13:05:55 So, thank you everyone for being here, especially those of you that are in a weird timezone, so thank you for for making the effort. 13:06:05 My name is Otto Cordero I'm an associate professor at MIT. And, broadly speaking, I'm interested in environmental microbiology, the evolution of microbes under ecology in the environment. 13:06:16 And so I'm going to tell you a little bit about this I also want to preface this by saying that I try to tailor this talk to the students. 13:06:26 Although I hope it will be also of interest for for the program participants. 13:06:34 However, for some of you that are very well seasoned environmental microbiologist. I suspect most of the things I'm going to talk about are not a very new. 13:06:44 However, if you stay here and maybe you can help me a bit hankies our questions. Now on the topic of questions. We told you this morning for the students. 13:06:53 The culture here is to ask. Ask. 13:06:56 Ask as much as you want. So I'm envisioning there will be a lot of interruptions I told my wife. I'll be here for a while because it's people like to ask questions. 13:07:06 So, there we go. 13:07:08 Alright, so first thing I would tell you is, why we should care about microbes. 13:07:15 And then you know it's like the this the first three lines of every other paper in microbiology are telling you why Microsoft so important and why they do everything that matters for us but, but I like to expand a bit more on that and give you a slightly 13:07:29 different perspective, hopefully. 13:07:32 So 13:07:35 perspective there is a bit more grounded on environmental microbiology so a lot of the things I'm going to tell you. 13:07:43 You know, are things that you may find if you open an environmental microbiology textbook which I really encourage you to do. 13:07:56 Um, so, so one of the first things you learn in environmental microbiology is wherever there is a source of energy that could sustain life in the planet microbes are they're taking advantage of it. 13:08:00 And so, and that's another way of saying that there is an extreme diversity of metabolisms and ways to generate that energy that sustains life, and really only microbes can do it, animals or plants do extremely narrow set of the possible chemical reactions 13:08:18 that mediate life. 13:08:21 The rest is all my groups. 13:08:24 Okay. And moreover, they're extremely abundant, and we're talking about mcgrigors of numbers there but they're very, very large numbers, there are similar one in soils and oceans, as well as you know, regardless of many of you know and and pretty much 13:08:42 on the planet. So, so another way to visualize this, I guess, is to compare our Earth against other planets nearby planets, such as Venus and Mars, and obviously there are a lot of differences but then you may write their spot. 13:08:58 A few things right so there is much more co2 on those planets and on earth, and the atmosphere of the Earth also has a lot of nitrogen, I believe that's mostly, there's a geological explanation for that. 13:09:12 Obviously there is water. And there is a while, oxygen is barely detectable if not undetectable in other planets that on earth there's there's quite a bit approximately. 13:09:26 20% of our atmosphere approximately, right. So, turns out that the reason why these numbers look the way they look is because there's life on this planet. 13:09:34 Right, so for example we need carbon. I mean, we are made of a lot of carbon and another of nitrogen. 13:09:43 And so, and that carbon goes into plants are for synthetic organisms by carbon fixation is presumably. 13:09:57 One of the reasons why there is so little carbon in the atmosphere also. Well, climate change, you know things are changing with anthropogenic input of carbon of co2 in the atmosphere. 13:10:00 Also, oxygen generated by photosynthesis, or it's nice to see you guys at the seminar room. 13:10:06 That's great. 13:10:19 It's very abundant abundant the thermosphere that was not the case before the sort of invention of photosynthesis by sino bacteria we believe so. so really microbes shape the planet and make life possible for all of us. 13:10:27 Um, so I'm going to go through a few of these examples that again this is kind of things that may not be totally new for the environmental my privileges. 13:10:35 However, I feel like environmental microbiology is our, our only a few of you in the in the audience. So, so perhaps these words to talk about these things. 13:10:45 So the case of nitrogen and for the rest of the talk, I will talk mostly talking about carbon. 13:10:50 But for the case of nitrogen is is quite remarkable. Because, I mean, as you know, we need nitrogen. 13:10:59 Proteins are made of amino acids that are reaching it. So nitrogen know life. 13:11:03 But where's the nitrogen come from there's a lot of nitrogen atmosphere. It needs to be fixed into convert to, to, to, to take it from air into an organism, it needs to be converted from from inorganic to organic nitrogen and namely ammonia, for example. 13:11:19 And so the only creatures on this planet that do that are microorganisms, especially bacteria. Many of many of which living soils and form a symbiotic relationships with legumes, for example, 13:11:34 or in the, in the ocean cyanobacteria are the are some of the primary nitrogen fixers in that brings the nitrogen that is that used to form for example a plant and the tissues in a plant right and create all this this order and all this structure. 13:12:06 There's a set of reactions that said Paquin will will tell you about during the class that take it back to the atmosphere. So that's a nitrogen cycle is completely mediated by by microorganisms. 13:12:18 One of the most. I think one of the strongest demonstrations of the relevance of microbes for the black. 13:12:29 Right, so, and what about carbon and nitrogen so so carbon comes into living beings. First, through carbon fixation, which is again taking that and Australian co2 and turning it into sugars, really. 13:12:49 And so, photosynthetic organisms can do that. 13:12:51 And so what you're seeing here is a hero. Yeah, we've got a question in the chat from Dimitri Petrov, okay, I'll just say it so everybody here can hear it as well he says What about fungi. 13:13:04 Yeah, yeah, I believe there is also. What about what about fun Yeah, I mean, I don't know, but I believe there. There's also. 13:13:12 I'm not really sure this but I believe the notification can also be performed by fungi and, and I'm not sure if there is a nitrogen fixing punter, I wouldn't be surprised if the case is just a just a second. 13:13:28 Um, yeah. So, um, so I was saying that what you see here is a. 13:13:35 It's an algal bloom near the coast of England, and then so we can see it from space, because it reflects it does have Garfield, and because I think what you're seeing here is Amanda hotly which is a calculator for that, that you can see it from from outer 13:13:54 space because he has his calcium carbonate shells. So that's a new carrier, that is not a bacterium, but the most abundant America abundant photosynthetic organisms in the planet are cyanobacteria, like for example probiotic caucus, which was discovered 13:14:09 by Penny Chism next door to me. 13:14:15 And, and so okay let's let's look at this cycling of carbon and this is probably. 13:14:21 I don't know if you can simplify this the picture with more, the sun must fix your to their plants and phytoplankton that, including several bacteria that that perform photosynthesis and on carbon fixation, and they will get these organisms are live forever, 13:14:37 they die, and they exude carbon and what happens with that. Well, it gets taken up by hits or traffic organisms that we spire it back to see you do that, I don't know if you can simplify the carbon cycle, more. 13:14:49 So, so let's look a little bit a death right so on the end of photosynthesis, as I told you there is the most abundant organisms. 13:15:11 most abundant are pro pro Caicos and scenic Of course, two types of sign of Materia that are extremely abundant in the planet, the picture on the right, tells you a little bit about our bond and they are pretty much everywhere, especially around the equator. 13:15:24 Right, so, so that's that's it, that's a simple statement. And so, so cyanobacteria extremely abundant also in lakes and so on, and collectively all these phytoplankton produce about 50% of the oxygen we breathe. 13:15:40 But I'm going to, I'm gearing up to tell you something that maybe it's not a surprise. For some of you, but I suspect, not everybody knows is what I'm what I'm going to tell you in the next few slides. 13:15:52 But if you look at plants. Right now this is the this is a tissue of a plant I just found a beautiful picture online, there are many look like this, with the cells in the tissue for plant and you look inside that you find you find the total blast, which 13:16:08 which is the organelles where photosynthesis happens right and it's just like an assign a bacterium photosynthesis happens inside these little organelles in a plant. 13:16:18 Okay, just, just keep that in the fridge will come back to this in his life. 13:16:24 She looked at the other side, the head hydrotherapy and aerobic respiration, it turns back. 13:16:32 Carbon back to co2 for example. 13:16:40 Well, you know, the usual equalised cell is really good at doing this is an experiment that you can do in a high school growing the color in a flask is exactly doing these taking glucose and turning into co2, it does go through, through like policies 13:16:52 to say cycle and whatnot. And, you know, nothing to nothing too special my any pretty much most bacteria can that we that we can easily work within the lab can do this no problem. 13:17:05 the plants with the organelles, you create yourself also have an organism that is dedicated to generate energy from respiration that's the mitochondria, the powerhouse of the cell. 13:17:21 And in that powerhouse of the cell, you get the DCA cycle happening. And then the electron transport chain that does the actual respiration and generating a lot of energy for the cell. 13:17:42 Well, as it turns out, I don't know if you guys knew that. I hope that somebody didn't know this because every time I think about it, and I'm Mind blown by these, Um, and it's something that I teach every year. 13:17:52 Right. Whereas operate like policies happens in the status, basic basic basic biology. 13:17:59 And it's something that I teach every year. This organelles mitochondria and surplus have their own genomes. 13:18:06 Anybody knows why that is. 13:18:09 Because they were, they were bacteria, the mitochondria, was an alpha particular curiam once upon a time, on the class. Sure enough, was assigned number two. 13:18:21 If you take on how do we know that because we we can get this DNA. 13:18:25 Without going into the details of how you do that, you can get it DNA, compared with the in the database of of bacteria and any, any organism has been sequence, and you can build a fellow journey, let's say, a genealogy, with the evolutionary history 13:18:41 of the organisms, and you find that the DNA sequences of the mitochondria and the top last cluster with the bacteria. 13:18:49 So this is a tiny three of life. 13:18:53 Very few organisms here I see my is a corn, the corn plant. 