 down again. We're talking about 100 nanometers. And proteins, which

are preons of proteins, are about another order of magnitude down again at 10 nanometers. So we'll come back to that. Sye scale is just a useful way of keeping track of things. So at this stage, we're at the highest level of about 10 micrometers, so the size of a cell. Some protists reproduce using gametes, so sexually in the way that humans do, whereas others reproduce asexually by binary fission, so there's really no commonality that they can reproduce in multiple different ways. One very interesting thing about eukaryotes is the range of metabolic or sort of nutritional mechanisms that they use. So some are autotrophic, which means loosely that they produce their own food, whereas others are heterotrophic, which,

loosely speaking, means that they eat food produced by other organisms. So humans and all animals are heterotrophic. So we don't produce our own food. We don't photosynthesize. We eat food, or we consume organic molecules that contain energy and their bonds between the atoms that have been processed by other forms of life. So that's heterotrophic. So some eukaryotes are autotrophic, so some photosynthesize, but others don't. So again, there's a diversity here. For those that don't, for the heterotrophes, there is a diversity there. So some phagotrophic, that means to absorb nutrient through phagocytosis. So that's when essentially the cell cytoplasm absorbs nutrients by enveloping them in the cell membrane. So phagocytosis occurs in the human body, but we don't

absorb our nutrition through phagocytosis. That would be a bit weird. That would be like eating through the skin, sort of. But a single cells can do that. So that's called fagotrophy. There's also osmetrophy. That's absorbing nutrients through osmosis, which is passage across a semi-permeable membrane. So that's different, again, to phagocytosis. And there's also saprotrophy, which is feeding on dead matter. That is how fungi absorb their nutrients. There's also parasitism, which just means eating smaller organisms. So some protists eat other protists or bacteria as well. So there's a diverse range of metabolic and nutrient strategies used here, as you would expect from such a diverse group. Now, to give a bit of a sense of the diversity here, I'm going to talk about a very

broad categorization of protists into three different types. Protizoa, protozoa, which means animal-like, protophyta, which means plant-like, and slime molds, which are fungus-like. Now, this is not really an exclusive categorization because there's ones that don't necessarily fit into any of these. Also, slime molds aren't the only type of fungus-like protists, and also this categorization, again, these don't form clades, so it's not an evolutionary categorization. But the purpose of this is not really to explain the evolutionary relationship between protists, which is generally not well understood anyway. Rather, the purpose is just to explain the different forms that they take and the different morphologies and metabolic strategies and so forth. And so for that purpose,

this classification system is useful. But bear in mind that, yeah, it's not like these are different species or anything like that. So let's talk about protozoa first. So protozoa are protests that are kind of like animals in the sense that they're generally free living and they feed on organic matter like other microorganisms or organic tissues. So these are heterotrophes. They're very abundant in aqueous environments and the soil. This group of protists includes flagellates, so they move around with the help of whip-like structures called flagella, and ciliates, which move using hair-like structures called cilia that kind of beat and help the organism to move, as well as amoeba, which moved by the use of protrusions of the cytoplasm that kind of move and stick out,

which are called pseudipodia. So the distinction here is basically just in terms of how they move. Is it using phlegelum? Is it using cilia or is it using pseudipodia? And these types of organisms are found pretty much anywhere where there's water, especially in aquatic environments, and mostly feed on other microorganisms or organic tissues. So these are heterotrophes and they move about, so they're mobile. And that's what makes them kind of animal-like. But there are other types of projects as well. So let's talk about the protophyter. These are the plant-like ones. These are mostly algae as well as lichens. So algae is another term that we need to explain. Algae doesn't have a precise definition in biology, but a typical

conception would be something like algae are eukaryotes that produce energy from photosynthesis, but lack the complex structures of higher plants. So algae are thought to be ancestral to higher plants, but they're much simpler than them, well, obviously being ancestral to them, but they do photosynthesize. So that's why they're obviously plant-like, because they carry out photosynthesis. And this includes organisms from unicellular microalgae to multicellular form. such as seaweed. It may be, come as a bit of surprise, but seaweed is actually not a plant. Many people think of it as a plant, but it isn't because it lacks all the more complicated structures that plants have, and it's actually a protest. Now, remember that I've sort of

been saying that protests are single cellular, and I've been emphasizing that throughout. That's technically speaking not true, because we've just seen a counter example to this, and you may have picked up on this before and been wondering why I've been saying this. The reason I talk about protests of being single cellular is that nearly all protests are single cellular, and for the most part, that's a good way to think about them. But it's strictly speaking not true, because there are some multicellular forms of protists, and seaweed as an example. Remember, technically, a protist is just any eukaryote that's not an animal plant or a fungus. And I'm not going to get into the technical definition of what makes something a

plant at this point, but it includes certain anatomical structures that you need to have to count as a plant, and seaweed doesn't have any of them. So therefore, even though it's multicellular and eukaryotic, and it photosynthesizes. Seweed doesn't count as a plant. It's a protist. Lichens are also very interesting. So these are kind of plant-like and maybe confused as plants, but it's actually a composite organism comprised of algae. Remember, these are essentially single cellular photosynthetic protists. Algae living on the filaments of fungi species in a mutualistic relationship. You probably know what lichen looks like. It kind of looks like a layer of bark, but it doesn't have to be on a tree. It can also be on rocks. So it's usually on some

sort of flat surface, like a rock or a tree. It's not actually part of a plant, though, nor is it a form of moss, although it could look a little bit like moss, but it's actually kind of a mutualistic combination of algae and fungi living together. It's a very strange phenomenon. But let's move on from lichen and talk about the last of the three different main types of protists that I'm going to cover, which are the slime molds. These are fungus-like organisms. Slime molds aren't the only type of more fungus-like protists, but I'm going to focus on these ones because they're interesting to get a lot of attention. So again, a slime mold is an informal name. It doesn't refer to a clade, but I'm going to use it here because it's helpful. So slime molds are several times, types of unrelated, but sort of

similar in lifestyle, eukaryotic organisms that can live freely as single cells, but also can aggregate together to form multicellular reproductive structures. So again, this is a very strange phenomena. They're not single cell, they're not multi-cell. They're kind of both, depending on the stage of life and also environmental circumstances. So when food is a by, Slime molds tend to exist as single-selled organisms and just move about doing their thing, eating food. But when food is in short supply, these organisms will congregate together and start moving as a single macroscopic body. And you can see this. So slime molds, you can look up pictures of them, they look quite disgusting. Many of them are bright yellow or green or some

