13:14:31 Hi, everyone. Thank you for coming and I presume you can hear me.
13:14:39 So what I'm going to try and do today is get over the shock of being the only biologist with no fees extremely the room doctor room full of physicists, but with hopefully overlapping interest and hopefully will ask questions because it's a first for many
13:14:54 for me over a month and a half first month a year and a half, first travel first talk in person. First or first visit to keep it up and who knows what else.
13:15:04 So with that introduction. What I'm going to try and do over the next hour or so is tell you why I think the system we've developed over many years which is the microbial mats system, in, in, in extreme environments is interesting and the kinds of questions
13:15:20 that have led somewhat willy nilly not quite serial monogamy from one project to another, and in all of those somehow I've veer towards talking to physicists, partly because I felt that they bring a completely different way of thinking that isn't is somewhat
13:15:38 alien to me and with enough tussles over years. We do get interesting results so that's really going to be the journey, I'm going to try and tell you about.
13:15:47 And I hope Daniels in the audience yes I see him. So he, we were just talking about this, just to break the ice. Everybody noticed the alliteration in diversity dynamics and defense, and another talk I gave Of course I gave was on microbes meta genomics
13:16:06 and mysteries and Daniel sharp back and he said, is that you know there's a word that describes specifically having a lot of ends in a sentence. So when you get tired and bored, look it up on your phone cell phones and let's see if we get the answer.
13:16:21 So what I'm going to try and do here is
13:16:26 go as quickly or as fast as anybody would want please do ask questions. And this is kind of the the team for everyone in a way, whose understanding organisms in the environment which is that you get an interesting phenotype but hopefully you start with
13:16:41 one. So that's on the upper left as well explain what that is and you wanted to link it back in some way to the environment and the approach we took and I'm going to lean heavily on that and as a counterpoint really interestingly to how otter described
13:16:56 it which is he talked a lot about Redux being important. I'm going to sort of shift to genomes and what they can tell us and and the dynamics there.
13:17:06 And so just to introduce it because I won't get to talk about it a lot. Is this process called phototaxis where all you do is put some cells down on a wet, others plate have light community, just a light bulb, and they'll actually start to move which
13:17:20 is making those fingers and they make these very regular fingers which I found fascinating and did not lend itself to an easy biological explanation, which is why I started talking to physicists and modelers.
13:17:36 So, in this next slide, just to sort of give you a bird's eye view of why cyanobacteria interesting. A lot of people wouldn't have to be convinced but maybe you would need some convincing.
13:17:49 So, what's interesting here is that, and, and, and, most of you heard auto stock yesterday. They really an ancient file them and they basically invented photosynthesis and you can't.
13:18:04 In fact, emphasize that more because that's where the oxygen came from that's why we're live in a way.
13:18:10 And they also, and also talked about this as well. They are were involved at some point pan organism and then gave rise to or plastics, which is where photosynthesis happens in every parent and every elder so that's quite a claim to fame.
13:18:26 And so what they are really a primary producers in a way, and I'll talk a little bit more about that, and they're there in in any environment to choose to look at.
13:18:37 They also fix nitrogen I'll talk about that more obviously they fixed carbon if they're doing photosynthesis. So, one can do a little bit of a good Duncan experiment to say, well that's not a bad partner to have in golf, because they they store phosphate
13:18:52 they fix nitrogen they fix carbon, and if they can spit out any of these things and you can control them, then it leads to the pathway of symbiosis which is also fascinating and, which we didn't talk very much about yesterday.
13:19:06 Another astonishing thing about them is that you can just dry them to Chris, put them back in water and they spring back to life and we know very little about the molecular mechanisms of, of how that happens.
13:19:23 But that is the great advantage now or disadvantage depending on how you look at it, of having over 2000 sequence antibacterial genomes. So there's a treasure trove of information that's out there that can be used to shore up to arguments or to build
13:19:27 Their heat and cold tolerant. These would probably interest is less of that.
13:19:41 up new hypotheses.
13:19:44 But on the other hand there are only a very few model organisms that have been developed.
13:19:52 So just very quickly what another fact thing that fascinates me about China bacteria, is they come in every shape and form the unicellular in in cases like this the spiral shape the filaments that move.
13:20:05 And they also actually have three dimensional structure for all of you who have thought about prokaryotes that's an amazing array of mythologies, and those mythologies I would argue also come with developmental changes and I'll come back to that a little
13:20:20 bit. So, then anything, but simple.
13:20:27 And now to dig a little deeper so just now looking into the self, what you see is, he has a cross section I should have put a spotlight of my Chrono Cross, and it's not a great picture but here what you can see a membrane.
13:20:41 That's another thing that didn't come up very much in the conversation yesterday is membranes are essential part of trying to do photosynthesis, which I've tried to show here this incredibly trivial cartoon but basically just to remind you, so it's in
13:20:57 So, in your head. There's a two fold two systems here for the system one and system two, and basically there's one splits water electrons can go through here go through the system one.
13:21:10 And there's a there's a reduction here and a production of ATP, all because there's a membrane in which you can separate these processes.
13:21:19 And this thing I want to show you in the next slide, but it's what's actually a light harvesting complex. So what it's doing is very efficient be capturing in the amount of light and funneling into the filter systems where the chart separation happens
13:21:36 and.
13:21:39 And the reason I bring this up is so you see it in all his glory here so each of these are rings of proteins, but they're all set up in such a way and possibly some of you interested in life and physics would be interested this funnel it efficiently into
13:21:54 these photos just.
13:21:58 And, again, you're very quiet so maybe I'll ask a question, you, this is, this is what happens in in higher plants and you don't see this colorful structure or any guesses about why sign of bacteria have this huge what's called an antenna complex, or
13:22:14 what is what advantage it might give them.
13:22:21 That's true. And, and also, each of these pigments absorb different wavelengths of light so even in very low light environments, they can survive when nobody else can.
13:22:32 So all of this. No, and I want to make one other point that also didn't come up that much I want to sort of dig much more into the genetics. Now, there are these complexes of operations which are just jeans strung together that are required to make these.
13:22:49 And it's not like you can just switch them on and switch them off. They're very tightly controlled and there's a beautiful phenomenon called chromatic adaptation which has been known for a very long time.
13:23:01 you can go the same bug in different wavelengths of light, and they change the structure of the fight populism to match the incoming light, so they are incredibly sophisticated in my opinion of I've seen and perceiving light and then making changes that
13:23:19 then make it more efficient for them to be in a certain environment.
13:23:26 Sorry.
13:23:28 More or less just care. Yeah, yeah. And also I should that's a good point to point out that these are the membranes in which they're engulf which are also complex to just shown us squiggles but that's not the case.
13:23:41 Yeah,
13:23:50 that's a good question. All the photosynthetic complexes are always in the membrane, and another point that's actually, I didn't point out their mobile.
13:23:59 So depending on on light intensity etc and actually even this whole big five a better song is suggested to move. And so I would say, given that rubbish goes the other major enzyme which, and that's not in the membranes.
13:24:14 But, but it's incredibly tightly packed in there. I don't have numbers, it would be good to have them
13:24:28 through the implication is just expands the range of wavelength and which can. That's right, but look mean the growth is limited by the light of life to get as opposed to phosphates and nitrogen and, for sure.
13:24:41 Light is and I'm building up that he was like being a resource in that way.
13:24:50 So again, this is kind of for the students over there. I don't see too many students at all but hopefully they're listening offline is the idea that you know model organisms have somebody pointed out that an hour of you would agree that model organisms
13:25:06 Nikolai East whatever have given us a tremendous foundation of knowledge which is why you can think of regulatory circuits and all of that.
