Um, diving deep. Diving into the muscle cell, a little bit into a different single cell bacteria. And our speaker, Renee Hoover would be talking about a little mystery about bacteria now. Environment. Please welcome Renee. Al right, hope that's over again. Okay, hi everybody. My name is Renee Hoover, and I'm a graduate student in the microbiology program here at U D. And like a lot of scientists, I like to solve mysteries. So I'm here to talk to you today about one of my favorite mysteries, which is how we can learn the when and where of bacteria eating iron. Now let's start off with something that might be a little more relatable. Imagine you have a garden. And in this garden you grow some prize cabbages. And there's something sneaking into your garden eating this cabbage. Now you're going to want to know who is eating this cabbage. You might want to know when this is happening, how this is happening, what else they might be doing, and how the activity of this cabbage being eaten is going to impact your overall garden ecosystem. Okay, now imagine a similar mystery only at a microscopic level in your garden soil, where instead of cabbage being eaten by a cute animal, we have ferrous iron and it's being eaten by these single celled bacteria. Now you're going to have these same questions. You're going to want to know who is eating this iron, when you're going to want to know the mechanisms, what else they might be doing. And you're really going to want to know how this can affect your gardens ecosystem. We want to know this because when bacteria eat iron, rust is formed. And this rust can be really sticky. And it can affect the mobility of important plant nutrients like phosphorus. And it can affect the mobility of heavy metals and dangerous compounds like arsenic or uranium. These tiny iron particles that are formed can also bind with other sticky substances that bacteria make. And when that happens, it can cause clogging in your pipes and your sump pumps and have these other effects. We really do want to understand the bacteria that eat iron and the mechanisms that they use to do this. So how can we solve these mysteries and what are the clues that we can look for? Now if we think back to the garden, there are different ways to learn about who is eating your cabbage. You could observe who interacts with the cabbage. It's a garden. Animals are big, they're often there one at a time. You might be able to have a steak out and catch your culprit. You could analyze changes to the cabbage. You could look for unique bite marks or a marker that the animal leaves behind on your cabbage. Or maybe you could match that animal to clues detected in the environment. Maybe you could find some footprints. So can we also use these approaches to learn about the bacteria that might be eating the iron? Okay, what about observing who interacts with the iron? Sadly no. While we can sequence the metagenomes from the soil and learn who's present, the communities of bacteria are really complex. We're talking about millions and billions of single felled organisms. Not just one or two cute bunnies. And just because we can see who's there, that doesn't tell us who is active or who is doing what activity on that bacterial scale. Now, how about analyzing changes to the iron? Can we find those unique bite marks left behind? And again, the answer is no. Even though when bacteria eat iron, they form rust. The rust they form is identical to the rust that forms when iron contacts oxygen. So we can't look at the rust and discern whether or not it was made by a certain bacteria or whether it was made by bacteria at all. Now, how about matching those bacteria to clues that we detect in the environment? A wild bacteria don't have feet to make footprints. They do have genes and proteins that get expressed. And these genes and proteins can be tied to specific activities. And we can sequence those and thereby learn what bacteria are present and doing certain activities. But first, we need to know which genes and proteins to look for. Just like in our garden, where there may be a lot of different footprints. And some of those may be made by animals that are just passing through, living their lives and not interacting with our cabbage. There are a lot of genes and proteins being made by bacteria in the environment that aren't associated with eating iron. So we need to know which ones are associated with eating iron, so that we can look specifically for those. So that's what I've been working on as part of my research. I've been curating a list of these genes and proteins by looking at their traits and characteristics, where they're located in the cell membrane, whether they're capable of interacting with iron. And making a list of these genes and proteins of interest. Now to take that one step further, I've refined that list by analyzing the galleon else family of bacteria. And this is a really neat family because they're known for their iron oxidizing members. But there is also a genus of bacteria in this family that does not eat iron. And that presents a great opportunity for me as the science detective because it let me compare and contrast the iron eating bacteria with the non iron eating bacteria in this same family. And find the genes that were specific to bacteria that met our previous criteria. And we're only present in bacteria that eat iron. So here's a summary of those results and the details don't matter. I know there's a lot going on and it's a little hard to read, But the important thing to realize is that wherever you see a shaded box, it represents a gene encoding for a protein that might be able to eat iron. Where it's shaded indicates that it's present in the genome of that bacteria. We see that not only are the known and more studied iron oxidase genes present, but we have a lot of potential iron oxidation genes present in only these iron eating genera. This list has given me a lot to go on. My next step was to actually look for these genes in a real environmental sample. So I looked for these genes in a metagenome sample, which is the whole community