other very prominent color. You might mistake them for being a fungus or even a weird type of plant, but they're actually neither, although they're kind of fungus-like. You can find videos where you see that they move over time and not like a plant that grows. They actually physically move across the ground or across a rock or something like that. Not quickly, but they do move in a visible time span. The reason they congregate together, I don't know if the details are fully understood, but it appears that that allows them to be more sensitive to airborne chemicals and help them detect food sources, which they can then move in the direction of. They can also change shape and function of the different parts of the body, so they can form fruiting bodies,

which are like stalks that project outwards and release spores that help them reproduce. So this is something that makes them a little bit like fungi in having these spores. But slime molds are extremely interesting because they kind of break a lot of our preconceptions of how life works, that you're an organism and that you reproduce. But these are kind of single cells that sometimes come together and then can move and specialize, kind of like it's an animal, but they're not animals. They don't have any permanent specialization of cells, and they can exist as single cells just fine. So really, really strange stuff.

As interesting as that all is, that concludes our discussion of the protists. Let's then move from protists to the yeasts. Protists are eukaryotes that aren't plants, animals, or fungi. There are some types of fungi that, while still being fungi, also come into the rubric of microbiology because they're single cellular. And these are called yeasts. So, again, it's a bit confusing here because I talked about fungus-like protists. But these are things that are not fungi, but are like fungi in some manner. Yeasts are fungi.

So they're part of the fungus kingdom. So fungi can be multi-celled, but they can be single-celled. When they're single-celled, they're called yeasts. I'm not going to talk a great deal about fungi. That will need to do a separate episode on that. But I'll just say briefly, fungi differ from both plants and animals. They differ from plants because they don't photosynthesize. They are not autotroats. They don't produce their own food, and they don't have any of the other structures that plants have either. However, they also differ from animals, because apart from being largely terrestrial, so fungi evolved on land, they don't come from the ocean. They don't eat their food in the way that animals do. Instead, they digest by excreting enzymes

into their environment. And that's what we mentioned before. Saprotrophy, feeding on dead matter. That's what fungi do. Another way that fungi differ from animals is that they have a cell wall, which animals don't. They just have a membrane. Fungi have a cell wall that's made of chitin and is analogous to the cell wall of plants, but the cell wall of plants is made of different material and is evolutionarily distinct. So fungi are a bit strange. Centuries ago, they were thought to be plants because they they're not motile, but they're not plants, and I've just mentioned some of the differences, but they're also not animals because they're very different, so their own kingdom. But this podcast isn't about fungi, it's about microorganisms, and yeast are the microscopic

type of fungi, because they're single-celled, and I'm not going to go into the details of yeast too much here, because there would just be a podcast on fungi, but I will mention the yeast species Saccharomyces syrivisae, which people are probably familiar with, because this is baker's yeast. This is a species that converts carbohydrates, like sugar essentially, to carbon dioxide and alcohols in a process called fermentation. So the products of this reaction are used in baking and production of alcoholic beverages and have been for thousands of years. So it's an extremely useful organism here. It's interesting to think that when we're producing bread, when the bread's rising or when the alcohol is fermenting,

that essentially what is happening here is that a fungus is digesting the food or the nutrients there and excreting waste product. If you think about it in that way, it kind of sounds very unappetizing. but as it turns out, waste products of other organisms can be very good for us, and that's an interesting phenomena. Yeasts are very common in the environment. Often they're found in sugar-rich materials, because that's what they digest. Naturally occurring yeasts are found on the skins of fruits and berries and some plant products, so they're very widespread. Yeasts can also be grown in the laboratory on either solid growth media or liquid broths, and that's how, for example, the baker's yeast is propagated, and so can just be grown in the laboratory as well as other yeast.

that have various culinary or medical uses. So that's a little bit about yeast. Yeasts are eukaryotes, so they're a similar size, broadly speaking, to protists, so say 10 micrometers. But now we're moving down, and we're getting smaller, because we're going to talk about bacteria and a little bit about archaea. So bacteria and archaea are prokaryotes. That means that they lack a nucleus. They lack many of the other organelles that are found inside eukaryotes, and they're also,

as a result of that, a lot smaller. So instead of around 10 micrometers, we're talking about one micrometer. Bacteria, because obviously they're a lot simpler, they're evolutionarily older. All life is thought to have evolved from maybe not exactly modern bacteria, but from ancestors that were very similar to bacteria. Now, bacteria occur in many different shapes and sizes. I've said that they're roughly one micrometer, but actually there's a lot of variation there. But also, the different morphologies of bacteria are quite interesting.

So there's sort of two main types that you'll often see in terms of the naming of bacterial species. They're often named after their shape because that's one of the easiest things to detect. You have to look at them. So the coxye are basically spherical, so they look like little circles if you look at them in a microscope. And the basili are rods. So they look like little rods or sort of rounded rectangles if you see them in the microscope. So coxae and basilii, if you see that sort of stem in name of a bacteria, that's usually just telling you its shape. There are other morphologies of bacteria as well.

So there are some that are kind of elongated rods that have like instead of being quite rounded at the ends, they're kind of strung into sort of thin strings. There are kind of corkscrew that form little helices or filaments. Some of the long and sort of crinkly ones are called spirochetes. There are others that have budding appendices like kind of little tails that stick out of them. So there's many different and quite exotic forms of bacteria. but coxswine and basile are sort of the two main forms. In terms of metabolism, just like protists, there are many different ways that bacteria gain energy.

So because of the great diversity of bacterial metabolism, there are a number of different sort of axes that we can divide things on or categories we can divide things into. So first, let's talk about the energy source. There's really only two possible sources of energy for any organism. Either the energy is gained from light or it's gained from oxidizing existing organic compounds. Usually, in the case of when we talked about protists, we talked about autotrophes in terms of organisms that produce their own energy through photosynthesis. In the bacterial world, though, it's a little bit more complicated because many bacterial species that get their energy from light are also autotrophes. So that means that they fix their own carbon into an organic form using an initial source of carbon dioxide.