13:25:14 And in the case of cyber bacteria that just a very few model systems and we can come back to why that's the case, but they've been used, obviously to study photosynthesis circadian clock, and Irene and I were talking a little bit about that nitrogen fixation
13:25:30 marine ecology.
13:25:32 Little bit of synthetic biology. But, and you can do all of these things which I believe you require to build to the next step. So you can, it's easy to do the biochemistry.
13:25:43 There's now more transcript omics inflammation, all this to say that to build a model organism takes a lot of stuff, and insider bacteria I think we're kind of there.
13:25:55 However, I would argue very strongly and coming from my own experience, going back to the story of for the taxes so beautiful phenomenon.
13:26:04 But if I think about it for a minute.
13:26:06 They are never growing on petri dishes at point 4% are gross. So they're always with somebody else and we've completely missed that story. And I think would actually be going very wrong directions potentially by shoehorning regulate the networks that
13:26:23 we find into that simple example of what's going on. For example that phototaxis that I showed you the fingers movie that may never happen in the environment, or if it happens, what's the proxy that actually happens in the environment is to me the question
13:26:37 to us.
13:26:38 So that's what actually led me really to start to look at environments where cyanobacteria important motility was important and fluctuations were important to try and understand what was going on in the system.
13:26:55 And to understand core foundation which is something I, again, think of not and some modeling approach, but just the dynamics between different organisms.
13:27:05 So not to beat a dead horse. At this point at a couple of things here, one that I find particularly interesting is in Yellowstone, everything's protected so you have to get permission to go in, but there is an incredible diversity of micro niches for
13:27:22 want of a better word. So one example, gives it away, is something called chocolate bar is incredibly high in iron, and yet you have bugs going in there.
13:27:34 Their son the bacteria growing in there so an obvious question to ask is how have they adapted to these environments and we know very little about them, but I would argue the tools are there to do it.
13:27:47 So, in a simple minded way so now instead of getting deeper into how we set up these experiments. You can think about these spring so this is October spring call for obvious reasons, where water's coming out of the geothermal events, and it cools and
13:28:04 it runs down these channels.
13:28:07 And once you can see, not so beautifully here, you can see these colored areas where the sign of bacteria has started to grow.
13:28:14 And what's beautiful about the system, to me, is there is this sweet spot here between about 70 degrees centigrade and 50 degrees centigrade, where cyanobacteria have their day in the sun, because above that they, for some reason, something we're thinking
13:28:31 about over a beer. There are no foot photosynthetic organisms about 72 degrees and archaea kind of take over.
13:28:39 Below 50 degrees, you get you carriers pesky you carriers Come, eat Grey's, the rest of it. But if you look at that area between the two, you can actually really set up the experiments to go.
13:28:53 Just look at cyanobacteria and and and this is a close up of what the math, look like they've got a top green layer which is where the side of bacteria are, and this is what we call it a week.
13:29:21 the structure you get which is about the size of my pinky to do all your experiments and.
13:29:22 Any questions about that. Yeah.
13:29:28 So,
13:29:34 no it doesn't love a flow, every day, more so in October spring the spring next door where we always are. We also work which is called mushroom spring, but let's come back to this idea of flow because there's a question I have in mind to pose here about
13:29:49 flow, and forming biofilms under flow.
13:29:54 These, these temperatures that you're mentioning have a stable, even through, through the day to day and for the seasons, actually.
13:30:04 So that's a sorry I should have mentioned that's another very attractive feature of this you can go them.
13:30:10 Winter you can go very easily but you put your mind to Japan, but you anytime of the year you can go. And it's also doesn't fluctuate between day and night.
13:30:23 One of the latest UK that in, in, in octopus and mushroom because of the way the springs are settled and this is a question that we've discussed ad nauseum with Daniel, that things can come up and bubble up and then because of stuff that happens in the
13:30:37 geochemistry of it, you can get fluctuations in temperature, the very regular basis, but by the time you come down to those temperatures is kind of steady, whereas mushroom is steady and a lower temperature, all the time.
13:30:52 Excuse me back.
13:30:54 Once you sample a block of a map like what you've described here, how does the map recover, does it grow from the bottom up from.
13:31:03 Yeah, that's a fascinating question. And if there's only phenomenal logical information that what happens and people have, you know, the early like Tom Brock and all that did experiments basically pulled out stuff and you basically see some of and I'm
13:31:18 going to talk about in excruciating detail. These filaments that come in, not the sign of bacteria, and then the sign of bacteria seem to follow them.
13:31:26 And it's slowly fills up, but when we took core samples and came back the next year, you could actually tell where it had been but more or less filled in, but without us knowing the details and what actually happened to that process.
13:31:44 So here's where things get yeah yeah how unique.
13:31:55 Very good. Outside of Yellowstone. Sorry, do they exist Oh yes, they exist in almost every hot spring. So you will always find cynical caucus and one variety or another, and we'll come back again to try to understand how different they are and does it
13:32:11 even matter.
13:32:13 So, yeah, so that's perfect lead into this question to this slide which is phylogenetic three which I assume I don't have to explain but happy to explain.
13:32:25 Okay.
13:32:27 An order you can look here is right at this part of it. Everything that says always stands for October spring. So these are all just to answer your question, I mean, these are all from octopus spring.
13:32:41 And you can see that if you go to the lower temperature parts of the map, you always pick out what we call type B, but at the higher parts, there was always this thing called type A, so this telling you just at the 16 s level, there's a distinction, but
13:32:57 you can go back year after year and you can find the Type A and the type B at those temperatures. And in fact, it was the genesis of all the experiments we did for the next five years, which to ask the somewhat naive and trivial question that does how
13:33:14 the 60 actually it's on the next slide when I just pulled it.
13:33:18 So really the question is, we call these rival types. Do they reflect the functional diversity we see because this is just one fingerprint of what's going on.
13:33:31 And and these are all the methods we use but I'll come back to that.
13:33:35 And then as we I've been telling you about I think what would the idea is to take all of this information and try to figure out, are there any rules we can come back to from looking at these as these systems, and I'll, that's really all I'm going to be
13:33:52 talking about. So what I'm going to try and tell you is three kind of short stories. They're not complete by any means but it was just sort of as teasers, and hopefully we can talk about it over the next week and a lot of this is published, most of it
13:34:05 is so we can always, you can always go back to that. So first I'll start with the comparative economics.
13:34:12 And just to give you a little flavor of how it's done.
13:34:16 All the gory details have been taken out. So you can't complain. So you start with the core samples like I showed you, and basically if you get everybody out of there you got what's called a message, you know, with a lot of caveats so if anybody cares
13:34:30 about I'm happy to talk about, and you get something then from this if you're interested in the red sausages, which is the cynical caucus, then you use an enrichment culture which allows these to grow.
13:34:42 And what we had against so these hopefully we'll get seared in your mind now the low temperature blue guys at OSPI temperature is OSA, and those were our reference genomes for proxies for these two temperatures.
13:34:57 And then what I had wanted to do and are getting much much closer is beautiful as Yellowstone, is there are problems is going back every year and doing certain experiments.
13:35:09 So the plan was that we would be able to grow them in the lab, we can do, and to build up a genetic system which is critical. I think to take the next steps.
13:35:20 And then to use them to build synthetic communities which is what we're doing a little bit with separate and hopefully to start to do evolution of populations, not with cynical sisters our model organism for cyanobacteria which has been sitting on a petri
13:35:34 dish for 25 years, but somebody that has relatively fresh out of the environment.