of bacteria from an iron rich fen. What I found is that a lot of these genes are present in the genomes of known iron oxidizers, like our friends, the galleon else who we see in orange. But we also see some of these genes in bacteria that aren't as well studied and may not have a connection where they're known as like an iron oxidizer. So that's really exciting because it expands our idea of who in the environment might be eating the iron. And also gives us clues when we look at these genes and proteins as to how. So this is ongoing and it's moving in a great direction where my next step is going to be looking at who is expressing these genes. We know who can make them. And now the next step will be determining who is imparting thoughts. If there's one thing that I want everyone to take away from my talk today, I hope you leave thinking that the bacteria they eat, iron are really cool and that it's important to learn about their genes and mechanisms. Because learning about that can help us understand the environmental impact of these bacteria and better understand how their activities in the environment where they are, how active they are when they're active, can help us understand the mobility of this phosphorus, arsenic, uranium, and other compounds. As well as finding perhaps some novel solutions to the more industrial concerns we have with the ways these bacteria can clog infrastructure. I would like to thank my lab mates, my collaborators, and my funding sources. Y'all are awesome and I will hear and take any questions. He. Great. Firstly, my question is about the trait that these bacteria have, that they eat iron. Why do you think it's been selected evolutionary? Yeah, that is a great question. Because as you might imagine, like if you were to look at a Redox ladder of how much energy a bacterial cell can actually get by eating iron, it's not a lot. It's at the edge of what's thermodynamically favorable. It's a hard life for them. It's not easy. You got to eat a lot of iron to get enough calories essentially, to sustain yourself. But I think the thing we find with bacteria is that there are so many of them and there's so much diversity that there's pretty much a bacteria for every niche. You know, if there's a food source out there, they're gonna find a way to exploit it and take advantage of it. And I would guess that, you know, iron may not be the easiest thing to eat, but if nobody else wants to eat it, you got no one to compete against. So it's kind of like, well, hey, hard to eat, but it's all mines. Thank you so much. Yeah. Oh yeah. Thank you for the presentation. Let's see. Thank you for the presentation. I was wondering, when you bring this bacteria into the environment, are there any unintended consequences that you're seeing in your research? Yeah, unintended. I mean, they are out in the environment. A lot of times we're not really inoculating them into the environment. We're trying to go out and isolate them from the environment. Which is rather challenging in itself and is one of the reasons that I'm doing this. Bioinformatics and genomics based work that I am is that iron oxidizing bacteria don't grow well in the lab. We try to catch them, we try to bring them into the lab, but we don't have any that we can really edit in a way where we can knock out genes and show functions. A lot of what we do is trying to work with the handful of isolates we have, but then also studying them in these big groups in the environment to learn what we can. That gives us clues to come back into the lab with as far as them being in the environment. We're also just really curious about the different traits and why we see them in some places more than others and how they function in different niches. I hope that. Yeah, so I really enjoyed the cabbage analogy. Okay, but I'm curious, are these bacterium actually eating the iron? Is the iron actually going into the bacteria or is it just the electronic equivalents from first sink on this Redox? Yeah. So you are they truly eating well, you know, that's a great question. And yeah, the iron itself doesn't enter the cell because they don't want those rust particles inside themselves that would be bad for business. And that's one of the clues I have when I whittled down my list of genes, is that because they do this oxidation outside where they're taking the electron off the iron and passing it through their cell membrane. There are certain traits we look for in these genes and proteins of interest. A lot of times it'll include being a multi heme cytochrome that's located in that outer membrane. Because they do need to interact with that extra cellular iron and get the electron into the cell. While technically. Yeah. Eats a, a little bit of a funny term essentially. Even as humans, when we eat, we're taking electrons off of carbon and using bacteria to do it. Yeah, exactly. So it's got microbes making us all work. Okay. So then what makes this truly unique, of course, is that it's able to do that from iron and not all bacterial species are able to do it, but it could also potentially use other metals to partner. Yeah. Yeah, there's definitely a potential there from that. And that's why whittling down this list of genes and proteins that we think might work for eating iron, we're really curious and then testing that to see if it's expressed at the same time that we see iron being oxidized in the environment. Because there is a chance that maybe they can oxidize other metals with that too. Maybe something that could oxidize iron could, if it's in the right redox range, be used to oxidize manganese or another metal too. And then not to nerd out too much, I apologize, but so your diagram was showing iron two going to iron three really? Does it really go after iron metal metal or is it going after iron two species? Yeah, it's usually going after iron two species. We'll find like a dissolved iron two. Or we think some of these multi heme cytochromes that extend a little bit past the outer cell membrane might be able to contact solid iron minerals, things like ferrihydrite or gert, and take the