13:18:59 Doesn't the eukaryotes on the left. 13:19:03 On the right, you have here the chloroplasts of of the mice plant clustering together with cynical Kaku so we sign a bacteria, and the mitochondria clustering together with other bacteria which is not appropriate to look at. 13:19:17 More on this later, but what what we what we think happened is that the origin of the critic cell is basically was just a dramatic event in which there was a fusion really have a couple of microbes. 13:19:36 Most likely Anakin in golf in a bacterium that could do an uncooperative material that can that had all the machinery to perform aerobic respiration. Later on, that organism and golfing a sign of bacterium, 13:19:52 which ended up being the last. So, the few fundamental biochemical reactions that generate energy that we eukaryotes can perform were pretty much stolen from bacteria. 13:20:07 So all of these different forms of metabolism were really invented by bacteria. 13:20:15 And just a cute detail before I turn the page. On this introduction. This is still happening. Nowadays, they are Amoeba, which is Pauline Ayla who involved, and really hijacked a china material and, and now we can do for the synthesis created this is 13:20:36 in the process presumably of evolving towards an Oregon L, they sign a bacterium inside, inside his Amoeba. Now the relationship, by the way, is they cannot be decoupled, as far as I understand, although I don't study and study of things. 13:20:51 So, on this and there are multiple examples of this type of your future events is extreme form of same symbiosis. 13:20:59 Alright, so that was my introduction and and what I wanted to do with this was to hopefully get you excited about microbes and tell you why. 13:21:09 Why is this important and you may have noticed, I did not mention at all. 13:21:15 disease. 13:21:18 You know, whatever bacterial infections and so on. Yes, this is very important. And we should care about it and we should provide funding for it, but I felt this introduction is a you know something more fundamental. 13:21:34 I also the non mentioned human microbiome, which are also very exciting and so on but this is more fundamental I think there are more fundamental reasons why we should care about micros. 13:21:45 All right, we've got a question. Yes, please. 13:21:49 Hi. Oh this is Trish in that tree that you were showing in the previous slide, I guess there's no clear answer to this but what do you think happened with the nucleus. 13:21:59 You think it was also an encouragement of some sort or, or, you know what the consensus. 13:22:05 I don't have a good idea of what is a consensus but I'm sure people have have thought about this. I'm just you should look up the. 13:22:13 There's a whole literature on the end of symbiosis theory for the origin of the eukaryotic cell active area of research. 13:22:26 Right. 13:22:27 Thank you for the questions by we keep keep asking if there is anything that pops up. 13:22:45 Alright so what I'm going to try to do next is actually really, what is the word ambitious, yes he's very ambitious. So, um, and, and by necessity I think I'm going to be superficial about, about certain things, The things I want to talk about should 13:22:54 probably be covered in a course that takes takes place through a whole semester. But I'm going to only they bought a few a few minutes to these. 13:23:05 Um, and again it's just to give you, especially for students to give hopefully give you a perspective of what we think are some of the organizing organizing principles of of microbial life. 13:23:19 And I should of course start by saying that we have, we really are far from understanding what are what are those general principles that explain the patterns that we see in in microbial communities for example so this is why it's such an ambitious thing 13:23:38 to try to do about it but I can try to give you a few a few ideas. So what we're going to be doing pretty much is sort of peeling an onion. 13:23:49 We're going to start with, with bio energetics, which is probably the most fundamental level of which we can we can think about this. 13:23:56 And I know other people probably Alfred department will talk about this, and that is much more qualified than me to talk about it. 13:24:08 We're going to talk about a little bit about division of labor and metabolic traders, and then a little bit more about ecology and physiology and I'm just going to give you a few examples of the things, like I said, this is you can you can have more than 13:24:23 one class, dedicated to these topics. 13:24:27 So, so let's start with the bio energetics. 13:24:31 And so the basic statement here is a life is fueled by observing. 13:24:37 Life is fueled by reduction oxidation reaction Redux reactions. And that's where the energy comes from that fuels life. 13:24:46 So I'm just a little bit about this, this thing that you can you many of you probably know already. In, especially the physicist I suppose the chemist in thermodynamics, there's a there's a way to describe a sample what would happen with our reaction, 13:25:01 you have these two reactions, as amb, they meet and the product cnd in you can ask is this reaction favorable is going to take place. And if so, is he going to consume energy or is he going to release energy. 13:25:17 And so under the way to think about this interval nomics is is with this concept of the free energy. Right. So in the example I'm giving you this is a useful thing to go through this through this example on the left. 13:25:30 So you have an initial your initial state with a reactants MB has a certain free energy, and the brothers down there, have a lower free energy. So there's a Delta free energy, the G. 13:25:47 Right. And in this case, is negative, because the products have a lower free energy. 13:25:52 And so that tells you that the reaction is gunning, meaning that he will he will release energy, which is a type of thing that that is useful for life. 13:26:11 Okay. 13:26:11 And so that that's those are important statements. 13:26:15 You may remember their reactions, don't happen spontaneously necessarily, they're required enzymes that that make it go through that activation energy barrier that push it up the barrier and other reaction can can move forward. 13:26:29 Okay. 13:26:33 So right so that's the basics of, you know how to think about this in terms of thermodynamics, but what does that delta G, where's that come from. I just want to calculate that what does it mean. 13:26:46 So in, in the. Here's an example of of a Redux reaction with, which is the oxidation of vehicles. This is glucose EC six age 12, or six, oxygen, and after being fully oxidized that produces co2 and water. 13:27:05 And so, glucose is being oxidized you donate. Donate electrons and oxygen is being reduced it takes the electrons is so the so called electron acceptor, and you should be hearing this, again, electron acceptor and electron docs. 13:27:27 So these are the Redux reactions. I'm like, and the statement. One of the statements I want to make. He said, you can calculate how much energy will be produced by this type of reaction, and people that are experts in this field, you give them some equations, 13:27:39 and they know how to calculate the amount of energy that they'll come out. This is not something that I do very frequently, but you can find it in textbooks and, and it can be done. 13:27:51 Um, and so, and the way to go. The way to or the reason why we can do this is because we know there's a table with the Redux potentials of this of the different have different half reactions. 13:28:04 So for example, and this results potentials are expressed in both on the referred with the letter E. 13:28:11 And so, for example the oxidation of glucose to co2 is a reaction, that is that is very negative in this in this tower, meaning that it has a high tendency to lose elections there how this how this can happen. 13:28:28 You know, it's a really good electron donor is what it does, you know, and on the other end of this table and there are these lines in between here because there are many many many many things on this electron tower that I'm not showing you here. 13:28:40 You have near the bottom you have oxygen, which happens to be a great electron acceptor is highly electro negative. I mean, it has a great tendency to get this. 13:28:53 These elements so when you couple them. Naturally, this reaction, you know as a high Delta. 13:29:01 Eat. In this case, the Delta, Delta. 13:29:04 The of the reduction potential. So this one being negative of there and this one being positive. You know that is large and. 13:29:13 And from this delta you can calculate the, there's a formula that tells you that the the free energy, and it goes by, in front of a constant F, and n is a number of electrons. 13:29:25 Mmm hmm. 13:29:28 And, by the way. Now this this goes way beyond what I want to talk in the class but these Delta gees are strong but it's important is they're strongly dependent on the conditions in the environment in particular pH, or the amount of hydrogen in the environment. 13:29:45 Right, as well as atmospheric pressure and so on. So they always refer to these these numbers they typically are in standard conditions like one atmosphere pH seven and so on. 13:29:57 But the point is here that you can go from this table with a reduction potentials. But tell you whether you know the, what is the gap in the tendency to give electrons versus receive electronic into reactants, you can try to convert that to energy in 13:30:19 of kilojoules. And so the reason why I'm telling you this is not so much because I want to tell you, tell you, or teach you about Redux chemistry. But there's one important thing that I, I need to extract from this is like I told you this a really long 13:30:36 tower, as we call it the Redux tower. 13:30:42 With all these health reactions. so you can go and see what would happen is the exercise that we do in our mental microbiology class. What happens if you couple glucose. 13:30:52 With I don't know night nitrate. 13:30:56 Well we the energy yield of that reaction versus oxygen or versus sulfate and what happens if you utilize acetate instead of glucose and so on and so forth. 13:31:06 So you can actually do all these calculations. 13:31:10 And the point here that I want to make is that, as you can see there. There are different possibilities for you right and depending on what is your electron acceptor or electron donor but let's say for the case for the sake of argument, depending on what 13:31:23 what is the electron acceptor, you have a different energy yield, and that energy deal determines how, you know, the energy that the organism has how much energy it has to grow. 13:31:35 So, just from this logic, we can expect that if there is oxygen and there's an organism that can perform aerobic respiration that gives you in the order of of 2000 plus kilojoules per mole of glucose. 13:31:51 That's going to be much more favorable than doing anaerobic respiration we nitrate, which I believe is in the order of hundreds of kilojoules promote. 13:32:03 Right. And then if you look in the table. Now, the reduction of nitrates utilize nitrate as an electron acceptor instead of oxygen. 13:32:10 It is more favorable than then using sulfate, for example, as an electron acceptor, and so on and so forth, there's a large number of possible electron acceptor and dogs as well. 13:32:23 So, so that's that's a, that's the first organizing principle. I would say that if you if you want to call it that way, which is this hierarchy of Redux reactions determines what organisms will grow, depending on the structure of environment. 13:32:40 And they also themselves structure, the environment. 