13:35:41 So, to tell you the punch line a little bit early. So if you look at for example sent any plots which is basically looking at gene arrangement along the genome, and you look at organisms, for example, folklore Akaka Susannah Bactrian from the oceans.
13:35:59 If you see two very closely related organisms, and you just plop them along the two axes, if they're in the same boxer, more or less in the same position, you get this straight line, more or less and in some cases you can get inversion, as you go further
13:36:16 and further away, you get less and less sentence.
13:36:21 Now, given the fact that we had these two organisms cynical gawkers OSA, and always be the first question we asked is, what does the sentence me look like.
13:36:33 And lo and behold the founders know center need to go off between these guys.
13:36:38 The only bars, you can see that kind of go all over the place or transposons which are basically hopping around. So this was the first and most amazing experiment that I had ever seen with two organisms look like each other they're 16 so look like they're
13:36:53 pretty much similar, and yet there's almost no sin between them, which is one of the so called rules that as you get further and further apart soon. The synchrony may break, but two very closely related organisms are not likely to show that.
13:37:09 So it's set out a whole train of thinking for me is, what is the how and the why of this phenomenon and how common is it is it something to do with extreme temperatures.
13:37:21 Is it an outlier. These are all questions that we can't get out of just looking at to genomes, but it's, I think fascinating questions.
13:37:30 Yeah.
13:37:33 Right.
13:37:44 That's, that's not an impossible hypothesis in this case I don't know that they're always drying up they can. It's a, it's a possibility that the DNA is breaking up when they're dried we don't really have any experimental evidence.
13:37:57 Though I would say that saw an organism called diner caucus with some of you may have heard of a is UV resistant does break up it's, but we have no evidence that cyanobacteria can do that, but they are very UV resistant so it's not an impossible idea.
13:38:23 Yeah.
13:38:28 Sorry we're doing a bad job with the microphones, but we should have announced that we need you to use the mics when you ask a question so the zoom participants can also hear.
13:38:38 So I think my question for the zoom participants was Sergei had this great hypothesis about if they dried out their genomes look at fracture they'd have to reassemble from scratch and I guess I was curious then with this predict that two isolates that
13:38:51 are very very closely related, even within the same rabbit type would be totally scrambled because of the drying up, you know.
13:38:57 Yeah, if it's a physical phenomenon like that.
13:39:00 I, you know, I have no evidence, one way or another, is an experiment you could do. Yeah, yeah.
13:39:10 I was leading to that I could do it, it hasn't been done. Thanks. we have an estimate how many million years separate those two glades is a welder. I don't know that, but if you address this to Daniel.
13:39:24 He will no doubt, say, it's a question we have mucked around without any clear idea, the one thing we know is that the caldera which erupted was about 300,000 years ago.
13:39:38 He has an adult want to split your can say that the work is done here.
13:39:41 Go ahead, Daniel, no so yes there's that okay we're starting to say this one timescale which is known, which is the time scale formation of the Yellowstone Caldera.
13:39:51 And if one assumes that diversity within the B group formed on that timescale which is sort of reasonable with mutation rates and generation times and so on.
13:40:00 Then the, the divergence of the B from the a is another factor of five or 10 longer than that.
13:40:08 3 million roughly then, if it's done maybe I mean it's one doesn't know. Maybe.
13:40:17 Maybe one quick follow up question to that is, um, is this level of scrutiny, high or low when comparing to other closely related strains, carry know as a very high what however you're defining sentence, there is no sentence, and I will show that in the
13:40:37 next slide, which is something a little more important but so far no evidence that this is a common feature.
13:40:48 You know, roughly, what are the gene content differences between these strains. Do they have, like, a very high overlap but they're all coming in the next couple of slides, but I'll be there in a minute.
13:41:03 And there was one other question.
13:41:06 Um, I think I've seen similar plots for like strains of Nikolai and they don't have this level of genome reorganization as I remember, it's something that's somewhat specific to cyanobacteria if you have any understanding of what why that why that is
13:41:19 why Santa Victor I do there's so much.
13:41:22 Sure it's true of all sino bacteria because I don't know that much of this, this has been done with close the proper focus and cynical caucus to some extent they do believe they're more.
13:41:33 They're more synthetic than these guys are killing the broker Cockers, you can go to much bigger genetic distances, and they're still synthetic salsa streamline genomes, other things going on, but all of this is a leading for me to say that this was,
13:41:49 I got deflected totally from our project, by looking at something like this, and I will answer, I hope some of the other questions that came up. So this is something this is just another way of showing the same data but i think it's it's in the spirit
13:42:03 of all of this. So this is the it's a closed circuit, you know, kind of vanilla favor about 3000 genes, two copies of identical 16 s, and kind of false force color.
13:42:16 And then if you look at outside is I believe oh so you know it doesn't really matter. It could be done any which way, just another way of showing the symphony.
13:42:27 And so now we can start digging into all the questions that were asked, which is that they are very closely related based on 16 s and identity of the amino acids and the symphony by some parameter is broken almost on average every to KB, but it's not
13:42:48 to say that opera on structure is broken up. There are very few instances where operations are broken usually because of transpose on has jumped in. So we did do a major analysis, which I won't die, you will have all the different kinds of transposons
13:43:05 they are. And actually you can look in the meta genome and actually can see evidence of these guys actively moving around.
13:43:14 So now what I'm going to do rather more quickly so just this is just an example, I think you get the picture.
13:43:20 I think what I'm going to try and do is now sort of position you to say we will be found all these things. We really didn't know quite how to go after them because we basically had, and we'll come back to it, just to reference genomes, and then a sparse
13:43:38 meta genome that we could recruit to say do you look like OSA or do you look like OSB, and most of it suggested that there was a lot more diversity around OSB which is the low temperature guy, and much less diversity, for OSA which is the high temperature
13:43:54 guy and I leave it at that and we can hopefully come back to what that might mean. Because what I want to do now is give you some examples of things we got by just gazing at these two genomes.
13:44:10 And this is not, I hope, just just so stories. I hope they'll build up into something that I would like to make as a hypothesis about what might be going on.
13:44:21 So what I'm going to skip to now is to show you one example of something we found very typical and just simply just compare the OSB genome that OSH you know you find quite a few examples of this, where there's a region that's flanked by transport zones.
13:44:51 And that was the focus that we use rather than to look at random genes to look at something that says, okay, we kind of understand what's going on here.
13:44:58 you can see that there's something either hopped into or got lost from OSA, but it basically shows you what looks like a pretty authentic offer on to do some.
13:45:00 And what these genes are I'll tell you in the next one is that it's a transporter so it allows these forcefulness which are also telling the next side to come in and then you have a very complex enzyme called a CP lies that can basically clean those bonds
13:45:17 bonds and make a long story short, this is what also phosphate which all of you know, looks like forcefulness have a phosphorus carbon bond which is difficult to break.
13:45:32 However, and again only. to my knowledge, only prokaryotes can make it.
13:45:37 It's not quite clear design should still be asked, Where fascinates in these hot springs come from, but clearly they're there. And nowadays, of course they're they're everywhere because then herbicides in in all sorts of things.
13:45:52 But to skip back to the story of what we actually found I'll just give you a bullet points can happy to talk in detail about it later. But it's important to realize that almost every nutrient in these hot springs is limiting there's almost no nitrogen
13:46:10 that almost no phosphorus. So it's really the sign of bacteria who are building up the fixed carbon storing phosphate and, which I'll show you in the next couple of slides, also fixing nitrogen.
13:46:23 So, what we found that again I'll just I'll just sort of give you the highlights of this, it seems that always be which is the low temperature guy is using the CP lies which is promiscuous so it can use almost any source of forcefulness.
