Biology Exam Preparation and Bacterial Classification

Okay, welcome to the online version of Biology 240. Today I wanted to start out by telling people how they could study for the exams because several students have asked me about how to study for this next exam. Flashcards are a great way to study for this exam. There are going to be many different details that you're going to have to memorize and the best way to do that is to hand write, not print, but hand write your flashcards. Many studies have shown that the act of writing information down actually helps you retain that information and recall it better later. So, handwrite flashcards and go through them when you can. Also, rewrite your notes, your lecture notes and your reading notes, and self-quiz yourself. So, just write questions regarding the material that you're learning and ask. yourself those questions later and see if you can recall that information. If you can't, you need to go back and study it again, and if you can, huzzah, move on. Okay, we're going to start on chapter 11. Here we're discussing prokaryotic classification, so basically bacteria, and we're going to cover not just bacteria today, we are also going to cover archaea. Eukaryotes will be covered in another chapter. This is the tree of life. I like showing this because it shows that there are many different types of bacteria. And in fact, we're going to talk about the fact that there are thousands of different types of bacteria. We are only going to cover a handful of them in this class. Today, we will cover archaea, seen down here. You can see that they are in a different branch of the tree of life from bacteria. And in fact, they are related to eukaryotes, which we talked about recently. Now we're going to start. by talking about bacteria in general. I want you to keep in mind that we have not been able to grow all bacteria in the laboratory, which means that we haven't been able to fully characterize them. And in fact there are hundreds, maybe thousands, of species that we haven't been able to characterize because we can't grow them in the lab. So we're going to start by talking about bacteria in general and we're going to talk first about their shapes and replication. Prokaryotes come in many different shapes. This ball form seen on top here is referred to as caucasus and it just looks like a little ball. If you take that ball and stretch it out a little bit it looks halfway between a caucasus and a bacillus. And that is called caucobacillus. Bacillus are also referred to as rod shaped and you can see that they are elongated. Here we have vibrio. Vibrio is comma shaped and this is very characteristic of vibrio. and this one happens to have flagella as well. Spirulium are rigid bacteria that have two bends in them and this is a rigid shape. This is not a shape that, you know, this bacteria happened to lay down this way and it looks like this. This is a rigid shape. These spirochetes have a, almost look like corkscrews and in fact they, when they move, they're referred to as moving in a corkscrew fashion. We talked about spirochetes when we talked about endoflagella a few chapters ago. These are flexible microbes and they tend to be able to be flexible. Down here we have pleomorphic bacteria. Now all of these have their particular shape because they have cell walls that help them retain their circular shape or their broad shape or their bacillus shape or their shape. Down here we have pleomorphic bacteria. that don't have cell walls and so they are able to take a variety of shapes. Now if you looked at a population, so many different, a group of microbes within the same species for these bacteria, they would all have the same shape unless they were replicating. But the pleomorphic, if you looked at a population of any one species of pleomorphic bacteria, they may have several different shapes. And then down here we have a star shape, and you can see that it's referred to as a star shape because it's pointy. It has these points on it to make it look like a star. Now cells can be arranged in many different ways, and the arrangement of the cells depends on the plane of replication and separation of daughter cells. So what do I mean by that? This is the plane of replication. This indicates that this bacteria will form a daughter cell, either on this side or on this side of this bacillus. Now these bacteria can be arranged singly as observed here or they could be found in pairs. The dye here in diplococci refers to the fact that these are often found in pairs and you can see that here and here and here. Now note that there are single microbes in this image, so you won't always see them in pairs, but most often you'll see them in pairs. These bacteria can also replicate one on end to each other in these chains, and these chains are referred to as streptococci. In this particular image you can see that there are very few individual microbes or pairs of microbes. They're in, most of the microbes in this image are in chains. Then you can have tetrads. The tetra here refers to four and so these are groups of four bacteria and you can see these on the stain here. And then if you have stacks of these four, these are referred to as sarkinae and this is due to the ability to replicate on three different planes. If the bacteria is a cocci and it can replicate on any plane, these form grape-like structures and are referred to as staphylococci. where the staple refers to grape-like and you can see that in this stain here. Now these bacteria as we said before or as I said before are not just found in cocci form they are also found in rod form bacilli form and these can have the same have similar arrangements to the cocci so you can have single diplo, diplo bacilli you can have streptobacilli in these chains You can also have palisades, and that's because these bacteria have ends to them. So you can have, if you have a plane of replication at one end or the other, you can have palisades that are formed, or you can have a V shape. And we'll talk about how these V shapes form in just a minute. Now bacteria can replicate a number of different ways. The most common way is by binary fission, but not all bacteria replicate this way, but many do. We've talked about binary fission before. You have chromosomes. The chromosomal DNA replicates that and that leads to elongation of the cell wall, the cell wall in the cytoplasmic membrane. And that also separates the chromosomal DNA. Then a cell wall forms, a cross wall forms, and the membrane invaginates. That just means that pinches in here. Eventually a cross wall or the cytoplasmic membrane completely separates the mother and the daughter cell and then you have the mother cell and the daughter cell completely separating. Now as we showed before up here the daughter cell doesn't always completely separate. You can see these have not completely separated but often the daughter cell will completely separate. Now this is different than snapping. So in snapping you have daughter cell that forms but it never completely separates from the mother cell and so here you have the separation the membrane and the cell wall have formed in between the daughter cell and the mother cell but they don't completely separate and here we have a hinge that forms in between these two cells and then another form of replication is bee snapping a great example of this is mycobacterium and this When mycobacterium replicate, there's an elongation stage. Separation and early division stage occurs in which the membrane forms in between the mother cell and the daughter cell. And then eventually you have the late division stage and you end up with V-snapping. Now note here that in the V-snapping stage, the mother and the daughter cell are still attached. Eventually that daughter cell is detached. daughter cell detaches and elongates and the cycle repeats itself. Another form of replication is spore formers. We're going to talk about spore formers in much greater detail when we get to fungi, but here's an example of a bacteria that can form spores. Actinomycetes or the order Actinomycetes. can form spores. And here we see vegetative cells and then we see spore formers. Now these are not two different species. These are one species, one type of bacteria in this image in two different stages. The vegetative cell that's actively metabolizing and replicating and these spore formers that carry the DNA of the cells. And here's a nice drawing showing the separation, the DNA in daughter cells that eventually get separated with these septums until you have eventual full separation of individual spores that are formed by actinomycetes. The next form of replication is budding. In budding you start out the same as you do with as you do with binary fission with a chromosome replicating and the bacteria elongating but then you have a bud that forms at one end of the bacteria. Eventually the chromosomal DNA all collects in the young bud and the daughter cell breaks off from the mother cell. The parent can make more offspring. when they bud off. So unlike other cell replication types for budding, individual mother cells can go on to make more than one daughter cell. And finally we have viviparity. In viviparity, the daughter cell forms within the mother cell. So here we have the mother cell, here's the daughter cell. The daughter cell becomes fully formed within the mother cell and eventually lyses out of the mother cell to form another daughter cell to be completely independent and then eventually forming its own offspring. And so here you can see a stain where the daughter cell is forming inside the mother cell and again here's the daughter cell and here's the mother cell and they're both sharing the membrane. A great example of this is epilepsym. And so here you can see epilepsym. There's the mother cell, there's the daughter cell. We've talked about this particular microbe in the past because it's incredibly big. Here's epilepsym compared to E. coli. This little tiny dot here is E. coli. And you can see that this bacteria is considerably larger than other bacteria like E. coli. And just another size comparison, here's paramecium, which is a eukaryote. And remember, in general, eukaryotes are bigger than bacteria. And yet here we have a bacteria that is significantly larger than this eukaryote. Bacteria can also form endospores. Endospores are a way for the bacteria to protect itself from the environment. by being in a state of