13:32:45 So for those of you that were in the morning in in George's tutorial, he talked about there being arrested column. This has been a rescue column is structured by this by the real either Redux chemistry. 13:32:58 And so I have a few slides about about this. Are there any questions, by the way. 13:33:07 One question coming. 13:33:25 Hi, I'm just curious how literally true this hierarchy thing is meaning like, Are there examples where bacteria will do two metabolism simultaneously with two different electron donors or something of that nature, like, Are there complexities or is it 13:33:28 really basically hold up 13:33:33 the editor and owner part. 13:33:36 I mean I'm not I don't think of it in this specific example but I believe that's possible. Because that's basically you know you can how you can, there are cases where customers can utilize more than one carbon source simultaneously, that carbon source 13:34:01 I don't think I know of an example where an organism is simultaneously to electronic acceptance. 13:34:07 That's, that's harder. 13:34:09 Right. 13:34:10 So there I think there's a certain asymmetry here and. 13:34:14 In, you know how flexible innovation can be with the electron acceptor versus electron donors. 13:34:22 So this question. One more question 13:34:26 here too. 13:34:30 I'm thinking, why is it that everyone isn't performing this reaction one right Oh, yeah. Yeah, great question. Yes, yes. 13:34:40 Exactly. Alright, so let me go to my next slide which hopefully answer this. Exactly. That's the question. 13:34:47 So the question. Yes, go ahead. Learn how, how do you sort of take into account the fact that maybe certain reactions are a little bit more hard to perform. 13:34:58 Maybe that's sort of the other side of the question I was just asked. Yeah, yeah, this is, this is a good point let's, let's talk about that in a second. 13:35:07 It's actually a really that we haven't understand your question, I think it's a really important point. 13:35:12 But let me get back to it later. Okay, cool. thanks. 13:35:16 So, to access question. So let's think about that being a rescue column that Josh was talking about earlier. 13:35:25 So I'm. 13:35:29 I'm. I'm going to speculate, but this is informed speculation about about what may happen during the development of those of those patterns that you see at the end and live in a graphical namely those bands with different colors. 13:35:42 What does it happen. So initially, you have. 13:35:49 First of all, you have, you need to have a photosynthetic organism that process the oxygen. Okay, let's assume that's there. And so you have light, and co2, and water. 13:36:00 I know you have a sign of bacteria, for example, that is growing, producing oxygen and releasing carbon in one way or another, the carbon that they, they fix, they they produce glucose, different sugars and they did this this is released in one way in 13:36:18 one way or another, sometimes because simply organisms die and the carbon is released. So now you have carbon and oxygen being released by the sign of bacteria. 13:36:26 So sure enough, yeah, if there may be sulfate neither there. No, but I mean yeah and organism can can wants to perform that. Good luck. They're not gonna they're not gonna win the competition against the aerobic is pirate of carbon. 13:36:41 And so that that leads to the growth of these heads or traffic Arabic organisms. But what will happen is, they will consume the oxygen. oxygen may become limiting. 13:36:52 In that case, actually. So then, so that then opens the niche. Create a new niche for this anaerobic organisms. 13:37:03 And so the next one. 13:37:05 Following going down that path that ladder of the results tower. The next one, maybe a nitrate reducer right because that's one of the reactions that has the highest free Delta, Delta free energy in the, in the table. 13:37:26 And once a nitrate is exhausted, then maybe you get another type of things some magnesium and stuff like that. 13:37:38 But ultimately you may get in this, in this systems. So faith with users, because salted is being provided from the bottom. 13:37:47 In any type of systems. 13:37:51 You know, and then that that's that's a hope that answers the question so he's actually this successive niche creation, through the depletion of the electron acceptance that leads to the emergence of the special butters, to some extent reproducible although 13:38:06 I am not sure if anybody has systematically studied how reproducible these dynamics are to do, you know, in a quantitative manner. 13:38:16 And then you get more complicated things like sulfate reduction. Lisa the production of certified in they are photosynthetic organisms that like to use salt hydrogen sulfide as some electron donor. 13:38:32 And this photosynthetic organisms have pigments. 13:38:39 For 13:38:39 bodies if you're still here. This is the pink berries of super was in March. This way they are pink. You have purple sulfur bacteria are utilizing different ways of light, and so on and then you start to get this this this beautiful colorful patterns. 13:38:54 But this is all flows from the, from Redux chemistry. 13:38:59 You know that that's why I'm telling you this, we don't have to at all. We don't have to think here about sales and how they grow and and this only rid of chemistry. 13:39:09 So one could make a simulation of these just using those the bio energetics So does that does. 13:39:16 All right. Um, so, And then second Oh yeah, this way. 13:39:29 Hey auto I have a question so is the claim that weakness of the bands relate to the weakness of the Delta ease. Is that what your speculation is because the thing that always confused me is why you get these kind of discrete bands. 13:39:43 Yeah, let's do continuous gradients. Yeah, yeah. Interesting question. 13:39:48 I, 13:39:53 I suppose. 13:39:56 The answer to your question could be yes. But I also the, I mean, there are opposite gradients right so there may be conditions. 13:40:05 I mean, like, 13:40:09 okay, so I'm gonna listen to a bit crazy. 13:40:12 Sorry. 13:40:15 I think what we look what it looks to our eyes as discreet bands is maybe more something like this. 13:40:25 Can you see what I'm wondering. 13:40:29 Yes or no. 13:40:33 No. 13:40:35 Yeah, we can see that, yeah okay so so you know so this could be the purpose of for bacteria and this is sort of the range in which the organism can grow, given the gradient of hydrogen sulfide and light, and whatnot. 13:40:49 If you move a little bit this way maybe there's not enough light, and it grows less and then there's another organism that takes in there and that appears as bands, but it's not. 13:41:00 It's not necessarily you know it's not like like this. 13:41:06 I'm not sure if this really answers your question but yes i mean they're also discreet. These are discrete metabolic groups that are from these reactions. 13:41:17 There is not something that is like a, like a purple surfer bacterium that 13:41:25 utilizes how sorry oxidizes hydrogen sulfide, there is something there is not like something that is almost an eye sulfite oxidase if either. That's it or not. 13:41:41 And, and, and there are discrete chemical species I think that, that, that are available so i think that's that's what happens. 13:41:48 Um Can I follow up on that I know. 13:41:51 I've always been very interested in this. 13:41:54 And it seems to make so much sense that there are these layers ordered by basically the Redux potential right. It's like predicting principle. 13:42:04 But at least on my end when I tried to look into literature, to what extent these cartoons have nicely ordered layers in order of Redux potential are actually true. 13:42:12 It seems like every external paper I found is, it's not at all that stratified. So to what extent this cartoon corresponds to like is there an ordering by Redux potential in these water Collins. 13:42:25 Yes. 13:42:28 I have I have examples, and dislikes. So this is this is still a cartoon. 13:42:32 And I'm glad you asked this because I wasn't sure if I should show this example so I'm just beating a dead horse. But this is obviously a cartoon of what, one could expect in the, in a, in a water column. 13:42:45 This is not done, they don't didn't make it up. This is based on observations. And so this may be this cartoon is beating a dead horse except, just to tell you that at the very bottom of this, of this ladder that you see metallic agents and managers are. 13:43:04 I mean, when there is no electron acceptor 13:43:09 available. You may, and there is no oxygen and, but there is some sort of some form of, there has to be hydrogen, for example. 13:43:21 Or, and or acetate, then, then you use that you start to get advantages. And so there are the advantages they utilize only hydrogen, and co2, and they utilize you to as an as an electron acceptor which is crazy to produce methane. 13:43:38 And so these are the very bottom of the, of the ladder. 13:43:45 And I have a quick question. Yeah, so the air pocket at the top of the column is the only thing sort of breaking the the symmetry otherwise you could have sort of resource like the chemicals diffuse in any direction you second sorry. 13:44:02 You like the reason that you expect that like the cartoon of the Redux potentials we have like this tower where like the top is the top is like greatest and the bottom is least and that is like directional but we don't like the chemical diffuse, a directional 13:44:18 The capital diffuse, a directional and so the gradient is being caused by the other two but I guess this means that there's a prediction that once the oxygen is gone, then the gradients should disappear. 13:44:27 No, no. 13:44:30 The gradient starts created by in the industry Nebraska column at sample, which is a cartoon. 13:44:36 But this is the same that happens in a. 13:44:48 And at the bottom you have sulfate, because in the ocean, there's a lot of sulfur and organic matter is so faded into things are running at the bottom liberating solve it. 13:44:52 Whenever you know if you're in a salt marsh and you're stagnant water you get the same type of gradient, you are at the top you have oxygen because of photosynthesis. 13:44:57 And then you have your gradient, and the rest the gradients appear because the chemical species are consumed. 13:45:04 And the consumption of certain chemical species opens a niche for the next one and the next one, and so on. 13:45:11 And so with respect to the question of whether this is our second sorry. 13:45:23 Oh, there we go. With respect to the question of whether this is relevant environment as well. I think the resounding yes. 13:45:30 and whether these. These gradients appear. 13:45:33 They may not be as beautiful as the. 13:45:46 I think radiance in the individual rescue column, and there's a bunch of other processes that affect the gradients, but they exist and so there are two examples here but I'm sure there's more. 13:45:49 The, the ability is a is a huge body of water, and it's highly stratified for for multiple reasons that are not necessarily related to microbes with for example these gradients of salt, create this certification in the in the in the water is very deep 13:46:08 as well. And, and so one of the favorite spots for environmental microbiology is to study, to study microbes. 13:46:17 And the reason is precisely so certified that you get these, these these chemical songs. So this is a type of pictures that you that you that people produce from this. 13:46:34 So, I mean let's go through this graph. 