So an autotrope is technically speaking, an organism that fixes its own carbon from the atmosphere, so from carbon dioxide, and then fixing, fixes meaning basically it incorporates it into organic molecules, as distinct from heterotrophes, which get their organic compounds from eating other species or consuming organic compounds directly, which is what humans and other animals do. So often those are kind of the same thing. If you're an autotrof, that means you get your energy from the sun. That's true for, I think, most, if not all, protests. But bacteria is more complicated, because there are,

what are called photo-autotrophes. That means that they get their energy from light. That's the photo part, and they fix their own carbon dioxide, hence the auto part. These are photosynthetic bacteria, including cyanobacteria. However, bacteria uniquely also have what are called chemo-autotrophes. So it's still auto, meaning it still fixes its carbon from carbon dioxide in the atmosphere. But instead of getting its energy from the sun, it gets its energy from chemical compounds. So how does this work? Well, basically these are organisms that get their energy from non-organic compounds, so hydrogen, sulfur, or nitrifying bacteria. So they can feed on sulfurous or nitrous compounds, which humans, and other animals can't. We have to feed on organic compounds. But there are types of bacteria

that can essentially eat things that no animal could possibly eat. They're not even organic compounds, and therefore they still need organic compounds, obviously, to form the structures of the cell proteins and lipids and so forth, but it gets that carbon dioxide from the atmosphere. So hence they're chemo-autotrophes. So very interesting, not something you see as far as I'm away in any eukaryotic organism. So that accounts for the autotrophes. They all fix their own carbon from the atmosphere. Some of them get the energy from the sun, so photo-autotropes. Some of them get it from a diversity of different non-organic chemical sources like sulfur and nitrous compounds. Those are the chemo-autotropes. Now let's look at those that get their carbon from

the source that's familiar to us, so existing organic compounds. So these are the heterotrophes. The most familiar type of heteroatroph is a chemohetrof. This is, this was mentioned in the context of protists. Humans are chemo-heterotrophes. What that means is that we get our energy from chemical sources, by oxidizing chemical sources, and we get our carbon from existing organic molecules. There are bacteria that also do this, including fermenting bacteria, for example, as well as bacteria that engage in both aerobic and anaerobic respiration. So some bacteria need oxygen, some don't. Mention that a little bit more later. But all that comes under chemohetorotrophs. But there are some bacteria that although they get their organic compounds from existing

organic sources, so they get their carbon from existing organic sources, but they still get their energy from the sun. And these are called photo heteroatrophes. So there are certain types of green non-sulf and purple non-sulfer bacteria. So these are fairly unique species, but what it means is that although they need to consume organic compounds, they can still produce their own energy. And again, as far as I'm aware, this combination does not occur in any Uco-Eotic organism. So this is why we need to make these distinctions. And we can't just talk about the hetero and autotrophes, as I did for the proteus, because bacteria can be strange.

They can make an interesting combination. So don't worry if you couldn't quite follow all of that. Complex terminology there, but the basic idea is that bacteria can get their energy in the way that plants do. They can also get it in the way that animals. do, but there are even more ways that they can get it, which involve basically feeding on weird stuff like sulfur and nitrous compounds, or by eating as well as photosynthesizing at the same time. I'm putting that loosely, obviously, but that's the idea of a photohetroph. So,

fascinating combinations possible in the bacterial world. Let's move on from metabolism and talk about some other aspects of bacteria. The bacteria have DNA, just like humans, but they have a lot less of it than humans and other animals. So bacterial genomes range from maybe 100,000 to about 10 million base pairs, so that's compared to a few billion base pairs of humans, so much, much smaller. Bacterial genomes, therefore, usually only encode from a few hundred to a few thousand genes, obviously because they don't have any of the organelles that eukaryotes do, so there's much, much simpler intracellular processes going on there. They also don't need many of the specialized proteins that are used for sensory organs or motor function or all of the other complicated

things that humans and other animals need because of their specialized organs and specialized cells. genes and bacterial genomes usually consist of a single continuous stretch of DNA, so they don't have very many introns, which are basically bits of genes that are not actually used to encode the protein that are kind of taken out in a sense. So basically bacterial genetics, although it's sort of similar in the basic concepts, so it's still based on DNA, it still has transcription and translation and so forth, if you remember, we've talked about that in previous episodes. That all still happens in bacteria, but it's just generally much simpler, and there's generally fewer proteins involved. and less complexity and fewer methods of regulating gene expression and all that other stuff. So it all points to a more sort of simple, more ancestral form of the cell. Another interesting aspect of bacterial genetics is that in addition to their normal chromosomal DNA, by the way, bacteria have a single usually circular chromosomes,

so they don't have multiple chromosomes like humans do. But in addition to that, bacteria can also possess what are called plasmids. So plasmid is an extra chromosomal, so separate from the mrsome. main DNA, small molecule of DNA that's usually circular and contain usually only a small number, like a handful of genes. Typically, they contain genes that are useful for the bacteria, like antibiotic resistance or conveying metabolic functions or perhaps virulence factors that might help the bacteria infect an organism. So plasmids can be passed between different bacteria. That's how they're sort of transmitted and replicate separately from the chromosomal DNA.

And studying the genetics of plasmids is very important. for understanding things like conferring new traits into bacteria or understanding the spread of antimicrobial resistance, for example, as well as the process by which we genetically modify organisms often involves introduction of plasmids, or at least propagation of material using plasmids, and eventually I'll get around to doing some episodes on genetic engineering and gene technology, and we'll talk about that in more detail then. I mentioned that fungi have a cell wall, which is something that makes them different from animals. bacteria also have a cell wall, which is interesting because animals don't have a cell wall.

The cell wall of a bacteria exists outside the membrane, so you've got your membrane of phospholipids, and then outside that is your cell wall. In bacteria, these are made of peptidoglycan, which is basically made of long polysaccharide, or sugar chains that are cross-linked by peptide bonds, which are found in proteins. So hence why, it's called peptidoglycan. Bacterial cell walls are different from the cell walls of both plants and fungi. The cell walls are plants made of cellulose. Those are fungi, as I mentioned, are made of chitin.

So although they will have cell walls, they're all made of different things. Also, although as far as I know, all bacteria have cell walls, there are different types of cell walls depending on the type of bacteria. So the two main ones are gram positive and gram negative. And these names are historical. They originate from the reaction of the cells to a gram stain, which is just a way of visualizing the cells. But they're structurally different. So the main difference is that a gram positive bacteria has a simpler structure.