a very low or stopped metabolic rate. So it's not metabolizing, it's not replicating. And that allows the bacteria to become resistant to changes in the environment. Now again, the vegetative cell is the cell that's actively replicating and metabolizing, but here we have endospores that are forming inside of vegetative cells. And this is another example of spores forming inside of cells. We've already gone through how an endospore forms so we're not going to go over that today. I will remind you that each vegetative cell can make one endospore which can germinate later to make one vegetative cell. Spores can form on the ends of the cells or at the terminus of the cell. They can also form at the center of the cell and typically any one species of bacteria will form endospores in either at the end or at the terminus or at the center. As for the different types of bacteria that can form endospores, here I'm showing Clostridium. An example of a gram-positive bacteria that can form endospores is Bacillus. Okay, so let's talk about classification next. Classification is just the way that we group bacteria together. How we... determine which ones are more related to others. The Burgese Manual of Determinative Bacteriology is a manual that lists all the types of bacteria that have ever been described. So if a researcher has described a bacteria in a laboratory it eventually makes it into the Burgese Manual. It's now called the Burgese Manual of Systematic Bacteriology. Now, back in the 1950s, you could describe all of the microbes that had ever been described and put them into one book. Now we have several volumes of books because we have described so many different types of bacteria. And these are no longer printed, as far as I know. Now I think they are just available online. I'd like to point out that the chair of Berkey's Manual Trust and past president of Berkey's International Society of Microbial Systematics, was formerly at UAA. So this is Dr. Fred Rainey. If you ever run into Dr. Rainey here in Anchorage because he still occasionally hangs out, tell him Dr. Katz said hi. Okay, classification. Continuing with classification. Taxonomy refers to the way that we classify microbes, what group we put them into. Now I've mentioned species a few times. When you think about when microbes and other living things are characterized, they're grouped according to how similar they are to other living things. Two individual living things are very similar to each other. They're referred to as, they are given species names. If they're a little more distant from each other, then they're in the same genus. If they're a little more distant from each other, they're family. And up here on kingdom, you can have very different organisms within this classification. One way to remember this taxonomy tree is to remember King Philip can order five golden spoons. Another way is just to remember the order of the names. Kingdom, phylum, class, order, family, genus, species. Where kingdom has is the biggest umbrella that contains the largest number of living things within that. I like to use an example. So we are Homo sapiens. Sapiens is the species that we are in. Homo is the genus. that we are in. Our kingdom is animals. So if you looked at if you had any animal that would be all of those animals would be in the kingdom animal. Chordates are animals with backbones. Mammals, so now we're getting a little more particulate, those are ones that have fur and hair and milk glands. Primates are mammals that have collarbones. Hominids are primates that have flat feet. faces and three-dimensional vision. So you can see with each of these levels we're becoming a little more specific. Now in bacteria we use the same taxonomy so we're talking today about bacteria that is a domain. These are in the kingdom of eubacteria. We can narrow eubacteria down even more so we can talk about phylum of bacteria. There are many different phylum. There are even more different classes, orders, families, and down here we're going to be referring to most bacteria by their genus and species name. One thing I want to point out is that the genus and the species are italicized, so when you're referring to the genus and species of microbes you should italicize those. Okay, so we have our tree of life again. We have bacteria and you can see that there are many different types of bacteria. These bacteria have been classified in many different ways. Right now they're mostly classified based on nucleic sequence homology, so that just means how much of their chromosomal sequence is similar or not similar to the chromosomal sequence of another living thing. But in the past, We have classified bacteria and other microbes and other living things based on protein sequence homology or RNA similarities or phenotypes including colony morphology or cell morphology or growth requirements or pathogenicity genes. So we've used many different ways to classify living things. Now we mostly use nucleic acid sequence. So for bacteria we use the 16S ribosomal This is a gene that's found in all bacteria and archaea. It has regions of highly conserved regions that are the same between just about any organism that's a bacteria or archaea. But then it has regions that are different. They have individual nucleotide differences. And this is showing the different regions of the 16S ribosomal. RNA gene. If we sequence the entire gene of the living organism, we can determine how similar it is to another organism by looking at how many individual nucleotides are similar or dissimilar between those organisms. Now bacteria, the domain of bacteria is really diverse. And another way of classifying bacteria is based on whether they are gram-negative. or gram-positive, and that's how we're going to group bacteria today. Within gram-positive bacteria, we have high GC content and low GC content. I'll talk about what that is in just a minute. Gram-negative bacteria can be grouped together based on their ability to use light as an energy source and whether they can fix nitrogen. There's lots of different ways that we're going to characterize gram-negative bacteria here in just a minute. We're going to start out by talking about the archaea and the deeply branching bacteria. Archaea, as I've mentioned before, were once thought to be bacteria, but we discovered in the 1970s, Carl Weiss discovered in the 1970s, that archaea are their own domain. And the deeply branching bacteria we'll talk about in just a minute. These are the oldest bacteria. So let's look at archaea. Archaea are not bacteria. They are their own classification. Many of them are extremophiles. There are two major phyla, the crinarcheota and the earcheota. Very few of them are known to cause disease. The book says that none of them are known to cause disease, and I gave an example a few weeks ago of one type of Archaea that is associated with periodontal disease. These are extremophiles. They are most often found in really extreme environments, like very warm environments. These are thermophiles or hyperthermophiles, indicating that they are most commonly found found and can replicate and survive in extremely high temperatures. There are also halophiles in the domain Archaea. Halophiles are microbes that can survive very high concentrations of salt, as seen here. These Archaea often share common features, or actually I should say all Archaea share common features, such as the lack of a true peptidoglycan or cell wall, and then cell membrane lipids that are different from bacterial cell membrane lipids in that they have branched hydrocarbon chains. So what does that look like? Here are the cell lipids of archaea and you can see that the lipids, the fatty part of this lipid, has branches on it. This carbon is attached to another carbon unlike the unbranched tails of eukaryotes or bacteria. So here's the eukaryotic or bacterial fossil lipid. Here's that phosphate head. Here's the ester linkage and here is the tail and there are no branches in this tail. Archaea have another difference as well. They have ether linkages here instead of ester linkages. And then we didn't really talk about isomers in chemistry, but the archaea have an L-glycerol and eukaryotes and bacteria. have a D-glycerol in their phospholipid. In addition to having branched tails, these tails can also be connected in archaea. So typically in bacteria and eukaryotes the tails are not connected and we have a phospholipid bilayer. In archaea these tails are sometimes connected. and so instead of having a phospholipid bilayer you have a monolayer. Methanogens or archaea that are associated with mammals they are able to convert carbon dioxide, hydrogen gas, and organic acids to methane gas. They produce about 10 trillion tons of methane. These are buried on the ocean floor so these ones are obviously not associated with mammals. They are able to digest sludge during sewage treatment and some live in the colons of mammals. Here I'm showing a cow. Cows happen to have a lot of archaea in their guts and produce a lot of methane. So do humans. Okay, back to bacteria. We're going to start out with the deeply branching bacteria. These are some of the oldest bacteria and these are thought to be relatives of the bacteria. that lived over two and a half billion years ago. We have evidence of bacteria that lived two and a half billion years ago in these tramadolites. These tramadolites are actually the waste products of films of bacteria and we know that these are somewhere between that these deeply branching bacteria lived somewhere between 542 million years ago to two and a half billion years ago. Some of the deeply branching bacteria include Aquaflex and Deinococcus. Aquaflex is the earliest branch of bacteria. These are hyperthermophiles that are able to grow in very high temperatures. Aquafax, for example, can grow best at somewhere between 85 to 95 degrees Celsius. They have a very small genome, about a third of the size of an E. coli. Dinococcus is interesting because it has an outer membrane that's similar to gram-negatives, gram-negative bacteria, and yet it stains gram-positive. These are mostly autotrophic. bacteria. So go back to your metabolism lecture and think about what autotrophic means. The next type of bacteria we're going to talk about is the phototrophic bacteria. Phototrophic refers to light so these are microbes that can get their energy from light. They can also be autotrophic. These are divided into five