13:46:40 They make these studies and in something very similar you can find in certain regions of the ocean. 13:46:40 in a little bit of detail because the colors are a little bit annoying if you're colorblind. 13:46:54 This is horrible. So, when you measure oxygen, so I, I'm, I show here. Oh to oxygen. See there is oxygen. 13:46:54 At high concentrations on the surface, and it's depleted. 13:46:58 As you go deeper, you know, and why is it depleted, because you have, as I told you before you have respiration that consumes oxygen. 13:47:06 So once that's completed. 13:47:09 Then what happens. Well, this For the synthetic organisms also release nitrate, no plans to release nitrate RG release nitrate. 13:47:31 So then you have your next electron acceptor and and so this nitrate, and this is the part where maybe you should look in in detail. This is brown line here right there is nitrate. 13:47:35 When you reduce nitrate. The you dump electrons into it, then you can That's right. 13:47:41 And this little repair orange is nitrate, is the result of that respiration reaction. 13:47:50 So, it's so you're seeing there that the real chemistry happen is is mediated by makers. The next one is manganese and, which is also this electron acceptor, and I'm not sure what's happening. 13:48:06 But anyway, that's enough to make the font and. And down here at the towards the bottom you get a lot of sulfate as I told you, because there is a lot of organic matter that contains sulfate. 13:48:21 And, and then you get a lot of of sulfate in the sediments, especially in bodies of water that are, that have an influence from from the ocean, like the Dead Sea. 13:48:35 And, and what you're mentioning here in the state I sold Fund, which is a product, the product of the reduction of subject. 13:48:42 So I'm just telling you that there is a lot of sulfate reduction happening at the bottom. 13:48:46 That's expect. 13:48:49 You know, so it to this extent I think this this data is is not applicable to this extent. Yes, this gradients appear and explain the parents that you see in the, in typically in bodies of water. 13:49:04 for those of you that don't know Boston mystic lake is the same story is a mystic Lake highly stratified by Redux chemistry, there is there's a paper from Aragon on this on this fact. 13:49:23 A few years ago. 13:49:27 And, and just to, I guess, now maybe beat a dead horse. This also happens in the ocean. And because the ocean is such a large part of the planet. This is important for for biochemical cycles there's less oxygen. 13:49:39 Oxygen minimum zones, near the coast of California near the coast of Peru and Chile, little bit Aquarius Well, the Indian Ocean and so on. And that near the coast of Namibia, I believe as well. 13:49:51 And where, where there is a lot less oxygen then, and the average, the ocean. Also, as you may expect probably near, really, the coastal areas that are highly populated. 13:50:06 There is a lot of organic matter being dumped by humans into the ocean. So a lot of respiration so that consumes the oxygen right. So, just killing, killing some of the natural live there. 13:50:20 And so in this in this oxygen minimum zones. These are. This is a graph that explains a little bit why you get those things, and it's essentially it's a combination of physical oceanography and microbiology, for, for reasons that are not relevant to microbiology, 13:50:38 you get a, you get a lot of nutrients, near the near the coastal regions. And then once you get a lot of nutrients so through these upwelling their phytoplankton blooms. 13:50:51 So I miss a lot of positivity in the ecosystem. That means a lot of organic matter like basically organic carbon and nitrogen that are being released, and a lot of respiration, which again, takes away the oxygen eventually. 13:51:06 Um, and then what happens is that you get the notification that process through which nitrate is converted and I tried and so eventually to to nitrogen gas, this is these are the regions of the ocean where this happening. 13:51:22 This is Redux chemistry, it may not be a beautiful Winogradsky column with the layers but but it's happening. And when you look at the data, you find things that are kind of similar to this, where there are regions that can be delineated where the, where 13:51:32 the certain metabolic activities are taking place. 13:51:38 Question over. Yeah, you told about the Redux sort of layers, but what about the essential nutrients which are needed for grows like nitrogen, phosphorus, how often they are rate limiting for this process instead of the energy being raised the image and. 13:51:55 Yeah, great question. I mean I guess the answer is the answer depends on case by case. 13:52:02 There are multiple examples where, where micronutrients are limiting probably some of the best known ones are in the case of iron. 13:52:13 For example, I don't is limiting for photosynthesis in the ocean. 13:52:16 Maybe limit as well for for nitrogen fixation 13:52:23 and and there may be there may be many, many other examples. 13:52:28 I cannot improvise right now but. 13:52:31 But yes, in many in many cases, micronutrients can be limiting. 13:52:37 And, and in some cases, microbes have ways to scavenge for these micronutrients. And that leads to interactions between my groups, through the sharing willing on a willing sharing of the, of the nutrient for example of iron, vitamins, stuff like that. 13:52:55 That's what I guess I can tell you something very general, it depends on the case by case but but yes it is it is relevant. 13:53:04 And it proves that in a situation where the micronutrients are limiting you don't really expect to see as as certification, or by Redux. 13:53:13 I'm not sure of that I guess the, I guess it would depend on which of their metabolic niches is being inhibited by the lack of the micro micro nutrient. 13:53:27 For example, there are. I mean, methanogens are are very finicky. They need any specific conditions for growth if those conditions are not there, then they may not grow and then things may end up at sulfate reduction and no Montana genesis for example. 13:53:47 But, but the logic still works. You know so because you still have, there is still a hierarchy of metabolic nations. There is governed by, by energetics. 13:53:59 One more question. 13:54:02 Do you find that as you go down. These stratified this table, or maybe on certain layers. Are you more likely than elsewhere defined microbial metabolic consortiums or in other words like are certain, you know, Redux reactions more likely to lead to Central 13:54:28 vague Association Yes, and others. Yes, resounding yes, Yes. I'll talk about this but yes, 13:54:28 yes. 13:54:30 And so I'll tell you a bit about it but, but, yes. And finally, now the vino rescue column writer, or even better microbial Matt. 13:54:39 All these patterns that may one way or another, manifest at really large scales of thousands of meters, you know what a column. You can also find them on a centimeter scale so even millimeters kills in a microbial mats. 13:54:53 And so I don't know depends where you live, but they're here near near Boston we can go to Super wizard marches so much, so much as a great for the things. 13:55:02 And then you can try to get out a core of soil of the fence and you find this this is really from simple wizard much. 13:55:11 And, you know, I, we could speculate what's in here but the green thing must be for the synthetic organisms. This purple thing here suspect is a purple surfer bacterium and so on. 13:55:24 You know, that maybe iron bacteria there i don't i don't know but but you get these really beautiful I think cake with the, with the layers, taking place there and that's that's that's a bio energetics, I think. 13:55:40 All right. Alright, so 13:55:44 I'm going to come to the last question, I think it's a really, really important question in a second. So, life is fueled by reduction oxidation reaction Redux reactions. 13:55:54 This is, I think needs to be mentioned is one of those organizing principle. There were a lot of really interesting questions by the way during the presentation and I I suspected you know many, many of you, especially the physicist, really have a different 13:56:08 perspective on this type of things for the environmental microbiologist. This is all news. And it's very relevant, we should we should all know it. 13:56:18 I don't have this sense this is an active area of research, but I think this may, this could potentially be a good active area of research for somebody that comes from that perspective, you know these questions of how why you have a discrete band or how 13:56:32 reproducibility is and so on or not questions that typically the microbiologist will naturally ask. 13:56:39 So anyway, is that it obviously the answer is no. So, so we keep peeling the onion. 13:56:48 And we keep peeling the onion. 13:56:53 Yes. So, um, so so thermodynamics tell you. 13:57:02 Really nothing about the pathway that our reaction will take and or the kinetics for the matter, as you guys some of you guys know, way better than me this. 13:57:13 And so frequently this reactions take place through complex enzymatic machineries, or even or even, even better, through multiple species. 13:57:25 So nothing tells you hear that this this work is performed by is by a single and same or even by a single species is a complex machinery so casing. 13:57:36 One of the most obvious cases. 13:57:39 Again the oxidation of glucose, that the basic reaction glucose and oxygen, pretty much never meet inside the cell. 13:57:47 So there's a whole series of conversions. This cascade of reactions that is somebody, somehow, somewhat complex to remember, and then organelles in the case of Eucharistic sales and there is a cycle and this electron transport chain that finally brings 13:58:07 So it's a really complex and cinematic machinery to. 13:58:12 Another important thing to keep in mind. Everything I've been talking about has been respiration and not you know like I guess the 99% of humans when you hear respiration you think oxygen by your breathing oxygen but as you probably saw you may have realized 13:58:29 realized already. I was talking about respiration with sulfate, you can happen with Iran, it can happen with manganese nitrate. So microbes can risk by rocks and, but I still respiration, in the sense that you're using an external electron acceptor and 13:58:46 and there is some in molecular machinery in the cells to, to, to dump electrons in it and engineering generate energy. However, there is also fermentation and that's fundamentally different interpretation you have only the upper part of like like policies, 13:59:02 and then they're in there is an internal electron acceptor inside the cell. These are still Redux reaction, which is with Redux reactions. Delta accessories and a plus. 13:59:15 There is a where electrons are dumped in there, becomes any dh, and then fermentation is all about the cycling of energy flows and NADH in order to continue dumping electrons into the cell needs to regenerate and 80 Plus, and it does so by transferring 13:59:33 the electrons from NADH into paperweight or, or, or other molecules derived from pi robot and. 13:59:42 And that leads to the production of a byproduct. This in itself doesn't generate any any energy, the cell does it only as far as when they're saying to regenerate regenerate. 13:59:55 Reducing power. 