Episode 112: Introduction to Microbiology

[MUSIC] Hello, you're listening to The Science of Everything Podcast Episode 112, introduction to microbiology. I'm your host, James Fodor, and 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 protests, yeasts, bacteria, and archaea, viruses, and pre-ons, with a little bit of discussion at the end about microbial growth and efforts to control microbial growth. Recommended pre-listening for this episode is episode 10 and 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, it's 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 worlds, including ancient India, especially associated with the Jane 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. 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 Antonyn Van Loenhook, 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 he's 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 a middle 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 derived 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 life forms would spontaneously arise from like rotting organic matter or just in an stagnant pool of water or something like that. Like flies, for example, were 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'd 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 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 exposed the boiling water to 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 boiling the water doesn't do anything to the water if it's then allowed to condense back or it does this kill any life that exists in it, but of course this wasn't understood at the time. So what Pestua did in 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 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 that prevented things from growing in the 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 micro organisms to grow in the in the broth after it was boiled. And so by shaping the necks of the 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, the 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 that 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 it to a healthy one. He also found that he could grow the bacteria in a nutrient broth, inject the not the blood but the broth with the bacteria growing it into a healthy animal and cause the disease. And he developed a set of postulates that are still used in medicine state called Cox postulates that are used to establish where there are given pathogenes 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 this game 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 that discovered it 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, but 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 of, 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 in purely in terms of size, but also complexity, and then move to the smaller, simpler ones. So we'll start with protests and then move to yeasts, then we'll talk about bacteria and archaea and finish with the some cellular organisms. So let's start with protests. Now protest 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 text. 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 protest is technically speaking any eukaryotic organism that is not an animal plan to our fungus. Remember, eukaryote is an organism whose cells contain a nucleus and generally other organelles as well. Eukaryotes are more complicated, more recently evolved types of organisms and they 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. Protests, 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 protest 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 protests 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 protests, so most are small, single-celled organisms, there's many different types of them, they're very diverse, we're just going to lump them all together and call them protests for the purpose here because they all protest 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. range of reproductive metabolic and other functions across protists. So again, the only distinguishing feature really of protists is that they are eukaryotic and single-celled. So of course, they're small, larger than pro-carriots, just to give you an idea. So protists are about the same 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 pro-carriot cell is about a tenth 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 factor, another order of magnitude down again at 10 nanometers. So we'll come back to that size scale as 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 efficient. 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 from other or produced by other organisms. So humans are, 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 in their bonds between the atoms that have been processed by other forms of life. So that's heterotrophic. So some eukaryotes are autotrophics, so some photosynthesize, but others don't. So again, there's a diversity here. For those that don't, for the heterotrophs, 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 phagotrophy. There's also osmetrophy. That's absorbing nutrients through osmosis, which is passage across a semipermeable membrane. So that's different again to phagocytosis. And there's also sapotrophy, 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, protozoa, protozoa, which means animal like, protofighta, 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 clays, 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. The protozoa are protists 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 tissue. So these are heterotrophs. They're very abundant in aqueous environments in the soil. This group of protists includes flagellates, so they move around with the help of whoop 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 is called pseudopodia. So the distinction here is basically just in terms of how they move. Is it using flagellum? Is it using cilia or is it using pseudopodia? 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 heterotrophs and they move about to their mobile and that's what makes them kind of animal like. But there are other types of approaches as well, so let's talk about the proto-fighter. 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 or 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, obviously being ancestral to them, but they do photosynthesize. So that's why they're obviously plant-like because they carry our photosynthesis. And this includes organisms from unicellular micro-algae to multicellular forms such as seaweed. It may be come as a bit of a surprise, but seaweed is actually not a plant. Many people think of it as a plant, but it isn't because it lacks all of 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 are 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 protests and seaweed as an example. Remember, technically a protest 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 seaweed doesn't count as a plant, it's a protest. Likens are also very interesting, so these are kind of plant-like and maybe confuse those plants, but it's actually a composite organism comprised of algae. Remember, these are essentially single-cellular photosynthetic protests. 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 protests that I'm going to cover, which are the slime moles. These are fungus-like organisms. Slime moles aren't the only type of more fungus-like protests, but I'm going to focus on these ones because they're interesting and get a lot of attention. So again, a slime mole is in informal name, it doesn't refer to a clade, but I'm going to use it here because it's helpful. So slime moles 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 phenomenon. They're not single-cell. They're not multicell. They're kind of both, depending on the stage of life and also environmental circumstances. So when food is abundant, slime moles tend to exist as single-celled 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. But you can see this. So slime moles, you can look at 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 over 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 moles are extremely interesting because they kind of break a lot of our preconceptions of how life works, that you know, 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 find, 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 out of 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 multicelled, but they can be single celled when they're single cell 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 autotroves, 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, sapratrophy, 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're not motile, but they're not plants, and I've just mentioned some of the differences. So they're also not animals, because they're very different, so they're 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, a serivisia, which people are probably familiar with because this is Bakers yeast. This is a species that converts carbohydrates, like sugar, essentially, to carbon dioxide, and alcohol is 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 yeast 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 saccharomyces yeast is propagated and so let's just be grown in the laboratory as well as other yeasts that have various culinary or medical uses. So that's a little bit about yeasts are eukaryotes, so they're similar size, broadly speaking, to protests, 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 there 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 monbacteria, 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 coxae are basically spherical, so they look like little circles. If you look at them in a microscope and the bacilli are rods, so they look like little rods or sort of rounded rectangles if you see them in the microscope. So coxae and bacilli, you see that stem in name of bacteria that's usually just telling you it's 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 end, they're kind of strung into thin strings. There are kind of corkscrew that are little form little helices or filaments. Some of the long and crinkly ones are called spiral keats. 