It's got the membrane, and then it's got the cell wall, a fairly thick cell wall, outside the membrane. In gram-negative bacteria, it's completely different. You've got the inner membrane, and then you've got a thin cell wall outside that, and then you've got a second membrane and outer membrane on the other side of the cell wall. So for gram-negative bacteria, the cell wall is a lot thinner, and it's wedged in between two membranes. So given that, you might understand how one is stained by the stain and the other isn't, but there's also a very big structural difference.

Bacteria are very commonly classified in terms of whether they're gram-positive or gram-negatives. That's one of the reasons I wanted to mention that. Many bacteria are motile, so they can move around. The best studied of the mechanisms by which they do this is the flagella, which is a long filament that's turned by a motor, and it can kind of be whipped like a whip and allows the bacteria to move. The bacterial phlegelm is made up of about 20 proteins, which form a reversible motor, so circular motion is found in the natural world.

Chemotaxis is an important phenomenon for bacteria, and it refers to the fact that bacteria that are motile will move either towards or away from certain stimuli. So these behaviors are called taxis, and they're mediated by chemicals, so hence chemotaxies. But there are other types of taxis as well. So chemotaxis is just a very common one that's metered by chemicals. Bacteria can also move towards or away from life, so that's phototaxis, or energy sources, so that's energy taxes, or even magnetic fields, so magnetotaxis.

And this is a very important way that bacteria can respond to stimuli, can find sources, food or avoid poisonous or toxic substances and they can find light if they're photosynthetic. So there's many applications of that. So bacteria do sense their environment, but obviously in a much simpler way than animals or plants do. Bacteria reproduce by binary fission, so that means essentially they just split in two, which produced two identical copies of the parent cells. So that's different from how reproduction works in animal cells, which use meiosis, which is a different mechanism that splits the DNA in a way that, generally speaking, the two daughter cells won't be identical to the parent cell. And if you want, there's a, I've done episodes on mitosis and meiosis

as well, so you can refer to those for more detail there, but binary efficient is a different type of cell division again that occurs in bacteria. And bacteria can grow very rapidly and multiply extremely quickly, as we'll see a little bit later. The final thing that I wanted to mention with respect to bacteria are endospores. Many types of gram-positive bacteria, so not all bacteria, but many types can form endospores. These are highly resilient and resistant dormant structures that is basically like the cell has gone into hibernation, essentially. So an endospor contains a core of DNA and ribosomes, which are basically factories that help to produce proteins from the DNA, protected by a rigid coat of peptidoglycan and proteins. So basically a cell wall.

But it's a small structure. Endosomes are much smaller than the bacteria as a whole. It's kind of like a reduced core. It's the minimum machinery and information necessary. to produce more bacteria, but it's inactive. So endospores show no detectable metabolism and can survive extreme physical and chemical stresses, including high UV, gamma radiation, detergents and disinfectants, extreme heat, freezing and thawing, pressure and desiccation. So endospores can survive, as I said, frozen for really arbitrarily long periods of time. It's thought that they can survive in space, they can survive very high UV and radiation, so they're extremely resilient. They can be killed with high enough temperatures, but you need very high temperatures. So it's more than regular boiling

to kill endospores. And it's fascinating that bacteria are able to survive in this way. Remember, it's not the bacteria itself that survives. So it's the endospores. So what the endospores will do is they'll survive in the harsh environment. And then when conditions are favorable, there's mechanisms that will allow the bacteria to then resuscitate themselves from that dormant state and then continue to divide. It's thought that bacterial endosports could be a mechanism by which life is able to move from one planetary body to another, which is a whole fascinating idea that life on Earth could have actually originated elsewhere in the soul system or even elsewhere in the galaxy and being transported on meteors or on comets or something through bacterial endospores,

which could theoretically survive the harsh conditions of space. But again, that is the topic for another podcast. We've finished with bacteria, but as a little addendum, I do want to talk about archaea. Now, archaea are actually a third domain of life. In the current standard classification, there's three domains of life. One of them is eukaryotes, which I talked about before in regards to progests. Yeasts are also eukaryotes. Then there are bacteria, which we've just been discussing. And then the third domain are archaea. Now, most people know about bacteria and eukaryotes, but archaea are a bit less well known. And one of the reasons for that is because they've only been discovered in the last, I think since the 60s or 70s, it's been really understood how

distinctive they are from bacteria. So at a superficial level, archaer are quite similar to bacteria. They're prokaryotes. They're similar. size to bacteria and they have many of the other same properties in terms of cell wall and metabolism and so forth. They lack nuclei and organelles. But one of the main differences between bacteria and why they're classified separately is that archaea actually have different RNA polymerase enzymes. So these are the enzymes that are used to help replicate the genome and also the enzymes that are used for the translation of the genome from DNA to proteins. they also use different enzymes, which are more similar to those used in eukaryotes compared to bacteria.

So it's thought that in some ways, Arquira are actually more similar to eukaryotes because of these very deep biochemical similarities. There are also differences in the membrane structure, so Arkeal membranes are made of molecules that are very different from those found in any other life forms, showing that they're only distantly related to bacteria and eukaryotes. So I think there was a time in which it was thought that Archaea were kind of like a transition from bacteria to eukaryotes because of the similarity. of the polymerase enzymes, but the realization that this membrane is so very different seems to

pull against that because they're not similar to membranes that are found in eukaryotes. There are also differences in the cell walls, so unlike bacteria, Archeia, lack peptidoglycan in the cell wall, so they have a different structure yet again of the cell wall from Archaia. Another thing about Arkea, and I don't really know why this is the case, is that no known species of Archa causes diseases in humans, even though Archaea are ubiquitous and found in almost all environments. Arquia was sort of originally studied and understood in the context of very extreme environments, like very high temperatures, volcanic vents, for example, or very high pH, acidic environments, or very salty environments, and species that can survive in those environments

are called extremophiles, as a sort of an informal term, because they can survive in extreme environments. But it's now known that Archaia, although some of them are extremophiles, many of them just live in ordinary environments just like bacteria do, and they're found all over the place. So I don't really know why no known species caused disease in humans. So that's all I have to say about archaea. Many of the other things that I would say are similar to what I'd say about bacteria, although they haven't been studied for as long as bacteria, but are similar in many other ways, but also different in some fundamentals that I just talked about.