13:59:57 And so you end up with things like lactate, which I bet at least one of you had yogurt for breakfast this morning, which is produced by lactic acid bacteria, that, that, That does this lactic acid fermentation. 14:00:15 And so and so. So you also have a lot of different fermentation pathways, and then things get a little bit more complicated. There is also are called fermentation. 14:00:26 I bet, at least one of you had alcohol. Last weekend. 14:00:29 And, and it's a very similar logic, in this case, don't electrons are dumped into acetaldehyde instead of Pyro bait, and you have co2 coming out and so on but it's essentially the recycling of nav and any of the H. 14:00:39 And sometimes people confused, partial respiration with fermentation fermentation is fundamentally this cycling of the electron carrier. 14:00:54 And this is a reaction that has a much lower. 14:00:56 Delta G than aerobic respiration, by the way, as you can see an order of magnitude less, but it's still very energetically favorite will index absence of oxygen. 14:01:06 So it's one of the first things that will happen when you don't have oxygen is fermentation. 14:01:11 Um, and so when you open an environmental microbiology textbook which I encourage you to do, you should probably find schemes like this. 14:01:23 And, and if you're in the right place googling about microbes in Arabic environments, you will find these type of things. And so, there is a fundamental traffic organization in microbial ecosystems, especially anaerobic microbial ecosystems. 14:01:41 That is not only the result of bio energetics say mentioning until now but also have these fermentation reactions. So in pretty much any, an aerobic ecosystem, such as for example, the cow, the room and have a cow or 14:02:02 whatever there is water is stagnant. What happens in the soils, sorry in the sediments, they become an aerobic and then you have this type of reactions, etc etc. 14:02:11 Most of the planet actually is where Microsoft is anaerobic, and 14:02:20 you have this anyway in those environments, you have this type of cascade, which starts with the composition of complex forms of organic matter right so for example plants and algae, or utilize it co2 from the atmosphere and light to create really complex 14:02:35 structures right the tissues of plants and whatnot, living in the end, and cellulose and the in the trunk of trees, etc etc really complex storage compounds such as carbohydrates, and eventually they need to be broken down because otherwise it's, think 14:02:55 of carbon and nitrogen and life wouldn't exist if there weren't microbes, which is what tearing the ocean foundering soils that break those things down. 14:03:05 And so they break down these compounds, primarily through hydrolysis. They have really complex and symmetric machineries that can break down this micro molecule so this is something that we studied in my lab is I find it quite fascinating. 14:03:21 And eventually that releases small sugars, things that are a bit more easy to digest, literally. 14:03:29 And then what happens in an anaerobic environment. The first thing that will happen is that those sugars will be fermented and then there'll be a number of different fermentation products to be lactate Nutri appropriate, you may be familiar with these 14:03:41 names, especially if you if you if you care about human microbiome. That's exactly what was happening is happening in the human microbiome this this awkward part here. 14:03:49 Right. 14:03:51 So, so before we start worrying about how microbes change our our our our our mood or if we if we they induce depression or shiny hair or not. This is the fundamental job of the microbes in the, in the gut. 14:04:07 This producing this fermentation products from which we, we can we get 14:04:15 our nutrition. 14:04:17 Right, so, um, now that the human gut continued on that note, as a very short residents time, there is a high flow through the gut. 14:04:27 And so reactions that are slow. Those near the near the delta t zero. There are not very energetically favorable 14:04:38 will will will have a hard time these organisms that perform those reactions will have a hard time remaining in the system, because they grow too slow, and they got his watch out I forget out with what frequency but somewhere in the order of one or two 14:04:55 days, I believe, I may be completely wrong but is quite fast, the turnover time of microbes in the gut. So, so those are low, low energy reactions may not take place. 14:05:07 However, where you have high resonance times like for example, I don't know, Like I said before stagnant water, and 14:05:19 I'm blanking out for the word here. 14:05:32 degraded. You have anaerobic environment with a really high response time. 14:05:34 Anyway, wherever they're stuck in in water, and you have organic matter, being being dumped there and it's been it's been 14:05:37 Also in the God of water really the car room and the car is huge. And so, there is a the Roman is a really large bioreactor with is a high residence time. 14:05:49 So then those low growing micros have a chance. 14:05:52 And then, for example, sulphide reduction can happen from those fermentation brothers. So, the users and electron donor lactate for example beautiful approximate, and they use sulfate, as the electron acceptor. 14:06:07 Right. This is a particular illustration where it's sulfate, with a very apparently very, very important they put it everywhere. If there is no sulfate, then you end up having ultimately Montana Genesis, which is down here. 14:06:21 And so and so this is the fundamental structure of this anaerobic ecosystems as you see the upper part down to the green box here with fermentation is conserved. 14:06:31 What changes is at the bottom because that depends on residence time and depends on the electron acceptor is available. 14:06:39 Okay, so that's, that's another really important concept I think. 14:06:48 Right. So, here's a naive question that I think some someone is the kind of question that is, I feel like somebody in this audience could ask because it's a question that may seems naive on the surface but it's actually really deep, and I think is a really 14:07:05 good question. 14:07:07 Why isn't there one or there's some kind of can do all of this. I'm not sure if this was clear. 14:07:13 When I was talking about this but there are organist there. These are niches for organisms there's an organism to be multiple organisms that their families hydrolysis, there are others that specialize in doing the fermentation. 14:07:25 There is a sulfate reducer there is taking this fermentation products and, and, and, and dumping them on sulfate and so on mythologize or the group of their own. 14:07:34 There are care. They don't touch the complex or organic micro most molecules are all and and in some cases they just use co2 and hydrogen, don't even take the fermentation approach. 14:07:48 At best, they, they can utilize acetate and and hydrogen. So why is there this division of labor. Right. Okay, so there are multiple answers to this. Again, it sort of depends on the, what why we're talking about. 14:08:04 But I think in general, we don't have a good, I don't know if there is a good sort of general principle for why this is not happening. It may be specific for certain cases. 14:08:19 However, we don't. There are many cases that are not well understood. And this is a fascinating area of research, I think, and and some of the most interesting cases I'm not talking about, for example in notification. 14:08:31 This is this is one of these amazing canonical examples of division of labor and. 14:08:39 But there is a couple things that can be set anyway. 14:08:44 So, the in the case of an Arabic environment some CS talking about this. And there is a there is a basic problem here with hydrogen fermentation reactions typically release hydrogen, and then hydrogen becomes in what sci fi if it's led to accumulate for 14:09:03 some of these reactions especially displaces a fantastic question that somebody asked earlier, especially for those reactions that are very close to the delta t equals zero that they're not very energetically favorable, the products of their reaction 14:09:20 inhibited, you have a product innovation. And so, and hydrogen is one of these products. And so, it's a byproduct of fermentation. And then you have on the other side, you have reactions, certain processes that consumer hydrogen. 14:09:32 For example, anaerobic respiration consumes it. So this upper. So, this part here of the graph, maybe producing hydrogen, and is far down here is consuming the hydrogen. 14:09:44 And so that every, maybe, you know, a basic reason why you cannot do both things. 14:10:00 Right, so, so, so one police it consumes, you cannot have one organism that does both, I believe, but what you do have is the consortium, as somebody asked earlier, you are what we call center fi organisms that consumed a hydrogen like methanogens. 14:10:12 energetic conditions for the, for mentors, so they can continue fermenting because they're removing their by their byproducts, hydrogen, which is inhibiting to the reaction. 14:10:21 So this is this is the fundamental example of form of cooperation if you will have seen trophy as we call it, in environmental microbiology, that is fundamental for life. 14:10:36 Right, is it's really it's really at the core of what's happening in this low energy environments like whether whenever there's a ton of Genesis, the room and have a cow. 14:10:46 Say Marines elements etc etc. 14:10:49 But auto, could you clarify for a second. 14:10:53 Is there some fundamental reason that you couldn't perform fermentation and anaerobic respiration in the same cell. You could do that by maintaining low product concentrations if you balance the rates correctly, right. 14:11:06 So you're saying that this is a cooperative process and I see that but is there a deeper reason that you couldn't perform these reactions together. I mean I think it'd be great to talk to somebody who studies this to to ask this to go deeper on this. 14:11:23 I find it, I find it hard to imagine that this process can be coupled in such a way that the hydrogen is immediately consumed. 14:11:35 I, I find it really hard to imagine this been possible but I can also not give you, I feel like I cannot give you a very satisfying answer. 14:11:47 And this may be a good question for maybe outfit, or somebody, somebody like that. 14:11:54 But to go beyond the beyond the basic intuition that I have that. 14:12:00 It seems really hard that we would have. 14:12:03 This, this, I mean beyond the basic I mean one can argue, but it's not the most satisfying argument that the molecular machinery becomes just way too expensive. 14:12:27 I mean, to limit on the Genesis unit fully dedicated organism that does that is a complex thing. And, and so on for some, and then you have to have this other reactions on top, and so on. 14:12:28 But but something that goes beyond, and, and, and, and what you're looking for, which is why you cannot use, you cannot maybe accumulate the net the hydrogen a little bit and then use it and flip 14:12:41 is hard for me I think to think of that I do. One question. the two processes you have up on the screen. 14:12:50 How many different genes do you need to carry them out. Is it like a small module that one of these species can pick up easily or it's a part of it depends it depends the rest the respiration respiration reactions take a huge amount of protein space to 14:13:06 say, like for example aerobic respiration that is holy through carrier machinery, there is a P is very expensive means a lot of a lot of genes are proteins, more than genes, it's just a large fraction of the broken. 