groups based on pigment and source of electron for photosynthesis. So over here you can see we have green bacteria and here we have purple bacteria. So the types of phototrophic bacteria are the blue-green bacteria also known as the cyanobacteria, green sulfur bacteria, green non-sulfur bacteria, purple sulfur bacteria, purple non-sulfur bacteria. Why do I keep referring to the sulfur? That's because the non-sulfur bacteria don't use sulfur as their electron acceptor in photosynthesis. Sulphur bacteria use the sulfur as their electron acceptor in photosynthesis. The cyanotrophic bacteria can be grouped as, can be classified as cyanobacteria or chlorobi or chloroflexi or proteobacteria. The protobacteria can be broken down into gamma proteobacteria or alpha proteobacteria and one genus of beta proteobacteria. I'm not going to make you learn the entire table, but I would like you to remember the parts in red here. So the cyanobacteria, you can see that we, the cyanobacteria are blue-green bacteria. The cyanobacteria, they're oxygen net bacteria. oxogenic which means they use oxygen in their photosynthesis and their electron donor in photosynthesis is water. And now you can go through the rest of this table and look at the type of photosynthesis that the bacteria use. Cyanobacteria is oxygenic all the rest are anoxygenic and that means they undergo photosynthesis without oxygen production. They also have different electron donors in photosynthesis, so remember those. And then remember what common name is associated with each of these. Okay, now we're moving on to gram-positive bacteria. Gram-positive bacteria are often classified as high GC content or low GC content. And that's how we're going to discuss them in our lectures here. The low GC microbes, gram positive bacteria, include Firmicutes, Clasifidia, Molecules, and Bacilli. And the high GC contact bacteria that we'll talk about are the Actinobacteria. This table also lists representative genre, and we're going to cover most of these, and special characteristics and diseases associated with each of these bacteria. What do I mean by GC content? Well remember that the nucleotides used in DNA are thiamine, adenine, guanine, and cytosine. Cytosine and guanine are also also referred to as the C's and the G's and if we take all of the nucleotides that are present and we count up the number of GC's we can determine the GC content. So in this example we have some DNA sequence And we have 120 nucleotides here. If we count up all of the GCs in the sequence, there are 42 of them. 42 divided by 120 multiplied by 100% is 35%. So this is less than 50%. So this would be a low GC content region. Now this is just one small part of chromosomal DNA. If you took... all of the chromosomal DNA in the if you looked at all of the GC content in chromosomal DNA you'd be able to determine whether the number of GCs was larger than 50%, that would be high GC content, or lower than 50%, that would be low GC content. Okay, let's start with our low GC gram-positive bacteria. And in this, the first low GC gram-positive bacteria that we're going to talk about are the Firmicutes. The Firmicutes include Clostridia. These are rod-shaped aldehyde anaerobes. that means that they can only grow in the absence of oxygen. Many of these produce toxins that are deadly to humans and we're going to talk about some of these when we get to diseases, gastrointestinal diseases and skin diseases. These form endospores and examples of these are C. perforinges which causes gangrene, C. botulinum which causes botulism, Clostridium difficile, which causes severe diarrhea, and Clostridium ketonii, which causes tetanus. And we'll be discussing all of those in the last six lectures of this class. Next, in our firmicutes, we have our molecules. These include mycoplasma, which is a facultative or obligate anaerobe, meaning Facultative meaning it can live in the absence or presence of oxygen or obligate anaerobe meaning that it cannot live in the presence of oxygen it has to live in the absence of oxygen. These lack cell walls and so you can see that they're pleomorphic. The membranes contain sterols which give the bacteria their strength and they colonize the mucous membranes of respiratory and urinary tract of humans. The next firmicute on our list are the bacilli. Bacillus is an aerobic and can be either aerobic or facultative anaerobic. Bacillus anthracis causes anthrax. Bacillus thuringiensis produces a toxin that's used by farmers and gardeners as an insecticide. It loosens the integrity of the, decreases the integrity of the intestine of insects, and that leads to the killing of the insects. Other bacilli are able to synthesize antibiotics. This is just showing a gram stain of bacillus, reminding you that these are in fact gram positive bacteria, and as I showed you before. bacillus can also form endospores and that's what we see in this endospore stain. Another type of bacilli is Listeria monocytogenes. Listeria monocytogenes is a bacteria that can invade and live within our cells. Each of these images over here refers to a different part of the life cycle here. So here you can see Listeria monocytogenes. cytogenesis attaches to the cell and enters in in a phagesome but is able to break out of that phagesome to replicate inside of the cell and then it takes over the actin of the host cell to move around it can use this f-actin to move around within the host cell but also to spread from one host cell to another thereby evading the host immune system and again it can break out of the vacuoles when it invades a new cell and take over the actin once again. It's an intracellular pathogen, meaning it lives inside the cell and it's a pathogen because it can cause damage to the host. That damage comes in the form of death to fetuses, bacteremia, and meningitis in immunocompromised hosts. The next bacilli that we're going to talk about are the lactobacillus. These are normal members of the normal microbiota. So these are the microbes that are associated with hosts on a regular basis. These can grow in and are found in the human mouth and the stomach and the intestinal tract and the vagina and in fact here what we're showing is vaginal epithelial cells with lactobacilli living with those cells. They inhibit the growth of pathogens within the body and that's one of the reasons that they're part of the normal microbiota. They're also used in the production of a number of different types of food including yogurt, buttermilk, and sauerkraut. They rarely cause infections and when they do they can cause blood infections. So you'll note that up here I said that they're in the mouth, stomach, intestinal tract, and vagina. They should not be in the blood. So when they get into the blood they can replicate and cause infections. Okay, other than that, they rarely cause disease. And the final firmicute that we will talk about are bacilli and cocci. We have bacilli streptococcus here. So this is a gram-positive bacteria that can cause streptococcus infections. Many of you may have had strep throat that was caused by streptococcus. And these, the last firmicutes. The last firmicute we'll talk about is Enterococcus, and that's a bacteria that's found in the gut. Firmicutes can also be cocci. Here we have Staphylococcus. This gram-positive bacteria forms these grape-like clusters. It's one of the most common inhabitants of humans, but it can also be a pathogen that produces toxins and enzymes that contribute to disease. We'll talk a lot about Staphylococcus and Streptococcus when we get to the last six chapters of our class. Okay, that's the last of our low GC content gram-positive bacteria. Now to move on to our high GC gram-positive bacteria. For these, we're going to discuss actinobacteria. Actinobacteria include a number of different microbes. The first one that we're going to talk about is tyrannobacterium. Tyrannobacterium are pleomorphic arobes and facultative anaerobes. These are able to produce metachromatic granules and you can see that with the metachromatic granule stain up here. These are not endospores and this is not a gram stain this is a stain for these metachromatic granules. Carinia bacterium can cause things like diphtheria infections and here you can see a pseudomembrane from a C. diphtheria infection. The next actinobacteria that we're going to talk about is mycobacterium. Mycobacterium can be differentiated from other gram positive bacteria by acid fast stains. When you do an acid fast stain, these microbes appear pink. These are aerobic rods that sometimes form filaments. They grow really slow. I've talked about this in class before. They can take up to 28 days to grow a colony on a plate. The slow growth is partially due to the mycolic acid in its cell walls. Some species are pathogens to animals and humans, including Mycobacterium tuberculosis, which we'll talk about in a few lectures. The only other actinobacteria that we're going to talk about is actinomyces, and we talked about these earlier. These are spore formers, and here you can see those spores once again here and here. These are the vegetative cells of actinomycetes, and these are the spores. These can cause disease primarily in immunocompromised patients, so if your immune system is working well, you will likely not get sick from actinomyces. These are important genres include actinomyces, nocaria, and streptomyces. Streptomyces recycle nutrients in the soil and are really important antibiotic producers. Nocaria is soil and water drilling aerobes that can degrade a variety of pollutants. And then actinomyces normally present in the oral cavity and throats of humans. So that's it for the gram-positive bacteria. Now we're going to move on to the gram-negative proteobacteria. These are the largest and most diverse group of bacteria. So we're going to discuss many of these different groups. Starting out with our alpha proteobacteria. You'll note that we are going to talk about alpha, beta, gamma, and delta, and epsilon proteobacteria. So keep track of this part of this word. This is alpha proteobacteria. First up are the nitrogen fixers. These are often found in soil. So here we have nitrogen fixing bacteria that can convert nitrogen from the air into ammonia. An example of this is azospirulium which produces chemicals that aid in nutrient uptake and rhizobium which produces ammonia which aids in plant growth and root production. And over here you can see a root from a plant. And