So that's why they are classified separately as their own domain of life. That concludes the discussion of prokaryotes. So remember, that's at the one micrometer level, about a tenth of size of plant and animal and protist cells. We're now going to go even smaller, so 100 nanometers. This is nanoscale we're talking about here, much smaller than you can see even with a good light microscope. You can see quite easily animal and plant cells, and with more difficulty, you can see bacterial cells using a light microscope, but you can't see viruses using a light microscope. Now, I think there may be one or two exceptions of really big viruses that you can

make out using a light microscope, but basically speaking, you can't see viruses using a light microscope. you need to use an electron microscope to see a virus because they're that small. And viruses are also very different from anything that we've talked about before. Even though prokaryotes and eukaryotes are very different, they're still both cells, they're cellular organisms, they have cell membranes, they have DNA, they have the proteins to translate that DNA and turn it into, well, other proteins, and they have cytosol, which is the fluid that fills the cell membrane. So they're similar in those basic respects.

Viruses are not like that at all. Viruses are what are called accellular, which means that they're not cells. So viruses mostly don't have a cell membrane. Viruses don't have cytosol. They don't have ribosomes, so they don't have the ability to convert DNA into protein. They don't have any of that machinery or any of the complexity that even prokaryotes do, let alone new carriotes. So a virus is structurally much simpler. A virus consists of basically genetic material, so it could be either DNA or RNA.

and we'll get to that in a moment, wrapped in protein. And sometimes there's also a membrane surrounding that. So these are called enveloped viruses. But in the simplest form, viruses are the way I think of them as just DNA or RNA wrapped in protein as a protective coat. Now, because they lack all of the machinery, especially ribosomes that are found in cells, viruses cannot survive or they cannot replicate outside of living cells. So the way they function is that they infect living cells, could be prokaryotes, could be eukaryots, and hijack the machinery and use that to replicate more

copies of themselves, which then are released and then go on to infect more cells. So they're entirely parasitic in this way. They can't live by themselves, or they can't replicate by themselves, I should say, because technically speaking, most biologists or the consensus is that viruses aren't even alive, although not everyone agrees with that, but because they can't reproduce autonomously, like all other types of life can, they're typically regarded as non-living, they are kind of like life because they can replicate, but they can't do so by themselves. They have to hijack another cells. So it's a bit of a complicated issue, but I usually regard them as not being alive, and they're certainly subcellular and sub-microscopic because you can't see them in a microscope.

So for this reason, I find them quite interesting, because they kind of break all the rules. A single virus particle, including the nucleic acid and the protein that protects it, is called a virion, and the protein coat surrounding the nucleic acid is called a capsid. Viruses then have a lipid envelope derived from the cell membrane also exists. So, for example, the influenza virus has a lipid envelope that it kind of steals from the cell that it was produced in. That's just really an extra source of protection as far as anyone, I think can help it to a new host cell, but the fact that it has some membrane surrounding it doesn't make it a cell. It's basically just the DNA wrapped in protein with a bit of stolen lipids surrounding it. Now, I mentioned viral genomes. The viral genomes are quite

interesting because unlike all other forms of life, they can hold their genetic material in two different forms, either in DNA or RNA. You may recall that RNA is thought to be evolutionarily older than DNA. In fact, this takes us all the way, way back to episode four, where I talked about the origin of life, and as part of that I discussed the RNA world theory, which is that RNA originated as the information-carrying molecule, but because RNA is less stable, for a bunch of reasons that I think I discussed then, is less stable than DNA. This function was later given to DNA. So currently the way it works is that most organisms, well, really all organisms apart from viruses, store their genetic material,

the genetic information as DNA. It's then transcribed into RNA, which then is translated into proteins, which make the proteins that then go on to carry out biological functions. Now, viruses are not like that, because some of them carry their information as DNA, but some of them carry it as RNA. Permanently as RNA. It's not like it's a RNA that temporarily takes the transcript and then it's converted to protein. No, that's all it is. It's just stored in as an RNA form. Within each of those, the DNA can be stored linearly or circularly. So that's also different because bacteria usually have circular DNA, but virus, it can be linear or it can be circular, so it wraps around. Also, it can be single-stranded or double-stranded. So you would know that in,

again, all forms of life other than viruses that I'm aware of, information is stored in double-strand DNA. So there's two strands. So there's essentially two copies of the information there, or the copy and the anti-copy in a sense, the complementary strand. But in some viral genomes, there's only a single strand of the genetic material that's stored there. So there's a huge diversity of forms that viruses can store their genetic material in, but it is always still there is a nucleic acid form. And depending on the way that the information is stored in the virus, the way in which the virus hijacks the host cells machinery has to adapt.

Because, for example, if it's an RNA virus, then what has to happen, in order to replicate its genome is that first the RNA has to be converted to DNA because cells don't replicate RNA, they replicate DNA. So they've got the machinery to do that. So this is why these are called retroviruses, because first the RNA needs to be converted back into DNA, and then the DNA is replicated, and then it's converted into RNA, which is then packaged to make up a new virus. So it can be quite complicated.

There's multiple steps involved here for some of these viruses. Viruses have very small genomes, unsurprisingly, because most most of the things that genomes would ordinarily code for, they don't need to code for. The only thing that they need to code for, really are the proteins that make up their capsids, so the protective protein coats, they need to code for that, and any proteins that they need to gain access to the cell and hijack its machinery. So it might need special proteins to allow it to take over the machinery of the cell. So those are the only things that it needs to code for.

It doesn't need anything else, because everything else it just grabs from its host cell. So the smallest virus is code for only two proteins and have a genome of only a few thousand, basis long. The largest viruses have a few thousand proteins and therefore a few million bases long. You know, on average you might say it's a few hundred proteins. It doesn't do a few hundred proteins that a virus needs, which is way less even than the simplest bacteria. Now, I should say, when I say that viruses hijacked the host machinery, what I mean by that is that they use all of the proteins and perhaps lipid structures as well, but mostly the proteins that are necessary for replicating the genetic material and also for translating

the genetic material into proteins. So like ribosomes, for example, viruses don't carry their own ribosomes in order they carry the genetic material to produce them. So they have to use those of an existing cell. And that's what I mean by hijack. Instead of the cell carrying on its own metabolic functions, the virus gets it to do its work for it. And so the process of a virus infecting a cell and then producing more viruses is usually called viral replication. not reproduction because viruses are not considered to be alive, so instead it said that they replicate. But this is a little confusing because DNA is also replicated, so don't get confused here. We're talking about vire replication, not DNA replication here.