13:46:45 Unlike OSA which seems to use very specific for spawn at isms. So it uses for spawning cases, which can only use for example, metal forcefully or amino accurate force for me and one could then potentially set up to do experiments in terms of evolution
13:47:01 and competition. But it turned out of course both of them can go first fascinated so that was a bit of a surprise to be, but I mean it's possible to do other experiments, but that's the line of thinking, we would use.
13:47:14 And it's just to point out that we do, we did make a mutant in a poly phosphate kinase which suggests that we can do geneticists very non trivial, but it sets us on the path of trying to do, genetic experiments with organisms from these extreme environments,
13:47:33 excuse was that a question.
13:47:35 So I might have missed it, and do these two types occupied different spatial niches the temperatures are different. So did you check the. A biotic environment rather the exam to see what resources are there like a different types of force.
13:47:50 So, so in terms of our guess is that as you go up the temperature gradient you mostly only get OSA very little OSB, and as you go down the gradient, it gets to be all of these variants of OSB.
13:48:07 So, so how different the environment micro environment is, is, is unclear because I'm getting a somebody asked, it's happening in flowing water so one might argue that the guys downstream where all of this other activities happening of you carriers etc
13:48:31 have more access to nutrients for example, on time.
13:48:34 Want to go a little fast.
13:48:38 Oh. So the other surprise we found so that was an example where there was a module that allows you to use fascinating one of them, and a slightly more attenuated form in the other species, right, so this is suggesting that these gene, these modules can
13:48:54 come in and out, and our I think it sets up, is to ask why which we don't have an answer to but it's a legitimate question to ask. When does one module kind of sweep through the entire population.
13:49:08 And since we only at that point had to isolate, you can't really ask this question very well, but you can with meta genomic data, and I'll come to that in a minute.
13:49:23 Yes, question.
13:49:24 These, the genes in this stretch that you were showing that are shared between A and B, how similar the idea the sequence level. Do you mean at the Franklin Regent.
13:49:37 Yes, they're very similar but not identical I don't believe.
13:49:42 Okay, so I've watched.
13:49:44 I mean, yeah, because I was thinking about you were mentioning horizontal gene transfer at some point right and so I was wondering if you know you could infer that these are probably come from the same source but they've been away from each other for
13:49:56 a bit so they've diverged but not a lot compared to the rest of the genome yeah so that's a beautiful question to ask, you know, how big is that module that comes in and when it came it what happened.
13:50:08 And I believe one can begin to answer that question.
13:50:14 To help differentiate between this temperature effect and possibly nutrients as you to the upstream downstream flow.
13:50:22 How How do these different string about just temperature wise today, what what are the optimal temperature they said differently. So we don't have a very good example of that but that's also something that we've been dying to set up need some experimental
13:50:35 some physicists is basically a temperature gradient that's kind of fino copies this three feet difference, and see that with both OSA and OSB, and ask it, what temperature does one peter out.
13:50:48 But then, first I would imagine you're stuck with x in exchange.
13:50:51 So I would argue that OSB, you don't see them at 70 degrees so at some point in that temperature gradient there petering out, and the reverse is happening for OS was just growing monoculture so that they can do.
13:51:10 But
13:51:10 if they have the same temperature as it does is no bad temperature.
13:51:15 I'm sure they won't have the exact temperature response, but the question I think that's more interesting to me is if there's subtle differences. So if they can go at 64 and not 66, what's happening at those temperatures.
13:51:30 If that is kind of where you're going with the being somewhere.
13:51:34 Right.
13:51:37 Yeah.
13:51:40 Yeah. Yeah, I agree. Maybe I just coming up. I mean, with all the stream level diversity within, within these and the amount of overlapping genes between the two which seems to depend on the cell and so on.
13:51:52 I think there's the whatever one would measure with a colonial strain in the lab might not tell one, tell them very much.
13:52:06 almost the last time was the last part of your sentence, nobody that trying to measure the temperature responsible colonial strain might not give one much clues of rule because of the diversity within the within the be.
13:52:15 I thought that you were asking about diversity you were just asking a simple question about temperature.
13:52:21 So, we know, we know the gross level right that always be does not survive at 70 and, but I imagine you have to go beyond that, get it any deeper understanding of what's going on, but you are right and it's something intriguing that you have to two organisms
13:52:38 that are not active and and really can't hack it at these two extremes, and so it does behoove us to know what's going on.
13:52:51 What about the role of mineral precipitation.
13:52:54 Because if you're growing a lower temperature you have a different mineral precipitation or a that could impose a different growth rate on the, on the colony to escape hospitalization.
13:53:06 I am sure that could be true but I don't know how much that affects growth rate, and as an old how much temperature base, but I think this leads to some of the questions that will be good to discuss is when you start changing a multitude of parameters,
13:53:20 you know, what you get out of it to something.
13:53:23 I find hard enough to think about, let alone design experiments that then I'm confident that we're getting is be here.
13:53:31 But mineralization is true does payroll and you may have seen in those master realism and realization, because just to get some intuition here What should we think of in terms of the the doubling time in these mats and natured.
13:53:43 Do people know this is like deja vu five years.
13:53:47 So we don't know in the math, although some people early, early on did it and I was going to look it up and I've got, but in the lab, it's about 24 hours, and we can push it to about 20.
13:53:58 And we haven't done it very regardless, we're setting up now we have set up to do it in light, dark we were growing them in continuous light which is the classic where you grow sign back to grow but, you know, dance is something more sophisticated haven't
13:54:12 done that, if you had to bet, would you think it's closer to 24 hours or more like four months, four months, but in the match.
13:54:23 Yeah.
13:54:24 So, but this raises the whole question that when you're sitting around, not dividing.
13:54:29 What are you doing, I mean, philosophical question but in the math we never, I mean the lab we never
13:54:40 were done any more question.
13:54:43 Yeah.
13:54:51 I mean, can you look at gene expression like directly in the map because then you could ask, you know, for the strains that you can then grow in the lab what growth rate.
13:55:01 Best, you know, mimics the observed gene expression patterns, and then we'll come to that at the very very end. Ok.
13:55:12 Okay, so I'm going to go a little bit faster. Oh shy.
13:55:28 I may have missed this but is the for what's causing this sort of gradient, who's on you know what part of the temperature is the hypothesis that they literally can't grow outside of the range or that they get out competed outside of the range.
13:55:35 Okay, okay. All right. I mean, both sides questions me as an experimental split ask, how would you set up something rigorously to ask that, and who was it who said, Oh yeah, Daniel was saying, but if you start using exceeding strains, one is like getting
13:55:52 It's like getting you in the lab and you in the lab and now you're all of us and I just don't believe that's true and you shouldn't either looking at the, The flexibility of those genomes right so I was, I almost feel and we're thinking about it very
13:56:07 hard, is we have some core samples. And if we have a lab set up.
13:56:13 Perfect, we can drop them into a whole matrix of different parameters and then just run that experiment, because either. I think that bothers me is the question of my takeaway say annoys me I'll get an answer.
13:56:29 But does it mean in terms of what's really happening in the math.
13:56:34 And to be perfectly frank with you because you're a physicist, but I mean you could propose to do an experiment like that, and you would get an answer.
13:56:42 But I didn't have satisfied would be to me.
13:56:47 So question at the back.
13:56:57 Okay, So, so the other surprise we found, And we were told.
13:56:59 There is no nitrogen fixation that happens about 55 degrees centigrade. And here was a genome that had every 23 KPPS that looked like that all the genes for nitrogen fixation so said I'll be damned Brian will try and figure this out.