then we have nitrifying bacteria. These are another type of alpha proteobacteria. These are able to take that ammonium from these nitrogen fixing bacteria that produce ammonia and that converted into ammonium. These nitrifying bacteria can take the ammonium and turn them into nitrate. This nitrate can be taken up by roots and used as a organic and use this compound to help the roots grow. And then that nitrate can be denitrified and turned into nitrogen. that's found in the air. Nitrifying bacteria oxidates nitrogenous compounds, providing electrons. They're important to the environment and for agriculture, and as you can see here with this root, they convert reduced nitrogenous compounds into nitrate, which is called nitrification, and a great example is Nitrobacter. Alpha proteobacteria also includes some pathogenic microbes such as Rickettsia. Rickettsia is transmitted through a bite of an arthropod, which is a type of insect. It causes several human diseases including rocky mountain spotted fever seen here. This is an image of Rickettsia. Another type of alpha proteobacteria is Brucella. This can cause brucellosis. It survives phagocytosis by white blood cells which helps it spread throughout the body. And so here you can see the symptoms with the clinical manifestations of grecelliosis, and you can see that it affects just about every part of the body. Now we're moving on to our beta proteobacteria. These are mostly pathogenic microbes, including Neisseria. Neisseria gonorrhea is a sexually transmitted bacteria that we're going to talk about in the very last chapter of our book. It inhabits the mucous membranes of mammals and can cause numerous diseases depending on which species of Neisseria you're discussing. This is Neisseria gonorrhea which is caused by sexually transmitted disease. But there are other species of Neisseria that can infect the brain and other parts of the body. Here we have Bordetella. Bordetella causes pertussis. These are the ciliated cells in the... in the airway of a mammal. This bacteria will attach to the cilia and kill the cilia, leading to an inability to breathe. And then down here we have Burkholderia. Burkholderia is able to colonize moist environmental surfaces and respiratory passages of cystic fibrosis patients, so patients who produce a lot of salt and very thick mucus. It's a bacteria that can infect both animals and humans through direct... contact via inhalation, ingestion, or open wounds. One of the nasty things about this bacteria is that the infection incubation period can be anywhere from a couple of days to a couple of years. This allows people to be infected without realizing it. The bacterium can also manage to survive outside of a host cell organism, allowing it to spread that way as well. Okay, moving on to gamma proteobacteria. There are a lot of different gamma proteobacteria. Here I'm showing a dichotomous key to help remember the different types of gamma proteobacteria. We're not going to talk about this one. We are going to talk about purple sulfur bacteria up next. Legionella will talk about Fibrio pseudomonas enterobacteria and some of these others. So let's start with gamma proteobacteria. These include purple sulfur bacteria. so it's purple and it uses sulfur in for the two of these are obligate anerbose they're able to oxidize hydrogen sulfur hydrogen hydrogen sulfide to sulfur they're found in sulfur rich zones because they need that sulfur they're also found in lakes fogs and oceans here i'm showing a worm that is completely covered in gram positive i'm sorry gram not gram-positive, but in these gamma proteobacteria, these purple sulfur bacteria. Another type of gamma proteobacteria are intracellular pathogens. Legionella causes Legionnaires disease, and we'll talk about that when we get to diseases of the lungs. Coxillia causes Q fever. This is a flu-like sickness caused by Coxillia burneti. It infects goats, sheep, cows, and other animals. then those animals are able to spread this infection to humans through the wind. They survive. These are both pathogens that can survive within white blood cells. White blood cells circulate throughout the body, so when these microbes get into the body, they can circulate and cause many different symptoms. The glycolytic facultative aneurysms are the largest groups of gamma proteobacteria. They're able to take in carbohydrates and break them down into an energy form using glycolysis and the pentose phosphate pathway. So hopefully you can remember those pathways from the chapter on metabolism. They're divided into three families. The Enterobacteriaceae include straight rods, oxidase negative to treat microbes that have Peritrichous flagella, so flagella that are all over the body or they can be non-modal. There are many different genres within the Enterobacteriaceae and you'll note that a lot of these can cause disease in humans. These two are rarely pathogenic to humans. Vibrio naceae are Vibrio, so remember that comma shaped bacteria. There are many different types of Vibrio. One example is Vibrio cholerae that can cause cholera in humans. And we'll talk about that one when we get to diseases of the digestive system. And then there are Pasteuraceae. These are, one example of that is Haemophilus, which causes meningitis in children, middle ear infections, and pneumonia. The last type of Gamma proteobacteria that we'll talk about are Pseudomonads. These are able to break down numerous organic compounds that are important pathogens of humans and animals. This is a great example of Pseudomonas. There are many different species of Pseudomonas. Some of them cause disease in humans. Pseudomonas can cause urinary tract infections, ear infections, and lung infections. And we'll talk about Pseudomonas in terms of skin infections in a couple of lectures. Other examples of gamma proteobacteria that are pseudomonads are Azovacter and Azovonus, which are non-pathogenic, so they don't cause disease, and they live in the soil. Moving on to delta proteobacteria, we're going to talk about the Sulfovibrio. This is a vibrio, so you can see that these are comma-shaped. These also happen to have flagella. They recycle sulfur in the environment and they are able to contribute to the corrosion of iron pipes. And in fact, that's what we see here. These are images of iron pipes used in plumbing and you can see that these are degrading and that is due to desulfovibrio. Another example of a delta proteobacteria are delavibrio. These are fascinating little microbes because these are a pathogen of gram-negative bacteria. So it's a gram-negative bacteria that can cause disease in other gram-negative bacteria. So here we have a gram-negative bacteria. Belovibrio is able to enter into this bacteria by getting through the outer membrane. It replicates within the gram-negative bacteria. And within 20, within... a short period of time, individual daughter cells from this Delivibrio are able to break out of that gram-negative bacteria to infect a new gram-negative bacteria. Okay, the last Delta proteobacteria that we'll talk about are the Myxobacteria. This is the life cycle of Myxobacteria. It's a fascinating microbe because it can live individually, but it can also form these mounds of cells. So this is not one big organism. This is lots of individual vegetative cells, actively replicating metabolizing cells. They form these mounds when there are very few nutrients around. Then these mounds can come together and form fruiting bodies that produce these pharyngeums. and these can release these myxospores. These myxospores can spread through the air and find a nutrient-rich area and then form these vegetative slime trails. These vegetative cells can form slime trails. replicate by binary fission and then when they deplete all the nutrients in that particular area they form more mounds and the cycle repeats. So those are the myxobacteria. That's it for the Delta proteobacteria. Now let's move on to the Epsilon proteobacteria. We're only going to talk about two of these. The first one is Campylobacter that can cause blood poisoning and intestinal inflammation. We'll talk about these when we get to intestinal diseases. And then helicobacter is a gram-negative epsilon proteobacteria that can cause ulcers and cancer in a small subset of patients who have helicobacter. And we're going to talk about these in much greater detail in a few lectures. Okay, other types of gram-negative bacteria include chlamydia. Chlamydia are obligate intracellular microbes, intracellular meaning that they can replicate within another host cell. So here we have the life cycle of chlamydia. An elementary body enters into a host cell. The elementary body transforms into a reticulate body. That reticulate body replicates within the cell and transforms back into these elementary bodies which are released and they can infect new cells. They can grow in mammals, birds, and some in vertebrates. Some of them are smaller than viruses and they are the chlamydia is the most commonly sexually transmitted bacteria in the United States and we'll talk about that more when we get to the last chapter of the last lecture of this class. Okay, we are almost done. The next type of gram-negative bacteria that we're going to talk about is the spirochetes. You'll remember these from one of the earlier lectures where we talked about microbes that have endoflagella and can move in corkscrew-like fashion. Those are the spirochetes. These are flexible organisms that have this wavy look to them. They're modal, as I just said. They have diverse metabolism and habitats. That just means they can eat lots of things, convert them to energy, and they can live in lots of different places. Two of the spirochetes that are able to cause disease in humans are Trepanema and Borrelia. Trepanema causes syphilis, which you can see here, and we'll talk about that when we get to the last lecture of the class. Borrelia causes Lyme disease, and we'll talk about that when we talk about diseases of the nervous system. The last group of bacteria that we're going to talk about are Bacteroides. These are able to live in the digestive tracts of humans and animals. Some of these species are also able to cause disease. And then Cytophagia are aquatic gliding bacteria that are important to the degradation of raw sewage. And that's it! If you want to learn a little more about spore formation, you can check out this YouTube video. That's it. Thank you.