Now, it consists of a series of stages. The first stage of vireplication is attachment, so the virus needs to attach to the cell membrane of the host cell that it's going to infect. There may be special proteins that allow it to do that to sort of latch on tight, or maybe specific receptors that it looks for, so it knows that it's found the right type of target cell. The next stage is called penetration or viral entry. This is when the virion, the viral particle, enters the host cell, usually through either receptor-mediated endocytosis or membrane fusion. If the bacteria has its own enveloped membrane,

then it can just fuse with the membrane of the host cell, and then it's sort of in already. So that's a reason why it might want that. If it doesn't have its own envelope, then a receptor-mediated endocytosis is basically a way that the bacteria can be tricked into letting the virion particle in. I'll do some episodes in the future about how that works when we talk more about the cell membrane.

But basically, this is a standard mechanism for the cell bringing in things that it needs, like nutrients, for example, but the virus can kind of trick that into bringing in the viral particle. The next stage is called uncoating. And this is when the virus sheds its capsid, so the protein coat is removed,

and this allows the genetic material to enter the cell directly. The uncoating process can occur either by degradation of the protein coat using viral enzymes or possibly just by using host enzymes, or may just occur through simple dissociation, so they just kind of fall off each other. Either way, the virul genomic nucleic acid is released into the cell. Once it's there, replication of the viral DNA can begin, or RNA can begin. And this involves a process by which proteins that the virus has brought with it,

allow the virus to hijack the cell's replication and translation machinery into producing more copies of itself instead of producing other proteins that it would normally be doing. So this is how the virus turns the infected cell, the host cell, into basically just a virus-making factory. So it sort of suspends and takes over existing functions and just turns it into pump out more and more viruses. Then during the assembly phase, all of the proteins that have been produced by expressing the genes that the virus itself brought with it using the host machinery, those proteins are then packaged up. So they form new virion particles. and by putting the DNA or RNA into the proteins and getting that all sort of packaged up.

And any post-translation modification occurs then at this stage as well. And then the last stage is release, where the virus, the virion particles are released from the cell. Usually this occurs from cell lysis, so the bursting of the cell, which kills the host cell, releasing all of the produced virion particles, which can then go and infect new cells. So the whole process is basically the virus comes in, it gets into the cell, it hijacks the cells machinery to produce more copies of it, and then when it's ready, it kills the cell releasing itself and more particles, more copies of itself, to then infect more cells. So it sounds pretty nasty if you think of it that way, and as I said, viruses are entirely

parasitic, they can't reproduce or replicate by themselves. Viruses are usually classified by phenotypic characteristics because it's very hard to establish evolutionary relationships for viruses, so morphology, the type of nucleic acid, which we talked about before, mode of replication, type of host organisms they infect, and. and type of diseases that they cause. One particular important type of viruses that I will mention, I'm not going to talk about the different types because it's too complicated here,

but I will mention one, and these are called bacteriophages. This is just a virus that infects and replicates within bacteria and archaea. And so it's distinct from viruses that infect eukaryotes. Bacteriophages can form in many different shapes, but a very common shape looks kind of like the Moonlander module, if you know what that looks like. It's sort of like it has a head and a neck

and then little legs that stick out. Now, obviously, that's not what. these are. These are just proteins that the protein capsid that I mentioned. But it kind of looks like that. It looks kind of like a little mosquito or I think of it as a moon lander. I'll put a picture up on the Facebook so you can see what I mean here. But bacteriophages often have this shape, though not all of them. This shape is just particularly useful because essentially the little leg structures help them to latch onto the cell wall and then they can be injected through this kind of neck. The nucleic acid can be injected into the cell. So the reason they have the shape is basically that it's a convenient

way of allowing them entry into the host cell. But bacterifages are very common. They can actually be used as a treatment for bacterial infections. You can use one microorganism against another. So that's why I wanted to mention them. Viruses will kill, or generally, at least they, if they're allowed to sort of replicate to completion, they will kill their host cell. And they do that through a number of ways. And particularly, they cause tissue damage through a number of ways as well. Most common cause of death is cell lifest that I mentioned, the bursting of the cell. Cell death can also be caused by just the cessation of its ordinary functions as it's taken over and suppressed by proteins that the virus brings with it that suppress ordinary cell activities so that it just instead focuses on pumping out

more viral particles. Sometimes virus has actually caused no changes to the infected cell and they can actually lie dormant within the cell for a long time, even years, and the cells show few signs of infection, which is quite interesting. And those sorts of infections are observed for some human diseases as well. There may be an initial phase where the infection produces a lot of symptoms, but then it kind of stabilizes. You still actually have the infection, but it's just dormant. I'm not entirely sure why that happens, but it's an interesting, it's an interesting phenomenon. All right, so we're almost at the end of our overview here. We've talked about protests, we've talked about yeast, we've talked about bacteria and archaea,

and we've talked about viruses. But there's one form of microbial agent left, and these are preons. And preons, you don't hear about very often because they're pretty unusual, they're only just sort of starting to be studied. Preons, because their proteins, are even smaller than viruses. Remember, viruses are made up of a bunch of proteins in nucleic acid, but a prion is really just one protein, whereas a virus is maybe 100 nanometers in size, a prion is maybe 10 or less nanometers in size, so it's very, very small, and about a million times smaller than a ucarotic cell, of course, which includes many proteins. But a preon isn't just any protein. A preon is a misfolded protein, and it's even more than

that, it's a misfolded protein that has the ability to transmit its misfolded shape to normal variants of the same protein. So they have the ability to kind of reproduce themselves in this way or replicate themselves. And some of these prions cause fatal and transmissible diseases in humans and other animals, particularly neurodegenerative diseases. Preons are particularly insidious. The reason they cause these diseases is because the misfolded form produces abnormal aggregates of the proteins. This is called amyloids. So they accumulate in the affected tissue and then can be transmitted to surrounding cells as well. are associated with tissue damage and cell depth because the cells can actually become filled up

with these huge crystalline structures of just aggregated proteins. And so they can't do anything. They're just full of this junk, essentially. The prion aggregates are stable. So once they begin to misfold and then accumulating this way, there's not really anything that can be done to reverse the process. So they're resistant to denaturation, so they can't be unfolded by chemical or physical means. They can't be destroyed by ordinary infection means or cooking because they're so stable. preons can cause neurodegenerative diseases, especially because they can aggregate in the extracellular space, which disrupts the function of, for example, nerve cells. And interestingly, the incubation period for preon diseases is long. So it takes a long time to build up these amyloids, which disrupts cellular function. So we're talking five to 20 years after infection. But once symptoms begin to appear, the disease has already progressed for a very long way, and there's nothing that can be done about it. So they're completely incurable.

eventually this leads to brain damage and eventually death. Thankfully, the diseases that are caused in this way, so Kuru is one of the best well-known ones, the only way that I think is known to transmit that is by eating the flesh of an infected person, or possibly an animal, but it was mainly transmitted, I think, by certain tribes in Papua New Guinea who engaged in a practice of ritual cannibalism.