13:57:13 But we didn't have an easy way to do it and I will tell you the story because I think it's a way to do experiments in situ the positives and the negatives of doing something like that, and two other things on the slide that are worth pointing out for
13:57:27 those of you not familiar with this is one is that just a side you can have this is producing hydrogen, and that is something that came up in orders talk yesterday.
13:57:38 Many organisms will produce hydrogen, and then they also have what are called uptake hydrogen is so they don't new you waste the resources put it right back to us for something.
13:57:50 Interestingly, as far as I know, when we looked at this, which was some years ago, there were no uptake hydrogen ss, so this is going to another part of the story, hopefully we'll have enough time to talk about is the utilization of resources that may
13:58:04 be signed or bacteria have figured out, it's fine to let the hydrogen out and let your comrades, use it.
13:58:11 But that's the beginning of the second story which is, if you're the primary producer, how much of this are you doing for yourself how much of this is feeding the rest of the map.
13:58:24 So basically what we resorted to was to take in situ measurements and at the time. Several years ago, it was a somewhat unique way of doing this and what is required, as opposed to persons who are willing to take measurements over a deal cycle to see
13:58:42 what is actually going on.
13:58:47 And I, as an aside, since I've been talking too much. I was told, you'll never be a card carrying ecologist unless you spend 24 hours in Yellowstone so I'm not a physicist and not a card carrying ecologist, guess what I am.
13:59:01 So this is typically the kind of measurements you can get, and and walk you through this somewhat quickly because I'm sure you'll get the drift, but this is over 24 light.
13:59:12 Here the dark period followed. And you can see that it's cloudy day the light levels, change, but you do get to be looking here, the amount of oxygen produced and then penetrating into the math, and this is happening every like dark cycle.
13:59:27 And then you can layer on top of this of other data. And in this case again I won't bore you with details but basically to show you more of the result.
13:59:39 And then what is possibly telling us something that was really interesting to us. So now you're looking at actual nitrogen is activity remains you froze the samples went back today Ward's lab in the nitrogen is a Sicilian reduction acid.
13:59:55 And you can see something that is would have been very easy to mix up, if, if an steno had not been a great scientist, and that as you can see nitrogen is levels are kind of low, but there's this little peak early in the morning, where it really goes
14:00:10 up six to 10 fold. And then in a few hours later, it kind of falls again.
14:00:17 And what we did to try and figure out what was happening there was to basically look at other parameters, including the expression of of NIF jeans and a whole lot of other genes for photosynthesis and nitrogen fixation.
14:00:32 But what we also did because they were antibodies available to the major fH protein, you can see that not only so this answer some question. Somebody asked, it's not just the transcripts that are changing, but proteins are also changing on a daily cycle.
14:00:50 And if you let that settle in your head for a bit. It actually means that these major complexes like photosynthesis and nitrogen fixation, the whole complex has been broken down and being remade.
14:01:02 So it's almost by the to graduate and I've shown you is the, If you think of cynical Caicos it's almost a different organism in the morning when is doing photosynthesis and at night when it's basically using glycogen to do fermentation.
14:01:17 So it has to be switching these roles on a diet, on a diet cycle. and the question that maybe we talked about it. But this idea that once you have this primary producer that does this.
14:01:32 Does it set up behaviors in the hetero tropes and everybody else who's living off the resources being produced.
14:01:46 I have a lot of questions.
14:01:48 Okay so, so nitrogen is famously sensitive to oxygen, sorry, nitrogen is famous famously very sensitive to oxygen.
14:01:56 And so you're saying that it's, it's not so I don't understand the temperature problem, maybe you can say some words about what the problem with 50 higher than 50 see is, and then also you, I mean you're showing us that that oxygen is being produced at
14:02:08 And then also, you, I mean you're showing us that that oxygen is being produced at the same site that the nitrogen as activity is happening and that, you know, there must be some strategy for making those things compatible with each other.
14:02:17 Maybe the strategy is just continued recycling of the nitrogen as every time it gets destroyed it gets recreated or something like this is this that compatible with the data that you showed us know, because it doesn't look like that it's happening over
14:02:29 a two year cycle, but I've come to you I mean your question is well taken. The only thing I would say I may be misspoke is it's not that it's, it didn't happen at 50 degrees.
14:02:40 That was the word on the street, and I was trying to say is that if you went in, at this time of day, you said there's no nitrogen fixation and that's what most people do they don't go into an experiment at four in the morning, but what we fail to because
14:02:54 we know that nitrogen is killed by oxygen if you're going to get an act, any activity, it's more likely to be in a period of the dark. So if you look very carefully, but I think we're getting into the weeds and you and I can talk about this the change
14:03:08 in nitrogen is activity, but to two may be of interest to everyone else is there modelers in this crowd, what we came up with this idea which basically is repeating what I already said is that there's a region here where everything you need for nitrogen
14:03:25 is to work happens to be there, which is that there's enough reductions. There's energy being produced by photosynthesis. And so, and and and the nitrogen is not being killed by the oxygen levels.
14:03:50 And this goes back to, I think, a very important part of how the math is structured that at certain times oxygen can build up in fact you can get eight times higher levels of oxygen in the map from saturation, but that's all being used up by the hetero
14:03:57 tropes. And so once you get to this point where there's a lot of photosynthesis going on. There's too much oxygen produced, and it kills the nitrogen is.
14:04:08 And so this cycle repeats itself every diet cycle, and I don't have the answer to this but I'll just leave it in your head as somebody was talking about.
14:04:18 I have in the case, there's a circadian clock in these guys. So is that part of what's happening here that you anticipate the fact that you're going to need for the systems, you're going to need nitrogen is and you start to do the expression, and the
14:04:33 buildup of the proteins before you're going to need them. So I leave this as a testable idea, we haven't actually done it but we're trying to do, and trying to grow.
14:04:44 Do you sign the bacteria under conditions in the lab where we can start to test this, because otherwise we have to resort to making all these measurements, essentially, in situ, we're just at a point not so feasible.
14:04:58 The Rocky.
14:04:59 Sorry, it's me.
14:05:01 It could you go back to the last slide where you had this in the US I am you know staining there the bottom.
14:05:09 Yeah. What is that, oh is that telling me. That's telling you that you have to look a little more closely, but you can look at the New Age expression.
14:05:20 And you can see that this is slightly delayed from the actual production of the Mr. Na, it reaches a peak in the evening, and then it's being degraded by noon.
14:05:33 So it's essentially telling you which is more or less what people believe is Mr. Na and protein levels don't have to be in sync with each other, and how that's happening and control of that is something we don't know, but I was compelled by the idea that
14:05:46 that you said that it was disassembling the nitrogen as it is and then building it again each day.
14:05:52 Because now, not the case for the photosynthetic oh yes it is.
14:05:56 And the day one and day two proteins are completely broken down because they're damaged by highlights, they're broken down, and there's a circadian rhythm.
14:06:05 So, you know, this is from Amanda's meta transcriptome data. Many of these genes follow a strict circadian clock right right but I always interpreted the RNA is, you know, okay so is that actually the protein levels in the 70s and that's why I showed
14:06:31 but also based on what we're imagining they're not, they are doubling and they do double at just about that dawn time point. So it's a possibility. But, I think.
14:06:44 I totally agree with you. I do feel that doing all of this in situ is a pain, and you can't get to the levels of quantification that you might ask, which is window, how much the cell division play a role in the switch we're ignoring essential in in the
14:07:07 mRNA or the. We calculated in the page, I remember it's like 1314, different, something like that.
14:07:15 So it's probably not cell division right.
14:07:18 One question.
14:07:20 Do you have any evidence that the physiology of the other microbes, not the sign of bacteria.