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 coxae and bacilli 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 autotrophs 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 autotrophs. So that means that they fix their own carbon into an organic form using an initial source of carbon dioxide. So an autotroph 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 heterotrophs 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 autotroph that means you get your energy from the sun. That's true for I think most if not all protists. But bacteria is more complicated because there are what are called photo autotrophs. That means that they get their energy from light, that's the photopart 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 autotrophs. So it's still auto, meaning it still fixes its carbon from carbon dioxide and 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 their chemo autotrophs. So very interesting, not something you see as far as I'm away in any eukaryotic organism. So that accounts for the autotrophs. They all fix their own carbon from the atmosphere. Some of them get the energy from the sun, so photo autotrophs, some of them get it from a diversity of different non-organic chemical sources, like sulfur and nitrous compounds. Those are the chemo autotrophs. Now let's look at those that get their carbon from the source of the smelly. So existing organic compounds. So these are the heterotrophs. The most familiar type of heterotroph is a chemo heterotroph. This was mentioned in the context of protests. Humans are chemo heterotrophs. What that means is that we get our energy from chemical sources, biocrystalline 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 chemo heterotrophs. 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 heterotrophs. So there are certain types of green non-sulfur and purple non-sulfur 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 eukaryotic organism. So this is why we need to make these distinctions. And we can't just talk about the heterotrophs as I did it for the protest, because bacteria can be strange. They can make interesting combinations. 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. And that loosely, but that's the idea of photo heterotroph. So fastening any 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 you carry out to do. So there's much, much simpler intracellular processes going on there. They also don't need many of those specialized proteins that use for sensory organs or motor function, or all the other complicated things that humans and other animals need, because of their specialized organs and specialized cells. Genes in 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 also 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. to play. Charismid is an extra chromosomal, so separate from the 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 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 polysaccharides or sugar chains that are crossed 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 that made of cellulose, those are fungi, as I mentioned, made of chitin, so although they all 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 are 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 if a 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 reasons, but there's also a very big structural difference. Bacteria are very commonly classified in terms of whether they're gram positive or gram negative, so it's one of the reasons I wanted to mention that. Many bacteria are motile, so they can move around. The best study 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 whipping and allows the bacteria to move. The bacteria for the Delam is made up of about 20 proteins, which form a reversible motor, so circular motion is found in the natural world. Chemo-taxis is an important phenomena 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 chemo-taxis. But there are other types of taxis as well. So chemo-taxis is just a very common one that's mediated by chemicals. They can also move towards or away from life, so that's photo-taxis or energy sources, so that's energy-taxis or even magnetic fields, so being needle-taxis. And this is a very important way that bacteria can respond to stimuli, can find sources of food or avoid poisonous 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. They're reproduced by binary efficient, so that means essentially they just split in two, which produce 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, 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 endospore 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 dislocation. 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. As fascinating the 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 endospores 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 solar system or even elsewhere in the galaxy and been transported on meteors or on comets or something through bacterial endospores, which could theoretically survive the harsh conditions of space. But again, that is 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. There's in the current standard classification, there's three domains of life. One of them is eukaryotes, which I talked about before in regards to protists, 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, archaea are quite similar bacteria to bacteria. They're pro-carriers, they're similar sized 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 archaea 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, archaea are actually more similar to eukaryotes because of these very deep biochemical similarities. There are also differences in the membrane structures, so archaea 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. That's the realization that this membrane is so very different, seems to put it against that, because they're not similar to membranes that are found in eukaryotes. There are also differences in the cell wall, so unlike bacteria, archaea lack peptidoglycan in the cell wall, so they have a different structure yet again of the cell wall from archaea. Another thing about archaea, and I don't really know why this is the case, is that no known species of archaea causes diseases in humans, even though archaea ubiquitous in found in almost all environments, archaea were sort of originally studied and understood in the context of very extreme environments, like very high temperatures, volcanic vents, for example, or very low pH, acidic environments, or very salty environments, and species that can survive in those environments are called extremeophiles, as a sort of informal term, because they can survive in extreme environments. But it's now known that archaea, although some of them are extremeophiles, many of them are just living ordinary environments, just like bacteria do, and they're found all over the place. So I don't really know why no known species cause 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 the size of plant and animal and protus cells. We're now going to go even smaller, so 100 nanometers, so 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 the 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, 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 Acellula, which means 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 pro-carriots do, little or new carriots. 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 this is 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 what the way they function is that they infect living cells, could be pro-carriots, 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, but they are kind of like life because they can replicate, but they can't do so by themselves, they have to hijack another cell. 