That's since been stopped, but there are still people who are infected with Kuru because of that very long incubation period. Similar diseases are observed. in cattle as well, such as so-called mad cow disease is a prion disease. And one of the reasons these are so insidious is precisely because there's very little way to treat or deal with prions, because as I said, it's very hard to denature them. They're resistant to chemical or physical destruction. They're not alive, so you can't kill them. So it requires extreme mechanisms to

deal with them. So I find prions very interesting because of they're extremely unusual characteristics, but they are fairly niche in terms of that there aren't very many known pre-on diseases and also the mechanisms by which they cause this propagation of the misfolded shape is not very well understood. Now, before we finish out, I want to say a few words about microbial growth and control. Often we're interested in preventing the growth of microbes to control disease, and so it's useful to know a bit about how this works. I mentioned that bacteria grow by binary fission, so dividing into two identical copies.

This can occur very quickly under optimal conditions, so bacteria can divide such that the population doubles every 10 minutes under optimal conditions. So you can go from hardly any to a huge number in a very short amount of time. This is why even leaving food out under optimal temperature and other conditions for a few hours can cause it to go bad. Microbial growth can be described using a mathematical model called a growth curve. This is an idealized description of the growth of bacteria, which occurs in four different phases. So the initial phase is the lag phase where growth is very slow, if not non-existent.

And so it's kind of just a flat line. If you think of the horizontal axis is time and the vertical axis is how many bacteria, then the lag phase, nothing much is happening. It's just kind of a flat line over time. And this is the phase during which individual bacteria are maturing, developing, adapting to their environment, responding to chemitaxis and other things, finding nutrients and getting settled in other words. And so no or very little division occurs during this phase.

but after the lag phase, once they've had time to acclimatize and grow, the bacteria will start to divide. And this leads to what's called the exponential phase, which is an exponential curve, a very rapid uptick and the number of bacteria, where you have rapid cell division and they just keep growing and dividing and propagating. Given infinite resources, this would continue forever. But of course, in any actual real circumstance, if you don't keep adding new nutrients, eventually the nutrients begin to be depleted. And this gives rise to the stationary phase, which is another horrible. horizontal line or near horizontal line occurring after the exponential phase. This is when the resources start to become limiting and the number of bacteria that are dying begins to equal out the number

of bacteria that are dividing and reproducing. Eventually that process continues so the scale tips so that more bacteria are dying than are being added to the population through binary efficient. And so this is called the death phase where the population drops off, possibly gradually or possibly dramatically, depending on the details. So the whole process of the growth curve, it looks like a curve that has a peak. So it starts off slow, goes up quickly, peaks, and then goes down. So what we generally want to do is reduce the rate at which the exponential phase goes up. You can't stop bacterial growth. You can, but it's used to require conditions that are rather inconvenient. So freezing substance stops bacterial growth. But when you thaw it,

the bacteria will keep growing again. This is a something that's often not understood. Many bacteria can survive freezing, and certainly their endosports can, as we discussed before. So freezing, something doesn't sterilize it. It just prevents the bacteria from growing. There are many factors that affect the rate at which bacteria grow. One is the level of salt. So this is how, basically how much water is available. These are two different ways of looking at the same thing. If there's a lot of water, then there's a lower salt content. Often a way to measure this is the water activity, which is the partial vapor pressure of water in a substance divided by the standard partial pressure, vapor pressure of water. Don't worry about that

technical definition. It's not very important. The water activity is just a number between zero and one that says how much water is in a substance. Substances with a high water activity tend to support more rapid growth of microorganisms because they need water to survive, just like any living organism. So bacteria tend to grow in values of up to 0.9. So anything like juice or milk or anything that's primarily liquidy will have values of around 0.9 or above. Pure water, of course, has exactly one. So things like that, bacteria can grow in very readily. Mold can grow in lower levels of water, so values as low as 0.8. That's why bread can have mold grow on it, but generally won't have bacteria grow on it, so there's not enough water there for bacteria,

but there's enough of mold, or at least some types of mold. Dried fruit has a value around 0.6, so there generally won't be anything growing on that. That's too low for mold. Mold will grow in things like fruit or other things as well over time. That's the way that. those things often will go bad because again the mold can grow on things that are still solid but have enough water for the mold to grow. Peanut butter has a water activity value of around 0.35 and this is why you will never see anything grow in peanut butter. You might if it's contaminated with something else but if it's just actual pure peanut butter then nothing will ever grow in that and this is why you don't need to refrigerate things like peanut butter or honey for that matter. Honey also has a very

low water activity. The reason nothing grows in them is just there isn't enough water there. I believe honey has been found in ancient Egyptian tombs, and I don't know if anyone tried it, but as far as I know, there's no reason why you wouldn't be able to eat that honey, because there's no reason anything will be able to grow in that. There's just not enough water. So that's a very important thing. That's why historically either drying things out or especially treating things with salt, so adding salt to meat, packing it in salt, is a way to preserve it, because it reduces the water content and therefore makes it harder for organisms to grow there. Moving on, temperature also, probably fairly obviously is a way to control the growth of microorganisms.

Low temperatures reduce the rate of microbial growth, essentially because they just make all reactions happen slower, so everything takes a bit longer. But importantly, low temperatures don't stop microbial growth. So you put something in the fridge, usually that's about four degrees. Microbial growth is slowed, but it does not stop. That's why things in the fridge won't last forever. Microbial growth will stop in the freezer, assuming it is actually reaching sub-zero temperatures. That's not always true, by the way.