14:07:26 Show it resulting 24 hour pattern in response to this, so desperately trying to figure out now and okay and, in the absence of that, do you know if the, if the other molecules designer bacteria secrete.
14:07:41 They presumably have this 24 hour rhythm is that buffered, as seen by the other bacteria or do you think they actually like these levels actually change in the context of the other.
14:08:02 I think they do and that's actually what we're trying to do so they were very cursory experiments trying to show the organic acids are being released by the sign of bacteria and like Palais and lactate that go up, presumably being used by the other abundant
14:08:04 organism, that's in there. So they are cycling, but whether that's having an impact on the actual replication of the other guys it's harder to do, which kind of jumping the gun to the kinds of things that's happened I and others are trying to do which
14:08:16 is to build a synthetic community with all its attendant problems to ask questions of that day.
14:08:27 I, I do.
14:08:32 Again the stuff that you were asking in the previous slide.
14:08:34 Do you know for sure that it's the same cell that switching and changing its, its transcription level or could be that there are sub populations that are just different that just rise and fall according to Dr P and that's the problem with this kind of
14:08:49 experiment. Even the nitrogen fixation when we tried to publish this and it's true. We're basically taking the whole map.
14:08:57 They could be somebody else is doing nitrogen fixation that's on a day cycle right now we know that's not true, but it's an, it's not do that.
14:09:09 So different some populations are doing different things, you know, is what you're arguing potentially yeah and the falling based on the environment. And I think that's a really, I went that route would like to go with the kinds of experiments and I,
14:09:22 you know, if I want talking so much more of a discussion about how to do these experiments, in a way, I mean I have my ideas, but quantifying this and building it up so we do the right experiment the model it is valuable.
14:09:37 So, I don't know much about this but couldn't you bring like single cells to the lab and just do transcriptome mix with them and just figured out you know if we could and we are and we will.
14:09:53 So, how much I haven't even come to the end, you can go another 25 minutes.
14:10:00 Okay, so I'm going to be very brief and and just really bug me if I'm saying something absolutely outrageous. But I just wanted to leave you not with the idea that here you have nitrogen fixation going on in a unicellular organisms.
14:10:14 So it's being temporarily separated from the photosynthesis, which is the oxygen generating process right that's the, that's the bottom line. But what I wanted to say is that is by not so that's these guys in the mat.
14:10:30 But, in fact, cyanobacteria have found a plethora of strategy is to try and do nitrogen fixation, including having specialized cells that are called head Croesus where they basically I mean it's incredible.
14:10:45 They basically break down for the system to which I'm sure you remember, is where oxygen is produced, so they basically kill that reaction you generate reduction, which is what they need an ATP just from for the system one, and that is happening in a
14:11:00 Spaceman every 14 cells becomes a hypnosis, which is another element, and this goes back to the question of development, then by no means doing this in an ad hoc fashion.
14:11:11 So that's what actresses, they can sometimes all just clump together. And so the filaments in the middle of the least oxygen and that's where you can get nitrogen fixation so essentially the same problem being solved in ways which I kind of find fascinating.
14:11:27 However, the one that is absolutely unbelievable is what Jonathan's there found, because one of the hallmarks of a sign of bacteria is that they have both system one and a half water system to and regenerate oxygen.
14:11:41 These guys called unpronounceable name is actually have basically shot to pieces their photo system, too.
14:11:53 So my some criteria and they're not they're not satisfactory anymore, but what they've become is basically nitrogen fixing organisms that feed.
14:12:02 Another unpronounceable marine organism. So, I want I just want to leave this thought in your head, that the genomic flexibility in these organisms is something you would just and actually when Jonathan did this work, I have to confess, I didn't even
14:12:17 believe it, it just seemed to fly in the face of all logic, but that I think should be an interesting lesson for us is that the rules that we assume to be can be broken.
14:12:35 Okay, so I'm wonderful very quickly through this because I started talking here at the TechCrunch talking at some point, I'm not sure when yet, but I don't know if he plans to talk about this.
14:12:46 Okay, but I'm go very quickly.
14:12:50 I can say some things. Okay, so no Danielle That can't be true.
14:12:58 No dad yeah that can be true. I think what I'll do is I just say my piece. And then when you get your turn on the stage, you can talk more about it I'm going to give my biologists view of the world.
14:13:12 So, again I skipped.
14:13:16 A lot of the detail or published if it if it strikes your imagination, but really it was to sort of sidestep the question that we only had two genomes and we had some evidence of all of this flexibility that was going on but no measure of it.
14:13:32 So after a lot of work that by Michelle and my, we basically came up with this idea that we could take the whole genome and describe primers across the whole genome and deep sequence just the regions and try to look at the single nucleotide polymorphous
14:13:49 and so jumping very far from what I showed you, which was changes in opera ironic structure or transposes down to the nitty gritty of what's happening in a gene or an orange energetic region.
14:14:03 And, and essentially then another part of this was to try and clear all the errors since this was done by car by leave a leave all of that detail out, but what it ends up telling us, based on statistical analysis is, how many leaves they are for any of
14:14:19 these regions, completely. For me, a novel way of thinking about this because you're not looking at genes you're not looking at whole organization, just looking at regions and trying to see how much allele diversity, there is which is not something I
14:14:36 know a lot about and I'll tell you more about it.
14:14:40 But what it allowed us to do then is to really look, obviously we did primers for the 16 s and four and just show you one but there were about 100 of these.
14:14:52 And you, if I walk you through this what you'll see is here, the green is the most abundant so this this was samples taken from 55 so that fits with them being like OSB which is the blue car, and then you can see here is OSA, and you can see all of these
14:15:11 aliens that are different at the 16 s level on a tree. And you can do that for all the protein or sandwich we had the full sequence. And you can see here now the picture looks very different.
14:15:19 So just to orient you hear some guy. That's the most frequent one, it's at 55. He has OSB and his OSA. So, without going into all the details I want to get to the defense bar and and Daniel I'm sure we'll do a better job at explaining this is essentially
14:15:38 saying that there is this diversity that we are kind of as a proxy for not getting whole genomes and not getting deep sequencing, but telling us about diversity that exists, not necessarily at the protein level because that's not what we're getting at,
14:15:56 but it's beginning to tell you that there. To me the most exciting part of this is, you don't have to go the conventional route of getting thousands of isolates or deep sequencing.
14:16:06 The completely different way of thinking about population variation.
14:16:15 So, essentially what this came up with this idea was to argue that you don't really necessarily have to say that there is a niche and overtime certain organ certain cyanobacteria in this case are selected for so that over time.
14:16:33 All the green and yellow guys are in one place all the purpose are in, in other words they're basically optimize for the niches, they're in, but what we seem to have found was that actually have what I think Michael decide coined this term we weren't
14:16:50 smart enough, called the music genome so really what you have our genomes that are scrambled at all times. But we don't read this is a hypothesis really, but we really don't have any evidence of how much this is happening.
14:17:07 And one thing we thought we could do is to start to look at individual genomes to see, is this really the case, and we're just starting to get that data outcome for them.
14:17:22 Question you're talking a lot about Gino type but I only care about phenotype. Okay, so that's a confession, I agree
14:17:31 to comment on what you think. This means for phenotype.
14:17:36 What it means I believe, is two ways to think about. One is, it has no done, or it has a profound effect. And how do I know which of those, it is right.
14:17:50 I'm just looking at genomes. I've seen things are recombining.
14:17:55 I can, I can say whatever I want.