Many studies have shown that the act of writing information down actually helps you retain that information and recall it better later. So, handwrite flashcards and go through them when you can. Also, rewrite your notes, your lecture notes and your reading notes, and self-quiz yourself.

So, just write questions regarding the material that you're learning and ask. yourself those questions later and see if you can recall that information. If you can't, you need to go back and study it again, and if you can, huzzah, move on. Okay, we're going to start on chapter 11. Here we're discussing prokaryotic classification, so basically bacteria, and we're going to cover not just bacteria today, we are also going to cover archaea. Eukaryotes will be covered in another chapter.

This is the tree of life. I like showing this because it shows that there are many different types of bacteria. And in fact, we're going to talk about the fact that there are thousands of different types of bacteria. We are only going to cover a handful of them in this class. Today, we will cover archaea, seen down here.

You can see that they are in a different branch of the tree of life from bacteria. And in fact, they are related to eukaryotes, which we talked about recently. Now we're going to start.

by talking about bacteria in general. I want you to keep in mind that we have not been able to grow all bacteria in the laboratory, which means that we haven't been able to fully characterize them. And in fact there are hundreds, maybe thousands, of species that we haven't been able to characterize because we can't grow them in the lab. So we're going to start by talking about bacteria in general and we're going to talk first about their shapes and replication. Prokaryotes come in many different shapes.

This ball form seen on top here is referred to as caucasus and it just looks like a little ball. If you take that ball and stretch it out a little bit it looks halfway between a caucasus and a bacillus. And that is called caucobacillus. Bacillus are also referred to as rod shaped and you can see that they are elongated. Here we have vibrio.

Vibrio is comma shaped and this is very characteristic of vibrio. and this one happens to have flagella as well. Spirulium are rigid bacteria that have two bends in them and this is a rigid shape.

This is not a shape that, you know, this bacteria happened to lay down this way and it looks like this. This is a rigid shape. These spirochetes have a, almost look like corkscrews and in fact they, when they move, they're referred to as moving in a corkscrew fashion. We talked about spirochetes when we talked about endoflagella a few chapters ago. These are flexible microbes and they tend to be able to be flexible.

Down here we have pleomorphic bacteria. Now all of these have their particular shape because they have cell walls that help them retain their circular shape or their broad shape or their bacillus shape or their shape. Down here we have pleomorphic bacteria. that don't have cell walls and so they are able to take a variety of shapes. Now if you looked at a population, so many different, a group of microbes within the same species for these bacteria, they would all have the same shape unless they were replicating.

But the pleomorphic, if you looked at a population of any one species of pleomorphic bacteria, they may have several different shapes. And then down here we have a star shape, and you can see that it's referred to as a star shape because it's pointy. It has these points on it to make it look like a star.

Now cells can be arranged in many different ways, and the arrangement of the cells depends on the plane of replication and separation of daughter cells. So what do I mean by that? This is the plane of replication.

This indicates that this bacteria will form a daughter cell, either on this side or on this side of this bacillus. Now these bacteria can be arranged singly as observed here or they could be found in pairs. The dye here in diplococci refers to the fact that these are often found in pairs and you can see that here and here and here. Now note that there are single microbes in this image, so you won't always see them in pairs, but most often you'll see them in pairs.

These bacteria can also replicate one on end to each other in these chains, and these chains are referred to as streptococci. In this particular image you can see that there are very few individual microbes or pairs of microbes. They're in, most of the microbes in this image are in chains. Then you can have tetrads. The tetra here refers to four and so these are groups of four bacteria and you can see these on the stain here.

And then if you have stacks of these four, these are referred to as sarkinae and this is due to the ability to replicate on three different planes. If the bacteria is a cocci and it can replicate on any plane, these form grape-like structures and are referred to as staphylococci. where the staple refers to grape-like and you can see that in this stain here.

Now these bacteria as we said before or as I said before are not just found in cocci form they are also found in rod form bacilli form and these can have the same have similar arrangements to the cocci so you can have single diplo, diplo bacilli you can have streptobacilli in these chains You can also have palisades, and that's because these bacteria have ends to them. So you can have, if you have a plane of replication at one end or the other, you can have palisades that are formed, or you can have a V shape. And we'll talk about how these V shapes form in just a minute. Now bacteria can replicate a number of different ways. The most common way is by binary fission, but not all bacteria replicate this way, but many do.

We've talked about binary fission before. You have chromosomes. The chromosomal DNA replicates that and that leads to elongation of the cell wall, the cell wall in the cytoplasmic membrane.

And that also separates the chromosomal DNA. Then a cell wall forms, a cross wall forms, and the membrane invaginates. That just means that pinches in here.

Eventually a cross wall or the cytoplasmic membrane completely separates the mother and the daughter cell and then you have the mother cell and the daughter cell completely separating. Now as we showed before up here the daughter cell doesn't always completely separate. You can see these have not completely separated but often the daughter cell will completely separate.

Now this is different than snapping. So in snapping you have daughter cell that forms but it never completely separates from the mother cell and so here you have the separation the membrane and the cell wall have formed in between the daughter cell and the mother cell but they don't completely separate and here we have a hinge that forms in between these two cells and then another form of replication is bee snapping a great example of this is mycobacterium and this When mycobacterium replicate, there's an elongation stage. Separation and early division stage occurs in which the membrane forms in between the mother cell and the daughter cell. And then eventually you have the late division stage and you end up with V-snapping.

Now note here that in the V-snapping stage, the mother and the daughter cell are still attached. Eventually that daughter cell is detached. daughter cell detaches and elongates and the cycle repeats itself. Another form of replication is spore formers. We're going to talk about spore formers in much greater detail when we get to fungi, but here's an example of a bacteria that can form spores.

Actinomycetes or the order Actinomycetes. can form spores. And here we see vegetative cells and then we see spore formers.

Now these are not two different species. These are one species, one type of bacteria in this image in two different stages. The vegetative cell that's actively metabolizing and replicating and these spore formers that carry the DNA of the cells.

And here's a nice drawing showing the separation, the DNA in daughter cells that eventually get separated with these septums until you have eventual full separation of individual spores that are formed by actinomycetes. The next form of replication is budding. In budding you start out the same as you do with as you do with binary fission with a chromosome replicating and the bacteria elongating but then you have a bud that forms at one end of the bacteria.

Eventually the chromosomal DNA all collects in the young bud and the daughter cell breaks off from the mother cell. The parent can make more offspring. when they bud off.

So unlike other cell replication types for budding, individual mother cells can go on to make more than one daughter cell. And finally we have viviparity. In viviparity, the daughter cell forms within the mother cell. So here we have the mother cell, here's the daughter cell.

The daughter cell becomes fully formed within the mother cell and eventually lyses out of the mother cell to form another daughter cell to be completely independent and then eventually forming its own offspring. And so here you can see a stain where the daughter cell is forming inside the mother cell and again here's the daughter cell and here's the mother cell and they're both sharing the membrane. A great example of this is epilepsym. And so here you can see epilepsym. There's the mother cell, there's the daughter cell.

We've talked about this particular microbe in the past because it's incredibly big. Here's epilepsym compared to E. coli.

This little tiny dot here is E. coli. And you can see that this bacteria is considerably larger than other bacteria like E.

coli. And just another size comparison, here's paramecium, which is a eukaryote. And remember, in general, eukaryotes are bigger than bacteria.

And yet here we have a bacteria that is significantly larger than this eukaryote. Bacteria can also form endospores. Endospores are a way for the bacteria to protect itself from the environment.

by being in a state of a very low or stopped metabolic rate. So it's not metabolizing, it's not replicating. And that allows the bacteria to become resistant to changes in the environment. Now again, the vegetative cell is the cell that's actively replicating and metabolizing, but here we have endospores that are forming inside of vegetative cells. And this is another example of spores forming inside of cells.

We've already gone through how an endospore forms so we're not going to go over that today. I will remind you that each vegetative cell can make one endospore which can germinate later to make one vegetative cell. Spores can form on the ends of the cells or at the terminus of the cell.

They can also form at the center of the cell and typically any one species of bacteria will form endospores in either at the end or at the terminus or at the center. As for the different types of bacteria that can form endospores, here I'm showing Clostridium. An example of a gram-positive bacteria that can form endospores is Bacillus.

