Scientist in the Forum - Janet Price | Tiny Campsites: Understanding Bacterial Communities

Hi there everybody and welcome to the Museum of Natural History here in the middle of Ann Arbor I’m so excited to get to talk to you today. So my name’s Janet Price I’m actually a graduate student here at the University and I have the privilege of working here on the fifth floor so I get to see this museum every single day and it’s it’s such a treasure and I’m so excited to tell you a little Bit about the research that’s going on here at the University So my research is especially interesting because we’ve now opened the new exhibit on the second floor all about life at the cell level So I’ll be talking about one of those things. You can see in the exhibit Bacteria, so a little bit about bacteria. They were among the first things alive here on the planet Earth They actually appeared about four billion years ago now to put that in perspective dinosaurs appear at about 240 million years ago which means bacteria are 16 times older than the dinosaurs and they’ve kind of got it figured out they were these tiny animals that we didn’t see until hundreds of years ago just because they were so Small and originally we kind of sorted them just by what they looked like So we made all the circle bacteria the same name and all the rod shape ones but now we’ve gotten much better at being able to tell them apart and base them based on their characteristics and We know that they don’t have a nucleus so the brain of the cell or the mitochondria which our cells use to power everything, but even without those things they’re able to eat and grow and communicate with one another and reproduce all without the things that we think are very important for our life and they’re tiny I mean tiny they are about one to three microns across and that means about 10,000 of them can sit on the head of a pin I’m not a very good seamstress so that equates to about 5,000 that can sit on the end of your pen so they’re tiny and they are everywhere and Normally when we think about them, we think about illnesses I got this bacteria and now I’m sick, but actually they do so many great things for us The reason that we have pickles is because they’re able to ferment in that juice and give us delicious pickles but they also help make our yogurts and our cheese and they’re Important for the processing of coffee and chocolate and for the adults in the crowd they make all of our favorite fermented beverages So without bacteria we would have- we would be missing a lot of the things that we take for granted Now, going a little bit back if you remember maybe back in high school You saw this old construction of what the kingdoms of life looked like? I always thought it was kind of a weird shape It kind of reminded me of a cat’s foot with all the little toe fingers being the different kingdoms of life So we’ve got our animals here. We’ve got our funguses and our plants But where are the bacteria? If you look really closely down here at the bottom, there are three little arrows.

That’s it 02:57 - This is what they thought all of life wasn’t that much of it was bacteria but as we learn more and as we get better with Genetics and understand DNA even more this is what our tree of life looks like now You can actually play with it on the second floor of the museum But you’ll see that animals take up a small portion and then plants and fungi And the rest of this is bacteria. That’s right about two-thirds of the life on this planet are bacteria So we’re grossly outnumbered and they can live pretty much anywhere So we found them at the very bottom of the ocean. We found them in volcanoes eating the lava to survive We’ve even found them in clouds where they’re able to fall back to the earth as rain So they’re everywhere and more importantly they’re inside us too They’re in our intestines and helping us to break down the food that we eat every single day And in fact, they outnumber us by a lot So if you were to count all of your cells and count all the bacteria on your body They would outnumber us about 10 of them to one of our cells So, understanding how they can survive in all these environments is kind of what we do My lab looks at Bacterial biofilms and these are just communities of bacteria Living together and they’ve found a way to stick to one another and to all these surfaces So if you’ve ever run in a stream without shoes on and you’ve slipped on a rock and you may have fallen in the water Well, that was a bacterial biofilm you stepped on. They use it to stick to that rock so they don’t get swept down the stream But as harmless as those rocks are sometimes that they can build up inside of our water pipes and this can get our water Contaminated or even block it so that we get sick. So Understanding how these bacterial communities develop is really important and I like to think of them as the bacteria Going camping and they’re really good at camping.

So 04:56 - Anytime they bump into a surface they can set up this camp And the first thing they do is make this protein Shell they make a tent for themselves to protect them from everything so that could be weather the environment Antibiotics that we try to kill them off with or even predators okay, maybe not bears but like really small worms and other bacteria that would try to cause them harm and this allows the bacteria to live everywhere in the Volcanoes and the clouds and it makes it really hard for us to get rid of them So when I work in the lab, this is what I see every day. These are Ecoli living in a biofilm and I think it’s kind of beautiful it looks kind of like a spiderweb or a bowl of spaghetti and With this they’re able to protect themselves from being scrubbed right off a plate and I know what you’re thinking great One bacteria get rid of it. Just get rid of all the e.coli. We don’t need it. I want to eat at Chipotle Anyway, I need to get rid of it But the problem is it’s not just e-coli. It’s pretty much everything. So here we have some examples So this is a yeast this is some bacteria that live in the dirt This is why you shouldn’t eat raw chicken, and they all make this same shape So it’s really important to these bacteria for their protection and their survival And in fact, the protection is so good If you put a drop of water or antibiotic, this is a side view right on top of the biofilm It wouldn’t soak in it doesn’t even distort the water drop. That’s how well these bacteria are protected from their environment And I want to understand How these cells are protecting themselves so that we can get rid of them better.

