Microorganisms and Carbon Cycle in Oceans

The last discussion question we talked about, I left those up and people wanted them, right? And we had just finished talking about the oceans. And we had talked about polygobacteria ubilicae, and we had talked about photosynthetic bacteria. Now, of course, there's lots of other things in the ocean, in the phytoplankton and the plankton. And there are lots of algae. And photosynthetic eukaryotes that also make up the microbial plankton that's available in the oceans. Okay, so I just want to mention that, but I won't cover it in this class so much. One of the really interesting things is it seems like what dominates in aquatic environments has to be able to take advantage of the light energy that enters the system. Actinobacteria, AC1, right? That has actinorhodopsin. Polygobacter ubique has its own proteorhodopsin, and it helps its energy. And then the cyanobacteria have that also. And just as a side, something you don't need to remember, but I think this is really interesting. When they... You know, biologists and biologists would sum up all the energy coming into the ocean that they knew about. And they count all the oceanic plants and they count the phytoplankton. And they'd say, well, there's this much energy coming in. And then there's this food web that depends upon it, right? There's small animals that eat the plankton. Whales eat the plankton. And it goes up through the full food chain. And they realized. There are way more higher organisms that were feeding off of what we knew about than we can account for. They couldn't account for all the food that was being generated until we discovered the rhodopsins, and then that balanced the equation. And that was only discovered in the last decade, so that's interesting. All right, now we're going to take a deep dive into the ocean, and we're going to go to deep-sea ocean vents. So if I hope you watch the videos I posted because the best way to experience These areas is to actually what? See video of it and the thing that's really amazing to me is that these systems are available that they exist. And can you imagine in 77 when these guys went down, and these are a bunch of geologists mostly, and they went down there just to see the geological formation and then when they looked at it there's all these living things down here. It was a huge discovery. So what's available in deep sea ocean vent? The physical environment, so there's volcanic activity between the plates, the temperature is about five to four hundred degrees centigrade. The oceans are about 5 degrees centigrade on average, but anything near it, the temperature increases. The pH will be acidic to neutral depending on the ocean vent. The water seeps into cracks around the vent, picks up hydrogen sulfide, iron, sulfur, ammonia, methane, and hydrogen from the magma and re-enters through chimneys, and there's over 500 known systems. And these have been characterized, and they're all along the tectonic plates in the ocean. And here's a diagram of that. You can see that here is sediments and stuff, and the seawater seeps into these cracks, and the magma's down here, and it will superheat this water. And so the water comes down because it's cold, and then it gets warmer, starts going up, and it will reenter in places of least resistance, and then these chimneys form. And the chimneys form from the sediments depositing. So very close to the Gemini, it's 350 degrees centigrade and nothing grows. That's too hot. But very quickly, as you move away from it, it'll get down into the 100 degree centigrade range. And as it happens, all of this stuff precipitates out. So you have all these compounds, and a lot of them are reduced compounds that have a lot of high energy electrons in them, right? And this whole system, instead of being charged by the sun, like... everything on the surface of the earth is this system depends on something completely different and it's the energy of the magma the earth's core so that that's completely different and if something happened to our sun or we you know the the planet got destroyed by a comet These systems would survive. If you haven't watched the movie, don't look up. I recommend it. It's pretty funny if you like dark humor. Alright, so, chemistry available. What's available? You have all these really good electron donors. And we've talked about some of these. Hydrogen, ammonia, hydrogen sulfide, methane. All these really good electron acceptors. Remember before when I said there's oxygen. at the bottom of the deep sea, right? Because of downwelling, and then there's nothing to use up the oxygen until you get to these deep sea ocean vents. So there is oxygen there. There's also nitrite and nitrate, which are good electron donors. Iron is actually not a bad, I'm sorry, oxygen, nitrate, and nitrate are good electron acceptors. And then there are other ones too, right? And if you think back to what you've learned about the electron tower and respiration, you can recognize some of these pairs, right? Hydrogen gas can pair with oxygen. Methane can pair with oxygen. We talked about ammonia pairing with oxygen, etc. So many reactions are possible. And as I've told you before, and I hope you've learned in this class, If there is a reaction that is chemically favorable, there will be a microorganism that takes advantage of it. Okay, so now let's ask you a question and see if you picked up what I'm throwing down here. What is available in the deep sea to use as a source of energy? Thank you. Give people a little bit more time. Okay. All right. So here is how people responded. Okay. People said, some people said, oh, there's probably organic compounds. A lot of people said inorganic compounds. And most people said inorganic compounds and organic compounds. And the right answer is inorganic compounds and organic compounds. So there are chemoautolithotrophs that will take these. And they will generate cells from them, cell carbon, and they'll generate cells. Well, those die, so there's going to be organic compounds available also. So good. And two people chose stickers bars. All right. Alright, so what are the kind of things that you see? What are the kind of organisms that you see? You see sulfide oxidizers, and what they will do is they'll take hydrogen sulfide and oxidize it to sulfate and couple that with the reduction of oxygen to water. You will see methanogens. Methanogens take hydrogen gas again, and they will convert with CO2 as the electron acceptor. and they will make methane. You will also see methylotrophs that do the opposite reaction. Right, so methane is produced by the deep sea ocean vents and also the methanogens make more methane. They will take the methane plus oxygen and convert it into water and CO2. And we'll be talking more about methylotrophs later. And then you have hydrogen oxidizers, organisms that will take hydrogen Couple it to sulfide or sulfur and make hydrogen sulfide. Some examples of the kind of organisms that you find here are Methanococcus genotii. Right? And here is just a little cocci, and these are found in deep sea ocean vents and can grow over 100 degrees centigrade. And Pyridicium abyssii, this is what it looks like when grown in liquid culture. It has a growth maximum over 100 degrees centigrade and can grow to temperatures of over 113 degrees centigrade. So 13 degrees above the temperature that... water would boil on the surface. Of course, water doesn't boil at deep sea ocean vents because the pressure is much higher. Water can be hundreds of, you know, three, four hundred degrees down there. So here, and then it makes really interesting things. Here's the cell right here, and then all this other stuff is like this lattice it makes for its cells to grow in. So it makes its own