Okay, so let's talk about classification next. Classification is just the way that we group bacteria together. How we...

determine which ones are more related to others. The Burgese Manual of Determinative Bacteriology is a manual that lists all the types of bacteria that have ever been described. So if a researcher has described a bacteria in a laboratory it eventually makes it into the Burgese Manual.

It's now called the Burgese Manual of Systematic Bacteriology. Now, back in the 1950s, you could describe all of the microbes that had ever been described and put them into one book. Now we have several volumes of books because we have described so many different types of bacteria. And these are no longer printed, as far as I know. Now I think they are just available online.

I'd like to point out that the chair of Berkey's Manual Trust and past president of Berkey's International Society of Microbial Systematics, was formerly at UAA. So this is Dr. Fred Rainey. If you ever run into Dr. Rainey here in Anchorage because he still occasionally hangs out, tell him Dr. Katz said hi.

Okay, classification. Continuing with classification. Taxonomy refers to the way that we classify microbes, what group we put them into. Now I've mentioned species a few times.

When you think about when microbes and other living things are characterized, they're grouped according to how similar they are to other living things. Two individual living things are very similar to each other. They're referred to as, they are given species names.

If they're a little more distant from each other, then they're in the same genus. If they're a little more distant from each other, they're family. And up here on kingdom, you can have very different organisms within this classification. One way to remember this taxonomy tree is to remember King Philip can order five golden spoons. Another way is just to remember the order of the names.

Kingdom, phylum, class, order, family, genus, species. Where kingdom has is the biggest umbrella that contains the largest number of living things within that. I like to use an example.

So we are Homo sapiens. Sapiens is the species that we are in. Homo is the genus. that we are in. Our kingdom is animals.

So if you looked at if you had any animal that would be all of those animals would be in the kingdom animal. Chordates are animals with backbones. Mammals, so now we're getting a little more particulate, those are ones that have fur and hair and milk glands.

Primates are mammals that have collarbones. Hominids are primates that have flat feet. faces and three-dimensional vision.

So you can see with each of these levels we're becoming a little more specific. Now in bacteria we use the same taxonomy so we're talking today about bacteria that is a domain. These are in the kingdom of eubacteria. We can narrow eubacteria down even more so we can talk about phylum of bacteria. There are many different phylum.

There are even more different classes, orders, families, and down here we're going to be referring to most bacteria by their genus and species name. One thing I want to point out is that the genus and the species are italicized, so when you're referring to the genus and species of microbes you should italicize those. Okay, so we have our tree of life again. We have bacteria and you can see that there are many different types of bacteria.

These bacteria have been classified in many different ways. Right now they're mostly classified based on nucleic sequence homology, so that just means how much of their chromosomal sequence is similar or not similar to the chromosomal sequence of another living thing. But in the past, We have classified bacteria and other microbes and other living things based on protein sequence homology or RNA similarities or phenotypes including colony morphology or cell morphology or growth requirements or pathogenicity genes.

So we've used many different ways to classify living things. Now we mostly use nucleic acid sequence. So for bacteria we use the 16S ribosomal This is a gene that's found in all bacteria and archaea.

It has regions of highly conserved regions that are the same between just about any organism that's a bacteria or archaea. But then it has regions that are different. They have individual nucleotide differences. And this is showing the different regions of the 16S ribosomal.

RNA gene. If we sequence the entire gene of the living organism, we can determine how similar it is to another organism by looking at how many individual nucleotides are similar or dissimilar between those organisms. Now bacteria, the domain of bacteria is really diverse. And another way of classifying bacteria is based on whether they are gram-negative. or gram-positive, and that's how we're going to group bacteria today.

Within gram-positive bacteria, we have high GC content and low GC content. I'll talk about what that is in just a minute. Gram-negative bacteria can be grouped together based on their ability to use light as an energy source and whether they can fix nitrogen. There's lots of different ways that we're going to characterize gram-negative bacteria here in just a minute. We're going to start out by talking about the archaea and the deeply branching bacteria.

Archaea, as I've mentioned before, were once thought to be bacteria, but we discovered in the 1970s, Carl Weiss discovered in the 1970s, that archaea are their own domain. And the deeply branching bacteria we'll talk about in just a minute. These are the oldest bacteria. So let's look at archaea. Archaea are not bacteria.

They are their own classification. Many of them are extremophiles. There are two major phyla, the crinarcheota and the earcheota. Very few of them are known to cause disease. The book says that none of them are known to cause disease, and I gave an example a few weeks ago of one type of Archaea that is associated with periodontal disease.

These are extremophiles. They are most often found in really extreme environments, like very warm environments. These are thermophiles or hyperthermophiles, indicating that they are most commonly found found and can replicate and survive in extremely high temperatures.

There are also halophiles in the domain Archaea. Halophiles are microbes that can survive very high concentrations of salt, as seen here. These Archaea often share common features, or actually I should say all Archaea share common features, such as the lack of a true peptidoglycan or cell wall, and then cell membrane lipids that are different from bacterial cell membrane lipids in that they have branched hydrocarbon chains.

So what does that look like? Here are the cell lipids of archaea and you can see that the lipids, the fatty part of this lipid, has branches on it. This carbon is attached to another carbon unlike the unbranched tails of eukaryotes or bacteria. So here's the eukaryotic or bacterial fossil lipid. Here's that phosphate head.

Here's the ester linkage and here is the tail and there are no branches in this tail. Archaea have another difference as well. They have ether linkages here instead of ester linkages.

And then we didn't really talk about isomers in chemistry, but the archaea have an L-glycerol and eukaryotes and bacteria. have a D-glycerol in their phospholipid. In addition to having branched tails, these tails can also be connected in archaea. So typically in bacteria and eukaryotes the tails are not connected and we have a phospholipid bilayer.

In archaea these tails are sometimes connected. and so instead of having a phospholipid bilayer you have a monolayer. Methanogens or archaea that are associated with mammals they are able to convert carbon dioxide, hydrogen gas, and organic acids to methane gas.

They produce about 10 trillion tons of methane. These are buried on the ocean floor so these ones are obviously not associated with mammals. They are able to digest sludge during sewage treatment and some live in the colons of mammals.

Here I'm showing a cow. Cows happen to have a lot of archaea in their guts and produce a lot of methane. So do humans. Okay, back to bacteria.

We're going to start out with the deeply branching bacteria. These are some of the oldest bacteria and these are thought to be relatives of the bacteria. that lived over two and a half billion years ago. We have evidence of bacteria that lived two and a half billion years ago in these tramadolites.

These tramadolites are actually the waste products of films of bacteria and we know that these are somewhere between that these deeply branching bacteria lived somewhere between 542 million years ago to two and a half billion years ago. Some of the deeply branching bacteria include Aquaflex and Deinococcus. Aquaflex is the earliest branch of bacteria.

These are hyperthermophiles that are able to grow in very high temperatures. Aquafax, for example, can grow best at somewhere between 85 to 95 degrees Celsius. They have a very small genome, about a third of the size of an E. coli. Dinococcus is interesting because it has an outer membrane that's similar to gram-negatives, gram-negative bacteria, and yet it stains gram-positive.

These are mostly autotrophic. bacteria. So go back to your metabolism lecture and think about what autotrophic means.

The next type of bacteria we're going to talk about is the phototrophic bacteria. Phototrophic refers to light so these are microbes that can get their energy from light. They can also be autotrophic. These are divided into five groups based on pigment and source of electron for photosynthesis. So over here you can see we have green bacteria and here we have purple bacteria.

So the types of phototrophic bacteria are the blue-green bacteria also known as the cyanobacteria, green sulfur bacteria, green non-sulfur bacteria, purple sulfur bacteria, purple non-sulfur bacteria. Why do I keep referring to the sulfur? That's because the non-sulfur bacteria don't use sulfur as their electron acceptor in photosynthesis.

Sulphur bacteria use the sulfur as their electron acceptor in photosynthesis. The cyanotrophic bacteria can be grouped as, can be classified as cyanobacteria or chlorobi or chloroflexi or proteobacteria. The protobacteria can be broken down into gamma proteobacteria or alpha proteobacteria and one genus of beta proteobacteria. I'm not going to make you learn the entire table, but I would like you to remember the parts in red here. So the cyanobacteria, you can see that we, the cyanobacteria are blue-green bacteria.