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 they're 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 coats 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, so 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 as 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 makes 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 RNA that temporarily takes the transcript and then's convinced protein. No, that's all it is, it's just the, it's just stored it 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, virus, it can be linear or it can be circular, so reps around. Also, it can be single-stranded or double-stranded. So you would know that in, again, all forms of life other than viruses I'm aware of, information is stored in double-stranded DNA. So there's two strands. So there's essentially two copies of the information there or the copy in the anti-copy in a sense of 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 as 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 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 codes, 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 viruses code for only two proteins and have a genome of only a few thousand bases 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 hijack 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 said that they replicate, but this is a little confusing because DNA is also replicated, so don't get confused. We're talking about viral replication, not DNA replication here. Now, it consists of a series of stages, the first stage of viral replication 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 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 the 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 viral particle in. I'll do some of the 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 capsids, 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 dissociations, so they just kind of fall off each other. Either way, the virulge 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 into basically just a virus-making factory, so it sort of suspends and takes over existing functions and just turns it into compound 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 virulge particles by putting the DNA 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 virulge particles are released from the cell. Usually this occurs from cell lysosome, bursting of the cell, which kills the host cell, releasing all of the produced virulge 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 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, type of nucleic acid, which we talked about before, mode of replication, type of host organisms they infect, and type of diseases that they cause. One particular important type of viruses that I will mention, I'm not going to talk talk about the different types because it's too complicated here, but I will mention one and these are called bacteria farges. This is just a virus that infects and replicates within bacteria and archaea. And so it's distinct for viruses that infect eukaryotes. Bacteria farges 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, these are just proteins that, um, that the protein capsid that I mentioned, but it kind of looks like that. It's, it looks kind of like a little mosquito or, or I think of it as a moonlander. I'll put a picture up on the Facebook so you can see what I mean here. But bacteria farges often have this shape, though not all of them. This shape is just particularly useful because essentially the, the little legs 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 this shape is basically that it's a convenient way of allowing them entry into the host cell. The bacteria farges 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 the 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 life as 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, the suppress ordinary cell activities so that it just instead focuses on pumping out more viral particles. Sometimes viruses actually cause 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, so show a few signs of infection, which is quite interesting. And those sorts of infections are observed for some human diseases. Well, there may be an initial phase where the infection produces a lot of symptoms, but then it kind of stabilizes. You should actually have the infection, but it's just dormant. Not entirely sure why that happens, but it's an interesting, interesting phenomenon. All right. So we're almost at the end of our overview here. We've talked about protests, we talked about yeast, we talked about bacteria in archaea and we 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 and nucleic acid, but a preon is really just one protein. Whereas a virus is maybe 100 nanometers in size, preon is maybe 10 or less nanometers in size, so it's very, very small and about a million times smaller than a eukaryotic 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 reproduce themselves in this way or replicate themselves. And some of these preons 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 is called amyloids. So they accumulate in the affected tissue and then can be transmitted to surrounding cells as well. And are associated with tissue damage and cell deaths because the cells can actually become filled up with these huge crystallized structures of just aggregated proteins. And so they can't do anything. They're just full of this junk, essentially. The preon aggregate gets a stable. So once they begin to misfold and then accumulate in 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. Animals 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 5 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 preon disease. And one of the reasons this is so insidious is precisely because there's very little way to treat or deal with preons. 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 preons very interesting because of their extremely unusual characteristics, but they are fairly niche in terms of that there aren't very many known preon diseases, and also the mechanisms by which they cause this propagation of the misfolder 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 condition, 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 as time and the vertical axis as 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, you know, chemotaxis 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 the what's called the exponential phase, which is an exponential curve, a very rapid uptick in 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 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, it 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 requires conditions that are rather inconvenient. So freezing substance stops bacterial growth, but when you thaw it, the bacteria will keep growing again. This is something that's often not understood. Many bacteria can survive freezing, and certainly their endospores 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 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 of vapor pressure of water. Don't worry about that. Technical definition is 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 when have bacteria grown, it'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 they generally won't be anything growing on that. That's too low for mold. Mold will grow on 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 out there. grow in that. There's just not enough water. So that's a very important thing. And 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 ask forever. microbial growth will stop in the freezer, assuming it is actually reaching subzero temperatures. That's not always true, by the way. Some freezers don't work as well as parts of the might be above 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 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 higher 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 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 weren'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 being 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 facultative anaerobes, 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 mounts, 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 the 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 lease into 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. There'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 you 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 antiseptic. 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 inhibit the growth of others, and enough to make something safe, usually, if done properly, of course. An antiseptic is different to a disinfectant. A disinfectant is applied to an inanimate object, so you disinfect the bench, but you use an antiseptic on your hands, for example. 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 it's 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 and a whiz tour from protests right through to pre-ans. 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 aggravator of your choice. Should 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 [email protected]. That's [email protected]. Always love to get your feedback. If you want, particularly to support the show, you can make a donation. Either we'll run 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. [Music]