little lattice, and this is what it looks like in a broth culture. So interesting. Now, those are just some examples I told you about. I want you to understand that these kind of chemolithotrophic reactions can take place, right? But I do want to focus on a few organisms just to give you an idea of some of the players. We're going to focus on two. One of them is Geoglobus ahangari. This is a earcheota, so it's an archaea. It is a modal caucus which is very unusual and is a thermophile. It grows from 65 to 90 degrees centigrade. Here's a little electron micrograph of it. You can see it's a little cocci. It shows the cytoplasmic membrane and then it also has a surface layer. That's what the S stands for. It uses iron as its terminal electron acceptor and it can grow using hydrogen as the electron donor. So if you go look at the electron tower that we've used before, you'll see hydrogen at the very top of that tower. You'll see iron just above water. So iron is a very good electron acceptor. So it takes hydrogen gas and it reduces iron 3 plus to iron 2 plus. Now, it can also grow chemohedrotrophically on acetate. So it's an important... acetate user in these environments. So that's an example of a chemolithotroph that's growing in a deep sea ocean vent and it's producing, it is a primary producer in this environment. Okay, alright so let's see if you can relate this. to something you've learned before. What do Geoglobus, a Hungarian, and Prochlorococcus have in common? Okay, I'm going to close this for a second and end this. So now let's try that again. Okay, let's close this again and let's go back because Dr. Postian forgot to mention something, right? Geoglobus of Hungary. It's actually when if it's a chemolithal autotroph, okay, it's an autotroph also. And I forgot to mention that, right? So it'll get most of its carbon from carbon dioxide, all right? It is not, all right? So I've forgotten to mention that. That's why we do top hat questions. It's one of the reasons. Okay, so let's begin again. Okay, here are your responses. And the correct answer is, they both use carbon dioxide as their source of carbon for the most part. Prochlorococcus, remember, is a photosynthetic bacterium, so it gets its energy from the sun. So, Prochlorococcus does not live in the deep sea. Okay, now another example I want to give you of a deep sea organism, a microorganism, is Thermococcus atlanticus. This organism is also an archaea, is an obligate anaerobe and a thermophile. However, it is a heterotroph that grows on proteinaceous substances, proteins, peptides, amino acids. So it actually will metabolize those and there are a few species that can use carbohydrates. Now this organism can grow at very high temperatures, right? And actually these are of great interest to biotechnology. So here is Thermococcus. Obviously it's a cocci, right? High temperature, obligate anaerobic. but can grow on proteinaceous substances. They're a great interest to biotechnology. Why aren't they interested in things like Geoglobus ahungari? Well, those organisms grow on difficult things like hydrogen gas. Hydrogen gas is explosive, so you don't want to have a giant fermenter, a million liter fermenter that you have to pump hydrogen gas in, because if you make a mistake and hydrogen gas gets out into the environment, boom, you know, it's not great for your plant if it explodes. A lot of the time they're not interested in growing organisms like that. This guy, right, will grow on very simple substrates. There's lots of waste protein we can use, right? And that waste protein can be used to grow this and then you can get and isolate the enzymes from it. Some of the enzymes we use in biotechnology now for PCR actually comes from organisms like this. Okay, one more organism we're going to cover at the deep sea, and then we're going to talk about the carbon cycle, right? And this is tube worms, and this is a great example. Many of the macro organisms that grow in this environment are actually feeding off of the bacteria that grow. You know, again, there's a whole food web, and that there's tiny little animals that feed off the bacteria, and then those animals are eaten by little bigger animals, little bigger animals. And you actually get shrimp and crabs and all sorts of stuff here. But there are also things like tube worms and mussels that actually have symbiotic relationships, mutualistic relationships with bacteria, and they thrive that way. So the worm uptakes CO2 and hydrogen gas using a hemoglobin protein. So it has a hemoglobin protein that is, and it has a circulatory system shown here. and it has a little heart that pumps it, right? And in this circulatory system, it will have, you know, these proteins that will bind CO2 and H2S, and that delivers it... two tissues in the organism. So here is the feeding body right here, and inside these tissues, you will have bacteria. And this bacteria is a mutualistic symbiont. So this is a beneficial relationship for both. The tube worm provides, you know, shelter and a source of food for the microorganism. And in return, The symbiont, the bacterial symbiont, oxidizes the H2S and fixes the CO2 into cell carbon and then shares that organic matter with the tomb worm. And these things are gigantic. They are, you know, they can be up to three meters tall, right, so they're very big. They're very big organisms. When the ships, the vessels, the submarines came down to the surface and they landed, they expected to hear a scrape when they landed on the surface. Like when these vessels would go down to the bottom, they'll hit the rocks and they'll scrape a little bit so they know they hit the bottom. Instead, when they hit the bottom, it went skoomch, and then blood came up around the portholes. of them, which kind of freaked them out. They're like, what's going on? And what they had done is they had landed in a tube worm patch and had hit the molecules. And as soon as the blood was released, it turned red. So that's the tube worms. All right, after that fun story, the last thing I'm going to cover is the carbon cycle. Fun fact, where does carbon come from? It comes from fusion in stars, right? The universe in the beginning was a lot of molecules, not even molecules, a lot of elementary particles floating around that then organized into atoms and they organized in hydrogen gas. That hydrogen gas would get pulled together, it forms stars. You know, you don't have to remember any of this, but I just think this is interesting. Forms stars and then hydrogen fuses into helium under the gravity weight of the star. And you get more and more fusions and all sorts of stuff gets made. And one of the things that gets made is carbon. When the star explodes, that gets released into the environment. If you look at the carbon on Earth, 99.5% of it is in rocks and sediments. 