So the easiest thing to think of 06:42 - Every cell in a biofilm they bring their own tent right you want to be protected. You should do something for it and so we looked The first thing we did is we looked at the side view of one of those biofilms through those wrinkles and we stained the cells in green and anything making that protein for the tent in orange and you can see There are a lot of cells underneath that aren’t even making a tent. They’re relying on their neighbors to protect themselves So we’ve got these orange cells that have packed everything to go camping. They’ve got the tent. They’ve got the food They’ve got the fire started. They’ve got a sink they got their neighbor’s kitchen sink. They have everything you need.

07:21 - meanwhile, we’ve got these other guys these under packers who may have brought their school backpack with their cell phone charger and But don’t worry you guys he brought the marshmallows we’re saved So what we see is that our biofilms are a mix of these two types of cells We’ve got about 30% of the over packers and 70% Under packers and this balance is really important. So here again, we have our biofilms and this time I used a red Dye to show where the tent is And if we have that good mix of under packers and over packers, we have this protected biofilm that grows really fast But if I make some mutations so that we only have over packers We get this weird flat biofilm that’s really stuck and we can’t get rid of it and it grows really slowly But on the other side if we make it all marshmallow bringers, Ta Da! It’s not making the tent any more we can wash it away It’s not protected and it grows really fast. But who cares if I can use water and get it off the surface, we’re fine So what I want to know is how can we trick the bacteria into bringing the marshmallows? So there could be a lot of reasons that the bacteria want to go camping I mean, there are a lot of reasons any of us want to go camping Can you think of an example for a reason why you would want to go camping? Nature being outdoors is a good reason to go camping You want to sleep outside? That’s also a good reason. I always went camping when I had family visiting because we love bonfires But so there are a million different things that the bacteria could be thinking about to want to set up camp It could be they found a great place to camp. They found the perfect location. It’s right by the river it’s under some nice trees or Maybe it’s a lot of cells maybe all of their friends are there and there’s enough of them around to want to protect themselves Or maybe they’re just stressed out and it’s raining the sun’s really bright.

They wanted something to protect them and 09:28 - One of these signals is the: “Tent! We should build a tent!” signal And maybe if we take that signal away we can confuse the bacteria. So they just want to bring marshmallows So what is this signal? We’ve had a little bit of hints. So here we looked at how much oxygen is available the further we went into our Biofilms, and we saw that the further we went into one of these wrinkles And again, we have the red cells making tent you can see that eventually once the oxygen gets so low Our cells aren’t making tents anymore So it’s almost like the bacteria on the outside are hyperventilating and breathing in all of that oxygen and leaving no oxygen for those underlying Cells and that’s what’s telling them to bring marshmallows So if I take the oxygen away they shouldn’t be protected and that’s exactly what I tried So I got to put our cells inside this giant plastic bubble that doesn’t have oxygen in it it’s just full of hydrogen and I Had to wear these space like gloves so that I could touch things on the inside. It was really interesting and Just to reminder what they normally look like with our normal mix in oxygen and our over packers and then when I took the oxygen away Ta Da! The mix of cells no longer was making that tent protein. I was so excited But of course you need controls and when I have just over packers They’re still making a tent. They’re still trying to protect themselves.

So 10:57 - Oxygen isn’t the only signal it’s seen like maybe the communication between the over packers and the under packers are really important So oxygen isn’t the only story but it’s part of it So hopefully today I’ve told you a little bit about our bacterial friends they were the first life-forms here on earth and they live everywhere from the sky and the volcanoes to us and The communities of bacteria that we see every day are called Biofilms and only about 30% of the people in those biofilms or bacteria in those biofilms are making the tent structures They need to protect everybody in the community and oxygen is part of that signal So if you want to learn more about microbes and anything That’s the size of my microbes that we can’t see without the aid of a microscope The new exhibit is on the second floor and is beautiful But I’d love to take any questions about research or bacteria So are your over packers and under packers are those like somehow like they’re genetically the same bacteria And they have some different Characteristics do you know like when you say like I added only over packers or only under packers like what separates those two groups? That’s a great question So in our normal biofilms when it’s making the tent, those are all exactly the same cells They don’t have any mutations from one another when I make it just the over packers or the under packers I’ve deleted one of the genes that we think are really important for making those two populations So by switching one on I can make it over packers by switching one off I can make him under packers So but understanding how that happens naturally We still don’t know because having just those two deletions isn’t enough by itself I really appreciate everybody stopping by and I hope you’ve learned something today. So have a fun day in the museum! .