14:13:21 Similarly, salted reduction mythologies etc These are all respiration is a complicated thing. 14:13:29 I guess I was asking to figure out whether this is just a phylogenetic accident or if it's, you know, this combination strategy, of the time with horizontal gene transfer or not. 14:13:40 No no no no, they said, I think this is a. 14:13:44 Be there from a generic since I'm sure somewhere there but I believe this is much, much more fundamental of it. 14:13:49 I don't think I don't think is. 14:13:52 I may be wrong but anything is possible to do both things at the same time. 14:13:57 In this particular case where their reactions that produce hydrogen on others and consume it. 14:14:03 I mean, you would have to have an organism that is switching back and forth. 14:14:06 The thing becomes kind of almost. 14:14:13 It's really hard to imagine for me. Can we just follow up on the surface question. Yeah. Could it be related to the fact that hydrogen is a gas, and it's not soluble or in other words if it's instead of hydrogen you had some byproducts, like carbon containing 14:14:27 byproduct. You could easily imagine that it could be either shared through the environment or coupled within the same cell. 14:14:38 Whereas for hydrogen as you say is it is almost unbreakable rule that it has to be transferred Why are they unlearned. 14:14:46 I'm not sure if that. 14:14:50 There are also other organisms that are defy the, the expectation of what's possible in life but that that transfer the electrons effectively not by hydrogen but by cables. 14:15:03 They really have these long Pillai and they attached to each other and they dump electrons in one another. 14:15:08 So, and it still is to sales when the things. 14:15:12 Like I said, I feel like I can, I can wave my, my hands but I feel like other people may may provide a better answer but I think the answer is the bio energetics the reactions are fundamentally, you know, 14:15:28 opposed, in the sense that, as hazard impression pressures, change the delta G of the reactions is changing as well, and it's becoming unfavorable for the mentor and it's becoming favorable favorable for the risk fire. 14:15:46 Just, just to follow up so in other words this is only possible if delta G to begin with was not very strongly negative so that the correct emulation of hydrogen could reverse it, etc. 14:15:58 So this does not happen. But one of the questions earlier, this has not happened when there's more energy available. This only happens, because there's product innovation because hydrogen accumulates and inhibits the fermentation reaction. 14:16:13 Yeah. 14:16:20 Do you think we know enough about the genetic manipulate ability of any of these organisms so that we could try and engineer an organism that could reduce both co2 and sulfate by transplanting genes, and then ask what happens when you try and give the 14:16:22 So here. 14:16:39 nice alternative sources. 14:16:46 Who asked this question is under. 14:16:52 You know, I mean I'll try to go with the question, and some of these organisms mythologies. Now what days I believe we're starting to get genetic tools. 14:17:05 I believe there's somebody in Berkeley that that uses crisper. 14:17:12 And there are other mythologies that are genetically front of others is not easy, 14:17:19 whether whether it is possible regardless of the complications. 14:17:24 Regardless of the complications of working with these organisms, which are significant. 14:17:28 Whether it's possible to, to engineer, I mean, whether it's biochemically possible for this reactions to be in the same cell. 14:17:39 I, I, I'm not sure I cannot tell you this is fundamentally impossible because of our chemistry, but I am pretty sure that is extremely, extremely difficult that is organism functions. 14:17:53 So it seems like it seems like if, if you had sort of infinite genetic manipulate ability. You could have the situation where you can turn on one pathway, with one small molecule inducer another with a different small molecule inducer, and both of those 14:18:09 should work because you're only trying to reduce one thing at one time. 14:18:13 And then if you turned on both of them, then you'd be able to answer the question that neither you nor I know the answer to is whether there's some fundamental biochemical and compatibility between trying to run both reactions at the same time. 14:18:26 Yeah, I guess so. 14:18:30 My. Yeah, I mean, 14:18:34 the however in empirically I think I wouldn't advise anybody to try that. 14:18:41 It's a unless you have the infinite genetic capabilities and infinite time. 14:18:47 A. 14:18:49 He may be extremely difficult to the south, so I suspect the better way of doing this is asking the, the experts and this time we may get an answer for why this is is possible or not possible. 14:19:04 That's gonna say that this is theoretically possible then maybe 14:19:10 someone asking online. 14:19:17 Go ahead, Jacob. 14:19:21 Sorry. Yeah, so I don't really have much experience with Redux reactions or anything but I was wondering, you said towards the beginning of the talk that the delta G Redux hierarchy is characterized and like the special standard conditions. 14:19:35 I was just curious like how flexible that is to changes in these conditions like the hierarchy, like, Are there any cases where bacteria or like bugs can change their conditions. 14:19:49 Yeah. 14:19:49 This is exactly this case example. Hydrogen concentration is, is one of the main factors that you need to take into account when calculating the delta t. 14:19:59 And it's by product of their reactions. So, Yeah. 14:20:04 Alright so then, so maybe I missed this but how does this change the driving of the spatial patterning that we saw towards the beginning. 14:20:13 Um, I mean, I had a slide on this earlier, there is how you can transfer all along the way. 14:20:19 And, and, yeah, which which in starts with a with a farming fermentation reactions. Okay. I mean, I guess, one could give more give more specific answer depending on the particular case but but that that's included, let's say in the, in the phenomenon 14:20:39 that we are in this certification. The number is taken into account. 14:20:44 Awesome. Thank you. 14:20:47 Um, alright so anyway, maybe, maybe one remark that's relevant. Some of you know that we ran metabolic forum. Last winter with a bunch of excellent lectures on these related topics and it's available online. 14:21:10 And it's generally good reading and you won't answer all of these questions but it will help. Yeah, yeah. 14:21:15 Anyway, I, the reason why I wanted to talk about these things because I just like, apparently, many of you. I think this is a really interesting problem. 14:21:24 Why don't we have one organism that does everything, here's here's an example. And you know we can we can think more about this but as we have seen from the questions and from my heart answers. 14:21:35 This is not an easy problem. 14:21:39 Can I ask a question another hot stupid question. Why do we have to have division of labor between organisms instead of like temporal niches or spatial niches compartmentalization or division between time would you see another kind of Redux things. 14:21:52 You mean you mean one organism that you separate in time or separated space and that happens that happens as well, for example, cyanobacteria. 14:22:03 The do. 14:22:04 Right. They the notification is inhibited with oxygen by oxygen and signed a bacteria produce oxygen. So there you have a chemical incompatibility, but they have these special cells that are shielded from the oxygen. 14:22:18 And so that's an example. 14:22:20 It is possible. And moreover, fascinating to me at least. This type of some of these copying the centerpiece. They're coupled by the transfer of electrons essentially between, between organisms. 14:22:36 Also take place between, between two different species that are spatially aggregated, so if you if you know the work of classical work of Victoria or finding Caltech about these type of things. 14:22:47 Their spatial aggregates organisms that clump together, where one is doing a certain reaction and the other ones doing the sulfate reduction and so on. 14:22:57 So in a way, they have the spatial separation and inspiration across different organisms. 14:23:04 Yeah. 14:23:06 So yeah what is hilarity could be a solution for this but it's fundamentally the same dividing the working in different cells 14:23:16 compartmentalization. 14:23:18 So, um, 14:23:22 but But anyway, even if that case wasn't wasn't convinced enough for you that this is, this is not there is a fundamental biochemical constraint here that that creates division of labor, then this one is even worse, because the notification is a reaction. 14:23:40 that says there is a series of reactions that take nitrate, all the way to nitrogen gas, and their organism without the full pathway. 14:23:51 And, and in many many cases they don't perform the full reaction. So if you remember that data from the, from the Black Sea. The people measured nitrate, which is no three, and as well as nitrate, and they saw accumulation of nitrate and but if you are 14:24:07 doing the full electrification, sorry. 14:24:19 It's not here so if you're doing the first is it purple line here. If you're doing the full day notification reaction this shouldn't be any accumulation of metrics. However, it happens. And this is something that my good friend separate is been working on. 14:24:25 So he'll probably tell you more about but this is basically faculty division of labor, there are organizations that can do the full thing, and the organisms that choose to the park, some have lots of genes some still keep them there but don't activate 14:24:40 them. And, and this is, this goes way beyond I mean beyond any hope of finding a by fundamental biochemical recent that explains the division of labor, this is, this is ecology, this is kinetics, etc. 14:24:53 So, but also relevant and and I don't have a slide on this but the same story with carbon right you have the full black colleges pathway and then TJ cycle and then feel too. 14:25:06 But a lot of organisms as we know very well when you grow them on a lot of sugars, e coli stops halfway and excrete acetate parts of respiration, and then somebody else can take that acetate again form of division of labor that is not 14:25:22 constrained by biochemistry is a different story. It's a release to one of the earlier questions I think it was an Iran who asked, what about all these enzymatic machinery needed for the reactions was more or less where the answer goes, they science, 14:25:36 these are expensive and symmetric machineries and, and at the end of the day it's a zero sum game where you put your, your proteome resources. 14:25:46 All right. Um, so, so I have talked about by energetics, we talked a little bit about division of labor. And as you can imagine there is much more to talk a much more to say about about division of labor and, and it's a really interesting topic as, as 14:26:04 you could have infer from the questions. 14:26:08 And the last thing I want to talk about is sort of the combination between ecology and physiology. And then I'm going to jump into microbial diversity. 14:26:17 So, so now I'm going to really focus on on carbon and something that I know a little bit more about which is what happens with carbon in the microbes in the ocean. 