80% of that is inorganic. So most of the carbon on Earth is not in organic systems, right? The oceans have a little bit. Methane hydrates have a little bit, fossil fuels have a little bit, the terrestrial biosphere has almost nothing. So you can see that most of the carbon in our environment is locked up in sediments and sitting on the surface and it's not in living systems, right? When we talk about the carbon cycle, we're talking about the cycling of carbon through living systems. So a lot of it's in the soil and humus and fossil fuels. When those get used or burned, it goes into the atmosphere. That will come back into land plants. It will also come back into aquatic environments, plants and phytoplankton. So carbon is a really interesting molecule. So the carbon that we're going to be mostly concerned about here is the carbon that's is by conversions of different microorganisms. And they will act on things like CO2. They will reduce the CO2 to organic carbon that then is used in cells. Heterotrophs will use that, right, to build their cells. The autotrophs will use it to make organic carbon. But there's also a whole class of organisms that can take methane. The methanotrophs convert that into organic carbon. Methane is a very reduced molecule, right? And they'll use that to generate energy and also organic carbon, right? Again, remember that carbon is about 50% of the cell's dry weight in all organisms. So carbon dioxide reduction is called fixation. Methane use is called methane oxidation. Now... We're going to talk a little bit about autotrophic pathways. These are pathways that take CO2 and fix it into cell carbon, carbon fixation. If you have taken a biology class that involves plants, you have been taught the Calvin cycle, right? And let's see, where is that? The reductive pentose phosphate cycle, a.k.a. the Calvin-Benson-Basham cycle. That's the classic one that gets hot. That's what's done in plants. There's actually one, two, three, four, five more known pathways that have been discovered in microorganisms that can fix CO2 into cell carbon. I do not expect you to remember these. I just want you to know that carbon fixation can happen in many different ways. We are going to talk about one, which is the reductive acetyl-CoA pathway because it involves an organism that I'm interested in, or that is interesting for the class. And there are very important organisms that do it in different places. Autotrophic microbes are very common, right? We've discovered more and more of them as we've gone on. We've talked about cyanobacteria. We've talked about green non-sulfur and green sulfur bacteria, and all the different things that these do. And these are just some examples. And these are photoautotrophs. But there's a bunch of chemolithoautotrophs. Nitrifiers. And we talked about nitrifiers and we talked about the nitrogen cycle, right? And these are organisms that will take nitrate and convert it into ammonia. I'm sorry, they'll take ammonia and convert it into nitrate. Sorry, I got it backwards. There's also hydrogen oxidizers. And there's sulfur oxidizers. These are reduced compounds, ammonia, hydrogen, sulfur, that are in the environment that organisms can take advantage of. Now, I think it's useful to give you an example of one other CO2 fixation pathway besides the Calvin cycle that you may have run into. Right? So why this one? It's probably the easiest to understand, and it's used in a significant number of chemolithal autotrophs. Methanogens will use it. There's other organisms that will use it. So what is it? You take CO2, and it depends on hydrogen gas and carbon dioxide. If they're in a present environment, you can use them. So it'll take CO2. And it will build one half of acetyl CoA, so it will make the methyl group. So CO2 is reduced by successive hydrogen reductions. Hydrogen is oxidized, the carbon is reduced, and you get methane on tetrahydrofolate. Tetrahydrofolate, you guys ever heard of the vitamin folic acid? Yes? That's what it's used. It's a one carbon carrier. You actually use it in your metabolism, but not to do this. So tetrahydrofolate has it, and you just reduce it to methane. The CO2 is reduced by carbon monoxide dehydrogenase, the CO, and this is put on the acetyl-CoA synthase complex. The CO2 goes on, the methane comes on, and with the use of an ATP, this makes acetyl-CoA. Right? So one other thing that's really interesting about this pathway is while it uses hydrogen gas, which is a high energy compound, it requires very little ATP to make acetyl-CoA. So in the Calvin cycle you take CO2 and you make ribulose, you make RuBisCO, right? Right? And then the RuBis- that is then turned and you actually end up taking out glyceraldehyde 3-phosphate. So another 3-carbon compound. And this time, you take out a 2-carbon compound called acetyl-CoA. Alright, so that's that pathway. And what I want you to remember is this. I don't want you to remember like the steps of the pathway or memorize any of the names that are given here. I want you to know that there are other ways of fixing CO2. And one example I gave you is the reductive acetyl-CoA pathway. It starts with CO2 and it uses hydrogen and one ATP to make acetyl-CoA. That's what I want you to get out of that. Starts with CO2, uses hydrogen, and it makes one acetyl-CoA at the cost of one ATP. Okay, finally, our last topic is methylotrophs. So we talked about the part of the pathway where CO2 is converted into organic carbon. We're now going to look at a part of the pathway where methane is converted into organic carbon. Methylatrophs oxidize methane and other C1 molecules as electron donors. This is the electron donor, right, and in their energy metabolism and as carbon sources. They are typically proteobacteria. They grow by aerobic respiration. And here is they have a lot of this process takes place in the membrane. And therefore because of that they need a lot of membranes. And they'll have these internal membranes that house the machinery for respiration. Okay, so this is how it works. So this is a the methyl monooxygenase is actually in the cytoplasm, right? The hydrogens will come in and when they're fixing hydrogen and right, they're fixing cell carbon. What they'll do is they'll take the CO4 methane and they'll oxidize it. You can see they're going through oxidations here and they'll oxidize all the CO2. And then as this goes through. This makes NADH. And you can guess where the NADH goes. It goes into electron transport chain. This is the same electron transport chain we talked about before. And that ends up pumping protons across the membrane and synthesizing ATP. So instead of using glucose and proteins and all the stuff that you eat to generate this proton gradient, This organism uses an enzyme methyl monooxygenase and then a few other enzymes to make CO2 Dumps the electrons under NADH and those electrons then go through the similar electron transport chain It's just using a different source. Okay, so methyl monooxygenase MMO is really important in this process. But again, look After you figure out the source in this little reaction here, the rest of the game is exactly the same. And that's how it works. Okay, so why can you do this? Well, if you look at the electron tower and you look at methane, it's right here, methane to CO2 is pretty high on that electron tower. Oxygen is very low. on that electron tower, okay? So wait a minute. So the aerobic methane oxidizer on there, but if you look, nitrite is actually pretty low on this tower too. And this reaction, you know, if oxygen is not around and you're in an anaerobic environment, but nitrite is present, this should probably work, right? Well, sure enough, they started looking for this, and they found it in 2010. A bacterium was found in anoxic sediment that could do this. Methylmerabilis oxyferra, and it uses methane as a carbon and energy source, and it uses nitrite as its electron acceptor, not oxygen. So it grows in environments where oxygen is not... present and in those environments and then again here's some cool diagrams of what this organism looks like right and it's a little bit of a bent rod and here's what it's doing right so it's kind of interesting it takes nitrite and it uses some of the electrons from the electron transport chain to reduce nitrite to nitrogen gas and oxygen NOD, nitric oxide dismutase, splits the nitrite, or the NO, right, into nitrogen gas and oxygen. It takes two NOs and splits it in nitrogen gas and oxygen, and then has the oxygen... to the PMMO, which is a paramplasmic, right, or it's a particulate methyl monooxygenase that hangs out in the membrane. So the only thing different than what I just showed you before is it starts with nitrite, makes its own