14:17:56 And it's that's why come to show this day. Let the very season, but it's to its to ask the question how do you set this up when you find a fascinating biological program, and no intuition about what is my way of thinking about it, is to say, are only
14:18:18 the son of bacteria doing this, and nobody else does this in that environment.
14:18:23 So something has triggered this, for example the breakage of who knows what, that's one part of the story, but to me the second most interesting part of the story is what effect does this.
14:18:45 And that's why I gave you those kind of just so stories where modules of nutrients are coming in at now is that all that's happening. And then I guess if you're in the room, no doubt.
14:18:52 What's the time scale at what is happening in sweeps which I never claimed to understand but, you know, how is that happening to me more interesting question.
14:18:59 That is why is that happening.
14:19:00 And I'll throw this out there because I get up at night thinking about this, this does. So, if, if a module is really useful for them, for example nitrogen is etc.
14:19:12 Would you hypothesize that everybody all cyanobacteria must be.
14:19:20 And if not, what would be a model
14:19:25 was a long.
14:19:27 Yeah.
14:19:37 I'm dyslexic so this one.
14:19:42 Yeah, I'm here.
14:22:35 One question
14:22:45 really close. Yeah.
14:22:49 But just in case I have a lot.
14:22:54 Yeah I yeah, I'll have the muscle.
14:22:58 Okay muscle.
14:23:05 Oh, but this is the last day, and that is about since I have to go through my 3ds The last one is the defense which I actually find really fascinating as well.
14:23:13 And that is the idea that we've looked at all of this through the years I did it with the idea that there was nothing to do with predators we had this beautiful region where nothing was happening and they were growing rapidly, but from the genome, and
14:23:27 All of you know what Christmas so I'll skip that. But one of the nice things about Christmas just to remind you is that that is a kind of order, such that these Christmas space has come in at the 5% and get lost at the older answer at the three prime
14:23:56 so there can be a time distribution potentially of seeing when these events are happening, which I think is really very cool way to do this. And what we found was and I go very quickly or all of this is one point I really want to make his first there's
14:24:03 differences between OSA and OSB and only to point out that OSA has a whole new type, type one he that has come in and it looks very much like another type point system that is in an organism that grows in this matter It looks like a whole crisper cast
14:24:24 system has come in by horizontal gene transfer the crisper repeats are the same as in this other organism, but none of the spaces or Jane says actually swapping all of these out but it's taken this whole module that that's an aside, but I want to show
14:24:40 you what we can do with something like this, which I think is interesting I'm always excited when I talk about the audience less so. but you can you can take a host Crispus sequence found in, I forget, whether it's always a always be.
14:24:57 And now, and these ones you're looking at viral read so we happen to get a very shallow viral from somebody who had done it. And you can see here that these viral rates are changing from this original one that in the host spacer itself that's not the
14:25:15 best way to put it, but you get what I'm saying.
14:25:18 And, you know, so So what, but we have a little bit of a breakthrough in that we found that that same region which no doubt you have memorized this region here.
14:25:30 If you translate it in one frame into amino acid space, you can see that all of those viral reads that I showed you are starting to pick up mutations, great because of those changes in the spaces.
14:25:45 But all of those I found really interesting that all of those changes have conserved amino acid changes. So the stage is kind of getting away from it, but it's constrained by the functionality and it turns out we were lucky that it was actually in a page
14:26:01 license line so this is the region, right here. And this happens amazingly to be the active site of the lifetime.
14:26:09 So there's only that much monkeying around that the stage can do to move away from.
14:26:15 Now, I think that we could use that very effectively as really an idea to ask how much of this is happening. By comparing hosts spaces and now we have a very large message, you know, and comparing them to virus sequencing and ask how common is this up,
14:26:36 particular proteins, more prone to be picked up as spaces, because the fish can't really change them too much.
14:26:46 Does that make sense.
14:26:52 I'll skip all of this because this is more detail, I'll just end up so we stay on time. But what we realized is with the two isolates the shallow matter genome, almost non existent array of spaces that we had that we really needed to go much deeper in
14:27:08 all of this. And we, we had the luxury of having this Jgi agreeing to do this. And what we did is we have now samples from over five years so somewhat this idea of the time scale from two different springs and from four different temperatures.
14:27:26 And we have them right now in the person who being analyzed, where we had the DNA sequencing, the meta transcript to make data over a complete dial cycle every two hours.
14:27:40 And then about 400 different single cell analysis, and we are getting ready post pandemic to start to build up the page as well and inside integral isolates.
14:27:50 So this is kind of the continuation of a thought that we started very small to genomes, as sort of blurry view of what's going on. And the hope is that with this much deeper data set, which seems to be panning out at least for the meta transcriptome it,
14:28:06 we get a much finer grained picture of what's happening in these mats.
14:28:15 So, you know what, how we are almost, almost done right. So what I'm going to do really is, return to this idea of what auto was talking in Belgium so that kind of full circle and Matt is that in these mats.
14:28:31 And that is that in these mats. Now, I sort of focused very much on the signer bacteria as being the primary producers, fixing carbon fixing nitrogen producing oxygen, and this whole other path of the mat as what is happening in terms of metabolism and
14:28:46 sharing resources is something we can. We're now going to start to do by looking at the metabolites looking at the transcriptome and looking at the meta genome, for example, something like what's up and you know we have no idea how representative OSA
14:29:02 and OSBR in terms of all the other genes that may be there, but we never really could capture.
14:29:11 And so this is kind of the simple model that we're working on in trying to get to the metabolites for example we know glycol eight is is produced by the sign of bacteria are they feeding the opposite Yannick photo tropes the pillar mentors, orange guys
14:29:38 you saw in that Matt and then what happens at night so that is pieces of data that suggests this might be happening and how do we test it. And that goes to really almost a final slide that WhatsApp and I talking and thinking about how we can build synthetic
14:29:45 communities, and we just kind of starting to think about that I'd love to talk more about it as kind of leave it at that.
14:29:53 So just to end up I hope to wrap up like a lesson. What I've given you some of the kind of insights we can get from, I would say very shallow comparative genomics and metagenomics and 30 some of the novel genes we found.
14:30:10 And the idea of the fluid gene pools pan genomes which we know less about. I skipped over didn't talk too much about but Gabriel bootstrapping Daniel fishes labs looking at recombination in the single cell data that we have.
14:30:26 Looking at the viruses. And then, social behavior which I talked the least about So, I will.
14:30:38 So what you're looking at here and I hope you find interesting is, so this is a combination of the cloth Lexi is thin light gray spaghetti. And these guys being cynical caucus, and there's red light coming in from this direction.
14:31:00 And you can see that the whole
14:31:04 mass, for want of a better word is moving towards the light over time. But I will tell you and I'm not showing you all the data that these which are the closure of Flexi are more tie, we don't know how, and they will spread all over a plate with no directionality.
14:31:21 The sino bacteria are highly protected, they're moving in one direction, and it almost seems like they're sticking to the core of taxi and driving these structures so this is all you know adjust so stories, or you're trying to do now is to separate these
14:31:39 guys and quantify this behavior. But I want to end on the note that one of the things we talked a lot about is jeans and biochemistry and also talked about the Redux, but I would like to argue goes back to, maybe would suppose I forget now, but this idea
14:31:52 idea of when you form a biofilm that sitting on a surface but there's water flowing over it. How does the signer bacteria respond and can they be tethered by the floor of Flexi moving, and then that builds up the biofilm as something we haven't thought
14:32:08 but I'm very interested in, so I'll kind of leave it at that. In terms of what I would like to say I think that's it. And for you and your group, put together these questions, and I hadn't seen them till yesterday, but it doesn't do a bad you know copy
14:32:27 copy of the kinds of questions that I've been talking about so I'd love to talk about it more and discuss it with you the next week or so. So I think I'll end there I mean I could talk about funding and all that but maybe I'll just.