The cyanobacteria, they're oxygen net bacteria. oxogenic which means they use oxygen in their photosynthesis and their electron donor in photosynthesis is water. And now you can go through the rest of this table and look at the type of photosynthesis that the bacteria use.

Cyanobacteria is oxygenic all the rest are anoxygenic and that means they undergo photosynthesis without oxygen production. They also have different electron donors in photosynthesis, so remember those. And then remember what common name is associated with each of these.

Okay, now we're moving on to gram-positive bacteria. Gram-positive bacteria are often classified as high GC content or low GC content. And that's how we're going to discuss them in our lectures here.

The low GC microbes, gram positive bacteria, include Firmicutes, Clasifidia, Molecules, and Bacilli. And the high GC contact bacteria that we'll talk about are the Actinobacteria. This table also lists representative genre, and we're going to cover most of these, and special characteristics and diseases associated with each of these bacteria.

What do I mean by GC content? Well remember that the nucleotides used in DNA are thiamine, adenine, guanine, and cytosine. Cytosine and guanine are also also referred to as the C's and the G's and if we take all of the nucleotides that are present and we count up the number of GC's we can determine the GC content.

So in this example we have some DNA sequence And we have 120 nucleotides here. If we count up all of the GCs in the sequence, there are 42 of them. 42 divided by 120 multiplied by 100% is 35%.

So this is less than 50%. So this would be a low GC content region. Now this is just one small part of chromosomal DNA. If you took...

all of the chromosomal DNA in the if you looked at all of the GC content in chromosomal DNA you'd be able to determine whether the number of GCs was larger than 50%, that would be high GC content, or lower than 50%, that would be low GC content. Okay, let's start with our low GC gram-positive bacteria. And in this, the first low GC gram-positive bacteria that we're going to talk about are the Firmicutes.

The Firmicutes include Clostridia. These are rod-shaped aldehyde anaerobes. that means that they can only grow in the absence of oxygen.

Many of these produce toxins that are deadly to humans and we're going to talk about some of these when we get to diseases, gastrointestinal diseases and skin diseases. These form endospores and examples of these are C. perforinges which causes gangrene, C.

botulinum which causes botulism, Clostridium difficile, which causes severe diarrhea, and Clostridium ketonii, which causes tetanus. And we'll be discussing all of those in the last six lectures of this class. Next, in our firmicutes, we have our molecules.

These include mycoplasma, which is a facultative or obligate anaerobe, meaning Facultative meaning it can live in the absence or presence of oxygen or obligate anaerobe meaning that it cannot live in the presence of oxygen it has to live in the absence of oxygen. These lack cell walls and so you can see that they're pleomorphic. The membranes contain sterols which give the bacteria their strength and they colonize the mucous membranes of respiratory and urinary tract of humans.

The next firmicute on our list are the bacilli. Bacillus is an aerobic and can be either aerobic or facultative anaerobic. Bacillus anthracis causes anthrax.

Bacillus thuringiensis produces a toxin that's used by farmers and gardeners as an insecticide. It loosens the integrity of the, decreases the integrity of the intestine of insects, and that leads to the killing of the insects. Other bacilli are able to synthesize antibiotics.

This is just showing a gram stain of bacillus, reminding you that these are in fact gram positive bacteria, and as I showed you before. bacillus can also form endospores and that's what we see in this endospore stain. Another type of bacilli is Listeria monocytogenes.

Listeria monocytogenes is a bacteria that can invade and live within our cells. Each of these images over here refers to a different part of the life cycle here. So here you can see Listeria monocytogenes. cytogenesis attaches to the cell and enters in in a phagesome but is able to break out of that phagesome to replicate inside of the cell and then it takes over the actin of the host cell to move around it can use this f-actin to move around within the host cell but also to spread from one host cell to another thereby evading the host immune system and again it can break out of the vacuoles when it invades a new cell and take over the actin once again. It's an intracellular pathogen, meaning it lives inside the cell and it's a pathogen because it can cause damage to the host.

That damage comes in the form of death to fetuses, bacteremia, and meningitis in immunocompromised hosts. The next bacilli that we're going to talk about are the lactobacillus. These are normal members of the normal microbiota. So these are the microbes that are associated with hosts on a regular basis. These can grow in and are found in the human mouth and the stomach and the intestinal tract and the vagina and in fact here what we're showing is vaginal epithelial cells with lactobacilli living with those cells.

They inhibit the growth of pathogens within the body and that's one of the reasons that they're part of the normal microbiota. They're also used in the production of a number of different types of food including yogurt, buttermilk, and sauerkraut. They rarely cause infections and when they do they can cause blood infections. So you'll note that up here I said that they're in the mouth, stomach, intestinal tract, and vagina.

They should not be in the blood. So when they get into the blood they can replicate and cause infections. Okay, other than that, they rarely cause disease. And the final firmicute that we will talk about are bacilli and cocci. We have bacilli streptococcus here.

So this is a gram-positive bacteria that can cause streptococcus infections. Many of you may have had strep throat that was caused by streptococcus. And these, the last firmicutes.

The last firmicute we'll talk about is Enterococcus, and that's a bacteria that's found in the gut. Firmicutes can also be cocci. Here we have Staphylococcus.

This gram-positive bacteria forms these grape-like clusters. It's one of the most common inhabitants of humans, but it can also be a pathogen that produces toxins and enzymes that contribute to disease. We'll talk a lot about Staphylococcus and Streptococcus when we get to the last six chapters of our class.

Okay, that's the last of our low GC content gram-positive bacteria. Now to move on to our high GC gram-positive bacteria. For these, we're going to discuss actinobacteria. Actinobacteria include a number of different microbes. The first one that we're going to talk about is tyrannobacterium.

Tyrannobacterium are pleomorphic arobes and facultative anaerobes. These are able to produce metachromatic granules and you can see that with the metachromatic granule stain up here. These are not endospores and this is not a gram stain this is a stain for these metachromatic granules. Carinia bacterium can cause things like diphtheria infections and here you can see a pseudomembrane from a C. diphtheria infection.

The next actinobacteria that we're going to talk about is mycobacterium. Mycobacterium can be differentiated from other gram positive bacteria by acid fast stains. When you do an acid fast stain, these microbes appear pink.

These are aerobic rods that sometimes form filaments. They grow really slow. I've talked about this in class before. They can take up to 28 days to grow a colony on a plate. The slow growth is partially due to the mycolic acid in its cell walls.

Some species are pathogens to animals and humans, including Mycobacterium tuberculosis, which we'll talk about in a few lectures. The only other actinobacteria that we're going to talk about is actinomyces, and we talked about these earlier. These are spore formers, and here you can see those spores once again here and here. These are the vegetative cells of actinomycetes, and these are the spores. These can cause disease primarily in immunocompromised patients, so if your immune system is working well, you will likely not get sick from actinomyces.

These are important genres include actinomyces, nocaria, and streptomyces. Streptomyces recycle nutrients in the soil and are really important antibiotic producers. Nocaria is soil and water drilling aerobes that can degrade a variety of pollutants. And then actinomyces normally present in the oral cavity and throats of humans.

So that's it for the gram-positive bacteria. Now we're going to move on to the gram-negative proteobacteria. These are the largest and most diverse group of bacteria.

So we're going to discuss many of these different groups. Starting out with our alpha proteobacteria. You'll note that we are going to talk about alpha, beta, gamma, and delta, and epsilon proteobacteria.

So keep track of this part of this word. This is alpha proteobacteria. First up are the nitrogen fixers.

These are often found in soil. So here we have nitrogen fixing bacteria that can convert nitrogen from the air into ammonia. An example of this is azospirulium which produces chemicals that aid in nutrient uptake and rhizobium which produces ammonia which aids in plant growth and root production.

And over here you can see a root from a plant. And then we have nitrifying bacteria. These are another type of alpha proteobacteria. These are able to take that ammonium from these nitrogen fixing bacteria that produce ammonia and that converted into ammonium. These nitrifying bacteria can take the ammonium and turn them into nitrate.

This nitrate can be taken up by roots and used as a organic and use this compound to help the roots grow. And then that nitrate can be denitrified and turned into nitrogen. that's found in the air. Nitrifying bacteria oxidates nitrogenous compounds, providing electrons.