oxygen from that, and then goes through the oxidation of methane, right? You get cell carbon the same way, you just can pull in the acetate, and then you use the same whole electron transport chain as you did before. So again, it's just a cute little way, and I just wanted to show you that, of an organism doing something anaerobically and just adding two enzymes to this whole process to get what it needed to do the reaction. Okay! So now we're going to talk a little bit about the carbon cycle and what's going on as far as the increase in CO2 in the atmosphere. And I want you to look at the whole global carbon cycle as shown here. If you take everything that's on here, and the black is the pre-industrial sinks and producers. So this is before humans started burning fossil fuels and putting them in the environment. And you look at the fluxes, right? The total, the red is post-industrial anthropogenic, and the total is 829 petagrams, right? The flux out, so when you add that all up, there's actually 10.7 petagrams difference. The total flux out is 10.7, right? And then there's 6.9 in. You know, just moving of the flux. So the 3.8 is a net addition. So if you look at the total flux through the pathway, through all of the carbon cycle here, and you look at the amount, the net addition, it's just 0.46%. So the amount going through the carbon cycle is huge, but we're adding a small amount every single year. And that's what the problem is, and that has effects. Note where microbes have a role, both out in respiration. So you see microbes, you know, there's respiration, there's burning, but there's also just metabolic activity and in photosynthesis. There's a lot of photosynthesis that happens in the oceans. There's a lot of photosynthesis that happens on the land. Okay, so why do I point that out? I want you to realize the amount that we are adding is very small, and that while it is a bad thing to do this, it's easily reversible just by making changes. We either increase the flux in somehow, or we decrease the flux out. All right, so in summary, there is a diversity of organic carbon metabolism. Right? You have proteins, polysaccharides, nucleic acids, and lipids. There's secreted enzymes that make these into monomers. All that organic things, carbon, can then be pulled in and used in central metabolism. You can do this with organic acids, alcohols, aromatic compounds, linear hydrocarbons, depending on the organism. And you get all sorts of stuff in central metabolism. You can use this to make carbon, right, and stels. You can also use it in your energy metabolism. All of this kind of stuff is taking place in cells, and there's a huge diversity of metabolism in microorganisms. Okay, since I still have 10 minutes, that is the end of what is going to be on the exam. But since I still have 10 minutes... I thought we could begin immunity, and I have posted our relationship with microbes, and so we can do some introductory comments on this. All right, so the last unit focuses on our relationship with microbes, and it's going to talk about... The microbes that associate with us, most of the ones that are beneficial, and it's going to talk about the pathogens. But the first thing I thought I'd talk about... When we talk about this, is I would talk about how do we defend ourselves against microorganisms and our immune systems. If we didn't have an immune system, and unfortunately there are poor, you know, unfortunate individuals that have mutations that they can't produce an effective immune system, they will die without huge interventions immediately or very quickly from all the bacterial infections that they get. All right, so here's the learning outcomes. So let's do a preconception. What do you think? Okay, so where do you think the immune system is? The immune system is found mostly in the blood and circular system. True or false? Okay, very good. We're pretty split. This is a common misconception. The correct answer is false. A lot of the immune system is not in your circulatory system. In fact, 70%, over 70% of your immune system is associated with your gastrointestinal tract, which makes perfect sense. This is a tube that goes through your body and there's a ton of stuff. that you eat that's full of microorganisms that your body has to protect you against. So it's not surprising that a lot of your immune system is around your gastrointestinal tract. I do that just to make you realize there's a lot of cool stuff we're going to learn when we talk about the immune system. All right, so let's talk a little bit of an overview of the immune system for a few minutes. There is a number of different parts of the immune system, and there's lots of parts that people don't think about. What do you guys think about when you think about immunity? White blood cells? What else? It starts with an A. Antibodies, right? Everybody thinks about antibodies. During the COVID-19 pandemic, a lot of researchers got involved in doing stuff with immunity that didn't know a lot about immunity, and they did experiments. that someone who didn't know a lot about immunity would do. So they'd focus on antibodies and not focus on other parts of the immune system. It was pretty interesting. Not that I'm an expert in it, but I wasn't writing grants for it. So overview, you have physical barriers, right? You have all sorts of antimicrobial mechanisms in your body that stop bacteria from growing. from your skin to your eyelashes to movement of material through your system, right? You have mucous membranes, and we'll talk about how those are used. You have other parts of the innate immunity, phagocytosis, which is part of what some white blood cells do. You have the inflammatory response that is really important. You then have acquired immunity, and this is specific adaptive immunity that fights infections for you. One thing that's really amazing about your immune system, you guys ever heard of the movie The Andromeda Strain? It was a book, and it's like some horrible disease comes from outer space and wipes out all humans. Your immune system would be able to stop a pathogen that came from outer space. And you'll understand that as we go through this, right? Okay, and that is because of a required specific adaptive immunity. There's antibody-mediated immunity, B cells, and cell-mediated immunity, T cells. All right, so let's go through a little bit of an immune system introduction for just a minute. All right, so what does the immune system do? The immune system can identify things that are not you that should not be there, right? And this is an identification of self, right? The immune system must differentiate self from non-self because you don't want your immune system attacking your own tissues. That's called an autoimmune disease and those can be very bad. Right? You may think, well, wait a minute, why is it so hard to tell the difference between a bacteria and me? We're obviously different. But at the molecular level, you're made of the same things. Here is the structure of lysozyme, an enzyme that you make. Here is the structure of tetanus toxin. And yeah, they look different, but they're both proteins. And at the molecular level, they can be more difficult. to differentiate. If you have lysozynes in your system, you're fine. If you have technotoxin in your system, you're not fine. Alright? The immune system creates lymphocytes that respond to many macromolecules. When created, they collectively respond to both self and non-self, but the ones that respond to self are eliminated. And we'll go through that whole mechanism when we talk about it. Again, cells are the proteins, sugars, and lipids floating around that are part of our body and are accessible to the immune system. Okay, why don't I end there and we'll pick it up on...