14:26:27 So, here again we have this is clearly a sketch of what happens in the water column again at the top you have for the synthetic organisms and disorders entity organisms for just not only the oxygen but also the fixed carbon and carbon is ultimately released 14:26:50 its release because organisms die the ice, they produce Polly soccer rights, etc etc. Sorry, my criminal oceanographers are fine convenient to think about all this carbon in two pools, the DOM and the pump DOM is the sole organic matter and farm is particular 14:27:05 to organic matter and reality is more like a continuum. But, but, 14:27:11 but anyway, it's a kind of operational definition. There are there are large things and there are things that are solvable. 14:27:28 And ultimately, Hydra traffic bacteria, as a group together, recycle all this carbon and nitrogen and remineralize it meaning that they turn back the carbon into an organic carbon, co2, and inorganic nitrogen they're getting nitrogen nitrogen nitrogen 14:27:39 gas. Now, that's a level of obstruction. But what happens if you start piecing this up and tearing it apart. 14:28:04 First of all, this, this doin vs pm. As I told you, is sort of a convention but in reality so continue right from truly solvable materials to call it to little creatures like phytoplankton that are also particulate to large things like fecal pellets and 14:28:07 and large aggregates of organic matter. So, we don't need to talk about this is not super interesting but the definition is really operational is what stick, what stays on a filter on a given filter size is larger than one micron is particularly 14:28:27 So, so here we go so for, let's let's go first to the om and enter the pure. So, this. 14:28:29 anyway. 14:28:37 This is the salt organic monitor there are a lot of a lot of different molecules there is actually extremely high diversity of tiny molecules, most of which are on characterized, but let's say glucose. 14:28:51 Glucose is also present. 14:28:53 And in ranges are extremely small. We're talking about nano Mahler ranges as far as people have measured. 14:29:00 And so just to give you a sense for your, your favorite organism equally has a, an affinity or sorry I'm not constant that is in the order of the micro molar. 14:29:12 And so, oops, sorry. For those of you that don't remember this is my sketch of mono kinetics, and the case. In this case the micro molar or what you find in the ocean is nanometer so way been way below their, their. 14:29:32 And so naturally as you perhaps can imagine competition for for these compounds happens at really low substrate concentrations. So the species that wins the competition is the one that can survive at the lowest substrate concentrations. 14:29:34 The what the organisms can really uptake. 14:29:51 And so this is this is what what typically emerges from studying the model that came was that, as a model and I don't know if you guys are familiar, but this is what you would expect us in a key most that there is an organism that wins the competition 14:30:06 is the one that can draw resources to the lowest level where others cannot grow as fast and not cannot survive the dilution rate. And so that's what happens, we think, as well, in, in the environment in the ocean, for example, and the organisms that can 14:30:21 can do this, typically had they had to be very small. Because they sort of surface to volume ratio is a problem. 14:30:28 They want to put transporters on that membrane. 14:30:32 And if the volume is too large, they don't, they're not enough to, you know, to transport the nutrients in the cell needs. And so in order way to increase the affinity effective affinity there the case, why affinity is all one over case is the, is to 14:30:47 make the cells very small. So, what happens here is that this organism can grow very fast and hide substitute concentrations they become irrelevant because the competition is happening on those subject concentrations, so you get the selection for the 14:31:00 small scale them the. There are a few of these organisms. But the most well known and the most numerically abundant abundant organism, in the, in the planet is a thing called Pileggi back to Weekly or, sorry 11 as well. 14:31:15 And as you can see this image is widely distributed across the ocean, the number of sales is 10 to the 28 I don't even know what the number means, I think is larger than the number of stars in the universe, some crazy stuff like that. 14:31:30 there many very many results, but they are tiny. They are less than a micro I think I have a micro, on average, They're tiny cells. 14:31:41 Incidentally, this is just a parentheses. Incidentally, this sorry living organism, you can make a fellow journey with the mitochondria, and it comes pretty close, is the mitochondria is close to the record Cialis, which are endorsing violence, just like 14:31:57 the mitochondria, they also live inside other cells, and these are 11 is they're not so far. So sorry 11 is sort of the crossing of our mitochondria, and the most abundant organism, on the planet, these type of things, blow my mind. 14:32:12 Then on the other side end of the spectrum you have this to me or particular organic matter, which is rich in micro molecules like carbohydrates and proteins and so on. 14:32:22 So, they also they're also gradients that stem out of the particles that attract microbes that can do chemo taxes and so on. 14:32:30 And 14:32:33 so what we have there on a particle is actually a very high concentration of carbon for example or nitrogen storing these micro molecules gradients, as I said, and these particles are scaffolds for the assembly of dense communities that were microbes 14:32:48 can interact. So unlike the previous case where competition for uptake and transport was the most likely the primary determinant of competitive outcomes in this case, some more complicated story interactions between micros may actually matter when when 14:33:07 when trying to understand why are there so many of these microbes in a, in a particular, you know in a particle, who wins this competition, so to say. 14:33:22 That happens there. 14:33:24 And so, also in this case we are on the other end of the spectrum so we had a high concentrations competition happens there. so perhaps the affinities or not that relevant. 14:33:35 But this maximum growth rate is, is what selected for, you know, like, equal life For example, there are many microbes on this particles that are kind of like equal like the various for example that drum on answers. 14:33:59 Alright, so this is data from my paper. A few years ago, showing this divide between the distribution of microbes on particles and free living. So as you go to the left here in this heat map. 14:34:04 and they can grow really fast, and also perform overflow when they're provided with enough sugar experiences. 14:34:14 These are this is less than a micro This is what you would consider free living. And then you have the other filter sizes, their their ranges of filter sizes. 14:34:25 They go all the way up to 200 microns. And then you see see a clear by modality here. Yeah, they said 11 that's a big factor is very abundant and the free living fraction as I told you before, and things that they come through Mona's and side effects, 14:34:56 Latin names. 14:34:58 certified are typical typical your typical police Saturday the greater, they become bond and on the large particles. But what you have here is his name's here no most for most of you these things don't mean anything they're just weird. 14:34:58 This is what we're talking about here a huge diversity, you know, things that have diverged millions and millions and millions of years ago, and they're as different as you can imagine, for example a Delta positive material, and a Firmicutes, these are 14:35:13 really two different creatures although to the it may look similar if you're able to see them. 14:35:22 Um. 14:35:22 Alright so this is pretty much, pretty much what he said. So, um, and that by the way I'm trying to proceed because I have to leave. 14:35:30 In 10 minutes. I have to go pick up my, my daughter. So, and my wife is going to be angry at me because I'm late already. But I have only a few a few more slides here. 14:35:42 So, a few years ago, Nate Cermak who was a PhD student at MIT, brilliant, brilliant guy. 14:35:50 He helped develop this this instrument. And I love your MIT of stock mentalities, they were able to make to wait single sales. 14:35:59 Okay, and how that happens is a story you can read a big, but what you have here is the results, the distributions of biomass inventor grams for individual cells have different species of money micros of there you have the organism have been talking about 14:36:16 for a while now start 11 or Pileggi bacteria, tiny tiny tiny cells. We're talking about for yourself like 10s of federal grant. 14:36:26 And then down here, all the cells are also small for the synthetic broker Cocos in down here, you have, especially down here Bieber is plenty this Think of it as your equal leg. 14:36:37 I had their traffic organism that can grow very well sugars proteins and stuff like that. And, and this one when it's growing fast in a, an exponential face. 14:36:47 It's a, the order of 1000 photographs orders of magnitude heavier larger than the than the, the one that specializes on the soul organic matter. This is plenty This is one that specializes on particles. 14:37:03 This one in particular, loves to the great other particles I know because we have it. 14:37:09 I'm all right and so that's consistent with the idea that you know like this size matters. In this case, and it's related to the affinities related to the ecological niche, although all these organisms are hitter trips that are expiring organic matter 14:37:24 is completely two different beasts completely two different micro environments and evolutionary histories and like that one can keep peeling that audience, and you will find more and more and more niches. 14:37:37 If you, if you like that concept. And, and more diversity. 14:37:44 So, you know, so that's why I had this last few slides, that's all great. But I don't want to leave you with the impression that we understand where the organizing principles apply. 14:37:54 By no means, I mean, you may have already gotten this impression from the discussion we had earlier, but by no means we're nowhere near what happens is that we keep peeling the onion and we find more patterns, more diversity. 14:38:08 I we don't know what point to stop. 14:38:10 You know, I think there's a tendency of the physicist, to say these are details, you should look at the the microscopic variables, we don't we don't really know exactly how to make that call. 14:38:22 I mean I am. 14:38:24 I like the way of thinking but I don't think we know how to make that call. Some people, for example by educating some of them stop at the bio energetics, they say microsurgery as catalysts in this. 14:38:35 But, of course, the the microbiologist like that so what to do anymore. so it's always a really big problem. 14:38:40 We don't really know what is the right level, which we should describe these things. So here's a, I'm going to just highlight two, I think is one paper more from the lab of Martin post, who was my boss with advisors is way before I before I started my 14:38:54 PC. 14:38:57 And with a this this idea of peeling the audience. So you heard about 16 as those of you in the class this morning, the tutorial from Josh. And so this is a fellow genetic three of summary microbes, based on 16 s, but you can take with us if he or illustrates 14:39:11 illustrates you can take any of these little pieces here. And so, look at it in a more fine grained level, for example, take a nucleotide difference as to say okay maybe this is a different organism. 