electrons off of like solid iron as well. Excellent, thank you. This is really fascinating. I'm curious how you chose this field of research. Oh boy. Um, I think it comes back to kind of solving mysteries. When I was doing my undergrad studies, I was really interested in the biological sciences. And then I ended up taking a microbiology class. And I was just really surprised by how much we didn't know. It seemed like a big frontier, just full of things to explore and things we didn't understand. Especially in the environmental microbiology, where there's just so much diversity and so many niches. So it just really captured my curiosity for solving these mysteries. I'm Jay Bancroft. I just was alluding to your mobility questions about phosphorus. You pick up on some of those non mobile things or applications that you were thinking about for that and sort of the side light. I came into this thinking, oh well we hate to have our battleships get eaten by this. Rust is a huge problem, but this is the natural recycling that we like. The new car. I know the military has a hell of a time getting rid of this new stuff. The carbon fiber stuff doesn't get rid of. Maybe there's sort of I don't know if you have any thoughts about that as sort of related to this binding problem. Thanks. Yeah. You mean thoughts on sort of contributing to corrosion or thoughts on just to them affecting bio geochemical cycling or applications? Ah, yeah. I mean, we're definitely curious to know if they participate in things like corrosion. The jury's still out on that. We do see them present in some biofilms on things you mentioned like a Navy ship or maybe an oil derrick. But until we know what genes to look for, we can't say whether they're actively contributing to iron oxidation in those environments. It's another downstream, bigger picture thing that this work would eventually help solve a mystery for when it comes to that phosphorus and those mobile elements in the soil, these iron particulates, they're just able to bind with some of that. In the case of phosphorus, it would be binding that and then preventing its uptake into a plant could affect the plant's health if that plant is then starved for phosphorus or needs more nutrients. But there's also evidence that in certain cases with plants, we'll find this iron plaque forming on the roots. And these iron plaques will absorb things like arsenic. And then the plant doesn't uptake that arsenic, which is really important to rice. And certain parts of agriculture where we don't want to see arsenic being taken up into the rice and into the grain because then that can bioaccumulate in us. I feel like there's lots of bigger picture applications and it's one small piece of such a huge puzzle. Yeah, I was going to ask about the application as well, but you just answered. Thank you. Yeah, no problem. I'm just wondering, your research focuses very specifically on one group of organisms and finding markers in that group that it does seem to connect to the iron consumption, if you will. Are there specific reasons that you think that will be generalizable outside that group of organisms? Or is it more informatics approach where we see these markers? We'll see these markers in other organisms and we'll start to see what's in common across the Malley. It is like a specific family. They're very common in freshwater and soil systems. They are very widespread. And we see them all over the world in a lot of different environments. From like permafrost to soils, to creeks and streams to even aquifers and the deep subsurface. These galleon alyce are in a lot of places. But you're right, they definitely aren't the only iron oxidizers out there. But they do share certain traits that are common. We find them in stream systems with iron oxidizers like E lepto Thr. They do share certain traits in terms of need to have those proteins in their outer membrane to contact the iron. We also see commonalities between this family and even like the deep sea hydrothermal vent iron oxidizers called the zeta proteobacteria. They use the same multi hem cytochromes or single hem cytochromes in the outer membrane. And there's a lot of conserved complexes and genes that they seem to share. I think what we learn here we can definitely extrapolate to other iron oxidizers and apply across a wide range of bacteria. Based on other physical similarities. Yeah, based on other similarities between the organisms themselves and between what a protein has to have to be an iron oxidase. There's just certain traits like having a hem redox center that can take and pass that electron. And the ability to either have a fused porn or a separate porn structure to breach the membrane. And yeah. Could I try what brought you to this research question in a different way? Sure. You said bacteria that need iron are cool. And you answered Tracy's question in a broad way. But why particular question Oh boy. Brought you to that? Yeah. Gosh, I've always liked the color orange. I mean, but I think what really drew me to these bacteria is I like getting out and I like hiking, trail running, and these are an organism that I'll actually see out in the environment to even as a kid, you'd see like these goopy orange looking deposits and creeks and streams. And I know we've got a bunch of them around Newark. And if any of you go hiking, the next time you're at White Clay or if you're down at Lum's Pond, take a look in some of those little streams and you might see these goopy orange iron mats that are being made. I think when I learned that like oh wow, wait, that's a bacteria that's not just a soil thing or something like leeching out of the soil like there are tiny little organisms making that like it really, I don't know, it kind of drew me to them as a bacteria and you know, they're fun, they're interesting, they're not especially well behaved like a model organism, but it makes it unique and really, really fun. Thank you, Renee. Alrighty.
Fall 2023 Spark! Symposium featuring Rene Hoover
From Jason Felton September 29, 2023
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