Now, of course, there's lots of other things in the ocean, in the phytoplankton and the plankton. And there are lots of algae. And photosynthetic eukaryotes that also make up the microbial plankton that's available in the oceans. Okay, so I just want to mention that, but I won't cover it in this class so much.

One of the really interesting things is it seems like what dominates in aquatic environments has to be able to take advantage of the light energy that enters the system. Actinobacteria, AC1, right? That has actinorhodopsin.

Polygobacter ubique has its own proteorhodopsin, and it helps its energy. And then the cyanobacteria have that also. And just as a side, something you don't need to remember, but I think this is really interesting.

When they... You know, biologists and biologists would sum up all the energy coming into the ocean that they knew about. And they count all the oceanic plants and they count the phytoplankton. And they'd say, well, there's this much energy coming in.

And then there's this food web that depends upon it, right? There's small animals that eat the plankton. Whales eat the plankton. And it goes up through the full food chain. And they realized.

There are way more higher organisms that were feeding off of what we knew about than we can account for. They couldn't account for all the food that was being generated until we discovered the rhodopsins, and then that balanced the equation. And that was only discovered in the last decade, so that's interesting. All right, now we're going to take a deep dive into the ocean, and we're going to go to deep-sea ocean vents.

So if I hope you watch the videos I posted because the best way to experience These areas is to actually what? See video of it and the thing that's really amazing to me is that these systems are available that they exist. And can you imagine in 77 when these guys went down, and these are a bunch of geologists mostly, and they went down there just to see the geological formation and then when they looked at it there's all these living things down here. It was a huge discovery. So what's available in deep sea ocean vent?

The physical environment, so there's volcanic activity between the plates, the temperature is about five to four hundred degrees centigrade. The oceans are about 5 degrees centigrade on average, but anything near it, the temperature increases. The pH will be acidic to neutral depending on the ocean vent.

The water seeps into cracks around the vent, picks up hydrogen sulfide, iron, sulfur, ammonia, methane, and hydrogen from the magma and re-enters through chimneys, and there's over 500 known systems. And these have been characterized, and they're all along the tectonic plates in the ocean. And here's a diagram of that. You can see that here is sediments and stuff, and the seawater seeps into these cracks, and the magma's down here, and it will superheat this water. And so the water comes down because it's cold, and then it gets warmer, starts going up, and it will reenter in places of least resistance, and then these chimneys form.

And the chimneys form from the sediments depositing. So very close to the Gemini, it's 350 degrees centigrade and nothing grows. That's too hot.

But very quickly, as you move away from it, it'll get down into the 100 degree centigrade range. And as it happens, all of this stuff precipitates out. So you have all these compounds, and a lot of them are reduced compounds that have a lot of high energy electrons in them, right? And this whole system, instead of being charged by the sun, like... everything on the surface of the earth is this system depends on something completely different and it's the energy of the magma the earth's core so that that's completely different and if something happened to our sun or we you know the the planet got destroyed by a comet These systems would survive.

If you haven't watched the movie, don't look up. I recommend it. It's pretty funny if you like dark humor.

Alright, so, chemistry available. What's available? You have all these really good electron donors. And we've talked about some of these.

Hydrogen, ammonia, hydrogen sulfide, methane. All these really good electron acceptors. Remember before when I said there's oxygen. at the bottom of the deep sea, right?

Because of downwelling, and then there's nothing to use up the oxygen until you get to these deep sea ocean vents. So there is oxygen there. There's also nitrite and nitrate, which are good electron donors. Iron is actually not a bad, I'm sorry, oxygen, nitrate, and nitrate are good electron acceptors.

And then there are other ones too, right? And if you think back to what you've learned about the electron tower and respiration, you can recognize some of these pairs, right? Hydrogen gas can pair with oxygen.

Methane can pair with oxygen. We talked about ammonia pairing with oxygen, etc. So many reactions are possible. And as I've told you before, and I hope you've learned in this class, If there is a reaction that is chemically favorable, there will be a microorganism that takes advantage of it.

Okay, so now let's ask you a question and see if you picked up what I'm throwing down here. What is available in the deep sea to use as a source of energy? Thank you.

Give people a little bit more time. Okay. All right. So here is how people responded.

Okay. People said, some people said, oh, there's probably organic compounds. A lot of people said inorganic compounds. And most people said inorganic compounds and organic compounds. And the right answer is inorganic compounds and organic compounds.

So there are chemoautolithotrophs that will take these. And they will generate cells from them, cell carbon, and they'll generate cells. Well, those die, so there's going to be organic compounds available also.

So good. And two people chose stickers bars. All right.

Alright, so what are the kind of things that you see? What are the kind of organisms that you see? You see sulfide oxidizers, and what they will do is they'll take hydrogen sulfide and oxidize it to sulfate and couple that with the reduction of oxygen to water. You will see methanogens. Methanogens take hydrogen gas again, and they will convert with CO2 as the electron acceptor.

and they will make methane. You will also see methylotrophs that do the opposite reaction. Right, so methane is produced by the deep sea ocean vents and also the methanogens make more methane. They will take the methane plus oxygen and convert it into water and CO2.

And we'll be talking more about methylotrophs later. And then you have hydrogen oxidizers, organisms that will take hydrogen Couple it to sulfide or sulfur and make hydrogen sulfide. Some examples of the kind of organisms that you find here are Methanococcus genotii.

Right? And here is just a little cocci, and these are found in deep sea ocean vents and can grow over 100 degrees centigrade. And Pyridicium abyssii, this is what it looks like when grown in liquid culture. It has a growth maximum over 100 degrees centigrade and can grow to temperatures of over 113 degrees centigrade.

So 13 degrees above the temperature that... water would boil on the surface. Of course, water doesn't boil at deep sea ocean vents because the pressure is much higher.

Water can be hundreds of, you know, three, four hundred degrees down there. So here, and then it makes really interesting things. Here's the cell right here, and then all this other stuff is like this lattice it makes for its cells to grow in. So it makes its own little lattice, and this is what it looks like in a broth culture.

So interesting. Now, those are just some examples I told you about. I want you to understand that these kind of chemolithotrophic reactions can take place, right?

But I do want to focus on a few organisms just to give you an idea of some of the players. We're going to focus on two. One of them is Geoglobus ahangari.

This is a earcheota, so it's an archaea. It is a modal caucus which is very unusual and is a thermophile. It grows from 65 to 90 degrees centigrade. Here's a little electron micrograph of it.