14:32:50 Thank you so much. Perfect timing. And I apologize to everybody for interrupting fluff questions we have a few minutes for more questions.
14:33:01 It's okay.
14:33:03 I don't have a question I was just answering your question.
14:33:09 So he was talking about measuring VR by Emory issue. Right. I was wondering if you didn't measure that population why, but you know, in these guests clusters it, you could probably guess right clusters where the IBM ratio within a cluster would be much
14:33:15 Yeah.
14:33:27 higher than the IBM and what you mean by cluster and just so the clusters with those bubbles in the sky.
14:33:51 Is that maybe the population within the cluster is recombining much more. So if that is totally a cartoon. And if you have to go back to real life stories, what would that potentially mean that you would be asking the question, is it local versus spread
14:33:53 is what local versus the these bubbles.
14:33:56 Oh, they could even be local because I guess the point is that once once they're diverse to once the sequences are diverged enough they were not very likely to recommend even if they were in the same space, but that's the data doesn't show that the data
14:34:12 shows that we combine have a very big distances, I see.
14:34:27 So a question about this are by am ratio.
14:34:32 Tell me more about. Yeah, so so so one of the things that we saw here was there's this mismatch between the clock, you get from like a 16 ASR and 18, or maybe other conserved core jeans, and what you get from my breakdown of Cincinnati.
14:34:45 So that could happen because recombination is happening at a very high rate. It could also happen, because there's some slow down in the mutation rate, perhaps there's higher conservation on some of these core genes that these high temperatures.
14:34:58 Are you guys able to separate out those two possibilities at all.
14:35:03 I mentioned in principle we can we hadn't done it
14:35:09 is what you're asking, what's this idea of the mismatch is an interesting one because when we first started with this you know 16 s was the Makkah for diversity and then we started looking at Symphony which gives you another measure, and then you look
14:35:23 at gene content and then you look at the level. You know what Daniel is looking at which is snips, and each of them gives you a different time scale or reason, and I really honestly don't know how one should think about it always does to the questions
14:35:39 just people's differently.
14:35:43 people's differently. Yeah, I think it's look interesting to look at the timescales that each of those gives like the difference between all those clocks and to point you towards this is fast recombination or slow mutation rates at least in some subset of genes that are highly
14:35:56 conserved at these high temperature.
14:35:59 You know the other idea that I that I hear about for why we don't have recombination across broad phylogenetic scales and microbial world is because sometimes that's enforced by just not existing together.
14:36:12 So in these extreme environments, you also kind of wonder, these environments that are 20 see difference, you know maybe the optimum in terms of their nucleotide identities and their proteins is 20% different, but they're within you know half a meter
14:36:26 of each other and therefore they're still somehow exchanging genetic material and that wouldn't happen in non extreme environments, and I just another.
14:36:50 I think the, you know, to put it out there. I think if we came up with a model or a hypothesis and then sent us the data allow us to answer these I'd be very comfortable working with someone doing something like that and we do have some of these data
14:36:54 sets that could be used.
14:36:56 But we have to bring up something else that's happened I was discussing yesterday, throw it out there to is the idea that sometimes we are we are constrained by the data set, we have, and maybe a smarter way to do it is to ask.
14:37:11 This is the question we want to ask, and see if there's a data set, we want to get as opposed to picking cherries out of the system.
14:37:22 I guess I'm still sort of hung up on collecting these core samples from the actual map. So, is it. You mentioned something about permissions being needed so I guess the question I am going to ask, I don't know if it's possible but if you take a core sample
14:37:37 and allow the map to recover. But in various stages of recovery you take core samples so you make multiple connections and you take core samples over time.
14:37:46 Do you actually see different processes recover at different rates so you can guess which part of the substrate does things. Yeah, I think that would be a beautiful experiment to do, and I think it can be done.
14:37:59 I guess what we're thinking about, which I think would not be trivial to do is can we start to build these rather thick mat in the lab and a long time ago before we had a major burn out in the algae house where we were growing them, you were able to get
14:38:14 these tech biofilms but how much they look like anything in the map or don't know, but there we could potentially do exactly what you're doing, pull something out and then see what processes come back, but would, I mean, again I will turn it back to you
14:38:38 No, I mean, sure, I guess like To me it's not so much a question of what I believe the synthetic system more.
14:38:44 If you really think extreme environmental conditions or nutrient variation or temperature variation whatever have you makes a difference, because usually those are things that will also change the way these communities get set up my teach you something
14:38:57 much better need to set up your synthetic system know if you only have static snapshots this right I guess I don't know how you come up with the way of building the synthetic sister.
14:39:08 I agree with you.
14:39:11 I sort of had a related question which was, which of the phenomena you talked about, would you not expect to see in a web mix system like cyanobacteria, and lakes, oceans like why Matt, I mean it's obviously striking but it wasn't clear any of these.
14:39:26 I don't know that you get any kind of stratified or growth biofilms in, in many systems, right. And one thing I didn't talk about was there actually in a very big extracellular matrix.
14:39:38 And we, you know, this biofilm is like jelly almost right. And in that jelly.
14:39:45 The question is who's producing that whole matrix of I don't know that there's an equivalent of that in. Well next system.
14:40:00 Oh, okay. What does that look. What are the other like ecological phenomena that are different than this because of the spatial structure. It wasn't clear to me that any of this stuff you showed us today is, I think I agree with you i mean i don't see
14:40:13 that it's only to do with specially structured extreme environments.
14:40:19 I wouldn't put five bucks on something like that, there's no necessity to suggest that, What I will say maybe is that when your cheek by jowl with it, with neighbors and with everybody else can recombination and using DNA be somewhat different.
14:40:38 And that could have different implication, just maybe I could add something on that so if you think of the point of view of fame age. If you're in a matter of the things held together, and you burst from one bacteria you're likely to find a close relative
14:40:50 nearby. If you're in the ocean with planktonic bacteria, you're not. The next one you find this was a kilometer away and not not necessarily extremely close relative, so that might make a difference, we don't understand it well enough to know.
14:41:03 And that could be tested by the spacer populations, right, that, that you could do, over, over distance and see how they're much closer when you're all next to each other.
14:41:14 And I think we can do that now we just had didn't have enough density.
14:41:22 I waited too.
14:41:24 Yeah.
14:41:24 Okay. Um, yeah so I was really curious about.
14:41:29 You mentioned that one of the lineages had much higher diversity. What you know about the population sizes of the USA vs OSB and if they have different faiths except abilities or population.
14:41:45 Does a second, different age susceptibilities or differences in their population dynamics or turnovers within the, you know, just processing, diversity generating processes is kind of what I'm what I'm so I do believe anecdotally that as you go up in
14:41:59 temperature and the matter. When you go higher, to about 70 degrees very mostly I've always say the maximum much in a much less dense, so maybe on some unit area that it's less dense than OSB, and then based on the genomes, it seems like there's much
14:42:16 less diversity around OSA than ours be fair is a very interesting question and we never could ask it. The only thing we did have, again it's so it's so shallow it's not worth talking about but when we did the first comparison of all the crisper spaces,
14:42:32 you know I say versus always be there were none shed.
14:42:36 But I suspect that will break down, when we have, you know, that was only about 100 odd spaces but we have much more, I would hope that we might find going back to your, you know, extending your question that at the high temperatures on the low temperatures,
14:42:51 they may be some common spaces but they'd be vastly different.
14:43:08 right if you're on zoom, they'll get a cookie.
14:43:09 do