They're important to the environment and for agriculture, and as you can see here with this root, they convert reduced nitrogenous compounds into nitrate, which is called nitrification, and a great example is Nitrobacter. Alpha proteobacteria also includes some pathogenic microbes such as Rickettsia. Rickettsia is transmitted through a bite of an arthropod, which is a type of insect. It causes several human diseases including rocky mountain spotted fever seen here. This is an image of Rickettsia.

Another type of alpha proteobacteria is Brucella. This can cause brucellosis. It survives phagocytosis by white blood cells which helps it spread throughout the body. And so here you can see the symptoms with the clinical manifestations of grecelliosis, and you can see that it affects just about every part of the body. Now we're moving on to our beta proteobacteria.

These are mostly pathogenic microbes, including Neisseria. Neisseria gonorrhea is a sexually transmitted bacteria that we're going to talk about in the very last chapter of our book. It inhabits the mucous membranes of mammals and can cause numerous diseases depending on which species of Neisseria you're discussing. This is Neisseria gonorrhea which is caused by sexually transmitted disease. But there are other species of Neisseria that can infect the brain and other parts of the body.

Here we have Bordetella. Bordetella causes pertussis. These are the ciliated cells in the...

in the airway of a mammal. This bacteria will attach to the cilia and kill the cilia, leading to an inability to breathe. And then down here we have Burkholderia. Burkholderia is able to colonize moist environmental surfaces and respiratory passages of cystic fibrosis patients, so patients who produce a lot of salt and very thick mucus. It's a bacteria that can infect both animals and humans through direct...

contact via inhalation, ingestion, or open wounds. One of the nasty things about this bacteria is that the infection incubation period can be anywhere from a couple of days to a couple of years. This allows people to be infected without realizing it. The bacterium can also manage to survive outside of a host cell organism, allowing it to spread that way as well. Okay, moving on to gamma proteobacteria.

There are a lot of different gamma proteobacteria. Here I'm showing a dichotomous key to help remember the different types of gamma proteobacteria. We're not going to talk about this one. We are going to talk about purple sulfur bacteria up next. Legionella will talk about Fibrio pseudomonas enterobacteria and some of these others.

So let's start with gamma proteobacteria. These include purple sulfur bacteria. so it's purple and it uses sulfur in for the two of these are obligate anerbose they're able to oxidize hydrogen sulfur hydrogen hydrogen sulfide to sulfur they're found in sulfur rich zones because they need that sulfur they're also found in lakes fogs and oceans here i'm showing a worm that is completely covered in gram positive i'm sorry gram not gram-positive, but in these gamma proteobacteria, these purple sulfur bacteria. Another type of gamma proteobacteria are intracellular pathogens. Legionella causes Legionnaires disease, and we'll talk about that when we get to diseases of the lungs.

Coxillia causes Q fever. This is a flu-like sickness caused by Coxillia burneti. It infects goats, sheep, cows, and other animals.

then those animals are able to spread this infection to humans through the wind. They survive. These are both pathogens that can survive within white blood cells. White blood cells circulate throughout the body, so when these microbes get into the body, they can circulate and cause many different symptoms.

The glycolytic facultative aneurysms are the largest groups of gamma proteobacteria. They're able to take in carbohydrates and break them down into an energy form using glycolysis and the pentose phosphate pathway. So hopefully you can remember those pathways from the chapter on metabolism.

They're divided into three families. The Enterobacteriaceae include straight rods, oxidase negative to treat microbes that have Peritrichous flagella, so flagella that are all over the body or they can be non-modal. There are many different genres within the Enterobacteriaceae and you'll note that a lot of these can cause disease in humans.

These two are rarely pathogenic to humans. Vibrio naceae are Vibrio, so remember that comma shaped bacteria. There are many different types of Vibrio. One example is Vibrio cholerae that can cause cholera in humans. And we'll talk about that one when we get to diseases of the digestive system.

And then there are Pasteuraceae. These are, one example of that is Haemophilus, which causes meningitis in children, middle ear infections, and pneumonia. The last type of Gamma proteobacteria that we'll talk about are Pseudomonads.

These are able to break down numerous organic compounds that are important pathogens of humans and animals. This is a great example of Pseudomonas. There are many different species of Pseudomonas.

Some of them cause disease in humans. Pseudomonas can cause urinary tract infections, ear infections, and lung infections. And we'll talk about Pseudomonas in terms of skin infections in a couple of lectures.

Other examples of gamma proteobacteria that are pseudomonads are Azovacter and Azovonus, which are non-pathogenic, so they don't cause disease, and they live in the soil. Moving on to delta proteobacteria, we're going to talk about the Sulfovibrio. This is a vibrio, so you can see that these are comma-shaped.

These also happen to have flagella. They recycle sulfur in the environment and they are able to contribute to the corrosion of iron pipes. And in fact, that's what we see here. These are images of iron pipes used in plumbing and you can see that these are degrading and that is due to desulfovibrio. Another example of a delta proteobacteria are delavibrio.

These are fascinating little microbes because these are a pathogen of gram-negative bacteria. So it's a gram-negative bacteria that can cause disease in other gram-negative bacteria. So here we have a gram-negative bacteria.

Belovibrio is able to enter into this bacteria by getting through the outer membrane. It replicates within the gram-negative bacteria. And within 20, within... a short period of time, individual daughter cells from this Delivibrio are able to break out of that gram-negative bacteria to infect a new gram-negative bacteria.

Okay, the last Delta proteobacteria that we'll talk about are the Myxobacteria. This is the life cycle of Myxobacteria. It's a fascinating microbe because it can live individually, but it can also form these mounds of cells.

So this is not one big organism. This is lots of individual vegetative cells, actively replicating metabolizing cells. They form these mounds when there are very few nutrients around.

Then these mounds can come together and form fruiting bodies that produce these pharyngeums. and these can release these myxospores. These myxospores can spread through the air and find a nutrient-rich area and then form these vegetative slime trails.

These vegetative cells can form slime trails. replicate by binary fission and then when they deplete all the nutrients in that particular area they form more mounds and the cycle repeats. So those are the myxobacteria.

That's it for the Delta proteobacteria. Now let's move on to the Epsilon proteobacteria. We're only going to talk about two of these.

The first one is Campylobacter that can cause blood poisoning and intestinal inflammation. We'll talk about these when we get to intestinal diseases. And then helicobacter is a gram-negative epsilon proteobacteria that can cause ulcers and cancer in a small subset of patients who have helicobacter.

And we're going to talk about these in much greater detail in a few lectures. Okay, other types of gram-negative bacteria include chlamydia. Chlamydia are obligate intracellular microbes, intracellular meaning that they can replicate within another host cell. So here we have the life cycle of chlamydia. An elementary body enters into a host cell.

The elementary body transforms into a reticulate body. That reticulate body replicates within the cell and transforms back into these elementary bodies which are released and they can infect new cells. They can grow in mammals, birds, and some in vertebrates. Some of them are smaller than viruses and they are the chlamydia is the most commonly sexually transmitted bacteria in the United States and we'll talk about that more when we get to the last chapter of the last lecture of this class.

Okay, we are almost done. The next type of gram-negative bacteria that we're going to talk about is the spirochetes. You'll remember these from one of the earlier lectures where we talked about microbes that have endoflagella and can move in corkscrew-like fashion.

Those are the spirochetes. These are flexible organisms that have this wavy look to them. They're modal, as I just said.

They have diverse metabolism and habitats. That just means they can eat lots of things, convert them to energy, and they can live in lots of different places. Two of the spirochetes that are able to cause disease in humans are Trepanema and Borrelia. Trepanema causes syphilis, which you can see here, and we'll talk about that when we get to the last lecture of the class.

Borrelia causes Lyme disease, and we'll talk about that when we talk about diseases of the nervous system. The last group of bacteria that we're going to talk about are Bacteroides. These are able to live in the digestive tracts of humans and animals. Some of these species are also able to cause disease. And then Cytophagia are aquatic gliding bacteria that are important to the degradation of raw sewage.

And that's it! If you want to learn a little more about spore formation, you can check out this YouTube video. That's it.

Thank you.

Transcript for:Biology Exam Preparation and Bacterial Classification

Transcript for:
Biology Exam Preparation and Bacterial Classification