You can see it's a little cocci. It shows the cytoplasmic membrane and then it also has a surface layer. That's what the S stands for. It uses iron as its terminal electron acceptor and it can grow using hydrogen as the electron donor. So if you go look at the electron tower that we've used before, you'll see hydrogen at the very top of that tower.

You'll see iron just above water. So iron is a very good electron acceptor. So it takes hydrogen gas and it reduces iron 3 plus to iron 2 plus. Now, it can also grow chemohedrotrophically on acetate.

So it's an important... acetate user in these environments. So that's an example of a chemolithotroph that's growing in a deep sea ocean vent and it's producing, it is a primary producer in this environment. Okay, alright so let's see if you can relate this. to something you've learned before.

What do Geoglobus, a Hungarian, and Prochlorococcus have in common? Okay, I'm going to close this for a second and end this. So now let's try that again.

Okay, let's close this again and let's go back because Dr. Postian forgot to mention something, right? Geoglobus of Hungary. It's actually when if it's a chemolithal autotroph, okay, it's an autotroph also.

And I forgot to mention that, right? So it'll get most of its carbon from carbon dioxide, all right? It is not, all right? So I've forgotten to mention that.

That's why we do top hat questions. It's one of the reasons. Okay, so let's begin again.

Okay, here are your responses. And the correct answer is, they both use carbon dioxide as their source of carbon for the most part. Prochlorococcus, remember, is a photosynthetic bacterium, so it gets its energy from the sun. So, Prochlorococcus does not live in the deep sea.

Okay, now another example I want to give you of a deep sea organism, a microorganism, is Thermococcus atlanticus. This organism is also an archaea, is an obligate anaerobe and a thermophile. However, it is a heterotroph that grows on proteinaceous substances, proteins, peptides, amino acids.

So it actually will metabolize those and there are a few species that can use carbohydrates. Now this organism can grow at very high temperatures, right? And actually these are of great interest to biotechnology. So here is Thermococcus. Obviously it's a cocci, right?

High temperature, obligate anaerobic. but can grow on proteinaceous substances. They're a great interest to biotechnology.

Why aren't they interested in things like Geoglobus ahungari? Well, those organisms grow on difficult things like hydrogen gas. Hydrogen gas is explosive, so you don't want to have a giant fermenter, a million liter fermenter that you have to pump hydrogen gas in, because if you make a mistake and hydrogen gas gets out into the environment, boom, you know, it's not great for your plant if it explodes. A lot of the time they're not interested in growing organisms like that.

This guy, right, will grow on very simple substrates. There's lots of waste protein we can use, right? And that waste protein can be used to grow this and then you can get and isolate the enzymes from it.

Some of the enzymes we use in biotechnology now for PCR actually comes from organisms like this. Okay, one more organism we're going to cover at the deep sea, and then we're going to talk about the carbon cycle, right? And this is tube worms, and this is a great example. Many of the macro organisms that grow in this environment are actually feeding off of the bacteria that grow.

You know, again, there's a whole food web, and that there's tiny little animals that feed off the bacteria, and then those animals are eaten by little bigger animals, little bigger animals. And you actually get shrimp and crabs and all sorts of stuff here. But there are also things like tube worms and mussels that actually have symbiotic relationships, mutualistic relationships with bacteria, and they thrive that way. So the worm uptakes CO2 and hydrogen gas using a hemoglobin protein.

So it has a hemoglobin protein that is, and it has a circulatory system shown here. and it has a little heart that pumps it, right? And in this circulatory system, it will have, you know, these proteins that will bind CO2 and H2S, and that delivers it... two tissues in the organism. So here is the feeding body right here, and inside these tissues, you will have bacteria.

And this bacteria is a mutualistic symbiont. So this is a beneficial relationship for both. The tube worm provides, you know, shelter and a source of food for the microorganism.

And in return, The symbiont, the bacterial symbiont, oxidizes the H2S and fixes the CO2 into cell carbon and then shares that organic matter with the tomb worm. And these things are gigantic. They are, you know, they can be up to three meters tall, right, so they're very big.

They're very big organisms. When the ships, the vessels, the submarines came down to the surface and they landed, they expected to hear a scrape when they landed on the surface. Like when these vessels would go down to the bottom, they'll hit the rocks and they'll scrape a little bit so they know they hit the bottom.

Instead, when they hit the bottom, it went skoomch, and then blood came up around the portholes. of them, which kind of freaked them out. They're like, what's going on? And what they had done is they had landed in a tube worm patch and had hit the molecules.

And as soon as the blood was released, it turned red. So that's the tube worms. All right, after that fun story, the last thing I'm going to cover is the carbon cycle.

Fun fact, where does carbon come from? It comes from fusion in stars, right? The universe in the beginning was a lot of molecules, not even molecules, a lot of elementary particles floating around that then organized into atoms and they organized in hydrogen gas.

That hydrogen gas would get pulled together, it forms stars. You know, you don't have to remember any of this, but I just think this is interesting. Forms stars and then hydrogen fuses into helium under the gravity weight of the star. And you get more and more fusions and all sorts of stuff gets made.

And one of the things that gets made is carbon. When the star explodes, that gets released into the environment. If you look at the carbon on Earth, 99.5% of it is in rocks and sediments. 80% of that is inorganic.

So most of the carbon on Earth is not in organic systems, right? The oceans have a little bit. Methane hydrates have a little bit, fossil fuels have a little bit, the terrestrial biosphere has almost nothing. So you can see that most of the carbon in our environment is locked up in sediments and sitting on the surface and it's not in living systems, right? When we talk about the carbon cycle, we're talking about the cycling of carbon through living systems.

So a lot of it's in the soil and humus and fossil fuels. When those get used or burned, it goes into the atmosphere. That will come back into land plants.

It will also come back into aquatic environments, plants and phytoplankton. So carbon is a really interesting molecule. So the carbon that we're going to be mostly concerned about here is the carbon that's is by conversions of different microorganisms. And they will act on things like CO2.

They will reduce the CO2 to organic carbon that then is used in cells. Heterotrophs will use that, right, to build their cells. The autotrophs will use it to make organic carbon.

But there's also a whole class of organisms that can take methane. The methanotrophs convert that into organic carbon. Methane is a very reduced molecule, right? And they'll use that to generate energy and also organic carbon, right? Again, remember that carbon is about 50% of the cell's dry weight in all organisms.