Some freezers don't work as well, or parts of them might be above freezing. freezing, so you want to check that. But it will stop in the freezer, but if you take it out of the freezer and let it thaw, then the microbial growth can resume, and so you shouldn't take something out of the freezer and let it thaw for a very extended period. You should just let it thaw for long enough, and then cook it immediately, or as soon as possible. Otherwise, you're giving the bacteria time to start growing again. The ideal growth temperature for bacteria is around 20 to 45 degrees, so roughly around human body temperature, you know, give or take 10 degrees or so. and that is sort of room temperature on a warmish, coolish warm day, up to sort of on the hotter day.

So generally, the high of the temperature is, so if it's a hot day or if you live in hot climates where you regularly get 30 plus degrees, it's even worse idea to leave food out in those conditions because the bacteria are going to go more rapidly. Now, if you increase the temperature above that, so you start to get to 60, 70, 80 degrees, bacteria can start to die. Some bacteria survive at high temperatures than others. To completely sterilize something, you usually have to raise it to a very high temperature. often above 100 degrees at high pressures for a certain period of time to count as completely sterilized,

which means killed everything, including endospores. But that's quite a high criteria. This is, though, why if you cook something, it usually should be safe, as long as you've cooked it properly. So, for example, bacteria can grow on meat. There's obviously a lot of organic material to eat there. Even if it's fairly fresh, maybe it's been kept in the fridge for a few days or something. There'll still be bacteria growing there, which is why it will go bad if it's left too long. but if you cook that meat, if you cook it all the way through and ensure that even the middle, which usually cooks the last, of the meat has reached a sufficiently high temperature, then that should kill all of the bacteria that were there.

It may not kill all the endospores, but the endospores aren't going to bother you if you're going to eat it pretty much immediately. So this is why sometimes, especially in more professional environments, you'll stick a thermometer into the meat and make sure that the center has reached a certain temperature to ensure that it's been cooked enough all the way through to kill any bacteria that might be there. Moving on, pH, so basically the acidity. Optimal activity for bacteria is usually around 7, which is close to the pH of the human body. There are some bacteria that are called acidophiles, which prefer very low pH conditions and can flourish in those, but that's fairly

unusual. So the fact that the human stomach has a pH of around 1 to 2, I think, is partly in order to kill bacteria that might reach there because generally they can't grow in those conditions. Oxygen also has an important effect on bacterial growth. So some bacteria are aerobes, which means they require oxygen. There's kind of two different types. There's obligate aerobes, which require oxygen to grow, and there's facultative aerobes, which require oxygen to grow to the maximal extent, but they will still grow without oxygen. They just won't grow as much. There are also anaerobes which grow in the absence of oxygen. So again, obligate anaerobes cannot grow when oxygen is around, they require the complete absence of oxygen, and then there are faculty of anerobes,

which grow best in low-oxygen environments, but they can tolerate some oxygen. So there's variation there, and that really just means that bacteria can grow in any context, whether there's air or there isn't air or, like, oxygen, they can still grow. It would just affect the type of bacteria that can grow. Radiation will kill bacteria, just as it kills any living organism, if there's insufficient amounts, particularly ultraviolet radiation, or I guess gamma radiation, but you're probably not going to be using gamma radiation, that's a bit extreme. Ultraviolet germicidal irradiation is a disinfection method that uses short wavelength ultraviolet light to kill microorganisms.

Basically, it does so by destroying the nucleic acids and disrupting their DNA so they can't make proteins, they can't reproduce. So this method is used to, I think, for a lot of fruits and vegetables to irradiate them to kill pathogens or microorganisms that might exist on them. Finally, there are also many chemicals that are toxic to bacteria, such as ethanol that can either kill or at least hinder their growth. So this is very useful for food preservation or disinfecting surfaces. Now there's a whole series, and I've just mentioned some of them, it's a whole series of microbial control methods that vary depending on the technique and what they can be applied to.

So there's just a couple of distinctions that I wanted to make here. Sterilization is referred to substances or techniques that can completely destroy any pathogens, including endospores, and it can only be used on inanimate objects for obvious reasons, and usually requires pretty extreme conditions, such as very high temperatures or steam under high pressure, for example, or large doses of radiation. A step down from sterilization is called disinfection. So disinfection is the destruction of pathogens, but not bacterial endospores. So endospores survive disinfection. Now, that's usually not a problem for most purposes, especially food purposes, because if eat a substance that has no living bacteria but has some endospores, those endospores will be

destroyed in the digestion process, and they really shouldn't affect you in any way, at least as far as I'm aware, that's not going to cause any problems. But if you disinfect something and then allow it to exist in an environment where bacterial growth can resume, then you may find that bacteria re-emerge. Again, this is usually only used on inanimate objects because there's still fairly harsh measures, but not as harsh as required for full sterilization. Then there's antisepsis. So an antiseptic is a chemical that is applied to the body surface or a body surface to destroy or inhibit bacterial growth or other pathogens. Antiseptics are chemical, by definition, and they are usually much less harsh, obviously, because you apply them to a body surface. So an example would be alcohol

that you use to sanitize your hands. That would be an antiseptic. Again, they're not going to kill all bacteria, but they should kill a large proportion of them and sort of inhibit the growth of others, and enough to make something safe, usually if done properly, of course. And an antiseptic is different to a disinfectant. A disinfectant is applied to an inanimate object. So you'll, you disinfect the bench, but you use an antiseptic on your hands, for example. So that's just the distinction there in terms of the terminology. And finally, there's chemotherapy, which are chemicals that are used internally to kill organisms or pathogens within host tissues. So that's just an overview of the different terminology that's used. And it is important to understand what should be used in what context,

and also exactly what effect is going to have. Is it going to kill everything? Is it just going to inhibit or is it going to inhibit most of them or all of them and, you know, how long will it take sort of for them to grow back if that's possible. But that brings us to an end to this podcast. Hopefully you found that interesting. We went through all of the microbial world in a whiz tour from Protists right through to Preon's. If you found this episode interesting, then feel free to help spread the news of the podcast by living a favorable review on iTunes or the podcast aggregator of your choice. Did I say aggravator? Podcast aggregator of your choice. If you'd like to make suggestions or ask a question or give other feedback, you can send me an email.

My email address is Fods12 at gmail.com. That's FODS12 at gmail.com. Always love to get your feedback. If you want particularly to support the show, you can make a donation, either one-off via PayPal or you can become a recurring donor via Patreon. The link should be in the show description, or you can go to my website, which is Fods12.podbean.com. I greatly appreciate all my Patreon supporters that allows me to devote more time to the show and get out more episodes for you guys. So thanks again for listening and I'll talk to you next time.