14:39:22 Instead of trying to collapse them all. 14:39:24 And then you keep finding more and more and more diversity, And so absurd. 14:39:43 And if you keep being, you know more specific you know the you you lower the threshold of similarity. The number of things increases disproportionately. 14:39:46 And then number of things that you find a number of different types. And so people have been posted about these micro diversity for a long time. 14:39:56 And so people have been posted about these micro diversity for a long time. And, and, and nowadays that we have full genome sequences and we can think of strains. So on this is this is a bit all this paper. 14:40:06 So on this is this is a bit all this paper. Now we have full genome sequences to play this game. You keep finding more and more and more and more and more. 14:40:18 And it's not clear at what point should we stop. It's not clear how to start explain the diversity is not clear just functionally relevant, etc etc. This is one of the problems we are facing these days. 14:40:23 This is also a relatively all paper from the level for the little has been very vocal on the, on the relevance of horizontal gene transfer, and how, you know, thinking of a species three sort of misleading and so on and so forth. 14:40:43 And very influential as well in in that arena. And I just want you to see just look at the top panel on the left. This is on the, on the horizontal axis you have the average nucleotide identity between tournament's what so when it is 100. 14:40:57 That means that every gene that you can align between these two genomes is perfectly aligned. 14:41:15 These blue this light blue dots here. 14:41:16 And what you have on the other axis is a percentage of shared genes. 14:41:16 And in their cases here. Take your again your favorite book equally. 14:41:18 What is his average 70 75%. 14:41:23 And many of you see color early like 97% percent this. So, there are 97, there are only 3% divergence. There, there are some points here as well, in blue, or whatever with any of these other organisms your senior which is kind of funny colors, almost 14:41:38 100% identity and 10 15% of the genes are different. 14:41:43 So that type of diversity that we keep discovering is really unclear how to explain it definitely the explanations are not in the bio energetics and not in those things, then you have we have to invoke ecology and evolution to try to understand things 14:41:56 and that's kind of an active arena. And finally, I want to leave you with with this, this tree of life that appear few years ago in nature microbiology from the love of your Banfield extremely influential work similar influential. 14:42:10 The main the main thing here is that the main news here is that the story is that what this purple plate on the right is called the CPR or candidates find out where the h. 14:42:25 m. 14:42:27 So just to be clear, what before this paper, the tree of life for me was, what's on the left, this thing. 14:42:35 After this paper. Now we know there's this whole thing here, which is, if you Sunday brunch length is a lot of diversity there. And so somehow I had been missed until now. 14:42:45 And this relates the question that was asked, I believe, I don't know who is this in the morning. 14:42:50 Whether the 60 minutes is a is has any biases universal primers. Yes. 14:42:56 This, this type of organisms in this current spelling radiation one of the many reasons why they were missed it from the service is because they have insurance in their 16 years. 14:43:20 So the this universal primers may not work really well, all this data comes from meta genomic sequencing the normal assembly assembly of genome so meta genomes, as well as single cell sequence in which is independent of whatever is in the 16 s, and then 14:43:22 assembling the thing they start to realize wow they're all just organisms. This is not an artifact. These are real things. And it's a very exciting area of research, to me at least, to understand the physiology of all these books, they are extremely hard 14:43:34 to cultivate I mean, I don't think, I don't know if they're going to be cultivated if there's anybody any, any cultivars available. But, and then the reason is also that they are seen by ions, in many cases, as far as I know the AP bio on spinning they're 14:43:49 always living next to another bacterium. There's a penis paper or one particular example, and, and they really they are not self sufficient, they, in many cases they lack the ability to synthesize essential amino acids, or you know, even nucleotides and 14:44:05 stuff like that. So they need to depend on other organisms a little. 14:44:10 Maybe parasites, or, or maybe they're mutually will not. 14:44:17 And again, just to emphasize with this. The fact that this is just only about six minutes but I want to show there yesterday, there's this amazing diversity, and you know as I was peeling the onion going from bio energetics to trade offs, to a little 14:44:31 bit of ecology with example of the DRM and the PM. 14:44:34 We are nowhere explaining been able to explain this diversity. It's also unclear whether we actually want to that. 14:44:43 So that's I think where a lot of exciting questions come in and it's funny, we know almost nothing in biology and this is kind of a frontier here. 14:44:54 So that, that's all structure function problem that appears in biology, you have it here as well. 14:44:59 Only in very few cases we can map. In, you can find a one to one mapping between the glades in the story of life and functions, and in very few cases, for example cyanobacteria their authentic photosynthesis. 14:45:13 Madonna genes are typically our care. 14:45:17 And there may be other things like that, there's definitely bacteria or many cases sulfate producers and so, but But otherwise, things are mixed around and then you know there's no easy way to map from from from composition species composition to function, 14:45:34 even from jeans to function so it's difficult. 14:45:39 Um, and so it's the one I wrote there is generally unclear at what level of genetic resolution once you describe communities is generally unclear, we don't notice, there may be a few examples are getting some direction so mark and others, etc. 14:45:51 It may be case specific, we don't. 14:45:54 So a few a few less lights, yes, no, no more data, anything just to wrap up in this building the onion exercise. As I told you, by energetics, to me at least is the first order of organizing principle. 14:46:11 And it's also important. I mean, the recent one of the best reasons in my mind, is why to study Microsoft because they are involved with the planet. 14:46:20 Whatever we see around. 14:46:22 If you see blue skies, is because there's there. there's kind of bacteria, and so on. 14:46:28 And there's also metabolic constraints, which as you realize they're sort of fully understood and and physiological trade offs etc. that explain some of the apparent division of labor that you see in microbial ecosystems. 14:46:44 Some of the division of labor, maybe a necessity in some is faculty. 14:46:50 And I think this is a very exciting arena separate for example as identified but I think it's a, it's a, it's a general problem in a really good interesting product. 14:47:02 Um, and, as I was telling you, just a couple of slides ago that you know once you start to get into the diversity of organisms. Then, not only organisms but the pathways and genes and etc. 14:47:12 Then, then the organizing principles, start to disappear. Now we need to start invoke ecology and now we find ourselves in the same arena as the plant ecology is that I've been trying to explain diversity for, for many years. 14:47:28 And so we need to consider perhaps predation interfacing to species interactions selfish elements and white and whatnot. 14:47:38 I know what the question is is that if you what you care is function which is a good argument that maybe ultimately what we should care about function is also clear, to what extent we need to consider the diversity of organisms to understand the function 14:47:50 or somebody to come is like to think, Microsoft just catalyst and I'm the only thing I need to know is, is Redux chemistry 14:48:02 omics genomics, in particular, is a blessing and a curse, because I think. 14:48:09 I think it's fair to say that although we have discovered amazing things like for example that candidate failure radiation is because of genomics. 14:48:19 At the same time, there has been a deterioration of the, of the quality of micro of science in microbiologist performed because for many years. I see I see is that kind of fading away now. 14:48:28 But for many years. There were many papers that were like here so microbes here so microbes there. There's more diversity here, and here, and that's it. 14:48:36 And so this is sort of descriptive stats is very dissatisfied and. And it's something we need to move away from. 14:48:44 And finally, I want to say that microbiology has been built on model organisms. And this is, I mean I don't want to give the wrong impression that I appreciate it because everything in molecular biology and physiology is because we have those models for 14:48:58 instance like a call I bacillus, we will call it etc. However, they are completely disconnected from their environments where they once lived in fact many of us organisms. 14:49:08 You can barely detected in the environment. And so and so, this is a crossroads where we are now, that sort of 14:49:17 transition point, if you will, between the distinction between the model organisms and amazing diversity and complexity of the within the environment, how do we marry the two. 14:49:31 And this is what I said. So I believe this is all I have. 14:49:39 Honestly episode like a super burning question. 14:49:40 Now, 14:49:42 You have to go. 14:49:44 Sorry, it's kind of almost 6pm here. 14:49:49 Um. 14:49:50 Anybody has anything to say I'll be I'll be around more if you want to talk. 14:49:54 I would love to talk in fact. 14:49:57 Well, thank you, auto others the same here. 14:50:01 Thank you very much for your patience. 14:50:08 All right. 14:50:09 I think it was, it was a great start. And there are obviously many problems and questions. And it might be fun to pick out a few questions that I think there is a fair bit of interest in the room. 14:50:24 And I don't know organize some Journal Club. 14:50:29 You know, just to pick a random question maybe not so random. 14:50:35 We had the little discussion of the sort of fundamental compatibility or in compatibility between different pathways, there were two very specific pathways on on the slide there, and there's definitely worked on that subject, it might be fun to just see 14:50:56 whether there is understanding. 14:50:59 So one of the relevant chemistry and microbiology, and I think we can entirely achieve that, in real time, well here. 14:51:11 And I guess another branding item is with auto waiting to start the second session remotely. We skipped on a very important thing. we've been get properly introduced to each other. 14:51:30 So, probably not the right moment to do it now because we have cookies waiting out there, but we'll do this properly tomorrow.