So carbon dioxide reduction is called fixation. Methane use is called methane oxidation. Now...

We're going to talk a little bit about autotrophic pathways. These are pathways that take CO2 and fix it into cell carbon, carbon fixation. If you have taken a biology class that involves plants, you have been taught the Calvin cycle, right?

And let's see, where is that? The reductive pentose phosphate cycle, a.k.a. the Calvin-Benson-Basham cycle. That's the classic one that gets hot. That's what's done in plants.

There's actually one, two, three, four, five more known pathways that have been discovered in microorganisms that can fix CO2 into cell carbon. I do not expect you to remember these. I just want you to know that carbon fixation can happen in many different ways.

We are going to talk about one, which is the reductive acetyl-CoA pathway because it involves an organism that I'm interested in, or that is interesting for the class. And there are very important organisms that do it in different places. Autotrophic microbes are very common, right?

We've discovered more and more of them as we've gone on. We've talked about cyanobacteria. We've talked about green non-sulfur and green sulfur bacteria, and all the different things that these do.

And these are just some examples. And these are photoautotrophs. But there's a bunch of chemolithoautotrophs. Nitrifiers.

And we talked about nitrifiers and we talked about the nitrogen cycle, right? And these are organisms that will take nitrate and convert it into ammonia. I'm sorry, they'll take ammonia and convert it into nitrate.

Sorry, I got it backwards. There's also hydrogen oxidizers. And there's sulfur oxidizers.

These are reduced compounds, ammonia, hydrogen, sulfur, that are in the environment that organisms can take advantage of. Now, I think it's useful to give you an example of one other CO2 fixation pathway besides the Calvin cycle that you may have run into. Right?

So why this one? It's probably the easiest to understand, and it's used in a significant number of chemolithal autotrophs. Methanogens will use it.

There's other organisms that will use it. So what is it? You take CO2, and it depends on hydrogen gas and carbon dioxide.

If they're in a present environment, you can use them. So it'll take CO2. And it will build one half of acetyl CoA, so it will make the methyl group. So CO2 is reduced by successive hydrogen reductions.

Hydrogen is oxidized, the carbon is reduced, and you get methane on tetrahydrofolate. Tetrahydrofolate, you guys ever heard of the vitamin folic acid? Yes? That's what it's used. It's a one carbon carrier.

You actually use it in your metabolism, but not to do this. So tetrahydrofolate has it, and you just reduce it to methane. The CO2 is reduced by carbon monoxide dehydrogenase, the CO, and this is put on the acetyl-CoA synthase complex. The CO2 goes on, the methane comes on, and with the use of an ATP, this makes acetyl-CoA.

Right? So one other thing that's really interesting about this pathway is while it uses hydrogen gas, which is a high energy compound, it requires very little ATP to make acetyl-CoA. So in the Calvin cycle you take CO2 and you make ribulose, you make RuBisCO, right?

Right? And then the RuBis- that is then turned and you actually end up taking out glyceraldehyde 3-phosphate. So another 3-carbon compound.

And this time, you take out a 2-carbon compound called acetyl-CoA. Alright, so that's that pathway. And what I want you to remember is this. I don't want you to remember like the steps of the pathway or memorize any of the names that are given here.

I want you to know that there are other ways of fixing CO2. And one example I gave you is the reductive acetyl-CoA pathway. It starts with CO2 and it uses hydrogen and one ATP to make acetyl-CoA.

That's what I want you to get out of that. Starts with CO2, uses hydrogen, and it makes one acetyl-CoA at the cost of one ATP. Okay, finally, our last topic is methylotrophs. So we talked about the part of the pathway where CO2 is converted into organic carbon.

We're now going to look at a part of the pathway where methane is converted into organic carbon. Methylatrophs oxidize methane and other C1 molecules as electron donors. This is the electron donor, right, and in their energy metabolism and as carbon sources. They are typically proteobacteria.

They grow by aerobic respiration. And here is they have a lot of this process takes place in the membrane. And therefore because of that they need a lot of membranes. And they'll have these internal membranes that house the machinery for respiration. Okay, so this is how it works.

So this is a the methyl monooxygenase is actually in the cytoplasm, right? The hydrogens will come in and when they're fixing hydrogen and right, they're fixing cell carbon. What they'll do is they'll take the CO4 methane and they'll oxidize it. You can see they're going through oxidations here and they'll oxidize all the CO2. And then as this goes through.

This makes NADH. And you can guess where the NADH goes. It goes into electron transport chain. This is the same electron transport chain we talked about before.

And that ends up pumping protons across the membrane and synthesizing ATP. So instead of using glucose and proteins and all the stuff that you eat to generate this proton gradient, This organism uses an enzyme methyl monooxygenase and then a few other enzymes to make CO2 Dumps the electrons under NADH and those electrons then go through the similar electron transport chain It's just using a different source. Okay, so methyl monooxygenase MMO is really important in this process.

But again, look After you figure out the source in this little reaction here, the rest of the game is exactly the same. And that's how it works. Okay, so why can you do this?

Well, if you look at the electron tower and you look at methane, it's right here, methane to CO2 is pretty high on that electron tower. Oxygen is very low. on that electron tower, okay?

So wait a minute. So the aerobic methane oxidizer on there, but if you look, nitrite is actually pretty low on this tower too. And this reaction, you know, if oxygen is not around and you're in an anaerobic environment, but nitrite is present, this should probably work, right? Well, sure enough, they started looking for this, and they found it in 2010. A bacterium was found in anoxic sediment that could do this. Methylmerabilis oxyferra, and it uses methane as a carbon and energy source, and it uses nitrite as its electron acceptor, not oxygen.

So it grows in environments where oxygen is not... present and in those environments and then again here's some cool diagrams of what this organism looks like right and it's a little bit of a bent rod and here's what it's doing right so it's kind of interesting it takes nitrite and it uses some of the electrons from the electron transport chain to reduce nitrite to nitrogen gas and oxygen NOD, nitric oxide dismutase, splits the nitrite, or the NO, right, into nitrogen gas and oxygen. It takes two NOs and splits it in nitrogen gas and oxygen, and then has the oxygen... to the PMMO, which is a paramplasmic, right, or it's a particulate methyl monooxygenase that hangs out in the membrane.

So the only thing different than what I just showed you before is it starts with nitrite, makes its own oxygen from that, and then goes through the oxidation of methane, right? You get cell carbon the same way, you just can pull in the acetate, and then you use the same whole electron transport chain as you did before. So again, it's just a cute little way, and I just wanted to show you that, of an organism doing something anaerobically and just adding two enzymes to this whole process to get what it needed to do the reaction. Okay!

So now we're going to talk a little bit about the carbon cycle and what's going on as far as the increase in CO2 in the atmosphere. And I want you to look at the whole global carbon cycle as shown here. If you take everything that's on here, and the black is the pre-industrial sinks and producers. So this is before humans started burning fossil fuels and putting them in the environment. And you look at the fluxes, right?

The total, the red is post-industrial anthropogenic, and the total is 829 petagrams, right? The flux out, so when you add that all up, there's actually 10.7 petagrams difference. The total flux out is 10.7, right? And then there's 6.9 in.

You know, just moving of the flux. So the 3.8 is a net addition. So if you look at the total flux through the pathway, through all of the carbon cycle here, and you look at the amount, the net addition, it's just 0.46%.

So the amount going through the carbon cycle is huge, but we're adding a small amount every single year. And that's what the problem is, and that has effects. Note where microbes have a role, both out in respiration.

So you see microbes, you know, there's respiration, there's burning, but there's also just metabolic activity and in photosynthesis. There's a lot of photosynthesis that happens in the oceans. There's a lot of photosynthesis that happens on the land. Okay, so why do I point that out? I want you to realize the amount that we are adding is very small, and that while it is a bad thing to do this, it's easily reversible just by making changes.

We either increase the flux in somehow, or we decrease the flux out. All right, so in summary, there is a diversity of organic carbon metabolism. Right?

You have proteins, polysaccharides, nucleic acids, and lipids. There's secreted enzymes that make these into monomers. All that organic things, carbon, can then be pulled in and used in central metabolism. You can do this with organic acids, alcohols, aromatic compounds, linear hydrocarbons, depending on the organism. And you get all sorts of stuff in central metabolism.

You can use this to make carbon, right, and stels. You can also use it in your energy metabolism. All of this kind of stuff is taking place in cells, and there's a huge diversity of metabolism in microorganisms.

Okay, since I still have 10 minutes, that is the end of what is going to be on the exam. But since I still have 10 minutes... I thought we could begin immunity, and I have posted our relationship with microbes, and so we can do some introductory comments on this.

All right, so the last unit focuses on our relationship with microbes, and it's going to talk about... The microbes that associate with us, most of the ones that are beneficial, and it's going to talk about the pathogens. But the first thing I thought I'd talk about... When we talk about this, is I would talk about how do we defend ourselves against microorganisms and our immune systems.

If we didn't have an immune system, and unfortunately there are poor, you know, unfortunate individuals that have mutations that they can't produce an effective immune system, they will die without huge interventions immediately or very quickly from all the bacterial infections that they get. All right, so here's the learning outcomes. So let's do a preconception.

What do you think? Okay, so where do you think the immune system is? The immune system is found mostly in the blood and circular system.

True or false? Okay, very good. We're pretty split.

This is a common misconception. The correct answer is false. A lot of the immune system is not in your circulatory system. In fact, 70%, over 70% of your immune system is associated with your gastrointestinal tract, which makes perfect sense. This is a tube that goes through your body and there's a ton of stuff.

that you eat that's full of microorganisms that your body has to protect you against. So it's not surprising that a lot of your immune system is around your gastrointestinal tract. I do that just to make you realize there's a lot of cool stuff we're going to learn when we talk about the immune system. All right, so let's talk a little bit of an overview of the immune system for a few minutes. There is a number of different parts of the immune system, and there's lots of parts that people don't think about.

What do you guys think about when you think about immunity? White blood cells? What else? It starts with an A. Antibodies, right?

Everybody thinks about antibodies. During the COVID-19 pandemic, a lot of researchers got involved in doing stuff with immunity that didn't know a lot about immunity, and they did experiments. that someone who didn't know a lot about immunity would do. So they'd focus on antibodies and not focus on other parts of the immune system. It was pretty interesting.

Not that I'm an expert in it, but I wasn't writing grants for it. So overview, you have physical barriers, right? You have all sorts of antimicrobial mechanisms in your body that stop bacteria from growing. from your skin to your eyelashes to movement of material through your system, right? You have mucous membranes, and we'll talk about how those are used.

You have other parts of the innate immunity, phagocytosis, which is part of what some white blood cells do. You have the inflammatory response that is really important. You then have acquired immunity, and this is specific adaptive immunity that fights infections for you. One thing that's really amazing about your immune system, you guys ever heard of the movie The Andromeda Strain?

It was a book, and it's like some horrible disease comes from outer space and wipes out all humans. Your immune system would be able to stop a pathogen that came from outer space. And you'll understand that as we go through this, right? Okay, and that is because of a required specific adaptive immunity. There's antibody-mediated immunity, B cells, and cell-mediated immunity, T cells.

All right, so let's go through a little bit of an immune system introduction for just a minute. All right, so what does the immune system do? The immune system can identify things that are not you that should not be there, right? And this is an identification of self, right?

The immune system must differentiate self from non-self because you don't want your immune system attacking your own tissues. That's called an autoimmune disease and those can be very bad. Right? You may think, well, wait a minute, why is it so hard to tell the difference between a bacteria and me?

We're obviously different. But at the molecular level, you're made of the same things. Here is the structure of lysozyme, an enzyme that you make. Here is the structure of tetanus toxin. And yeah, they look different, but they're both proteins.

And at the molecular level, they can be more difficult. to differentiate. If you have lysozynes in your system, you're fine. If you have technotoxin in your system, you're not fine.

Alright? The immune system creates lymphocytes that respond to many macromolecules. When created, they collectively respond to both self and non-self, but the ones that respond to self are eliminated.

And we'll go through that whole mechanism when we talk about it. Again, cells are the proteins, sugars, and lipids floating around that are part of our body and are accessible to the immune system. Okay, why don't I end there and we'll pick it up on...

Transcript for:Microorganisms and Carbon Cycle in Oceans

Transcript for:
Microorganisms and Carbon Cycle in Oceans